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/1jkt.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1jkt/1jkt.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1jkt/1jkt.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1jkt/1jkt.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1jkt.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1jkt.pdb" } 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 Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Time building chain proxies: 2.79, per 1000 atoms: 0.31 Number of scatterers: 8966 At special positions: 0 Unit cell: (58.37, 58.37, 212.61, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 850 8.00 N 744 7.00 C 2876 6.00 H 4488 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: 8.01 Conformation dependent library (CDL) restraints added in 1.0 seconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 3 sheets defined 31.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 113 through 133 removed outlier: 3.914A pdb=" N PHE A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.522A pdb=" N MET A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.651A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.752A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.524A pdb=" N GLN A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.819A pdb=" N ARG B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 113 through 133 removed outlier: 3.664A pdb=" N THR B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.269A pdb=" N THR B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.998A pdb=" N LEU B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.753A pdb=" N ARG B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 30 removed outlier: 3.736A pdb=" N PHE A 43 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 28 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 40 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 93 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 89 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 92 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A 81 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= C, first strand: chain 'B' and resid 43 through 45 82 hydrogen bonds defined for protein. 237 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: 7.55 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 4486 1.16 - 1.34: 1456 1.34 - 1.52: 2031 1.52 - 1.70: 1071 1.70 - 1.89: 14 Bond restraints: 9058 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" H PHE A 162 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN A 38 " pdb=" H GLN A 38 " 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 B 192 " pdb=" H GLU B 192 " 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 A 271 " pdb="HE22 GLN A 271 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 111 " pdb=" H LEU A 111 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.61: 90 102.61 - 110.47: 9016 110.47 - 118.34: 3303 118.34 - 126.20: 3941 126.20 - 134.06: 78 Bond angle restraints: 16428 Sorted by residual: angle pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" C LEU B 196 " ideal model delta sigma weight residual 113.18 99.40 13.78 1.21e+00 6.83e-01 1.30e+02 angle pdb=" N PHE B 183 " pdb=" CA PHE B 183 " pdb=" C PHE B 183 " ideal model delta sigma weight residual 112.87 125.82 -12.95 1.20e+00 6.94e-01 1.16e+02 angle pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" C PHE A 178 " ideal model delta sigma weight residual 110.17 126.12 -15.95 1.51e+00 4.39e-01 1.12e+02 angle pdb=" N LEU A 196 " pdb=" CA LEU A 196 " pdb=" C LEU A 196 " ideal model delta sigma weight residual 113.18 100.49 12.69 1.21e+00 6.83e-01 1.10e+02 angle pdb=" N PHE B 104 " pdb=" CA PHE B 104 " pdb=" C PHE B 104 " ideal model delta sigma weight residual 113.97 101.08 12.89 1.28e+00 6.10e-01 1.01e+02 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3662 17.98 - 35.97: 340 35.97 - 53.95: 149 53.95 - 71.94: 58 71.94 - 89.92: 17 Dihedral angle restraints: 4226 sinusoidal: 2310 harmonic: 1916 Sorted by residual: dihedral pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual 123.40 133.58 -10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C THR B 180 " pdb=" N THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual -122.00 -132.09 10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C LYS A 175 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " pdb=" CB LYS A 175 " ideal model delta harmonic sigma weight residual -122.60 -132.24 9.64 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 524 0.131 - 0.262: 137 0.262 - 0.393: 16 0.393 - 0.524: 6 0.524 - 0.655: 3 Chirality restraints: 686 Sorted by residual: chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA THR B 180 " pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CB THR B 180 " both_signs ideal model delta sigma weight residual False 2.53 1.92 0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" CA GLU A 192 " pdb=" N GLU A 192 " pdb=" C GLU A 192 " pdb=" CB GLU A 192 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.34e+00 ... (remaining 683 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 234 " 0.133 2.00e-02 2.50e+03 5.31e-02 8.47e+01 pdb=" CG TYR A 234 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 234 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 234 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 234 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 234 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 234 " 0.094 2.00e-02 2.50e+03 pdb=" HD1 TYR A 234 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 234 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 234 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 191 " 0.113 2.00e-02 2.50e+03 4.82e-02 6.98e+01 pdb=" CG TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 191 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 191 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 191 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 191 " 0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR B 191 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 191 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR B 191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 208 " 0.113 2.00e-02 2.50e+03 4.57e-02 6.26e+01 pdb=" CG TYR A 208 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 208 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 208 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 208 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 208 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 208 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 208 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR A 208 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR A 208 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 208 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 208 " -0.009 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.54: 131 1.54 - 2.31: 2796 2.31 - 3.07: 28697 3.07 - 3.84: 38033 3.84 - 4.60: 61742 Warning: very small nonbonded interaction distances. Nonbonded interactions: 131399 Sorted by model distance: nonbonded pdb=" HA LYS A 276 " pdb=" HZ2 LYS A 276 " model vdw 0.775 2.270 nonbonded pdb="HD12 LEU B 218 " pdb=" H GLY B 219 " model vdw 0.996 2.270 nonbonded pdb=" H ASN A 75 " pdb="HD22 ASN A 75 " model vdw 1.050 2.100 nonbonded pdb=" O THR A 225 " pdb=" H ASN A 228 " model vdw 1.052 1.850 nonbonded pdb=" HA ILE A 252 " pdb="HD12 LEU A 255 " model vdw 1.091 2.440 ... (remaining 131394 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 8 15.91 1 O 850 7.97 1 N 744 6.97 1 C 2876 5.97 1 H 4488 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: 4488 of 8966 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8966 n_use_u_iso = 8966 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 = 8966 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8966 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8966 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 9 through 11 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 58 through 68 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 101 through 104 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 106 through 108 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 113 through 133 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 142 through 144 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 186 through 189 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 196 through 209 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 222 through 231 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 238 through 241 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 246 through 255 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 266 through 271 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 273 through 275 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'B' and resid 9 through 11 helix_type = alpha pi *3_10 unknown } helix { serial_number = "15" helix_identifier = "15" selection = chain 'B' and resid 58 through 69 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 101 through 103 helix_type = alpha pi *3_10 unknown } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 113 through 133 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 142 through 144 helix_type = alpha pi *3_10 unknown } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 199 through 212 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'B' and resid 222 through 230 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'B' and resid 248 through 253 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'B' and resid 266 through 270 } sheet { first_strand = chain 'A' and resid 25 through 30 sheet_id = " A" strand { selection = chain 'A' and resid 39 through 45 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 43 and name N bond_start_previous = chain 'A' and resid 26 and name O } strand { selection = chain 'A' and resid 88 through 93 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 91 and name N bond_start_previous = chain 'A' and resid 42 and name O } strand { selection = chain 'A' and resid 79 through 84 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 83 and name N bond_start_previous = chain 'A' and resid 90 and name O } } sheet { first_strand = chain 'B' and resid 28 through 30 sheet_id = " B" strand { selection = chain 'B' and resid 39 through 41 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 41 and name N bond_start_previous = chain 'B' and resid 28 and name O } } sheet { first_strand = chain 'B' and resid 43 through 45 sheet_id = " C" strand { selection = chain 'B' and resid 88 through 90 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 89 and name N bond_start_previous = chain 'B' and resid 44 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1jkt_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4488 occupancy sum: 4488.00 (% of total atoms 50.10) Rotatable: count: 1226 occupancy sum: 1226.00 (% of total atoms 13.68) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8549 (all), 10.56 % free)-------------| | | | r_work= 0.3487 r_free= 0.4112 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958556 | | target function (ml) not normalized (work): 30267.121761 | | target function (ml) not normalized (free): 3647.010734 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.81 - 6.29 0.98 1324 168 0.3612 0.4250 4.6265 4.6744| | 2: 6.28 - 5.01 0.95 1261 150 0.3316 0.4130 4.1035 4.1876| | 3: 5.01 - 4.38 0.96 1313 141 0.3048 0.3765 3.9593 4.1225| | 4: 4.38 - 3.99 0.96 1271 167 0.3456 0.3921 3.8353 3.8742| | 5: 3.99 - 3.70 0.94 1269 134 0.3597 0.4227 3.6703 3.736| | 6: 3.70 - 3.49 0.90 1208 143 0.4145 0.4423 3.5068 3.5292| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.81 - 6.29 1324 168 0.57 47.00 1.03 0.05 2494.09| | 2: 6.28 - 5.01 1261 150 0.48 53.95 0.88 0.04 1381.54| | 3: 5.01 - 4.38 1313 141 0.60 44.72 1.05 0.04 742.67| | 4: 4.38 - 3.99 1271 167 0.59 45.77 1.00 0.04 612.41| | 5: 3.99 - 3.70 1269 134 0.52 51.28 1.02 0.04 452.69| | 6: 3.70 - 3.49 1208 143 0.47 55.01 0.99 0.03 305.83| |alpha: min = 0.03 max = 0.05 mean = 0.04| |beta: min = 305.83 max = 2494.09 mean = 1012.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.95 mean = 49.53| |phase err.(test): min = 1.00 max = 89.86 mean = 50.50| |-----------------------------------------------------------------------------| ----------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 0.095 4570 Z= 0.631 Angle : 1.826 19.340 6174 Z= 1.153 Chirality : 0.125 0.655 686 Planarity : 0.009 0.101 798 Dihedral : 19.361 89.293 1728 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 92.65 Ramachandran Plot: Outliers : 16.42 % Allowed : 22.45 % Favored : 61.13 % Rotamer: Outliers : 17.07 % Allowed : 17.07 % Favored : 65.85 % Cbeta Deviations : 0.00 % 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: -7.21 (0.23), residues: 548 helix: -5.22 (0.15), residues: 172 sheet: -2.89 (0.79), residues: 47 loop : -5.13 (0.22), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 48 TYR 0.108 0.023 TYR A 234 PHE 0.052 0.011 PHE B 251 TRP 0.043 0.007 TRP B 201 HIS 0.003 0.001 HIS A 131 Individual atomic B min max mean iso aniso Overall: 0.00 77.44 33.73 4.15 4478 0 Protein: 0.00 77.44 33.73 4.15 4478 0 Chain A: 0.00 77.44 33.35 N/A 2239 0 Chain B: 0.00 73.79 34.12 N/A 2239 0 Histogram: Values Number of atoms 0.00 - 7.74 79 7.74 - 15.49 0 15.49 - 23.23 10 23.23 - 30.98 2024 30.98 - 38.72 1429 38.72 - 46.46 430 46.46 - 54.21 303 54.21 - 61.95 94 61.95 - 69.70 64 69.70 - 77.44 45 |-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: 3.49 - 19.81 A, n_refl.=8549 (all), 10.56 % free)-------------| | | | r_work= 0.3487 r_free= 0.4112 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958556 | | target function (ml) not normalized (work): 30267.121761 | | target function (ml) not normalized (free): 3647.010734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3553 0.3487 0.4112 n_refl.: 8549 re-set all scales: r(all,work,free)=0.3553 0.3487 0.4112 n_refl.: 8549 remove outliers: r(all,work,free)=0.3545 0.3478 0.4112 n_refl.: 8544 overall B=38.85 to atoms: r(all,work,free)=0.3940 0.3881 0.4443 n_refl.: 8544 bulk-solvent and scaling: r(all,work,free)=0.2857 0.2765 0.3621 n_refl.: 8544 remove outliers: r(all,work,free)=0.2855 0.2765 0.3607 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.3174 1300.952 1107.908 1.348 0.971 0.356 13.859-11.604 100.00 90 12 0.2176 1680.008 1539.871 1.266 0.975 0.329 11.577-9.718 99.43 156 19 0.2370 1643.853 1535.873 1.342 0.979 0.321 9.700-8.140 99.66 262 33 0.2802 1318.742 1207.528 1.320 0.987 0.303 8.117-6.812 97.25 444 52 0.2708 923.512 849.358 1.079 0.998 0.251 6.812-5.705 94.76 721 93 0.2876 655.291 593.315 0.810 1.015 0.163 5.702-4.776 94.99 1247 137 0.2640 640.119 588.984 0.813 1.037 0.090 4.775-3.999 95.66 2113 265 0.2666 608.046 548.501 1.025 1.066 0.054 3.998-3.486 92.23 2521 281 0.3081 415.289 367.051 1.160 1.112 0.045 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.8814 b_overall=-15.0006 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.673268 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206479 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 0.2909 0.3685 0.0776 0.004 0.8 16.0 6.6 12.4 0 0.125 0.2878 0.3690 0.0812 0.004 0.8 15.9 6.4 12.4 0 0.250 0.2809 0.3680 0.0871 0.004 0.8 19.5 6.8 12.8 0 0.500 0.2739 0.3706 0.0966 0.005 0.9 19.0 6.2 12.8 0 1.000 0.2620 0.3709 0.1089 0.007 1.0 26.6 7.3 13.8 0 2.000 0.2535 0.3676 0.1142 0.009 1.2 35.2 8.2 14.8 0 3.000 0.2472 0.3682 0.1210 0.011 1.3 41.8 8.4 16.1 0 4.000 0.2424 0.3681 0.1257 0.013 1.4 46.8 9.9 16.7 0 5.000 0.2388 0.3686 0.1298 0.015 1.6 50.7 10.6 18.7 0 6.000 0.2353 0.3674 0.1321 0.016 1.6 55.4 10.8 19.1 0 7.000 0.2328 0.3658 0.1330 0.017 1.7 58.6 11.1 19.1 0 8.000 0.2305 0.3687 0.1383 0.019 1.9 62.3 12.4 20.1 0 9.000 0.2276 0.3673 0.1397 0.020 1.9 65.0 12.6 20.3 0 10.000 0.2373 0.3668 0.1295 0.016 1.6 51.1 10.4 17.7 0 6.337 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2328 0.3658 0.1330 0.017 1.7 58.6 11.1 19.1 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.28 36.58 13.30 2.945 72.831 0.206 0.066 23.19 36.58 13.40 3.426 73.180 0.006 0.065 22.72 36.58 13.86 3.564 73.243 0.026 0.063 21.73 36.57 14.83 4.949 73.520 0.103 0.058 21.18 36.56 15.38 6.568 73.952 0.206 0.056 20.92 36.58 15.66 7.631 74.225 0.310 0.055 20.57 36.60 16.02 9.104 74.776 0.413 0.053 20.43 36.60 16.17 9.870 75.009 0.516 0.052 20.33 36.62 16.29 10.517 75.205 0.619 0.052 20.24 36.63 16.39 11.058 75.369 0.723 0.051 20.17 36.63 16.46 11.519 75.508 0.826 0.051 20.11 36.64 16.53 11.990 75.657 0.929 0.051 19.99 36.65 16.66 12.852 75.959 1.032 0.050 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 23.19 36.58 13.40 3.426 73.180 0.006 0.065 Individual atomic B min max mean iso aniso Overall: 43.89 111.29 73.28 2.24 4478 0 Protein: 43.89 111.29 73.28 2.24 4478 0 Chain A: 43.89 111.29 73.17 N/A 2239 0 Chain B: 49.00 110.16 73.39 N/A 2239 0 Histogram: Values Number of atoms 43.89 - 50.63 6 50.63 - 57.37 8 57.37 - 64.11 65 64.11 - 70.85 2095 70.85 - 77.59 1487 77.59 - 84.33 365 84.33 - 91.07 241 91.07 - 97.81 94 97.81 - 104.55 68 104.55 - 111.29 49 =========================== Idealize ADP of riding H ========================== r_work=0.2319 r_free=0.3658 r_work=0.2326 r_free=0.3653 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2326 r_free= 0.3653 coordinate error (max.-lik. estimate): 0.84 A | | | | normalized target function (ls_wunit_k1) (work): 0.065674 | | target function (ls_wunit_k1) not normalized (work): 501.812345 | | target function (ls_wunit_k1) not normalized (free): 149.270838 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2469 0.2326 0.3653 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3669 0.3585 0.4366 n_refl.: 8543 remove outliers: r(all,work,free)=0.3669 0.3585 0.4366 n_refl.: 8543 overall B=-2.29 to atoms: r(all,work,free)=0.3618 0.3533 0.4332 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2449 0.2306 0.3626 n_refl.: 8543 remove outliers: r(all,work,free)=0.2449 0.2306 0.3626 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2461 721.868 651.683 1.442 0.963 0.366 13.859-11.604 100.00 90 12 0.1704 932.197 885.740 1.411 0.966 0.351 11.577-9.718 99.43 156 19 0.1906 912.135 871.314 1.351 0.968 0.307 9.700-8.140 99.66 262 33 0.2030 731.739 697.649 1.365 0.974 0.292 8.117-6.812 97.25 444 52 0.2104 512.435 489.270 1.134 0.981 0.263 6.812-5.705 94.76 721 93 0.2437 363.605 341.965 0.851 0.993 0.173 5.702-4.776 94.99 1247 137 0.2302 355.187 336.823 0.813 1.008 0.070 4.775-3.999 95.66 2113 265 0.2248 337.391 317.929 1.028 1.028 0.041 3.998-3.486 92.23 2521 281 0.2662 230.434 214.352 1.152 1.060 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-10.2934 ============================ 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 = 9.894221 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.094566 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 0.2675 0.3642 0.0967 0.004 0.8 15.9 6.0 13.8 0 0.125 0.2689 0.3650 0.0960 0.004 0.8 14.8 5.1 13.2 0 0.250 0.2670 0.3640 0.0970 0.004 0.8 16.2 5.3 13.8 0 0.500 0.2563 0.3636 0.1073 0.007 0.9 23.8 6.6 15.2 0 1.000 0.2516 0.3643 0.1127 0.010 1.2 35.6 8.4 16.9 0 2.000 0.2472 0.3636 0.1164 0.015 1.5 43.0 9.5 18.1 0 3.000 0.2417 0.3632 0.1214 0.018 1.7 47.7 10.6 18.9 0 4.000 0.2401 0.3630 0.1229 0.022 1.9 52.5 10.8 18.3 0 5.000 0.2378 0.3630 0.1252 0.025 2.1 55.1 10.8 18.3 0 6.000 0.2368 0.3632 0.1264 0.029 2.3 57.8 10.8 19.3 0 7.000 0.2390 0.3729 0.1339 0.027 2.5 72.4 16.6 27.8 0 8.000 0.2364 0.3712 0.1347 0.029 2.6 74.9 16.8 27.4 0 9.000 0.2346 0.3734 0.1388 0.031 2.7 78.5 18.8 28.5 0 10.000 0.2403 0.3631 0.1228 0.022 1.9 52.8 10.6 18.3 0 4.947 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2401 0.3630 0.1229 0.022 1.9 52.5 10.8 18.3 0 5.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.01 36.30 12.29 10.526 78.404 0.095 6.083 24.26 36.31 12.05 10.880 78.892 0.003 6.087 24.00 36.30 12.30 10.546 78.384 0.012 6.083 23.96 36.29 12.33 10.584 78.356 0.047 6.082 23.76 36.29 12.52 10.998 78.096 0.095 6.077 23.02 36.16 13.14 12.644 78.560 0.142 6.058 22.89 36.17 13.28 13.021 78.872 0.189 6.056 22.80 36.17 13.37 13.479 79.164 0.236 6.054 22.73 36.16 13.43 13.942 79.410 0.284 6.052 22.73 36.27 13.54 13.785 79.250 0.331 6.056 22.71 36.27 13.56 13.986 79.362 0.378 6.056 22.69 36.27 13.58 14.161 79.456 0.426 6.055 22.67 36.27 13.60 14.318 79.537 0.473 6.055 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.012 Accepted refinement result: 24.00 36.30 12.30 10.546 78.384 0.012 6.083 Individual atomic B min max mean iso aniso Overall: 41.94 107.89 70.95 2.12 4478 0 Protein: 41.94 107.89 70.95 2.12 4478 0 Chain A: 41.94 107.89 70.85 N/A 2239 0 Chain B: 49.22 107.75 71.05 N/A 2239 0 Histogram: Values Number of atoms 41.94 - 48.53 4 48.53 - 55.13 8 55.13 - 61.73 64 61.73 - 68.32 2029 68.32 - 74.92 1503 74.92 - 81.51 407 81.51 - 88.11 240 88.11 - 94.70 104 94.70 - 101.30 69 101.30 - 107.89 50 =========================== Idealize ADP of riding H ========================== r_work=0.2400 r_free=0.3630 r_work=0.2399 r_free=0.3630 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2399 r_free= 0.3630 coordinate error (max.-lik. estimate): 0.80 A | | | | normalized target function (ml) (work): 6.082839 | | target function (ml) not normalized (work): 46478.973946 | | target function (ml) not normalized (free): 5632.596862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2530 0.2399 0.3630 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3580 0.3490 0.4338 n_refl.: 8543 remove outliers: r(all,work,free)=0.3580 0.3490 0.4338 n_refl.: 8543 overall B=-7.85 to atoms: r(all,work,free)=0.3411 0.3312 0.4243 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2493 0.2363 0.3590 n_refl.: 8543 remove outliers: r(all,work,free)=0.2493 0.2363 0.3590 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2540 721.868 644.738 1.631 0.972 0.367 13.859-11.604 100.00 90 12 0.1737 932.197 878.922 1.518 0.973 0.344 11.577-9.718 99.43 156 19 0.1917 912.135 864.621 1.511 0.974 0.321 9.700-8.140 99.66 262 33 0.1971 731.739 692.363 1.526 0.978 0.308 8.117-6.812 97.25 444 52 0.2371 512.435 480.309 1.297 0.982 0.280 6.812-5.705 94.76 721 93 0.2738 363.605 333.740 0.967 0.988 0.190 5.702-4.776 94.99 1247 137 0.2455 355.187 330.976 0.880 0.996 0.084 4.775-3.999 95.66 2113 265 0.2300 337.391 312.122 1.033 1.006 0.021 3.998-3.486 92.23 2521 281 0.2509 230.434 210.473 1.108 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=3.0543 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2363 r_free=0.3590 After: r_work=0.2365 r_free=0.3590 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.219903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.124804 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 0.2536 0.3571 0.1035 0.013 1.5 51.6 10.6 18.1 0 0.125 0.2532 0.3570 0.1038 0.013 1.5 51.8 10.6 18.1 0 0.250 0.2526 0.3570 0.1044 0.012 1.4 51.7 10.8 18.1 0 0.500 0.2464 0.3584 0.1120 0.014 1.5 53.6 11.1 18.1 0 1.000 0.2409 0.3589 0.1180 0.013 1.8 54.6 10.9 18.5 0 2.000 0.2388 0.3588 0.1201 0.016 1.9 53.7 10.9 19.1 0 3.000 0.2374 0.3587 0.1213 0.018 1.9 53.6 10.9 19.1 0 4.000 0.2365 0.3589 0.1224 0.020 2.0 54.0 10.9 19.1 0 5.000 0.2355 0.3592 0.1237 0.022 2.1 55.7 10.9 19.1 0 6.000 0.2340 0.3596 0.1255 0.025 2.2 57.7 10.9 18.7 0 7.000 0.2326 0.3598 0.1272 0.028 2.3 58.9 11.1 18.9 0 8.000 0.2294 0.3606 0.1312 0.035 2.7 64.2 12.0 20.1 0 9.000 0.2280 0.3607 0.1327 0.038 2.9 66.3 12.0 20.3 0 10.000 0.2375 0.3589 0.1214 0.018 1.9 54.3 10.9 19.1 0 4.110 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2532 0.3570 0.1038 0.013 1.5 51.8 10.6 18.1 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.32 35.70 10.38 10.190 70.277 0.125 6.108 25.40 35.68 10.28 10.443 70.289 0.004 6.108 25.29 35.70 10.41 10.213 70.255 0.016 6.107 25.01 35.68 10.67 10.454 70.099 0.062 6.101 23.80 35.58 11.78 12.263 70.941 0.125 6.074 23.60 35.61 12.01 12.850 71.304 0.187 6.070 23.51 35.73 12.22 13.324 71.408 0.250 6.072 23.42 35.74 12.32 13.810 71.667 0.312 6.070 23.36 35.75 12.39 14.203 71.861 0.374 6.069 23.30 35.75 12.45 14.616 72.053 0.437 6.068 23.25 35.76 12.51 15.099 72.262 0.499 6.067 23.19 35.75 12.56 15.651 72.490 0.562 6.065 23.18 35.76 12.58 15.776 72.541 0.624 6.065 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.016 Accepted refinement result: 25.29 35.70 10.41 10.213 70.255 0.016 6.107 Individual atomic B min max mean iso aniso Overall: 34.46 100.10 63.06 2.04 4478 0 Protein: 34.46 100.10 63.06 2.04 4478 0 Chain A: 34.46 100.10 62.98 N/A 2239 0 Chain B: 43.34 99.80 63.13 N/A 2239 0 Histogram: Values Number of atoms 34.46 - 41.02 4 41.02 - 47.59 8 47.59 - 54.15 90 54.15 - 60.71 2087 60.71 - 67.28 1456 67.28 - 73.84 378 73.84 - 80.41 237 80.41 - 86.97 103 86.97 - 93.54 68 93.54 - 100.10 47 =========================== Idealize ADP of riding H ========================== r_work=0.2529 r_free=0.3570 r_work=0.2528 r_free=0.3571 ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2528 r_free= 0.3571 coordinate error (max.-lik. estimate): 0.75 A | | | | normalized target function (ml) (work): 6.107290 | | target function (ml) not normalized (work): 46665.799094 | | target function (ml) not normalized (free): 5635.107908 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.81 - 6.29 0.98 1321 168 0.2333 0.3199 6.6166 6.7043| | 2: 6.28 - 5.01 0.95 1261 149 0.2714 0.3509 6.2586 6.343| | 3: 5.01 - 4.38 0.96 1313 141 0.2421 0.3765 6.1748 6.4106| | 4: 4.38 - 3.99 0.95 1270 167 0.2551 0.3804 6.0337 6.1706| | 5: 3.99 - 3.70 0.94 1269 134 0.2666 0.3834 5.868 6.0293| | 6: 3.70 - 3.49 0.90 1207 143 0.2838 0.3902 5.6474 5.7437| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.81 - 6.29 1321 168 0.73 33.20 1.01 0.77 137719.20| | 2: 6.28 - 5.01 1261 149 0.61 44.13 0.98 0.70 91356.09| | 3: 5.01 - 4.38 1313 141 0.70 36.73 1.02 0.66 62687.59| | 4: 4.38 - 3.99 1270 167 0.68 38.32 0.98 0.70 52298.56| | 5: 3.99 - 3.70 1269 134 0.63 42.62 1.02 0.65 37671.65| | 6: 3.70 - 3.49 1207 143 0.64 41.94 0.97 0.61 22659.81| |alpha: min = 0.61 max = 0.77 mean = 0.68| |beta: min = 22659.81 max = 137719.20 mean = 68186.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.88 mean = 39.41| |phase err.(test): min = 0.21 max = 89.28 mean = 41.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2639 0.2528 0.3571 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3523 0.3438 0.4244 n_refl.: 8543 remove outliers: r(all,work,free)=0.3523 0.3438 0.4244 n_refl.: 8543 overall B=0.73 to atoms: r(all,work,free)=0.3536 0.3452 0.4252 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2634 0.2526 0.3540 n_refl.: 8543 remove outliers: r(all,work,free)=0.2634 0.2526 0.3540 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2525 840.997 753.941 1.787 0.978 0.390 13.859-11.604 100.00 90 12 0.1880 1086.036 1021.045 1.558 0.980 0.360 11.577-9.718 99.43 156 19 0.2055 1062.665 1002.591 1.507 0.979 0.328 9.700-8.140 99.66 262 33 0.2156 852.497 804.023 1.534 0.982 0.319 8.117-6.812 97.25 444 52 0.2481 597.002 557.742 1.311 0.986 0.309 6.812-5.705 94.76 721 93 0.2864 423.611 388.702 0.929 0.992 0.179 5.702-4.776 94.99 1247 137 0.2590 413.803 385.176 0.872 0.998 0.093 4.775-3.999 95.66 2113 265 0.2483 393.070 361.565 1.034 1.006 0.050 3.998-3.486 92.23 2521 281 0.2727 268.462 244.071 1.107 1.022 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=3.2747 ================= 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 : 0.3487 0.4112 0.010 1.826 0.0 77.4 33.7 0 0.000 1_bss: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_settarget: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_weight: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_xyzrec: 0.2328 0.3658 0.017 1.714 38.8 116.3 72.6 0 0.342 1_adp: 0.2319 0.3658 0.017 1.714 43.9 111.3 73.3 0 0.342 1_regHadp: 0.2326 0.3653 0.017 1.714 43.9 111.3 73.3 0 0.342 2_bss: 0.2306 0.3626 0.017 1.714 41.6 109.0 71.0 0 0.342 2_settarget: 0.2306 0.3626 0.017 1.714 41.6 109.0 71.0 0 0.342 2_updatecdl: 0.2306 0.3626 0.017 1.760 41.6 109.0 71.0 0 0.342 2_weight: 0.2306 0.3626 0.017 1.760 41.6 109.0 71.0 0 0.342 2_xyzrec: 0.2401 0.3630 0.022 1.943 41.6 109.0 71.0 0 0.376 2_adp: 0.2400 0.3630 0.022 1.943 41.9 107.9 71.0 0 0.376 2_regHadp: 0.2399 0.3630 0.022 1.943 41.9 107.9 71.0 0 0.376 3_bss: 0.2363 0.3590 0.022 1.943 34.1 100.0 63.1 0 0.376 3_settarget: 0.2363 0.3590 0.022 1.943 34.1 100.0 63.1 0 0.376 3_updatecdl: 0.2363 0.3590 0.022 1.953 34.1 100.0 63.1 0 0.376 3_setrh: 0.2365 0.3590 0.022 1.953 34.1 100.0 63.1 0 0.376 3_weight: 0.2365 0.3590 0.022 1.953 34.1 100.0 63.1 0 0.376 3_xyzrec: 0.2532 0.3570 0.013 1.454 34.1 100.0 63.1 0 0.375 3_adp: 0.2529 0.3570 0.013 1.454 34.5 100.1 63.1 0 0.375 3_regHadp: 0.2528 0.3571 0.013 1.454 34.5 100.1 63.1 0 0.375 end: 0.2526 0.3540 0.013 1.454 35.2 100.8 63.8 0 0.375 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1jkt_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1jkt_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.2400 Refinement macro-cycles (run) : 280.5900 Write final files (write_after_run_outputs) : 15.8200 Total : 309.6500 Total CPU time: 5.99 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:25 PDT -0700 (1716251725.64 s) Start R-work = 0.2765, R-free = 0.3607 Final R-work = 0.2526, R-free = 0.3540 =============================================================================== Job complete usr+sys time: 374.64 seconds wall clock time: 18 minutes 8.73 seconds (1088.73 seconds total)