============================== Collecting inputs ============================== ----------Processing X-ray data---------- ----------Processing PDB file(s)---------- Symmetric amino acids flipped Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "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: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 306, 'PCIS': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Time building chain proxies: 1.03, per 1000 atoms: 0.20 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 1.30 Conformation dependent library (CDL) restraints added in 112.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 565 1.05 - 1.25: 2357 1.25 - 1.44: 743 1.44 - 1.64: 1466 1.64 - 1.83: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" CA NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sigma weight residual 1.133 0.970 0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" NH2 ARG A 94 " pdb="HH22 ARG A 94 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" ND1 HIS A 117 " pdb=" HD1 HIS A 117 " 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 A 253 " pdb=" H ALA A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS A 168 " pdb=" HE2 HIS A 168 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 128 105.38 - 112.52: 5958 112.52 - 119.66: 1333 119.66 - 126.80: 1893 126.80 - 133.95: 34 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.38 99.63 13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 114.09 99.75 14.34 1.55e+00 4.16e-01 8.56e+01 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 110.97 101.49 9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.72 103.13 10.59 1.30e+00 5.92e-01 6.64e+01 angle pdb=" N ALA A 253 " pdb=" CA ALA A 253 " pdb=" C ALA A 253 " ideal model delta sigma weight residual 113.41 104.47 8.94 1.22e+00 6.72e-01 5.37e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1819 17.88 - 35.76: 147 35.76 - 53.63: 50 53.63 - 71.51: 30 71.51 - 89.39: 6 Dihedral angle restraints: 2052 sinusoidal: 967 harmonic: 1085 Sorted by residual: dihedral pdb=" N GLN A 348 " pdb=" C GLN A 348 " pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " ideal model delta harmonic sigma weight residual 122.80 114.22 8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 40 " pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sinusoidal sigma weight residual -90.00 -43.56 -46.44 2 1.50e+01 4.44e-03 1.12e+01 dihedral pdb=" CB GLU A 72 " pdb=" CG GLU A 72 " pdb=" CD GLU A 72 " pdb=" OE1 GLU A 72 " ideal model delta sinusoidal sigma weight residual 0.00 84.02 -84.02 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 2049 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 253 0.077 - 0.153: 95 0.153 - 0.229: 35 0.229 - 0.306: 10 0.306 - 0.382: 4 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA TRP A 298 " pdb=" N TRP A 298 " pdb=" C TRP A 298 " pdb=" CB TRP A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ALA A 280 " pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CB ALA A 280 " both_signs ideal model delta sigma weight residual False 2.48 2.80 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " -0.117 2.00e-02 2.50e+03 3.53e-02 5.00e+01 pdb=" CG TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 298 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 298 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 298 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 298 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 298 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 298 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 193 " -0.080 2.00e-02 2.50e+03 2.41e-02 2.33e+01 pdb=" CG TRP A 193 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 193 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 193 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 193 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 193 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 193 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP A 193 " 0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 193 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 193 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 193 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 317 " 0.057 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" CG TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 317 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 317 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 317 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 317 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 317 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 317 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR A 317 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 317 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 317 " -0.008 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.47: 38 1.47 - 2.25: 1195 2.25 - 3.03: 16091 3.03 - 3.82: 24076 3.82 - 4.60: 38651 Warning: very small nonbonded interaction distances. Nonbonded interactions: 80051 Sorted by model distance: nonbonded pdb=" HB3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 0.684 2.270 nonbonded pdb=" HG2 GLU A 87 " pdb=" HD1 HIS A 117 " model vdw 0.725 2.270 nonbonded pdb="HD13 ILE A 116 " pdb=" HB3 LEU A 124 " model vdw 0.838 2.440 nonbonded pdb=" HA ILE A 116 " pdb="HG21 VAL A 120 " model vdw 0.941 2.440 nonbonded pdb=" OE2 GLU A 122 " pdb=" HB3 PRO A 305 " model vdw sym.op. 0.998 2.620 z,x,y ... (remaining 80046 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 11 15.91 1 O 476 7.97 1 N 427 6.97 1 C 1617 5.97 1 H 2569 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3508 0.3511 0.3496 n_refl.: 13583 re-set all scales: r(all,work,free)=0.3508 0.3511 0.3496 n_refl.: 13583 remove outliers: r(all,work,free)=0.3508 0.3511 0.3496 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2155 0.2137 0.2480 n_refl.: 13580 add H (0.00, 0.00): r(all,work,free)=0.2175 0.2158 0.2485 n_refl.: 13580 remove outliers: r(all,work,free)=0.2175 0.2158 0.2485 n_refl.: 13580 |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2158 r_free= 0.2485 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 7.152319 | | target function (ml) not normalized (work): 92193.386102 | | target function (ml) not normalized (free): 4996.069920 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_2 ----------Setting up input files for Rosetta---------- Warning: temporarily removing residue A 900 NVA |-starting model--------------------------------------------------------------| | target_work(ml) = 7.15232 r_work = 0.2158 r_free = 0.2485 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 7.86 % favored = 71.38 % Rotamer outliers = 16.73 % C-beta deviations = 0 Clashscore = 66.15 RMS(bonds) = 0.0100 RMS(angles) = 1.67 MolProbity score = 4.05 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 1fb5_rosetta_in.pdb -mtzfile 1fb5_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1fb5_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2294 r_free = 0.2540 energy = -1427.61 rmsd = 1.365 *** 2: r_work = 0.2276 r_free = 0.2532 energy = -1639.33 rmsd = 1.389 *** 3: r_work = 0.2290 r_free = 0.2555 energy = -1574.46 rmsd = 1.402 4: r_work = 0.2273 r_free = 0.2544 energy = -1528.78 rmsd = 1.434 5: r_work = 0.2265 r_free = 0.2483 energy = -1517.85 rmsd = 1.333 *** |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 7.11345 r_work = 0.2265 r_free = 0.2483 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 2.52 % favored = 93.08 % Rotamer outliers = 0.00 % C-beta deviations = 2 Clashscore = 3.54 RMS(bonds) = 0.0253 RMS(angles) = 2.01 MolProbity score = 1.59 Merging back heteroatoms from original input file. ----------Running phenix.refine (with null strategy)---------- start r_work=0.4707 r_free=0.4347 1_bss r_work=0.1994 r_free=0.2294 end r_work=0.1993 r_free=0.2292 Ramachandran outliers = 2.52 % favored = 93.08 % Rotamer outliers = 0.00 % C-beta deviations = 2 Clashscore = 8.83 RMS(bonds) = 0.0910 RMS(angles) = 2.13 MolProbity score = 1.92 Resolution = 3.50 R-work = 0.1993 R-free = 0.2292 ----------Final results---------- Refined model: 1fb5_rosetta_phenix_001.pdb Final maps: 1fb5_rosetta_phenix_001.mtz Elapsed time: 16503.3s 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.