Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s 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: 1.58, per 1000 atoms: 0.18 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: 1.97 Conformation dependent library (CDL) restraints added in 360.0 milliseconds 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. 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: 0.63 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: 1.96 Time building geometry restraints manager: 2.30 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2998 r_free=0.3469 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2998 r_free=0.3469 ========================= Local real-space refinement ========================= Before: r_work=0.2998 r_free=0.3469 291 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 270 time to evaluate : 0.452 outliers start: 21 outliers final: 4 residues processed: 21 average time/residue: 0.2694 time to fit residues: 9.0745 After: r_work=0.3017 r_free=0.3503 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.830375 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152534 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 0.3040 0.3506 0.0466 0.002 0.5 2.1 0.0 0.6 0 0.125 0.3004 0.3508 0.0505 0.002 0.5 1.9 0.0 0.6 0 0.250 0.2941 0.3508 0.0567 0.003 0.6 2.2 0.0 0.6 0 0.500 0.2874 0.3522 0.0649 0.004 0.6 2.6 0.0 0.8 0 1.000 0.2802 0.3537 0.0735 0.005 0.7 4.7 0.0 1.8 0 2.000 0.2768 0.3547 0.0779 0.007 0.8 5.1 0.0 2.4 0 3.000 0.2736 0.3557 0.0822 0.008 1.0 6.7 0.0 3.6 0 4.000 0.2712 0.3541 0.0829 0.010 1.0 6.7 0.0 3.2 0 5.000 0.2700 0.3556 0.0855 0.011 1.1 8.3 0.0 4.8 0 6.000 0.2685 0.3549 0.0863 0.012 1.2 9.0 0.0 5.4 0 7.000 0.2676 0.3543 0.0867 0.013 1.3 11.4 0.0 7.6 0 8.000 0.2667 0.3544 0.0877 0.015 1.3 11.6 0.0 8.4 0 9.000 0.2659 0.3527 0.0868 0.016 1.4 13.1 0.0 9.0 0 10.000 0.2682 0.3547 0.0864 0.013 1.2 9.0 0.0 5.2 0 7.415 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3040 0.3506 0.0466 0.002 0.5 2.1 0.0 0.6 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.3040 r_free=0.3506 269 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 1.590 outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5069 time to fit residues: 4.6368 After: r_work=0.3041 r_free=0.3500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.41 35.00 4.59 11.856 115.379 0.153 0.118 30.66 33.37 2.71 15.728 119.839 0.005 0.120 30.43 33.35 2.92 15.724 119.762 0.019 0.118 29.66 33.40 3.74 16.074 119.580 0.076 0.113 28.98 33.52 4.54 16.777 119.440 0.153 0.109 28.52 33.68 5.16 17.571 119.413 0.229 0.106 28.24 33.91 5.67 18.293 119.450 0.305 0.104 28.02 34.02 6.00 18.791 119.462 0.381 0.103 27.87 34.13 6.25 19.202 119.498 0.458 0.102 27.75 34.20 6.45 19.764 119.572 0.534 0.101 27.63 34.28 6.64 20.344 119.695 0.610 0.101 27.54 34.37 6.83 20.913 119.817 0.686 0.100 27.42 34.44 7.02 21.754 120.079 0.763 0.100 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.019 Accepted refinement result: 30.43 33.35 2.92 15.724 119.762 0.019 0.118 Individual atomic B min max mean iso aniso Overall: 40.24 296.75 125.89 11.62 4450 0 Protein: 40.24 296.75 125.89 11.62 4450 0 Chain A: 40.24 296.75 123.59 N/A 2225 0 Chain B: 70.13 296.75 128.19 N/A 2225 0 Histogram: Values Number of atoms 40.24 - 65.89 3 65.89 - 91.54 442 91.54 - 117.19 1601 117.19 - 142.84 1375 142.84 - 168.49 620 168.49 - 194.14 255 194.14 - 219.80 80 219.80 - 245.45 37 245.45 - 271.10 15 271.10 - 296.75 22 =========================== Idealize ADP of riding H ========================== r_work=0.3043 r_free=0.3335 r_work=0.3043 r_free=0.3337 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.3043 r_free= 0.3337 coordinate error (max.-lik. estimate): 0.56 A | | | | normalized target function (ls_wunit_k1) (work): 0.117943 | | target function (ls_wunit_k1) not normalized (work): 1314.832356 | | target function (ls_wunit_k1) not normalized (free): 76.815158 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3056 0.3043 0.3337 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6188 0.6227 0.4667 n_refl.: 11703 remove outliers: r(all,work,free)=0.6188 0.6227 0.4667 n_refl.: 11703 overall B=-7.42 to atoms: r(all,work,free)=0.5996 0.6036 0.4520 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3018 0.3003 0.3327 n_refl.: 11703 remove outliers: r(all,work,free)=0.3018 0.3003 0.3327 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 0.3687 1674.768 1549.153 1.256 1.169 0.371 20.447-16.215 100.00 96 3 0.3099 1177.274 1108.505 0.979 1.157 0.337 16.132-12.745 100.00 194 11 0.2798 1140.175 1068.020 1.061 1.142 0.330 12.705-10.080 100.00 377 16 0.2636 1071.185 984.933 1.056 1.117 0.325 10.040-7.926 100.00 749 47 0.2560 830.304 778.687 1.009 1.078 0.277 7.906-6.254 99.81 1487 80 0.2900 512.619 471.663 0.972 1.014 0.208 6.249-4.933 100.00 3011 157 0.3054 442.842 392.376 1.050 0.911 0.192 4.931-4.001 99.68 5136 240 0.3187 373.224 328.448 1.327 0.760 0.121 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=2.7138 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.3003 r_free=0.3327 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 140 GLN Total number of N/Q/H flips: 2 r_work=0.3004 r_free=0.3326 ========================= Local real-space refinement ========================= Before: r_work=0.3004 r_free=0.3326 284 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 2.073 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4810 After: r_work=0.3004 r_free=0.3326 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.253625 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.075558 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 0.3026 0.3324 0.0298 0.002 0.4 1.4 0.0 0.4 0 0.016 0.3011 0.3324 0.0313 0.002 0.4 1.7 0.0 0.4 0 0.048 0.2990 0.3333 0.0343 0.002 0.5 1.8 0.0 0.4 0 0.097 0.2973 0.3337 0.0364 0.002 0.5 1.9 0.0 0.4 0 0.145 0.2958 0.3329 0.0371 0.002 0.5 1.8 0.0 0.4 0 0.193 0.2944 0.3322 0.0378 0.003 0.5 1.9 0.0 0.4 0 0.242 0.2934 0.3334 0.0399 0.003 0.5 1.9 0.0 0.2 0 0.290 0.2923 0.3336 0.0413 0.004 0.6 1.8 0.0 0.2 0 0.338 0.2968 0.3332 0.0364 0.002 0.5 1.9 0.0 0.4 0 0.161 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3026 0.3324 0.0298 0.002 0.4 1.4 0.0 0.4 0 0.016 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.3026 r_free=0.3324 286 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.520 outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4964 time to fit residues: 3.3095 After: r_work=0.3026 r_free=0.3326 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.26 33.26 3.00 19.628 129.568 0.076 6.510 32.38 33.54 1.16 18.030 140.741 0.002 6.520 31.46 33.26 1.80 17.327 140.298 0.009 6.503 29.24 33.06 3.82 18.505 135.323 0.038 6.472 28.62 33.25 4.63 19.531 133.279 0.076 6.467 28.49 33.27 4.78 20.087 132.646 0.113 6.467 28.41 33.21 4.80 20.524 132.533 0.151 6.466 28.31 33.25 4.95 21.051 132.756 0.189 6.464 28.23 33.29 5.07 21.530 132.969 0.227 6.463 28.17 33.34 5.17 21.898 133.126 0.264 6.463 28.12 33.40 5.28 22.270 133.300 0.302 6.462 28.08 33.43 5.35 22.608 133.457 0.340 6.462 28.05 33.46 5.41 22.912 133.597 0.378 6.461 max suggested for this run: 25.91 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.038 Accepted refinement result: 29.24 33.06 3.82 18.505 135.323 0.038 6.472 Individual atomic B min max mean iso aniso Overall: 58.88 284.33 129.83 12.85 4450 0 Protein: 58.88 284.33 129.83 12.85 4450 0 Chain A: 58.88 284.33 127.50 N/A 2225 0 Chain B: 66.69 284.33 132.16 N/A 2225 0 Histogram: Values Number of atoms 58.88 - 81.43 119 81.43 - 103.97 848 103.97 - 126.52 1253 126.52 - 149.06 1173 149.06 - 171.61 652 171.61 - 194.15 266 194.15 - 216.70 75 216.70 - 239.24 29 239.24 - 261.78 14 261.78 - 284.33 21 =========================== Idealize ADP of riding H ========================== r_work=0.2924 r_free=0.3306 r_work=0.2917 r_free=0.3322 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2917 r_free= 0.3322 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.470592 | | target function (ml) not normalized (work): 72134.160535 | | target function (ml) not normalized (free): 3622.880981 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2936 0.2917 0.3322 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6263 0.6300 0.4697 n_refl.: 11703 remove outliers: r(all,work,free)=0.6263 0.6300 0.4697 n_refl.: 11703 overall B=-6.89 to atoms: r(all,work,free)=0.6086 0.6124 0.4557 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2921 0.2901 0.3330 n_refl.: 11703 remove outliers: r(all,work,free)=0.2921 0.2901 0.3330 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 0.3673 1674.768 1548.000 1.248 1.150 0.371 20.447-16.215 100.00 96 3 0.3119 1177.274 1107.594 0.998 1.139 0.340 16.132-12.745 100.00 194 11 0.2768 1140.175 1066.318 1.082 1.126 0.333 12.705-10.080 100.00 377 16 0.2578 1071.185 987.636 1.051 1.104 0.325 10.040-7.926 100.00 749 47 0.2460 830.304 780.172 1.011 1.068 0.276 7.906-6.254 99.81 1487 80 0.2867 512.619 467.933 0.997 1.010 0.207 6.249-4.933 100.00 3011 157 0.2969 442.842 392.526 1.035 0.917 0.170 4.931-4.001 99.68 5136 240 0.3013 373.224 330.830 1.293 0.780 0.109 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=2.4049 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2901 r_free=0.3330 After: r_work=0.2901 r_free=0.3330 ================================== NQH flips ================================== r_work=0.2901 r_free=0.3330 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 266 ASN Total number of N/Q/H flips: 2 r_work=0.2901 r_free=0.3330 ========================= Local real-space refinement ========================= Before: r_work=0.2901 r_free=0.3330 291 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.051 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3765 After: r_work=0.2901 r_free=0.3330 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.937986 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.075361 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 0.2901 0.3332 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.018 0.2900 0.3331 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.053 0.2900 0.3332 0.0432 0.002 0.5 1.4 0.0 0.0 0 0.105 0.2899 0.3331 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.158 0.2898 0.3333 0.0435 0.002 0.5 1.4 0.0 0.0 0 0.210 0.2897 0.3334 0.0437 0.002 0.5 1.4 0.0 0.0 0 0.263 0.2893 0.3338 0.0445 0.002 0.5 1.5 0.0 0.0 0 0.315 0.2890 0.3339 0.0448 0.003 0.5 1.6 0.0 0.0 0 0.368 0.2899 0.3334 0.0435 0.002 0.5 1.4 0.0 0.0 0 0.175 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2901 0.3332 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.018 0.2900 0.3331 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.053 0.2899 0.3331 0.0431 0.002 0.5 1.4 0.0 0.0 0 0.158 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2901 r_free=0.3332 291 residues out of total 498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 0.653 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4869 After: r_work=0.2901 r_free=0.3332 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.01 33.32 4.31 20.730 135.545 0.075 6.473 31.62 33.24 1.62 17.655 142.547 0.002 6.516 31.30 33.12 1.82 17.170 142.921 0.009 6.509 29.45 33.11 3.66 18.560 140.238 0.038 6.479 28.22 33.47 5.25 20.748 138.398 0.075 6.462 27.87 33.41 5.54 21.260 137.829 0.113 6.455 27.69 33.53 5.84 21.901 138.034 0.151 6.452 27.70 33.46 5.76 21.999 137.698 0.188 6.451 27.62 33.53 5.91 22.363 137.945 0.226 6.450 27.55 33.60 6.05 22.743 138.227 0.264 6.449 27.53 33.61 6.08 22.935 138.313 0.301 6.449 27.50 33.64 6.14 23.205 138.509 0.339 6.448 27.47 33.66 6.19 23.448 138.676 0.377 6.447 max suggested for this run: 27.11 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.038 Accepted refinement result: 29.45 33.11 3.66 18.560 140.238 0.038 6.479 Individual atomic B min max mean iso aniso Overall: 65.91 272.44 132.20 10.57 4450 0 Protein: 65.91 272.44 132.20 10.57 4450 0 Chain A: 75.41 272.44 131.09 N/A 2225 0 Chain B: 65.91 272.44 133.32 N/A 2225 0 Histogram: Values Number of atoms 65.91 - 86.57 103 86.57 - 107.22 938 107.22 - 127.87 1170 127.87 - 148.52 1063 148.52 - 169.18 647 169.18 - 189.83 318 189.83 - 210.48 119 210.48 - 231.13 59 231.13 - 251.79 13 251.79 - 272.44 20 =========================== Idealize ADP of riding H ========================== r_work=0.2945 r_free=0.3311 r_work=0.2955 r_free=0.3315 ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2955 r_free= 0.3315 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ml) (work): 6.482520 | | target function (ml) not normalized (work): 72267.133865 | | target function (ml) not normalized (free): 3624.505411 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2771 0.3173 6.9685 6.9502| | 2: 6.35 - 5.04 1.00 2776 143 0.3082 0.3252 6.4459 6.4985| | 3: 5.04 - 4.40 1.00 2783 123 0.2996 0.3491 6.3845 6.4569| | 4: 4.40 - 4.00 0.99 2723 135 0.3193 0.3559 6.1086 6.1533| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 28.75 0.97 1.00 155177.45| | 2: 6.35 - 5.04 2776 143 0.65 39.94 1.03 1.00 115550.86| | 3: 5.04 - 4.40 2783 123 0.73 33.69 1.08 1.01 81212.37| | 4: 4.40 - 4.00 2723 135 0.68 37.77 1.04 1.01 52919.66| |alpha: min = 1.00 max = 1.01 mean = 1.00| |beta: min = 52919.66 max = 155177.45 mean = 101867.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.92 mean = 34.97| |phase err.(test): min = 0.00 max = 89.04 mean = 35.04| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2972 0.2955 0.3315 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6341 0.6377 0.4778 n_refl.: 11703 remove outliers: r(all,work,free)=0.6341 0.6377 0.4778 n_refl.: 11703 overall B=-1.73 to atoms: r(all,work,free)=0.6298 0.6334 0.4742 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2992 0.2976 0.3329 n_refl.: 11703 remove outliers: r(all,work,free)=0.2992 0.2976 0.3329 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 0.3644 1518.629 1410.501 1.330 1.022 0.370 20.447-16.215 100.00 96 3 0.3152 1067.517 1009.426 1.067 1.020 0.339 16.132-12.745 100.00 194 11 0.2788 1033.876 965.833 1.115 1.018 0.326 12.705-10.080 100.00 377 16 0.2636 971.318 897.400 1.106 1.014 0.321 10.040-7.926 100.00 749 47 0.2489 752.895 709.256 1.051 1.007 0.272 7.906-6.254 99.81 1487 80 0.2889 464.827 426.249 1.010 0.995 0.212 6.249-4.933 100.00 3011 157 0.3050 401.556 354.014 0.971 0.976 0.162 4.931-4.001 99.68 5136 240 0.3141 338.429 298.436 1.100 0.948 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-6.2011 ================= 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_updatephipsi: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_nqh: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_realsrl: 0.3017 0.3503 0.010 1.541 35.8 301.7 117.2 0 0.022 1_weight: 0.3017 0.3503 0.010 1.541 35.8 301.7 117.2 0 0.022 1_xyzrec: 0.3040 0.3506 0.002 0.509 35.8 301.7 117.2 0 0.199 1_realsrl2: 0.3041 0.3500 0.002 0.509 35.8 301.7 117.2 0 0.201 1_adp: 0.3043 0.3335 0.002 0.509 40.2 296.7 125.9 0 0.201 1_regHadp: 0.3043 0.3337 0.002 0.509 40.2 296.7 125.9 0 0.201 2_bss: 0.3003 0.3327 0.002 0.509 32.8 289.3 118.5 0 0.201 2_settarget: 0.3003 0.3327 0.002 0.509 32.8 289.3 118.5 0 0.201 2_updatephipsi: 0.3003 0.3327 0.002 0.509 32.8 289.3 118.5 0 0.201 2_updatecdl: 0.3003 0.3327 0.002 0.538 32.8 289.3 118.5 0 0.201 2_nqh: 0.3004 0.3326 0.002 0.538 32.8 289.3 118.5 0 0.203 2_realsrl: 0.3004 0.3326 0.002 0.538 32.8 289.3 118.5 0 0.203 2_weight: 0.3004 0.3326 0.002 0.538 32.8 289.3 118.5 0 0.203 2_xyzrec: 0.3026 0.3324 0.002 0.441 32.8 289.3 118.5 0 0.222 2_realsrl2: 0.3026 0.3326 0.002 0.441 32.8 289.3 118.5 0 0.222 2_adp: 0.2924 0.3306 0.002 0.441 58.9 284.3 129.8 0 0.222 2_regHadp: 0.2917 0.3322 0.002 0.441 58.9 284.3 129.8 0 0.222 3_bss: 0.2901 0.3330 0.002 0.441 52.0 277.4 122.9 0 0.222 3_settarget: 0.2901 0.3330 0.002 0.441 52.0 277.4 122.9 0 0.222 3_updatephipsi: 0.2901 0.3330 0.002 0.441 52.0 277.4 122.9 0 0.222 3_updatecdl: 0.2901 0.3330 0.002 0.462 52.0 277.4 122.9 0 0.222 3_setrh: 0.2901 0.3330 0.002 0.462 52.0 277.4 122.9 0 0.222 3_nqh: 0.2901 0.3330 0.002 0.462 52.0 277.4 122.9 0 0.224 3_realsrl: 0.2901 0.3330 0.002 0.462 52.0 277.4 122.9 0 0.224 3_weight: 0.2901 0.3330 0.002 0.462 52.0 277.4 122.9 0 0.224 3_xyzrec: 0.2901 0.3332 0.002 0.451 52.0 277.4 122.9 0 0.224 3_realsrl2: 0.2901 0.3332 0.002 0.451 52.0 277.4 122.9 0 0.224 3_adp: 0.2945 0.3311 0.002 0.451 65.9 272.4 132.2 0 0.224 3_regHadp: 0.2955 0.3315 0.002 0.451 65.9 272.4 132.2 0 0.224 end: 0.2976 0.3329 0.002 0.451 64.2 270.7 130.5 0 0.224 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2yhj_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2yhj_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.8900 Refinement macro-cycles (run) : 415.8100 Write final files (write_after_run_outputs) : 18.0100 Total : 440.7100 Total CPU time: 7.86 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:39 PDT -0700 (1716251739.87 s) Start R-work = 0.2998, R-free = 0.3469 Final R-work = 0.2976, R-free = 0.3329 =============================================================================== Job complete usr+sys time: 491.81 seconds wall clock time: 20 minutes 35.20 seconds (1235.20 seconds total)