Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_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 amber.topology_file_name=4amber_1jkt.prmtop amber.coordinate_file_name=4amber_1jkt.rst7 amber.order_file_name=4amber_1jkt.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_1jkt.order 4amber_1jkt.prmtop 4amber_1jkt.rst7 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 = "4phenix_1jkt.pdb" } default_model = "4phenix_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 } amber { use_amber = True topology_file_name = 4amber_1jkt.prmtop coordinate_file_name = 4amber_1jkt.rst7 order_file_name = 4amber_1jkt.order } } 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/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 8964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4482 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4482 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Time building chain proxies: 0.95, per 1000 atoms: 0.11 Number of scatterers: 8964 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 4486 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: 1.65 Conformation dependent library (CDL) restraints added in 182.9 milliseconds 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: 0.51 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: 1.34 Time building geometry restraints manager: 1.87 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: 4484 1.16 - 1.34: 1456 1.34 - 1.52: 2032 1.52 - 1.70: 1070 1.70 - 1.89: 14 Bond restraints: 9056 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 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 bond pdb=" N ALA B 41 " pdb=" H ALA B 41 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9051 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: 3937 126.20 - 134.06: 78 Bond angle restraints: 16424 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 16419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3676 17.86 - 35.72: 330 35.72 - 53.58: 143 53.58 - 71.43: 60 71.43 - 89.29: 15 Dihedral angle restraints: 4224 sinusoidal: 2310 harmonic: 1914 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 4221 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: 0.62 - 1.42: 84 1.42 - 2.21: 1778 2.21 - 3.01: 26540 3.01 - 3.80: 38987 3.80 - 4.60: 63821 Warning: very small nonbonded interaction distances. Nonbonded interactions: 131210 Sorted by model distance: nonbonded pdb=" HA LYS A 276 " pdb=" HZ1 LYS A 276 " model vdw 0.619 2.270 nonbonded pdb=" HG2 GLU B 59 " pdb=" HZ1 LYS B 175 " model vdw 0.865 2.270 nonbonded pdb=" HZ3 LYS B 46 " pdb="HH12 ARG B 58 " model vdw 0.937 2.100 nonbonded pdb="HD12 LEU B 218 " pdb=" H GLY B 219 " model vdw 0.996 2.270 nonbonded pdb=" HG1 THR A 35 " pdb=" H LEU A 37 " model vdw 1.046 2.100 ... (remaining 131205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_1jkt.prmtop atom order : 4amber_1jkt.order coordinates : 4amber_1jkt.rst7 ===================================== ... ===================================== ============================== 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 4486 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: 4486 of 8964 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8964 n_use_u_iso = 8964 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 = 8964 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8964 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8964 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 } amber { use_amber = True topology_file_name = "4amber_1jkt.prmtop" coordinate_file_name = "4amber_1jkt.rst7" order_file_name = "4amber_1jkt.order" } } output { prefix = "4phenix_1jkt_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4486 occupancy sum: 4486.00 (% of total atoms 50.08) Rotatable: count: 1226 occupancy sum: 1226.00 (% of total atoms 13.69) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8549 (all), 10.56 % free)-------------| | | | r_work= 0.3488 r_free= 0.4108 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958543 | | target function (ml) not normalized (work): 30267.023379 | | target function (ml) not normalized (free): 3646.820836 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3613 0.4246 4.6264 4.6743| | 2: 6.28 - 5.01 0.95 1261 150 0.3319 0.4120 4.1036 4.1872| | 3: 5.01 - 4.38 0.96 1313 141 0.3048 0.3760 3.9593 4.1226| | 4: 4.38 - 3.99 0.96 1271 167 0.3453 0.3929 3.8352 3.8747| | 5: 3.99 - 3.70 0.94 1269 134 0.3599 0.4216 3.6701 3.7348| | 6: 3.70 - 3.49 0.90 1208 143 0.4146 0.4422 3.507 3.5289| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 46.97 1.03 0.05 2491.85| | 2: 6.28 - 5.01 1261 150 0.48 53.94 0.88 0.04 1381.22| | 3: 5.01 - 4.38 1313 141 0.60 44.73 1.05 0.04 742.88| | 4: 4.38 - 3.99 1271 167 0.59 45.76 1.00 0.04 612.28| | 5: 3.99 - 3.70 1269 134 0.52 51.23 1.02 0.04 451.99| | 6: 3.70 - 3.49 1208 143 0.47 54.93 0.99 0.03 305.23| |alpha: min = 0.03 max = 0.05 mean = 0.04| |beta: min = 305.23 max = 2491.85 mean = 1011.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.92 mean = 49.50| |phase err.(test): min = 1.01 max = 89.49 mean = 50.47| |-----------------------------------------------------------------------------| ----------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= 0.3488 r_free= 0.4108 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958543 | | target function (ml) not normalized (work): 30267.023379 | | target function (ml) not normalized (free): 3646.820836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3553 0.3488 0.4108 n_refl.: 8549 re-set all scales: r(all,work,free)=0.3553 0.3488 0.4108 n_refl.: 8549 remove outliers: r(all,work,free)=0.3545 0.3479 0.4108 n_refl.: 8544 overall B=39.91 to atoms: r(all,work,free)=0.3961 0.3903 0.4454 n_refl.: 8544 bulk-solvent and scaling: r(all,work,free)=0.2858 0.2767 0.3608 n_refl.: 8544 remove outliers: r(all,work,free)=0.2856 0.2767 0.3594 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 0.3198 1301.171 1115.763 1.346 0.974 0.357 13.859-11.604 100.00 90 12 0.2180 1680.291 1540.162 1.296 0.978 0.341 11.577-9.718 99.43 156 19 0.2372 1644.130 1535.569 1.341 0.982 0.325 9.700-8.140 99.66 262 33 0.2803 1318.964 1207.170 1.314 0.989 0.308 8.117-6.812 97.25 444 52 0.2708 923.667 848.802 1.081 1.000 0.258 6.812-5.705 94.76 721 93 0.2875 655.401 593.519 0.805 1.016 0.162 5.702-4.776 94.99 1247 137 0.2640 640.227 589.037 0.817 1.038 0.097 4.775-3.999 95.66 2113 265 0.2667 608.149 548.585 1.034 1.065 0.067 3.998-3.486 92.23 2521 281 0.3084 415.359 367.119 1.171 1.110 0.044 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.8814 b_overall=-15.4094 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.974385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.202570 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 0.3056 0.3726 0.0670 0.015 2.1 2.5 1.8 10.4 1 0.125 0.2839 0.3701 0.0862 0.015 2.2 3.2 2.9 10.2 2 0.250 0.2591 0.3695 0.1104 0.017 2.4 4.4 2.7 13.0 2 0.500 0.2353 0.3714 0.1361 0.020 2.9 8.8 4.2 18.3 5 1.000 0.2123 0.3785 0.1661 0.026 3.6 16.5 6.8 22.6 14 2.000 0.2001 0.3796 0.1795 0.031 4.2 25.2 9.7 26.4 22 3.000 0.1923 0.3791 0.1869 0.036 4.7 35.2 10.8 28.9 28 4.000 0.1842 0.3839 0.1997 0.040 5.1 41.2 13.1 31.5 35 5.000 0.1813 0.3801 0.1988 0.044 5.7 48.3 14.8 30.5 40 6.000 0.2350 0.3649 0.1299 0.049 4.2 66.1 12.2 17.5 5 7.000 0.2290 0.3660 0.1370 0.055 4.8 67.3 12.6 17.7 10 8.000 0.1681 0.3839 0.2158 0.054 6.6 63.4 20.1 34.8 49 9.000 0.1657 0.3870 0.2214 0.057 6.9 68.5 21.7 37.2 52 10.000 0.2215 0.3754 0.1538 0.023 3.3 11.9 6.2 20.5 10 1.487 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2350 0.3649 0.1299 0.049 4.2 66.1 12.2 17.5 5 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.50 36.49 12.99 2.945 73.891 0.203 0.069 23.46 36.58 13.12 3.431 74.231 0.006 0.069 23.03 36.55 13.52 3.577 74.274 0.025 0.067 22.11 36.46 14.35 4.930 74.518 0.101 0.062 21.61 36.51 14.90 6.618 74.959 0.203 0.059 21.22 36.55 15.33 8.356 75.543 0.304 0.058 21.02 36.59 15.57 9.470 75.869 0.405 0.057 20.88 36.63 15.75 10.368 76.133 0.506 0.056 20.77 36.67 15.90 11.101 76.353 0.608 0.055 20.68 36.68 16.00 11.702 76.536 0.709 0.055 20.62 36.71 16.09 12.255 76.696 0.810 0.055 20.52 36.76 16.24 13.078 76.974 0.912 0.054 20.47 36.80 16.33 13.573 77.126 1.013 0.054 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: 23.46 36.58 13.12 3.431 74.231 0.006 0.069 Individual atomic B min max mean iso aniso Overall: 45.04 112.35 74.32 2.23 4478 0 Protein: 45.04 112.35 74.32 2.23 4478 0 Chain A: 45.04 112.35 74.20 N/A 2239 0 Chain B: 51.05 111.78 74.43 N/A 2239 0 Histogram: Values Number of atoms 45.04 - 51.77 6 51.77 - 58.50 10 58.50 - 65.23 74 65.23 - 71.96 2101 71.96 - 78.69 1470 78.69 - 85.42 374 85.42 - 92.15 239 92.15 - 98.89 87 98.89 - 105.62 67 105.62 - 112.35 50 =========================== Idealize ADP of riding H ========================== r_work=0.2346 r_free=0.3658 r_work=0.2346 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= 0.2346 r_free= 0.3653 coordinate error (max.-lik. estimate): 0.86 A | | | | normalized target function (ls_wunit_k1) (work): 0.068766 | | target function (ls_wunit_k1) not normalized (work): 525.441117 | | target function (ls_wunit_k1) not normalized (free): 149.820989 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2487 0.2346 0.3653 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3765 0.3688 0.4418 n_refl.: 8543 remove outliers: r(all,work,free)=0.3765 0.3688 0.4418 n_refl.: 8543 overall B=-2.37 to atoms: r(all,work,free)=0.3712 0.3633 0.4381 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2478 0.2339 0.3633 n_refl.: 8543 remove outliers: r(all,work,free)=0.2478 0.2339 0.3633 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 0.2779 709.383 625.690 1.390 0.963 0.361 13.859-11.604 100.00 90 12 0.1764 916.075 865.806 1.335 0.967 0.341 11.577-9.718 99.43 156 19 0.1906 896.360 857.422 1.363 0.970 0.322 9.700-8.140 99.66 262 33 0.2118 719.083 680.597 1.360 0.976 0.312 8.117-6.812 97.25 444 52 0.2212 503.572 475.149 1.116 0.985 0.263 6.812-5.705 94.76 721 93 0.2505 357.317 332.693 0.873 0.999 0.203 5.702-4.776 94.99 1247 137 0.2308 349.044 327.948 0.811 1.018 0.081 4.775-3.999 95.66 2113 265 0.2236 331.555 308.955 1.019 1.041 0.052 3.998-3.486 92.23 2521 281 0.2677 226.449 206.869 1.149 1.080 0.026 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-10.6442 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.231218 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.102964 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 0.2978 0.3678 0.0700 0.015 2.2 2.7 2.0 10.6 2 0.125 0.2797 0.3709 0.0911 0.015 2.5 3.9 3.3 12.0 2 0.250 0.2650 0.3644 0.0994 0.018 2.8 5.6 3.5 15.9 5 0.500 0.2493 0.3725 0.1232 0.023 3.6 11.4 7.7 20.3 11 1.000 0.2367 0.3793 0.1427 0.034 4.8 27.0 12.4 27.2 25 2.000 0.2303 0.3825 0.1522 0.043 5.8 42.8 15.7 33.7 40 3.000 0.2273 0.3804 0.1530 0.050 6.6 57.5 19.7 37.6 49 4.000 0.2247 0.3845 0.1598 0.058 7.4 65.2 20.4 38.6 55 5.000 0.2230 0.3848 0.1618 0.064 8.1 75.6 21.4 39.8 62 6.000 0.2217 0.3866 0.1649 0.069 8.6 87.1 21.9 43.7 66 7.000 0.2201 0.3869 0.1668 0.075 9.0 93.9 22.4 41.9 67 8.000 0.2201 0.3902 0.1702 0.080 9.6 106.5 24.5 44.9 73 9.000 0.2195 0.3918 0.1723 0.085 10.1 118.2 24.5 46.5 76 10.000 0.2472 0.3753 0.1281 0.024 3.8 12.9 8.0 22.8 14 1.116 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2650 0.3644 0.0994 0.018 2.8 5.6 3.5 15.9 5 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.50 36.44 9.94 10.669 79.477 0.103 6.071 26.55 36.46 9.92 11.026 80.151 0.003 6.073 26.48 36.45 9.96 10.700 79.452 0.013 6.071 26.36 36.46 10.10 10.964 79.283 0.051 6.067 25.60 36.35 10.75 12.661 79.452 0.103 6.048 25.34 36.30 10.96 13.185 79.933 0.154 6.044 25.14 36.41 11.27 13.592 80.113 0.206 6.045 25.01 36.41 11.40 14.025 80.376 0.257 6.043 24.92 36.42 11.50 14.421 80.593 0.309 6.043 24.85 36.43 11.58 14.770 80.770 0.360 6.042 24.80 36.43 11.63 15.075 80.918 0.412 6.041 24.75 36.43 11.67 15.346 81.042 0.463 6.041 24.72 36.42 11.70 15.591 81.149 0.515 6.040 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.013 Accepted refinement result: 26.48 36.45 9.96 10.700 79.452 0.013 6.071 Individual atomic B min max mean iso aniso Overall: 43.28 109.33 71.90 2.07 4478 0 Protein: 43.28 109.33 71.90 2.07 4478 0 Chain A: 43.28 108.95 71.82 N/A 2239 0 Chain B: 51.59 109.33 71.99 N/A 2239 0 Histogram: Values Number of atoms 43.28 - 49.88 5 49.88 - 56.49 9 56.49 - 63.09 98 63.09 - 69.70 2109 69.70 - 76.30 1443 76.30 - 82.91 373 82.91 - 89.51 231 89.51 - 96.12 95 96.12 - 102.72 68 102.72 - 109.33 47 =========================== Idealize ADP of riding H ========================== r_work=0.2648 r_free=0.3645 r_work=0.2648 r_free=0.3645 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2648 r_free= 0.3645 coordinate error (max.-lik. estimate): 0.87 A | | | | normalized target function (ml) (work): 6.070763 | | target function (ml) not normalized (work): 46386.698653 | | target function (ml) not normalized (free): 5614.297416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2752 0.2648 0.3645 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3702 0.3626 0.4345 n_refl.: 8543 remove outliers: r(all,work,free)=0.3702 0.3626 0.4345 n_refl.: 8543 overall B=0.00 to atoms: r(all,work,free)=0.3702 0.3626 0.4345 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2619 0.2514 0.3503 n_refl.: 8543 remove outliers: r(all,work,free)=0.2619 0.2514 0.3503 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 0.2649 709.383 624.396 1.657 0.991 0.390 13.859-11.604 100.00 90 12 0.1816 916.075 865.588 1.358 0.992 0.350 11.577-9.718 99.43 156 19 0.1912 896.360 846.273 1.352 0.990 0.320 9.700-8.140 99.66 262 33 0.2163 719.083 670.841 1.397 0.991 0.320 8.117-6.812 97.25 444 52 0.2401 503.572 464.515 1.239 0.992 0.290 6.812-5.705 94.76 721 93 0.3048 357.317 320.366 1.002 0.994 0.250 5.702-4.776 94.99 1247 137 0.2697 349.044 319.381 0.840 0.995 0.079 4.775-3.999 95.66 2113 265 0.2439 331.555 301.160 1.009 0.996 0.050 3.998-3.486 92.23 2521 281 0.2621 226.449 204.338 1.109 1.003 0.024 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=1.8391 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.033483 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.115110 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 0.2775 0.3513 0.0738 0.015 2.3 1.3 1.6 14.0 2 0.125 0.2626 0.3496 0.0870 0.016 2.5 2.3 2.0 13.6 3 0.250 0.2474 0.3527 0.1053 0.019 3.0 5.2 3.6 15.2 6 0.500 0.2514 0.3503 0.0989 0.018 2.8 5.6 3.5 15.9 5 1.000 0.2494 0.3503 0.1009 0.020 2.9 5.9 3.5 16.1 5 2.000 0.2475 0.3503 0.1027 0.025 3.0 6.4 3.5 16.1 6 3.000 0.2410 0.3510 0.1100 0.034 3.4 8.3 4.0 15.9 9 4.000 0.2375 0.3512 0.1138 0.039 3.7 9.5 4.0 15.9 12 5.000 0.2337 0.3520 0.1183 0.045 4.1 11.7 4.7 15.7 15 6.000 0.2316 0.3521 0.1204 0.049 4.4 12.8 4.7 15.9 17 7.000 0.2302 0.3523 0.1221 0.053 4.5 14.1 4.7 15.7 19 8.000 0.2284 0.3525 0.1241 0.057 4.8 15.5 5.1 15.9 21 9.000 0.2275 0.3526 0.1251 0.060 4.9 16.8 4.9 16.1 22 10.000 0.2514 0.3503 0.0989 0.018 2.8 5.6 3.5 15.9 5 1.017 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2626 0.3496 0.0870 0.016 2.5 2.3 2.0 13.6 3 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.26 34.96 8.70 10.317 79.181 0.115 6.073 26.24 34.86 8.63 10.753 79.743 0.003 6.072 26.20 34.98 8.78 10.370 79.145 0.014 6.072 25.90 35.01 9.10 10.690 78.963 0.058 6.065 24.64 34.85 10.21 12.559 79.924 0.115 6.040 24.41 35.07 10.66 13.194 80.193 0.173 6.040 24.23 35.08 10.85 13.858 80.574 0.230 6.038 24.10 35.09 10.98 14.444 80.874 0.288 6.036 24.01 35.10 11.09 14.948 81.113 0.345 6.035 23.94 35.11 11.17 15.382 81.308 0.403 6.034 23.89 35.12 11.24 15.750 81.466 0.460 6.033 23.84 35.13 11.29 16.071 81.600 0.518 6.033 23.81 35.14 11.33 16.352 81.715 0.576 6.033 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.014 Accepted refinement result: 26.20 34.98 8.78 10.370 79.145 0.014 6.072 Individual atomic B min max mean iso aniso Overall: 44.31 109.18 71.83 1.92 4478 0 Protein: 44.31 109.18 71.83 1.92 4478 0 Chain A: 44.31 108.73 71.80 N/A 2239 0 Chain B: 54.86 109.18 71.87 N/A 2239 0 Histogram: Values Number of atoms 44.31 - 50.80 5 50.80 - 57.28 9 57.28 - 63.77 220 63.77 - 70.26 2175 70.26 - 76.74 1299 76.74 - 83.23 344 83.23 - 89.72 231 89.72 - 96.20 87 96.20 - 102.69 67 102.69 - 109.18 41 =========================== Idealize ADP of riding H ========================== r_work=0.2620 r_free=0.3498 r_work=0.2619 r_free=0.3498 ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2619 r_free= 0.3498 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 6.071535 | | target function (ml) not normalized (work): 46392.595546 | | target function (ml) not normalized (free): 5609.756188 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2292 0.3043 6.5556 6.6769| | 2: 6.28 - 5.01 0.95 1261 149 0.2910 0.3479 6.2215 6.31| | 3: 5.01 - 4.38 0.96 1313 141 0.2607 0.3421 6.1226 6.3432| | 4: 4.38 - 3.99 0.95 1270 167 0.2562 0.3839 5.9847 6.1316| | 5: 3.99 - 3.70 0.94 1269 134 0.2829 0.3835 5.8487 6.017| | 6: 3.70 - 3.49 0.90 1207 143 0.3026 0.4262 5.6551 5.7567| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 32.96 1.02 0.91 123981.50| | 2: 6.28 - 5.01 1261 149 0.62 43.24 1.00 0.85 81354.49| | 3: 5.01 - 4.38 1313 141 0.72 35.23 0.99 0.80 55346.09| | 4: 4.38 - 3.99 1270 167 0.68 38.00 0.98 0.81 47731.42| | 5: 3.99 - 3.70 1269 134 0.61 43.94 0.98 0.73 36857.79| | 6: 3.70 - 3.49 1207 143 0.58 46.62 0.91 0.64 25736.22| |alpha: min = 0.64 max = 0.91 mean = 0.79| |beta: min = 25736.22 max = 123981.50 mean = 62490.78| |figures of merit: min = 0.01 max = 1.00 mean = 0.66| |phase err.(work): min = 0.00 max = 89.59 mean = 39.87| |phase err.(test): min = 2.19 max = 89.27 mean = 40.92| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2712 0.2619 0.3498 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3718 0.3651 0.4293 n_refl.: 8543 remove outliers: r(all,work,free)=0.3718 0.3651 0.4293 n_refl.: 8543 overall B=1.11 to atoms: r(all,work,free)=0.3744 0.3678 0.4310 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2692 0.2601 0.3469 n_refl.: 8543 remove outliers: r(all,work,free)=0.2692 0.2601 0.3469 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 0.2422 709.383 634.436 1.550 0.997 0.380 13.859-11.604 100.00 90 12 0.1681 916.075 869.768 1.406 0.999 0.359 11.577-9.718 99.43 156 19 0.1825 896.360 853.400 1.370 0.997 0.324 9.700-8.140 99.66 262 33 0.2157 719.083 672.242 1.416 0.997 0.319 8.117-6.812 97.25 444 52 0.2464 503.572 467.858 1.279 0.997 0.298 6.812-5.705 94.76 721 93 0.3012 357.317 321.812 1.041 0.997 0.268 5.702-4.776 94.99 1247 137 0.2847 349.044 319.037 0.842 0.996 0.079 4.775-3.999 95.66 2113 265 0.2548 331.555 301.076 1.006 0.993 0.059 3.998-3.486 92.23 2521 281 0.2839 226.449 203.284 1.089 0.995 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.9824 ================= 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 : 0.3488 0.4108 0.010 1.826 0.0 77.4 33.7 0 0.000 1_bss: 0.2767 0.3594 0.010 1.826 39.9 117.3 73.6 0 0.000 1_settarget: 0.2767 0.3594 0.010 1.826 39.9 117.3 73.6 0 0.000 1_weight: 0.2767 0.3594 0.010 1.826 39.9 117.3 73.6 0 0.000 1_xyzrec: 0.2350 0.3649 0.049 4.232 39.9 117.3 73.6 0 0.088 1_adp: 0.2346 0.3658 0.049 4.232 45.0 112.3 74.3 0 0.088 1_regHadp: 0.2346 0.3653 0.049 4.232 45.0 112.3 74.3 0 0.088 2_bss: 0.2339 0.3633 0.049 4.232 42.7 110.0 72.0 0 0.088 2_settarget: 0.2339 0.3633 0.049 4.232 42.7 110.0 72.0 0 0.088 2_updatecdl: 0.2339 0.3633 0.049 4.231 42.7 110.0 72.0 0 0.088 2_weight: 0.2339 0.3633 0.049 4.231 42.7 110.0 72.0 0 0.088 2_xyzrec: 0.2650 0.3644 0.018 2.814 42.7 110.0 72.0 0 0.626 2_adp: 0.2648 0.3645 0.018 2.814 43.3 109.3 71.9 0 0.626 2_regHadp: 0.2648 0.3645 0.018 2.814 43.3 109.3 71.9 0 0.626 3_bss: 0.2514 0.3503 0.018 2.814 43.3 109.3 71.9 0 0.626 3_settarget: 0.2514 0.3503 0.018 2.814 43.3 109.3 71.9 0 0.626 3_updatecdl: 0.2514 0.3503 0.018 2.798 43.3 109.3 71.9 0 0.626 3_setrh: 0.2514 0.3503 0.018 2.798 43.3 109.3 71.9 0 0.626 3_weight: 0.2514 0.3503 0.018 2.798 43.3 109.3 71.9 0 0.626 3_xyzrec: 0.2626 0.3496 0.016 2.479 43.3 109.3 71.9 0 0.677 3_adp: 0.2620 0.3498 0.016 2.479 44.3 109.2 71.8 0 0.677 3_regHadp: 0.2619 0.3498 0.016 2.479 44.3 109.2 71.8 0 0.677 end: 0.2601 0.3469 0.016 2.479 45.4 110.3 72.9 0 0.677 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1jkt_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_1jkt_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.5000 Refinement macro-cycles (run) : 191.8700 Write final files (write_after_run_outputs) : 11.2400 Total : 208.6100 Total CPU time: 4.04 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:42:24 PDT -0700 (1723221744.76 s) Start R-work = 0.2767, R-free = 0.3594 Final R-work = 0.2601, R-free = 0.3469 =============================================================================== Job complete usr+sys time: 252.08 seconds wall clock time: 10 minutes 57.37 seconds (657.37 seconds total)