============================== 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: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 82} Time building chain proxies: 0.54, per 1000 atoms: 0.19 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 0.66 Conformation dependent library (CDL) restraints added in 61.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Time building geometry restraints manager: 0.75 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: 1476 1.15 - 1.32: 248 1.32 - 1.49: 442 1.49 - 1.66: 665 1.66 - 1.83: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" NH1 ARG B 87 " pdb="HH12 ARG B 87 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS A 100 " pdb=" H HIS A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LYS B 108 " pdb=" H LYS B 108 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 75 " pdb=" H LEU A 75 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.19: 59 104.19 - 111.07: 3254 111.07 - 117.94: 912 117.94 - 124.81: 926 124.81 - 131.69: 70 Bond angle restraints: 5221 Sorted by residual: angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 112.92 102.67 10.25 1.23e+00 6.61e-01 6.95e+01 angle pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " ideal model delta sigma weight residual 115.55 123.69 -8.14 1.33e+00 5.65e-01 3.75e+01 angle pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL A 81 " pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 110.91 104.61 6.30 1.24e+00 6.50e-01 2.58e+01 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 110.80 120.70 -9.90 2.13e+00 2.20e-01 2.16e+01 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 964 25.86 - 51.72: 104 51.72 - 77.58: 14 77.58 - 103.44: 5 103.44 - 129.30: 1 Dihedral angle restraints: 1088 sinusoidal: 582 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta harmonic sigma weight residual 180.00 50.70 129.30 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" C ASP B 132 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual -122.60 -139.66 17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual 122.80 139.34 -16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 1085 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.134: 186 0.134 - 0.267: 45 0.267 - 0.401: 3 0.401 - 0.534: 2 0.534 - 0.667: 2 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA PHE B 135 " pdb=" N PHE B 135 " pdb=" C PHE B 135 " pdb=" CB PHE B 135 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.03e+00 pdb=" CG ASN A 134 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.003 2.00e-02 2.50e+03 6.76e-03 1.37e+00 pdb=" CG PHE B 135 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 135 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 135 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.003 2.00e-02 2.50e+03 9.20e-03 1.27e+00 pdb=" CG ASN B 134 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 134 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 90 1.84 - 2.53: 2680 2.53 - 3.22: 8880 3.22 - 3.91: 12220 3.91 - 4.60: 18232 Nonbonded interactions: 42102 Sorted by model distance: nonbonded pdb=" HG3 ARG A 89 " pdb="HH11 ARG A 89 " model vdw 1.154 2.270 nonbonded pdb=" HA GLU A 147 " pdb=" HB2 GLU A 150 " model vdw 1.325 2.440 nonbonded pdb="HH22 ARG A 94 " pdb="HD12 ILE A 104 " model vdw 1.340 2.270 nonbonded pdb=" O LEU A 74 " pdb=" H ASP A 76 " model vdw 1.363 1.850 nonbonded pdb=" HA2 GLY B 126 " pdb=" H THR B 140 " model vdw 1.423 2.270 ... (remaining 42097 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 257 7.97 1 N 229 6.97 1 C 865 5.97 1 H 1476 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3785 0.3757 0.4316 n_refl.: 7246 re-set all scales: r(all,work,free)=0.3785 0.3757 0.4316 n_refl.: 7246 remove outliers: r(all,work,free)=0.3784 0.3755 0.4316 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2245 0.2212 0.2876 n_refl.: 7245 add H (0.00, 0.00): r(all,work,free)=0.2322 0.2290 0.2924 n_refl.: 7245 remove outliers: r(all,work,free)=0.2322 0.2290 0.2924 n_refl.: 7245 |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2290 r_free= 0.2924 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 5.390417 | | target function (ml) not normalized (work): 37220.829002 | | target function (ml) not normalized (free): 1894.163436 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_18 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 5.39042 r_work = 0.2290 r_free = 0.2924 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 8.33 % favored = 81.55 % Rotamer outliers = 24.68 % C-beta deviations = 4 Clashscore = 23.72 RMS(bonds) = 0.0143 RMS(angles) = 1.97 MolProbity score = 3.64 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 1yab_rosetta_in.pdb -mtzfile 1yab_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yab_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2141 r_free = 0.2614 energy = -1023.28 rmsd = 1.108 *** 2: r_work = 0.2186 r_free = 0.2553 energy = -1079.09 rmsd = 1.193 *** 3: r_work = 0.2114 r_free = 0.2478 energy = -1056.60 rmsd = 1.150 *** 4: r_work = 0.2111 r_free = 0.2510 energy = -1051.62 rmsd = 1.096 5: r_work = 0.2121 r_free = 0.2465 energy = -1085.06 rmsd = 1.159 *** |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 5.31809 r_work = 0.2121 r_free = 0.2465 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 1.19 % favored = 97.02 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 2.48 RMS(bonds) = 0.0275 RMS(angles) = 2.19 MolProbity score = 1.20 ----------Running phenix.refine (with null strategy)---------- start r_work=0.3866 r_free=0.4295 1_bss r_work=0.1930 r_free=0.2391 end r_work=0.1930 r_free=0.2391 Ramachandran outliers = 1.19 % favored = 97.02 % Rotamer outliers = 0.00 % C-beta deviations = 1 Clashscore = 11.32 RMS(bonds) = 0.0926 RMS(angles) = 2.18 MolProbity score = 1.74 Resolution = 3.40 R-work = 0.1930 R-free = 0.2391 ----------Final results---------- Refined model: 1yab_rosetta_phenix_001.pdb Final maps: 1yab_rosetta_phenix_001.mtz Elapsed time: 4897.1s 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.