============================== 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: 8784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4334 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: 2.91 Conformation dependent library (CDL) restraints added in 400.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 3.31 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: 4332 1.15 - 1.31: 765 1.31 - 1.48: 1860 1.48 - 1.64: 1909 1.64 - 1.81: 6 Bond restraints: 8872 Sorted by residual: bond pdb=" N VAL A 100 " pdb=" H VAL A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N LYS B 46 " pdb=" H LYS B 46 " 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 B 140 " pdb="HE22 GLN B 140 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP B 292 " pdb=" H ASP B 292 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 253 " pdb=" H ILE A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8867 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 162 104.43 - 111.82: 9279 111.82 - 119.21: 2643 119.21 - 126.60: 3803 126.60 - 133.99: 71 Bond angle restraints: 15958 Sorted by residual: angle pdb=" N LEU B 37 " pdb=" CA LEU B 37 " pdb=" C LEU B 37 " ideal model delta sigma weight residual 110.14 119.17 -9.03 1.47e+00 4.63e-01 3.78e+01 angle pdb=" N VAL B 89 " pdb=" CA VAL B 89 " pdb=" CB VAL B 89 " ideal model delta sigma weight residual 111.00 117.48 -6.48 1.14e+00 7.69e-01 3.23e+01 angle pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" C ILE A 108 " ideal model delta sigma weight residual 110.53 115.72 -5.19 9.40e-01 1.13e+00 3.04e+01 angle pdb=" C GLU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 120.31 128.30 -7.99 1.52e+00 4.33e-01 2.76e+01 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 108.27 115.35 -7.08 1.37e+00 5.33e-01 2.67e+01 ... (remaining 15953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3255 17.72 - 35.43: 216 35.43 - 53.15: 69 53.15 - 70.87: 33 70.87 - 88.58: 11 Dihedral angle restraints: 3584 sinusoidal: 1626 harmonic: 1958 Sorted by residual: dihedral pdb=" C THR B 212 " pdb=" N THR B 212 " pdb=" CA THR B 212 " pdb=" CB THR B 212 " ideal model delta harmonic sigma weight residual -122.00 -135.87 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLU B 184 " pdb=" N GLU B 184 " pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta harmonic sigma weight residual -122.60 -135.02 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C ASN B 86 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " pdb=" CB ASN B 86 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 3581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 495 0.107 - 0.213: 154 0.213 - 0.320: 30 0.320 - 0.427: 15 0.427 - 0.533: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN A 86 " pdb=" N ASN A 86 " pdb=" C ASN A 86 " pdb=" CB ASN A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.013 2.00e-02 2.50e+03 3.89e-02 2.26e+01 pdb=" CD GLN B 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN B 61 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN B 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 264 " -0.005 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 264 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 264 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 264 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR B 264 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR B 264 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR B 264 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.014 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 130 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 130 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR B 130 " 0.041 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 26 1.64 - 2.38: 2855 2.38 - 3.12: 27212 3.12 - 3.86: 38333 3.86 - 4.60: 59693 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128119 Sorted by model distance: nonbonded pdb="HH12 ARG A 227 " pdb=" HB2 PRO A 311 " model vdw 0.896 2.270 nonbonded pdb="HH12 ARG B 227 " pdb=" HB2 PRO B 311 " model vdw 0.922 2.270 nonbonded pdb=" HE2 LYS B 257 " pdb=" HA LYS B 283 " model vdw 1.020 2.440 nonbonded pdb=" HE2 LYS A 257 " pdb=" HA LYS A 283 " model vdw 1.026 2.440 nonbonded pdb="HD21 ASN A 36 " pdb=" HE2 LYS B 283 " model vdw 1.089 2.270 ... (remaining 128114 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 4 15.91 1 O 904 7.97 1 N 728 6.97 1 C 2814 5.97 1 H 4334 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.5459 0.5499 0.4202 n_refl.: 11707 re-set all scales: r(all,work,free)=0.5459 0.5499 0.4202 n_refl.: 11707 remove outliers: r(all,work,free)=0.5462 0.5502 0.4202 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2951 0.2927 0.3427 n_refl.: 11703 add H (0.00, 0.00): r(all,work,free)=0.2993 0.2968 0.3484 n_refl.: 11703 remove outliers: r(all,work,free)=0.2993 0.2968 0.3484 n_refl.: 11703 |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2968 r_free= 0.3484 coordinate error (max.-lik. estimate): 0.66 A | | | | normalized target function (ml) (work): 7.422717 | | target function (ml) not normalized (work): 82748.452469 | | target function (ml) not normalized (free): 4154.786639 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_8 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 7.42272 r_work = 0.2968 r_free = 0.3484 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.00 % favored = 97.00 % Rotamer outliers = 4.22 % C-beta deviations = 11 Clashscore = 11.17 RMS(bonds) = 0.0102 RMS(angles) = 1.54 MolProbity score = 2.21 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 2yhj_rosetta_in.pdb -mtzfile 2yhj_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=2yhj_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.3369 r_free = 0.3592 energy = -3594.51 rmsd = 0.896 *** 2: r_work = 0.3255 r_free = 0.3518 energy = -3682.99 rmsd = 0.912 *** 3: r_work = 0.3419 r_free = 0.3622 energy = -3626.47 rmsd = 0.906 4: r_work = 0.3292 r_free = 0.3566 energy = -3710.97 rmsd = 0.918 5: r_work = 0.3387 r_free = 0.3658 energy = -3627.56 rmsd = 0.932 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 7.39865 r_work = 0.3255 r_free = 0.3518 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 99.29 % Rotamer outliers = 0.20 % C-beta deviations = 0 Clashscore = 1.03 RMS(bonds) = 0.0281 RMS(angles) = 1.93 MolProbity score = 0.80 ----------Running phenix.refine (with null strategy)---------- start r_work=0.6268 r_free=0.4845 1_bss r_work=0.2656 r_free=0.3292 end r_work=0.2656 r_free=0.3292 Ramachandran outliers = 0.00 % favored = 99.29 % Rotamer outliers = 0.20 % C-beta deviations = 0 Clashscore = 4.56 RMS(bonds) = 0.0918 RMS(angles) = 2.14 MolProbity score = 1.23 Resolution = 4.00 R-work = 0.2656 R-free = 0.3292 ----------Final results---------- Refined model: 2yhj_rosetta_phenix_001.pdb Final maps: 2yhj_rosetta_phenix_001.mtz Elapsed time: 24008.8s 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.