Hi,
I am afraid to say that something is very wrong with your refinement.
For example, the initial model is wrong, the mask is wrong and/or CTF
parameters are wrong.
Do your 2D class averages show protein-like features? Does your
initial model look reasonable?
Best regards,
Takanori Nakane
> Thanks Takanori. Resolution before CTFRefine is 8.9 A, i couldn't get
> better than this.
>
> Following is the run_model.star output FSC table of Refine3D
>
> data_model_class_1
>
> loop_
> _rlnSpectralIndex #1
> _rlnResolution #2
> _rlnAngstromResolution #3
> _rlnSsnrMap #4
> _rlnGoldStandardFsc #5
> _rlnFourierCompleteness #6
> _rlnReferenceSigma2 #7
> _rlnReferenceTau2 #8
> _rlnSpectralOrientabilityContribution #9
> 0 0.000000 999.000000 999.000000 1.000000
> 1.000000 3.039271e-09 3.036232e-06 0.000000
> 1 0.003030 330.000000 999.000000 1.000000
> 1.000000 3.313983e-08 3.310669e-05 5.917887e-05
> 2 0.006061 165.000000 999.000000 1.000000
> 1.000000 2.834714e-08 2.831879e-05 4.894759e-04
> 3 0.009091 110.000000 999.000000 1.000000
> 1.000000 2.244205e-08 2.241961e-05 0.001894
> 4 0.012121 82.500000 999.000000 1.000000
> 1.000000 1.473943e-08 1.472469e-05 0.006954
> 5 0.015152 66.000000 999.000000 1.000000
> 1.000000 1.006470e-08 1.005464e-05 0.008245
> 6 0.018182 55.000000 999.000000 1.000000
> 1.000000 6.430807e-09 6.424376e-06 0.013133
> 7 0.021212 47.142857 999.000000 1.000000
> 1.000000 4.697458e-09 4.692761e-06 0.015915
> 8 0.024242 41.250000 999.000000 1.000000
> 1.000000 3.794016e-09 3.790222e-06 0.032345
> 9 0.027273 36.666667 999.000000 0.999049
> 1.000000 3.233850e-09 3.230617e-06 0.065457
> 10 0.030303 33.000000 509.723944 0.992206
> 1.000000 2.969999e-09 1.513880e-06 0.058040
> 11 0.033333 30.000000 252.247974 0.984360
> 1.000000 2.766835e-09 6.979284e-07 0.066659
> 12 0.036364 27.500000 114.823041 0.966195
> 1.000000 2.947017e-09 3.383854e-07 0.049031
> 13 0.039394 25.384615 36.299630 0.899514
> 1.000000 3.547018e-09 1.287554e-07 0.048808
> 14 0.042424 23.571429 20.529078 0.833617
> 1.000000 4.501066e-09 9.240273e-08 0.036345
> 15 0.045455 22.000000 18.068204 0.814658
> 1.000000 4.487677e-09 8.108426e-08 0.034633
> 16 0.048485 20.625000 16.908402 0.804140
> 1.000000 3.574465e-09 6.043849e-08 0.058198
> 17 0.051515 19.411765 13.302209 0.762192
> 1.000000 3.260028e-09 4.336557e-08 0.054712
> 18 0.054545 18.333333 11.765598 0.738322
> 1.000000 3.464403e-09 4.076077e-08 0.043442
> 19 0.057576 17.368421 9.746735 0.698594
> 1.000000 3.970331e-09 3.869777e-08 0.035180
> 20 0.060606 16.500000 6.951958 0.618521
> 1.000000 3.837963e-09 2.668136e-08 0.036874
> 21 0.063636 15.714286 9.907047 0.702183
> 1.000000 3.310894e-09 3.280118e-08 0.058766
> 22 0.066667 15.000000 9.302637 0.688186
> 1.000000 3.409664e-09 3.171887e-08 0.052253
> 23 0.069697 14.347826 0.046791 3.022290e-04
> 0.000000 3.950329e-09 1.848379e-10 0.041263
> 24 0.072727 13.750000 0.046791 -0.00682
> 0.000000 4.260500e-09 1.993509e-10 0.027919
> 25 0.075758 13.200000 5.113473 0.538000
> 1.000000 4.082221e-09 2.087433e-08 0.023655
> 26 0.078788 12.692308 4.649721 0.512092
> 1.000000 4.320315e-09 2.008826e-08 0.017395
> 27 0.081818 12.222222 4.771700 0.519180
> 1.000000 4.651859e-09 2.219728e-08 0.017283
> 28 0.084848 11.785714 5.274460 0.546370
> 1.000000 4.341189e-09 2.289743e-08 0.024534
> 29 0.087879 11.379310 2.112394 0.299240
> 0.991113 4.475941e-09 9.454950e-09 0.020282
> 30 0.090909 11.000000 4.375935 0.495409
> 0.999956 4.638524e-09 2.029788e-08 0.017993
> 31 0.093939 10.645161 3.817018 0.457622
> 0.999938 4.574895e-09 1.746246e-08 0.011620
> 32 0.096970 10.312500 0.046791 -0.01266
> 0.000000 5.090813e-09 2.382017e-10 0.006043
> 33 0.100000 10.000000 0.173382 0.011037
> 0.000000 5.219388e-09 9.049489e-10 0.004702
> 34 0.103030 9.705882 0.046791 7.270886e-04
> 0.000000 5.033294e-09 2.355104e-10 0.003934
> 35 0.106061 9.428571 1.977962 0.283007
> 0.980173 5.190977e-09 1.026756e-08 0.002332
> 36 0.109091 9.166667 0.046791 -0.00118
> 0.000000 5.145647e-09 2.407674e-10 0.001391
> 37 0.112121 8.918919 1.072335 0.154572
> 0.451873 5.509750e-09 5.908297e-09 7.252224e-04
> 38 0.115152 8.684211 0.971698 0.138223
> 0.366854 5.742969e-09 5.580429e-09 5.191572e-04
> 39 0.118182 8.461538 0.046791 -0.00536
> 0.000000 5.602983e-09 2.621664e-10 2.818296e-04
> 40 0.121212 8.250000 0.046791 -0.00421
> 0.000000 5.724266e-09 2.678413e-10 1.955938e-04
> 41 0.124242 8.048780 0.213259 0.015691
> 0.000000 5.848579e-09 1.247262e-09 1.256604e-04
> 42 0.127273 7.857143 0.081286 0.002834
> 0.000000 6.098445e-09 4.957180e-10 7.936153e-05
> 43 0.130303 7.674419 0.046791 -0.00483
> 0.000000 5.885802e-09 2.753996e-10 5.268402e-05
> 44 0.133333 7.500000 0.420095 0.045757
> 0.001089 6.188234e-09 2.599646e-09 2.722632e-05
> 45 0.136364 7.333333 0.192184 0.013164
> 0.000000 6.409364e-09 1.231777e-09 2.424098e-05
> 46 0.139394 7.173913 0.046791 -7.64494e-04
> 0.000000 6.499672e-09 3.041230e-10 1.980919e-05
> 47 0.142424 7.021277 0.046791 6.916352e-04
> 0.000000 6.560100e-09 3.069504e-10 1.868118e-05
> 48 0.145455 6.875000 0.046791 -0.01169
> 0.000000 6.724800e-09 3.146568e-10 1.485480e-05
> 49 0.148485 6.734694 0.227418 0.017464
> 0.000000 6.951354e-09 1.580865e-09 1.351432e-05
> 50 0.151515 6.600000 0.069085 0.002092
> 0.000000 6.827112e-09 4.716480e-10 1.256239e-05
> 51 0.154545 6.470588 0.057605 0.001486
> 0.000000 7.154738e-09 4.121509e-10 1.114213e-05
> 52 0.157576 6.346154 0.089671 0.003397
> 0.000000 7.165733e-09 6.425579e-10 9.241038e-06
> 53 0.160606 6.226415 0.046791 -0.00390
> 0.000000 7.367394e-09 3.447241e-10 8.571254e-06
> 54 0.163636 6.111111 0.046791 2.460130e-04
> 0.000000 7.377381e-09 3.451914e-10 7.752445e-06
> 55 0.166667 6.000000 0.046791 4.277551e-04
> 0.000000 7.556618e-09 3.535780e-10 6.668082e-06
> 56 0.169697 5.892857 0.046791 -0.00710
> 0.000000 7.731845e-09 3.617769e-10 6.149462e-06
> 57 0.172727 5.789474 0.046791 -0.00801
> 0.000000 7.706908e-09 3.606101e-10 5.795120e-06
> 58 0.175758 5.689655 0.046791 -0.00111
> 0.000000 7.970649e-09 3.729507e-10 4.791571e-06
> 59 0.178788 5.593220 0.046791 -3.02845e-04
> 0.000000 8.011282e-09 3.748519e-10 4.751638e-06
> 60 0.181818 5.500000 0.046791 -0.00939
> 0.000000 8.109959e-09 3.794691e-10 4.250316e-06
> 61 0.184848 5.409836 0.046791 -0.00258
> 0.000000 8.302458e-09 3.884762e-10 3.715239e-06
> 62 0.187879 5.322581 0.108479 0.004812
> 0.000000 8.341882e-09 9.049187e-10 3.459086e-06
> 63 0.190909 5.238095 0.046791 -0.00108
> 0.000000 8.531299e-09 3.991838e-10 2.908744e-06
> 64 0.193939 5.156250 0.111172 0.005030
> 0.000000 8.545994e-09 9.500784e-10 3.188802e-06
> 65 0.196970 5.076923 0.046791 -0.00621
> 0.000000 8.803906e-09 4.119392e-10 2.483702e-06
> 66 0.200000 5.000000 0.074446 0.002406
> 0.000000 8.815924e-09 6.563064e-10 2.464602e-06
> 67 0.203030 4.925373 0.107835 0.004760
> 0.000000 8.897024e-09 9.594067e-10 2.159672e-06
> 68 0.206061 4.852941 0.046791 3.354429e-04
> 0.000000 9.197138e-09 4.303388e-10 1.859192e-06
> 69 0.209091 4.782609 0.112154 0.005111
> 0.000000 9.035874e-09 1.013412e-09 1.878826e-06
> 70 0.212121 4.714286 0.046791 -0.00563
> 0.000000 9.425886e-09 4.410419e-10 1.584559e-06
> 71 0.215152 4.647887 0.046791 -2.31483e-04
> 0.000000 9.354980e-09 4.377242e-10 1.456250e-06
> 72 0.218182 4.583333 0.102165 0.004315
> 0.000000 9.490783e-09 9.696232e-10 1.400821e-06
> 73 0.221212 4.520548 0.046791 -0.00227
> 0.000000 9.689360e-09 4.533700e-10 1.263722e-06
> 74 0.224242 4.459459 0.071373 0.002224
> 0.000000 9.690132e-09 6.916145e-10 1.096707e-06
> 75 0.227273 4.400000 0.046791 -0.00412
> 0.000000 9.933088e-09 4.647742e-10 1.012700e-06
> 76 0.230303 4.342105 0.046791 -2.15435e-04
> 0.000000 9.916654e-09 4.640052e-10 9.484011e-07
> 77 0.233333 4.285714 0.046791 -0.00334
> 0.000000 1.008880e-08 4.720599e-10 9.142882e-07
> 78 0.236364 4.230769 0.046791 -0.00236
> 0.000000 1.019339e-08 4.769538e-10 7.453590e-07
> 79 0.239394 4.177215 0.046791 -0.00183
> 0.000000 1.029314e-08 4.816214e-10 7.069748e-07
> 80 0.242424 4.125000 0.062970 0.001758
> 0.000000 1.046224e-08 6.588069e-10 6.206620e-07
> 81 0.245455 4.074074 0.090747 0.003473
> 0.000000 1.050475e-08 9.532708e-10 6.382405e-07
> 82 0.248485 4.024390 0.064055 0.001815
> 0.000000 1.068844e-08 6.846506e-10 5.280048e-07
> 83 0.251515 3.975904 0.046791 -0.00187
> 0.000000 1.074170e-08 5.026094e-10 4.819384e-07
> 84 0.254545 3.928571 0.069768 0.002131
> 0.000000 1.089448e-08 7.600832e-10 4.230262e-07
> 85 0.257576 3.882353 0.046791 -0.00653
> 0.000000 1.105754e-08 5.173879e-10 4.269524e-07
> 86 0.260606 3.837209 0.114923 0.005341
> 0.000000 1.109695e-08 1.275292e-09 3.564842e-07
> 87 0.263636 3.793103 0.063193 0.001770
> 0.000000 1.124659e-08 7.107055e-10 3.323456e-07
> 88 0.266667 3.750000 0.046791 -0.00838
> 0.000000 1.132569e-08 5.299348e-10 2.920896e-07
> 89 0.269697 3.707865 0.046791 -9.42386e-04
> 0.000000 1.142207e-08 5.344444e-10 2.849842e-07
> 90 0.272727 3.666667 0.058276 0.001518
> 0.000000 1.152943e-08 6.718903e-10 2.473628e-07
> 91 0.275758 3.626374 0.046791 -0.00215
> 0.000000 1.156117e-08 5.409529e-10 2.187241e-07
> 92 0.278788 3.586957 0.046791 4.446633e-04
> 0.000000 1.171880e-08 5.483287e-10 1.983572e-07
> 93 0.281818 3.548387 0.046791 -0.00192
> 0.000000 1.163338e-08 5.443317e-10 1.859423e-07
> 94 0.284848 3.510638 0.046791 -0.00278
> 0.000000 1.181429e-08 5.527968e-10 1.652119e-07
> 95 0.287879 3.473684 0.053051 0.001271
> 0.000000 1.181307e-08 6.266929e-10 1.457190e-07
> 96 0.290909 3.437500 0.101353 0.004252
> 0.000000 1.184533e-08 1.200562e-09 1.335276e-07
> 97 0.293939 3.402062 0.059693 0.001589
> 0.000000 1.198962e-08 7.156913e-10 1.208470e-07
> 98 0.296970 3.367347 0.108934 0.004848
> 0.000000 1.197328e-08 1.304298e-09 1.167373e-07
> 99 0.300000 3.333333 0.046791 -0.00201
> 0.000000 1.206087e-08 5.643343e-10 9.331324e-08
> 100 0.303030 3.300000 0.046791 -2.51660e-04
> 0.000000 1.208802e-08 5.656045e-10 9.142334e-08
> 101 0.306061 3.267327 0.085471 0.003110
> 0.000000 1.217928e-08 1.040975e-09 7.441690e-08
> 102 0.309091 3.235294 0.046791 -8.23557e-04
> 0.000000 1.225168e-08 5.732625e-10 7.409849e-08
> 103 0.312121 3.203883 0.046791 -0.00420
> 0.000000 1.222365e-08 5.719506e-10 6.614297e-08
> 104 0.315152 3.173077 0.124481 0.006165
> 0.000000 1.234777e-08 1.537057e-09 5.321699e-08
> 105 0.318182 3.142857 0.046791 -0.00600
> 0.000000 1.237358e-08 5.789661e-10 5.285381e-08
> 106 0.321212 3.113208 0.059568 0.001583
> 0.000000 1.245512e-08 7.419287e-10 4.437456e-08
> 107 0.324242 3.084112 0.046791 4.626701e-04
> 0.000000 1.251852e-08 5.857479e-10 4.078762e-08
> 108 0.327273 3.055556 0.046791 -2.12945e-04
> 0.000000 1.255517e-08 5.874629e-10 3.680849e-08
> 109 0.330303 3.027523 0.093341 0.003658
> 0.000000 1.270808e-08 1.186181e-09 3.113079e-08
> 110 0.333333 3.000000 0.046791 -0.00190
> 0.000000 1.267878e-08 5.932465e-10 2.832362e-08
> 111 0.336364 2.972973 0.054006 0.001314
> 0.000000 1.279730e-08 6.911252e-10 2.401383e-08
> 112 0.339394 2.946429 0.046791 6.621227e-05
> 0.000000 1.283731e-08 6.006643e-10 2.186627e-08
> 113 0.342424 2.920354 0.076760 0.002547
> 0.000000 1.289001e-08 9.894334e-10 1.882097e-08
> 114 0.345455 2.894737 0.046791 -0.00470
> 0.000000 1.300281e-08 6.084082e-10 1.673825e-08
> 115 0.348485 2.869565 0.046791 -0.00252
> 0.000000 1.294199e-08 6.055621e-10 1.539296e-08
> 116 0.351515 2.844828 0.046791 9.480361e-04
> 0.000000 1.313424e-08 6.145576e-10 1.316700e-08
> 117 0.354545 2.820513 0.046791 -0.00189
> 0.000000 1.310934e-08 6.133926e-10 1.114247e-08
> 118 0.357576 2.796610 0.104634 0.004506
> 0.000000 1.319692e-08 1.380853e-09 9.941482e-09
> 119 0.360606 2.773109 0.046791 5.818334e-04
> 0.000000 1.328818e-08 6.217606e-10 8.713432e-09
> 120 0.363636 2.750000 0.046791 7.206302e-04
> 0.000000 1.327001e-08 6.209107e-10 8.129833e-09
> 121 0.366667 2.727273 0.046791 -0.00161
> 0.000000 1.345320e-08 6.294818e-10 6.978053e-09
> 122 0.369697 2.704918 0.046791 2.777700e-04
> 0.000000 1.336609e-08 6.254063e-10 6.199321e-09
> 123 0.372727 2.682927 0.105458 0.004571
> 0.000000 1.353111e-08 1.426966e-09 5.647392e-09
> 124 0.375758 2.661290 0.046791 -0.00229
> 0.000000 1.357237e-08 6.350582e-10 4.763764e-09
> 125 0.378788 2.640000 0.046791 -3.91353e-04
> 0.000000 1.356615e-08 6.347672e-10 4.432637e-09
> 126 0.381818 2.619048 0.079898 0.002745
> 0.000000 1.374641e-08 1.098306e-09 3.994019e-09
> 127 0.384848 2.598425 0.046791 -1.18548e-04
> 0.000000 1.366147e-08 6.392270e-10 3.959614e-09
> 128 0.387879 2.578125 0.046791 5.272071e-07
> 0.000000 1.379496e-08 6.454733e-10 3.398765e-09
> 129 0.390909 2.558140 0.075543 0.002473
> 0.000000 1.381728e-08 1.043800e-09 3.254885e-09
> 130 0.393939 2.538462 0.046791 -7.66372e-04
> 0.000000 1.388465e-08 6.496696e-10 3.054919e-09
> 131 0.396970 2.519084 0.054460 0.001335
> 0.000000 1.398919e-08 7.618502e-10 2.916856e-09
> 132 0.400000 2.500000 0.086723 0.003194
> 0.000000 1.392891e-08 1.207962e-09 2.906855e-09
> 133 0.403030 2.481203 0.046791 -0.00186
> 0.000000 1.411636e-08 6.605117e-10 2.766220e-09
> 134 0.406061 2.462687 0.046791 -0.00122
> 0.000000 1.410264e-08 6.598696e-10 2.764794e-09
> 135 0.409091 2.444444 0.046791 -9.87213e-05
> 0.000000 1.419972e-08 6.644119e-10 2.635484e-09
> 136 0.412121 2.426471 0.046791 3.277832e-04
> 0.000000 1.424616e-08 6.665848e-10 2.764923e-09
> 137 0.415152 2.408759 0.050685 0.001165
> 0.000000 1.423852e-08 7.216771e-10 2.660820e-09
> 138 0.418182 2.391304 0.112395 0.005131
> 0.000000 1.438915e-08 1.617261e-09 2.558729e-09
> 139 0.421212 2.374101 0.089747 0.003403
> 0.000000 1.432491e-08 1.285618e-09 2.714669e-09
> 140 0.424242 2.357143 0.053673 0.001299
> 0.000000 1.445509e-08 7.758499e-10 2.743497e-09
> 141 0.427273 2.340426 0.046791 -0.00414
> 0.000000 1.448992e-08 6.779908e-10 2.727285e-09
> 142 0.430303 2.323944 0.046791 5.488994e-04
> 0.000000 1.452087e-08 6.794390e-10 2.663981e-09
> 143 0.433333 2.307692 0.046791 4.162485e-04
> 0.000000 1.460544e-08 6.833959e-10 2.607739e-09
> 144 0.436364 2.291667 0.046791 -0.00153
> 0.000000 1.459931e-08 6.831093e-10 2.817174e-09
> 145 0.439394 2.275862 0.046791 4.946964e-04
> 0.000000 1.472359e-08 6.889243e-10 2.784068e-09
> 146 0.442424 2.260274 0.063089 0.001764
> 0.000000 1.469022e-08 9.267975e-10 2.689685e-09
> 147 0.445455 2.244898 0.046791 -0.00183
> 0.000000 1.479634e-08 6.923282e-10 2.650972e-09
> 148 0.448485 2.229730 0.098333 0.004024
> 0.000000 1.486379e-08 1.461596e-09 2.738972e-09
> 149 0.451515 2.214765 0.046791 -0.00161
> 0.000000 1.485642e-08 6.951394e-10 2.764782e-09
> 150 0.454545 2.200000 0.046791 -0.00110
> 0.000000 1.497707e-08 7.007849e-10 2.543608e-09
> 151 0.457576 2.185430 0.046791 -0.00181
> 0.000000 1.492252e-08 6.982321e-10 2.720339e-09
> 152 0.460606 2.171053 0.046791 -8.42192e-04
> 0.000000 1.504269e-08 7.038552e-10 2.507497e-09
> 153 0.463636 2.156863 0.046791 -9.68522e-04
> 0.000000 1.505980e-08 7.046556e-10 2.656932e-09
> 154 0.466667 2.142857 0.087881 0.003274
> 0.000000 1.510814e-08 1.327725e-09 2.540383e-09
> 155 0.469697 2.129032 0.046791 -0.00379
> 0.000000 1.520866e-08 7.116210e-10 2.457483e-09
> 156 0.472727 2.115385 0.046791 -0.00149
> 0.000000 1.516997e-08 7.098104e-10 2.499745e-09
> 157 0.475758 2.101911 0.046791 9.751904e-04
> 0.000000 1.531908e-08 7.167875e-10 2.441705e-09
> 158 0.478788 2.088608 0.065303 0.001882
> 0.000000 1.528790e-08 9.983476e-10 2.398193e-09
> 159 0.481818 2.075472 0.048485 0.001070
> 0.000000 1.536086e-08 7.447768e-10 2.213627e-09
> 160 0.484848 2.062500 0.046791 -4.43055e-04
> 0.000000 1.542858e-08 7.219110e-10 2.183093e-09
> 161 0.487879 2.049689 0.046791 -5.19663e-04
> 0.000000 1.539804e-08 7.204820e-10 2.246372e-09
> 162 0.490909 2.037037 0.046791 1.154401e-04
> 0.000000 1.554626e-08 7.274175e-10 2.061196e-09
> 163 0.493939 2.024540 0.076059 0.002504
> 0.000000 1.555028e-08 1.182739e-09 2.061341e-09
> 164 0.496970 2.012195 0.046791 -0.00263
> 0.000000 1.562836e-08 7.312587e-10 1.936159e-09
> 165 0.500000 2.000000 0.046791 8.184090e-04
> 0.000000 1.564676e-08 7.321198e-10 1.912812e-09
> 166 0.503030 1.987952 0.046791 7.212602e-04
> 0.000000 1.565628e-08 7.325652e-10 1.834726e-09
> 167 0.506061 1.976048 0.066702 0.001959
> 0.000000 1.579452e-08 1.053530e-09 1.687895e-09
> 168 0.509091 1.964286 0.046791 -7.23162e-05
> 0.000000 1.573990e-08 7.364777e-10 1.693392e-09
> 169 0.512121 1.952663 0.051530 0.001202
> 0.000000 1.586045e-08 8.172854e-10 1.626278e-09
> 170 0.515152 1.941176 0.046791 5.093044e-05
> 0.000000 1.588604e-08 7.433157e-10 1.555120e-09
> 171 0.518182 1.929825 0.056989 0.001456
> 0.000000 1.592782e-08 9.077164e-10 1.486633e-09
> 172 0.521212 1.918605 0.046791 -9.84665e-04
> 0.000000 1.605333e-08 7.511434e-10 1.310867e-09
> 173 0.524242 1.907514 0.046791 2.406135e-04
> 0.000000 1.598522e-08 7.479564e-10 1.365487e-09
> 174 0.527273 1.896552 0.046791 -8.89537e-05
> 0.000000 1.613033e-08 7.547465e-10 1.251096e-09
> 175 0.530303 1.885714 0.046791 -4.47142e-04
> 0.000000 1.611454e-08 7.540076e-10 1.174961e-09
> 176 0.533333 1.875000 0.046791 4.765055e-04
> 0.000000 1.620845e-08 7.584016e-10 1.131067e-09
> 177 0.536364 1.864407 0.046791 -0.00110
> 0.000000 1.627290e-08 7.614174e-10 1.036264e-09
> 178 0.539394 1.853933 0.046791 -0.00193
> 0.000000 1.624001e-08 7.598784e-10 1.030453e-09
> 179 0.542424 1.843575 0.046791 -0.00111
> 0.000000 1.640893e-08 7.677820e-10 9.111693e-10
> 180 0.545455 1.833333 0.046791 -9.26278e-04
> 0.000000 1.635232e-08 7.651332e-10 8.886851e-10
> 181 0.548485 1.823204 0.046791 -1.57150e-04
> 0.000000 1.649187e-08 7.716630e-10 7.996929e-10
> 182 0.551515 1.813187 0.118846 0.005674
> 0.000000 1.650989e-08 1.962140e-09 7.716341e-10
> 183 0.554545 1.803279 0.046791 5.627601e-04
> 0.000000 1.656179e-08 7.749345e-10 7.125076e-10
> 184 0.557576 1.793478 0.057744 0.001492
> 0.000000 1.666375e-08 9.622237e-10 6.597182e-10
> 185 0.560606 1.783784 0.046791 7.682734e-05
> 0.000000 1.661549e-08 7.774471e-10 6.124900e-10
> 186 0.563636 1.774194 0.046791 -8.95054e-04
> 0.000000 1.676708e-08 7.845401e-10 5.729267e-10
> 187 0.566667 1.764706 0.046791 9.869904e-04
> 0.000000 1.678311e-08 7.852902e-10 5.454015e-10
> 188 0.569697 1.755319 0.046791 4.476934e-04
> 0.000000 1.687080e-08 7.893932e-10 4.885343e-10
> 189 0.572727 1.746032 0.046791 5.140315e-04
> 0.000000 1.695544e-08 7.933538e-10 4.583657e-10
> 190 0.575758 1.736842 0.062051 0.001710
> 0.000000 1.693554e-08 1.050866e-09 4.200987e-10
> 191 0.578788 1.727749 0.046791 -8.61961e-04
> 0.000000 1.707653e-08 7.990197e-10 4.097779e-10
> 192 0.581818 1.718750 0.068635 0.002067
> 0.000000 1.705154e-08 1.170338e-09 3.667196e-10
> 193 0.584848 1.709845 0.046791 5.288265e-04
> 0.000000 1.718393e-08 8.040448e-10 3.493061e-10
> 194 0.587879 1.701031 0.085613 0.003119
> 0.000000 1.723078e-08 1.475181e-09 3.230998e-10
> 195 0.590909 1.692308 0.046791 -0.00198
> 0.000000 1.727572e-08 8.083395e-10 3.068551e-10
> 196 0.593939 1.683673 0.046791 1.451081e-04
> 0.000000 1.742897e-08 8.155105e-10 2.866063e-10
> 197 0.596970 1.675127 0.046791 -0.00103
> 0.000000 1.733365e-08 8.110504e-10 2.732911e-10
> 198 0.600000 1.666667 0.046791 3.981471e-04
> 0.000000 1.752002e-08 8.197706e-10 2.524526e-10
> 199 0.603030 1.658291 0.046791 -8.15709e-04
> 0.000000 1.754968e-08 8.211584e-10 2.484132e-10
> 200 0.606061 1.650000 0.046791 -9.45257e-04
> 0.000000 2.247772e-08 1.051744e-09 8.279940e-11
>
>
> Thanks
>
>
> Humayun
>
>
>
>
>
>
> On Wed, Dec 11, 2019 at 11:57 AM Takanori Nakane
> <[log in to unmask]>
> wrote:
>
>> Hi,
>>
>> What is the resolution "before per particle CTFRefine"?
>>
>> Can you cite the FSC table in run_model.star?
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>
>> > Hi,
>> >
>> > I am struggling with a situation of tilt data refinement. The
>> refinement
>> > before per particle CTFRefine runs fine and ends with converged map.
>> Both
>> > half maps look fine from the final round but the merged map
>> > run_class001.mrc has nothing in it, it's all dust. Any ideas why?
>> >
>> > Auto-refine: Refinement has converged, stopping now...
>> > Auto-refine: + Final reconstruction from all particles is saved as:
>> > Refine3D/job014/run_class001.mrc
>> > Auto-refine: + Final model parameters are stored in:
>> > Refine3D/job014/run_model.star
>> > Auto-refine: + Final data parameters are stored in:
>> > Refine3D/job014/run_data.star
>> > Auto-refine: + Final resolution (without masking) is: 8.91892
>> > Auto-refine: + But you may want to run relion_postprocess to mask the
>> > unfil.mrc maps and calculate a higher resolution FSC
>> > --
>> >
>> > ______________________
>> >
>> > Regards,
>> >
>> > Humayun Sharif, PhD
>> >
>> > Research Fellow | Wu Lab
>> > BCMP, Harvard Medical School
>> >
>> > Immune Disease Institute
>> > PCMM, Boston Children's Hospital
>> > 3 Blackfan Circle | Boston
>> > MA, 02115, USA
>> > P:+1-857-218-9051
>> >
>> > ########################################################################
>> >
>> > To unsubscribe from the CCPEM list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
>> >
>>
>>
>>
>
> --
>
> ______________________
>
> Regards,
>
> Humayun Sharif, PhD
>
> Research Fellow | Wu Lab
> BCMP, Harvard Medical School
>
> Immune Disease Institute
> PCMM, Boston Children's Hospital
> 3 Blackfan Circle | Boston
> MA, 02115, USA
> P:+1-857-218-9051
>
> ########################################################################
>
> To unsubscribe from the CCPEM list, click the following link:
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>
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