Hmm - that looks almost too good - Mask volumes are expected to be less
than 1..
<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>
And the rotation angles etc look as though chains A B C & D could be
symmetry euivalents?
rotation ~ 90 0 180 - ie a crystallographic two fold
Are you sure you arent giving PARROT a model with actual symmetry
equivalent molecules?
Eleanor
On Fri, 25 Jun 2021 at 14:38, Savvas Savvides <[email protected]>
wrote:
> There you go Eleanor
>
> Best wishes, — Savvas
>
> --------
>
>
> # Task 41 parrot running cparrot
> # Mini-MTZ input to HKLIN:
> # Data type parameter job annotation
> # Reflections F_SIGF 39 il_phaser.1.259: NULL_dname
> imported by job 39
> # Phases ABCD 39 il_phaser.1.259: NULL_dname
> imported by job 39
> mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
> colin-fo F_SIGF_F,F_SIGF_SIGF
> colin-phifom ABCD_PHI,ABCD_FOM
> seqin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
> pdbin-mr
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
> mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
> xmlout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
> cycles 3
> anisotropy-correction
> solvent-content 0.6
> ncs-mask-filter-radius 20.0
>
> <B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
> <html> <!-- CCP4 HTML LOGFILE -->
> <hr>
> <pre>
>
> ###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 7.1.014: cparrot version 1.0.6 : 20/04/21##
> ###############################################################
> User: root Run date: 25/ 6/2021 Run time: 12:41:49
>
>
> Please reference: Collaborative Computational Project, Number 4. 2011.
> "Overview of the CCP4 suite and current developments". Acta Cryst. D67,
> 235-242.
> as well as any specific reference in the program write-up.
>
> <!--SUMMARY_END--></FONT></B>
>
> Copyright 2008-2010 Kevin Cowtan and University of York.
>
> <B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN-->
> $TEXT:Reference: $$ Please reference $$
>
> 'Recent developments in classical density modification.'
> Cowtan K. (2010) Acta Cryst. D66, 470-478.
>
> $$<!--SUMMARY_END--></FONT></B>
>
> mtzin /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
> colin-fo F_SIGF_F,F_SIGF_SIGF
> colin-phifom ABCD_PHI,ABCD_FOM
> seqin
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/seqin.fasta
> pdbin-mr
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
> mtzout /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklout.mtz
> xmlout
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/program.xml
> cycles 3
> anisotropy-correction
> solvent-content 0.6
> ncs-mask-filter-radius 20.0
>
>
> PDB file:
> /Applications/ccp4-7.1/lib/data/reference_structures/reference-1tqw.pdb
> Number of atoms read: 9432
> PDB file:
> /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/XYZIN_MR-coordinates.pdb
> Number of atoms read: 7264
>
> MTZ file: /Users/savvass/CCP4I2_PROJECTS/julie/CCP4_JOBS/job_41/hklin.mtz
> Number of reflections: 22867 Number of columns: 7
>
> Applying anisotropy correction:
> | -0.05391, 8.59e-17, 0.1649|
> | 8.59e-17, -0.1351, -3.06e-17|
> | 0.1649, -3.06e-17, -0.5043|
>
> NCS from atomic model:
>
> NCS operator found relating chains A and B
> Polar rotation/deg: 89.9215,-0.233543,179.754
> Euler rotation/deg: -57.6965,179.708,122.771
> Source: xyz = ( -5.624, 9.951, 36.36)
> Target: xyz = ( -5.528, 38.96, 64.43)
>
> NCS operator found relating chains B and A
> Polar rotation/deg: 90.0785,179.766,179.754
> Euler rotation/deg: 57.2294,179.708,-122.303
> Source: xyz = ( -5.528, 38.96, 64.43)
> Target: xyz = ( -5.624, 9.951, 36.36)
>
> NCS operator found relating chains C and D
> Polar rotation/deg: 90.1347,-0.132348,178.552
> Euler rotation/deg: -100.677,178.528,79.5875
> Source: xyz = ( -17.66, 33.01, 93.38)
> Target: xyz = ( -17.88, 16.06, 7.398)
>
> NCS operator found relating chains D and C
> Polar rotation/deg: 89.8653,179.868,178.552
> Euler rotation/deg: 100.412,178.528,-79.3228
> Source: xyz = ( -17.88, 16.06, 7.398)
> Target: xyz = ( -17.66, 33.01, 93.38)
>
>
> -- 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
> $$
>
>
> On 25 Jun 2021, at 15:34, Eleanor Dodson <[email protected]>
> wrote:
>
> The extract from the log file looks OK - can you send the whole log.txt?
> Eleanor
>
> On Fri, 25 Jun 2021 at 12:09, Savvas Savvides <[email protected]>
> wrote:
>
>> 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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