Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { 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: 0.00s 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: 1.47, per 1000 atoms: 0.16 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: 2.28 Conformation dependent library (CDL) restraints added in 282.9 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. 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: 0.62 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: 1.89 Time building geometry restraints manager: 2.61 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2765 r_free=0.3607 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2765 r_free=0.3607 ========================= Local real-space refinement ========================= Before: r_work=0.2765 r_free=0.3607 233 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 149 time to evaluate : 0.627 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 53 residues processed: 84 average time/residue: 0.3082 time to fit residues: 32.7113 After: r_work=0.2796 r_free=0.3641 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.886377 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.204903 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 0.2912 0.3674 0.0762 0.005 1.0 19.9 1.6 9.3 0 0.125 0.2895 0.3684 0.0790 0.004 0.9 17.6 1.8 9.3 0 0.250 0.2850 0.3690 0.0840 0.005 0.9 18.4 1.8 9.3 0 0.500 0.2760 0.3697 0.0937 0.006 1.0 20.4 1.8 9.8 0 1.000 0.2649 0.3711 0.1062 0.008 1.1 26.7 2.0 11.0 0 2.000 0.2569 0.3711 0.1142 0.010 1.2 36.1 1.8 12.2 0 3.000 0.2504 0.3714 0.1210 0.012 1.4 39.5 1.8 14.0 0 4.000 0.2455 0.3723 0.1267 0.013 1.5 44.1 1.8 15.0 0 5.000 0.2425 0.3707 0.1281 0.015 1.6 50.0 2.7 14.8 0 6.000 0.2383 0.3712 0.1329 0.017 1.7 54.8 2.2 17.1 0 7.000 0.2358 0.3703 0.1345 0.018 1.8 57.0 2.7 16.5 0 8.000 0.2322 0.3727 0.1406 0.020 2.0 61.0 2.7 18.5 0 9.000 0.2299 0.3725 0.1426 0.021 2.0 62.6 2.7 18.7 0 10.000 0.2421 0.3714 0.1294 0.015 1.6 50.1 1.8 15.9 0 5.943 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2912 0.3674 0.0762 0.005 1.0 19.9 1.6 9.3 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2912 r_free=0.3674 199 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.779 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 5 residues processed: 46 average time/residue: 0.5881 time to fit residues: 40.1669 After: r_work=0.2981 r_free=0.3705 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.81 37.05 7.24 2.945 72.831 0.205 0.114 29.55 36.96 7.41 3.377 73.195 0.006 0.112 28.91 36.88 7.98 3.835 73.357 0.026 0.108 27.62 36.71 9.09 6.533 74.042 0.102 0.099 26.79 36.69 9.90 9.386 74.912 0.205 0.093 26.11 36.74 10.63 12.048 75.876 0.307 0.089 25.75 36.78 11.03 13.703 76.414 0.410 0.086 25.50 36.81 11.31 14.989 76.828 0.512 0.085 25.30 36.83 11.53 16.075 77.187 0.615 0.084 24.76 36.87 12.11 19.234 78.339 0.717 0.080 24.64 36.89 12.24 20.143 78.627 0.820 0.079 24.55 36.90 12.35 20.901 78.866 0.922 0.079 24.38 36.91 12.53 22.181 79.323 1.025 0.078 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: 29.55 36.96 7.41 3.377 73.195 0.006 0.112 Individual atomic B min max mean iso aniso Overall: 42.74 113.20 73.31 2.24 4478 0 Protein: 42.74 113.20 73.31 2.24 4478 0 Chain A: 42.74 111.29 73.20 N/A 2239 0 Chain B: 49.76 113.20 73.42 N/A 2239 0 Histogram: Values Number of atoms 42.74 - 49.78 6 49.78 - 56.83 9 56.83 - 63.88 61 63.88 - 70.92 2102 70.92 - 77.97 1504 77.97 - 85.01 373 85.01 - 92.06 237 92.06 - 99.11 84 99.11 - 106.15 66 106.15 - 113.20 36 =========================== Idealize ADP of riding H ========================== r_work=0.2955 r_free=0.3696 r_work=0.2948 r_free=0.3691 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2948 r_free= 0.3691 coordinate error (max.-lik. estimate): 0.86 A | | | | normalized target function (ls_wunit_k1) (work): 0.111799 | | target function (ls_wunit_k1) not normalized (work): 854.255303 | | target function (ls_wunit_k1) not normalized (free): 152.904372 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3028 0.2948 0.3691 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3932 0.3880 0.4372 n_refl.: 8543 remove outliers: r(all,work,free)=0.3932 0.3880 0.4372 n_refl.: 8543 overall B=-8.18 to atoms: r(all,work,free)=0.3785 0.3729 0.4260 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2963 0.2889 0.3577 n_refl.: 8543 remove outliers: r(all,work,free)=0.2963 0.2889 0.3577 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 0.2885 739.071 649.840 1.655 0.983 0.373 13.859-11.604 100.00 90 12 0.2115 954.413 881.847 1.564 0.985 0.361 11.577-9.718 99.43 156 19 0.2420 933.874 868.614 1.600 0.985 0.353 9.700-8.140 99.66 262 33 0.2719 749.178 692.959 1.578 0.988 0.352 8.117-6.812 97.25 444 52 0.2915 524.647 478.622 1.302 0.993 0.312 6.812-5.705 94.76 721 93 0.3050 372.271 335.621 0.918 1.000 0.200 5.702-4.776 94.99 1247 137 0.2796 363.652 332.851 0.863 1.009 0.112 4.775-3.999 95.66 2113 265 0.2858 345.431 309.345 1.031 1.019 0.078 3.998-3.486 92.23 2521 281 0.3199 235.926 208.686 1.115 1.039 0.035 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.5550 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2889 r_free=0.3577 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 172 ASN Total number of N/Q/H flips: 2 r_work=0.2888 r_free=0.3577 ========================= Local real-space refinement ========================= Before: r_work=0.2888 r_free=0.3577 157 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.647 outliers start: 6 outliers final: 4 residues processed: 6 average time/residue: 0.8478 time to fit residues: 8.7299 After: r_work=0.2888 r_free=0.3578 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.011223 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.099419 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 0.2923 0.3601 0.0677 0.003 0.6 8.4 1.3 2.4 0 0.125 0.2848 0.3584 0.0736 0.003 0.7 10.2 1.3 2.2 0 0.250 0.2777 0.3592 0.0815 0.004 0.7 11.9 1.5 3.9 0 0.500 0.2696 0.3617 0.0922 0.006 0.9 16.3 1.5 5.9 0 1.000 0.2600 0.3628 0.1028 0.010 1.2 23.3 1.8 8.3 0 2.000 0.2544 0.3639 0.1095 0.013 1.4 31.0 2.2 11.6 0 3.000 0.2508 0.3654 0.1146 0.016 1.6 37.6 2.4 15.7 0 4.000 0.2474 0.3643 0.1170 0.019 1.8 40.2 2.7 16.1 0 5.000 0.2451 0.3661 0.1210 0.021 2.0 46.0 3.3 17.9 0 6.000 0.2428 0.3667 0.1240 0.024 2.1 50.5 3.5 20.3 0 7.000 0.2404 0.3667 0.1263 0.027 2.3 55.9 3.6 22.8 0 8.000 0.2388 0.3674 0.1287 0.029 2.5 60.6 4.2 23.4 0 9.000 0.2373 0.3678 0.1305 0.031 2.6 62.8 5.1 23.4 0 10.000 0.2524 0.3645 0.1121 0.015 1.6 36.8 2.4 14.8 0 3.506 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2848 0.3584 0.0736 0.003 0.7 10.2 1.3 2.2 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2848 r_free=0.3584 156 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.301 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 11 average time/residue: 0.4212 time to fit residues: 8.4393 After: r_work=0.2863 r_free=0.3602 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.63 36.02 7.39 10.537 72.576 0.099 6.164 28.87 35.89 7.02 10.792 73.505 0.003 6.164 28.47 36.00 7.53 10.665 72.497 0.012 6.159 28.30 35.98 7.68 10.746 72.437 0.050 6.156 26.75 35.73 8.98 12.510 73.481 0.099 6.121 26.53 35.81 9.28 13.120 73.713 0.149 6.118 26.32 35.78 9.46 13.834 74.109 0.199 6.114 26.18 35.76 9.59 14.482 74.427 0.249 6.111 26.07 35.75 9.68 15.056 74.688 0.298 6.109 25.98 35.74 9.76 15.609 74.928 0.348 6.107 25.93 35.74 9.81 15.989 75.086 0.398 6.105 25.86 35.72 9.86 16.504 75.292 0.447 6.104 25.80 35.71 9.90 16.978 75.476 0.497 6.102 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: 28.47 36.00 7.53 10.665 72.497 0.012 6.159 Individual atomic B min max mean iso aniso Overall: 36.70 105.19 64.98 1.97 4478 0 Protein: 36.70 105.19 64.98 1.97 4478 0 Chain A: 36.70 101.96 65.00 N/A 2239 0 Chain B: 51.41 105.19 64.95 N/A 2239 0 Histogram: Values Number of atoms 36.70 - 43.55 5 43.55 - 50.40 7 50.40 - 57.25 333 57.25 - 64.10 2222 64.10 - 70.94 1226 70.94 - 77.79 324 77.79 - 84.64 205 84.64 - 91.49 65 91.49 - 98.34 72 98.34 - 105.19 19 =========================== Idealize ADP of riding H ========================== r_work=0.2847 r_free=0.3600 r_work=0.2846 r_free=0.3600 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2846 r_free= 0.3600 coordinate error (max.-lik. estimate): 0.77 A | | | | normalized target function (ml) (work): 6.158781 | | target function (ml) not normalized (work): 47059.246184 | | target function (ml) not normalized (free): 5645.941280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2925 0.2846 0.3600 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3738 0.3678 0.4247 n_refl.: 8543 remove outliers: r(all,work,free)=0.3738 0.3678 0.4247 n_refl.: 8543 overall B=3.96 to atoms: r(all,work,free)=0.3807 0.3750 0.4300 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2909 0.2835 0.3543 n_refl.: 8543 remove outliers: r(all,work,free)=0.2909 0.2835 0.3543 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 0.2699 824.508 727.871 1.600 1.002 0.379 13.859-11.604 100.00 90 12 0.2241 1064.743 969.121 1.470 1.002 0.365 11.577-9.718 99.43 156 19 0.2226 1041.829 979.988 1.534 1.000 0.361 9.700-8.140 99.66 262 33 0.2537 835.782 779.080 1.515 1.002 0.359 8.117-6.812 97.25 444 52 0.2844 585.296 532.814 1.288 1.003 0.334 6.812-5.705 94.76 721 93 0.3089 415.305 373.418 0.953 1.005 0.244 5.702-4.776 94.99 1247 137 0.2825 405.690 370.536 0.858 1.006 0.128 4.775-3.999 95.66 2113 265 0.2851 385.363 345.206 1.015 1.006 0.076 3.998-3.486 92.23 2521 281 0.3053 263.199 234.282 1.125 1.013 0.028 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=3.3028 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2835 r_free=0.3543 After: r_work=0.2835 r_free=0.3543 ================================== NQH flips ================================== r_work=0.2835 r_free=0.3543 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.2835 r_free=0.3543 ========================= Local real-space refinement ========================= Before: r_work=0.2835 r_free=0.3543 146 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.220 revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.5932 time to fit residues: 4.0287 After: r_work=0.2836 r_free=0.3543 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.281837 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.099369 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 0.2836 0.3515 0.0679 0.005 0.7 13.3 1.3 0.8 0 0.125 0.2832 0.3515 0.0683 0.005 0.7 13.3 1.3 0.8 0 0.250 0.2825 0.3515 0.0690 0.005 0.7 13.2 1.3 0.8 0 0.500 0.2796 0.3518 0.0723 0.008 0.8 13.5 1.5 0.8 0 1.000 0.2706 0.3526 0.0821 0.016 1.3 17.4 1.5 1.2 0 2.000 0.2602 0.3514 0.0912 0.015 1.5 31.8 1.6 3.5 0 3.000 0.2562 0.3524 0.0962 0.019 1.9 36.1 2.0 3.9 0 4.000 0.2524 0.3531 0.1006 0.022 2.0 41.5 2.4 7.1 0 5.000 0.2498 0.3544 0.1045 0.026 2.3 47.7 3.6 9.6 0 6.000 0.2470 0.3568 0.1099 0.029 2.8 58.6 3.8 12.2 0 7.000 0.2460 0.3574 0.1114 0.029 2.9 58.8 4.2 12.8 0 8.000 0.2443 0.3584 0.1141 0.031 3.2 64.1 4.4 13.6 1 9.000 0.2434 0.3595 0.1162 0.032 3.3 66.3 4.9 15.7 1 10.000 0.2575 0.3517 0.0942 0.018 1.8 32.4 1.6 3.3 0 3.641 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2602 0.3514 0.0912 0.015 1.5 31.8 1.6 3.5 0 3.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2602 r_free=0.3514 138 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.540 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 17 average time/residue: 0.1789 time to fit residues: 5.2505 After: r_work=0.2613 r_free=0.3531 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.13 35.31 9.17 9.353 75.548 0.099 6.219 26.36 35.34 8.98 9.658 75.555 0.003 6.224 26.13 35.31 9.17 9.353 75.548 0.012 6.219 25.85 35.27 9.41 9.636 75.388 0.050 6.213 24.68 34.93 10.25 11.400 76.008 0.099 6.184 24.39 34.88 10.49 12.213 76.573 0.149 6.178 24.17 34.84 10.67 13.190 77.070 0.199 6.173 24.11 34.95 10.84 13.299 77.082 0.248 6.174 24.03 34.95 10.92 13.789 77.309 0.298 6.172 23.96 34.94 10.98 14.207 77.493 0.348 6.171 23.91 34.94 11.03 14.564 77.644 0.397 6.170 23.87 34.94 11.07 14.873 77.772 0.447 6.169 23.84 34.94 11.10 15.140 77.879 0.497 6.168 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: 26.13 35.31 9.17 9.353 75.548 0.012 6.219 Individual atomic B min max mean iso aniso Overall: 40.66 109.15 68.94 1.97 4478 0 Protein: 40.66 109.15 68.94 1.97 4478 0 Chain A: 40.66 105.92 68.96 N/A 2239 0 Chain B: 55.37 109.15 68.92 N/A 2239 0 Histogram: Values Number of atoms 40.66 - 47.51 5 47.51 - 54.36 7 54.36 - 61.21 333 61.21 - 68.06 2222 68.06 - 74.91 1226 74.91 - 81.76 324 81.76 - 88.61 205 88.61 - 95.45 65 95.45 - 102.30 72 102.30 - 109.15 19 =========================== Idealize ADP of riding H ========================== r_work=0.2613 r_free=0.3531 r_work=0.2613 r_free=0.3530 ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2613 r_free= 0.3530 coordinate error (max.-lik. estimate): 0.72 A | | | | normalized target function (ml) (work): 6.219126 | | target function (ml) not normalized (work): 47520.339741 | | target function (ml) not normalized (free): 5732.633177 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2392 0.3039 6.7172 6.7748| | 2: 6.28 - 5.01 0.95 1261 149 0.2756 0.3572 6.3629 6.4611| | 3: 5.01 - 4.38 0.96 1313 141 0.2589 0.3899 6.2989 6.561| | 4: 4.38 - 3.99 0.95 1270 167 0.2691 0.3641 6.155 6.2748| | 5: 3.99 - 3.70 0.94 1269 134 0.2743 0.3796 5.9795 6.139| | 6: 3.70 - 3.49 0.90 1207 143 0.2843 0.3976 5.7564 5.8471| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.75 31.58 1.00 0.97 155810.17| | 2: 6.28 - 5.01 1261 149 0.62 43.47 1.00 0.90 110642.21| | 3: 5.01 - 4.38 1313 141 0.70 36.87 1.01 0.85 80516.22| | 4: 4.38 - 3.99 1270 167 0.68 38.42 0.98 0.89 66620.56| | 5: 3.99 - 3.70 1269 134 0.63 42.15 1.01 0.83 47330.52| | 6: 3.70 - 3.49 1207 143 0.64 41.47 0.95 0.77 28673.33| |alpha: min = 0.77 max = 0.97 mean = 0.87| |beta: min = 28673.33 max = 155810.17 mean = 82494.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.74 mean = 38.91| |phase err.(test): min = 0.00 max = 89.42 mean = 40.64| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2704 0.2609 0.3518 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3672 0.3597 0.4308 n_refl.: 8543 remove outliers: r(all,work,free)=0.3672 0.3597 0.4308 n_refl.: 8543 overall B=1.82 to atoms: r(all,work,free)=0.3710 0.3637 0.4335 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2699 0.2603 0.3507 n_refl.: 8543 remove outliers: r(all,work,free)=0.2699 0.2603 0.3507 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 0.2520 824.508 742.687 1.567 0.997 0.379 13.859-11.604 100.00 90 12 0.1949 1064.743 997.509 1.421 0.997 0.359 11.577-9.718 99.43 156 19 0.2008 1041.829 992.786 1.502 0.995 0.359 9.700-8.140 99.66 262 33 0.2190 835.782 787.961 1.485 0.997 0.358 8.117-6.812 97.25 444 52 0.2569 585.296 538.343 1.289 0.998 0.327 6.812-5.705 94.76 721 93 0.2920 415.305 375.037 0.945 1.000 0.217 5.702-4.776 94.99 1247 137 0.2697 405.690 371.113 0.901 1.001 0.177 4.775-3.999 95.66 2113 265 0.2620 385.363 347.509 1.014 1.001 0.078 3.998-3.486 92.23 2521 281 0.2767 263.199 235.864 1.121 1.008 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=3.1862 ================= 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_updatephipsi: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_nqh: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_realsrl: 0.2796 0.3641 0.011 1.834 38.8 116.3 72.6 0 0.034 1_weight: 0.2796 0.3641 0.011 1.834 38.8 116.3 72.6 0 0.034 1_xyzrec: 0.2912 0.3674 0.005 0.982 38.8 116.3 72.6 0 0.224 1_realsrl2: 0.2981 0.3705 0.005 0.982 38.8 116.3 72.6 0 0.256 1_adp: 0.2955 0.3696 0.005 0.982 42.7 113.2 73.3 0 0.256 1_regHadp: 0.2948 0.3691 0.005 0.982 42.7 113.2 73.3 0 0.256 2_bss: 0.2889 0.3577 0.005 0.982 34.6 105.0 65.1 0 0.256 2_settarget: 0.2889 0.3577 0.005 0.982 34.6 105.0 65.1 0 0.256 2_updatephipsi: 0.2889 0.3577 0.005 0.982 34.6 105.0 65.1 0 0.256 2_updatecdl: 0.2889 0.3577 0.005 1.044 34.6 105.0 65.1 0 0.256 2_nqh: 0.2888 0.3577 0.005 1.044 34.6 105.0 65.1 0 0.256 2_realsrl: 0.2888 0.3578 0.005 1.044 34.6 105.0 65.1 0 0.256 2_weight: 0.2888 0.3578 0.005 1.044 34.6 105.0 65.1 0 0.256 2_xyzrec: 0.2848 0.3584 0.003 0.664 34.6 105.0 65.1 0 0.336 2_realsrl2: 0.2863 0.3602 0.003 0.664 34.6 105.0 65.1 0 0.340 2_adp: 0.2847 0.3600 0.003 0.664 36.7 105.2 65.0 0 0.340 2_regHadp: 0.2846 0.3600 0.003 0.664 36.7 105.2 65.0 0 0.340 3_bss: 0.2835 0.3543 0.003 0.664 40.7 109.2 68.9 0 0.340 3_settarget: 0.2835 0.3543 0.003 0.664 40.7 109.2 68.9 0 0.340 3_updatephipsi: 0.2835 0.3543 0.003 0.664 40.7 109.2 68.9 0 0.340 3_updatecdl: 0.2835 0.3543 0.003 0.708 40.7 109.2 68.9 0 0.340 3_setrh: 0.2835 0.3543 0.003 0.708 40.7 109.2 68.9 0 0.340 3_nqh: 0.2835 0.3543 0.003 0.708 40.7 109.2 68.9 0 0.340 3_realsrl: 0.2836 0.3543 0.003 0.708 40.7 109.2 68.9 0 0.340 3_weight: 0.2836 0.3543 0.003 0.708 40.7 109.2 68.9 0 0.340 3_xyzrec: 0.2602 0.3514 0.015 1.540 40.7 109.2 68.9 0 0.378 3_realsrl2: 0.2613 0.3531 0.015 1.540 40.7 109.2 68.9 0 0.380 3_adp: 0.2613 0.3531 0.015 1.540 40.7 109.2 68.9 0 0.380 3_regHadp: 0.2613 0.3530 0.015 1.540 40.7 109.2 68.9 0 0.380 end: 0.2603 0.3507 0.015 1.540 42.5 111.0 70.8 0 0.380 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1jkt_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1jkt_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0300 Refinement macro-cycles (run) : 422.5900 Write final files (write_after_run_outputs) : 16.1400 Total : 445.7600 Total CPU time: 7.91 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:29 PDT -0700 (1716251729.94 s) Start R-work = 0.2765, R-free = 0.3607 Final R-work = 0.2603, R-free = 0.3507 =============================================================================== Job complete usr+sys time: 490.39 seconds wall clock time: 20 minutes 20.87 seconds (1220.87 seconds total)