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 <[email protected]> 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>