============================== 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: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 197, 'PCIS': 2} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.76, per 1000 atoms: 0.22 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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: 0.77 Conformation dependent library (CDL) restraints added in 140.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Time building geometry restraints manager: 0.86 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: 1751 1.15 - 1.33: 431 1.33 - 1.50: 638 1.50 - 1.68: 707 1.68 - 1.85: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" N3 GSH A 500 " pdb=" HN3 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.00e-02 1.00e+04 2.57e+02 bond pdb=" N2 GSH A 500 " pdb=" HN2 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.10e-02 8.26e+03 2.12e+02 bond pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CB2 GSH A 500 " pdb="HB23 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.44e+02 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.06: 254 107.06 - 114.81: 4243 114.81 - 122.56: 1410 122.56 - 130.32: 522 130.32 - 138.07: 15 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N TYR A 164 " pdb=" CA TYR A 164 " pdb=" C TYR A 164 " ideal model delta sigma weight residual 114.31 102.34 11.97 1.29e+00 6.01e-01 8.61e+01 angle pdb="HN11 GSH A 500 " pdb=" N1 GSH A 500 " pdb="HN12 GSH A 500 " ideal model delta sigma weight residual 111.04 138.07 -27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" N ASP A 62 " pdb=" CA ASP A 62 " pdb=" C ASP A 62 " ideal model delta sigma weight residual 114.04 103.69 10.35 1.24e+00 6.50e-01 6.97e+01 angle pdb=" CA2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" O2 GSH A 500 " ideal model delta sigma weight residual 120.61 109.21 11.40 1.39e+00 5.18e-01 6.72e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 115.47 104.89 10.58 1.31e+00 5.83e-01 6.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1213 13.48 - 26.97: 109 26.97 - 40.45: 57 40.45 - 53.94: 18 53.94 - 67.42: 20 Dihedral angle restraints: 1417 sinusoidal: 663 harmonic: 754 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CA HIS A 150 " pdb=" CB HIS A 150 " ideal model delta harmonic sigma weight residual 122.80 130.92 -8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " pdb=" CE MET A 132 " ideal model delta sinusoidal sigma weight residual 180.00 120.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1414 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.084: 254 1.084 - 2.167: 0 2.167 - 3.250: 0 3.250 - 4.334: 0 4.334 - 5.417: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 2.76 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" CA HIS A 150 " pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CB HIS A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 500 " 0.313 2.00e-02 2.50e+03 2.24e-01 7.49e+02 pdb=" CA2 GSH A 500 " 0.101 2.00e-02 2.50e+03 pdb=" CA3 GSH A 500 " 0.137 2.00e-02 2.50e+03 pdb=" N3 GSH A 500 " 0.034 2.00e-02 2.50e+03 pdb=" O2 GSH A 500 " -0.303 2.00e-02 2.50e+03 pdb=" HN3 GSH A 500 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 156 " -0.131 2.00e-02 2.50e+03 5.15e-02 7.95e+01 pdb=" CG TYR A 156 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 156 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 156 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 156 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 156 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 156 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR A 156 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 156 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 156 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 156 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 201 " 0.100 2.00e-02 2.50e+03 3.02e-02 3.64e+01 pdb=" CG TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 201 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 201 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 201 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 201 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 201 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 201 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 201 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 201 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.87: 142 1.87 - 2.55: 3363 2.55 - 3.23: 10953 3.23 - 3.92: 14318 3.92 - 4.60: 22275 Nonbonded interactions: 51051 Sorted by model distance: nonbonded pdb="HG13 ILE A 109 " pdb=" H ALA A 110 " model vdw 1.183 2.270 nonbonded pdb="HH12 ARG A 103 " pdb="HE21 GLN A 204 " model vdw 1.249 2.100 nonbonded pdb=" HD2 PHE A 122 " pdb=" HE1 MET A 165 " model vdw 1.275 2.270 nonbonded pdb=" HA PHE A 7 " pdb="HD22 LEU A 55 " model vdw 1.279 2.440 nonbonded pdb=" HB3 GLU A 30 " pdb="HD11 LEU A 32 " model vdw 1.331 2.440 ... (remaining 51046 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 14 15.91 1 O 316 7.97 1 N 282 6.97 1 C 1138 5.97 1 H 1756 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3024 0.3019 0.3086 n_refl.: 4185 re-set all scales: r(all,work,free)=0.3024 0.3019 0.3086 n_refl.: 4185 remove outliers: r(all,work,free)=0.3035 0.3030 0.3086 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.2182 0.2184 0.2159 n_refl.: 4182 add H (0.20, 21.00): r(all,work,free)=0.2173 0.2184 0.2159 n_refl.: 4182 add H (0.18, 16.00): r(all,work,free)=0.2173 0.2184 0.2159 n_refl.: 4182 add H (0.18, 16.00): r(all,work,free)=0.2151 0.2148 0.2172 n_refl.: 4182 remove outliers: r(all,work,free)=0.2151 0.2148 0.2172 n_refl.: 4182 |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.2148 r_free= 0.2172 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.493163 | | target function (ml) not normalized (work): 24433.773781 | | target function (ml) not normalized (free): 2720.126665 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_4 ----------Setting up input files for Rosetta---------- Warning: temporarily removing residue A 500 GSH |-starting model--------------------------------------------------------------| | target_work(ml) = 6.49316 r_work = 0.2148 r_free = 0.2172 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 8.70 % favored = 71.01 % Rotamer outliers = 9.57 % C-beta deviations = 0 Clashscore = 39.19 RMS(bonds) = 0.0091 RMS(angles) = 1.56 MolProbity score = 3.65 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 1u87_rosetta_in.pdb -mtzfile 1u87_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1u87_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2577 r_free = 0.3161 energy = -1137.35 rmsd = 0.963 *** 2: r_work = 0.2624 r_free = 0.3155 energy = -1242.66 rmsd = 1.000 *** 3: r_work = 0.2546 r_free = 0.3037 energy = -1243.19 rmsd = 0.983 *** 4: r_work = 0.2583 r_free = 0.3110 energy = -1228.04 rmsd = 0.978 5: r_work = 0.2593 r_free = 0.3102 energy = -1236.06 rmsd = 0.969 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.57479 r_work = 0.2546 r_free = 0.3037 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 99.52 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 1.44 RMS(bonds) = 0.0198 RMS(angles) = 1.61 MolProbity score = 0.88 Merging back heteroatoms from original input file. ----------Running phenix.refine (with null strategy)---------- start r_work=0.4087 r_free=0.4753 1_bss r_work=0.1870 r_free=0.2501 end r_work=0.1863 r_free=0.2498 Ramachandran outliers = 0.00 % favored = 99.52 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 6.28 RMS(bonds) = 0.0913 RMS(angles) = 2.09 MolProbity score = 1.35 Resolution = 3.50 R-work = 0.1863 R-free = 0.2498 ----------Final results---------- Refined model: 1u87_rosetta_phenix_001.pdb Final maps: 1u87_rosetta_phenix_001.mtz Elapsed time: 7231.3s 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.