============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/dev/shm/nigel/phenix-1.20.1-4487/modules/chem_data/mon_lib" Total number of atoms: 10709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1791 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1774 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1789 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1760 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1808 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1787 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 1.95, per 1000 atoms: 0.18 Number of scatterers: 10709 At special positions: 0 Unit cell: (93.4462, 93.4462, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 986 8.00 N 925 7.00 C 3305 6.00 H 5475 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: 2.64 Conformation dependent library (CDL) restraints added in 307.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Time building geometry restraints manager: 2.93 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: 5475 1.15 - 1.32: 909 1.32 - 1.49: 1985 1.49 - 1.66: 2363 1.66 - 1.83: 36 Bond restraints: 10768 Sorted by residual: bond pdb=" N LEU D 57 " pdb=" H LEU D 57 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR D 56 " pdb=" H TYR D 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA D 79 " pdb=" H ALA D 79 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN C 37 " pdb="HE21 GLN C 37 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU D 66 " pdb=" H GLU D 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.11: 95 104.11 - 111.63: 12425 111.63 - 119.14: 2968 119.14 - 126.66: 4055 126.66 - 134.17: 45 Bond angle restraints: 19588 Sorted by residual: angle pdb=" N PHE C 3 " pdb=" CA PHE C 3 " pdb=" C PHE C 3 " ideal model delta sigma weight residual 111.69 119.66 -7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C HIS A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 126.47 -6.63 1.25e+00 6.40e-01 2.81e+01 angle pdb=" N GLN E 111 " pdb=" CA GLN E 111 " pdb=" C GLN E 111 " ideal model delta sigma weight residual 108.48 116.85 -8.37 1.65e+00 3.67e-01 2.58e+01 angle pdb=" N LYS D 4 " pdb=" CA LYS D 4 " pdb=" C LYS D 4 " ideal model delta sigma weight residual 112.38 118.50 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N ASN F 64 " pdb=" CA ASN F 64 " pdb=" C ASN F 64 " ideal model delta sigma weight residual 107.23 115.01 -7.78 1.67e+00 3.59e-01 2.17e+01 ... (remaining 19583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3748 17.94 - 35.88: 328 35.88 - 53.82: 138 53.82 - 71.76: 38 71.76 - 89.70: 14 Dihedral angle restraints: 4266 sinusoidal: 2176 harmonic: 2090 Sorted by residual: dihedral pdb=" CA GLU D 32 " pdb=" C GLU D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLU C 2 " pdb=" C GLU C 2 " pdb=" N PHE C 3 " pdb=" CA PHE C 3 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C GLN D 28 " pdb=" N GLN D 28 " pdb=" CA GLN D 28 " pdb=" CB GLN D 28 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 4263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 653 0.090 - 0.181: 165 0.181 - 0.271: 24 0.271 - 0.361: 7 0.361 - 0.452: 2 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA GLN D 28 " pdb=" N GLN D 28 " pdb=" C GLN D 28 " pdb=" CB GLN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE C 3 " pdb=" N PHE C 3 " pdb=" C PHE C 3 " pdb=" CB PHE C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU C 83 " pdb=" N LEU C 83 " pdb=" C LEU C 83 " pdb=" CB LEU C 83 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 848 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 40 " -0.031 2.00e-02 2.50e+03 1.17e-02 5.43e+00 pdb=" CG TRP D 40 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP D 40 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP D 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 40 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 40 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 40 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP D 40 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP D 40 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 40 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 40 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 40 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP D 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " 0.029 2.00e-02 2.50e+03 1.03e-02 4.23e+00 pdb=" CG TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 40 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 40 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " 0.007 2.00e-02 2.50e+03 8.98e-03 2.42e+00 pdb=" CG TYR A 56 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " -0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.012 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.27: 26 1.27 - 2.10: 1182 2.10 - 2.93: 28699 2.93 - 3.77: 48990 3.77 - 4.60: 78719 Warning: very small nonbonded interaction distances. Nonbonded interactions: 157616 Sorted by model distance: nonbonded pdb=" HE2 LYS E 4 " pdb=" HE2 PHE F 85 " model vdw 0.437 2.270 nonbonded pdb=" HE2 PHE B 3 " pdb=" CE LYS B 4 " model vdw 0.479 2.750 nonbonded pdb=" O LEU A 109 " pdb=" HE3 LYS C 46 " model vdw sym.op. 0.570 2.620 x,y+1,z nonbonded pdb="HD22 LEU E 20 " pdb="HD12 ILE E 50 " model vdw 0.593 2.440 nonbonded pdb="HD23 LEU E 91 " pdb=" HE3 LYS E 95 " model vdw 0.689 2.440 ... (remaining 157611 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 18 15.91 1 O 986 7.97 1 N 925 6.97 1 C 3305 5.97 1 H 5475 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 10709 At special positions: 0 Unit cell: (93.4462, 93.4462, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.4002 0.3982 0.4350 n_refl.: 25915 re-set all scales: r(all,work,free)=0.4002 0.3982 0.4350 n_refl.: 25915 remove outliers: r(all,work,free)=0.3980 0.3959 0.4350 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2621 0.2596 0.3090 n_refl.: 25903 add H (0.00, 0.00): r(all,work,free)=0.2743 0.2719 0.3191 n_refl.: 25903 remove outliers: r(all,work,free)=0.2743 0.2719 0.3191 n_refl.: 25903 |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2719 r_free= 0.3191 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 6.160398 | | target function (ml) not normalized (work): 151447.233801 | | target function (ml) not normalized (free): 8269.366924 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_24 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.1604 r_work = 0.2719 r_free = 0.3191 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 2.19 % favored = 82.66 % Rotamer outliers = 11.77 % C-beta deviations = 1 Clashscore = 35.08 RMS(bonds) = 0.0104 RMS(angles) = 1.40 MolProbity score = 3.54 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 2pej_rosetta_in.pdb -mtzfile 2pej_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=2pej_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2580 r_free = 0.3142 energy = -4146.69 rmsd = 1.137 *** 2: r_work = 0.2586 r_free = 0.3174 energy = -4212.58 rmsd = 1.146 3: r_work = 0.2600 r_free = 0.3152 energy = -4087.18 rmsd = 1.132 4: r_work = 0.2595 r_free = 0.3138 energy = -4078.89 rmsd = 1.110 *** 5: r_work = 0.2575 r_free = 0.3131 energy = -4222.32 rmsd = 1.129 *** |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.10887 r_work = 0.2575 r_free = 0.3131 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.16 % favored = 97.97 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 1.31 RMS(bonds) = 0.0224 RMS(angles) = 1.65 MolProbity score = 0.86 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4343 r_free=0.4832 1_bss r_work=0.2021 r_free=0.2483 end r_work=0.2021 r_free=0.2483 Ramachandran outliers = 0.16 % favored = 97.97 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 7.48 RMS(bonds) = 0.0918 RMS(angles) = 1.88 MolProbity score = 1.42 Resolution = 3.40 R-work = 0.2021 R-free = 0.2483 ----------Final results---------- Refined model: 2pej_rosetta_phenix_001.pdb Final maps: 2pej_rosetta_phenix_001.mtz Elapsed time: 25468.1s 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.