Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2pej.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2pej/2pej.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 10709 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1791 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1774 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1789 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1760 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1808 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1787 Classifications: {'peptide': 109} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Time building chain proxies: 3.22, per 1000 atoms: 0.30 Number of scatterers: 10709 At special positions: 0 Unit cell: (93.4462, 93.4462, 411.544, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 986 8.00 N 925 7.00 C 3305 6.00 H 5475 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=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: 9.14 Conformation dependent library (CDL) restraints added in 1.2 seconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.565A pdb=" N GLU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 53 through 62 removed outlier: 4.092A pdb=" N LEU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 85 removed outlier: 4.792A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 110 removed outlier: 4.577A pdb=" N SER A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.012A pdb=" N ARG B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 3.777A pdb=" N GLU B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 62 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 85 removed outlier: 4.725A pdb=" N GLU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 Processing helix chain 'C' and resid 3 through 33 removed outlier: 3.767A pdb=" N GLU C 32 " --> pdb=" O GLN C 28 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 33 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 47 removed outlier: 3.632A pdb=" N SER C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.758A pdb=" N LEU C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 109 removed outlier: 5.207A pdb=" N GLU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Proline residue: C 87 - end of helix removed outlier: 3.508A pdb=" N SER C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 31 removed outlier: 3.529A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 65 through 108 removed outlier: 4.567A pdb=" N GLU D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Proline residue: D 87 - end of helix Processing helix chain 'E' and resid 4 through 30 removed outlier: 3.560A pdb=" N GLU E 9 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.561A pdb=" N ALA E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU E 62 " --> pdb=" O GLU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.669A pdb=" N LEU E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 108 removed outlier: 3.535A pdb=" N GLY E 99 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 33 removed outlier: 3.800A pdb=" N LEU F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 47 Processing helix chain 'F' and resid 53 through 63 removed outlier: 3.770A pdb=" N GLU F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 84 removed outlier: 3.730A pdb=" N GLU F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 108 removed outlier: 3.596A pdb=" N LEU F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN F 93 " --> pdb=" O MET F 89 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.86 Time building geometry restraints manager: 5.42 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: 5475 1.15 - 1.32: 909 1.32 - 1.49: 1985 1.49 - 1.66: 2363 1.66 - 1.83: 36 Bond restraints: 10768 Sorted by residual: bond pdb=" N LEU D 57 " pdb=" H LEU D 57 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR D 56 " pdb=" H TYR D 56 " 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 D 79 " pdb=" H ALA D 79 " 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 C 37 " pdb="HE21 GLN C 37 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU D 66 " pdb=" H GLU D 66 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 96.60 - 104.11: 95 104.11 - 111.63: 12425 111.63 - 119.14: 2968 119.14 - 126.66: 4055 126.66 - 134.17: 45 Bond angle restraints: 19588 Sorted by residual: angle pdb=" N PHE C 3 " pdb=" CA PHE C 3 " pdb=" C PHE C 3 " ideal model delta sigma weight residual 111.69 119.66 -7.97 1.23e+00 6.61e-01 4.20e+01 angle pdb=" C HIS A 48 " pdb=" N PRO A 49 " pdb=" CA PRO A 49 " ideal model delta sigma weight residual 119.84 126.47 -6.63 1.25e+00 6.40e-01 2.81e+01 angle pdb=" N GLN E 111 " pdb=" CA GLN E 111 " pdb=" C GLN E 111 " ideal model delta sigma weight residual 108.48 116.85 -8.37 1.65e+00 3.67e-01 2.58e+01 angle pdb=" N LYS D 4 " pdb=" CA LYS D 4 " pdb=" C LYS D 4 " ideal model delta sigma weight residual 112.38 118.50 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N ASN F 64 " pdb=" CA ASN F 64 " pdb=" C ASN F 64 " ideal model delta sigma weight residual 107.23 115.01 -7.78 1.67e+00 3.59e-01 2.17e+01 ... (remaining 19583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4334 17.94 - 35.88: 348 35.88 - 53.82: 177 53.82 - 71.76: 57 71.76 - 89.70: 14 Dihedral angle restraints: 4930 sinusoidal: 2840 harmonic: 2090 Sorted by residual: dihedral pdb=" CA GLU D 32 " pdb=" C GLU D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLU C 2 " pdb=" C GLU C 2 " pdb=" N PHE C 3 " pdb=" CA PHE C 3 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C GLN D 28 " pdb=" N GLN D 28 " pdb=" CA GLN D 28 " pdb=" CB GLN D 28 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 653 0.090 - 0.181: 165 0.181 - 0.271: 24 0.271 - 0.361: 7 0.361 - 0.452: 2 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA GLN D 28 " pdb=" N GLN D 28 " pdb=" C GLN D 28 " pdb=" CB GLN D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE C 3 " pdb=" N PHE C 3 " pdb=" C PHE C 3 " pdb=" CB PHE C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA LEU C 83 " pdb=" N LEU C 83 " pdb=" C LEU C 83 " pdb=" CB LEU C 83 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 848 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 40 " -0.031 2.00e-02 2.50e+03 1.17e-02 5.43e+00 pdb=" CG TRP D 40 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP D 40 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP D 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 40 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 40 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 40 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 40 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP D 40 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP D 40 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 40 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 40 " 0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 40 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP D 40 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 40 " 0.029 2.00e-02 2.50e+03 1.03e-02 4.23e+00 pdb=" CG TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 40 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 40 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 40 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 40 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 40 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 40 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 40 " -0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 40 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 40 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 56 " 0.007 2.00e-02 2.50e+03 8.98e-03 2.42e+00 pdb=" CG TYR A 56 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 56 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 56 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 56 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 56 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 56 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR A 56 " -0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 56 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 56 " -0.012 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.27: 26 1.27 - 2.10: 952 2.10 - 2.93: 28374 2.93 - 3.77: 48439 3.77 - 4.60: 77822 Warning: very small nonbonded interaction distances. Nonbonded interactions: 155613 Sorted by model distance: nonbonded pdb=" HE2 LYS E 4 " pdb=" HE2 PHE F 85 " model vdw 0.437 2.270 nonbonded pdb=" HE2 PHE B 3 " pdb=" CE LYS B 4 " model vdw 0.479 2.750 nonbonded pdb=" O LEU A 109 " pdb=" HE3 LYS C 46 " model vdw sym.op. 0.570 2.620 x,y+1,z nonbonded pdb="HD22 LEU E 20 " pdb="HD12 ILE E 50 " model vdw 0.593 2.440 nonbonded pdb="HD23 LEU E 91 " pdb=" HE3 LYS E 95 " model vdw 0.689 2.440 ... (remaining 155608 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 18 15.91 1 O 986 7.97 1 N 925 6.97 1 C 3305 5.97 1 H 5475 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 5475 of 10709 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 10709 n_use_u_iso = 10709 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 10709 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (10709 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 10709 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 5 through 32 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 35 through 47 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 53 through 62 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 65 through 85 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 87 through 110 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 5 through 31 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 35 through 47 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 53 through 62 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 65 through 85 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 87 through 109 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'C' and resid 3 through 33 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'C' and resid 35 through 47 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'C' and resid 53 through 63 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'C' and resid 65 through 109 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'D' and resid 4 through 31 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'D' and resid 35 through 47 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'D' and resid 53 through 63 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'D' and resid 65 through 108 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'E' and resid 4 through 30 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'E' and resid 37 through 40 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'E' and resid 42 through 45 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'E' and resid 53 through 62 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'E' and resid 65 through 85 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'E' and resid 87 through 108 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'F' and resid 5 through 33 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'F' and resid 35 through 47 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'F' and resid 53 through 63 } helix { serial_number = "28" helix_identifier = "28" selection = chain 'F' and resid 65 through 84 } helix { serial_number = "29" helix_identifier = "29" selection = chain 'F' and resid 86 through 108 } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2pej_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 5475 occupancy sum: 5475.00 (% of total atoms 53.37) Rotatable: count: 1628 occupancy sum: 1628.00 (% of total atoms 15.87) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2921 153 0.4360 0.4718 7.382 7.48| | 2: 6.98 - 5.58 1.00 2800 148 0.4215 0.5156 6.69 6.77| | 3: 5.58 - 4.89 0.99 2720 172 0.3241 0.3521 6.1102 6.1196| | 4: 4.89 - 4.45 0.99 2703 139 0.3764 0.4024 5.9987 6.0922| | 5: 4.45 - 4.13 0.99 2734 139 0.4458 0.4594 5.7787 5.9358| | 6: 4.13 - 3.89 0.99 2654 143 0.4796 0.5068 5.5643 5.7591| | 7: 3.89 - 3.70 0.99 2711 136 0.4992 0.5177 5.3566 5.4641| | 8: 3.70 - 3.54 0.99 2685 135 0.4835 0.5326 5.105 5.1893| | 9: 3.54 - 3.40 1.00 2668 154 0.4775 0.4950 4.9066 4.9642| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 19.99 - 6.98 2921 153 0.49 51.09 0.92 0.50 544086.03| | 2: 6.98 - 5.58 2800 148 0.30 66.73 0.95 0.53 214995.99| | 3: 5.58 - 4.89 2720 172 0.69 35.94 1.11 0.64 42450.73| | 4: 4.89 - 4.45 2703 139 0.79 27.26 1.44 0.80 27205.46| | 5: 4.45 - 4.13 2734 139 0.79 26.83 1.66 0.95 19864.90| | 6: 4.13 - 3.89 2654 143 0.78 28.28 1.78 1.04 13980.59| | 7: 3.89 - 3.70 2711 136 0.78 28.46 1.82 1.08 9226.84| | 8: 3.70 - 3.54 2685 135 0.77 29.33 1.76 1.05 6022.37| | 9: 3.54 - 3.40 2668 154 0.81 26.83 1.72 0.96 3599.32| |alpha: min = 0.50 max = 1.08 mean = 0.83| |beta: min = 3599.32 max = 544086.03 mean = 102556.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.99 mean = 35.92| |phase err.(test): min = 0.00 max = 89.77 mean = 35.86| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 5293 Z= 0.680 Angle : 1.400 9.726 7134 Z= 0.922 Chirality : 0.084 0.452 851 Planarity : 0.004 0.013 913 Dihedral : 18.241 89.696 2067 Min Nonbonded Distance : 0.751 Molprobity Statistics. All-atom Clashscore : 33.12 Ramachandran Plot: Outliers : 2.19 % Allowed : 15.16 % Favored : 82.66 % Rotamer: Outliers : 11.77 % Allowed : 11.09 % Favored : 77.13 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.00 (0.23), residues: 640 helix: -3.54 (0.15), residues: 557 sheet: None (None), residues: 0 loop : -4.73 (0.48), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 103 TYR 0.018 0.004 TYR B 56 PHE 0.016 0.002 PHE C 44 TRP 0.026 0.005 TRP D 40 HIS 0.005 0.002 HIS A 101 Individual atomic B min max mean iso aniso Overall: 78.72 190.99 119.02 0.81 5234 0 Protein: 78.72 190.99 119.02 0.81 5234 0 Chain A: 78.72 132.62 102.27 N/A 876 0 Chain B: 94.80 147.44 118.99 N/A 867 0 Chain C: 85.82 131.82 108.29 N/A 876 0 Chain D: 84.11 124.52 104.22 N/A 860 0 Chain E: 118.58 190.99 151.35 N/A 883 0 Chain F: 108.44 147.31 128.51 N/A 872 0 Histogram: Values Number of atoms 78.72 - 89.95 313 89.95 - 101.17 702 101.17 - 112.40 1380 112.40 - 123.63 856 123.63 - 134.86 864 134.86 - 146.08 713 146.08 - 157.31 118 157.31 - 168.54 78 168.54 - 179.76 76 179.76 - 190.99 134 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25915 (all), 5.09 % free)------------| | | | r_work= 0.4270 r_free= 0.4614 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 5.895891 | | target function (ml) not normalized (work): 145015.334724 | | target function (ml) not normalized (free): 7902.559553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 re-set all scales: r(all,work,free)=0.4288 0.4270 0.4614 n_refl.: 25915 remove outliers: r(all,work,free)=0.4266 0.4247 0.4614 n_refl.: 25903 overall B=-17.33 to atoms: r(all,work,free)=0.3800 0.3778 0.4198 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 remove outliers: r(all,work,free)=0.2653 0.2628 0.3103 n_refl.: 25903 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 19.988-16.886 98.02 93 6 0.4981 1064.578 868.154 1.015 0.889 0.304 16.855-15.102 97.06 96 3 0.3850 1222.025 1136.069 1.082 0.884 0.305 15.055-13.543 96.90 117 8 0.3123 1277.787 1208.209 1.082 0.887 0.296 13.531-12.124 98.40 177 8 0.2353 1772.472 1690.272 1.270 0.886 0.298 12.122-10.863 98.00 231 14 0.2470 1913.581 1885.994 1.269 0.887 0.253 10.859-9.734 96.81 316 18 0.2173 1837.359 1794.637 1.328 0.888 0.250 9.728-8.719 98.71 440 18 0.2370 1558.782 1516.125 1.331 0.888 0.242 8.719-7.816 98.08 582 32 0.2649 1152.027 1095.392 1.318 0.888 0.235 7.812-7.000 98.44 835 46 0.3179 832.644 767.986 1.214 0.888 0.227 6.996-6.272 99.42 1131 61 0.3629 543.615 499.913 1.102 0.888 0.210 6.270-5.619 99.76 1581 82 0.3397 434.382 397.799 0.922 0.888 0.170 5.619-5.035 99.26 2133 136 0.2723 456.309 441.157 0.978 0.887 0.145 5.034-4.511 99.59 2966 163 0.2174 514.948 493.021 1.118 0.887 0.133 4.511-4.041 99.19 4079 206 0.2150 428.987 409.503 1.196 0.886 0.102 4.041-3.621 99.33 5632 291 0.2586 273.439 257.563 1.179 0.885 0.034 3.621-3.400 99.53 4175 227 0.2771 176.375 161.769 1.056 0.884 0.036 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9964 b_overall=0.3094 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.952115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.199475 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2826 0.3261 0.0435 0.004 0.7 7.9 1.6 9.9 0 0.125 0.2786 0.3238 0.0453 0.004 0.7 8.1 1.4 10.2 0 0.250 0.2760 0.3232 0.0471 0.004 0.7 8.6 1.6 9.9 0 0.500 0.2724 0.3226 0.0502 0.005 0.7 9.4 1.2 10.1 0 1.000 0.2695 0.3213 0.0518 0.006 0.8 11.4 1.9 10.1 0 2.000 0.2654 0.3172 0.0518 0.008 0.9 13.3 2.2 10.4 0 3.000 0.2635 0.3168 0.0533 0.009 1.0 16.5 2.3 11.3 0 4.000 0.2619 0.3159 0.0540 0.010 1.1 18.6 2.8 11.8 0 5.000 0.2592 0.3140 0.0547 0.012 1.2 20.4 2.7 11.9 0 6.000 0.2585 0.3137 0.0551 0.013 1.3 23.1 3.6 12.1 0 7.000 0.2577 0.3134 0.0557 0.014 1.3 24.4 3.6 12.8 0 8.000 0.2559 0.3123 0.0564 0.015 1.4 26.3 3.6 13.1 0 9.000 0.2544 0.3117 0.0573 0.016 1.4 27.3 3.9 13.1 0 10.000 0.2567 0.3127 0.0560 0.015 1.4 25.7 3.8 12.8 0 8.476 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2826 0.3261 0.0435 0.004 0.7 7.9 1.6 9.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.26 32.61 4.35 0.568 101.402 0.199 0.093 28.32 32.67 4.36 1.749 101.456 0.006 0.093 27.98 32.43 4.45 1.896 101.451 0.025 0.091 27.36 31.95 4.59 3.184 101.494 0.100 0.087 26.49 31.20 4.72 8.427 102.610 0.199 0.081 26.66 31.47 4.82 6.367 102.202 0.299 0.083 26.20 31.05 4.85 9.890 103.228 0.399 0.080 25.92 30.83 4.91 13.948 104.238 0.499 0.077 25.86 30.81 4.95 14.766 104.464 0.598 0.077 25.82 30.80 4.98 15.411 104.642 0.698 0.076 25.72 30.73 5.01 16.719 105.043 0.798 0.075 25.68 30.72 5.04 17.330 105.215 0.898 0.075 25.63 30.68 5.05 18.149 105.458 0.997 0.075 max suggested for this run: 20.28 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.997 Accepted refinement result: 25.63 30.68 5.05 18.149 105.458 0.997 0.075 Individual atomic B min max mean iso aniso Overall: 58.91 225.75 109.99 13.99 5234 0 Protein: 58.91 225.75 109.99 13.99 5234 0 Chain A: 58.91 179.53 92.80 N/A 876 0 Chain B: 73.63 187.91 110.13 N/A 867 0 Chain C: 64.28 204.26 100.39 N/A 876 0 Chain D: 62.93 183.86 95.68 N/A 860 0 Chain E: 96.25 225.75 142.23 N/A 883 0 Chain F: 87.44 188.27 118.23 N/A 872 0 Histogram: Values Number of atoms 58.91 - 75.60 482 75.60 - 92.28 1211 92.28 - 108.96 1139 108.96 - 125.65 1068 125.65 - 142.33 575 142.33 - 159.01 401 159.01 - 175.70 240 175.70 - 192.38 84 192.38 - 209.06 23 209.06 - 225.75 11 =========================== Idealize ADP of riding H ========================== r_work=0.2563 r_free=0.3068 r_work=0.2547 r_free=0.3042 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2547 r_free= 0.3042 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.072717 | | target function (ls_wunit_k1) not normalized (work): 1787.672389 | | target function (ls_wunit_k1) not normalized (free): 140.277261 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2573 0.2547 0.3042 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3729 0.3703 0.4197 n_refl.: 25903 remove outliers: r(all,work,free)=0.3729 0.3703 0.4197 n_refl.: 25903 overall B=-0.11 to atoms: r(all,work,free)=0.3727 0.3700 0.4195 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2533 0.2505 0.3048 n_refl.: 25903 remove outliers: r(all,work,free)=0.2533 0.2505 0.3048 n_refl.: 25903 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 19.988-16.886 98.02 93 6 0.4965 794.855 657.846 0.782 0.994 0.281 16.855-15.102 97.06 96 3 0.3770 912.411 834.996 0.872 0.990 0.295 15.055-13.543 96.90 117 8 0.3120 954.045 902.506 0.926 0.991 0.300 13.531-12.124 98.40 177 8 0.2207 1323.395 1265.533 1.084 0.992 0.300 12.122-10.863 98.00 231 14 0.2153 1428.753 1415.323 1.037 0.992 0.235 10.859-9.734 96.81 316 18 0.1919 1371.842 1351.037 1.098 0.994 0.230 9.728-8.719 98.71 440 18 0.1980 1163.846 1145.572 1.103 0.994 0.227 8.719-7.816 98.08 582 32 0.2233 860.148 836.421 1.103 0.994 0.223 7.812-7.000 98.44 835 46 0.2624 621.684 591.752 1.021 0.994 0.200 6.996-6.272 99.42 1131 61 0.3079 405.884 383.201 0.944 0.994 0.170 6.270-5.619 99.76 1581 82 0.3076 324.327 303.157 0.838 0.995 0.150 5.619-5.035 99.26 2133 136 0.2539 340.698 328.497 0.871 0.995 0.115 5.034-4.511 99.59 2966 163 0.2144 384.480 371.087 0.988 0.995 0.100 4.511-4.041 99.19 4079 206 0.2167 320.298 309.009 1.054 0.995 0.070 4.041-3.621 99.33 5632 291 0.2808 204.160 191.640 1.024 0.995 0.030 3.621-3.400 99.53 4175 227 0.3133 131.688 118.354 0.907 0.994 0.025 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.3800 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.674141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.041729 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2511 0.3036 0.0524 0.003 0.5 6.8 1.6 6.7 0 0.125 0.2455 0.2987 0.0531 0.003 0.6 8.2 1.6 7.8 0 0.250 0.2407 0.2948 0.0541 0.004 0.7 9.5 1.4 9.0 0 0.500 0.2370 0.2911 0.0541 0.006 0.8 10.9 1.7 10.1 0 1.000 0.2341 0.2898 0.0557 0.010 1.1 12.8 2.2 10.2 0 2.000 0.2321 0.2888 0.0567 0.015 1.3 13.8 2.3 10.4 0 3.000 0.2306 0.2878 0.0571 0.020 1.5 15.3 2.5 10.2 0 4.000 0.2298 0.2874 0.0576 0.022 1.6 16.2 2.2 10.2 0 5.000 0.2253 0.2818 0.0565 0.022 1.9 27.4 4.7 15.4 0 6.000 0.2244 0.2811 0.0567 0.025 2.1 31.1 5.5 16.6 0 7.000 0.2235 0.2806 0.0571 0.027 2.2 31.5 5.5 17.2 0 8.000 0.2226 0.2796 0.0570 0.029 2.3 32.6 6.2 17.2 0 9.000 0.2219 0.2796 0.0577 0.032 2.5 34.2 6.7 18.1 0 10.000 0.2315 0.2881 0.0566 0.018 1.4 14.4 2.2 10.1 0 3.337 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2370 0.2911 0.0541 0.006 0.8 10.9 1.7 10.1 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.70 29.11 5.41 19.074 122.002 0.042 5.879 30.27 34.15 3.88 16.953 133.111 0.001 5.962 26.41 30.88 4.47 15.644 128.094 0.005 5.910 24.61 29.46 4.85 17.939 125.746 0.021 5.863 23.79 28.88 5.09 19.033 123.895 0.042 5.843 23.56 28.74 5.18 19.508 123.434 0.063 5.837 23.49 28.73 5.24 19.879 123.416 0.083 5.835 23.29 28.63 5.34 19.903 123.138 0.104 5.830 23.26 28.63 5.37 20.051 123.137 0.125 5.830 23.24 28.63 5.39 20.192 123.172 0.146 5.829 23.22 28.63 5.41 20.314 123.212 0.167 5.829 23.21 28.63 5.42 20.420 123.252 0.188 5.828 23.21 28.64 5.43 20.511 123.286 0.209 5.828 max suggested for this run: 24.40 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.146 Accepted refinement result: 23.24 28.63 5.39 20.192 123.172 0.146 5.829 Individual atomic B min max mean iso aniso Overall: 53.86 220.64 112.28 16.20 5234 0 Protein: 53.86 220.64 112.28 16.20 5234 0 Chain A: 53.86 179.66 95.54 N/A 876 0 Chain B: 68.53 186.78 112.44 N/A 867 0 Chain C: 60.39 204.49 102.29 N/A 876 0 Chain D: 57.83 183.12 98.33 N/A 860 0 Chain E: 91.15 220.64 143.97 N/A 883 0 Chain F: 82.34 184.96 120.61 N/A 872 0 Histogram: Values Number of atoms 53.86 - 70.53 247 70.53 - 87.21 841 87.21 - 103.89 1165 103.89 - 120.57 1145 120.57 - 137.25 834 137.25 - 153.93 523 153.93 - 170.61 306 170.61 - 187.28 120 187.28 - 203.96 36 203.96 - 220.64 17 =========================== Idealize ADP of riding H ========================== r_work=0.2324 r_free=0.2863 r_work=0.2329 r_free=0.2862 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2329 r_free= 0.2862 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.828103 | | target function (ml) not normalized (work): 143278.081135 | | target function (ml) not normalized (free): 7872.957537 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2357 0.2329 0.2862 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3717 0.3693 0.4147 n_refl.: 25903 remove outliers: r(all,work,free)=0.3717 0.3693 0.4147 n_refl.: 25903 overall B=-0.83 to atoms: r(all,work,free)=0.3692 0.3667 0.4125 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2350 0.2322 0.2868 n_refl.: 25903 remove outliers: r(all,work,free)=0.2350 0.2322 0.2868 n_refl.: 25903 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 19.988-16.886 98.02 93 6 0.4906 794.855 663.902 0.821 0.980 0.290 16.855-15.102 97.06 96 3 0.3803 912.411 830.107 0.848 0.975 0.285 15.055-13.543 96.90 117 8 0.3149 954.045 900.588 0.841 0.979 0.261 13.531-12.124 98.40 177 8 0.2279 1323.395 1257.708 0.958 0.978 0.250 12.122-10.863 98.00 231 14 0.2211 1428.753 1408.104 1.027 0.980 0.225 10.859-9.734 96.81 316 18 0.1947 1371.842 1348.699 1.091 0.983 0.220 9.728-8.719 98.71 440 18 0.2020 1163.846 1140.686 1.104 0.983 0.221 8.719-7.816 98.08 582 32 0.2323 860.148 831.546 1.107 0.985 0.211 7.812-7.000 98.44 835 46 0.2849 621.684 584.229 1.026 0.986 0.201 6.996-6.272 99.42 1131 61 0.3189 405.884 379.799 0.975 0.988 0.171 6.270-5.619 99.76 1581 82 0.3265 324.327 299.609 0.860 0.990 0.141 5.619-5.035 99.26 2133 136 0.2354 340.698 327.902 0.894 0.993 0.116 5.034-4.511 99.59 2966 163 0.1798 384.480 372.626 1.007 0.996 0.101 4.511-4.041 99.19 4079 206 0.1742 320.298 310.048 1.073 0.999 0.061 4.041-3.621 99.33 5632 291 0.2276 204.160 193.708 1.063 1.004 0.016 3.621-3.400 99.53 4175 227 0.2651 131.688 120.389 0.920 1.008 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-2.9777 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2322 r_free=0.2868 After: r_work=0.2323 r_free=0.2868 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.879276 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037199 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2338 0.2882 0.0543 0.005 0.8 11.4 1.4 9.6 0 0.125 0.2331 0.2873 0.0542 0.005 0.8 11.2 1.6 9.6 0 0.250 0.2325 0.2868 0.0543 0.005 0.8 11.2 1.7 9.6 0 0.500 0.2313 0.2860 0.0547 0.006 0.9 11.4 1.7 9.7 0 1.000 0.2267 0.2834 0.0567 0.012 1.2 15.2 2.0 10.1 0 2.000 0.2244 0.2820 0.0576 0.016 1.6 17.0 2.2 9.7 0 3.000 0.2220 0.2819 0.0599 0.016 2.0 23.3 3.1 11.8 0 4.000 0.2207 0.2825 0.0618 0.018 2.2 28.0 4.4 13.1 0 5.000 0.2195 0.2819 0.0624 0.021 2.4 30.0 4.8 13.5 0 6.000 0.2187 0.2811 0.0624 0.024 2.6 28.8 4.4 12.3 0 7.000 0.2177 0.2806 0.0628 0.026 2.8 33.6 4.8 13.8 0 8.000 0.2170 0.2807 0.0637 0.028 2.9 35.2 5.2 14.3 0 9.000 0.2166 0.2800 0.0635 0.030 3.1 34.6 5.0 14.3 0 10.000 0.2226 0.2818 0.0592 0.015 1.8 22.2 2.7 11.1 0 3.440 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2331 0.2873 0.0542 0.005 0.8 11.2 1.6 9.6 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.31 28.73 5.42 20.072 123.249 0.037 5.835 29.02 32.99 3.97 17.413 131.899 0.001 5.960 27.89 32.09 4.20 16.991 131.762 0.005 5.945 25.79 30.48 4.69 18.748 128.345 0.019 5.906 24.20 29.33 5.14 18.408 125.181 0.037 5.857 23.74 28.99 5.25 18.933 124.417 0.056 5.841 23.49 28.77 5.28 19.345 124.119 0.074 5.832 23.34 28.64 5.30 19.694 123.994 0.093 5.827 23.25 28.60 5.35 19.979 124.065 0.112 5.824 23.19 28.57 5.38 20.247 124.165 0.130 5.822 23.08 28.54 5.46 20.346 123.521 0.149 5.820 23.06 28.53 5.47 20.454 123.546 0.167 5.819 23.03 28.52 5.49 20.546 123.571 0.186 5.819 max suggested for this run: 24.65 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.186 Accepted refinement result: 23.03 28.52 5.49 20.546 123.571 0.186 5.819 Individual atomic B min max mean iso aniso Overall: 48.02 223.41 112.10 17.29 5234 0 Protein: 48.02 223.41 112.10 17.29 5234 0 Chain A: 48.02 183.20 95.21 N/A 876 0 Chain B: 63.77 191.73 112.14 N/A 867 0 Chain C: 56.40 204.72 102.08 N/A 876 0 Chain D: 52.00 186.06 98.19 N/A 860 0 Chain E: 85.31 223.41 143.75 N/A 883 0 Chain F: 76.50 186.75 120.79 N/A 872 0 Histogram: Values Number of atoms 48.02 - 65.56 127 65.56 - 83.10 713 83.10 - 100.64 1212 100.64 - 118.18 1216 118.18 - 135.72 898 135.72 - 153.26 555 153.26 - 170.80 332 170.80 - 188.34 119 188.34 - 205.88 46 205.88 - 223.41 16 =========================== Idealize ADP of riding H ========================== r_work=0.2303 r_free=0.2852 r_work=0.2304 r_free=0.2853 ----------X-ray data---------- |--(resolution: 3.40 - 19.99 A, n_refl.=25903 (all), 5.09 % free)------------| | | | r_work= 0.2304 r_free= 0.2853 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ml) (work): 5.818368 | | target function (ml) not normalized (work): 143038.746958 | | target function (ml) not normalized (free): 7866.759413 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.99 - 6.98 0.98 2910 153 0.2469 0.3000 7.1141 7.2633| | 2: 6.98 - 5.58 1.00 2800 148 0.3250 0.3977 6.4889 6.6077| | 3: 5.58 - 4.89 0.99 2720 172 0.2217 0.2746 6.0205 6.1097| | 4: 4.89 - 4.45 0.99 2703 139 0.1687 0.2066 5.8205 5.9519| | 5: 4.45 - 4.13 0.99 2734 139 0.1657 0.2100 5.6595 5.8651| | 6: 4.13 - 3.89 0.99 2654 143 0.1970 0.2766 5.5338 5.7582| | 7: 3.89 - 3.70 0.99 2711 136 0.2191 0.2744 5.3827 5.5974| | 8: 3.70 - 3.54 0.99 2684 135 0.2547 0.3027 5.2 5.2909| | 9: 3.54 - 3.40 1.00 2668 154 0.2550 0.3113 5.0036 5.0985| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 19.99 - 6.98 2910 153 0.73 30.62 1.00 0.99 290881.43| | 2: 6.98 - 5.58 2800 148 0.52 49.35 1.00 0.97 126593.26| | 3: 5.58 - 4.89 2720 172 0.78 28.14 1.00 0.98 36546.71| | 4: 4.89 - 4.45 2703 139 0.86 20.26 1.01 1.01 22426.18| | 5: 4.45 - 4.13 2734 139 0.87 19.87 1.01 1.03 16931.32| | 6: 4.13 - 3.89 2654 143 0.84 23.09 1.04 1.03 13444.40| | 7: 3.89 - 3.70 2711 136 0.82 25.29 1.02 1.01 10362.05| | 8: 3.70 - 3.54 2684 135 0.79 28.20 0.99 0.98 7399.47| | 9: 3.54 - 3.40 2668 154 0.81 26.38 0.98 0.91 4840.97| |alpha: min = 0.91 max = 1.03 mean = 0.99| |beta: min = 4840.97 max = 290881.43 mean = 61169.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 89.98 mean = 28.02| |phase err.(test): min = 0.00 max = 89.99 mean = 28.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2332 0.2304 0.2853 n_refl.: 25903 re-set all scales: r(all,work,free)=0.3722 0.3697 0.4151 n_refl.: 25903 remove outliers: r(all,work,free)=0.3722 0.3697 0.4151 n_refl.: 25903 overall B=-0.99 to atoms: r(all,work,free)=0.3691 0.3667 0.4124 n_refl.: 25903 bulk-solvent and scaling: r(all,work,free)=0.2333 0.2305 0.2855 n_refl.: 25903 remove outliers: r(all,work,free)=0.2333 0.2305 0.2855 n_refl.: 25903 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 19.988-16.886 98.02 93 6 0.4909 794.855 663.713 0.831 0.975 0.290 16.855-15.102 97.06 96 3 0.3827 912.411 829.165 0.859 0.971 0.285 15.055-13.543 96.90 117 8 0.3148 954.045 900.246 0.850 0.975 0.261 13.531-12.124 98.40 177 8 0.2317 1323.395 1256.110 0.967 0.974 0.250 12.122-10.863 98.00 231 14 0.2236 1428.753 1407.668 1.037 0.976 0.225 10.859-9.734 96.81 316 18 0.1979 1371.842 1347.242 1.100 0.979 0.221 9.728-8.719 98.71 440 18 0.2044 1163.846 1139.262 1.112 0.980 0.221 8.719-7.816 98.08 582 32 0.2362 860.148 830.218 1.116 0.982 0.211 7.812-7.000 98.44 835 46 0.2903 621.684 582.471 1.034 0.983 0.202 6.996-6.272 99.42 1131 61 0.3243 405.884 378.831 0.989 0.986 0.182 6.270-5.619 99.76 1581 82 0.3280 324.327 299.411 0.863 0.989 0.141 5.619-5.035 99.26 2133 136 0.2333 340.698 327.964 0.891 0.992 0.111 5.034-4.511 99.59 2966 163 0.1749 384.480 373.403 1.009 0.997 0.101 4.511-4.041 99.19 4079 206 0.1680 320.298 310.677 1.078 1.001 0.061 4.041-3.621 99.33 5632 291 0.2197 204.160 194.389 1.077 1.008 0.014 3.621-3.400 99.53 4175 227 0.2593 131.688 120.681 0.923 1.013 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.5619 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4270 0.4614 0.010 1.400 78.7 191.0 119.0 0 0.000 1_bss: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_settarget: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_weight: 0.2628 0.3103 0.010 1.400 61.4 173.7 101.7 0 0.000 1_xyzrec: 0.2826 0.3261 0.004 0.674 61.4 173.7 101.7 0 0.225 1_adp: 0.2563 0.3068 0.004 0.674 58.9 225.7 110.0 0 0.225 1_regHadp: 0.2547 0.3042 0.004 0.674 58.9 225.7 110.0 0 0.225 2_bss: 0.2505 0.3048 0.004 0.674 58.8 225.6 109.9 0 0.225 2_settarget: 0.2505 0.3048 0.004 0.674 58.8 225.6 109.9 0 0.225 2_updatecdl: 0.2505 0.3048 0.004 0.730 58.8 225.6 109.9 0 0.225 2_weight: 0.2505 0.3048 0.004 0.730 58.8 225.6 109.9 0 0.225 2_xyzrec: 0.2370 0.2911 0.006 0.825 58.8 225.6 109.9 0 0.221 2_adp: 0.2324 0.2863 0.006 0.825 53.9 220.6 112.3 0 0.221 2_regHadp: 0.2329 0.2862 0.006 0.825 53.9 220.6 112.3 0 0.221 3_bss: 0.2322 0.2868 0.006 0.825 53.0 219.8 111.4 0 0.221 3_settarget: 0.2322 0.2868 0.006 0.825 53.0 219.8 111.4 0 0.221 3_updatecdl: 0.2322 0.2868 0.006 0.848 53.0 219.8 111.4 0 0.221 3_setrh: 0.2323 0.2868 0.006 0.848 53.0 219.8 111.4 0 0.221 3_weight: 0.2323 0.2868 0.006 0.848 53.0 219.8 111.4 0 0.221 3_xyzrec: 0.2331 0.2873 0.005 0.806 53.0 219.8 111.4 0 0.222 3_adp: 0.2303 0.2852 0.005 0.806 48.0 223.4 112.1 0 0.222 3_regHadp: 0.2304 0.2853 0.005 0.806 48.0 223.4 112.1 0 0.222 end: 0.2305 0.2855 0.005 0.806 47.0 222.4 111.1 0 0.222 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2pej_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2pej_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 16.6800 Refinement macro-cycles (run) : 385.2600 Write final files (write_after_run_outputs) : 24.5300 Total : 426.4700 Total CPU time: 8.12 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:38:53 PDT -0700 (1716251933.98 s) Start R-work = 0.2628, R-free = 0.3103 Final R-work = 0.2305, R-free = 0.2855 =============================================================================== Job complete usr+sys time: 520.78 seconds wall clock time: 21 minutes 54.92 seconds (1314.92 seconds total)