============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 7468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3250 Classifications: {'peptide': 199} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "B" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 4218 Classifications: {'peptide': 267} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 246} Time building chain proxies: 1.29, per 1000 atoms: 0.17 Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 682 8.00 N 628 7.00 C 2366 6.00 H 3778 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 17 " distance=2.03 Simple disulfide: pdb=" SG CYS B 209 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 264 " 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: 1.77 Conformation dependent library (CDL) restraints added in 165.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 886 Time building geometry restraints manager: 1.97 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: 3777 1.15 - 1.32: 698 1.32 - 1.49: 1420 1.49 - 1.67: 1630 1.67 - 1.84: 19 Bond restraints: 7544 Sorted by residual: bond pdb=" N VAL B 256 " pdb=" H VAL B 256 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 700 " pdb=" H GLU A 700 " 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 B 114 " pdb=" H SER B 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND1 HIS A 563 " pdb=" HD1 HIS A 563 " 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 B 195 " pdb=" H HIS B 195 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 392 106.21 - 113.18: 8799 113.18 - 120.15: 2310 120.15 - 127.12: 2204 127.12 - 134.09: 31 Bond angle restraints: 13736 Sorted by residual: angle pdb=" N VAL B 78 " pdb=" CA VAL B 78 " pdb=" C VAL B 78 " ideal model delta sigma weight residual 112.43 120.71 -8.28 9.20e-01 1.18e+00 8.10e+01 angle pdb=" C LEU B 76 " pdb=" N PRO B 77 " pdb=" CA PRO B 77 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C LEU B 197 " pdb=" N PRO B 198 " pdb=" CA PRO B 198 " ideal model delta sigma weight residual 119.56 127.99 -8.43 1.02e+00 9.61e-01 6.83e+01 angle pdb=" N ILE B 213 " pdb=" CA ILE B 213 " pdb=" C ILE B 213 " ideal model delta sigma weight residual 112.90 105.33 7.57 9.60e-01 1.09e+00 6.21e+01 angle pdb=" N ARG A 511 " pdb=" CA ARG A 511 " pdb=" C ARG A 511 " ideal model delta sigma weight residual 108.45 118.26 -9.81 1.26e+00 6.30e-01 6.06e+01 ... (remaining 13731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 2728 17.57 - 35.14: 191 35.14 - 52.71: 70 52.71 - 70.28: 25 70.28 - 87.84: 4 Dihedral angle restraints: 3018 sinusoidal: 1459 harmonic: 1559 Sorted by residual: dihedral pdb=" CA LYS A 585 " pdb=" CB LYS A 585 " pdb=" CG LYS A 585 " pdb=" CD LYS A 585 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLN B 159 " pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " pdb=" CD GLN B 159 " ideal model delta sinusoidal sigma weight residual 60.00 113.33 -53.33 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" C HIS B 195 " pdb=" N HIS B 195 " pdb=" CA HIS B 195 " pdb=" CB HIS B 195 " ideal model delta harmonic sigma weight residual -122.60 -115.04 -7.56 0 2.50e+00 1.60e-01 9.15e+00 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 349 0.080 - 0.160: 177 0.160 - 0.240: 54 0.240 - 0.320: 12 0.320 - 0.400: 4 Chirality restraints: 596 Sorted by residual: chirality pdb=" CA PRO B 2 " pdb=" N PRO B 2 " pdb=" C PRO B 2 " pdb=" CB PRO B 2 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA GLN B 21 " pdb=" N GLN B 21 " pdb=" C GLN B 21 " pdb=" CB GLN B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA HIS B 195 " pdb=" N HIS B 195 " pdb=" C HIS B 195 " pdb=" CB HIS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 593 not shown) Planarity restraints: 1091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 44 " -0.125 2.00e-02 2.50e+03 5.17e-02 8.01e+01 pdb=" CG TYR B 44 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 44 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 44 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 44 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 44 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 44 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 44 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR B 44 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 44 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR B 44 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 600 " 0.122 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR A 600 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 600 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 600 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 600 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 600 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 600 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 600 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 600 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 600 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 54 " 0.112 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG TYR B 54 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 54 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR B 54 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 54 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 54 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 54 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 54 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 54 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR B 54 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 54 " 0.006 2.00e-02 2.50e+03 ... (remaining 1088 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 115 1.73 - 2.45: 4531 2.45 - 3.17: 24552 3.17 - 3.88: 32886 3.88 - 4.60: 50977 Nonbonded interactions: 113061 Sorted by model distance: nonbonded pdb=" HA HIS A 559 " pdb=" HA ALA A 592 " model vdw 1.014 2.440 nonbonded pdb="HH22 ARG A 545 " pdb=" HG3 PRO A 703 " model vdw 1.092 2.270 nonbonded pdb=" HA ARG A 636 " pdb="HH11 ARG A 636 " model vdw 1.130 2.270 nonbonded pdb="HD22 LEU A 512 " pdb="HH21 ARG A 611 " model vdw 1.155 2.270 nonbonded pdb=" OE1 GLU A 613 " pdb=" H GLU A 613 " model vdw 1.278 1.850 ... (remaining 113056 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 14 15.96 2 O 682 7.97 1 N 628 6.97 1 C 2366 5.97 2 H 3778 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 7468 At special positions: 0 Unit cell: (89.84, 89.84, 124.63, 90, 90, 120) Space group: P 61 (No. 169) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3536 0.3506 0.4119 n_refl.: 10454 re-set all scales: r(all,work,free)=0.3536 0.3506 0.4119 n_refl.: 10454 remove outliers: r(all,work,free)=0.3536 0.3506 0.4114 n_refl.: 10449 bulk-solvent and scaling: r(all,work,free)=0.2269 0.2242 0.2777 n_refl.: 10449 add H (0.00, 0.00): r(all,work,free)=0.2322 0.2297 0.2804 n_refl.: 10449 remove outliers: r(all,work,free)=0.2322 0.2297 0.2804 n_refl.: 10449 |--(resolution: 3.09 - 30.50 A, n_refl.=10449 (all), 5.10 % free)------------| | | | r_work= 0.2297 r_free= 0.2804 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.329940 | | target function (ml) not normalized (work): 62767.686369 | | target function (ml) not normalized (free): 3461.676123 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_14 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.32994 r_work = 0.2297 r_free = 0.2804 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 4.98 % favored = 82.25 % Rotamer outliers = 5.28 % C-beta deviations = 0 Clashscore = 35.90 RMS(bonds) = 0.0095 RMS(angles) = 1.71 MolProbity score = 3.29 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 1m10_rosetta_in.pdb -mtzfile 1m10_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1m10_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2121 r_free = 0.2823 energy = -2468.58 rmsd = 1.600 *** 2: r_work = 0.2132 r_free = 0.2850 energy = -2455.81 rmsd = 1.463 3: r_work = 0.2105 r_free = 0.2868 energy = -2486.57 rmsd = 1.403 4: r_work = 0.2159 r_free = 0.2858 energy = -2474.94 rmsd = 1.722 5: r_work = 0.2115 r_free = 0.2889 energy = -2439.97 rmsd = 1.624 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.24561 r_work = 0.2121 r_free = 0.2823 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.43 % favored = 95.89 % Rotamer outliers = 0.24 % C-beta deviations = 0 Clashscore = 2.28 RMS(bonds) = 0.0240 RMS(angles) = 1.95 MolProbity score = 1.29 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4013 r_free=0.4257 1_bss r_work=0.2006 r_free=0.2733 end r_work=0.2006 r_free=0.2733 Ramachandran outliers = 0.43 % favored = 95.89 % Rotamer outliers = 0.24 % C-beta deviations = 0 Clashscore = 7.23 RMS(bonds) = 0.0909 RMS(angles) = 2.07 MolProbity score = 1.68 Resolution = 3.09 R-work = 0.2006 R-free = 0.2733 ----------Final results---------- Refined model: 1m10_rosetta_phenix_001.pdb Final maps: 1m10_rosetta_phenix_001.mtz Elapsed time: 15254.7s 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.