Polish後の3D auto-refineの標準出力

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2019年6月4日 (火) 11:37時点におけるKttn (トーク | 投稿記録)による版

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RELION version: 3.0.5 
Precision: BASE=double, CUDA-ACC=single 

 === RELION MPI setup ===
 + Number of MPI processes             = 5
 + Number of threads per MPI process  = 3
 + Total number of threads therefore  = 15
 + Master  (0) runs on host            = relion-docker
 + Slave     1 runs on host            = relion-docker
 + Slave     2 runs on host            = relion-docker
 + Slave     3 runs on host            = relion-docker
 + Slave     4 runs on host            = relion-docker
 =================
 uniqueHost relion-docker has 4 ranks.
 Slave 1 will distribute threads over devices  0
 Thread 0 on slave 1 mapped to device 0
 Thread 1 on slave 1 mapped to device 0
 Thread 2 on slave 1 mapped to device 0
 Slave 2 will distribute threads over devices  1
 Thread 0 on slave 2 mapped to device 1
 Thread 1 on slave 2 mapped to device 1
 Thread 2 on slave 2 mapped to device 1
 Slave 3 will distribute threads over devices  2
 Thread 0 on slave 3 mapped to device 2
 Thread 1 on slave 3 mapped to device 2
 Thread 2 on slave 3 mapped to device 2
 Slave 4 will distribute threads over devices  3
 Thread 0 on slave 4 mapped to device 3
 Thread 1 on slave 4 mapped to device 3
 Thread 2 on slave 4 mapped to device 3
 Running CPU instructions in double precision. 
 Estimating initial noise spectra 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 1
 Auto-refine: Resolution= 53.1 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 999 degrees; and in offsets= 999 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   0/   0 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 14.24 degrees; offsets= 5.51 pixels
 Auto-refine: WARNING: The angular accuracy is worse than 10 degrees, so basically you cannot align your particles (yet)!
 Auto-refine: WARNING: You probably need not worry if the accuracy improves during the next few iterations.
 Auto-refine: WARNING: However, if the problem persists it may lead to spurious FSC curves, so be wary of inflated resolution estimates...
 Auto-refine: WARNING: Sometimes it is better to tune resolution yourself by adjusting T in a 3D-classification with a single class.
 CurrentResolution= 53.1 Angstroms, which requires orientationSampling of at least 30 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 1
   4/   4 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 53.1 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       19.9125 Angstroms
 Maximization ...
   7/   7 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 2
 Auto-refine: Resolution= 19.9125 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 22.4263 degrees; and in offsets= 2.57111 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   0/   0 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 6.205 degrees; offsets= 2.532 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 19.9125 Angstroms, which requires orientationSampling of at least 11.25 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 2
   3/   3 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       12.2538 Angstroms
 Maximization ...
   9/   9 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 3
 Auto-refine: Resolution= 12.2538 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 22.3741 degrees; and in offsets= 2.40324 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   1/   1 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 2.467 degrees; offsets= 0.968 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 12.2538 Angstroms, which requires orientationSampling of at least 6.92308 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 3
   5/   5 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       16.7684 Angstroms
 Maximization ...
  20/  20 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 4
 Auto-refine: Resolution= 5.58947 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 4.94432 degrees; and in offsets= 0.756971 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.677 degrees; offsets= 0.633 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 5.58947 Angstroms, which requires orientationSampling of at least 3.18584 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 4
   7/   7 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       16.7684 Angstroms
 Maximization ...
1.58/1.58 min ............................................................~~(,_,">
 Auto-refine: Iteration= 5
 Auto-refine: Resolution= 5.13871 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 4.86417 degrees; and in offsets= 0.738034 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.447 degrees; offsets= 0.549 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 5.13871 Angstroms, which requires orientationSampling of at least 2.92683 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 5
   7/   7 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       16.7684 Angstroms
 Maximization ...
1.57/1.57 min ............................................................~~(,_,">
 Auto-refine: Iteration= 6
 Auto-refine: Resolution= 4.82727 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 4.83247 degrees; and in offsets= 0.710338 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.376 degrees; offsets= 0.523 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 4.82727 Angstroms, which requires orientationSampling of at least 2.74809 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 6
   8/   8 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       16.7684 Angstroms
 Maximization ...
1.52/1.52 min ............................................................~~(,_,">
 Auto-refine: Iteration= 7
 Auto-refine: Resolution= 4.75522 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 5.27068 degrees; and in offsets= 0.756547 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.418 degrees; offsets= 0.529 pixels
 Auto-refine: Angular step= 7.5 degrees; local searches= false
 Auto-refine: Offset search range= 5 pixels; offset step= 1 pixels
 CurrentResolution= 4.75522 Angstroms, which requires orientationSampling of at least 2.70677 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 24192
 OrientationalSampling= 15 NrOrientations= 1152
 TranslationalSampling= 2 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 774144
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 1 NrTranslations= 84
=============================
 Expectation iteration 7
   8/   8 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       12.744 Angstroms
 Maximization ...
  54/  54 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 8
 Auto-refine: Resolution= 4.82727 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 5.23629 degrees; and in offsets= 0.776253 pixels (no gain for 2 iter) 
 Estimating accuracies in the orientational assignment ... 
   4/   4 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.452 degrees; offsets= 0.529 pixels
 Auto-refine: Angular step= 3.75 degrees; local searches= false
 Auto-refine: Offset search range= 1.94063 pixels; offset step= 0.39675 pixels
 CurrentResolution= 4.82727 Angstroms, which requires orientationSampling of at least 2.74809 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 193536
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 0.7935 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 6193152
 OrientationalSampling= 3.75 NrOrientations= 73728
 TranslationalSampling= 0.39675 NrTranslations= 84
=============================
 Expectation iteration 8
  10/  10 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.95625 Angstroms
 Maximization ...
1.53/1.53 min ............................................................~~(,_,">
 Auto-refine: Iteration= 9
 Auto-refine: Resolution= 3.93333 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 3.84319 degrees; and in offsets= 0.533073 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.756 degrees; offsets= 0.3 pixels
 Auto-refine: Angular step= 3.75 degrees; local searches= false
 Auto-refine: Offset search range= 1.94063 pixels; offset step= 0.39675 pixels
 CurrentResolution= 3.93333 Angstroms, which requires orientationSampling of at least 2.25 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 193536
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 0.7935 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 6193152
 OrientationalSampling= 3.75 NrOrientations= 73728
 TranslationalSampling= 0.39675 NrTranslations= 84
=============================
 Expectation iteration 9
  15/  15 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.95625 Angstroms
 Maximization ...
1.03/1.03 min ............................................................~~(,_,">
 Auto-refine: Iteration= 10
 Auto-refine: Resolution= 3.88537 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 2.51214 degrees; and in offsets= 0.336198 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.708 degrees; offsets= 0.3 pixels
 Auto-refine: Angular step= 3.75 degrees; local searches= false
 Auto-refine: Offset search range= 1.94063 pixels; offset step= 0.39675 pixels
 CurrentResolution= 3.88537 Angstroms, which requires orientationSampling of at least 2.22222 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 193536
 OrientationalSampling= 7.5 NrOrientations= 9216
 TranslationalSampling= 0.7935 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 6193152
 OrientationalSampling= 3.75 NrOrientations= 73728
 TranslationalSampling= 0.39675 NrTranslations= 84
=============================
 Expectation iteration 10
  15/  15 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.95625 Angstroms
 Maximization ...
1.27/1.27 min ............................................................~~(,_,">
 Auto-refine: Iteration= 11
 Auto-refine: Resolution= 3.88537 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 2.48805 degrees; and in offsets= 0.317819 pixels (no gain for 2 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.691 degrees; offsets= 0.3 pixels
 Auto-refine: Angular step= 1.875 degrees; local searches= true
 Auto-refine: Offset search range= 1.5891 pixels; offset step= 0.225 pixels
 CurrentResolution= 3.88537 Angstroms, which requires orientationSampling of at least 2.22222 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 5550
 OrientationalSampling= 3.75 NrOrientations= 150
 TranslationalSampling= 0.45 NrTranslations= 37
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 177600
 OrientationalSampling= 1.875 NrOrientations= 1200
 TranslationalSampling= 0.225 NrTranslations= 148
=============================
 Expectation iteration 11
  13/  13 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
1.28/1.28 min ............................................................~~(,_,">
 Auto-refine: Iteration= 12
 Auto-refine: Resolution= 3.5011 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 1.77862 degrees; and in offsets= 0.242095 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.484 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 1.875 degrees; local searches= true
 Auto-refine: Offset search range= 1.5891 pixels; offset step= 0.225 pixels
 CurrentResolution= 3.5011 Angstroms, which requires orientationSampling of at least 2 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 5735
 OrientationalSampling= 3.75 NrOrientations= 155
 TranslationalSampling= 0.45 NrTranslations= 37
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 183520
 OrientationalSampling= 1.875 NrOrientations= 1240
 TranslationalSampling= 0.225 NrTranslations= 148
=============================
 Expectation iteration 12
  15/  15 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
1.30/1.30 min ............................................................~~(,_,">
 Auto-refine: Iteration= 13
 Auto-refine: Resolution= 3.5011 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 1.1691 degrees; and in offsets= 0.165272 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.469 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.9375 degrees; local searches= true
 Auto-refine: Offset search range= 0.826362 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.5011 Angstroms, which requires orientationSampling of at least 2 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 3045
 OrientationalSampling= 1.875 NrOrientations= 145
 TranslationalSampling= 0.3 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 97440
 OrientationalSampling= 0.9375 NrOrientations= 1160
 TranslationalSampling= 0.15 NrTranslations= 84
=============================
 Expectation iteration 13
  15/  15 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
1.28/1.28 min ............................................................~~(,_,">
 Auto-refine: Iteration= 14
 Auto-refine: Resolution= 3.35368 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 0.866585 degrees; and in offsets= 0.111316 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.409 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.9375 degrees; local searches= true
 Auto-refine: Offset search range= 0.826362 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.35368 Angstroms, which requires orientationSampling of at least 1.91489 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 3150
 OrientationalSampling= 1.875 NrOrientations= 150
 TranslationalSampling= 0.3 NrTranslations= 21
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 100800
 OrientationalSampling= 0.9375 NrOrientations= 1200
 TranslationalSampling= 0.15 NrTranslations= 84
=============================
 Expectation iteration 14
  19/  19 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.45/3.45 min ............................................................~~(,_,">
 Auto-refine: Iteration= 15
 Auto-refine: Resolution= 3.38936 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 0.60348 degrees; and in offsets= 0.0910626 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   2/   2 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.393 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.46875 degrees; local searches= true
 Auto-refine: Offset search range= 0.455313 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.38936 Angstroms, which requires orientationSampling of at least 1.93548 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1485
 OrientationalSampling= 0.9375 NrOrientations= 165
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 47520
 OrientationalSampling= 0.46875 NrOrientations= 1320
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 15
  24/  24 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
1.45/1.45 min ............................................................~~(,_,">
 Auto-refine: Iteration= 16
 Auto-refine: Resolution= 3.35368 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 0.412177 degrees; and in offsets= 0.064671 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.38 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.46875 degrees; local searches= true
 Auto-refine: Offset search range= 0.455313 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.35368 Angstroms, which requires orientationSampling of at least 1.91489 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1260
 OrientationalSampling= 0.9375 NrOrientations= 140
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 40320
 OrientationalSampling= 0.46875 NrOrientations= 1120
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 16
  24/  24 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.45/3.45 min ............................................................~~(,_,">
 Auto-refine: Iteration= 17
 Auto-refine: Resolution= 3.31875 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 0.287416 degrees; and in offsets= 0.079345 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.387 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.46875 degrees; local searches= true
 Auto-refine: Offset search range= 0.455313 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.31875 Angstroms, which requires orientationSampling of at least 1.89474 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1260
 OrientationalSampling= 0.9375 NrOrientations= 140
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 40320
 OrientationalSampling= 0.46875 NrOrientations= 1120
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 17
  24/  24 sec ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.62/3.62 min ............................................................~~(,_,">
 Auto-refine: Iteration= 18
 Auto-refine: Resolution= 3.35368 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 0.266466 degrees; and in offsets= 0.106059 pixels (no gain for 2 iter) 
 Estimating accuracies in the orientational assignment ... 
   4/   4 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.406 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.234375 degrees; local searches= true
 Auto-refine: Offset search range= 0.530297 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.35368 Angstroms, which requires orientationSampling of at least 1.91489 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1305
 OrientationalSampling= 0.46875 NrOrientations= 145
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 41760
 OrientationalSampling= 0.234375 NrOrientations= 1160
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 18
1.05/1.05 min ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.47/3.47 min ............................................................~~(,_,">
 Auto-refine: Iteration= 19
 Auto-refine: Resolution= 3.31875 (no gain for 0 iter) 
 Auto-refine: Changes in angles= 0.197337 degrees; and in offsets= 0.0839578 pixels (no gain for 0 iter) 
 Estimating accuracies in the orientational assignment ... 
   2/   2 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.38 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.234375 degrees; local searches= true
 Auto-refine: Offset search range= 0.530297 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.31875 Angstroms, which requires orientationSampling of at least 1.89474 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1485
 OrientationalSampling= 0.46875 NrOrientations= 165
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 47520
 OrientationalSampling= 0.234375 NrOrientations= 1320
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 19
1.07/1.07 min ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.63/3.63 min ............................................................~~(,_,">
 Auto-refine: Iteration= 20
 Auto-refine: Resolution= 3.31875 (no gain for 1 iter) 
 Auto-refine: Changes in angles= 0.141606 degrees; and in offsets= 0.0779309 pixels (no gain for 1 iter) 
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.389 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.234375 degrees; local searches= true
 Auto-refine: Offset search range= 0.530297 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.31875 Angstroms, which requires orientationSampling of at least 1.89474 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1485
 OrientationalSampling= 0.46875 NrOrientations= 165
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 47520
 OrientationalSampling= 0.234375 NrOrientations= 1320
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 20
1.05/1.05 min ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
3.63/3.63 min ............................................................~~(,_,">
 Auto-refine: Iteration= 21
 Auto-refine: Resolution= 3.31875 (no gain for 2 iter) 
 Auto-refine: Changes in angles= 0.135306 degrees; and in offsets= 0.0842628 pixels (no gain for 2 iter) 
 Auto-refine: Refinement has converged, entering last iteration where two halves will be combined...
 Auto-refine: The last iteration will use data to Nyquist frequency, which may take more CPU and RAM.
 Estimating accuracies in the orientational assignment ... 
   3/   3 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 0.393 degrees; offsets= 0.2 pixels
 Auto-refine: Angular step= 0.234375 degrees; local searches= true
 Auto-refine: Offset search range= 0.530297 pixels; offset step= 0.15 pixels
 CurrentResolution= 3.31875 Angstroms, which requires orientationSampling of at least 1.89474 degrees for a particle of diameter 200 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 1395
 OrientationalSampling= 0.46875 NrOrientations= 155
 TranslationalSampling= 0.3 NrTranslations= 9
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 44640
 OrientationalSampling= 0.234375 NrOrientations= 1240
 TranslationalSampling= 0.15 NrTranslations= 36
=============================
 Expectation iteration 21
1.07/1.07 min ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       9.65454 Angstroms
 Maximization ...
7.30/7.30 min ............................................................~~(,_,">
 Auto-refine: Refinement has converged, stopping now... 
 Auto-refine: + Final reconstruction from all particles is saved as: Refine3D/job052/run_class001.mrc
 Auto-refine: + Final model parameters are stored in: Refine3D/job052/run_model.star
 Auto-refine: + Final data parameters are stored in: Refine3D/job052/run_data.star
 Auto-refine: + Final resolution (already with masking) is: 2.87027