Polish後の3D auto-refineの標準出力
提供: Eospedia
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