Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 2.79, per 1000 atoms: 0.32 Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4334 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: 7.28 Conformation dependent library (CDL) restraints added in 1.2 seconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 10 sheets defined 10.7% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing sheet with id= A, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.183A pdb=" N LEU A 41 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG A 137 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU A 158 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 139 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR A 156 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A 141 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N SER A 154 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ARG A 143 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASP A 152 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 68 through 78 removed outlier: 3.602A pdb=" N ARG A 116 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 205 through 210 removed outlier: 5.984A pdb=" N SER A 265 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYS A 273 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 223 through 227 removed outlier: 4.011A pdb=" N GLN A 249 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 57 through 63 removed outlier: 6.380A pdb=" N VAL A 132 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 60 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 130 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 62 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 128 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 195 through 199 removed outlier: 4.199A pdb=" N LEU B 41 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG B 137 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU B 158 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR B 139 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR B 156 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 141 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER B 154 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG B 143 " --> pdb=" O ASP B 152 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP B 152 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 68 through 78 removed outlier: 3.575A pdb=" N ARG B 116 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 204 through 210 removed outlier: 6.658A pdb=" N LYS B 237 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 207 " --> pdb=" O LYS B 237 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN B 239 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU B 209 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS B 241 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.998A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 57 through 63 removed outlier: 6.378A pdb=" N VAL B 132 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 60 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR B 130 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 62 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 128 " --> pdb=" O ILE B 62 " (cutoff:3.500A) 162 hydrogen bonds defined for protein. 441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4332 1.15 - 1.31: 765 1.31 - 1.48: 1860 1.48 - 1.64: 1909 1.64 - 1.81: 6 Bond restraints: 8872 Sorted by residual: bond pdb=" N VAL A 100 " pdb=" H VAL A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N LYS B 46 " pdb=" H LYS B 46 " 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 B 140 " pdb="HE22 GLN B 140 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP B 292 " pdb=" H ASP B 292 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 253 " pdb=" H ILE A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8867 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 162 104.43 - 111.82: 9279 111.82 - 119.21: 2643 119.21 - 126.60: 3803 126.60 - 133.99: 71 Bond angle restraints: 15958 Sorted by residual: angle pdb=" N LEU B 37 " pdb=" CA LEU B 37 " pdb=" C LEU B 37 " ideal model delta sigma weight residual 110.14 119.17 -9.03 1.47e+00 4.63e-01 3.78e+01 angle pdb=" N VAL B 89 " pdb=" CA VAL B 89 " pdb=" CB VAL B 89 " ideal model delta sigma weight residual 111.00 117.48 -6.48 1.14e+00 7.69e-01 3.23e+01 angle pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" C ILE A 108 " ideal model delta sigma weight residual 110.53 115.72 -5.19 9.40e-01 1.13e+00 3.04e+01 angle pdb=" C GLU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 120.31 128.30 -7.99 1.52e+00 4.33e-01 2.76e+01 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 108.27 115.35 -7.08 1.37e+00 5.33e-01 2.67e+01 ... (remaining 15953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3781 17.72 - 35.43: 252 35.43 - 53.15: 113 53.15 - 70.87: 53 70.87 - 88.58: 11 Dihedral angle restraints: 4210 sinusoidal: 2252 harmonic: 1958 Sorted by residual: dihedral pdb=" C THR B 212 " pdb=" N THR B 212 " pdb=" CA THR B 212 " pdb=" CB THR B 212 " ideal model delta harmonic sigma weight residual -122.00 -135.87 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLU B 184 " pdb=" N GLU B 184 " pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta harmonic sigma weight residual -122.60 -135.02 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C ASN B 86 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " pdb=" CB ASN B 86 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 495 0.107 - 0.213: 154 0.213 - 0.320: 30 0.320 - 0.427: 15 0.427 - 0.533: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN A 86 " pdb=" N ASN A 86 " pdb=" C ASN A 86 " pdb=" CB ASN A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.013 2.00e-02 2.50e+03 3.89e-02 2.26e+01 pdb=" CD GLN B 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN B 61 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN B 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 264 " -0.005 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 264 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 264 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 264 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR B 264 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR B 264 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR B 264 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.014 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 130 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 130 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR B 130 " 0.041 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 26 1.64 - 2.38: 2701 2.38 - 3.12: 27057 3.12 - 3.86: 38097 3.86 - 4.60: 59430 Warning: very small nonbonded interaction distances. Nonbonded interactions: 127311 Sorted by model distance: nonbonded pdb="HH12 ARG A 227 " pdb=" HB2 PRO A 311 " model vdw 0.896 2.270 nonbonded pdb="HH12 ARG B 227 " pdb=" HB2 PRO B 311 " model vdw 0.922 2.270 nonbonded pdb=" HE2 LYS B 257 " pdb=" HA LYS B 283 " model vdw 1.020 2.440 nonbonded pdb=" HE2 LYS A 257 " pdb=" HA LYS A 283 " model vdw 1.026 2.440 nonbonded pdb="HD21 ASN A 36 " pdb=" HE2 LYS B 283 " model vdw 1.089 2.270 ... (remaining 127306 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 4 15.91 1 O 904 7.97 1 N 728 6.97 1 C 2814 5.97 1 H 4334 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: 4334 of 8784 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8784 n_use_u_iso = 8784 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 = 8784 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8784 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8784 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 54 through 56 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 93 through 104 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 171 through 173 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 176 through 179 helix_type = alpha pi *3_10 unknown } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 211 through 216 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 267 through 269 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'B' and resid 54 through 56 helix_type = alpha pi *3_10 unknown } helix { serial_number = "8" helix_identifier = "8" selection = chain 'B' and resid 93 through 104 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'B' and resid 171 through 173 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'B' and resid 176 through 179 helix_type = alpha pi *3_10 unknown } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 211 through 215 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 267 through 269 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 195 through 199 sheet_id = " A" strand { selection = chain 'A' and resid 40 through 45 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 45 and name N bond_start_previous = chain 'A' and resid 195 and name O } strand { selection = chain 'A' and resid 127 through 144 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 144 and name N bond_start_previous = chain 'A' and resid 40 and name O } strand { selection = chain 'A' and resid 151 through 168 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 168 and name N bond_start_previous = chain 'A' and resid 127 and name O } strand { selection = chain 'A' and resid 80 through 82 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 154 and name O } } sheet { first_strand = chain 'A' and resid 68 through 78 sheet_id = " B" strand { selection = chain 'A' and resid 111 through 121 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 120 and name N bond_start_previous = chain 'A' and resid 69 and name O } } sheet { first_strand = chain 'A' and resid 205 through 210 sheet_id = " C" strand { selection = chain 'A' and resid 238 through 244 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 239 and name N bond_start_previous = chain 'A' and resid 205 and name O } strand { selection = chain 'A' and resid 294 through 302 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 300 and name N bond_start_previous = chain 'A' and resid 238 and name O } strand { selection = chain 'A' and resid 259 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 264 and name N bond_start_previous = chain 'A' and resid 297 and name O } strand { selection = chain 'A' and resid 272 through 277 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 277 and name N bond_start_previous = chain 'A' and resid 261 and name O } } sheet { first_strand = chain 'A' and resid 223 through 227 sheet_id = " D" strand { selection = chain 'A' and resid 313 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 316 and name N bond_start_previous = chain 'A' and resid 224 and name O } strand { selection = chain 'A' and resid 249 through 255 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 254 and name N bond_start_previous = chain 'A' and resid 315 and name O } strand { selection = chain 'A' and resid 285 through 291 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 291 and name N bond_start_previous = chain 'A' and resid 249 and name O } } sheet { first_strand = chain 'A' and resid 57 through 63 sheet_id = " E" strand { selection = chain 'A' and resid 128 through 133 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 132 and name N bond_start_previous = chain 'A' and resid 58 and name O } } sheet { first_strand = chain 'B' and resid 195 through 199 sheet_id = " F" strand { selection = chain 'B' and resid 40 through 45 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 45 and name N bond_start_previous = chain 'B' and resid 195 and name O } strand { selection = chain 'B' and resid 127 through 144 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 144 and name N bond_start_previous = chain 'B' and resid 40 and name O } strand { selection = chain 'B' and resid 151 through 168 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 168 and name N bond_start_previous = chain 'B' and resid 127 and name O } strand { selection = chain 'B' and resid 80 through 82 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 82 and name N bond_start_previous = chain 'B' and resid 154 and name O } } sheet { first_strand = chain 'B' and resid 68 through 78 sheet_id = " G" strand { selection = chain 'B' and resid 111 through 121 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 120 and name N bond_start_previous = chain 'B' and resid 69 and name O } } sheet { first_strand = chain 'B' and resid 204 through 210 sheet_id = " H" strand { selection = chain 'B' and resid 237 through 244 sense = *parallel antiparallel unknown bond_start_current = chain 'B' and resid 237 and name N bond_start_previous = chain 'B' and resid 205 and name O } strand { selection = chain 'B' and resid 294 through 302 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 300 and name N bond_start_previous = chain 'B' and resid 238 and name O } strand { selection = chain 'B' and resid 259 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 264 and name N bond_start_previous = chain 'B' and resid 297 and name O } strand { selection = chain 'B' and resid 272 through 277 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 277 and name N bond_start_previous = chain 'B' and resid 261 and name O } } sheet { first_strand = chain 'B' and resid 223 through 227 sheet_id = " I" strand { selection = chain 'B' and resid 313 through 318 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 316 and name N bond_start_previous = chain 'B' and resid 224 and name O } strand { selection = chain 'B' and resid 249 through 255 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 254 and name N bond_start_previous = chain 'B' and resid 315 and name O } strand { selection = chain 'B' and resid 285 through 291 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 291 and name N bond_start_previous = chain 'B' and resid 249 and name O } } sheet { first_strand = chain 'B' and resid 57 through 63 sheet_id = " J" strand { selection = chain 'B' and resid 128 through 133 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 132 and name N bond_start_previous = chain 'B' and resid 58 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2yhj_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4334 occupancy sum: 4334.00 (% of total atoms 49.51) Rotatable: count: 1252 occupancy sum: 1252.00 (% of total atoms 14.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2869 154 0.5470 0.4516 5.0219 4.6882| | 2: 6.35 - 5.04 1.00 2777 143 0.5707 0.3865 4.0914 4.1453| | 3: 5.04 - 4.40 1.00 2783 123 0.6252 0.4330 3.9538 4.0152| | 4: 4.40 - 4.00 0.99 2723 135 0.6724 0.5113 3.6055 3.6227| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2869 154 0.51 50.27 0.85 0.03 2262.31| | 2: 6.35 - 5.04 2777 143 0.43 57.38 2.00 0.04 1473.91| | 3: 5.04 - 4.40 2783 123 0.59 44.81 2.34 0.05 841.25| | 4: 4.40 - 4.00 2723 135 0.61 43.53 2.67 0.06 378.44| |alpha: min = 0.03 max = 0.06 mean = 0.04| |beta: min = 378.44 max = 2262.31 mean = 1251.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.88 mean = 49.03| |phase err.(test): min = 0.00 max = 89.64 mean = 49.15| |-----------------------------------------------------------------------------| ----------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 0.113 4538 Z= 0.660 Angle : 1.541 9.034 6170 Z= 1.009 Chirality : 0.123 0.533 700 Planarity : 0.007 0.028 792 Dihedral : 15.468 88.583 1622 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.22 % Allowed : 6.83 % Favored : 88.96 % Cbeta Deviations : 2.09 % 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: -0.48 (0.32), residues: 566 helix: -0.38 (0.69), residues: 42 sheet: 0.26 (0.29), residues: 286 loop : -0.96 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 116 TYR 0.045 0.007 TYR B 264 PHE 0.018 0.005 PHE B 316 TRP 0.046 0.009 TRP A 162 HIS 0.008 0.002 HIS A 146 Individual atomic B min max mean iso aniso Overall: 34.09 300.00 115.49 16.58 4450 0 Protein: 34.09 300.00 115.49 16.58 4450 0 Chain A: 34.09 300.00 113.10 N/A 2225 0 Chain B: 38.50 300.00 117.88 N/A 2225 0 Histogram: Values Number of atoms 34.09 - 60.68 195 60.68 - 87.27 913 87.27 - 113.86 1318 113.86 - 140.45 1013 140.45 - 167.04 585 167.04 - 193.64 250 193.64 - 220.23 97 220.23 - 246.82 41 246.82 - 273.41 14 273.41 - 300.00 24 |-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: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 re-set all scales: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 remove outliers: r(all,work,free)=0.5853 0.5894 0.4411 n_refl.: 11703 overall B=1.75 to atoms: r(all,work,free)=0.5901 0.5942 0.4442 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 remove outliers: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3727 4797.975 4480.474 1.327 1.203 0.370 20.447-16.215 100.00 96 3 0.3168 3372.726 3174.597 1.053 1.189 0.340 16.132-12.745 100.00 194 11 0.2772 3266.441 3051.447 1.121 1.171 0.329 12.705-10.080 100.00 377 16 0.2682 3068.794 2812.929 1.067 1.142 0.309 10.040-7.926 100.00 749 47 0.2594 2378.704 2226.653 1.035 1.095 0.278 7.906-6.254 99.81 1487 80 0.3015 1468.580 1345.750 1.035 1.018 0.228 6.249-4.933 100.00 3011 157 0.3075 1268.682 1121.341 1.068 0.895 0.177 4.931-4.001 99.68 5136 240 0.3089 1069.236 942.207 1.427 0.716 0.137 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.8620 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.781473 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153546 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3037 0.3487 0.0450 0.002 0.5 1.6 0.0 3.2 0 0.125 0.2999 0.3477 0.0478 0.002 0.5 1.4 0.0 3.2 0 0.250 0.2935 0.3498 0.0563 0.003 0.5 1.9 0.0 2.8 0 0.500 0.2860 0.3506 0.0646 0.003 0.6 2.7 0.2 2.8 0 1.000 0.2785 0.3527 0.0741 0.005 0.7 3.2 0.0 4.0 0 2.000 0.2750 0.3550 0.0799 0.007 0.8 4.7 0.2 3.6 0 3.000 0.2722 0.3535 0.0813 0.008 0.9 6.0 0.4 4.4 0 4.000 0.2710 0.3555 0.0845 0.009 1.0 9.0 1.1 5.0 0 5.000 0.2695 0.3542 0.0848 0.011 1.1 9.1 1.6 6.6 0 6.000 0.2681 0.3541 0.0860 0.012 1.1 9.8 1.6 6.8 0 7.000 0.2670 0.3562 0.0892 0.013 1.2 11.2 1.8 7.8 0 8.000 0.2660 0.3571 0.0911 0.014 1.3 13.8 2.3 8.6 0 9.000 0.2646 0.3565 0.0919 0.015 1.4 14.4 1.9 9.2 0 10.000 0.2681 0.3565 0.0884 0.012 1.2 12.3 1.8 7.6 0 7.391 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2999 0.3477 0.0478 0.002 0.5 1.4 0.0 3.2 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.99 34.77 4.78 11.856 115.379 0.154 0.114 30.27 33.48 3.21 15.602 119.793 0.005 0.116 30.04 33.43 3.39 15.563 119.708 0.019 0.115 29.29 33.32 4.02 15.706 119.471 0.077 0.110 28.64 33.34 4.70 16.378 119.348 0.154 0.106 28.21 33.50 5.29 17.132 119.325 0.230 0.103 27.91 33.65 5.74 17.707 119.310 0.307 0.102 27.71 33.80 6.09 18.342 119.365 0.384 0.100 27.55 33.89 6.34 19.002 119.484 0.461 0.099 27.44 34.01 6.57 19.486 119.531 0.537 0.099 27.34 34.05 6.71 20.052 119.657 0.614 0.098 27.23 34.11 6.89 20.735 119.852 0.691 0.098 27.14 34.17 7.03 21.319 120.009 0.768 0.097 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.077 Accepted refinement result: 29.29 33.32 4.02 15.706 119.471 0.077 0.110 Individual atomic B min max mean iso aniso Overall: 34.40 296.75 125.32 12.06 4450 0 Protein: 34.40 296.75 125.32 12.06 4450 0 Chain A: 34.40 296.75 123.04 N/A 2225 0 Chain B: 62.08 296.75 127.59 N/A 2225 0 Histogram: Values Number of atoms 34.40 - 60.64 3 60.64 - 86.87 331 86.87 - 113.10 1477 113.10 - 139.34 1450 139.34 - 165.57 736 165.57 - 191.81 283 191.81 - 218.04 92 218.04 - 244.28 41 244.28 - 270.51 14 270.51 - 296.75 23 =========================== Idealize ADP of riding H ========================== r_work=0.2929 r_free=0.3332 r_work=0.2924 r_free=0.3333 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2924 r_free= 0.3333 coordinate error (max.-lik. estimate): 0.60 A | | | | normalized target function (ls_wunit_k1) (work): 0.109416 | | target function (ls_wunit_k1) not normalized (work): 1219.764251 | | target function (ls_wunit_k1) not normalized (free): 75.647089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2943 0.2924 0.3333 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6139 0.6177 0.4627 n_refl.: 11703 remove outliers: r(all,work,free)=0.6139 0.6177 0.4627 n_refl.: 11703 overall B=-2.27 to atoms: r(all,work,free)=0.6080 0.6119 0.4582 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2912 0.2892 0.3324 n_refl.: 11703 remove outliers: r(all,work,free)=0.2912 0.2892 0.3324 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3680 1676.747 1557.192 1.186 1.177 0.370 20.447-16.215 100.00 96 3 0.3083 1178.666 1114.428 0.938 1.165 0.336 16.132-12.745 100.00 194 11 0.2666 1141.522 1072.722 1.008 1.149 0.328 12.705-10.080 100.00 377 16 0.2569 1072.451 994.536 1.001 1.124 0.321 10.040-7.926 100.00 749 47 0.2428 831.285 786.557 0.974 1.083 0.282 7.906-6.254 99.81 1487 80 0.2748 513.224 477.177 0.957 1.016 0.213 6.249-4.933 100.00 3011 157 0.2918 443.366 397.739 1.039 0.908 0.183 4.931-4.001 99.68 5136 240 0.3096 373.665 331.962 1.337 0.750 0.103 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.4980 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.490875 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.074027 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2947 0.3339 0.0392 0.002 0.4 1.4 0.0 2.0 0 0.017 0.2919 0.3334 0.0415 0.002 0.4 1.7 0.0 2.0 0 0.051 0.2885 0.3338 0.0453 0.002 0.4 1.6 0.0 2.0 0 0.102 0.2858 0.3336 0.0478 0.002 0.4 1.6 0.0 2.0 0 0.153 0.2839 0.3339 0.0500 0.002 0.5 1.8 0.0 2.0 0 0.204 0.2825 0.3339 0.0514 0.002 0.5 2.1 0.0 2.0 0 0.255 0.2814 0.3334 0.0520 0.003 0.5 2.2 0.0 2.2 0 0.307 0.2807 0.3339 0.0531 0.003 0.5 2.4 0.0 2.0 0 0.358 0.2850 0.3340 0.0489 0.002 0.5 1.7 0.0 2.0 0 0.170 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2947 0.3339 0.0392 0.002 0.4 1.4 0.0 2.0 0 0.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.47 33.39 3.92 19.741 134.248 0.074 6.504 32.38 33.82 1.45 17.423 144.395 0.002 6.525 31.58 33.67 2.08 16.965 143.691 0.009 6.510 29.55 33.52 3.97 18.209 140.524 0.037 6.477 28.56 33.85 5.28 20.253 139.026 0.074 6.467 28.25 33.65 5.40 20.059 137.221 0.111 6.467 28.10 33.62 5.52 20.581 137.087 0.148 6.466 28.00 33.58 5.58 21.065 137.239 0.185 6.465 27.93 33.59 5.66 21.439 137.369 0.222 6.465 27.89 33.59 5.69 21.605 137.387 0.259 6.464 27.86 33.63 5.77 21.850 137.492 0.296 6.464 27.80 33.65 5.85 22.196 137.689 0.333 6.463 27.78 33.66 5.87 22.314 137.723 0.370 6.463 max suggested for this run: 26.85 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.037 Accepted refinement result: 29.55 33.52 3.97 18.209 140.524 0.037 6.477 Individual atomic B min max mean iso aniso Overall: 58.77 298.75 135.43 12.79 4450 0 Protein: 58.77 298.75 135.43 12.79 4450 0 Chain A: 58.77 298.75 133.05 N/A 2225 0 Chain B: 70.09 289.48 137.82 N/A 2225 0 Histogram: Values Number of atoms 58.77 - 82.77 72 82.77 - 106.76 801 106.76 - 130.76 1242 130.76 - 154.76 1266 154.76 - 178.76 686 178.76 - 202.76 251 202.76 - 226.76 74 226.76 - 250.75 27 250.75 - 274.75 12 274.75 - 298.75 19 =========================== Idealize ADP of riding H ========================== r_work=0.2955 r_free=0.3352 r_work=0.2962 r_free=0.3369 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2962 r_free= 0.3369 coordinate error (max.-lik. estimate): 0.57 A | | | | normalized target function (ml) (work): 6.476993 | | target function (ml) not normalized (work): 72205.520959 | | target function (ml) not normalized (free): 3629.386355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2981 0.2962 0.3369 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6403 0.6440 0.4819 n_refl.: 11703 remove outliers: r(all,work,free)=0.6403 0.6440 0.4819 n_refl.: 11703 overall B=-13.65 to atoms: r(all,work,free)=0.6056 0.6096 0.4545 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2966 0.2945 0.3388 n_refl.: 11703 remove outliers: r(all,work,free)=0.2966 0.2945 0.3388 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3731 1470.483 1359.744 1.312 1.127 0.372 20.447-16.215 100.00 96 3 0.3102 1033.673 973.472 1.048 1.120 0.339 16.132-12.745 100.00 194 11 0.2684 1001.098 934.732 1.089 1.109 0.329 12.705-10.080 100.00 377 16 0.2626 940.524 865.623 1.088 1.090 0.329 10.040-7.926 100.00 749 47 0.2465 729.025 686.214 1.042 1.060 0.282 7.906-6.254 99.81 1487 80 0.2914 450.090 410.266 1.028 1.009 0.215 6.249-4.933 100.00 3011 157 0.3025 388.825 343.163 1.036 0.927 0.179 4.931-4.001 99.68 5136 240 0.3077 327.699 289.094 1.235 0.808 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=5.6330 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2945 r_free=0.3388 After: r_work=0.2945 r_free=0.3388 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.832061 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.080069 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2946 0.3384 0.0439 0.002 0.4 1.7 0.0 1.8 0 0.017 0.2945 0.3384 0.0439 0.002 0.4 1.6 0.0 1.8 0 0.052 0.2944 0.3384 0.0440 0.002 0.4 1.6 0.0 1.8 0 0.104 0.2943 0.3383 0.0441 0.002 0.4 1.7 0.0 1.8 0 0.157 0.2941 0.3382 0.0441 0.002 0.4 1.6 0.0 1.8 0 0.209 0.2939 0.3381 0.0442 0.002 0.4 1.6 0.0 1.8 0 0.261 0.2938 0.3383 0.0445 0.002 0.4 1.6 0.0 1.8 0 0.313 0.2934 0.3383 0.0449 0.003 0.4 1.7 0.0 1.8 0 0.366 0.2943 0.3383 0.0441 0.002 0.4 1.7 0.0 1.8 0 0.174 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2941 0.3382 0.0441 0.002 0.4 1.6 0.0 1.8 0 0.209 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.41 33.82 4.41 21.383 134.793 0.080 6.349 31.55 33.63 2.07 18.130 141.501 0.002 6.388 31.22 33.54 2.31 17.694 141.954 0.010 6.380 29.14 33.61 4.47 19.396 139.109 0.040 6.349 28.19 33.62 5.43 21.252 137.568 0.080 6.333 27.98 33.60 5.62 21.837 137.148 0.120 6.328 27.96 33.61 5.65 22.123 136.849 0.160 6.326 27.88 33.65 5.77 22.485 137.038 0.200 6.325 27.79 33.70 5.91 22.938 137.380 0.240 6.324 27.77 33.73 5.96 23.117 137.435 0.280 6.323 27.77 33.68 5.91 23.128 137.493 0.320 6.322 27.66 33.75 6.09 23.724 137.956 0.360 6.321 27.68 33.76 6.08 23.608 137.867 0.400 6.321 max suggested for this run: 26.96 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 31.22 33.54 2.31 17.694 141.954 0.010 6.380 Individual atomic B min max mean iso aniso Overall: 88.80 280.10 135.92 7.72 4450 0 Protein: 88.80 280.10 135.92 7.72 4450 0 Chain A: 88.80 280.10 133.81 N/A 2225 0 Chain B: 92.75 270.83 138.03 N/A 2225 0 Histogram: Values Number of atoms 88.80 - 107.93 596 107.93 - 127.06 1347 127.06 - 146.19 1152 146.19 - 165.32 774 165.32 - 184.45 357 184.45 - 203.58 132 203.58 - 222.71 51 222.71 - 241.84 16 241.84 - 260.97 7 260.97 - 280.10 18 =========================== Idealize ADP of riding H ========================== r_work=0.3122 r_free=0.3354 r_work=0.3141 r_free=0.3352 ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.3141 r_free= 0.3352 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.386134 | | target function (ml) not normalized (work): 71192.627342 | | target function (ml) not normalized (free): 3556.837526 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2866 154 0.2837 0.3128 6.8578 6.8052| | 2: 6.35 - 5.04 1.00 2776 143 0.3218 0.3335 6.3343 6.3761| | 3: 5.04 - 4.40 1.00 2783 123 0.3347 0.3602 6.3028 6.3477| | 4: 4.40 - 4.00 0.99 2723 135 0.3525 0.3640 6.0277 6.0466| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2866 154 0.77 28.43 0.96 0.88 116969.91| | 2: 6.35 - 5.04 2776 143 0.65 40.31 1.05 0.91 88927.99| | 3: 5.04 - 4.40 2783 123 0.71 34.96 1.14 0.93 64423.92| | 4: 4.40 - 4.00 2723 135 0.66 39.64 1.12 0.96 44001.26| |alpha: min = 0.88 max = 0.96 mean = 0.92| |beta: min = 44001.26 max = 116969.91 mean = 79046.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.86 mean = 35.76| |phase err.(test): min = 0.00 max = 87.53 mean = 35.97| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.3151 0.3141 0.3352 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6491 0.6527 0.4916 n_refl.: 11703 remove outliers: r(all,work,free)=0.6491 0.6527 0.4916 n_refl.: 11703 overall B=-20.68 to atoms: r(all,work,free)=0.5976 0.6015 0.4503 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3081 0.3070 0.3319 n_refl.: 11703 remove outliers: r(all,work,free)=0.3081 0.3070 0.3319 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3697 1470.483 1358.615 1.301 1.157 0.373 20.447-16.215 100.00 96 3 0.3127 1033.673 973.425 1.043 1.147 0.341 16.132-12.745 100.00 194 11 0.2735 1001.098 930.982 1.075 1.133 0.332 12.705-10.080 100.00 377 16 0.2704 940.524 862.785 1.096 1.110 0.334 10.040-7.926 100.00 749 47 0.2532 729.025 685.741 1.073 1.073 0.300 7.906-6.254 99.81 1487 80 0.2943 450.090 413.074 1.013 1.012 0.234 6.249-4.933 100.00 3011 157 0.3147 388.825 342.881 1.065 0.914 0.214 4.931-4.001 99.68 5136 240 0.3299 327.699 287.453 1.279 0.772 0.144 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=9.3065 ================= 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 : 0.5891 0.4411 0.010 1.541 34.1 300.0 115.5 0 0.000 1_bss: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_settarget: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_weight: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_xyzrec: 0.2999 0.3477 0.002 0.505 35.8 301.7 117.2 0 0.190 1_adp: 0.2929 0.3332 0.002 0.505 34.4 296.7 125.3 0 0.190 1_regHadp: 0.2924 0.3333 0.002 0.505 34.4 296.7 125.3 0 0.190 2_bss: 0.2892 0.3324 0.002 0.505 32.1 294.5 123.0 0 0.190 2_settarget: 0.2892 0.3324 0.002 0.505 32.1 294.5 123.0 0 0.190 2_updatecdl: 0.2892 0.3324 0.002 0.574 32.1 294.5 123.0 0 0.190 2_weight: 0.2892 0.3324 0.002 0.574 32.1 294.5 123.0 0 0.190 2_xyzrec: 0.2947 0.3339 0.002 0.417 32.1 294.5 123.0 0 0.238 2_adp: 0.2955 0.3352 0.002 0.417 58.8 298.8 135.4 0 0.238 2_regHadp: 0.2962 0.3369 0.002 0.417 58.8 298.8 135.4 0 0.238 3_bss: 0.2945 0.3388 0.002 0.417 45.1 285.1 121.8 0 0.238 3_settarget: 0.2945 0.3388 0.002 0.417 45.1 285.1 121.8 0 0.238 3_updatecdl: 0.2945 0.3388 0.002 0.460 45.1 285.1 121.8 0 0.238 3_setrh: 0.2945 0.3388 0.002 0.460 45.1 285.1 121.8 0 0.238 3_weight: 0.2945 0.3388 0.002 0.460 45.1 285.1 121.8 0 0.238 3_xyzrec: 0.2941 0.3382 0.002 0.432 45.1 285.1 121.8 0 0.239 3_adp: 0.3122 0.3354 0.002 0.432 88.8 280.1 135.9 0 0.239 3_regHadp: 0.3141 0.3352 0.002 0.432 88.8 280.1 135.9 0 0.239 end: 0.3070 0.3319 0.002 0.432 68.1 259.4 115.2 0 0.239 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2yhj_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2yhj_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.8400 Refinement macro-cycles (run) : 295.4000 Write final files (write_after_run_outputs) : 18.3900 Total : 326.6300 Total CPU time: 6.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:10 PDT -0700 (1716251770.11 s) Start R-work = 0.2998, R-free = 0.3469 Final R-work = 0.3070, R-free = 0.3319 =============================================================================== Job complete usr+sys time: 400.25 seconds wall clock time: 18 minutes 58.20 seconds (1138.20 seconds total)