============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped None 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: 7874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Time building chain proxies: 1.38, per 1000 atoms: 0.18 Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 786 8.00 N 644 7.00 C 2466 6.00 H 3946 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: 1.79 Conformation dependent library (CDL) restraints added in 176.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3934 1.15 - 1.32: 712 1.32 - 1.49: 1460 1.49 - 1.66: 1768 1.66 - 1.83: 52 Bond restraints: 7926 Sorted by residual: bond pdb=" NE1 TRP B 28 " pdb=" CE2 TRP B 28 " ideal model delta sigma weight residual 1.370 1.483 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" N SER A 112 " pdb=" H SER A 112 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" ND2 ASN B 107 " pdb="HD22 ASN B 107 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN B 131 " pdb=" H GLN B 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.14: 87 105.14 - 112.40: 9571 112.40 - 119.66: 1859 119.66 - 126.92: 2837 126.92 - 134.18: 20 Bond angle restraints: 14374 Sorted by residual: angle pdb=" N ASP B 232 " pdb=" CA ASP B 232 " pdb=" CB ASP B 232 " ideal model delta sigma weight residual 114.17 108.16 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " pdb=" CZ ARG A 64 " ideal model delta sigma weight residual 124.40 117.23 7.17 1.40e+00 5.10e-01 2.62e+01 angle pdb=" N PRO B 234 " pdb=" CA PRO B 234 " pdb=" CB PRO B 234 " ideal model delta sigma weight residual 103.31 107.82 -4.51 8.90e-01 1.26e+00 2.57e+01 angle pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " ideal model delta sigma weight residual 124.40 117.32 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N PRO B 202 " pdb=" CA PRO B 202 " pdb=" CB PRO B 202 " ideal model delta sigma weight residual 103.19 107.64 -4.45 9.00e-01 1.23e+00 2.45e+01 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2625 17.84 - 35.68: 301 35.68 - 53.52: 161 53.52 - 71.37: 60 71.37 - 89.21: 19 Dihedral angle restraints: 3166 sinusoidal: 1510 harmonic: 1656 Sorted by residual: dihedral pdb=" CA ASP A 122 " pdb=" C ASP A 122 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP B 122 " pdb=" C ASP B 122 " pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta harmonic sigma weight residual 180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 402 0.037 - 0.075: 108 0.075 - 0.112: 81 0.112 - 0.149: 23 0.149 - 0.187: 22 Chirality restraints: 636 Sorted by residual: chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 219 " pdb=" CA THR A 219 " pdb=" OG1 THR A 219 " pdb=" CG2 THR A 219 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB THR B 73 " pdb=" CA THR B 73 " pdb=" OG1 THR B 73 " pdb=" CG2 THR B 73 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 633 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 239 " -0.113 2.00e-02 2.50e+03 4.19e-02 5.26e+01 pdb=" CG TYR B 239 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 239 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 239 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 239 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 239 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 239 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR B 239 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 TYR B 239 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR B 239 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 246 " -0.035 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" CG HIS B 246 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 246 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 246 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 246 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 246 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS B 246 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS B 246 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 246 " 0.034 2.00e-02 2.50e+03 1.68e-02 6.34e+00 pdb=" CG HIS A 246 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 246 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 246 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 246 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 246 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 246 " 0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 63 1.67 - 2.40: 3135 2.40 - 3.13: 24071 3.13 - 3.87: 33793 3.87 - 4.60: 51974 Warning: very small nonbonded interaction distances. Nonbonded interactions: 113036 Sorted by model distance: nonbonded pdb=" O LEU B 182 " pdb=" HG SER B 183 " model vdw 0.936 1.850 nonbonded pdb=" HB2 GLN B 184 " pdb="HG11 VAL B 195 " model vdw 1.002 2.440 nonbonded pdb="HG13 VAL A 188 " pdb=" HB2 ALA B 252 " model vdw sym.op. 1.043 2.440 -x+y+1,-x+1,z nonbonded pdb="HG13 VAL B 195 " pdb=" H THR B 196 " model vdw 1.203 2.270 nonbonded pdb=" HG2 PRO B 140 " pdb=" HG3 GLU B 193 " model vdw 1.204 2.440 ... (remaining 113031 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: 5 Type Number sf(0) Gaussians S 32 15.96 2 O 786 7.97 1 N 644 6.97 1 C 2466 5.97 2 H 3946 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.2958 0.2934 0.3409 n_refl.: 9258 re-set all scales: r(all,work,free)=0.2958 0.2934 0.3409 n_refl.: 9258 remove outliers: r(all,work,free)=0.2957 0.2934 0.3409 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2323 0.2300 0.2784 n_refl.: 9255 add H (0.00, 0.00): r(all,work,free)=0.2339 0.2315 0.2800 n_refl.: 9255 remove outliers: r(all,work,free)=0.2339 0.2315 0.2800 n_refl.: 9255 |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2315 r_free= 0.2800 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.015620 | | target function (ml) not normalized (work): 53003.629840 | | target function (ml) not normalized (free): 2700.529622 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_16 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.01562 r_work = 0.2315 r_free = 0.2800 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 2.96 % favored = 90.71 % Rotamer outliers = 23.77 % C-beta deviations = 0 Clashscore = 15.75 RMS(bonds) = 0.0070 RMS(angles) = 1.40 MolProbity score = 3.27 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 1w60_rosetta_in.pdb -mtzfile 1w60_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1w60_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2071 r_free = 0.2901 energy = -2727.35 rmsd = 1.198 *** 2: r_work = 0.2085 r_free = 0.2950 energy = -2876.45 rmsd = 1.269 3: r_work = 0.2115 r_free = 0.2840 energy = -2709.86 rmsd = 1.223 *** 4: r_work = 0.2054 r_free = 0.2906 energy = -2706.44 rmsd = 1.406 5: r_work = 0.2049 r_free = 0.2897 energy = -2756.38 rmsd = 1.179 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 5.90907 r_work = 0.2115 r_free = 0.2840 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.79 % favored = 95.26 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 2.54 RMS(bonds) = 0.0245 RMS(angles) = 1.90 MolProbity score = 1.37 ----------Running phenix.refine (with null strategy)---------- start r_work=0.3304 r_free=0.3922 1_bss r_work=0.1951 r_free=0.2699 end r_work=0.1951 r_free=0.2699 Ramachandran outliers = 0.79 % favored = 95.26 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 6.35 RMS(bonds) = 0.0907 RMS(angles) = 2.16 MolProbity score = 1.68 Resolution = 3.14 R-work = 0.1951 R-free = 0.2699 ----------Final results---------- Refined model: 1w60_rosetta_phenix_001.pdb Final maps: 1w60_rosetta_phenix_001.mtz Elapsed time: 20649.4s 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.