** Welcome to Simulator ** Version : 0.25 Compiled : May 5 2021 Mode : Scripted Output filename : betgal_1elec_per_angSq.mrc Make a 3d scattering potential? : -320 Number of threads : 16 PDB file name : bgal_flat.pdb Add another type of particle? : no Output pixel size (Angstroms) : 1.0 Linear scaling of per atom bFactor : 1.0 Per atom (xtal) bFactor added to all atoms : 4.0 wanted size is 320 Create a tilt-series as well? : no Create a particle stack? : 1 Making a particle stack with 1 images wanted defocus (Angstroms) : 8000 wanted additional phase shift x * PI radians, i.e. 0.5 for PI/2 shift. : 0electrons/Ang^2 in a frame at the specimen : 1.5 electrons/Pixel/sec : 3.0 number of frames per movie (micrograph or tilt) : 1 Set expert options? : yes Use an existing set of orientations : no Linear scaling water intensity : 1.0 fraction of the defocus to add as astigmatism : 0.0 Accelrating volatage (kV) : 300 Objective aperture diameter in micron : 100 Spherical aberration constant in millimeters : 2.7 Std deviation of error to use in shifts, astigmatism, rotations etc. : 0.0Pre-exposure in electron/A^2 : 0 minimum padding of images with solvent : 32 minimum thickness in Z : 10 Propagation distance in angstrom : 5 Rotation of tilt-axis from Y (degrees) : 0.0 Standard deviation on angles in plane (degrees) : 2.0 Standard deviation on tilt-angles (degrees) : 0.1 Standard deviation on magnification (fraction) : 0.0001 Beam-tilt in X (milli radian) : 0.0 Beam-tilt in Y (milli radian) : 0.0 Beam-tilt particle shift in X (Angstrom) : 0.0 Beam-tilt particle shift in Y (Angstrom) : 0.0 Max particles is 0 here In constructor real total current 32824 32824 32824 Number of particles initialized 1 PDB center of mass at 93.002000 93.002000 93.002000 (x,y,z Angstrom) Setting origin there. There are 32824 non-water atoms in the specimen. Current number of PDBs 1 Using extra phase shift of 0.000000 radians Got here emulate is 0.000000 There are 1 tilts for Tilt 0, scaling the pixel size from 1.000 to 1.000 Working on iParticle 0/ 1 For the particle stack, stretching the defocus by 0.00 percent and randmozing the astigmatism angle -90,90Scaling the defocus by 1.000000 to match the def at 300 KeV AVG BFACTOR FROM PDB IS 19.164429 max/min xyz, 90.431000,-90.431000 68.182007,-68.181999 45.899002,-45.898998 min is 10.000000, shift is 0, max_depth is 91 for frame 0 the size neigborhood is 2 using neighborhood of 125.00 vox^3 for waters and 125.00 vox^3 for non-waters Starting projected water calc with sizeN 5, 5 Finishing projected water calc wanted size is 407 Is single particle is 1 size pre rot padding 380 335 0.000000 rot size post rot 1 padding 787 742 0.000000 rot size post rot 2 padding 787 742 padX 407 padY 407 padZ 0 rot vol dimension in Ang 787.00 x 742.00 y 104.00 z Drift for iTilt 0, iFrame 0 is 0.0000 Ang Atoms per nm^3 31.422, vol (in Ang^3) 787.00 742.00 104.00 specimen volume is 6.073e+04 nm expecting 1.908e+06 waters cuttoff is 1.908314e+06 5.925180e+07 0.967793 -0.967793 waters added 1.933e+06 (101.28%) Using a rmsd of 2.250000 for water perturbation wZ 104 csZ 104,rotZ 104 Working on iTilt 0 at 119.805107 degrees for frame 0 rotated_Z 104 nSlabs 21 nSlabs 21 iSlab 6 lSlab 5 Found a scattering cetner of mass at -53.511 Ang Exposure is 1.500 for frame -53.511456 -5.000000 -2.476191 Propagator distance is -5.000e+00 Angstroms, with offset for CTF of -5.101e+01 Angstroms for the specimen. 0 out of bounds of 32824 = percent 8.00000e+03 8.00000e+03 Astigmatism params are 0.000e+00 8.365e+01 SEED is 1639468828480218300e ./simulator_ctf_303DESKTOP-2HAG7BR.sh: line 3: ctffind: command not found tail: cannot open 'fit_303DESKTOP-2HAG7BR_1.txt.txt' for reading: No such file or directory Failed on the following record : From Line : From /groups/grigorieff/home/himesb/cisTEM_downstream_bah/src/core/numeric_text_file.cpp:261 void NumericTextFile::ReadLine(float *)