============================== 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: 8905 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4443 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 1.66, per 1000 atoms: 0.19 Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4498 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: 2.40 Conformation dependent library (CDL) restraints added in 195.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Time building geometry restraints manager: 2.66 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: 4496 1.15 - 1.31: 769 1.31 - 1.48: 1661 1.48 - 1.64: 2002 1.64 - 1.81: 46 Bond restraints: 8974 Sorted by residual: bond pdb=" N GLY B 56 " pdb=" H GLY B 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 22 " pdb=" H GLN A 22 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG B 88 " pdb=" HE ARG B 88 " 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 A 144 " pdb=" H LEU A 144 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B 118 " pdb=" HE2 HIS B 118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8969 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.54: 115 104.54 - 111.91: 10297 111.91 - 119.29: 2244 119.29 - 126.66: 3608 126.66 - 134.03: 30 Bond angle restraints: 16294 Sorted by residual: angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 111.11 124.42 -13.31 1.20e+00 6.94e-01 1.23e+02 angle pdb=" N GLU B 14 " pdb=" CA GLU B 14 " pdb=" C GLU B 14 " ideal model delta sigma weight residual 112.23 102.63 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" N ARG B 286 " pdb=" CA ARG B 286 " pdb=" C ARG B 286 " ideal model delta sigma weight residual 112.87 104.22 8.65 1.20e+00 6.94e-01 5.20e+01 angle pdb=" N ARG A 286 " pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 112.83 120.50 -7.67 1.22e+00 6.72e-01 3.96e+01 ... (remaining 16289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3199 15.89 - 31.78: 195 31.78 - 47.67: 77 47.67 - 63.56: 54 63.56 - 79.45: 14 Dihedral angle restraints: 3539 sinusoidal: 1696 harmonic: 1843 Sorted by residual: dihedral pdb=" C ASP A 287 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 131.25 -8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual -180.00 -137.85 -42.15 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 3536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 495 0.097 - 0.194: 152 0.194 - 0.291: 22 0.291 - 0.388: 1 0.388 - 0.485: 3 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ARG A 286 " pdb=" N ARG A 286 " pdb=" C ARG A 286 " pdb=" CB ARG A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " -0.140 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG PHE A 171 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 171 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 171 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 171 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 171 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " 0.084 2.00e-02 2.50e+03 2.57e-02 2.63e+01 pdb=" CG TRP B 251 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 251 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP B 251 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 251 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 251 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 251 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 11 " 0.072 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 11 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 11 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 11 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 11 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 11 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 11 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.75: 107 1.75 - 2.46: 5136 2.46 - 3.17: 29832 3.17 - 3.89: 39137 3.89 - 4.60: 59445 Nonbonded interactions: 133657 Sorted by model distance: nonbonded pdb=" HD2 PHE A 171 " pdb=" HA2 GLY A 197 " model vdw 1.033 2.270 nonbonded pdb=" HH TYR B 11 " pdb=" HG2 LYS B 15 " model vdw sym.op. 1.245 2.270 -y+1,-x+1,-z+1 nonbonded pdb=" HE3 LYS A 93 " pdb="HH22 ARG B 259 " model vdw sym.op. 1.356 2.270 y+1/2,-x+1/2,z nonbonded pdb=" O LEU A 170 " pdb=" H LEU A 173 " model vdw 1.370 1.850 nonbonded pdb=" H GLU A 157 " pdb=" HG3 GLU A 157 " model vdw 1.448 2.270 ... (remaining 133652 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 24 15.91 1 O 823 7.97 1 N 729 6.97 1 C 2831 5.97 1 H 4498 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.4304 0.4287 0.4514 n_refl.: 9579 re-set all scales: r(all,work,free)=0.4304 0.4287 0.4514 n_refl.: 9579 remove outliers: r(all,work,free)=0.4284 0.4268 0.4475 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2593 0.2577 0.2880 n_refl.: 9561 add H (0.00, 0.00): r(all,work,free)=0.2653 0.2637 0.2944 n_refl.: 9561 remove outliers: r(all,work,free)=0.2653 0.2637 0.2944 n_refl.: 9561 |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2637 r_free= 0.2944 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 6.963292 | | target function (ml) not normalized (work): 63045.645011 | | target function (ml) not normalized (free): 3570.453008 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_5 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.96329 r_work = 0.2637 r_free = 0.2944 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 2.36 % favored = 92.38 % Rotamer outliers = 3.40 % C-beta deviations = 0 Clashscore = 18.43 RMS(bonds) = 0.0053 RMS(angles) = 1.32 MolProbity score = 2.64 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 1wl3_rosetta_in.pdb -mtzfile 1wl3_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1wl3_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2553 r_free = 0.2925 energy = -3464.98 rmsd = 1.149 *** 2: r_work = 0.2508 r_free = 0.2931 energy = -3483.81 rmsd = 1.145 3: r_work = 0.2511 r_free = 0.2947 energy = -3471.22 rmsd = 1.161 4: r_work = 0.2513 r_free = 0.2863 energy = -3472.54 rmsd = 1.153 *** 5: r_work = 0.2492 r_free = 0.2836 energy = -3496.24 rmsd = 1.160 *** |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.83521 r_work = 0.2492 r_free = 0.2836 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.18 % favored = 97.82 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 1.35 RMS(bonds) = 0.0244 RMS(angles) = 1.75 MolProbity score = 0.90 ----------Running phenix.refine (with null strategy)---------- start r_work=0.5289 r_free=0.6068 1_bss r_work=0.1926 r_free=0.2600 end r_work=0.1926 r_free=0.2600 Ramachandran outliers = 0.18 % favored = 97.82 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 6.97 RMS(bonds) = 0.0916 RMS(angles) = 1.97 MolProbity score = 1.42 Resolution = 3.50 R-work = 0.1926 R-free = 0.2600 ----------Final results---------- Refined model: 1wl3_rosetta_phenix_001.pdb Final maps: 1wl3_rosetta_phenix_001.mtz Elapsed time: 18350.7s 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.