============================== 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: 3448 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3448 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Time building chain proxies: 0.79, per 1000 atoms: 0.23 Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 338 8.00 N 305 7.00 C 1069 6.00 H 1729 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: 0.76 Conformation dependent library (CDL) restraints added in 137.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Time building geometry restraints manager: 0.85 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: 1726 1.15 - 1.31: 311 1.31 - 1.48: 654 1.48 - 1.65: 767 1.65 - 1.82: 11 Bond restraints: 3469 Sorted by residual: bond pdb=" CD GLU A 325 " pdb=" OE1 GLU A 325 " ideal model delta sigma weight residual 1.249 1.413 -0.164 1.90e-02 2.77e+03 7.49e+01 bond pdb=" N SER A 273 " pdb=" H SER A 273 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N SER A 235 " pdb=" H SER A 235 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 329 " pdb="HH22 ARG A 329 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASN A 174 " pdb=" H ASN A 174 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 96.85 - 107.61: 528 107.61 - 118.37: 4323 118.37 - 129.13: 1425 129.13 - 139.89: 9 139.89 - 150.65: 1 Bond angle restraints: 6286 Sorted by residual: angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 150.65 -39.35 2.30e+00 1.89e-01 2.93e+02 angle pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " pdb=" NE ARG A 213 " ideal model delta sigma weight residual 112.00 134.35 -22.35 2.20e+00 2.07e-01 1.03e+02 angle pdb=" N ASP A 202 " pdb=" CA ASP A 202 " pdb=" C ASP A 202 " ideal model delta sigma weight residual 107.32 118.69 -11.37 1.65e+00 3.67e-01 4.75e+01 angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 112.68 104.82 7.86 1.33e+00 5.65e-01 3.50e+01 angle pdb=" C VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta sigma weight residual 110.52 101.59 8.93 1.57e+00 4.06e-01 3.24e+01 ... (remaining 6281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1155 17.94 - 35.89: 131 35.89 - 53.83: 59 53.83 - 71.77: 18 71.77 - 89.72: 2 Dihedral angle restraints: 1365 sinusoidal: 676 harmonic: 689 Sorted by residual: dihedral pdb=" C THR A 261 " pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" CB THR A 261 " ideal model delta harmonic sigma weight residual -122.00 -133.67 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C VAL A 265 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.88e+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 122.80 132.91 -10.11 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 1362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 197 0.092 - 0.183: 58 0.183 - 0.275: 13 0.275 - 0.366: 2 0.366 - 0.458: 1 Chirality restraints: 271 Sorted by residual: 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 5.24e+00 chirality pdb=" CA THR A 261 " pdb=" N THR A 261 " pdb=" C THR A 261 " pdb=" CB THR A 261 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 268 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " 0.012 2.00e-02 2.50e+03 1.08e-02 3.52e+00 pdb=" CG PHE A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 232 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 232 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 232 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 232 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 232 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 333 " -0.019 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 333 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 333 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 333 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 333 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 333 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 333 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 333 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 333 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 333 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 247 " -0.002 2.00e-02 2.50e+03 7.99e-03 1.92e+00 pdb=" CG TYR A 247 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 247 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 247 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 247 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 247 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 247 " -0.001 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 110 1.82 - 2.51: 2893 2.51 - 3.21: 10969 3.21 - 3.90: 14997 3.90 - 4.60: 22785 Nonbonded interactions: 51754 Sorted by model distance: nonbonded pdb="HH11 ARG A 262 " pdb=" HB ILE A 304 " model vdw sym.op. 1.119 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb=" HB3 SER A 126 " pdb=" HD1 PHE A 232 " model vdw sym.op. 1.225 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb="HD22 LEU A 330 " pdb="HD11 ILE A 334 " model vdw 1.269 2.440 nonbonded pdb=" HB3 ASP A 202 " pdb="HG23 VAL A 205 " model vdw 1.288 2.440 nonbonded pdb=" HG3 GLU A 133 " pdb=" HG SER A 240 " model vdw sym.op. 1.307 2.270 -x+2,-x+y+1,-z+1 ... (remaining 51749 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 7 15.96 2 O 338 7.97 1 N 305 6.97 1 C 1069 5.97 2 H 1729 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.4394 0.4373 0.4786 n_refl.: 6717 re-set all scales: r(all,work,free)=0.4394 0.4373 0.4786 n_refl.: 6717 remove outliers: r(all,work,free)=0.4389 0.4368 0.4786 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2954 0.2953 0.2991 n_refl.: 6712 add H (0.10, 61.00): r(all,work,free)=0.2951 0.2953 0.2991 n_refl.: 6712 add H (0.10, 56.00): r(all,work,free)=0.2950 0.2953 0.2991 n_refl.: 6712 add H (0.10, 56.00): r(all,work,free)=0.2956 0.2956 0.2962 n_refl.: 6712 remove outliers: r(all,work,free)=0.2956 0.2956 0.2962 n_refl.: 6712 |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2956 r_free= 0.2962 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 6.710381 | | target function (ml) not normalized (work): 42899.466069 | | target function (ml) not normalized (free): 2123.896024 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_23 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.71038 r_work = 0.2956 r_free = 0.2962 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 3.20 % favored = 82.19 % Rotamer outliers = 20.63 % C-beta deviations = 3 Clashscore = 25.54 RMS(bonds) = 0.0128 RMS(angles) = 1.79 MolProbity score = 3.60 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 2ogu_rosetta_in.pdb -mtzfile 2ogu_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=2ogu_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2660 r_free = 0.3213 energy = -1236.27 rmsd = 1.255 *** 2: r_work = 0.2696 r_free = 0.3395 energy = -1234.76 rmsd = 1.251 3: r_work = 0.2696 r_free = 0.3242 energy = -1175.41 rmsd = 1.288 4: r_work = 0.2657 r_free = 0.3231 energy = -1138.01 rmsd = 1.272 5: r_work = 0.2647 r_free = 0.3283 energy = -1195.09 rmsd = 1.278 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.62464 r_work = 0.2660 r_free = 0.3213 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 98.17 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 0.29 RMS(bonds) = 0.0263 RMS(angles) = 1.97 MolProbity score = 0.61 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4284 r_free=0.4900 1_bss r_work=0.2480 r_free=0.3017 end r_work=0.2480 r_free=0.3017 Ramachandran outliers = 0.00 % favored = 98.17 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 5.22 RMS(bonds) = 0.0926 RMS(angles) = 2.13 MolProbity score = 1.28 Resolution = 3.23 R-work = 0.2480 R-free = 0.3017 ----------Final results---------- Refined model: 2ogu_rosetta_phenix_001.pdb Final maps: 2ogu_rosetta_phenix_001.mtz Elapsed time: 9919.2s 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.