============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/dev/shm/nigel/phenix-1.20.1-4487/modules/chem_data/mon_lib" Total number of atoms: 4856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 144} Chain: "C" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2428 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 144} Time building chain proxies: 0.95, per 1000 atoms: 0.20 Number of scatterers: 4856 At special positions: 0 Unit cell: (102.513, 104.593, 105.694, 90, 90, 90) Space group: I 21 21 21 (No. 24) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 12 33.99 S 4 16.00 O 482 8.00 N 382 7.00 C 1558 6.00 H 2418 1.00 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 added/changed 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 new custom angles: 0 Total number of changed 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 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed 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 new custom angles: 0 Total number of changed 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 : Auto - 3.50 Amino 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: 1.05 Conformation dependent library (CDL) restraints added in 161.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.19: 2414 1.19 - 1.39: 976 1.39 - 1.60: 1480 1.60 - 1.81: 3 1.81 - 2.02: 25 Bond restraints: 4898 Sorted by residual: bond pdb=" N VAL C 572 " pdb=" H VAL C 572 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MSE A 470 " pdb=" H MSE A 470 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N CYS A 456 " pdb=" H CYS A 456 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 449 " pdb=" H VAL A 449 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN C 468 " pdb="HD21 ASN C 468 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4893 not shown) Histogram of bond angle deviations from ideal: 96.68 - 103.60: 39 103.60 - 110.52: 4917 110.52 - 117.44: 1798 117.44 - 124.36: 2024 124.36 - 131.29: 120 Bond angle restraints: 8898 Sorted by residual: angle pdb=" C HIS A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.76 125.62 -5.86 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C HIS C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta sigma weight residual 119.78 124.36 -4.58 1.03e+00 9.43e-01 1.98e+01 angle pdb=" C ASP A 558 " pdb=" N PRO A 559 " pdb=" CA PRO A 559 " ideal model delta sigma weight residual 119.76 123.72 -3.96 1.00e+00 1.00e+00 1.57e+01 angle pdb=" C VAL C 497 " pdb=" N LYS C 498 " pdb=" CA LYS C 498 " ideal model delta sigma weight residual 120.38 125.51 -5.13 1.37e+00 5.33e-01 1.40e+01 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 108.74 113.88 -5.14 1.38e+00 5.25e-01 1.39e+01 ... (remaining 8893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 1757 16.89 - 33.77: 127 33.77 - 50.65: 53 50.65 - 67.54: 16 67.54 - 84.42: 3 Dihedral angle restraints: 1956 sinusoidal: 930 harmonic: 1026 Sorted by residual: dihedral pdb=" C VAL C 572 " pdb=" N VAL C 572 " pdb=" CA VAL C 572 " pdb=" CB VAL C 572 " ideal model delta harmonic sigma weight residual -122.00 -129.82 7.82 0 2.50e+00 1.60e-01 9.78e+00 dihedral pdb=" C VAL A 572 " pdb=" N VAL A 572 " pdb=" CA VAL A 572 " pdb=" CB VAL A 572 " ideal model delta harmonic sigma weight residual -122.00 -129.79 7.79 0 2.50e+00 1.60e-01 9.71e+00 dihedral pdb=" CB GLU C 574 " pdb=" CG GLU C 574 " pdb=" CD GLU C 574 " pdb=" OE1 GLU C 574 " ideal model delta sinusoidal sigma weight residual 0.00 -84.42 84.42 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 1953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 198 0.044 - 0.088: 121 0.088 - 0.132: 47 0.132 - 0.176: 17 0.176 - 0.220: 7 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA GLU C 556 " pdb=" N GLU C 556 " pdb=" C GLU C 556 " pdb=" CB GLU C 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU A 556 " pdb=" N GLU A 556 " pdb=" C GLU A 556 " pdb=" CB GLU A 556 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 573 " pdb=" N ILE A 573 " pdb=" C ILE A 573 " pdb=" CB ILE A 573 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 387 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 523 " 0.023 2.00e-02 2.50e+03 1.27e-02 3.64e+00 pdb=" CG HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" ND1 HIS A 523 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A 523 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 523 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 523 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 HIS A 523 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS A 523 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 HIS A 523 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " 0.004 2.00e-02 2.50e+03 7.38e-03 1.63e+00 pdb=" CG PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 467 " -0.012 2.00e-02 2.50e+03 7.27e-03 1.59e+00 pdb=" CG PHE A 467 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 467 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 467 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 467 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 467 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 467 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 467 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 467 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 467 " -0.001 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.03: 257 2.03 - 2.72: 7497 2.72 - 3.41: 16347 3.41 - 4.11: 22074 4.11 - 4.80: 34986 Nonbonded interactions: 81161 Sorted by model distance: nonbonded pdb=" HA ASP A 504 " pdb=" HE2 PHE C 467 " model vdw 1.334 2.270 nonbonded pdb=" HE2 PHE A 467 " pdb=" HA ASP C 504 " model vdw 1.337 2.270 nonbonded pdb=" O GLU C 485 " pdb="HD22 ASN C 490 " model vdw 1.340 1.850 nonbonded pdb=" O GLU A 485 " pdb="HD22 ASN A 490 " model vdw 1.343 1.850 nonbonded pdb="HH22 ARG A 550 " pdb=" OE1 GLU A 554 " model vdw 1.350 1.850 ... (remaining 81156 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: 6 Type Number sf(0) Gaussians Se 12 33.79 1 S 4 15.91 1 O 482 7.97 1 N 382 6.97 1 C 1558 5.97 1 H 2418 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 4856 At special positions: 0 Unit cell: (102.513, 104.593, 105.694, 90, 90, 90) Space group: I 21 21 21 (No. 24) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.5909 0.5906 0.5815 n_refl.: 6670 re-set all scales: r(all,work,free)=0.5909 0.5906 0.5815 n_refl.: 6670 remove outliers: r(all,work,free)=0.5634 0.5640 0.5266 n_refl.: 6654 bulk-solvent and scaling: r(all,work,free)=0.2872 0.2874 0.2834 n_refl.: 6654 add H (0.30, 59.00): r(all,work,free)=0.2860 0.2874 0.2834 n_refl.: 6654 add H (0.27, 54.00): r(all,work,free)=0.2859 0.2874 0.2834 n_refl.: 6654 add H (0.27, 54.00): r(all,work,free)=0.2826 0.2827 0.2804 n_refl.: 6654 remove outliers: r(all,work,free)=0.2825 0.2826 0.2804 n_refl.: 6653 |--(resolution: 3.60 - 36.79 A, n_refl.=6653 (all), 4.72 % free)-------------| | | | r_work= 0.2826 r_free= 0.2804 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 7.067996 | | target function (ml) not normalized (work): 44804.023835 | | target function (ml) not normalized (free): 2217.361508 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_10 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 7.068 r_work = 0.2826 r_free = 0.2804 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.00 % favored = 97.33 % Rotamer outliers = 5.76 % C-beta deviations = 0 Clashscore = 7.01 RMS(bonds) = 0.0080 RMS(angles) = 1.17 MolProbity score = 2.09 Rosetta command-line arguments: -parser:protocol /dev/shm/bkpoon/software/rosetta_src_2021.16.61629_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 4iy2_rosetta_in.pdb -mtzfile 4iy2_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=4iy2_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2761 r_free = 0.3091 energy = -1808.30 rmsd = 1.315 *** 2: r_work = 0.2736 r_free = 0.2978 energy = -1856.44 rmsd = 1.376 *** 3: r_work = 0.2642 r_free = 0.2952 energy = -1797.78 rmsd = 1.308 *** DEBUG dumping error message ERROR: Rosetta exited with status 1 stderr output: ERROR: error computing X-ray target ERROR:: Exit from: src/core/scoring/cryst/PhenixInterface.cc line: 158 [ ERROR ]: Caught exception: File: src/core/scoring/cryst/PhenixInterface.cc:158 [ ERROR ] UtilityExitException ERROR: error computing X-ray target AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. --------------------------------------------------------------- [ ERROR ]: Error(s) were encountered when running jobs. 1 jobs failed; Check the output further up for additional error messages. ---------------------------------------------------------------