Dear colleagues, I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a MacBookPro (OSX 10.15.7) and keep getting the following error report as the program is in the process of outputting SigmaA statistics.
Below, I provide two pieces of information:
(1) The Error message
(2) The last page of the ouput file where the program ends up crashing with the
error message.
Thank you in advance for any insights/input on this issue.
Best wishes,
Savvas
----------------------------
Error Report for Job 41: Density modification - PARROT
-ERROR- CTaskParrot:9 Error in wrapper parrot 0.0:: Failed starting external
process
- this can be due to a number of things, but usually is due to the command used
by subprocess/QProcess not working for some reason.
Missing input files, bad commands, non-functional programs etc. Check log files
and stdout.
Process: cparrot
-ERROR- CTaskParrot:47 Error in wrapper parrot 0.0:: Error in checking
external process after completion
exit status and code: -11 -11
———--------------------
-- Cycle: 1 --------------------------------
Suggested radius for solvent mask determination: 5.68666
NCS operator: 1
NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10
Contiguity score: 1.000 Self-overlap score: 0.151
NXop refinement- correlation before: 0.539, after: 0.581
NXop old: -57.7 179.7 122.8 -5.6 10.0 36.4 -5.5 39.0 64.4
NXop new: 105.8 180.0 -74.1 -7.4 11.2 40.1 -7.3 37.8 60.9
NCS operator: 2
NCS masking: Mask volume as fraction of ASU: 1.00 Multiplicity: 10
Contiguity score: 1.000 Self-overlap score: 0.154
NXop refinement- correlation before: 0.528, after: 0.577
NXop old: 57.2 179.7 -122.3 -5.5 39.0 64.4 -5.6 10.0 36.4
NXop new: -94.6 179.8 85.4 -3.8 36.5 60.3 -3.8 12.5 40.6
NCS operator: 3
NCS masking: Mask volume as fraction of ASU: 0.95 Multiplicity: 9
Contiguity score: 0.999 Self-overlap score: 0.149
NXop refinement- correlation before: 0.447, after: 0.606
NXop old: -100.7 178.5 79.6 -17.7 33.0 93.4 -17.9 16.1 7.4
NXop new: -140.4 179.8 39.7 -9.8 36.7 79.4 -9.9 12.4 21.6
NCS operator: 4
NCS masking: Mask volume as fraction of ASU: 0.89 Multiplicity: 9
Contiguity score: 0.998 Self-overlap score: 0.179
NXop refinement- correlation before: 0.423, after: 0.588
NXop old: 100.4 178.5 -79.3 -17.9 16.1 7.4 -17.7 33.0 93.4
NXop new: 144.0 179.8 -36.0 -24.0 11.7 20.5 -23.7 37.5 80.6
<B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
NCS operator statistics:
Operator_number Mask_volume/ASU Correlation
1 1.001 0.911
2 0.998 0.912
3 0.954 0.863
4 0.888 0.854
<!--SUMMARY_END--></FONT></B>
$TABLE :Cycle 1 Electron density histograms:
$GRAPHS :Protein:N:1,4,5,6::Solvent:N:1,7,8::Simulation:N:1,3,4: $$
rho_min rho_max Simulatn P_init P_trgt P_mod S_init S_mod $$
$$
-0.317 -0.282 0.000 0.000 0.017 0.008 0.000 0.000
-0.282 -0.247 0.000 0.000 0.026 0.014 0.000 0.000
-0.247 -0.212 0.002 0.002 0.036 0.024 0.000 0.000
-0.212 -0.177 0.007 0.007 0.045 0.039 0.000 0.000
-0.177 -0.143 0.022 0.019 0.057 0.056 0.003 0.000
-0.143 -0.108 0.050 0.048 0.064 0.076 0.020 0.000
-0.108 -0.073 0.093 0.094 0.071 0.081 0.069 0.000
-0.073 -0.038 0.142 0.147 0.070 0.090 0.156 0.000
-0.038 -0.003 0.172 0.175 0.072 0.091 0.234 0.000
-0.003 0.032 0.172 0.173 0.068 0.085 0.237 1.000
0.032 0.067 0.141 0.141 0.063 0.075 0.167 0.000
0.067 0.101 0.099 0.094 0.057 0.071 0.080 0.000
0.101 0.136 0.056 0.053 0.053 0.063 0.026 0.000
0.136 0.171 0.029 0.026 0.049 0.053 0.006 0.000
0.171 0.206 0.011 0.012 0.044 0.048 0.001 0.000
0.206 0.241 0.004 0.005 0.038 0.038 0.000 0.000
0.241 0.276 0.001 0.002 0.033 0.033 0.000 0.000
0.276 0.311 0.000 0.001 0.030 0.025 0.000 0.000
0.311 0.345 0.000 0.000 0.025 0.016 0.000 0.000
0.345 0.380 0.000 0.000 0.021 0.014 0.000 0.000
$$
Gamma 0.24162
Log likelihood: 2.920853e+04 Log likelihood (free): 0.000000e+00
$TABLE :Cycle 1 SigmaA statistics:
$GRAPHS :SigmaA statistics:N:1,2,3: $$
1/resol^2 sigmaA(s) sigmaA(w) $$
$$
0.012 0.682 0.675
0.025 0.629 0.635
0.035 0.659 0.664
0.043 0.666 0.670
0.051 0.619 0.638
0.059 0.515 0.593
0.066 0.452 0.656
$$
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