============================== 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: 7982 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7982 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 1.42, per 1000 atoms: 0.18 Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3920 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: 1.97 Conformation dependent library (CDL) restraints added in 179.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Time building geometry restraints manager: 2.17 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: 3919 1.15 - 1.32: 661 1.32 - 1.48: 1834 1.48 - 1.65: 1688 1.65 - 1.82: 21 Bond restraints: 8123 Sorted by residual: bond pdb=" NH1 ARG A 84 " pdb="HH11 ARG A 84 " 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 476 " pdb="HH22 ARG A 476 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR A 399 " pdb=" H THR A 399 " 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 A 279 " pdb="HH22 ARG A 279 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP A 159 " pdb=" HE1 TRP A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 414 106.96 - 113.72: 8838 113.72 - 120.48: 2791 120.48 - 127.23: 2538 127.23 - 133.99: 74 Bond angle restraints: 14655 Sorted by residual: angle pdb=" OE1 GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 122.60 112.79 9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" CG GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 116.40 126.40 -10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" N GLY A 21 " pdb=" CA GLY A 21 " pdb=" C GLY A 21 " ideal model delta sigma weight residual 114.90 124.70 -9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 114.67 108.55 6.12 1.10e+00 8.26e-01 3.10e+01 ... (remaining 14650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 2995 14.82 - 29.65: 142 29.65 - 44.47: 59 44.47 - 59.29: 43 59.29 - 74.12: 20 Dihedral angle restraints: 3259 sinusoidal: 1438 harmonic: 1821 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual 60.00 109.93 -49.93 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 255 0.056 - 0.112: 233 0.112 - 0.168: 47 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" C PRO A 469 " pdb=" CB PRO A 469 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL A 349 " pdb=" N VAL A 349 " pdb=" C VAL A 349 " pdb=" CB VAL A 349 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 182 " pdb=" N VAL A 182 " pdb=" C VAL A 182 " pdb=" CB VAL A 182 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.051 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" CG TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.051 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" CG TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.052 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" CG PHE A 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 192 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 192 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 192 " 0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 410 1.94 - 2.61: 9016 2.61 - 3.27: 26771 3.27 - 3.94: 35377 3.94 - 4.60: 53388 Nonbonded interactions: 124962 Sorted by model distance: nonbonded pdb=" O PRO A 215 " pdb="HH22 ARG A 279 " model vdw 1.279 1.850 nonbonded pdb=" HG2 ARG A 75 " pdb=" HD3 PRO A 76 " model vdw 1.320 2.440 nonbonded pdb=" HB3 GLN A 27 " pdb="HH21 ARG A 30 " model vdw 1.321 2.270 nonbonded pdb=" HG3 GLU A 334 " pdb=" HD3 PRO A 336 " model vdw 1.355 2.440 nonbonded pdb="HH22 ARG A 291 " pdb=" HE1 HIS A 394 " model vdw 1.358 2.100 ... (remaining 124957 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 11 15.96 2 O 707 7.97 1 N 703 6.97 1 C 2641 5.97 2 H 3920 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3997 0.3910 0.4798 n_refl.: 10132 re-set all scales: r(all,work,free)=0.3997 0.3910 0.4798 n_refl.: 10132 remove outliers: r(all,work,free)=0.3796 0.3691 0.4798 n_refl.: 10127 bulk-solvent and scaling: r(all,work,free)=0.2365 0.2364 0.2376 n_refl.: 10127 add H (0.07, 0.00): r(all,work,free)=0.2364 0.2364 0.2376 n_refl.: 10127 add H (0.07, 0.00): r(all,work,free)=0.2358 0.2359 0.2353 n_refl.: 10127 remove outliers: r(all,work,free)=0.2358 0.2359 0.2353 n_refl.: 10127 |--(resolution: 3.10 - 52.13 A, n_refl.=10127 (all), 10.01 % free)------------| | | | r_work= 0.2359 r_free= 0.2353 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ml) (work): 6.910794 | | target function (ml) not normalized (work): 62978.063512 | | target function (ml) not normalized (free): 6992.208967 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_13 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.91079 r_work = 0.2359 r_free = 0.2353 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 1.81 % favored = 85.94 % Rotamer outliers = 2.24 % C-beta deviations = 0 Clashscore = 28.95 RMS(bonds) = 0.0051 RMS(angles) = 1.25 MolProbity score = 2.86 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 1fp9_rosetta_in.pdb -mtzfile 1fp9_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1fp9_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2154 r_free = 0.2964 energy = -3425.89 rmsd = 0.893 *** 2: r_work = 0.2155 r_free = 0.2976 energy = -3297.32 rmsd = 1.018 3: r_work = 0.2103 r_free = 0.2953 energy = -3402.04 rmsd = 0.973 *** 4: r_work = 0.2155 r_free = 0.2982 energy = -3512.20 rmsd = 1.000 5: r_work = 0.2191 r_free = 0.2974 energy = -3414.08 rmsd = 0.943 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.93485 r_work = 0.2103 r_free = 0.2953 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 98.80 % Rotamer outliers = 0.25 % C-beta deviations = 1 Clashscore = 0.75 RMS(bonds) = 0.0233 RMS(angles) = 1.75 MolProbity score = 0.74 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4112 r_free=0.5758 1_bss r_work=0.1953 r_free=0.2811 end r_work=0.1953 r_free=0.2811 Ramachandran outliers = 0.00 % favored = 98.80 % Rotamer outliers = 0.25 % C-beta deviations = 1 Clashscore = 5.64 RMS(bonds) = 0.0912 RMS(angles) = 1.98 MolProbity score = 1.31 Resolution = 3.10 R-work = 0.1953 R-free = 0.2811 ----------Final results---------- Refined model: 1fp9_rosetta_phenix_001.pdb Final maps: 1fp9_rosetta_phenix_001.mtz Elapsed time: 17374.5s 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.