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 <eleanor.dod...@york.ac.uk> 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 <savvas.savvi...@ugent.be
> <mailto:savvas.savvi...@ugent.be>> 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
> $$
>
>
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
smime.p7s
Description: S/MIME cryptographic signature
