=== RELION MPI setup === + Number of MPI processes = 4 + Master (0) runs on host = perk + Slave 1 runs on host = perk + Slave 2 runs on host = perk + Slave 3 runs on host = perk ================= + Reading Refine3D/job245/run_data.star... - Using pixel size calculated from magnification and detector pixel size in the input STAR file: 1.137 + Using movie pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.5685 A + Using coord. pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 1.137 A + Using dose per frame from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.9333 e/A^2 + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job245/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job245/run_half2_class001_unfil.mrc - Mask: MaskCreate/job238/mask.mrc + Masking references ... + Transforming references ... + Initializing motion estimator ... + using parameters from: Polish/job251/opt_params.txt s_vel: 0.951, s_div: 16815, s_acc: 1.05 + Performing loop over all micrographs ... 000/??? sec ~~(,_,"> [oo] 0.02/6.93 hrs ~~(,_,"> 0.04/7.04 hrs ~~(,_,"> 0.06/7.00 hrs ~~(,_,"> 0.08/7.11 hrs ~~(,_,"> 0.09/7.01 hrs ~~(,_,"> 0.11/6.91 hrs ~~(,_,"> 0.13/6.90 hrs .~~(,_,"> 0.14/6.72 hrs .~~(,_,"> 0.16/6.61 hrs .~~(,_,"> 0.17/6.58 hrs .~~(,_,"> 0.20/6.71 hrs .~~(,_,"> 0.21/6.73 hrs .~~(,_,"> 0.23/6.60 hrs ..~~(,_,"> 0.24/6.51 hrs ..~~(,_,"> 0.25/6.43 hrs ..~~(,_,"> 0.27/6.38 hrs ..~~(,_,"> 0.29/6.37 hrs ..~~(,_,"> 0.31/6.42 hrs ..~~(,_,"> 0.33/6.49 hrs ...~~(,_,"> 0.34/6.49 hrs ...~~(,_,"> 0.37/6.57 hrs ...~~(,_,"> 0.38/6.55 hrs ...~~(,_,"> 0.40/6.54 hrs ...~~(,_,"> 0.41/6.52 hrs ...~~(,_,"> 0.43/6.53 hrs ...~~(,_,"> 0.45/6.51 hrs ....~~(,_,"> 0.46/6.41 hrs ....~~(,_,"> 0.47/6.34 hrs ....~~(,_,"> 0.49/6.37 hrs ....~~(,_,"> 0.50/6.34 hrs ....~~(,_,"> 0.52/6.31 hrs ....~~(,_,"> 0.53/6.25 hrs .....~~(,_,"> 0.54/6.19 hrs .....~~(,_,"> 0.55/6.09 hrs .....~~(,_,"> 0.56/6.06 hrs .....~~(,_,"> 0.57/6.03 hrs .....~~(,_,"> 0.59/5.98 hrs .....~~(,_,"> 0.60/6.02 hrs ......~~(,_,"> 0.62/5.99 hrs ......~~(,_,"> 0.63/5.93 hrs ......~~(,_,"> 0.64/5.91 hrs ......~~(,_,"> 0.66/5.92 hrs ......~~(,_,"> 0.68/5.94 hrs ......~~(,_,"> 0.69/5.92 hrs ......~~(,_,"> 0.70/5.91 hrs .......~~(,_,"> 0.72/5.93 hrs .......~~(,_,"> 0.74/5.94 hrs .......~~(,_,"> 0.75/5.92 hrs .......~~(,_,"> 0.77/5.92 hrs .......~~(,_,"> 0.78/5.92 hrs .......~~(,_,"> 0.80/5.92 hrs ........~~(,_,"> 0.82/5.93 hrs ........~~(,_,"> 0.83/5.93 hrs ........~~(,_,"> 0.85/5.92 hrs ........~~(,_,"> 0.86/5.92 hrs ........~~(,_,"> 0.87/5.90 hrs ........~~(,_,"> 0.89/5.92 hrs .........~~(,_,"> 0.90/5.90 hrs .........~~(,_,"> 0.92/5.89 hrs .........~~(,_,"> 0.94/5.91 hrs .........~~(,_,"> 0.95/5.92 hrs .........~~(,_,"> 0.97/5.91 hrs .........~~(,_,"> 0.99/5.93 hrs ..........~~(,_,"> 1.00/5.92 hrs ..........~~(,_,"> 1.02/5.92 hrs ..........~~(,_,"> 1.04/5.94 hrs ..........~~(,_,"> 1.05/5.93 hrs ..........~~(,_,"> 1.07/5.93 hrs ..........~~(,_,"> 1.08/5.94 hrs ..........~~(,_,"> 1.10/5.94 hrs ...........~~(,_,"> 1.12/5.95 hrs ...........~~(,_,"> 1.13/5.95 hrs ...........~~(,_,"> 1.14/5.93 hrs ...........~~(,_,"> 1.16/5.93 hrs ...........~~(,_,"> 1.18/5.94 hrs ...........~~(,_,"> 1.19/5.93 hrs ............~~(,_,"> 1.21/5.93 hrs ............~~(,_,"> 1.22/5.93 hrs ............~~(,_,"> 1.24/5.92 hrs ............~~(,_,"> 1.25/5.92 hrs ............~~(,_,"> 1.27/5.91 hrs ............~~(,_,"> 1.28/5.91 hrs .............~~(,_,"> 1.30/5.90 hrs .............~~(,_,"> 1.31/5.90 hrs .............~~(,_,"> 1.33/5.89 hrs .............~~(,_,"> 1.34/5.88 hrs .............~~(,_,"> 1.36/5.89 hrs .............~~(,_,"> 1.37/5.89 hrs .............~~(,_,"> 1.39/5.89 hrs ..............~~(,_,"> 1.41/5.90 hrs ..............~~(,_,"> 1.42/5.91 hrs ..............~~(,_,"> 1.44/5.92 hrs ..............~~(,_,"> 1.46/5.92 hrs ..............~~(,_,"> 1.47/5.93 hrs ..............~~(,_,"> 1.49/5.93 hrs ...............~~(,_,"> 1.51/5.93 hrs ...............~~(,_,"> 1.52/5.93 hrs ...............~~(,_,"> 1.54/5.93 hrs ...............~~(,_,"> 1.55/5.93 hrs ...............~~(,_,"> 1.57/5.92 hrs ...............~~(,_,"> 1.58/5.93 hrs ................~~(,_,"> 1.60/5.93 hrs ................~~(,_,"> 1.62/5.93 hrs ................~~(,_,"> 1.63/5.94 hrs ................~~(,_,"> 1.65/5.95 hrs ................~~(,_,"> 1.67/5.96 hrs ................~~(,_,"> 1.69/5.97 hrs ................~~(,_,"> 1.71/5.97 hrs .................~~(,_,"> 1.72/5.98 hrs .................~~(,_,"> 1.74/5.97 hrs .................~~(,_,"> 1.75/5.97 hrs .................~~(,_,"> 1.77/5.98 hrs .................~~(,_,"> 1.79/5.99 hrs .................~~(,_,"> 1.81/5.99 hrs ..................~~(,_,"> 1.83/6.00 hrs ..................~~(,_,"> 1.84/5.99 hrs ..................~~(,_,"> 1.85/5.99 hrs ..................~~(,_,"> 1.87/5.98 hrs ..................~~(,_,"> 1.88/5.96 hrs ..................~~(,_,"> 1.89/5.96 hrs ...................~~(,_,"> 1.91/5.96 hrs ...................~~(,_,"> 1.93/5.97 hrs ...................~~(,_,"> 1.95/5.98 hrs ...................~~(,_,"> 1.96/5.99 hrs ...................~~(,_,"> 1.98/5.98 hrs ...................~~(,_,"> 2.00/5.99 hrs ...................~~(,_,"> 2.01/5.99 hrs ....................~~(,_,"> 2.03/5.99 hrs ....................~~(,_,"> 2.04/5.99 hrs ....................~~(,_,"> 2.06/5.98 hrs ....................~~(,_,"> 2.07/5.98 hrs ....................~~(,_,"> 2.09/5.97 hrs ....................~~(,_,"> 2.10/5.97 hrs .....................~~(,_,"> 2.12/5.98 hrs .....................~~(,_,"> 2.13/5.97 hrs .....................~~(,_,"> 2.15/5.97 hrs .....................~~(,_,"> 2.16/5.97 hrs .....................~~(,_,"> 2.18/5.97 hrs .....................~~(,_,"> 2.19/5.97 hrs ......................~~(,_,"> 2.21/5.97 hrs ......................~~(,_,"> 2.23/5.97 hrs ......................~~(,_,"> 2.25/5.98 hrs ......................~~(,_,"> 2.26/5.97 hrs ......................~~(,_,"> 2.27/5.97 hrs ......................~~(,_,"> 2.29/5.97 hrs .......................~~(,_,"> 2.31/5.98 hrs .......................~~(,_,"> 2.32/5.98 hrs .......................~~(,_,"> 2.34/5.98 hrs .......................~~(,_,"> 2.36/5.98 hrs .......................~~(,_,"> 2.37/5.98 hrs .......................~~(,_,"> 2.39/5.98 hrs .......................~~(,_,"> 2.40/5.98 hrs ........................~~(,_,"> 2.42/5.98 hrs ........................~~(,_,"> 2.43/5.97 hrs ........................~~(,_,"> 2.45/5.98 hrs ........................~~(,_,"> 2.47/5.97 hrs ........................~~(,_,"> 2.48/5.97 hrs ........................~~(,_,"> 2.49/5.97 hrs .........................~~(,_,"> 2.51/5.96 hrs .........................~~(,_,"> 2.52/5.96 hrs .........................~~(,_,"> 2.54/5.96 hrs .........................~~(,_,"> 2.55/5.96 hrs .........................~~(,_,"> 2.56/5.95 hrs .........................~~(,_,"> 2.58/5.94 hrs ..........................~~(,_,"> 2.59/5.93 hrs ..........................~~(,_,"> 2.60/5.93 hrs ..........................~~(,_,"> 2.62/5.93 hrs ..........................~~(,_,"> 2.64/5.94 hrs ..........................~~(,_,"> 2.65/5.94 hrs ..........................~~(,_,"> 2.67/5.94 hrs ..........................~~(,_,"> 2.69/5.94 hrs ...........................~~(,_,"> 2.71/5.95 hrs ...........................~~(,_,"> 2.72/5.95 hrs ...........................~~(,_,"> 2.74/5.96 hrs ...........................~~(,_,"> 2.75/5.94 hrs ...........................~~(,_,"> 2.76/5.93 hrs ...........................~~(,_,"> 2.78/5.93 hrs ............................~~(,_,"> 2.79/5.93 hrs ............................~~(,_,"> 2.81/5.93 hrs ............................~~(,_,"> 2.83/5.93 hrs ............................~~(,_,"> 2.84/5.93 hrs ............................~~(,_,"> 2.86/5.93 hrs ............................~~(,_,"> 2.88/5.94 hrs .............................~~(,_,"> 2.89/5.93 hrs .............................~~(,_,"> 2.90/5.93 hrs .............................~~(,_,"> 2.91/5.92 hrs .............................~~(,_,"> 2.93/5.92 hrs .............................~~(,_,"> 2.94/5.91 hrs .............................~~(,_,"> 2.96/5.92 hrs ..............................~~(,_,"> 2.98/5.92 hrs ..............................~~(,_,"> 2.99/5.93 hrs ..............................~~(,_,"> 3.01/5.92 hrs ..............................~~(,_,"> 3.02/5.91 hrs ..............................~~(,_,"> 3.04/5.92 hrs ..............................~~(,_,"> 3.05/5.92 hrs ..............................~~(,_,"> 3.07/5.92 hrs ...............................~~(,_,"> 3.08/5.92 hrs ...............................~~(,_,"> 3.10/5.92 hrs ...............................~~(,_,"> 3.11/5.92 hrs ...............................~~(,_,"> 3.13/5.91 hrs ...............................~~(,_,"> 3.14/5.91 hrs ...............................~~(,_,"> 3.16/5.92 hrs ................................~~(,_,"> 3.18/5.91 hrs ................................~~(,_,"> 3.19/5.91 hrs ................................~~(,_,"> 3.21/5.91 hrs ................................~~(,_,"> 3.22/5.92 hrs ................................~~(,_,"> 3.24/5.91 hrs ................................~~(,_,"> 3.25/5.91 hrs .................................~~(,_,"> 3.27/5.91 hrs .................................~~(,_,"> 3.28/5.91 hrs .................................~~(,_,"> 3.30/5.90 hrs .................................~~(,_,"> 3.31/5.91 hrs .................................~~(,_,"> 3.32/5.90 hrs .................................~~(,_,"> 3.34/5.90 hrs .................................~~(,_,"> 3.35/5.89 hrs ..................................~~(,_,"> 3.36/5.88 hrs ..................................~~(,_,"> 3.38/5.88 hrs ..................................~~(,_,"> 3.39/5.88 hrs ..................................~~(,_,"> 3.40/5.87 hrs ..................................~~(,_,"> 3.41/5.86 hrs ..................................~~(,_,"> 3.42/5.86 hrs ...................................~~(,_,"> 3.44/5.85 hrs ...................................~~(,_,"> 3.45/5.85 hrs ...................................~~(,_,"> 3.47/5.86 hrs ...................................~~(,_,"> 3.48/5.85 hrs ...................................~~(,_,"> 3.50/5.85 hrs ...................................~~(,_,"> 3.51/5.85 hrs ....................................~~(,_,"> 3.52/5.84 hrs ....................................~~(,_,"> 3.54/5.84 hrs ....................................~~(,_,"> 3.56/5.85 hrs ....................................~~(,_,"> 3.57/5.84 hrs ....................................~~(,_,"> 3.58/5.84 hrs ....................................~~(,_,"> 3.60/5.84 hrs ....................................~~(,_,"> 3.62/5.84 hrs .....................................~~(,_,"> 3.63/5.84 hrs .....................................~~(,_,"> 3.65/5.84 hrs .....................................~~(,_,"> 3.66/5.83 hrs .....................................~~(,_,"> 3.67/5.83 hrs .....................................~~(,_,"> 3.69/5.83 hrs .....................................~~(,_,"> 3.70/5.83 hrs ......................................~~(,_,"> 3.72/5.83 hrs ......................................~~(,_,"> 3.73/5.83 hrs ......................................~~(,_,"> 3.75/5.83 hrs ......................................~~(,_,"> 3.76/5.82 hrs ......................................~~(,_,"> 3.78/5.82 hrs ......................................~~(,_,"> 3.79/5.82 hrs .......................................~~(,_,"> 3.80/5.82 hrs .......................................~~(,_,"> 3.81/5.81 hrs .......................................~~(,_,"> 3.83/5.81 hrs .......................................~~(,_,"> 3.84/5.81 hrs .......................................~~(,_,"> 3.85/5.80 hrs .......................................~~(,_,"> 3.87/5.80 hrs .......................................~~(,_,"> 3.88/5.79 hrs ........................................~~(,_,"> 3.89/5.79 hrs ........................................~~(,_,"> 3.90/5.78 hrs ........................................~~(,_,"> 3.91/5.78 hrs ........................................~~(,_,"> 3.93/5.77 hrs ........................................~~(,_,"> 3.94/5.77 hrs ........................................~~(,_,"> 3.95/5.76 hrs .........................................~~(,_,"> 3.96/5.76 hrs .........................................~~(,_,"> 3.97/5.75 hrs .........................................~~(,_,"> 3.99/5.75 hrs .........................................~~(,_,"> 4.00/5.75 hrs .........................................~~(,_,"> 4.02/5.75 hrs .........................................~~(,_,"> 4.03/5.75 hrs ..........................................~~(,_,"> 4.05/5.75 hrs ..........................................~~(,_,"> 4.06/5.75 hrs ..........................................~~(,_,"> 4.07/5.75 hrs ..........................................~~(,_,"> 4.09/5.75 hrs ..........................................~~(,_,"> 4.10/5.74 hrs ..........................................~~(,_,"> 4.12/5.74 hrs ...........................................~~(,_,"> 4.12/5.73 hrs ...........................................~~(,_,"> 4.14/5.73 hrs ...........................................~~(,_,"> 4.15/5.73 hrs ...........................................~~(,_,"> 4.16/5.72 hrs ...........................................~~(,_,"> 4.17/5.72 hrs ...........................................~~(,_,"> 4.19/5.72 hrs ...........................................~~(,_,"> 4.20/5.71 hrs ............................................~~(,_,"> 4.21/5.71 hrs ............................................~~(,_,"> 4.22/5.70 hrs ............................................~~(,_,"> 4.24/5.70 hrs ............................................~~(,_,"> 4.25/5.69 hrs ............................................~~(,_,"> 4.26/5.69 hrs ............................................~~(,_,"> 4.27/5.69 hrs .............................................~~(,_,"> 4.29/5.69 hrs .............................................~~(,_,"> 4.30/5.69 hrs .............................................~~(,_,"> 4.32/5.69 hrs .............................................~~(,_,"> 4.34/5.69 hrs .............................................~~(,_,"> 4.35/5.69 hrs .............................................~~(,_,"> 4.37/5.69 hrs ..............................................~~(,_,"> 4.38/5.69 hrs ..............................................~~(,_,"> 4.39/5.69 hrs ..............................................~~(,_,"> 4.41/5.69 hrs ..............................................~~(,_,"> 4.43/5.69 hrs ..............................................~~(,_,"> 4.44/5.69 hrs ..............................................~~(,_,"> 4.45/5.69 hrs ..............................................~~(,_,"> 4.47/5.69 hrs ...............................................~~(,_,"> 4.48/5.68 hrs ...............................................~~(,_,"> 4.49/5.68 hrs ...............................................~~(,_,"> 4.50/5.68 hrs ...............................................~~(,_,"> 4.52/5.68 hrs ...............................................~~(,_,"> 4.53/5.67 hrs ...............................................~~(,_,"> 4.55/5.67 hrs ................................................~~(,_,"> 4.56/5.67 hrs ................................................~~(,_,"> 4.58/5.67 hrs ................................................~~(,_,"> 4.59/5.67 hrs ................................................~~(,_,"> 4.60/5.67 hrs ................................................~~(,_,"> 4.62/5.67 hrs ................................................~~(,_,"> 4.64/5.67 hrs .................................................~~(,_,"> 4.65/5.67 hrs .................................................~~(,_,"> 4.67/5.67 hrs .................................................~~(,_,"> 4.68/5.67 hrs .................................................~~(,_,"> 4.69/5.67 hrs .................................................~~(,_,"> 4.71/5.67 hrs .................................................~~(,_,"> 4.72/5.67 hrs ..................................................~~(,_,"> 4.74/5.67 hrs ..................................................~~(,_,"> 4.75/5.67 hrs ..................................................~~(,_,"> 4.76/5.66 hrs ..................................................~~(,_,"> 4.77/5.66 hrs ..................................................~~(,_,"> 4.79/5.66 hrs ..................................................~~(,_,"> 4.80/5.65 hrs ..................................................~~(,_,"> 4.82/5.65 hrs ...................................................~~(,_,"> 4.83/5.66 hrs ...................................................~~(,_,"> 4.84/5.65 hrs ...................................................~~(,_,"> 4.85/5.65 hrs ...................................................~~(,_,"> 4.87/5.64 hrs ...................................................~~(,_,"> 4.88/5.64 hrs ...................................................~~(,_,"> 4.89/5.64 hrs ....................................................~~(,_,"> 4.91/5.64 hrs ....................................................~~(,_,"> 4.92/5.63 hrs ....................................................~~(,_,"> 4.93/5.63 hrs ....................................................~~(,_,"> 4.94/5.63 hrs ....................................................~~(,_,"> 4.95/5.62 hrs ....................................................~~(,_,"> 4.97/5.62 hrs .....................................................~~(,_,"> 4.97/5.61 hrs .....................................................~~(,_,"> 4.99/5.61 hrs .....................................................~~(,_,"> 5.00/5.60 hrs .....................................................~~(,_,"> 5.01/5.60 hrs .....................................................~~(,_,"> 5.03/5.60 hrs .....................................................~~(,_,"> 5.04/5.60 hrs .....................................................~~(,_,"> 5.06/5.60 hrs ......................................................~~(,_,"> 5.07/5.61 hrs ......................................................~~(,_,"> 5.09/5.61 hrs ......................................................~~(,_,"> 5.10/5.61 hrs ......................................................~~(,_,"> 5.12/5.61 hrs ......................................................~~(,_,"> 5.13/5.60 hrs ......................................................~~(,_,"> 5.14/5.60 hrs .......................................................~~(,_,"> 5.15/5.59 hrs .......................................................~~(,_,"> 5.16/5.59 hrs .......................................................~~(,_,"> 5.17/5.58 hrs .......................................................~~(,_,"> 5.18/5.58 hrs .......................................................~~(,_,"> 5.19/5.57 hrs .......................................................~~(,_,"> 5.19/5.56 hrs ........................................................~~(,_,"> 5.20/5.56 hrs ........................................................~~(,_,"> 5.21/5.55 hrs ........................................................~~(,_,"> 5.22/5.55 hrs ........................................................~~(,_,"> 5.23/5.54 hrs ........................................................~~(,_,"> 5.24/5.54 hrs ........................................................~~(,_,"> 5.25/5.53 hrs ........................................................~~(,_,"> 5.26/5.52 hrs .........................................................~~(,_,"> 5.27/5.52 hrs .........................................................~~(,_,"> 5.28/5.51 hrs .........................................................~~(,_,"> 5.28/5.50 hrs .........................................................~~(,_,"> 5.29/5.50 hrs .........................................................~~(,_,"> 5.30/5.49 hrs .........................................................~~(,_,"> 5.31/5.48 hrs ..........................................................~~(,_,"> 5.32/5.48 hrs ..........................................................~~(,_,"> 5.33/5.47 hrs ..........................................................~~(,_,"> 5.34/5.47 hrs ..........................................................~~(,_,"> 5.35/5.46 hrs ..........................................................~~(,_,"> 5.36/5.46 hrs ..........................................................~~(,_,"> 5.36/5.45 hrs ...........................................................~~(,_,"> 5.37/5.45 hrs ...........................................................~~(,_,"> 5.38/5.44 hrs ...........................................................~~(,_,"> 5.39/5.43 hrs ...........................................................~~(,_,"> 5.40/5.43 hrs ...........................................................~~(,_,"> 5.41/5.42 hrs ...........................................................~~(,_,"> 5.41/5.41 hrs ............................................................~~(,_,"> + Fitting B/k-factors between 10 and 50 pixels, or 20 and 4.0932 Angstrom ... + Combining frames for all micrographs ... 000/??? sec ~~(,_,"> [oo] 0.10/6.12 hrs ~~(,_,"> 0.19/6.00 hrs .~~(,_,"> 0.28/5.80 hrs ..~~(,_,"> 0.36/5.70 hrs ...~~(,_,"> 0.45/5.63 hrs ....~~(,_,"> 0.52/5.49 hrs .....~~(,_,"> 0.61/5.51 hrs ......~~(,_,"> 0.69/5.45 hrs .......~~(,_,"> 0.78/5.47 hrs ........~~(,_,"> 0.87/5.49 hrs .........~~(,_,"> === RELION MPI setup === + Number of MPI processes = 4 + Master (0) runs on host = perk + Slave 1 runs on host = perk + Slave 2 runs on host = perk + Slave 3 runs on host = perk ================= + Reading Refine3D/job245/run_data.star... - Using pixel size calculated from magnification and detector pixel size in the input STAR file: 1.137 + Using movie pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.5685 A + Using coord. pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 1.137 A + Using dose per frame from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.9333 e/A^2 - Motion has already been estimated for all micrographs - Will only recombine frames for 1245 unfinished micrographs + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job245/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job245/run_half2_class001_unfil.mrc - Mask: MaskCreate/job238/mask.mrc + Masking references ... + Transforming references ... + Fitting B/k-factors between 10 and 50 pixels, or 20 and 4.0932 Angstrom ... + Combining frames for all micrographs ... 000/??? sec ~~(,_,"> [oo] 0.07/4.49 hrs ~~(,_,"> 0.14/4.50 hrs .~~(,_,"> 0.21/4.45 hrs ..~~(,_,"> 0.29/4.47 hrs ...~~(,_,"> 0.36/4.53 hrs ....~~(,_,"> 0.43/4.52 hrs .....~~(,_,"> 0.51/4.52 hrs ......~~(,_,">-------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 27499 on node perk exited on signal 15 (Terminated). -------------------------------------------------------------------------- === RELION MPI setup === + Number of MPI processes = 8 + Master (0) runs on host = perk + Slave 1 runs on host = perk + Slave 2 runs on host = perk + Slave 3 runs on host = perk + Slave 4 runs on host = perk + Slave 5 runs on host = perk + Slave 6 runs on host = perk + Slave 7 runs on host = perk ================= + Reading Refine3D/job245/run_data.star... - Using pixel size calculated from magnification and detector pixel size in the input STAR file: 1.137 + Using movie pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.5685 A + Using coord. pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 1.137 A + Using dose per frame from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.9333 e/A^2 - Motion has already been estimated for all micrographs - Will only recombine frames for 1097 unfinished micrographs + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job245/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job245/run_half2_class001_unfil.mrc - Mask: MaskCreate/job238/mask.mrc + Masking references ... + Transforming references ... + Fitting B/k-factors between 10 and 50 pixels, or 20 and 4.0932 Angstrom ... + Combining frames for all micrographs ... 000/??? sec ~~(,_,"> [oo] 0.07/4.62 hrs ~~(,_,">-------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 33012 on node perk exited on signal 15 (Terminated). -------------------------------------------------------------------------- === RELION MPI setup === + Number of MPI processes = 4 + Master (0) runs on host = perk + Slave 1 runs on host = perk + Slave 2 runs on host = perk + Slave 3 runs on host = perk ================= + Reading Refine3D/job245/run_data.star... - Using pixel size calculated from magnification and detector pixel size in the input STAR file: 1.137 + Using movie pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.5685 A + Using coord. pixel size from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 1.137 A + Using dose per frame from MotionCorr/job007/frames/19Apr15_bMR4nd_162-10_0001.star: 0.9333 e/A^2 - Motion has already been estimated for all micrographs - Will only recombine frames for 1076 unfinished micrographs + Reading references ... + The names of the reference half maps and the mask were taken from the PostProcess STAR file. - Half map 1: Refine3D/job245/run_half1_class001_unfil.mrc - Half map 2: Refine3D/job245/run_half2_class001_unfil.mrc - Mask: MaskCreate/job238/mask.mrc + Masking references ... + Transforming references ... + Fitting B/k-factors between 10 and 50 pixels, or 20 and 4.0932 Angstrom ... + Combining frames for all micrographs ... 000/??? sec ~~(,_,"> [oo] 0.05/3.44 hrs ~~(,_,"> 0.11/3.63 hrs .~~(,_,"> 0.17/3.74 hrs ..~~(,_,"> 0.23/3.81 hrs ...~~(,_,"> 0.28/3.73 hrs ....~~(,_,"> 0.33/3.74 hrs .....~~(,_,"> 0.39/3.74 hrs ......~~(,_,"> 0.45/3.74 hrs .......~~(,_,"> 0.50/3.74 hrs ........~~(,_,"> 0.56/3.77 hrs ........~~(,_,"> 0.62/3.82 hrs .........~~(,_,"> 0.68/3.83 hrs ..........~~(,_,"> 0.74/3.85 hrs ...........~~(,_,"> 0.81/3.87 hrs ............~~(,_,"> 0.87/3.90 hrs .............~~(,_,"> 0.92/3.88 hrs ..............~~(,_,"> 0.99/3.91 hrs ...............~~(,_,"> 1.05/3.94 hrs ................~~(,_,"> 1.11/3.94 hrs ................~~(,_,"> 1.17/3.94 hrs .................~~(,_,"> 1.23/3.95 hrs ..................~~(,_,"> 1.29/3.95 hrs ...................~~(,_,"> 1.35/3.94 hrs ....................~~(,_,"> 1.41/3.96 hrs .....................~~(,_,"> 1.47/3.96 hrs ......................~~(,_,"> 1.53/3.96 hrs .......................~~(,_,"> 1.58/3.94 hrs ........................~~(,_,"> 1.65/3.96 hrs ........................~~(,_,"> 1.71/3.95 hrs .........................~~(,_,"> 1.77/3.96 hrs ..........................~~(,_,"> 1.82/3.95 hrs ...........................~~(,_,"> 1.88/3.95 hrs ............................~~(,_,"> 1.95/3.97 hrs .............................~~(,_,"> 2.01/3.97 hrs ..............................~~(,_,"> 2.06/3.96 hrs ...............................~~(,_,"> 2.12/3.95 hrs ................................~~(,_,"> 2.17/3.95 hrs .................................~~(,_,"> 2.22/3.93 hrs .................................~~(,_,"> 2.28/3.93 hrs ..................................~~(,_,"> 2.33/3.92 hrs ...................................~~(,_,"> 2.39/3.92 hrs ....................................~~(,_,"> 2.45/3.92 hrs .....................................~~(,_,"> 2.50/3.91 hrs ......................................~~(,_,"> 2.56/3.92 hrs .......................................~~(,_,"> 2.62/3.91 hrs ........................................~~(,_,"> 2.68/3.92 hrs .........................................~~(,_,"> 2.74/3.92 hrs .........................................~~(,_,"> 2.80/3.93 hrs ..........................................~~(,_,"> 2.86/3.93 hrs ...........................................~~(,_,"> 2.93/3.94 hrs ............................................~~(,_,"> 2.98/3.94 hrs .............................................~~(,_,"> 3.04/3.94 hrs ..............................................~~(,_,"> 3.10/3.94 hrs ...............................................~~(,_,"> 3.16/3.93 hrs ................................................~~(,_,"> 3.21/3.93 hrs .................................................~~(,_,"> 3.27/3.93 hrs .................................................~~(,_,"> 3.32/3.92 hrs ..................................................~~(,_,"> 3.38/3.92 hrs ...................................................~~(,_,"> 3.44/3.92 hrs ....................................................~~(,_,"> 3.48/3.90 hrs .....................................................~~(,_,"> 3.51/3.87 hrs ......................................................~~(,_,"> 3.54/3.83 hrs .......................................................~~(,_,"> 3.56/3.80 hrs ........................................................~~(,_,"> 3.59/3.78 hrs .........................................................~~(,_,"> 3.62/3.75 hrs .........................................................~~(,_,"> 3.64/3.71 hrs ..........................................................~~(,_,"> 3.66/3.67 hrs ...........................................................~~(,_,"> 3.66/3.66 hrs ............................................................~~(,_,"> + Combining all EPS and STAR files ... + Done! + Written logfile in Polish/job252/logfile.pdf + Written new particle STAR file in Polish/job252/shiny.star