============================== 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: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'CIS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'CIS': 1, 'TRANS': 82} Time building chain proxies: 1.69, per 1000 atoms: 0.25 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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: 1.97 Conformation dependent library (CDL) restraints added in 297.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Time building geometry restraints manager: 2.22 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: 3382 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" NE2 GLN A 33 " pdb="HE21 GLN A 33 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA E 82 " pdb=" H ALA E 82 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " 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 D 116 " pdb="HE21 GLN D 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE F 86 " pdb=" H PHE F 86 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2144 127.35 - 133.97: 26 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2476 26.78 - 53.56: 262 53.56 - 80.34: 51 80.34 - 107.12: 5 107.12 - 133.91: 2 Dihedral angle restraints: 2796 sinusoidal: 1274 harmonic: 1522 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 2793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 7.99e-04 1.91e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 48 1.52 - 2.29: 1738 2.29 - 3.06: 20457 3.06 - 3.83: 30156 3.83 - 4.60: 47763 Warning: very small nonbonded interaction distances. Nonbonded interactions: 100162 Sorted by model distance: nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 nonbonded pdb=" HA GLN C 116 " pdb=" HB2 ALA C 117 " model vdw 0.871 2.440 nonbonded pdb=" HG2 ARG B 94 " pdb="HH11 ARG B 94 " model vdw 0.985 2.270 nonbonded pdb=" HA MET F 13 " pdb=" HB2 SER F 14 " model vdw 1.040 2.440 ... (remaining 100157 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 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3394 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.3233 0.3206 0.3573 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3233 0.3206 0.3573 n_refl.: 8745 remove outliers: r(all,work,free)=0.3229 0.3204 0.3559 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2103 0.2011 0.2945 n_refl.: 8739 add H (0.00, 0.00): r(all,work,free)=0.2160 0.2066 0.3022 n_refl.: 8739 remove outliers: r(all,work,free)=0.2155 0.2061 0.3022 n_refl.: 8738 |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2061 r_free= 0.3022 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.227441 | | target function (ml) not normalized (work): 49003.730647 | | target function (ml) not normalized (free): 5605.241729 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_9 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.22744 r_work = 0.2061 r_free = 0.3022 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 4.77 % favored = 81.62 % Rotamer outliers = 25.33 % C-beta deviations = 0 Clashscore = 44.43 RMS(bonds) = 0.0030 RMS(angles) = 0.85 MolProbity score = 3.91 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 3fm7_rosetta_in.pdb -mtzfile 3fm7_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=3fm7_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2560 r_free = 0.3079 energy = -2629.34 rmsd = 1.759 *** 2: r_work = 0.2526 r_free = 0.3082 energy = -2475.52 rmsd = 1.637 3: r_work = 0.2557 r_free = 0.3064 energy = -2610.72 rmsd = 1.594 *** 4: r_work = 0.2583 r_free = 0.3023 energy = -2652.84 rmsd = 1.796 *** 5: r_work = 0.2567 r_free = 0.3060 energy = -2653.79 rmsd = 1.558 |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.24243 r_work = 0.2583 r_free = 0.3023 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 1.67 % favored = 94.03 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 2.93 RMS(bonds) = 0.0207 RMS(angles) = 1.95 MolProbity score = 1.48 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4595 r_free=0.4285 1_bss r_work=0.2107 r_free=0.2853 end r_work=0.2107 r_free=0.2853 Ramachandran outliers = 1.67 % favored = 94.03 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 7.77 RMS(bonds) = 0.0905 RMS(angles) = 2.15 MolProbity score = 1.83 Resolution = 3.50 R-work = 0.2107 R-free = 0.2853 ----------Final results---------- Refined model: 3fm7_rosetta_phenix_001.pdb Final maps: 3fm7_rosetta_phenix_001.mtz Elapsed time: 14784.4s 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.