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### CCP4 PROGRAM SUITE: Phaser 2.5.7 ###
#####################################################################################
User: jmht42
Run time: Fri Feb 13 14:17:55 2015
Version: 2.5.7
Release Date: Wed Jan 14 13:55:29 2015
If you use this software please cite:
$TEXT:Reference1: $$ $$
"Phaser Crystallographic Software"
A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni & R.J. Read
J. Appl. Cryst. (2007). 40, 658-674
PDF
$$
*************************************************************************************
*** Phaser Module: PREPROCESSOR 2.5.7 ***
*************************************************************************************
ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT
$TEXT:Script: $$ Baubles Markup $$
MODE MR_AUTO
HKLIN &
/volatile/jmht42/testset/percent/1UCS/ROSETTA_MR_0/MRBUMP/search_c1_tl100_r3_allato &
m_mrbump/input/1UCS.mtz
LABIN F=F SIGF=SIGF
COMPosition PROTein MW 6906.275 NUM 1
ENSEmble autoMR PDBFile &
/volatile/jmht42/testset/percent/1UCS/ROSETTA_MR_0/MRBUMP/search_c1_tl100_r3_allato &
m_mrbump/data/loc0_ALL_c1_tl100_r3_allatom/unmod/MODEL_UNMOD_loc0_ALL_c1_tl100_r3_a &
llatom.pdb RMS 0.100
SEARCH ENSEmble autoMR NUM 1
XYZOUT ON
JOBS 1
PACK CUTOFF 5
SGALTERNATIVE SELECT NONE
ROOT phaser_loc0_ALL_c1_tl100_r3_allatom_UNMOD
KILL TIME 360
END
$$
CPU Time: 0 days 0 hrs 0 mins 0.00 secs ( 0.00 secs)
Finished: Fri Feb 13 14:17:55 2015
*************************************************************************************
*** Phaser Module: READ DATA FROM MTZ FILE 2.5.7 ***
*************************************************************************************
Data read from mtz file:
/volatile/jmht42/testset/percent/1UCS/ROSETTA_MR_0/MRBUMP/search_c1_tl100_r3_allat
om_mrbump/input/1UCS.mtz
Space-Group Name (Hall Symbol): P 21 21 21 ( P 2ac 2ab)
Space-Group Number: 19
Unit Cell: 32.50 39.50 44.64 90.00 90.00 90.00
Column Labels Selected: F SIGF
Resolution on Mtz file: 0.62 29.58
Resolution Selected: 0.62 22.32
Number of Reflections in Selected Resolution Range: 118502
CPU Time: 0 days 0 hrs 0 mins 0.13 secs ( 0.13 secs)
Finished: Fri Feb 13 14:17:55 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
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: Ensemble autoMR
Automatic (best predicted) search order WILL be used
One test spacegroup
P 21 21 21
CPU Time: 0 days 0 hrs 0 mins 0.22 secs ( 0.22 secs)
Finished: Fri Feb 13 14:17:55 2015
*************************************************************************************
*** Phaser Module: CELL CONTENT ANALYSIS 2.5.7 ***
*************************************************************************************
Space-Group Name (Hall Symbol): P 21 21 21 ( P 2ac 2ab)
Space-Group Number: 19
Unit Cell: 32.50 39.50 44.64 90.00 90.00 90.00
MW of "average" protein to which Matthews applies: 6907
Resolution for Matthews calculation: 0.62
Z MW VM % solvent rel. freq.
1 6907 2.07 40.71 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 ---------------------------------------------
2.08 --------------------------------------------------
2.00 ************************************************ (COMPOSITION*1)
1.92 ---------------------------------------
1.85 --------------------------
1.79 --------------
1.72 ------
1.67 --
1.61 -
1.56 -
1.52 -
1.47 -
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25 -
$TABLE : Cell Content Analysis:
$SCATTER
:N*Composition vs Probability:0|2x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.956149
$$
Most probable VM for resolution = 2.06225
Most probable MW of protein in asu for resolution = 6947.66
CPU Time: 0 days 0 hrs 0 mins 0.26 secs ( 0.26 secs)
Finished: Fri Feb 13 14:17:55 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Composition Table
-----------------
Total Scattering = 22519.9
Ensemble Fraction Scattering
autoMR 100.30%
CPU Time: 0 days 0 hrs 0 mins 0.26 secs ( 0.26 secs)
Finished: Fri Feb 13 14:17:55 2015
*************************************************************************************
*** Phaser Module: ANISOTROPY CORRECTION 2.5.7 ***
*************************************************************************************
------------------------------
DATA FOR ANISOTROPY CORRECTION
------------------------------
Resolution of All Data (Number): 0.62 22.32 (118502)
Resolution of Selected Data (Number): 0.62 22.32 (118502)
---------------------
ANISOTROPY CORRECTION
---------------------
Protocol cycle #1 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Protocol cycle #2 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Protocol cycle #3 of 3
Refinement protocol for this macrocycle:
BIN SCALES: REFINE
ANISOTROPY: REFINE
SOLVENT K: FIX
SOLVENT B: FIX
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 2 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222311.193 222581.182 269.989
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.298
Resharpening B (to restore strong direction of diffraction): -0.186
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222581.182 222581.185 0.003
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.298
Resharpening B (to restore strong direction of diffraction): -0.186
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222581.185 222581.188 0.003
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.298
Resharpening B (to restore strong direction of diffraction): -0.186
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.298
Resharpening B (to restore strong direction of diffraction): -0.186
--------------
ABSOLUTE SCALE
--------------
Scale factor to put input Fs on absolute scale
Wilson Scale: 0.970961
Wilson B-factor: 3.98566
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 10.70 secs ( 10.70 secs)
Finished: Fri Feb 13 14:18:05 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
eLLG Values Computed for All Data
---------------------------------
eLLG with all data for ensemble "autoMR": 40815.8
Automatic (Best Predicted) Search Order
---------------------------------------
Search Order determined by best expected LLG
#1: Ensemble autoMR
CPU Time: 0 days 0 hrs 0 mins 10.74 secs ( 10.74 secs)
Finished: Fri Feb 13 14:18:05 2015
*************************************************************************************
*** Phaser Module: TRANSLATIONAL NON-CRYSTALLOGRAPHIC SYMMETRY 2.5.7 ***
*************************************************************************************
Unit Cell: 32.50 39.50 44.64 90.00 90.00 90.00
-------------------------------------
DATA FOR TRANSLATIONAL NCS CORRECTION
-------------------------------------
Intensity Moments for Data
--------------------------
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: 2.69
2nd Moment Acentric: 1.98
Resolution for Twin Analysis (85% I/SIGI > 3): 1.55A (HiRes=0.62A)
$TABLE : Intensity distribution for Data:
$GRAPHS
:Cumulative intensity distribution (acentric and centric):N:1,2,3,4,5,6:
$$
Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser
$$ loggraph $$
0 0 0 0 0 0
0.04 0.0392106 0.0030343 0.0318108 0.158519 0.104993
0.08 0.0768837 0.0115132 0.0687874 0.222703 0.180617
0.12 0.11308 0.0245815 0.107123 0.270966 0.232012
0.16 0.147856 0.0414833 0.141245 0.310843 0.27533
0.2 0.181269 0.0615519 0.1736 0.345279 0.307636
0.24 0.213372 0.0842006 0.2031 0.375794 0.334068
0.28 0.244216 0.108914 0.238309 0.403299 0.361968
0.32 0.273851 0.13524 0.265498 0.428392 0.389134
0.36 0.302324 0.162786 0.294454 0.451494 0.419971
0.4 0.32968 0.191208 0.321234 0.472911 0.443465
0.44 0.355964 0.220208 0.34652 0.492878 0.464023
0.48 0.381217 0.24953 0.370718 0.511578 0.477239
0.52 0.405479 0.278952 0.397771 0.529158 0.488987
0.56 0.428791 0.308287 0.423056 0.54574 0.504405
0.6 0.451188 0.337373 0.444399 0.561422 0.516153
0.64 0.472708 0.366075 0.463431 0.576289 0.5279
0.68 0.493383 0.394281 0.486813 0.590413 0.546256
0.72 0.513248 0.421896 0.507749 0.603856 0.558003
0.76 0.532334 0.448846 0.527732 0.616672 0.567548
0.8 0.550671 0.475069 0.5469 0.628907 0.586637
0.84 0.56829 0.500518 0.566612 0.640603 0.599119
0.88 0.585217 0.525156 0.583605 0.651798 0.609398
0.92 0.601481 0.548959 0.600462 0.662525 0.621145
0.96 0.617107 0.571908 0.617047 0.672813 0.637298
1 0.632121 0.593994 0.633225 0.682689 0.648311
1.04 0.646545 0.615215 0.648722 0.692179 0.65859
1.08 0.660404 0.635573 0.664492 0.701302 0.67254
1.12 0.67372 0.655074 0.679717 0.710082 0.681351
1.16 0.686514 0.673732 0.692632 0.718534 0.693833
1.2 0.698806 0.691559 0.706226 0.726678 0.707783
1.24 0.710616 0.708574 0.718733 0.734529 0.712922
1.28 0.721963 0.724795 0.730016 0.742101 0.721733
1.32 0.732865 0.740245 0.741572 0.749408 0.730543
1.36 0.743339 0.754946 0.751495 0.756463 0.737885
1.4 0.753403 0.768922 0.762507 0.763276 0.743759
1.44 0.763072 0.782197 0.772567 0.769861 0.751836
1.48 0.772362 0.794797 0.780587 0.776226 0.758443
1.52 0.781288 0.806747 0.788608 0.782381 0.767254
1.56 0.789864 0.818072 0.796221 0.788335 0.772394
1.6 0.798103 0.828799 0.805329 0.794097 0.779001
1.64 0.80602 0.838951 0.813214 0.799674 0.784141
1.68 0.813626 0.848554 0.820555 0.805076 0.78928
1.72 0.820934 0.857633 0.828847 0.810307 0.792952
1.76 0.827955 0.866211 0.837004 0.815376 0.803231
1.8 0.834701 0.874311 0.842985 0.820287 0.812041
1.84 0.841183 0.881957 0.848423 0.825049 0.817181
1.88 0.84741 0.889169 0.853861 0.829666 0.823054
1.92 0.853393 0.895971 0.858347 0.834143 0.831131
1.96 0.859142 0.902382 0.862153 0.838487 0.834068
2 0.864665 0.908422 0.868951 0.842701 0.837004
$$
---------------------
ANISOTROPY CORRECTION
---------------------
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222581.188 222581.189 0.001
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.299
Resharpening B (to restore strong direction of diffraction): -0.186
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222581.189 222581.197 0.008
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.299
Resharpening B (to restore strong direction of diffraction): -0.186
Performing Minimization...
Done
--- Convergence before iteration limit (50) at cycle 1 ---
Start-this-macrocycle End-this-macrocycle Change-this-macrocycle
222581.197 222581.197 0.000
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.299
Resharpening B (to restore strong direction of diffraction): -0.186
Refined Anisotropy Parameters
-----------------------------
Principal components of anisotropic part of B affecting observed amplitudes:
eigenB (A^2) direction cosines (orthogonal coordinates)
0.112 -0.0000 0.0000 1.0000
0.074 1.0000 -0.0000 0.0000
-0.186 0.0000 1.0000 -0.0000
Anisotropic deltaB (i.e. range of principal components): 0.299
Resharpening B (to restore strong direction of diffraction): -0.186
Intensity Moments after Anisotropy Correction
---------------------------------------------
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: 2.70
2nd Moment Acentric: 1.98
Resolution for Twin Analysis (85% I/SIGI > 3): 1.55A (HiRes=0.62A)
$TABLE : Intensity distribution after Anisotropy Correction:
$GRAPHS
:Cumulative intensity distribution (acentric and centric):N:1,2,3,4,5,6:
$$
Z ACent_theor ACent_twin ACent_obser Cent_theor Cent_obser
$$ loggraph $$
0 0 0 0 0 0
0.04 0.0392106 0.0030343 0.0316748 0.158519 0.106461
0.08 0.0768837 0.0115132 0.0689233 0.222703 0.179148
0.12 0.11308 0.0245815 0.107667 0.270966 0.234214
0.16 0.147856 0.0414833 0.140973 0.310843 0.27533
0.2 0.181269 0.0615519 0.17292 0.345279 0.306167
0.24 0.213372 0.0842006 0.203507 0.375794 0.334802
0.28 0.244216 0.108914 0.238037 0.403299 0.363436
0.32 0.273851 0.13524 0.264954 0.428392 0.389868
0.36 0.302324 0.162786 0.294182 0.451494 0.419971
0.4 0.32968 0.191208 0.320691 0.472911 0.440529
0.44 0.355964 0.220208 0.346248 0.492878 0.463289
0.48 0.381217 0.24953 0.370854 0.511578 0.478708
0.52 0.405479 0.278952 0.397635 0.529158 0.488987
0.56 0.428791 0.308287 0.423872 0.54574 0.506608
0.6 0.451188 0.337373 0.443991 0.561422 0.516153
0.64 0.472708 0.366075 0.463023 0.576289 0.5279
0.68 0.493383 0.394281 0.48627 0.590413 0.542584
0.72 0.513248 0.421896 0.507749 0.603856 0.558737
0.76 0.532334 0.448846 0.527325 0.616672 0.56975
0.8 0.550671 0.475069 0.546221 0.628907 0.587372
0.84 0.56829 0.500518 0.566748 0.640603 0.599119
0.88 0.585217 0.525156 0.584149 0.651798 0.610132
0.92 0.601481 0.548959 0.601006 0.662525 0.621145
0.96 0.617107 0.571908 0.616504 0.672813 0.63583
1 0.632121 0.593994 0.633768 0.682689 0.650514
1.04 0.646545 0.615215 0.64913 0.692179 0.657856
1.08 0.660404 0.635573 0.664084 0.701302 0.67254
1.12 0.67372 0.655074 0.679173 0.710082 0.680617
1.16 0.686514 0.673732 0.692632 0.718534 0.693098
1.2 0.698806 0.691559 0.706362 0.726678 0.706314
1.24 0.710616 0.708574 0.719141 0.734529 0.712922
1.28 0.721963 0.724795 0.730288 0.742101 0.720999
1.32 0.732865 0.740245 0.741028 0.749408 0.731278
1.36 0.743339 0.754946 0.751631 0.756463 0.73862
1.4 0.753403 0.768922 0.762235 0.763276 0.743759
1.44 0.763072 0.782197 0.771615 0.769861 0.754038
1.48 0.772362 0.794797 0.780859 0.776226 0.762115
1.52 0.781288 0.806747 0.78888 0.782381 0.767988
1.56 0.789864 0.818072 0.795949 0.788335 0.771659
1.6 0.798103 0.828799 0.804377 0.794097 0.776799
1.64 0.80602 0.838951 0.81335 0.799674 0.783407
1.68 0.813626 0.848554 0.82205 0.805076 0.78928
1.72 0.820934 0.857633 0.829391 0.810307 0.795888
1.76 0.827955 0.866211 0.836324 0.815376 0.806167
1.8 0.834701 0.874311 0.843393 0.820287 0.812041
1.84 0.841183 0.881957 0.849239 0.825049 0.820117
1.88 0.84741 0.889169 0.853045 0.829666 0.823789
1.92 0.853393 0.895971 0.857803 0.834143 0.831131
1.96 0.859142 0.902382 0.863241 0.838487 0.834802
2 0.864665 0.908422 0.87031 0.842701 0.839941
$$
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
Space Group : P 21 21 21
Patterson Symmetry: P m m m
Resolution of All Data (Number): 0.62 22.32 (118502)
Resolution of Patterson (Number): 5.00 9.97 (251)
There were no non-origin Patterson peaks
No translational ncs found or input
tNCS/Twin Detection Table
-------------------------
No NCS translation vector
-Second Moments- --P-values--
Centric Acentric untwinned twin frac <5%
Theoretical for untwinned 3.00 2.00
Theoretical for perfect twin 2.00 1.50
Initial (data as input) 2.69 1.98+/-0.052 0.346 1
After Anisotropy Correction 2.70 1.98+/-0.052 0.337 1
Resolution for Twin Analysis (85% I/SIGI > 3): 1.55A (HiRes=0.62A)
------------
OUTPUT FILES
------------
No files output
CPU Time: 0 days 0 hrs 0 mins 18.33 secs ( 18.33 secs)
Finished: Fri Feb 13 14:18:13 2015
*************************************************************************************
*** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.7 ***
*************************************************************************************
Search Order (next search *):
#1: Ensemble autoMR *
CPU Time: 0 days 0 hrs 0 mins 18.33 secs ( 18.33 secs)
Finished: Fri Feb 13 14:18:13 2015
*************************************************************************************
*** Phaser Module: MOLECULAR REPLACEMENT ROTATION FUNCTION 2.5.7 ***
*************************************************************************************
---------------------
ANISOTROPY CORRECTION
---------------------
No refinement of parameters
------------------------
TRANSLATIONAL NCS VECTOR
------------------------
Space Group : P 21 21 21
Patterson Symmetry: P m m m
Resolution of All Data (Number): 0.62 22.32 (118502)
Resolution of Patterson (Number): 5.00 9.97 (251)
There were no non-origin Patterson peaks
No translational ncs found or input
--------------------------
DATA FOR ROTATION FUNCTION
--------------------------
Expected LLG
------------
Target = 120.000
eLLG = 120.078 (at 4.77A)
eLLG indicates that placement of ensemble "autoMR" will be straightforward
The data are sufficient to exceed the eLLG target
High resolution limit imposed by expected LLG = 4.77
Outliers with a probability less than 1e-06 will be rejected
There were 1 (0.0008%) reflections rejected
H K L reso F probability
22 9 44 0.82 58.500 2.075e-07
Resolution of All Data (Number): 0.62 22.32 (118502)
Resolution of Selected Data (Number): 4.77 22.32 (326)
-------------------
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 (203)
- half number of centrics (123/2)
= -264
With correction for SigF,
Wilson log(likelihood) = -263.274
----------
ENSEMBLING
----------
Ensemble Generation: autoMR
---------------------------
Ensemble configured for structure factor interpolation
Ensemble configured to resolution 4.77
PDB file # 1: MODEL_UNMOD_loc0_ALL_c1_tl100_r3_allatom.pdb
This pdb file contains 7 models
The input RmsD of model #1 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #1 with respect to the real structure is 0.24
The input RmsD of model #2 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #2 with respect to the real structure is 0.24
The input RmsD of model #3 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #3 with respect to the real structure is 0.24
The input RmsD of model #4 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #4 with respect to the real structure is 0.24
The input RmsD of model #5 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #5 with respect to the real structure is 0.24
The input RmsD of model #6 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #6 with respect to the real structure is 0.24
The input RmsD of model #7 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #7 with respect to the real structure is 0.24
Input VRMS delta = 0.000000
VRMS delta lower/upper limit = 0.000000 / 9.388516
Final VRMS delta = 0.000000
Electron Density Calculation
0% 100%
|===============================| DONE
Weighting Structure Factors
0% 100%
|===================================================================| DONE
Ensembling Table
----------------
Resolution of Ensembles: 4.768
Ensemble Scat% Radius Model# Rel-B RMS
autoMR 100.3 18.53 1 -0.0 0.238
2 -0.0 0.238
3 -0.0 0.238
4 -0.0 0.238
5 -0.0 0.238
6 -0.0 0.238
7 -0.0 0.238
Ensemble Generation for Spherical Harmonic Decomposition: autoMR
----------------------------------------------------------------
Ensemble configured for spherical harmonic decomposition
Ensemble configured to resolution 4.77
PDB file # 1: MODEL_UNMOD_loc0_ALL_c1_tl100_r3_allatom.pdb
This pdb file contains 7 models
The input RmsD of model #1 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #1 with respect to the real structure is 0.24
The input RmsD of model #2 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #2 with respect to the real structure is 0.24
The input RmsD of model #3 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #3 with respect to the real structure is 0.24
The input RmsD of model #4 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #4 with respect to the real structure is 0.24
The input RmsD of model #5 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #5 with respect to the real structure is 0.24
The input RmsD of model #6 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #6 with respect to the real structure is 0.24
The input RmsD of model #7 with respect to the real structure is 0.10
Allowed range (resolution and radius dependent) is 0.24 to 3.09
The initial RmsD of model #7 with respect to the real structure is 0.24
Input VRMS delta = 0.000000
VRMS delta lower/upper limit = 0.000000 / 9.388516
Final VRMS delta = 0.000000
Electron Density Calculation
0% 100%
|===============================| DONE
Weighting Structure Factors
0% 100%
|==========| DONE
Elmn for Search Ensemble
Elmn Calculation for Search Ensemble
0% 100%
|=======================================================================| DONE
Target Function: FAST LERF1
-------------------------
ROTATION FUNCTION #1 OF 1
-------------------------
Search Ensemble: autoMR
Sampling: 7.36 degrees
Known MR solutions
(empty solution set - no components)
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 54% of top
There were 925 sites over 67.5% of top
925 peaks selected
The sites over 67.5% are:
# Euler1 Euler2 Euler3 FSS Z-score
1 67.3 74.1 322.0 100.000 3.64
2 68.0 74.9 323.3 97.591 3.55
3 58.4 69.9 105.4 95.580 3.48
#SITES = 925: OUTPUT TRUNCATED TO 3 SITES
Top 925 rotations before clustering will be rescored
Calculating Likelihood for RF #1 of 1
0% 100%
|===================terminate called after throwing an instance of 'phaser::error'
what(): Program internal error in source file DataMR.cc (line 576)
*** Consistency check (V > 0) failed. ***
Please email this log file with some supporting information and data to cimr-phaser@lists.cam.ac.uk