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### PHENIX: Phaser 2.8.3 ###
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User: rwerther
Run time: Fri Mar 27 13:12:27 2020
Version: 2.8.3
Release Date: Wed Oct 16 22:41:51 2019 (svn 8451) (git 7473, f5edf81... )
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
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*** Phaser Module: PREPROCESSOR 2.8.3 ***
******************************************************************************************
CELL 63.841 119.741 165.101 90 90 90
COMPOSITION BY ASU
COMPOSITION PROTEIN SEQ "/Users/rwerther/Desktop/3022Natalia/3022Complex.pir" NUM 1
ELLG HIRES ON
ENSEMBLE complex PDB "/Users/rwerther/Desktop/3022Natalia/3022pin7_refine_19complex.pdb" ID 1
ENSEMBLE complex ESTIMATOR oeffner
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 "3022Natalia_phaser"
SEARCH ENSEMBLE complex
SEARCH ENSEMBLE complex
SGALT BASE P 2ac 2ab
SPACEGROUP P 21 21 21
TNCS RLIST ADD ON
XYZOUT ON
CPU Time: 0 days 0 hrs 0 mins 0.04 secs ( 0.04 secs)
Finished: Fri Mar 27 13:12:27 2020
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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 = 2
** Search Method: FAST
** Input Search Order:
** #1 complex
** #2 complex
** Automatic (best predicted) search order WILL be used
CPU Time: 0 days 0 hrs 0 mins 0.05 secs ( 0.05 secs)
Finished: Fri Mar 27 13:12:27 2020
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*** Phaser Module: CELL CONTENT ANALYSIS 2.8.3 ***
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Space-Group Name (Hall Symbol): P 21 21 21 ( P 2ac 2ab)
Space-Group Number: 19
Unit Cell: 63.84 119.74 165.10 90.00 90.00 90.00
--------------------
SPACE GROUP ANALYSIS
--------------------
Input Space Group: P 21 21 21
(a) Space groups derived by translation (screw) symmetry
--------------------------------------------------------
Z Space Group Hall Symbol
----
4 P 21 21 21 P 2ac 2ab
P 2 2 2 P 2 2
P 2 2 21 P 2c 2
P 21 2 2 P 2c 2 (z,x,y)
P 2 21 2 P 2c 2 (y,z,x)
P 21 21 2 P 2 2ab
P 2 21 21 P 2 2ab (z,x,y)
P 21 2 21 P 2 2ab (y,z,x)
----
(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
----
1 P 1 P 1
---
---
---
---
4 P 21 21 21 P 2ac 2ab
P 2 2 2 P 2 2
P 2 2 21 P 2c 2
P 21 2 2 * P 2c 2 (z,x,y)
P 2 21 2 * P 2c 2 (y,z,x)
P 21 21 2 P 2 2ab
P 2 21 21 * P 2 2ab (z,x,y)
P 21 2 21 * P 2 2ab (y,z,x)
----
Composition is of type: PROTEIN
MW to which Matthews applies: 39147
Resolution for Matthews calculation: 2.45
Z MW VM % solvent rel. freq.
1 39147 8.06 84.74 0.005
2 78293 4.03 69.48 0.045
3 117440 2.69 54.22 0.883
4 156587 2.02 38.96 1.000 <== most probable
5 195733 1.61 23.70 0.007
6 234880 1.34 8.44 0.005
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 * (COMPOSITION*1)
6.25 -
5.56 -
5.00 -
4.55 -
4.17 --
3.85 *** (COMPOSITION*2)
3.57 -----
3.33 -------
3.12 ------------
2.94 -----------------
2.78 -------------------------
2.63 ********************************* (COMPOSITION*3)
2.50 -----------------------------------------
2.38 -----------------------------------------------
2.27 --------------------------------------------------
2.17 -------------------------------------------------
2.08 ------------------------------------------
2.00 ******************************* (COMPOSITION*4)
1.92 --------------------
1.85 -----------
1.79 -----
1.72 --
1.67 -
1.61 -
1.56 * (COMPOSITION*5)
1.52 -
1.47 -
1.43 -
1.39 -
1.35 -
1.32 * (COMPOSITION*6)
1.28 -
1.25 -
Most probable VM for resolution = 2.25636
Most probable MW of protein in asu for resolution = 139838
CPU Time: 0 days 0 hrs 0 mins 0.17 secs ( 0.17 secs)
Finished: Fri Mar 27 13:12:27 2020
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*** Phaser Module: ANISOTROPY CORRECTION 2.8.3 ***
******************************************************************************************
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46969)
Outlier Rejection
-----------------
There were 20 reflections of 46989 (0.0426%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.403 1.129 9.294e-07 true false
1 0 50 3.30 25.708 0.964 4.504e-07 true false
1 0 52 3.17 30.082 1.130 4.912e-08 true false
1 3 1 33.15 24.215 0.438 3.351e-11 true false
1 3 51 3.22 16.374 0.438 8.519e-08 true false
1 18 3 6.57 16.081 0.310 1.088e-07 true false
2 0 52 3.16 36.667 1.365 1.793e-09 true false
2 3 50 3.27 26.607 0.687 3.527e-12 true false
2 3 51 3.21 21.406 0.534 5.827e-10 true false
2 6 3 16.17 14.107 0.259 7.724e-07 true false
2 6 47 3.44 15.019 0.324 3.162e-07 true false
2 15 35 4.03 13.918 0.337 9.557e-07 true false
3 6 49 3.28 19.942 0.522 2.504e-09 true false
3 48 2 2.48 15.684 0.615 1.864e-07 true false
4 3 49 3.29 18.726 0.535 8.506e-09 true false
5 7 47 3.32 17.504 0.495 2.828e-08 true false
6 4 48 3.25 15.200 0.372 2.685e-07 true false
9 3 33 4.07 17.132 0.484 4.081e-08 true false
11 36 15 2.79 16.142 0.281 1.016e-07 true false
12 42 2 2.51 15.280 0.567 2.716e-07 true false
---------------------
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
-----------------
There were 20 reflections of 46989 (0.0426%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.403 1.129 9.294e-07 true false
1 0 50 3.30 25.708 0.964 4.504e-07 true false
1 0 52 3.17 30.082 1.130 4.912e-08 true false
1 3 1 33.15 24.215 0.438 3.351e-11 true false
1 3 51 3.22 16.374 0.438 8.519e-08 true false
1 18 3 6.57 16.081 0.310 1.088e-07 true false
2 0 52 3.16 36.667 1.365 1.793e-09 true false
2 3 50 3.27 26.607 0.687 3.527e-12 true false
2 3 51 3.21 21.406 0.534 5.827e-10 true false
2 6 3 16.17 14.107 0.259 7.724e-07 true false
2 6 47 3.44 15.019 0.324 3.162e-07 true false
2 15 35 4.03 13.918 0.337 9.557e-07 true false
3 6 49 3.28 19.942 0.522 2.504e-09 true false
3 48 2 2.48 15.684 0.615 1.864e-07 true false
4 3 49 3.29 18.726 0.535 8.506e-09 true false
5 7 47 3.32 17.504 0.495 2.828e-08 true false
6 4 48 3.25 15.200 0.372 2.685e-07 true false
9 3 33 4.07 17.132 0.484 4.081e-08 true false
11 36 15 2.79 16.142 0.281 1.016e-07 true false
12 42 2 2.51 15.280 0.567 2.716e-07 true false
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 3 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-179169.304 -178366.705 802.598
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
7.439 1.0000 0.0000 0.0000
-1.543 -0.0000 -0.0000 1.0000
-5.896 -0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.335
Outlier Rejection
-----------------
There were 22 reflections of 46989 (0.0468%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.541 1.136 8.668e-07 true false
1 0 50 3.30 27.431 1.028 1.877e-07 true false
1 0 52 3.17 29.701 1.115 5.955e-08 true false
1 3 1 33.15 29.168 0.527 2.471e-13 true false
1 3 51 3.22 16.483 0.441 7.647e-08 true false
1 9 5 12.12 14.139 0.235 7.439e-07 true false
1 18 3 6.57 15.534 0.300 1.875e-07 true false
2 0 0 31.92 27.343 1.378 2.200e-07 true false
2 0 52 3.16 35.505 1.322 3.207e-09 true false
2 3 50 3.27 28.430 0.734 5.890e-13 true false
2 3 51 3.21 21.195 0.529 7.171e-10 true false
2 6 3 16.17 14.819 0.272 3.804e-07 true false
2 6 47 3.44 14.642 0.316 4.601e-07 true false
3 0 49 3.33 25.342 1.136 5.720e-07 true false
3 6 49 3.28 21.343 0.559 6.291e-10 true false
4 3 49 3.29 20.281 0.580 1.842e-09 true false
5 7 47 3.32 19.045 0.539 6.191e-09 true false
6 4 48 3.25 15.897 0.389 1.346e-07 true false
7 4 47 3.26 14.603 0.553 5.303e-07 true false
9 3 33 4.07 18.460 0.522 1.101e-08 true false
More than 20 outliers (see VERBOSE output)
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 2 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-178312.970 -178312.289 0.681
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
7.457 1.0000 0.0000 0.0000
-1.539 -0.0000 -0.0000 1.0000
-5.917 -0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.374
Outlier Rejection
-----------------
There were 23 reflections of 46989 (0.0489%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.618 1.139 8.341e-07 true false
1 0 50 3.30 27.502 1.031 1.810e-07 true false
1 0 52 3.17 29.721 1.116 5.895e-08 true false
1 3 1 33.15 29.715 0.537 1.437e-13 true false
1 3 51 3.22 16.535 0.442 7.265e-08 true false
1 9 5 12.12 14.301 0.238 6.332e-07 true false
1 18 3 6.57 15.535 0.300 1.874e-07 true false
2 0 0 31.92 27.857 1.403 1.703e-07 true false
2 0 52 3.16 35.515 1.322 3.191e-09 true false
2 3 50 3.27 28.511 0.736 5.439e-13 true false
2 3 51 3.21 21.200 0.529 7.138e-10 true false
2 6 3 16.17 14.981 0.275 3.239e-07 true false
2 6 47 3.44 14.645 0.316 4.586e-07 true false
3 0 49 3.33 25.401 1.139 5.553e-07 true false
3 6 49 3.28 21.402 0.561 5.939e-10 true false
4 3 49 3.29 20.337 0.581 1.743e-09 true false
4 6 48 3.32 13.880 0.347 9.955e-07 true false
5 7 47 3.32 19.090 0.540 5.925e-09 true false
6 4 48 3.25 15.943 0.391 1.286e-07 true false
7 4 47 3.26 14.644 0.555 5.093e-07 true false
More than 20 outliers (see VERBOSE output)
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 3 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-178294.884 -178293.575 1.309
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
7.525 1.0000 0.0000 0.0000
-1.511 -0.0000 -0.0000 1.0000
-6.014 -0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.539
Outlier Rejection
-----------------
There were 23 reflections of 46989 (0.0489%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.930 1.154 7.124e-07 true false
1 0 50 3.30 28.156 1.055 1.300e-07 true false
1 0 52 3.17 29.791 1.119 5.690e-08 true false
1 3 1 33.15 32.000 0.578 1.497e-14 true false
1 3 51 3.22 16.746 0.448 5.900e-08 true false
1 9 5 12.12 14.955 0.249 3.300e-07 true false
1 18 3 6.57 15.524 0.299 1.895e-07 true false
2 0 0 31.92 30.001 1.511 5.866e-08 true false
2 0 52 3.16 35.598 1.326 3.061e-09 true false
2 3 50 3.27 29.194 0.754 2.783e-13 true false
2 3 51 3.21 21.241 0.530 6.856e-10 true false
2 6 3 16.17 15.662 0.288 1.645e-07 true false
2 6 47 3.44 14.669 0.317 4.478e-07 true false
3 0 49 3.33 25.998 1.166 4.108e-07 true false
3 6 49 3.28 21.910 0.574 3.597e-10 true false
4 3 49 3.29 20.823 0.595 1.081e-09 true false
4 6 48 3.32 14.206 0.355 7.205e-07 true false
5 7 47 3.32 19.537 0.553 3.815e-09 true false
6 4 48 3.25 16.143 0.395 1.055e-07 true false
7 4 47 3.26 14.828 0.562 4.252e-07 true false
More than 20 outliers (see VERBOSE output)
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
7.525 1.0000 0.0000 0.0000
-1.511 -0.0000 -0.0000 1.0000
-6.014 -0.0000 1.0000 0.0000
Anisotropic deltaB (i.e. range of principal components): 13.539
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 55.1931
Wilson B-factor: 39.1971
--------------------------------
DATA AFTER ANISOTROPY CORRECTION
--------------------------------
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46966)
Outlier Rejection
-----------------
There were 23 reflections of 46989 (0.0489%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.930 1.154 7.124e-07 true false
1 0 50 3.30 28.156 1.055 1.300e-07 true false
1 0 52 3.17 29.791 1.119 5.690e-08 true false
1 3 1 33.15 32.000 0.578 1.497e-14 true false
1 3 51 3.22 16.746 0.448 5.900e-08 true false
1 9 5 12.12 14.955 0.249 3.300e-07 true false
1 18 3 6.57 15.524 0.299 1.895e-07 true false
2 0 0 31.92 30.001 1.511 5.866e-08 true false
2 0 52 3.16 35.598 1.326 3.061e-09 true false
2 3 50 3.27 29.194 0.754 2.783e-13 true false
2 3 51 3.21 21.241 0.530 6.856e-10 true false
2 6 3 16.17 15.662 0.288 1.645e-07 true false
2 6 47 3.44 14.669 0.317 4.478e-07 true false
3 0 49 3.33 25.998 1.166 4.108e-07 true false
3 6 49 3.28 21.910 0.574 3.597e-10 true false
4 3 49 3.29 20.823 0.595 1.081e-09 true false
4 6 48 3.32 14.206 0.355 7.205e-07 true false
5 7 47 3.32 19.537 0.553 3.815e-09 true false
6 4 48 3.25 16.143 0.395 1.055e-07 true false
7 4 47 3.26 14.828 0.562 4.252e-07 true false
More than 20 outliers (see VERBOSE output)
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 12.29 secs ( 12.29 secs)
Finished: Fri Mar 27 13:12:39 2020
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*** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY 2.8.3 ***
******************************************************************************************
Unit Cell: 63.84 119.74 165.10 90.00 90.00 90.00
---------------------
MAXIMUM NMOL ANALYSIS
---------------------
Stoichiometry of search components:
"complex"
Molecular weight of components: 42831.1
Volume of asymmetric unit: 315524
Packing to solvent content: 20%
Maximum automatic NMOL number: 4
-------------------------------------
DATA FOR TRANSLATIONAL NCS CORRECTION
-------------------------------------
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46969)
Outlier Rejection
-----------------
There were 20 reflections of 46989 (0.0426%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
0 3 51 3.23 24.403 1.129 9.294e-07 true false
1 0 50 3.30 25.708 0.964 4.504e-07 true false
1 0 52 3.17 30.082 1.130 4.912e-08 true false
1 3 1 33.15 24.215 0.438 3.351e-11 true false
1 3 51 3.22 16.374 0.438 8.519e-08 true false
1 18 3 6.57 16.081 0.310 1.088e-07 true false
2 0 52 3.16 36.667 1.365 1.793e-09 true false
2 3 50 3.27 26.607 0.687 3.527e-12 true false
2 3 51 3.21 21.406 0.534 5.827e-10 true false
2 6 3 16.17 14.107 0.259 7.724e-07 true false
2 6 47 3.44 15.019 0.324 3.162e-07 true false
2 15 35 4.03 13.918 0.337 9.557e-07 true false
3 6 49 3.28 19.942 0.522 2.504e-09 true false
3 48 2 2.48 15.684 0.615 1.864e-07 true false
4 3 49 3.29 18.726 0.535 8.506e-09 true false
5 7 47 3.32 17.504 0.495 2.828e-08 true false
6 4 48 3.25 15.200 0.372 2.685e-07 true false
9 3 33 4.07 17.132 0.484 4.081e-08 true false
11 36 15 2.79 16.142 0.281 1.016e-07 true false
12 42 2 2.51 15.280 0.567 2.716e-07 true false
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: 4.08
2nd Moment Acentric: 2.76
Resolution for Twin Analysis (85% I/SIGI > 3): 3.11A (HiRes= 2.45A)
---------------------
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: 4.02
2nd Moment Acentric: 2.70
Resolution for Twin Analysis (85% I/SIGI > 3): 3.11A (HiRes= 2.45A)
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector not set
Space Group (without translational symmetry):P 2 2 2
Patterson Symmetry: P m m m
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Patterson (Number): 5.00 10.00 (5054)
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)
58.8%: FRAC -0.0000 +0.3333 +0.0000 (ORTH 0.0 39.9 0.0)
Patterson Top (All) = 58.80%
There were 476 peaks
Patterson Top (Non-origin) = 58.80%
Patterson Origin Vector Distance = 15
There were 468 non-origin peaks
Patterson Top (Cutoff) = 58.80%
Patterson cutoff = 20%
There was 1 non-origin peak over cutoff
Patterson Top (Large Cell) = 58.80%
Unit Cell dimension was not smaller than origin Patterson vector distance
There was 1 non-origin and large cell peak over cutoff
Patterson Top (Analysis) = 58.80%
Peaks within minimum Patterson vector distance of one another were deleted
There was 1 widely separated non-origin peak over cutoff
There was 1 non-origin distinct peak (i.e. over 20% of origin peak and more than 15
angstroms from the origin)
Patterson Peaks Table
---------------------
Sorted by Height
Height Distance Vector
58.8% 39.9 : FRAC +0.0000 +0.3333 +0.0000 (ORTH 0.0 39.9 0.0)
Unit Cell: 63.84 119.74 165.10 90.00 90.00 90.00
Patterson Peaks Expanded by Symmetry
------------------------------------
Sorted by distance from origin in unit cell [(0,0,0),(1,1,1)]
Height Distance Vector
58.8% 39.9 : FRAC +0.0000 +0.3333 +0.0000 (ORTH 0.0 39.9 0.0)
Frequency Top = 0 0 2 height=99.6239
-------------
NMOL ANALYSIS
-------------
Estimate NMOL from Patterson spatial frequency analysis
Four measures of reliability of the NMOL estimate are given
(1) %Top:
Strength of the frequency analysis signal
Indicator is strong when %Top > 95
(2) tolfrac:
The maximum fractional difference (in x, y, or z) between the freq*tNCS-vector and
an exact unit cell repeat
Indicator is strong when tolfrac < 0.02
(3) tolorth:
The length of the vector difference between freq*tncs-vector and a unit cell repeat
in orthogonal Angstroms
Indicator is strong when tolorth < 5
(4) complete:
Most tNCS vectors in tNCS must be present
Translational NCS Analysis Table
--------------------------------
C*=Commensurate Modulation
C* NMOL %Patt tNCS-vector %Freq Frequencies tol-orth tol-frac repeat-dist
T 3 58.8 +0.0000 +0.3333 +0.0000 96.9 0 3 3 0.03 0.000233 39.9A
-------
RESULTS
-------
Strong modulation present
NMOL not input
NMOL and VECTOR set to values from analysis
tNCS vector = 0 0.333256 5.6684e-19
tNCS NMOL = 3
------------------------------------------------------------------------------------------
Advisory: NMOL (3) set by analysis. If structure solution fails consider other tNCS
------------------------------------------------------------------------------------------
----------------------------
TRANSLATIONAL NCS REFINEMENT
----------------------------
Special Position Perturbation
-----------------------------
NCS translation on special position with M = 4
NCS translation vector = 0 0.333256 0
Starting point for refinement will be shifted from special position.
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Data (Number): 2.45 50.01 (46966)
NCS translation has been perturbed in X
NCS translation has been perturbed in Y
NCS translation has been perturbed in Z
NCS translation perturbed by (orthogonal angstroms): 0.409 0.409 0.409
NCS translation has been set to -0.00640083 0.329843 -0.00247506
Protocol cycle #1 of 3
Refinement protocol for this macrocycle:
ROTATION: FIX
TRANSLATION: REFINE
VARIANCES: REFINE
Protocol cycle #2 of 3
Refinement protocol for this macrocycle:
ROTATION: FIX
TRANSLATION: REFINE
VARIANCES: REFINE
Protocol cycle #3 of 3
Refinement protocol for this macrocycle:
ROTATION: FIX
TRANSLATION: REFINE
VARIANCES: REFINE
There is 1 tncs parameter set to refine
Refining tNCS parameters
0% 100%
|==| DONE
TNCS REFINEMENT #1 OF 1
-----------------------
Performing Optimization...
Done
--- Convergence before iteration limit (100) at cycle 8 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-186408.029 -176168.878 10239.151
Ncs Translation Vector = -0.0162 0.3332 -0.0038
Rotational Deviation of NCS related structure = 0.0000 0.0000 0.0000
for effective molecular radius = 26.605
D corresponding to RMS deviation of NCS related structure:
Range (Resolution 50.005 - 2.452): 0.9962 - 0.5549
Performing Optimization...
Done
--- Convergence before iteration limit (100) at cycle 91 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-176168.878 -174717.070 1451.808
Ncs Translation Vector = -0.0055 0.3333 -0.0000
Rotational Deviation of NCS related structure = 0.0000 0.0000 0.0000
for effective molecular radius = 26.605
D corresponding to RMS deviation of NCS related structure:
Range (Resolution 50.005 - 2.452): 0.9222 - 0.0971
Performing Optimization...
Done
--- Convergence before iteration limit (100) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
-174717.070 -174717.049 0.021
Ncs Translation Vector = -0.0055 0.3333 0.0000
Rotational Deviation of NCS related structure = 0.0000 0.0000 0.0000
for effective molecular radius = 26.605
D corresponding to RMS deviation of NCS related structure:
Range (Resolution 50.005 - 2.452): 0.9222 - 0.0971
Translational NCS Refinement
----------------------------
Test rotation #1
Final angle : 0.0000 0.0000 0.0000
Final vector : -0.0055 0.3333 0.0000
tNCS D-values by resolution (low-high) : 0.9222 0.0971
Weighted Intensity Moments after tNCS (best) refinement
-------------------------------------------------------
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: 3.24
2nd Moment Acentric: 2.19
Resolution for Twin Analysis (85% I/SIGI > 3): 3.11A (HiRes= 2.45A)
Histogram of Epsilon Factors
----------------------------
Minimum EpsFac = 0.0778
Maximum EpsFac = 2.8444
Mean EpsFac = 1.0078 for 46989 reflections
Mid EpsFac Bin Value
| 0 2456 4912 7368 9824 12280
V | | | | | |
0.0
0.1 ** (292)
0.2 ** (373)
0.3 *** (703)
0.4 *** (670)
0.5 ******* (1691)
0.6 ********** (2235)
0.7 ************** (3427)
0.8 ************************************ (8625)
0.9 ************************************************** (12283)
1.0 *** (592)
1.1 ***** (1228)
1.2 ************* (3102)
1.3 ****************** (4227)
1.4 ********* (1967)
1.5 ***** (1225)
1.6 **** (926)
1.7 ** (467)
1.8 *** (528)
1.9 **** (882)
2.0 ** (391)
2.1 * (116)
2.2 * (202)
2.3 * (166)
2.4 * (237)
2.5 * (144)
2.6 * (112)
2.7 * (106)
2.8 * (72)
2.9
3.0
--------
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 3.01 2.00
Theoretical for perfect twin 2.00 1.50
Initial (data as input) 4.08 2.76+/-0.031 1 1
After Anisotropy Correction 4.02 2.70+/-0.031 1 1
After Anisotropy and tNCS 3.24 2.19+/-0.031 1 1
P-value < 0.01 for < 5% twinned is considered worth investigating
Resolution for Twin Analysis (85% I/SIGI > 3): 3.11A (HiRes= 2.45A)
---------------------------------------
DATA AFTER TRANSLATIONAL NCS CORRECTION
---------------------------------------
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46979)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 1 mins 4.91 secs ( 64.91 secs)
Finished: Fri Mar 27 13:13:33 2020
******************************************************************************************
*** 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 1 mins 4.92 secs ( 64.92 secs)
Finished: Fri Mar 27 13:13:33 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
TNCS Checks
-----------
Number of copies per TNCS set = 3
------------------------------------------------------------------------------------------
Warning: Number of search copies for complex (2) not divisible by 3
Number of search copies edited
------------------------------------------------------------------------------------------
TNCS search components
----------------------
Ensemble | input | search: sets number
complex 2 1 3
CPU Time: 0 days 0 hrs 1 mins 4.93 secs ( 64.93 secs)
Finished: Fri Mar 27 13:13:33 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
Composition Table
-----------------
Total Scattering = 127423
Search occupancy factor = 1 (default)
Ensemble Frac.Scat. (Search Frac.Scat.)
complex 111.14% 111.14%
------------------------------------------------------------------------------------------
Warning: Total search request exceeds scattering specified in composition. Composition
increased to resolve the discrepancy.
------------------------------------------------------------------------------------------
** Composition increased
from 127423
to 429152
Composition Table
-----------------
Total Scattering = 429152
Search occupancy factor = 1 (default)
Ensemble Frac.Scat. (Search Frac.Scat.)
complex 33.00% 33.00%
CPU Time: 0 days 0 hrs 1 mins 4.95 secs ( 64.95 secs)
Finished: Fri Mar 27 13:13:33 2020
******************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.8.3 ***
******************************************************************************************
Space-Group Name (Hall Symbol): P 21 21 21 ( P 2ac 2ab)
Space-Group Number: 19
Unit Cell: 63.84 119.74 165.10 90.00 90.00 90.00
--------------------
SPACE GROUP ANALYSIS
--------------------
Input Space Group: P 21 21 21
(a) Space groups derived by translation (screw) symmetry
--------------------------------------------------------
Z Space Group Hall Symbol
----
4 P 21 21 21 P 2ac 2ab
P 2 2 2 P 2 2
P 2 2 21 P 2c 2
P 21 2 2 P 2c 2 (z,x,y)
P 2 21 2 P 2c 2 (y,z,x)
P 21 21 2 P 2 2ab
P 2 21 21 P 2 2ab (z,x,y)
P 21 2 21 P 2 2ab (y,z,x)
----
(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
----
1 P 1 P 1
---
---
---
---
4 P 21 21 21 P 2ac 2ab
P 2 2 2 P 2 2
P 2 2 21 P 2c 2
P 21 2 2 * P 2c 2 (z,x,y)
P 2 21 2 * P 2c 2 (y,z,x)
P 21 21 2 P 2 2ab
P 2 21 21 * P 2 2ab (z,x,y)
P 21 2 21 * P 2 2ab (y,z,x)
----
Composition is of type: PROTEIN
MW to which Matthews applies: 131843
Resolution for Matthews calculation: 2.45
Z MW VM % solvent rel. freq.
1 131843 2.39 48.60 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 *********************************************** (COMPOSITION*1)
2.27 --------------------------------------------------
2.17 -------------------------------------------------
2.08 ------------------------------------------
2.00 -------------------------------
1.92 --------------------
1.85 -----------
1.79 -----
1.72 --
1.67 -
1.61 -
1.56 -
1.52 -
1.47 -
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25 -
Most probable VM for resolution = 2.25636
Most probable MW of protein in asu for resolution = 139838
CPU Time: 0 days 0 hrs 1 mins 5.04 secs ( 65.04 secs)
Finished: Fri Mar 27 13:13:33 2020
******************************************************************************************
*** Phaser Module: EXPERIMENTAL ERROR CORRECTION PREPARATION 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
-----------------------------
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 1 mins 7.99 secs ( 67.99 secs)
Finished: Fri Mar 27 13:13:36 2020
******************************************************************************************
*** Phaser Module: EXPECTED LLG OF ENSEMBLES 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
Resolution of Data (Selected): 2.452 (2.45181)
Number of Reflections (Selected): 46989 (46979)
eLLG Target: 225
----------
ENSEMBLING
----------
Ensemble: complex
-----------------
PDB file # 1: 3022pin7_refine_19complex.pdb
This file contains 1 model
The input RmsD of model #1 with respect to the real structure is 0.432
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 = 2.45181
Default RMSD = 0.1 0.2 0.4 0.8 1.6 3.2
Minimum solvent = 20%
Maximum number of polyalanine residues = 1519 (-full-)
Alanine residues for eLLG target = 195
Table of Alanine Residues for eLLG Target
-----------------------------------------
---RMSD---
eLLG-target | 0.10 0.20 0.40 0.80 1.60 3.20
225 | 195 203 237 399 1302 -full-
196 | 182 190 221 372 1215 -full-
169 | 169 176 205 346 1128 -full-
144 | 156 162 189 319 1041 -full-
121 | 143 149 173 292 955 -full-
100 | 130 135 158 266 868 -full-
81 | 117 122 142 239 781 -full-
64 | 104 108 126 212 694 -full-
49 | 91 95 110 186 607 -full-
36 | 78 81 94 159 520 -full-
25 | 65 67 79 133 434 -full-
16 | 52 54 63 106 347 -full-
9 | 39 40 47 79 260 -full-
4 | 26 27 31 53 173 1125
1 | 13 13 15 26 86 562
--------------
MONOMERIC ELLG
--------------
Expected LLG (eLLG)
-------------------
eLLG: eLLG of ensemble alone
eLLG RMSD frac-scat Ensemble
1474.6 0.432 0.33000 complex
Resolution for eLLG target
--------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso Ensemble
4.795 complex
Resolution for eLLG target: data collection
-------------------------------------------
eLLG-reso: Resolution to achieve target eLLG (225) with perfect data
eLLG-reso Ensemble
4.797 complex
eLLG indicates that placement of a single copy of ensemble "complex" should be easy
Expected LLG (eLLG): Chains
---------------------------
eLLG: eLLG of chain alone
eLLG RMSD frac-scat chain Ensemble
503.7 0.432 0.19288 " A" complex
64.7 0.432 0.06910 " F" complex
62.7 0.432 0.06803 " G" complex
0.00000 0.432 0.00000 " H" complex
Resolution for eLLG target: Chains
----------------------------------
eLLG-reso: Resolution to achieve target eLLG (225)
eLLG-reso chain Ensemble
3.429 " A" complex
> 2.45(all) " F" complex
> 2.45(all) " G" complex
> 2.45(all) " H" complex
--------------------
HOMO-OLIGOMERIC ELLG
--------------------
Number of copies for eLLG target
--------------------------------
eLLG-target RMSD frac-scat-known frac-scat num-copies Ensemble
225 0.432 0.00000 0.33000 1 complex
CPU Time: 0 days 0 hrs 1 mins 10.87 secs ( 70.87 secs)
Finished: Fri Mar 27 13:13:39 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Search Order (next search *) (placed +):
** #1 complex,complex, complex *
CPU Time: 0 days 0 hrs 1 mins 10.88 secs ( 70.88 secs)
Finished: Fri Mar 27 13:13:39 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT ROTATION FUNCTION 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
--------------------------
DATA FOR ROTATION FUNCTION
--------------------------
High resolution limit unaltered by RMS of ensemble
High resolution limit lowered by expected LLG = 4.79
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 4.79 50.01 (6620)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
-------------------
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 (5368)
- half number of centrics (1252/2)
= -5994
With correction for SigF,
Wilson log(likelihood) = -3825.24
----------
ENSEMBLING
----------
Ensemble Generation: complex
----------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 4.79
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 4.79451
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
33.0 30.6 1 -56.1 0.432 0.000 0.432 complex
-----------------
ROTATION FUNCTION
-----------------
Ensemble configured to resolution 4.79
Elmn for Search Ensemble
Elmn Calculation for Search Ensemble
0% 100%
|===========================================================================| DONE
Target Function: FAST LERF1
-------------------------
ROTATION FUNCTION #1 OF 1
-------------------------
Search Ensemble: complex
Translational Ncs: Rotational spacegroup changed to P1
Sampling: 4.48 degrees
Spherical Harmonics
-------------------
Elmn for Data
Elmn Calculation for Data
0% 100%
|================================================================================| DONE
Scanning the Range of Beta Angles
---------------------------------
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 52.5% of top
There were 41 sites over 52.5% of top
41 peaks selected
The sites over 52.5% are:
# Euler1 Euler2 Euler3 FSS Z-score
1 123.6 179.2 124.9 100.000 12.39
2 14.1 179.5 196.3 98.531 12.20
3 236.7 178.9 239.7 94.465 11.70
#Sites = 41: output truncated to 3 sites
Top 41 rotations before clustering will be rescored
Calculating Likelihood for RF #1 of 1
0% 100%
|==========================================| DONE
Mean and Standard Deviation
---------------------------
Scoring 500 randomly sampled rotations
Generating Statistics for RF #1 of 1
0% 100%
|========================================================================| DONE
Highest Score (Z-score): 109.074 (11.28)
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
Also store peaks over 60% of top
There were 6 sites over 60% of top
The sites over 60% are:
# Euler1 Euler2 Euler3 LLG Z-score Split #Group FSS-this-ang/FSS-top
1 14.1 179.5 196.3 109.07 11.28 0.0 5 98.531/ 98.531
2 123.6 179.2 124.9 107.37 11.20 179.2 6 100.000/ 100.000
3 176.4 1.2 7.3 93.89 10.53 179.3 5 91.694/ 91.694
#SITES = 6: OUTPUT TRUNCATED TO 3 SITES
Rotation Function Results
Top1: ENSEMBLE complex EULER 14.109 179.477 196.255 RF=109.1 RFZ=11.28
Rotation Function Table: complex
--------------------------------
(Z-scores from Fast Rotation Function)
#SET Top (Z) Second (Z) Third (Z)
1 109.07 11.28 107.37 11.20 93.89 10.53
---------------
FINAL SELECTION
---------------
Select by Percentage of Top value: 75%
Top RF = 109.074
Purge RF mean = -119.197
Number of sets stored before final selection = 1
Number of solutions stored before final selection = 6
Number of sets stored (deleted) after final selection = 1 (0)
Number of solutions stored (deleted) after final selection = 6 (0)
Percent used for purge = 60.000%
Includes deep search down percent = 15%
Number of solutions stored above (below) deep threshold = 5 (1)
Rotation Function Final Selection Table
---------------------------------------
Rotation list length by SET
SET# Start Final Deleted Set (*) Deep: Start Final Deleted Set (*)
1 5 5 - 6 6 -
ALL 5 5 6 6
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 1 mins 41.44 secs ( 101.44 secs)
Finished: Fri Mar 27 13:14:11 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT TRANSLATION FUNCTION 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
-----------------------------
DATA FOR TRANSLATION FUNCTION
-----------------------------
High Resolution Limit imposed by RF list = 4.79
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 4.79 50.01 (6620)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
-------------------
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 (5368)
- half number of centrics (1252/2)
= -5994
With correction for SigF,
Wilson log(likelihood) = -3825.24
------------------------
ALTERNATIVE SPACE GROUPS
------------------------
Space Group(s) to be tested:
P 21 21 21
----------
ENSEMBLING
----------
Ensemble Generation
-------------------
Resolution of Ensembles: 4.79451
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
33.0 30.6 1 -56.1 0.432 0.000 0.432 complex
Trace Generation: complex
-------------------------
This trace is from coordinates
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 3.00 2.00
---------------------
TRANSLATION FUNCTIONS
---------------------
Target Function: FAST LETF1
Translation Packing Function applied: top peak will pack
Translation Packing Cutoff: 50%
Sampling: 1.20 Angstroms
----------------------------
TRANSLATION FUNCTION #1 OF 1
----------------------------
SOLU SET
SOLU SPAC P 21 21 21
SOLU TRIAL ENSEMBLE complex EULER 14.109 179.477 196.255 RF 109.1 RFZ 11.28
SOLU TRIAL ENSEMBLE complex EULER 123.602 179.209 124.943 RF 107.4 RFZ 11.20
SOLU TRIAL ENSEMBLE complex EULER 176.403 1.250 7.279 RF 93.9 RFZ 10.53
SOLU TRIAL ENSEMBLE complex EULER 326.381 1.602 36.508 RF 91.1 RFZ 10.39
SOLU TRIAL ENSEMBLE complex EULER 338.178 3.575 200.947 RF 62.2 RFZ 8.96
SOLU TRIAL ENSEMBLE complex EULER 183.540 175.869 11.524 RF 21.3 RFZ 6.95 # DEEP
This TF set has 6 trial orientations
# Euler Rot-LLG RF RFZ Ensemble
1 14.1 179.5 196.3 109.1 109.1 11.3 complex
2 123.6 179.2 124.9 107.4 107.4 11.2 complex
3 176.4 1.2 7.3 93.9 93.9 10.5 complex
4 326.4 1.6 36.5 91.1 91.1 10.4 complex
5 338.2 3.6 200.9 62.2 62.2 9.0 complex
----- angles below here for deep search only -----
6 183.5 175.9 11.5 21.3 21.3 6.9 complex
5 trial orientations in initial search
1 trial orientations in deep search
Scoring 504 randomly sampled orientations and translations
Generating Statistics for TF SET #1 of 1
0% 100%
|=======| DONE
Mean Score (Sigma): -382.37 (51.83)
SET #1 of 1 TRIAL #1 of 5
-------------------------
Ensemble complex Euler 14.11 179.48 196.26
Doing Fast Translation Function FFT...
Done
Packing Fast Search Translations...
4287 peaks
500 peaks over 179.838 checked for packing
Translation peak 1 first to be kept
Done
New Top Packing Fast Translation Function FSS = 777.25 (TFZ=17.9) at Trial #1
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 7 sites over 67.5% of top
7 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.519 0.494 0.001 777.25 17.92
2 0.520 0.162 0.001 773.08 17.81
3 0.520 0.328 0.001 717.03 16.34
#Sites = 7: output truncated to 3 sites
Top 7 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #1 of 5
0% 100%
|========| DONE
Packing LLG Translations: pass 1 of 11...
7 peaks
1 peaks over 355.89 checked for packing
Translation peak 1 first to be kept
Done
Exit: found a peak that packs
New Top (ML) Translation Function LLG = 355.89 (TFZ=17.9) at Trial #1
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 7 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 0.519 0.494 0.001 355.89 17.92 0.0 1 777.25/ 777.25
2 0.520 0.328 0.001 354.10 16.34 19.9 1 717.03/ 717.03
3 0.520 0.162 0.001 349.39 17.81 37.0 1 773.08/ 773.08
#SITES = 7: OUTPUT TRUNCATED TO 3 SITES
SET #1 of 1 TRIAL #2 of 5
-------------------------
Ensemble complex Euler 123.60 179.21 124.94
Doing Fast Translation Function FFT...
Done
Current Top Packing Fast Translation Function FSS = 777.25 (TFZ=17.9)
Current Top (ML) Packing Translation Function LLG = 355.89 (TFZ=17.9)
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 3 sites over 67.5% of top
3 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.996 0.005 0.999 730.81 16.86
2 0.996 0.338 0.999 723.44 16.67
3 0.996 0.172 1.000 686.25 15.68
Top 3 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #2 of 5
0% 100%
|====| DONE
Packing LLG Translations: pass 1 of 1...
3 peaks
1 peaks over 355.89 checked for packing
Translation peak 1 first to be kept
Done
Exit: found a peak that packs
New Top (ML) Translation Function LLG = 356.26 (TFZ=15.7) at Trial #2
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 3 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 0.996 0.172 1.000 356.26 15.68 0.0 1 686.25/ 686.25
2 0.996 0.005 0.999 352.36 16.86 19.9 1 730.81/ 730.81
3 0.996 0.338 0.999 350.55 16.67 19.9 1 723.44/ 723.44
SET #1 of 1 TRIAL #3 of 5
-------------------------
Ensemble complex Euler 176.40 1.25 7.28
Doing Fast Translation Function FFT...
Done
Current Top Packing Fast Translation Function FSS = 777.25 (TFZ=17.9)
Current Top (ML) Packing Translation Function LLG = 356.26 (TFZ=15.7)
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 5 sites over 67.5% of top
5 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.983 0.490 0.498 651.39 15.51
2 0.982 0.158 0.498 648.77 15.44
3 0.982 0.324 0.498 600.87 14.16
#Sites = 5: output truncated to 3 sites
Top 5 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #3 of 5
0% 100%
|======| DONE
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 5 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 0.982 0.324 0.498 259.88 14.16 0.0 1 600.87/ 600.87
2 0.983 0.490 0.498 259.82 15.51 19.9 1 651.39/ 651.39
3 0.982 0.158 0.498 253.70 15.44 19.9 1 648.77/ 648.77
#SITES = 5: OUTPUT TRUNCATED TO 3 SITES
SET #1 of 1 TRIAL #4 of 5
-------------------------
Ensemble complex Euler 326.38 1.60 36.51
Doing Fast Translation Function FFT...
Done
Current Top Packing Fast Translation Function FSS = 777.25 (TFZ=17.9)
Current Top (ML) Packing Translation Function LLG = 356.26 (TFZ=15.7)
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 5 sites over 67.5% of top
5 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.526 0.006 0.497 662.40 16.02
2 0.526 0.338 0.497 654.75 15.81
3 0.526 0.172 0.497 602.32 14.40
#Sites = 5: output truncated to 3 sites
Top 5 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #4 of 5
0% 100%
|======| DONE
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 5 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 0.526 0.006 0.497 237.73 16.02 0.0 1 662.40/ 662.40
2 0.526 0.172 0.497 233.75 14.40 19.9 1 602.32/ 602.32
3 0.526 0.338 0.497 226.43 15.81 37.0 1 654.75/ 654.75
#SITES = 5: OUTPUT TRUNCATED TO 3 SITES
SET #1 of 1 TRIAL #5 of 5
-------------------------
Ensemble complex Euler 338.18 3.57 200.95
Doing Fast Translation Function FFT...
Done
Current Top Packing Fast Translation Function FSS = 777.25 (TFZ=17.9)
Current Top (ML) Packing Translation Function LLG = 356.26 (TFZ=15.7)
Top Peaks Without Clustering
Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
There were 3 sites over 67.5% of top
3 peaks selected
The sites over 67.5% are:
# Frac X Frac Y Frac Z FSS Z-score
1 0.020 0.498 0.507 474.14 12.34
2 0.020 0.166 0.507 460.28 11.96
3 0.020 0.331 0.506 439.80 11.39
Top 3 translations before clustering will be rescored
Calculating Likelihood for TF SET #1 of 1 TRIAL #5 of 5
0% 100%
|====| DONE
Top Peaks With Clustering
Select peaks over 75% of top (i.e. 0.75*(top-mean)+mean)
There were 3 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 0.020 0.498 0.507 135.70 12.34 0.0 1 474.14/ 474.14
2 0.020 0.166 0.507 134.09 11.96 37.5 1 460.28/ 460.28
3 0.020 0.331 0.506 132.99 11.39 20.0 1 439.80/ 439.80
-------------------------
DEEP TRANSLATION FUNCTION
-------------------------
Best TFZ is over Z-score cutoff for definite solution (8.00)
Do NOT search deep in trial orientation list
Translation Function Results
Top1: ENSEMBLE complex EULER 123.602 179.209 124.943 FRAC 0.985 0.838 1.000 TF=356.3
Translation Function Table
--------------------------
SET ROT*deep Top (Z) Second (Z) Third (Z) SpaceGroup Ensemble
1 1 355.9 17.92 354.1 16.34 349.4 17.81 P 21 21 21 complex
1 2 356.3 15.68 352.4 16.86 350.5 16.67 P 21 21 21 complex
1 3 259.9 14.16 259.8 15.51 253.7 15.44 P 21 21 21 complex
1 4 237.7 16.02 233.7 14.40 226.4 15.81 P 21 21 21 complex
1 5 135.7 12.34 134.1 11.96 133.0 11.39 P 21 21 21 complex
--- ---
---------------
FINAL SELECTION
---------------
LLG will be used for purge, not FSS
Top TF = 356.26
Top TFZ = 17.92
Mean TF = -382.37
Percent used for purge = 75%
Cutoff for acceptance = 171.6
TFZ used for final selection = 8.95971
Number of solutions over TF final cutoff = 12
Number of solutions over TFZ final cutoff = 15
Number of solutions over TF & TFZ cutoff = 12
Number of solutions stored before final selection = 23
Number of solutions stored (deleted) after final selection = 15 (8)
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 1 mins 52.37 secs ( 112.37 secs)
Finished: Fri Mar 27 13:14:23 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.8.3 ***
******************************************************************************************
---------
ENSEMBLES
---------
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 3.00 2.00
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "complex" Point Group: 1
Clash background has NOT been packed at 10.00%
----------------
PACKING FUNCTION
----------------
There are 15 solutions to pack
Packing analysis
0% 100%
|================| DONE
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 0.477 -- 1 2 1 356.26 15.68 P 21 21 21
2 2 0.477 -- 1 1 1 355.89 17.92 P 21 21 21
3 3 0.477 -- 1 1 2 354.10 16.34 P 21 21 21
4 4 0.477 -- 1 2 2 352.36 16.86 P 21 21 21
5 5 0.477 -- 1 2 3 350.55 16.67 P 21 21 21
6 6 0.716 -- 1 1 3 349.39 17.81 P 21 21 21
7 7 0.716 -- 1 3 1 259.88 14.16 P 21 21 21
8 8 0.716 -- 1 3 2 259.82 15.51 P 21 21 21
9 9 0.716 -- 1 3 3 253.70 15.44 P 21 21 21
10 10 0.716 -- 1 4 1 237.73 16.02 P 21 21 21
11 11 0.716 -- 1 4 2 233.75 14.40 P 21 21 21
12 12 0.716 -- 1 4 3 226.43 15.81 P 21 21 21
13 13 0.239 -- 1 5 1 135.70 12.34 P 21 21 21
14 14 0.239 -- 1 5 2 134.09 11.96 P 21 21 21
15 15 0.239 -- 1 5 3 132.99 11.39 P 21 21 21
15 accepted of 15 solutions
15 pack of 15 accepted solutions
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 2 mins 4.00 secs ( 124.00 secs)
Finished: Fri Mar 27 13:14:42 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
High resolution limit imposed by solution list = 4.79
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 4.79 50.01 (6620)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
-------------------
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 (5368)
- half number of centrics (1252/2)
= -5994
With correction for SigF,
Wilson log(likelihood) = -3825.24
----------
ENSEMBLING
----------
Ensemble Generation
-------------------
Resolution of Ensembles: 4.79451
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
33.0 30.6 1 -56.1 0.432 0.000 0.432 complex
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 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 are 15 solutions to refine
Refining solutions
0% 100%
|================| DONE
REFINING SET #1 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 1.00 0.17 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 0.50 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 0.84 1.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 23 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
355.746 575.938 220.192
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 321.3 179.7 324.9 FRAC 0.98 0.18 1.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 208.4 179.5 207.8 FRAC 1.00 0.50 1.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 30.1 177.6 34.1 FRAC 0.99 0.85 0.99 BFAC -0.12
REFINING SET #2 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.52 0.49 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 0.83 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 1.16 0.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 20 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
356.397 684.805 328.408
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 207.7 178.3 33.6 FRAC 0.53 0.48 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 211.7 178.5 33.0 FRAC 0.50 0.83 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 34.8 177.9 214.3 FRAC 0.51 1.17 0.01 BFAC -0.12
REFINING SET #3 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.52 0.33 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 0.66 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 0.99 0.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 19 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
354.634 575.969 221.335
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 146.3 179.7 330.0 FRAC 0.52 0.32 0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 210.6 177.7 34.6 FRAC 0.52 0.65 -0.01 BFAC -0.12
SOLU 6DIM ENSE complex EULER 28.8 179.5 208.2 FRAC 0.50 1.00 0.00 BFAC -0.12
REFINING SET #4 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 1.00 0.01 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 0.34 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 0.67 1.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 20 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
351.758 575.979 224.220
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 209.1 179.5 208.6 FRAC 1.00 -0.00 1.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 30.4 177.6 34.5 FRAC 0.98 0.35 0.99 BFAC -0.12
SOLU 6DIM ENSE complex EULER 321.6 179.7 325.2 FRAC 0.98 0.68 1.00 BFAC -0.12
REFINING SET #5 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 1.00 0.34 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 0.67 1.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 123.6 179.2 124.9 FRAC 0.99 1.00 1.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 16 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
350.010 684.865 334.855
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 214.6 177.8 214.1 FRAC 0.99 0.33 1.01 BFAC -0.12
SOLU 6DIM ENSE complex EULER 32.3 178.5 33.6 FRAC 1.00 0.67 1.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 28.8 178.3 34.7 FRAC 0.97 1.02 1.00 BFAC -0.12
REFINING SET #6 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.52 0.16 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 0.50 0.00 BFAC 0.00
SOLU 6DIM ENSE complex EULER 14.1 179.5 196.3 FRAC 0.51 0.83 0.00 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 20 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
350.017 684.768 334.751
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 34.7 177.9 214.2 FRAC 0.51 0.17 0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 207.9 178.3 33.8 FRAC 0.53 0.48 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 211.6 178.4 32.9 FRAC 0.50 0.83 -0.00 BFAC -0.12
REFINING SET #7 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.32 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.66 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.97 0.99 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 20 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
260.131 684.821 424.690
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 328.2 1.5 213.2 FRAC 1.00 0.33 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 145.4 2.1 34.1 FRAC 0.99 0.67 0.49 BFAC -0.12
SOLU 6DIM ENSE complex EULER 330.6 1.7 215.3 FRAC 0.97 0.98 0.50 BFAC -0.12
REFINING SET #8 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.49 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.82 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.97 1.16 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 16 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
259.838 575.967 316.129
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 151.0 0.5 28.5 FRAC 1.00 0.50 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 32.2 0.3 151.5 FRAC 0.98 0.82 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 329.6 2.4 214.5 FRAC 0.98 1.15 0.51 BFAC -0.12
REFINING SET #9 OF 15
---------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.16 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.98 0.49 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 176.4 1.2 7.3 FRAC 0.97 0.82 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 18 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
254.036 684.870 430.834
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 145.3 2.2 34.2 FRAC 0.99 0.17 0.49 BFAC -0.12
SOLU 6DIM ENSE complex EULER 331.4 1.7 214.5 FRAC 0.97 0.48 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 327.8 1.5 213.6 FRAC 1.00 0.83 0.50 BFAC -0.12
REFINING SET #10 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.53 0.01 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.52 0.34 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.51 0.67 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 19 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
237.318 684.874 447.556
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 151.5 1.7 214.5 FRAC 0.53 0.02 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 325.3 2.2 34.1 FRAC 0.51 0.33 0.49 BFAC -0.12
SOLU 6DIM ENSE complex EULER 147.9 1.5 213.4 FRAC 0.50 0.67 0.50 BFAC -0.12
REFINING SET #11 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.53 0.17 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.52 0.51 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.52 0.84 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 22 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
233.298 684.835 451.538
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 148.0 1.5 213.4 FRAC 0.50 0.17 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 151.6 1.7 214.3 FRAC 0.53 0.52 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 325.4 2.1 34.1 FRAC 0.51 0.83 0.49 BFAC -0.12
REFINING SET #12 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.53 0.34 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.52 0.67 0.50 BFAC 0.00
SOLU 6DIM ENSE complex EULER 326.4 1.6 36.5 FRAC 0.52 1.00 0.50 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 20 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
226.040 575.973 349.933
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 149.8 2.4 214.3 FRAC 0.51 0.35 0.51 BFAC -0.12
SOLU 6DIM ENSE complex EULER 215.8 0.3 147.9 FRAC 0.52 0.68 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 330.8 0.5 28.7 FRAC 0.50 1.00 0.50 BFAC -0.12
REFINING SET #13 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.02 0.50 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 0.83 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 1.16 0.51 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 22 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
133.993 575.962 441.969
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 150.6 0.5 28.9 FRAC 0.00 0.50 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 33.7 0.3 150.0 FRAC -0.02 0.82 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 329.9 2.4 214.1 FRAC -0.01 1.15 0.51 BFAC -0.12
REFINING SET #14 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.02 0.17 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 0.50 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 0.83 0.51 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 19 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
132.680 575.961 443.281
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 330.1 2.4 214.0 FRAC -0.01 0.15 0.51 BFAC -0.12
SOLU 6DIM ENSE complex EULER 150.9 0.5 28.5 FRAC 0.00 0.50 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 38.9 0.3 144.7 FRAC -0.02 0.82 0.50 BFAC -0.12
REFINING SET #15 OF 15
----------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.02 0.33 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 0.66 0.51 BFAC 0.00
SOLU 6DIM ENSE complex EULER 338.2 3.6 200.9 FRAC 0.01 1.00 0.51 BFAC 0.00
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 18 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
131.254 684.851 553.597
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 328.2 1.5 213.2 FRAC -0.00 0.33 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 145.3 2.1 34.2 FRAC -0.01 0.67 0.49 BFAC -0.12
SOLU 6DIM ENSE complex EULER 331.6 1.7 214.4 FRAC -0.03 0.98 0.50 BFAC -0.12
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Calculating Duplicates for 15 solutions
0% 100%
|================| DONE
13 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) = 685.074
Top LLG (packs) = 685.074
Mean LLG = -382.366
Percent used for purge = 75%
Cutoff for acceptance = 418.2
All Z-scores over 8.95971 retained
Number high TFZ retained = 0
Overall cutoff for acceptance (excluding high TFZ) = 576.6
Number of solutions stored before purge = 15
Number of solutions stored (deleted) after purge = 15 (0)
---------------
TFZ EQUIVALENTS
---------------
Translational NCS present
Refined TFZ equivalent not accurate and therefore not calculated
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 11 233.7 60.5 17.9 685.1 41.4 n/a P 21 21 21 1.112
--- 1 5 350.5 59.1 16.7 685.1 41.4 n/a P 21 21 21 1.112
--- 1 7 259.9 60.2 14.2 685.1 41.4 n/a P 21 21 21 1.112
--- 1 10 237.7 60.5 16.0 685.0 41.4 n/a P 21 21 21 1.112
--- 1 9 253.7 60.2 15.4 685.0 41.4 n/a P 21 21 21 1.112
--- 1 6 349.4 59.2 17.8 685.0 41.4 n/a P 21 21 21 1.112
--- 1 15 133.0 62.2 11.4 685.0 41.4 n/a P 21 21 21 1.112
--- 1 2 355.9 59.1 17.9 684.7 41.4 n/a P 21 21 21 1.112
2 --- 13 135.7 62.2 16.9 577.3 46.0 n/a P 21 21 21 n/a
--- 2 12 226.4 60.6 15.8 577.3 46.0 n/a P 21 21 21 n/a
--- 2 14 134.1 62.0 12.0 577.1 46.1 n/a P 21 21 21 n/a
--- 2 4 352.4 59.0 16.9 577.0 46.0 n/a P 21 21 21 n/a
--- 2 3 354.1 59.1 16.3 577.0 46.0 n/a P 21 21 21 n/a
--- 2 1 356.3 59.0 15.7 576.9 46.1 n/a P 21 21 21 n/a
--- 2 8 259.8 60.2 15.5 576.6 46.0 n/a P 21 21 21 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (15 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
complex 1 0.432 +0.000/+0.000 ( 0.432/ 0.432 )
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC P 21 21 21
SOLU 6DIM ENSE complex EULER 148.0 1.5 213.4 FRAC 0.50 0.17 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 151.6 1.7 214.3 FRAC 0.53 0.52 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 325.4 2.1 34.1 FRAC 0.51 0.83 0.49 BFAC -0.12
No files output
CPU Time: 0 days 0 hrs 3 mins 5.06 secs ( 185.06 secs)
Finished: Fri Mar 27 13:15:43 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Current is Best Solution (first search)
** Current solution has 3 components
** New Best LLG = 685.1 (resolution = 4.79)
** Best Component so far = complex
CPU Time: 0 days 0 hrs 3 mins 5.11 secs ( 185.11 secs)
Finished: Fri Mar 27 13:15:43 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Solutions will be refined to highest resolution
** Resolution for refinement: 2.45181
** Protocol for MR refinement is DEFAULT
** VRMS (variances) of ensemble(s) WILL be refined
CPU Time: 0 days 0 hrs 3 mins 6.40 secs ( 186.40 secs)
Finished: Fri Mar 27 13:15:44 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46979)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
-------------------
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 (42134)
- half number of centrics (4845/2)
= -44556
With correction for SigF,
Wilson log(likelihood) = -40782.6
----------
ENSEMBLING
----------
Ensemble Generation: complex
----------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 2.45
Electron Density Calculation
0% 100%
|=======| DONE
Ensemble Generation
-------------------
Resolution of Ensembles: 2.45181
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
33.0 30.6 1 -8.1 0.432 0.000 0.432 complex
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 3.00 2.00
----------
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 are 2 solutions to refine
Refining solutions
0% 100%
|===| DONE
REFINING SET #1 OF 2
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 148.0 1.5 213.4 FRAC 0.50 0.17 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 151.6 1.7 214.3 FRAC 0.53 0.52 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 325.4 2.1 34.1 FRAC 0.51 0.83 0.49 BFAC -0.12
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 3 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
2332.053 2582.603 250.550
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 138.7 1.6 222.6 FRAC 0.50 0.17 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 145.8 2.1 220.8 FRAC 0.53 0.52 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 323.9 2.0 35.4 FRAC 0.50 0.83 0.50 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
REFINING SET #2 OF 2
--------------------
Initial Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 150.6 0.5 28.9 FRAC 0.00 0.50 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 33.7 0.3 150.0 FRAC -0.02 0.82 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 329.9 2.4 214.1 FRAC -0.01 1.15 0.51 BFAC -0.12
Performing Optimization...
Done
--- Convergence before iteration limit (50) at cycle 5 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
1844.174 2091.320 247.146
Final Parameters:
SOLU SET
SOLU 6DIM ENSE complex EULER 274.6 0.2 265.5 FRAC 0.00 0.50 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 328.5 2.0 217.5 FRAC -0.03 0.81 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 320.3 2.5 224.2 FRAC -0.02 1.15 0.51 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Calculating Duplicates for 2 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) = 2581.76
Top LLG (packs) = 2581.76
Mean LLG = -382.366
Percent used for purge = 75%
Cutoff for acceptance = 1840.7
All Z-scores over 8.95971 retained
Number high TFZ retained = 0
Overall cutoff for acceptance (excluding high TFZ) = 2090.4
Number of solutions stored before purge = 2
Number of solutions stored (deleted) after purge = 2 (0)
---------------
TFZ EQUIVALENTS
---------------
Translational NCS present
Refined TFZ equivalent not accurate and therefore not calculated
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 2331.9 45.4 17.9 2581.8 44.3 n/a P 21 21 21 1.199
2 --- 2 1844.9 50.5 16.9 2090.4 49.5 n/a P 21 21 21 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (2 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
complex 1 0.432 -0.171/-0.171 ( 0.123/ 0.123 )
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC P 21 21 21
SOLU 6DIM ENSE complex EULER 138.7 1.6 222.6 FRAC 0.50 0.17 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 145.8 2.1 220.8 FRAC 0.53 0.52 0.50 BFAC -0.12
SOLU 6DIM ENSE complex EULER 323.9 2.0 35.4 FRAC 0.50 0.83 0.50 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
No files output
CPU Time: 0 days 0 hrs 3 mins 38.81 secs ( 218.81 secs)
Finished: Fri Mar 27 13:16:18 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** Refinement may have introduced clashes
** Packing will be checked
CPU Time: 0 days 0 hrs 3 mins 38.85 secs ( 218.85 secs)
Finished: Fri Mar 27 13:16:18 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT PACKING ANALYSIS 2.8.3 ***
******************************************************************************************
---------
ENSEMBLES
---------
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 3.00 2.00
-----------------
ENSEMBLE SYMMETRY
-----------------
Ensemble "complex" Point Group: 1
Clash background has NOT been packed at 10.00%
----------------
PACKING FUNCTION
----------------
There are 2 solutions 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 0.716 -- P 21 21 21 RFZ=10.4 TFZ=14.4 +TNCS PAK=1 LLG=685 LLG=2582 PAK=1
2 2 0 -- P 21 21 21 RFZ=9.0 TFZ=12.3 +TNCS PAK=0 LLG=577 LLG=2090 PAK=0
2 accepted of 2 solutions
2 pack of 2 accepted solutions
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 3 mins 39.68 secs ( 219.68 secs)
Finished: Fri Mar 27 13:16:18 2020
******************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.8.3 ***
******************************************************************************************
-----------------
TRANSLATIONAL NCS
-----------------
tNCS vector = -0.00554301 0.333265 0
tNCS NMOL = 3
-------------------------------
DATA FOR REFINEMENT AND PHASING
-------------------------------
Outlier Rejection
-----------------
There were 10 reflections of 46989 (0.0213%) rejected as outliers
- outliers with a Wilson probability less than 1e-06
- measurements expected to contain fewer than 0.01 bits of information
H K L reso Eo^2 sigma probability wilson low-info
2 0 52 3.16 25.598 0.953 4.756e-07 true false
2 3 50 3.27 23.141 0.598 1.065e-10 true false
2 3 51 3.21 15.649 0.390 1.726e-07 true false
3 6 49 3.28 17.389 0.455 3.112e-08 true false
4 3 49 3.29 16.555 0.473 7.225e-08 true false
4 7 47 3.36 15.165 0.347 2.754e-07 true false
5 7 47 3.32 22.391 0.634 2.307e-10 true false
6 4 48 3.25 19.418 0.476 4.130e-09 true false
7 4 47 3.26 17.779 0.673 2.384e-08 true false
23 9 16 2.63 17.860 0.487 1.972e-08 true false
Resolution of All Data (Number): 2.45 50.01 (46989)
Resolution of Selected Data (Number): 2.45 50.01 (46979)
Translational NCS:
Vector = -0.0055 0.3333 0.0000
Rotation = 0.0000 0.0000 0.0000
D values (lores-hires)= 0.9222- 0.0971
-------------------
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 (42134)
- half number of centrics (4845/2)
= -44556
With correction for SigF,
Wilson log(likelihood) = -40782.6
----------
ENSEMBLING
----------
Ensemble Generation
-------------------
Resolution of Ensembles: 2.45181
Scat% Radius Model# Rel-B RMS DRMS VRMS Ensemble
33.0 30.6 1 -8.1 0.432 0.000 0.432 complex
Trace Generation
----------------
Ensemble Trace-type Length Sampling Close-contact
complex C-alpha 419 3.00 2.00
-------
SCORING
-------
There are 2 solutions to score
Scoring solutions
0% 100%
|===| DONE
---------------
FIND DUPLICATES
---------------
Check for nearly equivalent solutions
Calculating Duplicates for 2 solutions
0% 100%
|===| DONE
No duplicate solutions found
---------------------
FIND TEMPLATE MATCHES
---------------------
No Template Solution(s) for comparison
---------------
TFZ EQUIVALENTS
---------------
Translational NCS present
Refined TFZ equivalent not accurate and therefore not calculated
-------
RESULTS
-------
Refinement Table (Sorted)
-------------------------
Refinement to full resolution
#out =#out #in =T (Start LLG Rval TFZ) (Refined LLG Rval TFZ==) SpaceGroup Cntrst
Top1 --- 1 2581.8 44.3 n/a 2581.8 44.3 n/a P 21 21 21 1.199
2 --- 2 2090.4 49.5 n/a 2090.4 49.5 n/a P 21 21 21 n/a
Refinement Table (Variance Ranges)
----------------------------------
Range of delta-VRMS and VRMS given over current solution list (2 solution(s))
Ensemble Model# RMS Delta-VRMS min/max (VRMS min/max)
complex 1 0.432 -0.171/-0.171 ( 0.123/ 0.123 )
------------
OUTPUT FILES
------------
Calculation of Map Coefficients
-------------------------------
1 top map coefficients calculated
Map coefficient calculated for top solution #1
SOLU SPAC P 21 21 21
SOLU 6DIM ENSE complex EULER 41.3 178.4 42.6 FRAC -0.50 -0.33 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 34.2 177.9 40.8 FRAC -0.53 0.02 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 143.9 2.0 35.4 FRAC -1.00 0.17 -0.00 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
No files output
CPU Time: 0 days 0 hrs 3 mins 43.67 secs ( 223.67 secs)
Finished: Fri Mar 27 13:16:22 2020
******************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.8.3 ***
******************************************************************************************
** There were 2 solutions
** Pdb and/or Mtz files have been written with results for 1 of these solutions
** Solution #1 written to PDB file: 3022Natalia_phaser.1.pdb
** Solution #1 written to MTZ file: 3022Natalia_phaser.1.mtz
Solution #1 annotation (history):
SOLU SET RFZ=10.4 TFZ=14.4 +TNCS PAK=1 LLG=685 LLG=2582 PAK=1 LLG=2582
SOLU SPAC P 21 21 21
SOLU 6DIM ENSE complex EULER 41.3 178.4 42.6 FRAC -0.50 -0.33 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 34.2 177.9 40.8 FRAC -0.53 0.02 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 143.9 2.0 35.4 FRAC -1.00 0.17 -0.00 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
Solution #2 annotation (history):
SOLU SET RFZ=9.0 TFZ=12.3 +TNCS PAK=0 LLG=577 LLG=2090 PAK=0 LLG=2090
SOLU SPAC P 21 21 21
SOLU 6DIM ENSE complex EULER 265.4 179.8 85.5 FRAC -0.00 -0.00 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 211.5 178.0 37.5 FRAC 0.03 0.31 -0.00 BFAC -0.12
SOLU 6DIM ENSE complex EULER 140.3 2.5 224.2 FRAC -0.48 -0.15 0.01 BFAC -0.12
SOLU ENSEMBLE complex VRMS DELTA -0.1714 #RMSD 0.43 #VRMS 0.12
CPU Time: 0 days 0 hrs 3 mins 43.79 secs ( 223.79 secs)
Finished: Fri Mar 27 13:16:23 2020
--------
ADVISORY
--------
NMOL (3) set by analysis. If structure solution fails consider other tNCS
--------
WARNINGS
--------
------------------------------------------------------------------------------------------
Warning: Number of search copies for complex (2) not divisible by 3
Number of search copies edited
------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------
Warning: Total search request exceeds scattering specified in composition. Composition
increased to resolve the discrepancy.
------------------------------------------------------------------------------------------
--------------------
EXIT STATUS: SUCCESS
--------------------
CPU Time: 0 days 0 hrs 3 mins 43.81 secs ( 223.81 secs)
Finished: Fri Mar 27 13:16:23 2020