============================== 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: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 280, 'PCIS': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.20 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 1.13 Conformation dependent library (CDL) restraints added in 159.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2407 1.16 - 1.34: 725 1.34 - 1.52: 904 1.52 - 1.70: 706 1.70 - 1.88: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" N GLU A 257 " pdb=" H GLU A 257 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 123 " pdb="HH11 ARG A 123 " 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 A 25 " pdb=" HE ARG A 25 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 7 " pdb=" H MET A 7 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 215 " pdb="HH11 ARG A 215 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.31: 128 103.31 - 110.98: 4961 110.98 - 118.66: 1711 118.66 - 126.34: 1854 126.34 - 134.02: 35 Bond angle restraints: 8689 Sorted by residual: angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 114.48 102.68 11.80 1.19e+00 7.06e-01 9.84e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.03 100.14 10.89 1.11e+00 8.12e-01 9.62e+01 angle pdb=" N TYR A 237 " pdb=" CA TYR A 237 " pdb=" C TYR A 237 " ideal model delta sigma weight residual 111.36 101.53 9.83 1.09e+00 8.42e-01 8.13e+01 angle pdb=" N THR A 64 " pdb=" CA THR A 64 " pdb=" C THR A 64 " ideal model delta sigma weight residual 110.14 96.77 13.37 1.51e+00 4.39e-01 7.84e+01 angle pdb=" N ASP A 182 " pdb=" CA ASP A 182 " pdb=" C ASP A 182 " ideal model delta sigma weight residual 110.23 97.58 12.65 1.45e+00 4.76e-01 7.61e+01 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1569 17.47 - 34.93: 188 34.93 - 52.40: 73 52.40 - 69.86: 26 69.86 - 87.33: 12 Dihedral angle restraints: 1868 sinusoidal: 904 harmonic: 964 Sorted by residual: dihedral pdb=" C HIS A 86 " pdb=" N HIS A 86 " pdb=" CA HIS A 86 " pdb=" CB HIS A 86 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C LEU A 150 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C LEU A 131 " pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " ideal model delta harmonic sigma weight residual -122.60 -112.34 -10.26 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 1865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 200 0.107 - 0.215: 103 0.215 - 0.322: 47 0.322 - 0.429: 11 0.429 - 0.536: 4 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ASN A 53 " pdb=" N ASN A 53 " pdb=" C ASN A 53 " pdb=" CB ASN A 53 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU A 150 " pdb=" N LEU A 150 " pdb=" C LEU A 150 " pdb=" CB LEU A 150 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.157 2.00e-02 2.50e+03 6.46e-02 1.25e+02 pdb=" CG TYR A 78 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.125 2.00e-02 2.50e+03 pdb=" HD1 TYR A 78 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 78 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR A 78 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 78 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 265 " -0.144 2.00e-02 2.50e+03 5.64e-02 9.54e+01 pdb=" CG TYR A 265 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 265 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 265 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 265 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 265 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 265 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR A 265 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 265 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR A 265 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 265 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.131 2.00e-02 2.50e+03 5.19e-02 8.08e+01 pdb=" CG TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR A 170 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 170 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 170 " -0.016 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 207 1.80 - 2.50: 4384 2.50 - 3.20: 16080 3.20 - 3.90: 22187 3.90 - 4.60: 33487 Nonbonded interactions: 76345 Sorted by model distance: nonbonded pdb=" HE2 PHE A 221 " pdb=" HB3 LYS A 258 " model vdw sym.op. 1.102 2.270 -y+1,x-y,z-1/3 nonbonded pdb=" HA VAL A 285 " pdb="HG12 VAL A 290 " model vdw 1.137 2.440 nonbonded pdb="HH12 ARG A 123 " pdb=" HA ASP A 288 " model vdw 1.169 2.270 nonbonded pdb=" H GLY A 27 " pdb="HG13 VAL A 72 " model vdw 1.177 2.270 nonbonded pdb=" HB2 ALA A 60 " pdb="HG21 VAL A 197 " model vdw 1.192 2.440 ... (remaining 76340 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 9 15.91 1 O 423 7.97 1 N 390 6.97 1 C 1490 5.97 1 H 2407 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.2638 0.2640 0.2618 n_refl.: 7571 re-set all scales: r(all,work,free)=0.2638 0.2640 0.2618 n_refl.: 7571 remove outliers: r(all,work,free)=0.2638 0.2640 0.2618 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1873 0.1867 0.1921 n_refl.: 7570 add H (0.00, 0.00): r(all,work,free)=0.2046 0.2040 0.2101 n_refl.: 7570 remove outliers: r(all,work,free)=0.2046 0.2040 0.2101 n_refl.: 7570 |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.2040 r_free= 0.2101 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 6.558263 | | target function (ml) not normalized (work): 44733.912491 | | target function (ml) not normalized (free): 4962.864273 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_6 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.55826 r_work = 0.2040 r_free = 0.2101 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 8.19 % favored = 69.62 % Rotamer outliers = 27.16 % C-beta deviations = 2 Clashscore = 83.49 RMS(bonds) = 0.0162 RMS(angles) = 2.31 MolProbity score = 4.32 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 1xgo_rosetta_in.pdb -mtzfile 1xgo_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1xgo_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2912 r_free = 0.3147 energy = -1733.73 rmsd = 1.465 *** 2: r_work = 0.2957 r_free = 0.3165 energy = -1764.20 rmsd = 1.346 3: r_work = 0.2948 r_free = 0.3131 energy = -1716.10 rmsd = 1.732 *** 4: r_work = 0.2900 r_free = 0.3143 energy = -1723.73 rmsd = 1.339 5: r_work = 0.2947 r_free = 0.3199 energy = -1747.75 rmsd = 1.386 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.71383 r_work = 0.2948 r_free = 0.3131 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 1.37 % favored = 95.90 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 1.91 RMS(bonds) = 0.0268 RMS(angles) = 2.10 MolProbity score = 1.24 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4592 r_free=0.4716 1_bss r_work=0.2019 r_free=0.2526 end r_work=0.2019 r_free=0.2526 Ramachandran outliers = 1.37 % favored = 95.90 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 8.48 RMS(bonds) = 0.0919 RMS(angles) = 2.16 MolProbity score = 1.74 Resolution = 3.51 R-work = 0.2019 R-free = 0.2526 ----------Final results---------- Refined model: 1xgo_rosetta_phenix_001.pdb Final maps: 1xgo_rosetta_phenix_001.mtz Elapsed time: 9591.5s 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.