============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped Residue "B GLU 180": "OE1" <-> "OE2" 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: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 185, 'PCIS': 1} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 185, 'PCIS': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.18 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 1.38 Conformation dependent library (CDL) restraints added in 130.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Time building geometry restraints manager: 1.53 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: 2954 1.16 - 1.33: 935 1.33 - 1.51: 1032 1.51 - 1.69: 1101 1.69 - 1.86: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" N SER A 131 " pdb=" H SER A 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 122 " pdb="HH11 ARG A 122 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA A 95 " pdb=" H ALA A 95 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG B 78 " pdb="HH22 ARG B 78 " 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 191 " pdb=" H GLN A 191 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.85: 324 106.85 - 113.67: 6801 113.67 - 120.49: 2030 120.49 - 127.31: 1705 127.31 - 134.13: 30 Bond angle restraints: 10890 Sorted by residual: angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 114.56 103.25 11.31 1.27e+00 6.20e-01 7.92e+01 angle pdb=" N VAL B 109 " pdb=" CA VAL B 109 " pdb=" C VAL B 109 " ideal model delta sigma weight residual 110.30 103.58 6.72 9.70e-01 1.06e+00 4.81e+01 angle pdb=" N ARG B 159 " pdb=" CA ARG B 159 " pdb=" C ARG B 159 " ideal model delta sigma weight residual 112.92 104.87 8.05 1.23e+00 6.61e-01 4.29e+01 angle pdb=" N VAL A 47 " pdb=" CA VAL A 47 " pdb=" C VAL A 47 " ideal model delta sigma weight residual 111.05 103.32 7.73 1.25e+00 6.40e-01 3.83e+01 angle pdb=" N LEU A 90 " pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 114.39 106.42 7.97 1.45e+00 4.76e-01 3.02e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2224 18.01 - 36.02: 144 36.02 - 54.02: 44 54.02 - 72.03: 20 72.03 - 90.04: 4 Dihedral angle restraints: 2436 sinusoidal: 1114 harmonic: 1322 Sorted by residual: dihedral pdb=" CB GLU B 180 " pdb=" CG GLU B 180 " pdb=" CD GLU B 180 " pdb=" OE1 GLU B 180 " ideal model delta sinusoidal sigma weight residual 0.00 90.04 -90.04 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 26 " pdb=" CG GLU B 26 " pdb=" CD GLU B 26 " pdb=" OE1 GLU B 26 " ideal model delta sinusoidal sigma weight residual 0.00 -88.21 88.21 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " ideal model delta sinusoidal sigma weight residual -180.00 -120.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 283 0.065 - 0.129: 133 0.129 - 0.194: 50 0.194 - 0.258: 13 0.258 - 0.323: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL B 109 " pdb=" N VAL B 109 " pdb=" C VAL B 109 " pdb=" CB VAL B 109 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TYR B 62 " pdb=" N TYR B 62 " pdb=" C TYR B 62 " pdb=" CB TYR B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 148 " 0.157 2.00e-02 2.50e+03 6.20e-02 1.15e+02 pdb=" CG TYR A 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 148 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 148 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 148 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 148 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 TYR A 148 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 148 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR A 148 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 148 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 141 " 0.107 2.00e-02 2.50e+03 3.96e-02 4.70e+01 pdb=" CG PHE A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 141 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE A 141 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 141 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " -0.105 2.00e-02 2.50e+03 3.17e-02 4.02e+01 pdb=" CG TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 138 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP B 138 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 138 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 138 " -0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 138 " 0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 138 " -0.021 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 245 1.88 - 2.56: 5793 2.56 - 3.24: 19194 3.24 - 3.92: 24770 3.92 - 4.60: 37824 Nonbonded interactions: 87826 Sorted by model distance: nonbonded pdb=" HE3 MET B 178 " pdb="HD22 LEU B 203 " model vdw 1.201 2.440 nonbonded pdb=" H ALA B 127 " pdb=" H ARG B 128 " model vdw 1.227 2.100 nonbonded pdb=" O GLN B 125 " pdb=" H ALA B 127 " model vdw 1.252 1.850 nonbonded pdb=" H LEU B 36 " pdb=" H LEU B 37 " model vdw 1.342 2.100 nonbonded pdb=" HG3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 1.436 2.270 ... (remaining 87821 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 8 15.96 2 O 586 7.97 1 N 520 6.97 1 C 1908 5.97 2 H 2954 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.2964 0.2933 0.3481 n_refl.: 8215 re-set all scales: r(all,work,free)=0.2964 0.2933 0.3481 n_refl.: 8215 remove outliers: r(all,work,free)=0.2964 0.2933 0.3481 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2248 0.2220 0.2749 n_refl.: 8215 add H (0.00, 0.00): r(all,work,free)=0.2273 0.2245 0.2774 n_refl.: 8215 remove outliers: r(all,work,free)=0.2273 0.2245 0.2774 n_refl.: 8215 |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2245 r_free= 0.2774 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.965962 | | target function (ml) not normalized (work): 54362.363768 | | target function (ml) not normalized (free): 2923.743411 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_15 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.96596 r_work = 0.2245 r_free = 0.2774 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 5.73 % favored = 73.44 % Rotamer outliers = 7.05 % C-beta deviations = 0 Clashscore = 29.98 RMS(bonds) = 0.0099 RMS(angles) = 1.43 MolProbity score = 3.42 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 1u9o_rosetta_in.pdb -mtzfile 1u9o_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1u9o_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2346 r_free = 0.2906 energy = -2441.18 rmsd = 1.630 *** 2: r_work = 0.2314 r_free = 0.2866 energy = -2464.66 rmsd = 1.046 *** 3: r_work = 0.2345 r_free = 0.2906 energy = -2463.56 rmsd = 1.142 4: r_work = 0.2451 r_free = 0.2964 energy = -2449.92 rmsd = 1.099 5: r_work = 0.2357 r_free = 0.2939 energy = -2452.87 rmsd = 1.290 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.83715 r_work = 0.2314 r_free = 0.2866 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 97.66 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 0.50 RMS(bonds) = 0.0263 RMS(angles) = 1.69 MolProbity score = 0.75 ----------Running phenix.refine (with null strategy)---------- start r_work=0.3919 r_free=0.4305 1_bss r_work=0.1725 r_free=0.2387 end r_work=0.1725 r_free=0.2387 Ramachandran outliers = 0.00 % favored = 97.66 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 4.52 RMS(bonds) = 0.0917 RMS(angles) = 1.97 MolProbity score = 1.30 Resolution = 3.31 R-work = 0.1725 R-free = 0.2387 ----------Final results---------- Refined model: 1u9o_rosetta_phenix_001.pdb Final maps: 1u9o_rosetta_phenix_001.mtz Elapsed time: 13947.9s 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.