============================== 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: 3086 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1543 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Time building chain proxies: 0.61, per 1000 atoms: 0.20 Number of scatterers: 3086 At special positions: 0 Unit cell: (70.8199, 70.8199, 70.01, 90, 90, 120) Space group: P 65 (No. 170) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 308 8.00 N 280 7.00 C 954 6.00 H 1544 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: 0.70 Conformation dependent library (CDL) restraints added in 74.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 360 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.10: 1544 1.10 - 1.21: 0 1.21 - 1.33: 308 1.33 - 1.44: 336 1.44 - 1.56: 918 Bond restraints: 3106 Sorted by residual: bond pdb=" N GLY A 104 " pdb=" H GLY A 104 " 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 93 " pdb=" H ALA A 93 " 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 48 " pdb=" H HIS B 48 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 10 " pdb=" H GLY A 10 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N SER B 103 " pdb=" H SER B 103 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 3101 not shown) Histogram of bond angle deviations from ideal: 102.64 - 108.90: 1201 108.90 - 115.16: 2931 115.16 - 121.42: 737 121.42 - 127.67: 747 127.67 - 133.93: 16 Bond angle restraints: 5632 Sorted by residual: angle pdb=" N HIS A 46 " pdb=" CA HIS A 46 " pdb=" C HIS A 46 " ideal model delta sigma weight residual 108.79 114.62 -5.83 1.53e+00 4.27e-01 1.45e+01 angle pdb=" N ALA B 50 " pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 108.13 114.63 -6.50 1.72e+00 3.38e-01 1.43e+01 angle pdb=" N HIS B 46 " pdb=" CA HIS B 46 " pdb=" C HIS B 46 " ideal model delta sigma weight residual 109.07 115.09 -6.02 1.61e+00 3.86e-01 1.40e+01 angle pdb=" N THR A 86 " pdb=" CA THR A 86 " pdb=" C THR A 86 " ideal model delta sigma weight residual 108.96 114.59 -5.63 1.59e+00 3.96e-01 1.26e+01 angle pdb=" N ALA A 109 " pdb=" CA ALA A 109 " pdb=" C ALA A 109 " ideal model delta sigma weight residual 112.93 108.80 4.13 1.33e+00 5.65e-01 9.65e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1088 17.29 - 34.57: 54 34.57 - 51.86: 20 51.86 - 69.15: 4 69.15 - 86.44: 2 Dihedral angle restraints: 1168 sinusoidal: 526 harmonic: 642 Sorted by residual: dihedral pdb=" CA HIS B 46 " pdb=" C HIS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU B 101 " pdb=" C LEU B 101 " pdb=" N ALA B 102 " pdb=" CA ALA B 102 " ideal model delta harmonic sigma weight residual 180.00 162.95 17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 69 " pdb=" C ILE B 69 " pdb=" N GLU B 70 " pdb=" CA GLU B 70 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 152 0.034 - 0.067: 46 0.067 - 0.101: 23 0.101 - 0.135: 17 0.135 - 0.168: 6 Chirality restraints: 244 Sorted by residual: chirality pdb=" CA VAL B 47 " pdb=" N VAL B 47 " pdb=" C VAL B 47 " pdb=" CB VAL B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ILE A 18 " pdb=" N ILE A 18 " pdb=" C ILE A 18 " pdb=" CB ILE A 18 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.19e-01 ... (remaining 241 not shown) Planarity restraints: 494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 20 " -0.000 2.00e-02 2.50e+03 4.94e-03 7.31e-01 pdb=" CG PHE B 20 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 20 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 20 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 20 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE B 20 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE B 20 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 20 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 45 " 0.004 2.00e-02 2.50e+03 4.84e-03 7.02e-01 pdb=" CG PHE A 45 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 45 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 45 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 45 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 45 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 45 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 45 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 20 " 0.003 2.00e-02 2.50e+03 3.91e-03 4.58e-01 pdb=" CG PHE A 20 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 20 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 20 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 20 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 20 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 20 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 20 " -0.001 2.00e-02 2.50e+03 ... (remaining 491 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.08: 168 2.08 - 2.69: 4385 2.69 - 3.29: 8530 3.29 - 3.90: 10967 3.90 - 4.50: 16312 Nonbonded interactions: 40362 Sorted by model distance: nonbonded pdb=" H GLY A 96 " pdb="HD21 ASN B 26 " model vdw sym.op. 1.477 2.100 -x+1,-y+1,z+1/2 nonbonded pdb=" O ALA B 4 " pdb=" H PHE B 20 " model vdw 1.502 1.850 nonbonded pdb=" OE2 GLU A 21 " pdb=" HE1 TRP A 32 " model vdw 1.545 1.850 nonbonded pdb=" O LEU B 42 " pdb=" H GLY B 94 " model vdw 1.609 1.850 nonbonded pdb=" H VAL A 47 " pdb=" O GLY A 52 " model vdw 1.623 1.850 ... (remaining 40357 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: 4 Type Number sf(0) Gaussians O 308 7.97 1 N 280 6.97 1 C 954 5.97 1 H 1544 1.00 1 sf(0) = scattering factor at diffraction angle 0. Number of scatterers: 3086 At special positions: 0 Unit cell: (70.8199, 70.8199, 70.01, 90, 90, 120) Space group: P 65 (No. 170) ----------F(model) initialization---------- Twinning will be detected automatically. start: r(all,work,free)=0.4423 0.4443 0.4253 n_refl.: 2197 re-set all scales: r(all,work,free)=0.4423 0.4443 0.4253 n_refl.: 2197 remove outliers: r(all,work,free)=0.4385 0.4403 0.4253 n_refl.: 2192 bulk-solvent and scaling: r(all,work,free)=0.2048 0.2008 0.2412 n_refl.: 2192 add H (0.00, 0.00): r(all,work,free)=0.2083 0.2050 0.2385 n_refl.: 2192 remove outliers: r(all,work,free)=0.2083 0.2050 0.2385 n_refl.: 2192 |--(resolution: 3.60 - 46.13 A, n_refl.=2192 (all), 9.99 % free)-------------| | | | r_work= 0.2050 r_free= 0.2385 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 6.153419 | | target function (ml) not normalized (work): 12140.696100 | | target function (ml) not normalized (free): 1395.056476 | |-----------------------------------------------------------------------------| End of input processing ======================= ROSETTA/PHENIX X-ray refinement ======================= Output directory: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/rosetta_11 ----------Setting up input files for Rosetta---------- |-starting model--------------------------------------------------------------| | target_work(ml) = 6.15342 r_work = 0.2050 r_free = 0.2385 | |-----------------------------------------------------------------------------| Validation statistics (starting model): Ramachandran outliers = 0.93 % favored = 90.74 % Rotamer outliers = 3.85 % C-beta deviations = 0 Clashscore = 2.92 RMS(bonds) = 0.0050 RMS(angles) = 1.07 MolProbity score = 2.05 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 4xcr_rosetta_in.pdb -mtzfile 4xcr_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=4xcr_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -nstruct 1 Generating 5 models on 1 processors... 1: r_work = 0.2066 r_free = 0.3403 energy = -1477.27 rmsd = 0.951 *** 2: r_work = 0.2042 r_free = 0.3530 energy = -1448.04 rmsd = 0.950 3: r_work = 0.2019 r_free = 0.3447 energy = -1413.26 rmsd = 0.939 4: r_work = 0.2002 r_free = 0.3403 energy = -1422.32 rmsd = 0.935 *** 5: r_work = 0.2123 r_free = 0.3362 energy = -1431.24 rmsd = 0.967 *** |-after ROSETTA---------------------------------------------------------------| | target_work(ml) = 6.03173 r_work = 0.2123 r_free = 0.3362 | |-----------------------------------------------------------------------------| Validation statistics after ROSETTA: Ramachandran outliers = 0.00 % favored = 98.15 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 0.65 RMS(bonds) = 0.0170 RMS(angles) = 1.74 MolProbity score = 0.71 ----------Running phenix.refine (with null strategy)---------- start r_work=0.4859 r_free=0.4299 1_bss r_work=0.1776 r_free=0.3310 end r_work=0.1776 r_free=0.3310 Ramachandran outliers = 0.00 % favored = 98.15 % Rotamer outliers = 0.00 % C-beta deviations = 0 Clashscore = 2.60 RMS(bonds) = 0.0900 RMS(angles) = 2.08 MolProbity score = 1.05 Resolution = 3.60 R-work = 0.1776 R-free = 0.3310 ----------Final results---------- Refined model: 4xcr_rosetta_phenix_001.pdb Final maps: 4xcr_rosetta_phenix_001.mtz Elapsed time: 5624.8s 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.