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 mailto:[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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] // 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>