Starting phenix.refine on Mon May 20 17:17:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4443 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 2.73, per 1000 atoms: 0.31 Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.14 Conformation dependent library (CDL) restraints added in 1.0 seconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 75.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.515A pdb=" N PHE A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.888A pdb=" N LYS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 35' Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 61 through 85 removed outlier: 3.620A pdb=" N HIS A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 102 through 123 removed outlier: 3.560A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 149 Processing helix chain 'A' and resid 156 through 166 removed outlier: 3.736A pdb=" N GLY A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 187 through 211 Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 263 through 281 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'B' and resid 14 through 27 removed outlier: 3.646A pdb=" N PHE B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.528A pdb=" N LYS B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 61 through 84 removed outlier: 3.626A pdb=" N HIS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.513A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.568A pdb=" N GLN B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 166 removed outlier: 3.649A pdb=" N GLY B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 187 through 211 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 263 through 281 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' 281 hydrogen bonds defined for protein. 843 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: 6.96 Time building geometry restraints manager: 4.64 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: 4496 1.15 - 1.31: 769 1.31 - 1.48: 1661 1.48 - 1.64: 2002 1.64 - 1.81: 46 Bond restraints: 8974 Sorted by residual: bond pdb=" N GLY B 56 " pdb=" H GLY B 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 22 " pdb=" H GLN A 22 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG B 88 " pdb=" HE ARG B 88 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 144 " pdb=" H LEU A 144 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B 118 " pdb=" HE2 HIS B 118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8969 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.54: 115 104.54 - 111.91: 10297 111.91 - 119.29: 2244 119.29 - 126.66: 3608 126.66 - 134.03: 30 Bond angle restraints: 16294 Sorted by residual: angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 111.11 124.42 -13.31 1.20e+00 6.94e-01 1.23e+02 angle pdb=" N GLU B 14 " pdb=" CA GLU B 14 " pdb=" C GLU B 14 " ideal model delta sigma weight residual 112.23 102.63 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" N ARG B 286 " pdb=" CA ARG B 286 " pdb=" C ARG B 286 " ideal model delta sigma weight residual 112.87 104.22 8.65 1.20e+00 6.94e-01 5.20e+01 angle pdb=" N ARG A 286 " pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 112.83 120.50 -7.67 1.22e+00 6.72e-01 3.96e+01 ... (remaining 16289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3699 15.89 - 31.78: 227 31.78 - 47.67: 111 47.67 - 63.56: 81 63.56 - 79.45: 14 Dihedral angle restraints: 4132 sinusoidal: 2289 harmonic: 1843 Sorted by residual: dihedral pdb=" C ASP A 287 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 131.25 -8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual -180.00 -137.85 -42.15 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 495 0.097 - 0.194: 152 0.194 - 0.291: 22 0.291 - 0.388: 1 0.388 - 0.485: 3 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ARG A 286 " pdb=" N ARG A 286 " pdb=" C ARG A 286 " pdb=" CB ARG A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " -0.140 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG PHE A 171 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 171 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 171 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 171 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 171 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " 0.084 2.00e-02 2.50e+03 2.57e-02 2.63e+01 pdb=" CG TRP B 251 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 251 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP B 251 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 251 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 251 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 251 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 11 " 0.072 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 11 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 11 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 11 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 11 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 11 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 11 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.75: 88 1.75 - 2.46: 4884 2.46 - 3.17: 29588 3.17 - 3.89: 38737 3.89 - 4.60: 58955 Nonbonded interactions: 132252 Sorted by model distance: nonbonded pdb=" HD2 PHE A 171 " pdb=" HA2 GLY A 197 " model vdw 1.033 2.270 nonbonded pdb=" HH TYR B 11 " pdb=" HG2 LYS B 15 " model vdw sym.op. 1.245 2.270 -y+1,-x+1,-z+1 nonbonded pdb=" HE3 LYS A 93 " pdb="HH22 ARG B 259 " model vdw sym.op. 1.356 2.270 y+1/2,-x+1/2,z nonbonded pdb=" O LEU A 170 " pdb=" H LEU A 173 " model vdw 1.370 1.850 nonbonded pdb=" H GLU A 157 " pdb=" HG3 GLU A 157 " model vdw 1.448 2.270 ... (remaining 132247 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 24 15.91 1 O 823 7.97 1 N 729 6.97 1 C 2831 5.97 1 H 4498 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: 4498 of 8905 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8905 n_use_u_iso = 8905 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 = 8905 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8905 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8905 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 12 through 27 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 30 through 35 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 43 through 54 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 61 through 85 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 96 through 100 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 102 through 123 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 126 through 149 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 156 through 166 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 168 through 182 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 187 through 211 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 230 through 238 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 240 through 247 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 251 through 260 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 263 through 281 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 283 through 285 helix_type = alpha pi *3_10 unknown } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 14 through 27 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 30 through 34 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 43 through 54 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 61 through 84 } helix { serial_number = "20" helix_identifier = "20" selection = chain 'B' and resid 96 through 100 } helix { serial_number = "21" helix_identifier = "21" selection = chain 'B' and resid 102 through 123 } helix { serial_number = "22" helix_identifier = "22" selection = chain 'B' and resid 126 through 149 } helix { serial_number = "23" helix_identifier = "23" selection = chain 'B' and resid 156 through 166 } helix { serial_number = "24" helix_identifier = "24" selection = chain 'B' and resid 168 through 182 } helix { serial_number = "25" helix_identifier = "25" selection = chain 'B' and resid 187 through 211 } helix { serial_number = "26" helix_identifier = "26" selection = chain 'B' and resid 230 through 238 } helix { serial_number = "27" helix_identifier = "27" selection = chain 'B' and resid 240 through 248 } helix { serial_number = "28" helix_identifier = "28" selection = chain 'B' and resid 251 through 261 } helix { serial_number = "29" helix_identifier = "29" selection = chain 'B' and resid 263 through 281 } helix { serial_number = "30" helix_identifier = "30" selection = chain 'B' and resid 283 through 285 helix_type = alpha pi *3_10 unknown } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1wl3_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4498 occupancy sum: 4498.00 (% of total atoms 50.51) Rotatable: count: 1300 occupancy sum: 1300.00 (% of total atoms 14.60) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.98 2477 144 0.4989 0.4770 4.495 5.1259| | 2: 5.55 - 4.41 0.96 2311 121 0.3871 0.4311 3.6506 3.6312| | 3: 4.41 - 3.85 0.93 2220 112 0.4708 0.5130 3.3519 3.4414| | 4: 3.85 - 3.50 0.88 2062 132 0.4868 0.5658 3.1476 3.3492| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2477 144 0.45 54.77 0.83 0.03 995.04| | 2: 5.55 - 4.41 2311 121 0.46 55.10 1.34 0.02 444.27| | 3: 4.41 - 3.85 2220 112 0.63 41.12 1.62 0.03 154.61| | 4: 3.85 - 3.50 2062 132 0.56 47.24 1.53 0.03 126.03| |alpha: min = 0.02 max = 0.03 mean = 0.03| |beta: min = 126.03 max = 995.04 mean = 451.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.52| |phase err.(work): min = 0.00 max = 89.98 mean = 49.80| |phase err.(test): min = 0.00 max = 89.87 mean = 48.86| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.085 4476 Z= 0.343 Angle : 1.323 14.340 6012 Z= 0.928 Chirality : 0.095 0.485 673 Planarity : 0.005 0.053 772 Dihedral : 15.841 79.450 1703 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 2.36 % Allowed : 5.26 % Favored : 92.38 % Rotamer: Outliers : 3.40 % Allowed : 7.43 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.27), residues: 551 helix: -2.44 (0.18), residues: 445 sheet: None (None), residues: 0 loop : -2.62 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 TYR 0.056 0.011 TYR A 11 PHE 0.085 0.007 PHE A 171 TRP 0.056 0.008 TRP B 251 HIS 0.001 0.000 HIS B 118 Individual atomic B min max mean iso aniso Overall: 21.36 100.34 56.13 1.48 4407 0 Protein: 21.36 100.34 56.13 1.48 4407 0 Chain A: 24.53 91.36 59.78 N/A 2198 0 Chain B: 21.36 100.34 52.50 N/A 2209 0 Histogram: Values Number of atoms 21.36 - 29.26 126 29.26 - 37.16 321 37.16 - 45.05 629 45.05 - 52.95 817 52.95 - 60.85 833 60.85 - 68.75 769 68.75 - 76.65 497 76.65 - 84.54 290 84.54 - 92.44 121 92.44 - 100.34 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 re-set all scales: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 remove outliers: r(all,work,free)=0.4621 0.4602 0.4849 n_refl.: 9561 overall B=23.46 to atoms: r(all,work,free)=0.5303 0.5276 0.5612 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 remove outliers: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4381 1220.303 1224.065 1.165 1.112 0.405 16.951-13.495 94.17 95 2 0.3095 1758.562 1726.307 0.965 1.108 0.377 13.466-10.728 99.01 188 12 0.2313 2173.838 2118.815 1.052 1.095 0.368 10.715-8.517 98.92 348 19 0.1972 2052.862 2022.519 1.059 1.081 0.351 8.515-6.766 98.37 689 37 0.2427 1366.340 1306.911 0.994 1.051 0.326 6.761-5.374 96.29 1294 80 0.2758 856.308 812.122 0.876 1.007 0.279 5.373-4.268 96.39 2549 123 0.2287 952.347 913.140 0.992 0.935 0.223 4.267-3.500 89.96 3807 225 0.2939 675.635 628.033 1.221 0.844 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.4189 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.840600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168723 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 0.2560 0.2780 0.0220 0.004 0.6 4.0 1.1 3.2 0 0.125 0.2533 0.2764 0.0231 0.004 0.7 4.4 0.9 3.4 0 0.250 0.2485 0.2767 0.0283 0.004 0.7 4.4 0.9 3.2 0 0.500 0.2417 0.2778 0.0362 0.006 0.7 5.5 0.9 3.4 0 1.000 0.2356 0.2797 0.0441 0.009 0.9 8.3 1.1 3.0 0 2.000 0.2307 0.2811 0.0504 0.010 1.1 9.8 1.1 3.2 0 3.000 0.2194 0.2861 0.0668 0.009 0.9 8.7 1.5 3.4 0 4.000 0.2174 0.2865 0.0691 0.010 1.0 9.3 1.8 3.6 0 5.000 0.2231 0.2846 0.0615 0.015 1.4 11.5 1.3 3.4 0 6.000 0.2142 0.2903 0.0761 0.012 1.2 12.5 2.2 4.0 0 7.000 0.2126 0.2890 0.0764 0.014 1.3 14.0 2.4 4.5 0 8.000 0.2113 0.2897 0.0784 0.015 1.3 14.6 2.2 4.2 0 9.000 0.2100 0.2906 0.0806 0.016 1.4 15.5 2.4 4.7 0 10.000 0.2157 0.2886 0.0728 0.011 1.1 10.9 1.6 4.0 0 5.920 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2560 0.2780 0.0220 0.004 0.6 4.0 1.1 3.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.60 27.80 2.20 1.044 79.246 0.169 0.074 25.62 27.52 1.90 2.192 79.340 0.005 0.074 25.22 27.59 2.37 2.301 79.374 0.021 0.072 24.38 27.83 3.44 3.349 79.494 0.084 0.067 23.22 28.21 4.99 7.305 80.329 0.169 0.061 22.89 28.31 5.42 8.717 80.703 0.253 0.060 22.68 28.39 5.71 9.669 80.992 0.337 0.059 22.39 28.53 6.13 11.130 81.486 0.422 0.057 22.26 28.64 6.38 11.948 81.730 0.506 0.056 22.15 28.70 6.55 12.703 81.949 0.591 0.056 22.01 28.78 6.78 13.616 82.251 0.675 0.055 21.95 28.78 6.83 14.022 82.365 0.759 0.055 21.84 28.86 7.01 14.728 82.596 0.844 0.054 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 25.62 27.52 1.90 2.192 79.340 0.005 0.074 Individual atomic B min max mean iso aniso Overall: 50.64 120.38 79.78 1.50 4407 0 Protein: 50.64 120.38 79.78 1.50 4407 0 Chain A: 53.40 112.38 83.28 N/A 2198 0 Chain B: 50.64 120.38 76.31 N/A 2209 0 Histogram: Values Number of atoms 50.64 - 57.61 167 57.61 - 64.59 414 64.59 - 71.56 731 71.56 - 78.54 830 78.54 - 85.51 799 85.51 - 92.48 651 92.48 - 99.46 455 99.46 - 106.43 247 106.43 - 113.41 108 113.41 - 120.38 5 =========================== Idealize ADP of riding H ========================== r_work=0.2562 r_free=0.2752 r_work=0.2550 r_free=0.2743 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2550 r_free= 0.2743 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ls_wunit_k1) (work): 0.073609 | | target function (ls_wunit_k1) not normalized (work): 666.459272 | | target function (ls_wunit_k1) not normalized (free): 43.830304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2550 0.2743 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5296 0.5269 0.5600 n_refl.: 9561 remove outliers: r(all,work,free)=0.5296 0.5269 0.5600 n_refl.: 9561 overall B=1.06 to atoms: r(all,work,free)=0.5329 0.5302 0.5635 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2563 0.2551 0.2769 n_refl.: 9561 remove outliers: r(all,work,free)=0.2563 0.2551 0.2769 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4016 516.480 520.938 1.293 1.076 0.410 16.951-13.495 94.17 95 2 0.3000 744.293 743.602 0.996 1.074 0.373 13.466-10.728 99.01 188 12 0.2266 920.054 898.795 1.086 1.063 0.366 10.715-8.517 98.92 348 19 0.1900 868.852 858.673 1.090 1.053 0.350 8.515-6.766 98.37 689 37 0.2337 578.289 556.990 1.007 1.030 0.332 6.761-5.374 96.29 1294 80 0.2718 362.423 345.241 0.898 0.997 0.288 5.373-4.268 96.39 2549 123 0.2308 403.071 386.642 0.982 0.942 0.227 4.267-3.500 89.96 3807 225 0.2927 285.955 265.931 1.172 0.876 0.135 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.1932 ============================ 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 = 3.267807 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046546 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 0.2626 0.2766 0.0140 0.002 0.4 2.2 0.9 2.3 0 0.008 0.2573 0.2767 0.0194 0.002 0.4 2.2 0.9 2.5 0 0.023 0.2526 0.2769 0.0243 0.002 0.4 2.5 0.9 2.5 0 0.045 0.2472 0.2749 0.0276 0.002 0.4 2.5 0.9 2.5 0 0.068 0.2433 0.2737 0.0304 0.002 0.5 2.5 0.9 2.8 0 0.091 0.2394 0.2750 0.0356 0.003 0.5 2.6 0.9 2.3 0 0.114 0.2373 0.2742 0.0369 0.003 0.5 2.6 0.9 2.5 0 0.136 0.2355 0.2740 0.0385 0.003 0.5 2.6 1.1 2.5 0 0.159 0.2451 0.2767 0.0316 0.002 0.5 2.5 0.9 2.5 0 0.076 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2626 0.2766 0.0140 0.002 0.4 2.2 0.9 2.3 0 0.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.26 27.66 1.40 11.425 88.579 0.047 6.203 26.74 28.42 1.67 11.677 89.439 0.001 6.214 25.71 28.08 2.37 11.780 89.195 0.006 6.179 24.03 28.30 4.27 12.175 89.867 0.023 6.129 23.50 28.53 5.04 13.435 90.587 0.047 6.115 23.41 28.44 5.03 13.455 90.472 0.070 6.113 23.27 28.52 5.25 14.031 90.726 0.093 6.110 23.14 28.63 5.48 14.677 91.014 0.116 6.107 23.11 28.64 5.53 14.949 91.112 0.140 6.106 23.04 28.70 5.66 15.381 91.286 0.163 6.105 23.01 28.73 5.72 15.674 91.398 0.186 6.104 22.96 28.79 5.84 16.117 91.568 0.209 6.103 22.93 28.82 5.89 16.407 91.675 0.233 6.103 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 25.71 28.08 2.37 11.780 89.195 0.006 6.179 Individual atomic B min max mean iso aniso Overall: 59.08 130.25 82.09 2.85 4407 0 Protein: 59.08 130.25 82.09 2.85 4407 0 Chain A: 59.82 122.57 84.79 N/A 2198 0 Chain B: 59.08 130.25 79.40 N/A 2209 0 Histogram: Values Number of atoms 59.08 - 66.20 244 66.20 - 73.31 842 73.31 - 80.43 1077 80.43 - 87.55 926 87.55 - 94.67 678 94.67 - 101.78 372 101.78 - 108.90 197 108.90 - 116.02 52 116.02 - 123.13 16 123.13 - 130.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.2571 r_free=0.2808 r_work=0.2569 r_free=0.2816 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2569 r_free= 0.2816 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.178149 | | target function (ml) not normalized (work): 55936.956863 | | target function (ml) not normalized (free): 3170.882243 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2582 0.2569 0.2816 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5398 0.5370 0.5718 n_refl.: 9561 remove outliers: r(all,work,free)=0.5398 0.5370 0.5718 n_refl.: 9561 overall B=0.17 to atoms: r(all,work,free)=0.5403 0.5375 0.5724 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2578 0.2564 0.2814 n_refl.: 9561 remove outliers: r(all,work,free)=0.2578 0.2564 0.2814 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4204 516.480 533.083 1.266 1.095 0.420 16.951-13.495 94.17 95 2 0.2894 744.293 746.473 0.981 1.094 0.375 13.466-10.728 99.01 188 12 0.2229 920.054 902.620 1.053 1.082 0.370 10.715-8.517 98.92 348 19 0.1894 868.852 854.501 1.037 1.069 0.342 8.515-6.766 98.37 689 37 0.2369 578.289 556.441 0.975 1.042 0.331 6.761-5.374 96.29 1294 80 0.2875 362.423 344.779 0.908 1.002 0.300 5.373-4.268 96.39 2549 123 0.2374 403.071 385.808 0.997 0.935 0.230 4.267-3.500 89.96 3807 225 0.2833 285.955 266.532 1.199 0.851 0.123 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.0306 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2564 r_free=0.2814 After: r_work=0.2564 r_free=0.2814 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.448618 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.047912 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 0.2564 0.2815 0.0251 0.002 0.4 2.5 0.9 2.3 0 0.007 0.2564 0.2815 0.0251 0.002 0.4 2.5 0.9 2.3 0 0.022 0.2562 0.2815 0.0253 0.002 0.4 2.5 0.9 2.3 0 0.045 0.2561 0.2815 0.0255 0.002 0.4 2.5 0.9 2.3 0 0.067 0.2559 0.2813 0.0255 0.002 0.4 2.5 0.9 2.3 0 0.089 0.2554 0.2811 0.0257 0.003 0.4 2.5 0.9 2.3 0 0.111 0.2549 0.2810 0.0261 0.003 0.4 2.5 0.9 2.3 0 0.134 0.2547 0.2807 0.0260 0.003 0.4 2.5 0.9 2.3 0 0.156 0.2560 0.2815 0.0255 0.002 0.4 2.5 0.9 2.3 0 0.074 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2547 0.2807 0.0260 0.003 0.4 2.5 0.9 2.3 0 0.156 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.47 28.07 2.60 11.909 90.545 0.048 6.179 26.52 28.54 2.02 11.612 91.588 0.001 6.216 25.30 28.06 2.76 12.016 90.535 0.006 6.174 23.57 28.33 4.76 12.291 91.813 0.024 6.119 23.09 28.57 5.48 13.406 92.303 0.048 6.106 22.89 28.68 5.79 13.960 92.515 0.072 6.102 22.76 28.79 6.02 14.559 92.761 0.096 6.100 22.74 28.81 6.07 14.740 92.790 0.120 6.099 22.66 28.86 6.20 15.226 93.012 0.144 6.097 22.61 28.91 6.30 15.588 93.167 0.168 6.096 22.55 28.96 6.41 16.002 93.344 0.192 6.096 22.52 28.99 6.47 16.313 93.470 0.216 6.095 22.48 29.02 6.54 16.622 93.594 0.240 6.094 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 25.30 28.06 2.76 12.016 90.535 0.006 6.174 Individual atomic B min max mean iso aniso Overall: 57.75 129.05 82.24 2.89 4407 0 Protein: 57.75 129.05 82.24 2.89 4407 0 Chain A: 60.02 121.31 84.94 N/A 2198 0 Chain B: 57.75 129.05 79.55 N/A 2209 0 Histogram: Values Number of atoms 57.75 - 64.88 105 64.88 - 72.01 763 72.01 - 79.14 1074 79.14 - 86.27 996 86.27 - 93.40 736 93.40 - 100.53 434 100.53 - 107.66 210 107.66 - 114.79 66 114.79 - 121.92 19 121.92 - 129.05 4 =========================== Idealize ADP of riding H ========================== r_work=0.2530 r_free=0.2806 r_work=0.2528 r_free=0.2805 ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2528 r_free= 0.2805 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.173794 | | target function (ml) not normalized (work): 55897.532934 | | target function (ml) not normalized (free): 3174.882747 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.97 2463 143 0.2489 0.2859 6.5666 6.6691| | 2: 5.55 - 4.41 0.96 2310 121 0.2371 0.2447 6.2109 6.239| | 3: 4.41 - 3.85 0.93 2220 112 0.2538 0.2946 6.0324 6.13| | 4: 3.85 - 3.50 0.88 2061 131 0.2899 0.3013 5.8151 5.9521| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2463 143 0.72 32.05 0.99 0.96 88918.82| | 2: 5.55 - 4.41 2310 121 0.76 29.72 1.00 0.99 51642.45| | 3: 4.41 - 3.85 2220 112 0.78 27.57 1.04 0.98 28990.78| | 4: 3.85 - 3.50 2061 131 0.75 31.34 0.95 0.92 20963.79| |alpha: min = 0.92 max = 0.99 mean = 0.96| |beta: min = 20963.79 max = 88918.82 mean = 49245.31| |figures of merit: min = 0.00 max = 1.00 mean = 0.75| |phase err.(work): min = 0.00 max = 89.99 mean = 30.19| |phase err.(test): min = 0.00 max = 89.28 mean = 30.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2543 0.2528 0.2805 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5400 0.5372 0.5727 n_refl.: 9561 remove outliers: r(all,work,free)=0.5400 0.5372 0.5727 n_refl.: 9561 overall B=-0.13 to atoms: r(all,work,free)=0.5396 0.5368 0.5722 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2543 0.2528 0.2806 n_refl.: 9561 remove outliers: r(all,work,free)=0.2543 0.2528 0.2806 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4199 516.480 532.660 1.265 1.101 0.420 16.951-13.495 94.17 95 2 0.2901 744.293 746.188 0.975 1.099 0.375 13.466-10.728 99.01 188 12 0.2218 920.054 902.326 1.050 1.087 0.370 10.715-8.517 98.92 348 19 0.1892 868.852 853.296 1.035 1.073 0.342 8.515-6.766 98.37 689 37 0.2351 578.289 555.991 0.975 1.045 0.331 6.761-5.374 96.29 1294 80 0.2862 362.423 345.056 0.911 1.002 0.300 5.373-4.268 96.39 2549 123 0.2339 403.071 386.333 0.998 0.932 0.220 4.267-3.500 89.96 3807 225 0.2762 285.955 267.455 1.219 0.843 0.124 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.2960 ================= 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 : 0.4622 0.4889 0.005 1.323 21.4 100.3 56.1 0 0.000 1_bss: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_settarget: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_weight: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_xyzrec: 0.2560 0.2780 0.004 0.625 44.8 123.8 79.6 0 0.147 1_adp: 0.2562 0.2752 0.004 0.625 50.6 120.4 79.8 0 0.147 1_regHadp: 0.2550 0.2743 0.004 0.625 50.6 120.4 79.8 0 0.147 2_bss: 0.2551 0.2769 0.004 0.625 51.7 121.4 80.8 0 0.147 2_settarget: 0.2551 0.2769 0.004 0.625 51.7 121.4 80.8 0 0.147 2_updatecdl: 0.2551 0.2769 0.004 0.649 51.7 121.4 80.8 0 0.147 2_weight: 0.2551 0.2769 0.004 0.649 51.7 121.4 80.8 0 0.147 2_xyzrec: 0.2626 0.2766 0.002 0.422 51.7 121.4 80.8 0 0.256 2_adp: 0.2571 0.2808 0.002 0.422 59.1 130.3 82.1 0 0.256 2_regHadp: 0.2569 0.2816 0.002 0.422 59.1 130.3 82.1 0 0.256 3_bss: 0.2564 0.2814 0.002 0.422 59.2 130.4 82.3 0 0.256 3_settarget: 0.2564 0.2814 0.002 0.422 59.2 130.4 82.3 0 0.256 3_updatecdl: 0.2564 0.2814 0.002 0.481 59.2 130.4 82.3 0 0.256 3_setrh: 0.2564 0.2814 0.002 0.481 59.2 130.4 82.3 0 0.256 3_weight: 0.2564 0.2814 0.002 0.481 59.2 130.4 82.3 0 0.256 3_xyzrec: 0.2547 0.2807 0.003 0.445 59.2 130.4 82.3 0 0.255 3_adp: 0.2530 0.2806 0.003 0.445 57.7 129.1 82.2 0 0.255 3_regHadp: 0.2528 0.2805 0.003 0.445 57.7 129.1 82.2 0 0.255 end: 0.2528 0.2806 0.003 0.445 57.6 128.9 82.1 0 0.255 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1wl3_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1wl3_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.2400 Refinement macro-cycles (run) : 296.2500 Write final files (write_after_run_outputs) : 16.5900 Total : 326.0800 Total CPU time: 6.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:30 PDT -0700 (1716251730.66 s) Start R-work = 0.2579, R-free = 0.2869 Final R-work = 0.2528, R-free = 0.2806 =============================================================================== Job complete usr+sys time: 394.08 seconds wall clock time: 18 minutes 15.95 seconds (1095.95 seconds total)