============================== 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: 6280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6280 Classifications: {'peptide': 404} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 388, 'PCIS': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N THR A 217 " occ=0.50 ... (12 atoms not shown) pdb="HG23 THR A 217 " occ=0.00 residue: pdb=" N TYR A 381 " occ=0.60 ... (19 atoms not shown) pdb=" HH TYR A 381 " occ=0.00 Time building chain proxies: 1.20, per 1000 atoms: 0.19 Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 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 12 16.00 O 612 8.00 N 555 7.00 C 2066 6.00 H 3035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 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: 1.53 Conformation dependent library (CDL) restraints added in 150.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Time building geometry restraints manager: 1.69 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: 3035 1.15 - 1.32: 568 1.32 - 1.49: 1477 1.49 - 1.66: 1273 1.66 - 1.84: 22 Bond restraints: 6375 Sorted by residual: bond pdb=" N THR A 403 " pdb=" H THR A 403 " 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 228 " pdb=" H VAL A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 89 " pdb=" H MET A 89 " 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 A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER A 232 " pdb=" H SER A 232 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.02: 217 106.02 - 113.10: 6605 113.10 - 120.19: 2340 120.19 - 127.27: 2193 127.27 - 134.35: 34 Bond angle restraints: 11389 Sorted by residual: angle pdb=" N ASP A 73 " pdb=" CA ASP A 73 " pdb=" C ASP A 73 " ideal model delta sigma weight residual 110.35 119.54 -9.19 1.40e+00 5.10e-01 4.31e+01 angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 114.75 107.29 7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" N GLN A 47 " pdb=" CA GLN A 47 " pdb=" C GLN A 47 " ideal model delta sigma weight residual 113.50 107.61 5.89 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N ASN A 320 " pdb=" CA ASN A 320 " pdb=" C ASN A 320 " ideal model delta sigma weight residual 108.69 116.64 -7.95 1.77e+00 3.19e-01 2.02e+01 angle pdb=" CA PHE A 404 " pdb=" C PHE A 404 " pdb=" O PHE A 404 " ideal model delta sigma weight residual 121.00 134.22 -13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 11384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 2265 16.41 - 32.81: 224 32.81 - 49.22: 87 49.22 - 65.63: 32 65.63 - 82.03: 9 Dihedral angle restraints: 2617 sinusoidal: 1119 harmonic: 1498 Sorted by residual: dihedral pdb=" CA PRO A 141 " pdb=" C PRO A 141 " pdb=" N ALA A 142 " pdb=" CA ALA A 142 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP A 277 " pdb=" C TRP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 273 0.066 - 0.133: 106 0.133 - 0.199: 54 0.199 - 0.265: 12 0.265 - 0.332: 3 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA TRP A 124 " pdb=" N TRP A 124 " pdb=" C TRP A 124 " pdb=" CB TRP A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP A 249 " pdb=" N TRP A 249 " pdb=" C TRP A 249 " pdb=" CB TRP A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE A 364 " pdb=" N PHE A 364 " pdb=" C PHE A 364 " pdb=" CB PHE A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 445 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " -0.002 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" CG PHE A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 37 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 37 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 37 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 37 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 312 " -0.011 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" CG PHE A 312 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 312 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 312 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 312 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 312 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 312 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 312 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 124 " 0.013 2.00e-02 2.50e+03 7.84e-03 2.46e+00 pdb=" CG TRP A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 124 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 124 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 124 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 124 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 124 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 124 " -0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 59 1.69 - 2.42: 2680 2.42 - 3.14: 20671 3.14 - 3.87: 30286 3.87 - 4.60: 45948 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99644 Sorted by model distance: nonbonded pdb=" HG1 THR A 217 " pdb="HD22 ASN A 28 " model vdw sym.op. 0.960 2.100 -x+1,-x+y,-z+1/3 nonbonded pdb="HD22 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 0.960 2.100 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" ND2 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 1.028 2.600 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" HG1 THR A 217 " pdb=" ND2 ASN A 28 " model vdw sym.op. 1.028 2.600 -x+1,-x+y,-z+1/3 nonbonded pdb=" HB3 PHE A 149 " pdb=" HE3 MET A 175 " model vdw 1.257 2.440 ... (remaining 99639 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 12 15.96 2 O 612 7.97 1 N 555 6.97 1 C 2066 5.97 2 H 3035 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 90, 90, 120) Space group: P 31 2 1 (No. 152) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3024 0.3004 0.3449 n_refl.: 8335 re-set all scales: r(all,work,free)=0.3024 0.3004 0.3449 n_refl.: 8335 remove outliers: r(all,work,free)=0.3024 0.3004 0.3449 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2136 0.2118 0.2515 n_refl.: 8334 add H (0.00, 0.00): r(all,work,free)=0.2148 0.2130 0.2516 n_refl.: 8334 remove outliers: r(all,work,free)=0.2148 0.2130 0.2516 n_refl.: 8334 |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2130 r_free= 0.2516 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 6.331014 | | target function (ml) not normalized (work): 50268.249862 | | target function (ml) not normalized (free): 2530.211080 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_19 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.33101 r_work = 0.2130 r_free = 0.2516 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.75 % favored = 91.54 % Rotamer outliers = 7.81 % C-beta deviations = 0 Clashscore = 11.15 RMS(bonds) = 0.0083 RMS(angles) = 1.37 MolProbity score = 2.74 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 2a8z_rosetta_in.pdb -mtzfile 2a8z_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=2a8z_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.1958 r_free = 0.2764 energy = -2691.49 rmsd = 0.754 *** 2: r_work = 0.2002 r_free = 0.2787 energy = -2698.81 rmsd = 0.778 3: r_work = 0.1943 r_free = 0.2661 energy = -2799.09 rmsd = 0.765 *** 4: r_work = 0.1916 r_free = 0.2710 energy = -2636.02 rmsd = 0.751 5: r_work = 0.1962 r_free = 0.2792 energy = -2673.15 rmsd = 0.744 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.24403 r_work = 0.1943 r_free = 0.2661 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 98.76 % Rotamer outliers = 0.30 % C-beta deviations = 0 Clashscore = 0.48 RMS(bonds) = 0.0211 RMS(angles) = 1.72 MolProbity score = 0.67 ----------Running phenix.refine (with null strategy)---------- start r_work=0.3242 r_free=0.3747 1_bss r_work=0.1728 r_free=0.2468 end r_work=0.1728 r_free=0.2468 Ramachandran outliers = 0.00 % favored = 98.76 % Rotamer outliers = 0.30 % C-beta deviations = 0 Clashscore = 4.30 RMS(bonds) = 0.0904 RMS(angles) = 1.98 MolProbity score = 1.21 Resolution = 3.20 R-work = 0.1728 R-free = 0.2468 ----------Final results---------- Refined model: 2a8z_rosetta_phenix_001.pdb Final maps: 2a8z_rosetta_phenix_001.mtz Elapsed time: 12703.9s 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.