----------------------------------------------------------------- | Read more about this program in the following publication: | | Scheres ea. (2007) Structure, 15, 1167-1177 | | | | *** Please cite it if this program is of use to you! *** | ----------------------------------------------------------------- --> Maximum-likelihood multi-reference 3D-refinement Initial reference volume : input/mlData/icoFiltered.vol Experimental images: : input/mlData/phantom_images.xmd Angular sampling rate : 15 Symmetry group: : c1 Output rootname : tmpLink/xmipp_mpi_mlf_refine3d_02/mlf3d Convergence criterion : 5e-05 ----------------------------------------------------------------- --> projecting 1 volumes x 81 projections... ----------------------------------------------------------------- --> Multi-reference refinement --> using a maximum-likelihood in Fourier-space (MLF) target --> with CTF correction Input images : input/mlData/phantom_images.xmd (104) Reference image(s) : tmpLink/xmipp_mpi_mlf_refine3d_02/mlf3d_extra/projections.xmd Output rootname : tmpLink/xmipp_mpi_mlf_refine3d_02/mlf3d_mlf2d Stopping criterium : 5e-05 initial sigma offset : 3 Psi sampling interval : 15 degrees Translational searches : 3 pixels Low resolution limit : 999 Ang High resolution limit : 0 Ang Check mirrors : true + Assuming images have been phase flipped + CTF group 1 contains 52 images + CTF group 2 contains 52 images ----------------------------------------------------------------- --> Estimating initial noise models from average power spectra ... --> 3D-EM volume refinement: iteration 1 of 2 Reading angle information ... Sorting projections ... Running iteration 0 with lambda= 0.2 Reading angle information ... Reading angle information ... Sorting projections ... Sorting projections ... Running iteration 0 with lambda= 0.2 Running iteration 0 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 0.613853 1st block: 0.613853 2nd block: 4.46218e-05 residual: 0.000313636 Running iteration 1 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 3939.12 1st block: 3939.12 2nd block: 0.0138652 residual: 0.00914726 Running iteration 1 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 270.244 1st block: 270.244 2nd block: 0.00142932 residual: 0.00114875 Running iteration 1 with lambda= 0.2 Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 0.626214 1st block: 0.612036 2nd block: 5.88328e-05 residual: 0.000831297 Running iteration 2 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 41.2982 1st block: 41.2252 2nd block: 0.00102525 residual: 0.00188056 Running iteration 2 with lambda= 0.2 Weighted error: 145.225 1st block: 145.246 2nd block: 0.00298472 residual: 0.0103074 Running iteration 2 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 0.623396 1st block: 0.600704 2nd block: 6.2898e-05 residual: 0.00147352 Running iteration 3 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 0.586534 1st block: 0.558098 2nd block: 6.26761e-05 residual: 0.00217838 Running iteration 4 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 14.0275 1st block: 13.961 2nd block: 0.000700341 residual: 0.0020578 Running iteration 3 with lambda= 0.2 Weighted error: 41.777 1st block: 41.4345 2nd block: 0.0024034 residual: 0.0114094 Running iteration 3 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 7.10549 1st block: 7.05424 2nd block: 0.000451212 residual: 0.00199801 Running iteration 4 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 32.8078 1st block: 32.3988 2nd block: 0.00110004 residual: 0.0116995 Running iteration 4 with lambda= 0.2 Backprojection of residual images Weighted error: 0.546522 1st block: 0.513964 2nd block: 6.15972e-05 residual: 0.00291597 Running iteration 5 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 4.32523 1st block: 4.2842 2nd block: 0.000303625 residual: 0.00186193 Running iteration 5 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 0.510039 1st block: 0.474369 2nd block: 6.02607e-05 residual: 0.00367052 Running iteration 6 with lambda= 0.2 Weighted error: 29.0319 1st block: 28.624 2nd block: 0.000964618 residual: 0.0120259 Running iteration 5 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 2.90255 1st block: 2.86848 2nd block: 0.000212352 residual: 0.00171092 Running iteration 6 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 0.478118 1st block: 0.440027 2nd block: 5.88358e-05 residual: 0.00443368 Running iteration 7 with lambda= 0.2 Weighted error: 25.9347 1st block: 25.5069 2nd block: 0.000747832 residual: 0.0122341 Running iteration 6 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Backprojection of residual images Weighted error: 2.08272 1st block: 2.05352 2nd block: 0.000155562 residual: 0.00157024 Running iteration 7 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 0.450291 1st block: 0.410262 2nd block: 5.72926e-05 residual: 0.005201 Running iteration 8 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 23.547 1st block: 23.1155 2nd block: 0.000723137 residual: 0.0124202 Running iteration 7 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 1.57886 1st block: 1.55316 2nd block: 0.000117809 residual: 0.00144855 Running iteration 8 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 0.425935 1st block: 0.384323 2nd block: 5.56471e-05 residual: 0.00597007 Running iteration 9 with lambda= 0.2 Weighted error: 21.4519 1st block: 21.0178 2nd block: 0.000686088 residual: 0.0125371 Running iteration 8 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 1.25617 1st block: 1.23303 2nd block: 9.1798e-05 residual: 0.00134854 Running iteration 9 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 1.04286 1st block: 1.0216 2nd block: 7.30903e-05 residual: 0.00126977 Time of 10 iterations: Elapsed time: User(2.79) System(0.01) Projection of residual volume; kappa = 0.5 Weighted error: 19.6414 1st block: 19.2113 2nd block: 0.000677768 residual: 0.0125968 Running iteration 9 with lambda= 0.2 Weighted error: 0.404456 1st block: 0.361524 2nd block: 5.39197e-05 residual: 0.00673955 Time of 10 iterations: Elapsed time: User(2.82) System(0.01) INIT_TIME: 0.020195 PROCESS_TIME: 2.81178 FINISH_TIME: 0.110382 Backprojection of residual images INIT_TIME: 0.013065 PROCESS_TIME: 2.87257 FINISH_TIME: 0.111255 Projection of residual volume; kappa = 0.5 Weighted error: 18.0232 1st block: 17.6002 2nd block: 0.000663881 residual: 0.0125932 Time of 10 iterations: Elapsed time: User(3.06) System(0) INIT_TIME: 0.020195 PROCESS_TIME: 3.08009 FINISH_TIME: 0.070531 --> calculating 3D-SSNR ... --> 3D-EM volume refinement: iteration 2 of 2 --> projecting 1 volumes x 81 projections... ----------------------------------------------------------------- Reading angle information ... Sorting projections ... Running iteration 0 with lambda= 0.2 Reading angle information ... Reading angle information ... Sorting projections ... Sorting projections ... Running iteration 0 with lambda= 0.2 Running iteration 0 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 1002.51 1st block: 1002.51 2nd block: 2.5232e-05 residual: 6.59726e-06 Running iteration 1 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 2.18637 1st block: 2.18637 2nd block: 2.00507e-08 residual: 1.41266e-08 Running iteration 1 with lambda= 0.2 Weighted error: 29.6267 1st block: 29.6267 2nd block: 2.0266e-07 residual: 2.53716e-07 Running iteration 1 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 279.372 1st block: 279.375 2nd block: 5.31516e-06 residual: 3.56853e-06 Running iteration 2 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 19.3312 1st block: 19.3275 2nd block: 7.22231e-08 residual: 6.99934e-07 Running iteration 2 with lambda= 0.2 Backprojection of residual images Weighted error: 1.24639 1st block: 1.24624 2nd block: 7.12841e-09 residual: 2.99113e-08 Running iteration 2 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 131.563 1st block: 131.529 2nd block: 3.98529e-06 residual: 5.06627e-06 Running iteration 3 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 0.864249 1st block: 0.863996 2nd block: 5.88662e-09 residual: 5.08697e-08 Running iteration 3 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 14.7163 1st block: 14.7102 2nd block: 7.98931e-08 residual: 1.24267e-06 Running iteration 3 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 0.658589 1st block: 0.658293 2nd block: 4.50342e-09 residual: 7.44869e-08 Running iteration 4 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 78.9009 1st block: 78.8712 2nd block: 1.90094e-06 residual: 6.54674e-06 Running iteration 4 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 11.921 1st block: 11.9136 2nd block: 7.78725e-08 residual: 1.81966e-06 Running iteration 4 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 0.529944 1st block: 0.529619 2nd block: 3.80267e-09 residual: 1.01188e-07 Running iteration 5 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 53.1495 1st block: 53.1187 2nd block: 1.17246e-06 residual: 8.62826e-06 Running iteration 5 with lambda= 0.2 Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 9.95678 1st block: 9.94872 2nd block: 7.72438e-08 residual: 2.43698e-06 Running iteration 5 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Weighted error: 0.442595 1st block: 0.442247 2nd block: 3.24951e-09 residual: 1.31451e-07 Running iteration 6 with lambda= 0.2 Backprojection of residual images Projection of residual volume; kappa = 0.5 Backprojection of residual images Weighted error: 38.8233 1st block: 38.7925 2nd block: 6.90402e-07 residual: 1.12278e-05 Running iteration 6 with lambda= 0.2 Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 8.4834 1st block: 8.47485 2nd block: 7.3506e-08 residual: 3.10788e-06 Running iteration 6 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 0.380224 1st block: 0.379855 2nd block: 2.81146e-09 residual: 1.65735e-07 Running iteration 7 with lambda= 0.2 Weighted error: 30.298 1st block: 30.2662 2nd block: 4.46121e-07 residual: 1.42953e-05 Running iteration 7 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Projection of residual volume; kappa = 0.5 Weighted error: 7.34374 1st block: 7.33483 2nd block: 6.80217e-08 residual: 3.85073e-06 Running iteration 7 with lambda= 0.2 Weighted error: 24.9706 1st block: 24.9373 2nd block: 2.94924e-07 residual: 1.791e-05 Running iteration 8 with lambda= 0.2 Weighted error: 0.334142 1st block: 0.333753 2nd block: 2.44883e-09 residual: 2.04458e-07 Running iteration 8 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 21.5035 1st block: 21.4682 2nd block: 2.0851e-07 residual: 2.20033e-05 Running iteration 9 with lambda= 0.2 Projection of residual volume; kappa = 0.5 Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 6.44777 1st block: 6.43854 2nd block: 6.15356e-08 residual: 4.67984e-06 Running iteration 8 with lambda= 0.2 Weighted error: 0.299246 1st block: 0.298835 2nd block: 2.14005e-09 residual: 2.47897e-07 Running iteration 9 with lambda= 0.2 Backprojection of residual images Backprojection of residual images Projection of residual volume; kappa = 0.5 Weighted error: 19.1671 1st block: 19.1296 2nd block: 1.51187e-07 residual: 2.66404e-05 Time of 10 iterations: Elapsed time: User(1.67) System(0) Projection of residual volume; kappa = 0.5 Weighted error: 0.272322 1st block: 0.271888 2nd block: 1.87943e-09 residual: 2.96283e-07 Time of 10 iterations: Elapsed time: User(1.73) System(0) Projection of residual volume; kappa = 0.5 Weighted error: 5.73643 1st block: 5.72687 2nd block: 5.47447e-08 residual: 5.60729e-06 Running iteration 9 with lambda= 0.2 Backprojection of residual images INIT_TIME: 0.012656 PROCESS_TIME: 1.77188 FINISH_TIME: 0.077526 INIT_TIME: 0.020316 PROCESS_TIME: 1.71066 FINISH_TIME: 0.134249 Projection of residual volume; kappa = 0.5 Weighted error: 5.16794 1st block: 5.15803 2nd block: 4.81057e-08 residual: 6.64133e-06 Time of 10 iterations: Elapsed time: User(1.88) System(0.01) INIT_TIME: 0.02255 PROCESS_TIME: 1.92692 FINISH_TIME: 0.071933 --> calculating 3D-SSNR ... --> Optimization was stopped before convergence was reached!