[phenixbb] Rosetta installation problems
Luca Jovine
Luca.Jovine at ki.se
Sat Oct 6 06:05:50 PDT 2018
I don’t think the two things are related, but - when running under Mac OS the refinement tests of Rosetta (3.9 = 2018.09.60072) with PHENIX 1.14-3260 - I am also getting a (different) RuntimeError. The same test suite worked just fine with 1.13, so maybe there’s some general Rosetta compatibility issue with 1.14?
Best, Luca
On 6 Oct 2018, at 15:12, Simone Pellegrino <simonpelle81 at gmail.com<mailto:simonpelle81 at gmail.com>> wrote:
Dear all,
I encounter a problem running the rosetta.run_tests after having compiled rosetta for interfacing with phenix. I have the following error:
DEBUG dumping error message
ERROR: Rosetta exited with status 139
stderr output:
Segmentation fault (core dumped)
Traceback (most recent call last):
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module>
run(sys.argv[1:], create_dir=True)
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
debug=params.output.debug)
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
self.run_jobs()
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 387, in run_jobs
check_result(result)
File "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py", line 378, in check_result
raise RuntimeError("Aborted due to error in job %d." % result.job_id)
RuntimeError: Aborted due to error in job 1.
Could you please help me in solving this issue?
Many thanks in advance
Best regards
Simone
--
Dr. Simone Pellegrino
I.G.B.M.C.
1, Rue Laurent Fries
67404 Illkirch Cedex
France
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//
OSX> rosetta.run_tests
Running Rosetta refinement tests
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz
phenix.rosetta_refine /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2
============================== Collecting inputs ==============================
----------Processing X-ray data----------
F-obs:
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=495
Type of sigmas: double, size=495
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 1.0000
Number of F-obs in resolution range: 495
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max = 22.4416
d_min = 1.8007
R-free flags:
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
Observation type: None
Type of data: int, size=495
Type of sigmas: None
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 1.0000
Test (R-free flags) flag value: 1
Number of work/free reflections by resolution:
work free %free
bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%
bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%
bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%
bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%
bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%
bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%
bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%
bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%
bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%
bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%
overall 475 20 4.0%
----------Processing PDB file(s)----------
Monomer Library directory:
"/usr/local/phenix/phenix-1.14-3260/modules/chem_data/mon_lib"
Total number of atoms: 66
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 59
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 7, 59
Classifications: {'peptide': 7}
Modifications used: {'COO': 1}
Link IDs: {'TRANS': 6}
Chain: " "
Number of atoms: 7
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 7, 7
Classifications: {'water': 7}
Link IDs: {None: 6}
Time building chain proxies: 0.06, per 1000 atoms: 0.91
Number of scatterers: 66
At special positions: 0
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Number of sites at special positions: 0
Number of scattering types: 3
Type Number sf(0)
O 21 8.00
N 12 7.00
C 33 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Custom bonds:
Warning: Ignoring bond with distance_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
Total number of custom bonds: 0
Custom angles:
Warning: Ignoring angle with angle_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
atom_selection_3 = None
Total number of custom angles: 0
Custom dihedrals:
Warning: Ignoring dihedral with angle_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
atom_selection_3 = None
atom_selection_4 = None
Total number of custom dihedrals: 0
Custom planarities:
Warning: Ignoring planarity with with sigma <= 0:
atom_selection = None
None
Total number of custom planarities: 0
Custom parallelities:
Warning: Ignoring parallelity with empty atom selection.
Total number of custom parallelities: 0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : False - 3.50
Amimo acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.01
Conformation dependent library (CDL) restraints added in 3.8 milliseconds
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 12
Time building geometry restraints manager: 0.03 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.29: 13
1.29 - 1.36: 11
1.36 - 1.42: 7
1.42 - 1.49: 6
1.49 - 1.55: 22
Bond restraints: 59
Sorted by residual:
bond pdb=" N GLY A 1 "
pdb=" CA GLY A 1 "
ideal model delta sigma weight residual
1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01
bond pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
ideal model delta sigma weight residual
1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00
bond pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
ideal model delta sigma weight residual
1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00
bond pdb=" CA ASN A 2 "
pdb=" C ASN A 2 "
ideal model delta sigma weight residual
1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00
bond pdb=" CA ASN A 6 "
pdb=" C ASN A 6 "
ideal model delta sigma weight residual
1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00
... (remaining 54 not shown)
Histogram of bond angle deviations from ideal:
107.05 - 110.59: 8
110.59 - 114.13: 19
114.13 - 117.67: 11
117.67 - 121.21: 23
121.21 - 124.75: 18
Bond angle restraints: 79
Sorted by residual:
angle pdb=" N ASN A 3 "
pdb=" CA ASN A 3 "
pdb=" C ASN A 3 "
ideal model delta sigma weight residual
108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00
angle pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
ideal model delta sigma weight residual
108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00
angle pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
pdb=" O GLN A 4 "
ideal model delta sigma weight residual
120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00
angle pdb=" CA GLN A 5 "
pdb=" C GLN A 5 "
pdb=" O GLN A 5 "
ideal model delta sigma weight residual
120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00
angle pdb=" C GLN A 4 "
pdb=" N GLN A 5 "
pdb=" CA GLN A 5 "
ideal model delta sigma weight residual
123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00
... (remaining 74 not shown)
Histogram of dihedral angle deviations from ideal:
0.04 - 14.51: 26
14.51 - 28.98: 5
28.98 - 43.45: 1
43.45 - 57.92: 1
57.92 - 72.39: 1
Dihedral angle restraints: 34
sinusoidal: 15
harmonic: 19
Sorted by residual:
dihedral pdb=" CA ASN A 3 "
pdb=" C ASN A 3 "
pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
ideal model delta harmonic sigma weight residual
180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00
dihedral pdb=" CB GLN A 5 "
pdb=" CG GLN A 5 "
pdb=" CD GLN A 5 "
pdb=" OE1 GLN A 5 "
ideal model delta sinusoidal sigma weight residual
0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00
dihedral pdb=" CB GLN A 4 "
pdb=" CG GLN A 4 "
pdb=" CD GLN A 4 "
pdb=" OE1 GLN A 4 "
ideal model delta sinusoidal sigma weight residual
0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00
... (remaining 31 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.024: 1
0.024 - 0.047: 1
0.047 - 0.071: 1
0.071 - 0.094: 1
0.094 - 0.118: 2
Chirality restraints: 6
Sorted by residual:
chirality pdb=" CA GLN A 5 "
pdb=" N GLN A 5 "
pdb=" C GLN A 5 "
pdb=" CB GLN A 5 "
both_signs ideal model delta sigma weight residual
False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01
chirality pdb=" CA ASN A 6 "
pdb=" N ASN A 6 "
pdb=" C ASN A 6 "
pdb=" CB ASN A 6 "
both_signs ideal model delta sigma weight residual
False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01
chirality pdb=" CA ASN A 2 "
pdb=" N ASN A 2 "
pdb=" C ASN A 2 "
pdb=" CB ASN A 2 "
both_signs ideal model delta sigma weight residual
False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01
... (remaining 3 not shown)
Planarity restraints: 13
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03 1.87e+00
pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03
pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03
pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03
pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03
pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03
pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03
pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00
pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03
pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03
pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00
pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03
pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03
pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03
... (remaining 10 not shown)
Histogram of nonbonded interaction distances:
2.53 - 3.00: 50
3.00 - 3.48: 107
3.48 - 3.95: 243
3.95 - 4.42: 255
4.42 - 4.90: 523
Nonbonded interactions: 1178
Sorted by model distance:
nonbonded pdb=" OH TYR A 7 "
pdb=" O HOH 11 "
model vdw sym.op.
2.525 2.440 -x+1,y-1/2,-z+1
nonbonded pdb=" O HOH 11 "
pdb=" OH TYR A 7 "
model vdw sym.op.
2.525 2.440 -x+1,y+1/2,-z+1
nonbonded pdb=" O HOH 14 "
pdb=" O HOH 13 "
model vdw sym.op.
2.634 2.440 x,y-1,z
nonbonded pdb=" O HOH 13 "
pdb=" O HOH 14 "
model vdw sym.op.
2.634 2.440 x,y+1,z
nonbonded pdb=" N GLY A 1 "
pdb=" O GLY A 1 "
model vdw
2.665 2.496
... (remaining 1173 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
============================== Scattering factors =============================
----------X-ray scattering dictionary----------
Number of scattering types: 3
Type Number sf(0) Gaussians
O 21 7.97 2
N 12 6.97 2
C 33 5.97 2
sf(0) = scattering factor at diffraction angle 0.
Number of scatterers: 66
At special positions: 0
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
----------F(model) initialization----------
Twinning will be detected automatically.
start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495
re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495
remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493
remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493
|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 % free)--------------|
| |
| r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.00 A |
| |
| normalized target function (ml) (work): 2.637727 |
| target function (ml) not normalized (work): 1247.644901 |
| target function (ml) not normalized (free): 60.766973 |
|-----------------------------------------------------------------------------|
End of input processing
======================= ROSETTA/PHENIX X-ray refinement =======================
Output directory:
/usr/local/rosetta/rosetta-2018.09.60072/test/rosetta_1
----------Setting up input files for Rosetta----------
/usr/local/rosetta/rosetta-2018.09.60072/main/source
|-starting model--------------------------------------------------------------|
| target_work(ml) = 2.63773 r_work = 0.1758 r_free = 0.1728 |
|-----------------------------------------------------------------------------|
Validation statistics (starting model):
Ramachandran outliers = 0.00 %
favored = 100.00 %
Rotamer outliers = 0.00 %
C-beta deviations = 0
Clashscore = 0.00
RMS(bonds) = 0.0000
RMS(angles) = 0.00
MolProbity score = 0.50
Rosetta command-line arguments:
-parser:protocol /usr/local/rosetta/rosetta-2018.09.60072/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml
-s 1yjp_rosetta_in.pdb
-mtzfile 1yjp_rosetta_data.mtz
-run:preserve_header
-crystal_refine
-parser:script_vars symmdef=1yjp_rosetta.symm
-parser:script_vars bfactstrat=individual
-parser:script_vars map_type=Auto
-nstruct 1
Generating 2 models on 1 processors...
1: r_work = 0.4326 r_free = 0.4380 energy = -19.44 rmsd = 26.004 ***
2: r_work = 0.3910 r_free = 0.5014 energy = 34.57 rmsd = 12.233
|-after ROSETTA---------------------------------------------------------------|
| target_work(ml) = 3.3273 r_work = 0.4326 r_free = 0.4380 |
|-----------------------------------------------------------------------------|
Validation statistics after ROSETTA:
Ramachandran outliers = 0.00 %
favored = 100.00 %
Rotamer outliers = 0.00 %
C-beta deviations = 1
Clashscore = 18.69
RMS(bonds) = 0.0000
RMS(angles) = 0.00
MolProbity score = 1.77
----------Running phenix.refine (with null strategy)----------
start r_work=0.4915 r_free=0.4690
1_bss r_work=0.3789 r_free=0.4327
end r_work=0.3789 r_free=0.4327
Ramachandran outliers = 0.00 %
favored = 100.00 %
Rotamer outliers = 0.00 %
C-beta deviations = 1
Clashscore = 19.05
RMS(bonds) = 0.0000
RMS(angles) = 0.00
MolProbity score = 1.78
----------Final results----------
Refined model: 1yjp_rosetta_phenix_001.pdb
Final maps: 1yjp_rosetta_phenix_001.mtz
Elapsed time: 669.9s
Citation:
DiMaio F., Echols N., Headd J.J., Terwilliger T.C., Adams P.D., and Baker D.
(2013). Improved low-resolution crystallographic refinement with Phenix and
Rosetta. Nat Methods 10, 1102-4.
phenix.rosetta_refine /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.pdb /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz number_of_models=2 nproc=2
============================== Collecting inputs ==============================
----------Processing X-ray data----------
F-obs:
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=495
Type of sigmas: double, size=495
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 1.0000
Number of F-obs in resolution range: 495
Number of F-obs<0 (these reflections will be rejected): 0
Number of F-obs=0 (these reflections will be used in refinement): 0
Refinement resolution range: d_max = 22.4416
d_min = 1.8007
R-free flags:
/usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
Miller array info: /usr/local/phenix/phenix-1.14-3260/modules/phenix_regression/refinement/data/1yjp.mtz:R-free-flags
Observation type: None
Type of data: int, size=495
Type of sigmas: None
Number of Miller indices: 495
Anomalous flag: False
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Systematic absences: 0
Centric reflections: 199
Resolution range: 22.4416 1.80066
Completeness in resolution range: 0.895118
Completeness with d_max=infinity: 0.895118
Wavelength: 1.0000
Test (R-free flags) flag value: 1
Number of work/free reflections by resolution:
work free %free
bin 1: 22.4433 - 3.8734 [61/70] 59 2 3.3%
bin 2: 3.8734 - 3.0770 [53/58] 49 4 7.5%
bin 3: 3.0770 - 2.6887 [49/55] 46 3 6.1%
bin 4: 2.6887 - 2.4432 [37/40] 35 2 5.4%
bin 5: 2.4432 - 2.2683 [62/66] 60 2 3.2%
bin 6: 2.2683 - 2.1347 [51/56] 49 2 3.9%
bin 7: 2.1347 - 2.0278 [50/55] 46 4 8.0%
bin 8: 2.0278 - 1.9396 [49/56] 49 0 0.0%
bin 9: 1.9396 - 1.8650 [43/50] 42 1 2.3%
bin 10: 1.8650 - 1.8007 [40/47] 40 0 0.0%
overall 475 20 4.0%
----------Processing PDB file(s)----------
Monomer Library directory:
"/usr/local/phenix/phenix-1.14-3260/modules/chem_data/mon_lib"
Total number of atoms: 66
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 59
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 7, 59
Classifications: {'peptide': 7}
Modifications used: {'COO': 1}
Link IDs: {'TRANS': 6}
Chain: " "
Number of atoms: 7
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 7, 7
Classifications: {'water': 7}
Link IDs: {None: 6}
Time building chain proxies: 0.06, per 1000 atoms: 0.91
Number of scatterers: 66
At special positions: 0
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
Number of sites at special positions: 0
Number of scattering types: 3
Type Number sf(0)
O 21 8.00
N 12 7.00
C 33 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Custom bonds:
Warning: Ignoring bond with distance_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
Total number of custom bonds: 0
Custom angles:
Warning: Ignoring angle with angle_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
atom_selection_3 = None
Total number of custom angles: 0
Custom dihedrals:
Warning: Ignoring dihedral with angle_ideal = None:
atom_selection_1 = None
atom_selection_2 = None
atom_selection_3 = None
atom_selection_4 = None
Total number of custom dihedrals: 0
Custom planarities:
Warning: Ignoring planarity with with sigma <= 0:
atom_selection = None
None
Total number of custom planarities: 0
Custom parallelities:
Warning: Ignoring parallelity with empty atom selection.
Total number of custom parallelities: 0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : False - 3.50
Amimo acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 0.01
Conformation dependent library (CDL) restraints added in 2.9 milliseconds
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 12
Time building geometry restraints manager: 0.01 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.29: 13
1.29 - 1.36: 11
1.36 - 1.42: 7
1.42 - 1.49: 6
1.49 - 1.55: 22
Bond restraints: 59
Sorted by residual:
bond pdb=" N GLY A 1 "
pdb=" CA GLY A 1 "
ideal model delta sigma weight residual
1.451 1.507 -0.056 1.60e-02 3.91e+03 1.23e+01
bond pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
ideal model delta sigma weight residual
1.522 1.553 -0.030 1.18e-02 7.18e+03 6.53e+00
bond pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
ideal model delta sigma weight residual
1.460 1.485 -0.025 1.17e-02 7.31e+03 4.40e+00
bond pdb=" CA ASN A 2 "
pdb=" C ASN A 2 "
ideal model delta sigma weight residual
1.524 1.498 0.025 1.26e-02 6.30e+03 4.00e+00
bond pdb=" CA ASN A 6 "
pdb=" C ASN A 6 "
ideal model delta sigma weight residual
1.526 1.504 0.022 1.28e-02 6.10e+03 2.85e+00
... (remaining 54 not shown)
Histogram of bond angle deviations from ideal:
107.05 - 110.59: 8
110.59 - 114.13: 19
114.13 - 117.67: 11
117.67 - 121.21: 23
121.21 - 124.75: 18
Bond angle restraints: 79
Sorted by residual:
angle pdb=" N ASN A 3 "
pdb=" CA ASN A 3 "
pdb=" C ASN A 3 "
ideal model delta sigma weight residual
108.90 113.48 -4.58 1.63e+00 3.76e-01 7.90e+00
angle pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
ideal model delta sigma weight residual
108.02 111.93 -3.91 1.78e+00 3.16e-01 4.84e+00
angle pdb=" CA GLN A 4 "
pdb=" C GLN A 4 "
pdb=" O GLN A 4 "
ideal model delta sigma weight residual
120.33 122.27 -1.94 1.08e+00 8.57e-01 3.23e+00
angle pdb=" CA GLN A 5 "
pdb=" C GLN A 5 "
pdb=" O GLN A 5 "
ideal model delta sigma weight residual
120.38 122.31 -1.93 1.09e+00 8.42e-01 3.13e+00
angle pdb=" C GLN A 4 "
pdb=" N GLN A 5 "
pdb=" CA GLN A 5 "
ideal model delta sigma weight residual
123.00 120.57 2.43 1.38e+00 5.25e-01 3.09e+00
... (remaining 74 not shown)
Histogram of dihedral angle deviations from ideal:
0.04 - 14.51: 26
14.51 - 28.98: 5
28.98 - 43.45: 1
43.45 - 57.92: 1
57.92 - 72.39: 1
Dihedral angle restraints: 34
sinusoidal: 15
harmonic: 19
Sorted by residual:
dihedral pdb=" CA ASN A 3 "
pdb=" C ASN A 3 "
pdb=" N GLN A 4 "
pdb=" CA GLN A 4 "
ideal model delta harmonic sigma weight residual
180.00 166.21 13.79 0 5.00e+00 4.00e-02 7.60e+00
dihedral pdb=" CB GLN A 5 "
pdb=" CG GLN A 5 "
pdb=" CD GLN A 5 "
pdb=" OE1 GLN A 5 "
ideal model delta sinusoidal sigma weight residual
0.00 -72.39 72.39 2 3.00e+01 1.11e-03 4.85e+00
dihedral pdb=" CB GLN A 4 "
pdb=" CG GLN A 4 "
pdb=" CD GLN A 4 "
pdb=" OE1 GLN A 4 "
ideal model delta sinusoidal sigma weight residual
0.00 54.08 -54.08 2 3.00e+01 1.11e-03 3.50e+00
... (remaining 31 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.024: 1
0.024 - 0.047: 1
0.047 - 0.071: 1
0.071 - 0.094: 1
0.094 - 0.118: 2
Chirality restraints: 6
Sorted by residual:
chirality pdb=" CA GLN A 5 "
pdb=" N GLN A 5 "
pdb=" C GLN A 5 "
pdb=" CB GLN A 5 "
both_signs ideal model delta sigma weight residual
False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01
chirality pdb=" CA ASN A 6 "
pdb=" N ASN A 6 "
pdb=" C ASN A 6 "
pdb=" CB ASN A 6 "
both_signs ideal model delta sigma weight residual
False 2.51 2.62 -0.11 2.00e-01 2.50e+01 2.86e-01
chirality pdb=" CA ASN A 2 "
pdb=" N ASN A 2 "
pdb=" C ASN A 2 "
pdb=" CB ASN A 2 "
both_signs ideal model delta sigma weight residual
False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.80e-01
... (remaining 3 not shown)
Planarity restraints: 13
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 7 " -0.006 2.00e-02 2.50e+03 9.66e-03 1.87e+00
pdb=" CG TYR A 7 " 0.022 2.00e-02 2.50e+03
pdb=" CD1 TYR A 7 " -0.004 2.00e-02 2.50e+03
pdb=" CD2 TYR A 7 " -0.008 2.00e-02 2.50e+03
pdb=" CE1 TYR A 7 " -0.001 2.00e-02 2.50e+03
pdb=" CE2 TYR A 7 " 0.002 2.00e-02 2.50e+03
pdb=" CZ TYR A 7 " -0.011 2.00e-02 2.50e+03
pdb=" OH TYR A 7 " 0.006 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN A 2 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00
pdb=" CG ASN A 2 " -0.021 2.00e-02 2.50e+03
pdb=" OD1 ASN A 2 " 0.008 2.00e-02 2.50e+03
pdb=" ND2 ASN A 2 " 0.007 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA GLN A 4 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00
pdb=" C GLN A 4 " -0.019 2.00e-02 2.50e+03
pdb=" O GLN A 4 " 0.007 2.00e-02 2.50e+03
pdb=" N GLN A 5 " 0.006 2.00e-02 2.50e+03
... (remaining 10 not shown)
Histogram of nonbonded interaction distances:
2.53 - 3.00: 50
3.00 - 3.48: 107
3.48 - 3.95: 243
3.95 - 4.42: 255
4.42 - 4.90: 523
Nonbonded interactions: 1178
Sorted by model distance:
nonbonded pdb=" OH TYR A 7 "
pdb=" O HOH 11 "
model vdw sym.op.
2.525 2.440 -x+1,y-1/2,-z+1
nonbonded pdb=" O HOH 11 "
pdb=" OH TYR A 7 "
model vdw sym.op.
2.525 2.440 -x+1,y+1/2,-z+1
nonbonded pdb=" O HOH 14 "
pdb=" O HOH 13 "
model vdw sym.op.
2.634 2.440 x,y-1,z
nonbonded pdb=" O HOH 13 "
pdb=" O HOH 14 "
model vdw sym.op.
2.634 2.440 x,y+1,z
nonbonded pdb=" N GLY A 1 "
pdb=" O GLY A 1 "
model vdw
2.665 2.496
... (remaining 1173 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
============================== Scattering factors =============================
----------X-ray scattering dictionary----------
Number of scattering types: 3
Type Number sf(0) Gaussians
O 21 7.97 2
N 12 6.97 2
C 33 5.97 2
sf(0) = scattering factor at diffraction angle 0.
Number of scatterers: 66
At special positions: 0
Unit cell: (21.937, 4.866, 23.477, 90, 107.08, 90)
Space group: P 1 21 1 (No. 4)
----------F(model) initialization----------
Twinning will be detected automatically.
start: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495
re-set all scales: r(all,work,free)=0.2072 0.2084 0.1924 n_refl.: 495
remove outliers: r(all,work,free)=0.2103 0.2117 0.1924 n_refl.: 493
bulk-solvent and scaling: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493
remove outliers: r(all,work,free)=0.1755 0.1758 0.1728 n_refl.: 493
|--(resolution: 1.80 - 22.44 A, n_refl.=493 (all), 4.06 % free)--------------|
| |
| r_work= 0.1758 r_free= 0.1728 coordinate error (max.-lik. estimate): 0.00 A |
| |
| normalized target function (ml) (work): 2.637727 |
| target function (ml) not normalized (work): 1247.644901 |
| target function (ml) not normalized (free): 60.766973 |
|-----------------------------------------------------------------------------|
End of input processing
======================= ROSETTA/PHENIX X-ray refinement =======================
Output directory:
/usr/local/rosetta/rosetta-2018.09.60072/test/rosetta_2
----------Setting up input files for Rosetta----------
/usr/local/rosetta/rosetta-2018.09.60072/main/source
|-starting model--------------------------------------------------------------|
| target_work(ml) = 2.63773 r_work = 0.1758 r_free = 0.1728 |
|-----------------------------------------------------------------------------|
Validation statistics (starting model):
Ramachandran outliers = 0.00 %
favored = 100.00 %
Rotamer outliers = 0.00 %
C-beta deviations = 0
Clashscore = 0.00
RMS(bonds) = 0.0000
RMS(angles) = 0.00
MolProbity score = 0.50
Rosetta command-line arguments:
-parser:protocol /usr/local/rosetta/rosetta-2018.09.60072/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml
-s 1yjp_rosetta_in.pdb
-mtzfile 1yjp_rosetta_data.mtz
-run:preserve_header
-crystal_refine
-parser:script_vars symmdef=1yjp_rosetta.symm
-parser:script_vars bfactstrat=individual
-parser:script_vars map_type=Auto
-nstruct 1
Generating 2 models on 2 processors...
Traceback (most recent call last):
File "/usr/local/phenix/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module>
DEBUG dumping error message
ERROR: Rosetta exited with status -9
stderr output:
run(sys.argv[1:], create_dir=True)
File "/usr/local/phenix/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
debug=params.output.debug)
File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
self.run_jobs()
File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 396, in run_jobs
check_result(result)
File "/usr/local/phenix/phenix-1.14-3260/modules/phenix/phenix/rosetta/refine.py", line 382, in check_result
raise RuntimeError("File '%s' not found." % result.file_name)
RuntimeError: File 'None' not found.
OSX>
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