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/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+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/1wl3.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" 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" } 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: 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: 1.52, per 1000 atoms: 0.17 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: 2.19 Conformation dependent library (CDL) restraints added in 282.1 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. 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: 0.62 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: 1.97 Time building geometry restraints manager: 2.51 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2579 r_free=0.2869 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2579 r_free=0.2869 ========================= Local real-space refinement ========================= Before: r_work=0.2579 r_free=0.2869 241 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 225 time to evaluate : 0.388 revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.2684 time to fit residues: 6.2817 After: r_work=0.2591 r_free=0.2903 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.379105 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170234 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 0.2555 0.2822 0.0267 0.003 0.5 2.9 0.0 1.1 0 0.125 0.2512 0.2802 0.0290 0.003 0.5 2.9 0.0 1.1 0 0.250 0.2436 0.2806 0.0371 0.003 0.6 3.4 0.0 1.3 0 0.500 0.2356 0.2787 0.0431 0.004 0.6 4.2 0.0 1.7 0 1.000 0.2277 0.2841 0.0563 0.006 0.8 5.7 0.0 1.7 0 2.000 0.2226 0.2877 0.0651 0.007 0.9 7.4 0.0 2.3 0 3.000 0.2200 0.2869 0.0669 0.009 1.0 8.3 0.0 2.8 0 4.000 0.2176 0.2906 0.0730 0.010 1.1 9.3 0.0 3.4 0 5.000 0.2158 0.2891 0.0733 0.012 1.1 10.6 0.0 3.6 0 6.000 0.2140 0.2887 0.0747 0.013 1.2 11.7 0.0 4.5 0 7.000 0.2125 0.2872 0.0748 0.014 1.3 12.8 0.0 4.5 0 8.000 0.2110 0.2879 0.0769 0.015 1.4 13.5 0.0 5.3 0 9.000 0.2101 0.2876 0.0775 0.016 1.4 14.3 0.0 5.1 0 10.000 0.2157 0.2888 0.0730 0.012 1.1 10.7 0.0 3.6 0 6.190 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2512 0.2802 0.0290 0.003 0.5 2.9 0.0 1.1 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2512 r_free=0.2802 224 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 1.648 outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6227 time to fit residues: 5.7482 After: r_work=0.2538 r_free=0.2793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.38 27.93 2.55 1.044 79.246 0.170 0.072 25.40 27.70 2.30 2.208 79.341 0.005 0.072 25.01 27.68 2.67 2.372 79.387 0.021 0.069 23.70 27.70 4.01 5.181 79.808 0.085 0.063 23.12 27.88 4.76 6.823 80.181 0.170 0.060 22.82 27.99 5.17 7.989 80.483 0.255 0.058 22.59 28.08 5.49 9.081 80.819 0.340 0.057 22.32 28.22 5.91 10.436 81.275 0.426 0.056 22.20 28.28 6.08 11.092 81.465 0.511 0.055 22.11 28.33 6.22 11.656 81.630 0.596 0.055 21.94 28.42 6.48 12.657 81.962 0.681 0.054 21.88 28.46 6.59 13.129 82.098 0.766 0.054 21.77 28.54 6.77 13.875 82.336 0.851 0.053 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.021 Accepted refinement result: 25.01 27.68 2.67 2.372 79.387 0.021 0.069 Individual atomic B min max mean iso aniso Overall: 51.34 122.44 79.88 1.79 4407 0 Protein: 51.34 122.44 79.88 1.79 4407 0 Chain A: 53.52 116.46 83.37 N/A 2198 0 Chain B: 51.34 122.44 76.40 N/A 2209 0 Histogram: Values Number of atoms 51.34 - 58.45 182 58.45 - 65.56 474 65.56 - 72.67 786 72.67 - 79.78 808 79.78 - 86.89 846 86.89 - 94.00 615 94.00 - 101.11 379 101.11 - 108.22 244 108.22 - 115.33 67 115.33 - 122.44 6 =========================== Idealize ADP of riding H ========================== r_work=0.2501 r_free=0.2768 r_work=0.2489 r_free=0.2757 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2489 r_free= 0.2757 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.068862 | | target function (ls_wunit_k1) not normalized (work): 623.475725 | | target function (ls_wunit_k1) not normalized (free): 44.082811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2504 0.2489 0.2757 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5274 0.5242 0.5663 n_refl.: 9561 remove outliers: r(all,work,free)=0.5274 0.5242 0.5663 n_refl.: 9561 overall B=-0.17 to atoms: r(all,work,free)=0.5268 0.5237 0.5657 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2522 0.2505 0.2800 n_refl.: 9561 remove outliers: r(all,work,free)=0.2522 0.2505 0.2800 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 0.3979 514.674 515.482 1.430 1.012 0.420 16.951-13.495 94.17 95 2 0.2792 741.689 757.778 1.060 1.016 0.365 13.466-10.728 99.01 188 12 0.2168 916.836 901.396 1.150 1.011 0.360 10.715-8.517 98.92 348 19 0.1802 865.813 862.136 1.154 1.009 0.340 8.515-6.766 98.37 689 37 0.2302 576.266 561.749 1.064 1.001 0.340 6.761-5.374 96.29 1294 80 0.2745 361.155 339.760 0.897 0.990 0.280 5.373-4.268 96.39 2549 123 0.2274 401.661 384.322 0.957 0.971 0.220 4.267-3.500 89.96 3807 225 0.2866 284.955 266.965 1.078 0.954 0.140 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.5810 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2505 r_free=0.2800 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 225 ASN A 244 GLN A 248 ASN A 282 ASN B 201 GLN Total number of N/Q/H flips: 6 r_work=0.2506 r_free=0.2792 ========================= Local real-space refinement ========================= Before: r_work=0.2506 r_free=0.2792 233 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.086 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2068 After: r_work=0.2506 r_free=0.2792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.450732 wxc_scale = 0.025 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.046791 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 0.2572 0.2823 0.0251 0.002 0.4 2.1 0.0 0.0 0 0.009 0.2532 0.2817 0.0285 0.002 0.4 2.1 0.0 0.0 0 0.026 0.2479 0.2811 0.0332 0.002 0.4 2.1 0.0 0.0 0 0.053 0.2432 0.2782 0.0350 0.002 0.4 2.8 0.0 0.2 0 0.079 0.2402 0.2762 0.0360 0.002 0.5 2.8 0.0 0.2 0 0.105 0.2373 0.2762 0.0388 0.003 0.5 3.4 0.0 0.2 0 0.131 0.2352 0.2755 0.0403 0.003 0.5 3.6 0.0 0.2 0 0.158 0.2342 0.2743 0.0401 0.003 0.5 3.8 0.0 0.4 0 0.184 0.2419 0.2783 0.0364 0.002 0.4 2.7 0.0 0.2 0 0.088 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2479 0.2811 0.0332 0.002 0.4 2.1 0.0 0.0 0 0.053 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2479 r_free=0.2811 235 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.956 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3483 After: r_work=0.2479 r_free=0.2811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.79 28.11 3.32 11.472 87.495 0.047 6.161 25.64 28.70 3.06 11.802 88.391 0.001 6.181 24.63 28.03 3.40 11.605 87.458 0.006 6.152 23.17 28.32 5.16 12.350 88.221 0.023 6.103 22.67 28.59 5.92 13.288 88.957 0.047 6.091 22.48 28.56 6.08 13.366 88.948 0.070 6.088 22.36 28.63 6.27 13.796 89.148 0.094 6.086 22.24 28.72 6.48 14.366 89.426 0.117 6.084 22.19 28.75 6.55 14.634 89.531 0.140 6.083 22.13 28.81 6.68 15.043 89.709 0.164 6.082 22.09 28.87 6.78 15.336 89.828 0.187 6.081 22.05 28.90 6.85 15.620 89.942 0.211 6.081 22.00 28.95 6.95 16.082 90.121 0.234 6.080 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: 24.63 28.03 3.40 11.605 87.458 0.006 6.152 Individual atomic B min max mean iso aniso Overall: 51.32 123.00 79.63 2.25 4407 0 Protein: 51.32 123.00 79.63 2.25 4407 0 Chain A: 53.22 115.88 83.07 N/A 2198 0 Chain B: 51.32 123.00 76.21 N/A 2209 0 Histogram: Values Number of atoms 51.32 - 58.48 157 58.48 - 65.65 511 65.65 - 72.82 826 72.82 - 79.99 841 79.99 - 87.16 837 87.16 - 94.33 592 94.33 - 101.49 379 101.49 - 108.66 214 108.66 - 115.83 44 115.83 - 123.00 6 =========================== Idealize ADP of riding H ========================== r_work=0.2463 r_free=0.2803 r_work=0.2462 r_free=0.2802 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2462 r_free= 0.2802 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.150923 | | target function (ml) not normalized (work): 55690.459999 | | target function (ml) not normalized (free): 3169.493989 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2481 0.2462 0.2802 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5274 0.5243 0.5670 n_refl.: 9561 remove outliers: r(all,work,free)=0.5274 0.5243 0.5670 n_refl.: 9561 overall B=1.18 to atoms: r(all,work,free)=0.5311 0.5280 0.5708 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2476 0.2458 0.2784 n_refl.: 9561 remove outliers: r(all,work,free)=0.2476 0.2458 0.2784 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 0.3819 514.674 514.503 1.406 1.011 0.420 16.951-13.495 94.17 95 2 0.2673 741.689 753.361 1.089 1.014 0.375 13.466-10.728 99.01 188 12 0.2142 916.836 905.796 1.155 1.010 0.369 10.715-8.517 98.92 348 19 0.1754 865.813 860.786 1.138 1.008 0.349 8.515-6.766 98.37 689 37 0.2239 576.266 560.087 1.063 1.000 0.348 6.761-5.374 96.29 1294 80 0.2842 361.155 337.905 0.896 0.989 0.278 5.373-4.268 96.39 2549 123 0.2247 401.661 383.451 0.958 0.970 0.217 4.267-3.500 89.96 3807 225 0.2745 284.955 267.734 1.070 0.952 0.118 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.2134 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2458 r_free=0.2784 After: r_work=0.2458 r_free=0.2784 ================================== NQH flips ================================== r_work=0.2458 r_free=0.2784 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 201 GLN B 22 GLN Total number of N/Q/H flips: 3 r_work=0.2458 r_free=0.2784 ========================= Local real-space refinement ========================= Before: r_work=0.2458 r_free=0.2784 233 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 0.987 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3812 time to fit residues: 1.7099 After: r_work=0.2459 r_free=0.2790 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.703405 wxc_scale = 0.030 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049387 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 0.2460 0.2788 0.0328 0.002 0.4 2.2 0.0 0.0 0 0.011 0.2459 0.2787 0.0328 0.002 0.4 2.2 0.0 0.0 0 0.034 0.2457 0.2789 0.0331 0.002 0.4 2.4 0.0 0.0 0 0.067 0.2457 0.2787 0.0331 0.002 0.4 2.4 0.0 0.0 0 0.101 0.2455 0.2790 0.0335 0.002 0.4 2.5 0.0 0.0 0 0.135 0.2452 0.2787 0.0335 0.002 0.4 2.6 0.0 0.0 0 0.168 0.2445 0.2782 0.0338 0.003 0.4 2.8 0.0 0.0 0 0.202 0.2437 0.2776 0.0340 0.004 0.4 3.0 0.0 0.0 0 0.236 0.2456 0.2789 0.0333 0.002 0.4 2.4 0.0 0.0 0 0.112 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2460 0.2788 0.0328 0.002 0.4 2.2 0.0 0.0 0 0.011 0.2459 0.2787 0.0328 0.002 0.4 2.2 0.0 0.0 0 0.034 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2460 r_free=0.2788 235 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.885 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8776 After: r_work=0.2460 r_free=0.2788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.60 27.88 3.28 11.478 88.597 0.049 6.152 25.52 28.47 2.95 11.718 89.317 0.001 6.179 24.45 27.84 3.38 11.614 88.557 0.006 6.146 22.99 28.17 5.17 12.278 89.271 0.025 6.099 22.45 28.44 6.00 13.422 90.177 0.049 6.085 22.19 28.54 6.36 13.903 90.430 0.074 6.080 22.17 28.50 6.33 13.998 90.394 0.099 6.080 22.08 28.57 6.49 14.496 90.629 0.123 6.079 22.04 28.59 6.55 14.782 90.749 0.148 6.078 21.98 28.65 6.67 15.178 90.923 0.173 6.077 21.93 28.69 6.76 15.533 91.072 0.198 6.076 21.90 28.72 6.82 15.844 91.198 0.222 6.076 21.85 28.77 6.92 16.213 91.343 0.247 6.075 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: 24.45 27.84 3.38 11.614 88.557 0.006 6.146 Individual atomic B min max mean iso aniso Overall: 51.80 125.40 80.73 2.59 4407 0 Protein: 51.80 125.40 80.73 2.59 4407 0 Chain A: 55.89 116.48 84.10 N/A 2198 0 Chain B: 51.80 125.40 77.37 N/A 2209 0 Histogram: Values Number of atoms 51.80 - 59.16 92 59.16 - 66.52 527 66.52 - 73.88 840 73.88 - 81.24 917 81.24 - 88.60 854 88.60 - 95.96 604 95.96 - 103.32 342 103.32 - 110.68 201 110.68 - 118.04 27 118.04 - 125.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.2445 r_free=0.2784 r_work=0.2444 r_free=0.2783 ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2444 r_free= 0.2783 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 6.145313 | | target function (ml) not normalized (work): 55639.666947 | | target function (ml) not normalized (free): 3169.629317 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2396 0.2812 6.5265 6.6519| | 2: 5.55 - 4.41 0.96 2310 121 0.2274 0.2428 6.1854 6.2119| | 3: 4.41 - 3.85 0.93 2220 112 0.2469 0.2954 6.0074 6.152| | 4: 3.85 - 3.50 0.88 2061 131 0.2843 0.3015 5.7934 5.9369| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 31.66 0.99 0.94 86190.89| | 2: 5.55 - 4.41 2310 121 0.76 29.46 1.01 0.97 50336.41| | 3: 4.41 - 3.85 2220 112 0.79 27.50 1.04 0.94 28330.76| | 4: 3.85 - 3.50 2061 131 0.75 30.75 0.93 0.86 20173.94| |alpha: min = 0.86 max = 0.97 mean = 0.93| |beta: min = 20173.94 max = 86190.89 mean = 47828.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.75| |phase err.(work): min = 0.00 max = 89.98 mean = 29.87| |phase err.(test): min = 0.00 max = 88.61 mean = 29.95| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2463 0.2444 0.2783 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5312 0.5280 0.5711 n_refl.: 9561 remove outliers: r(all,work,free)=0.5312 0.5280 0.5711 n_refl.: 9561 overall B=0.60 to atoms: r(all,work,free)=0.5331 0.5299 0.5730 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2461 0.2442 0.2786 n_refl.: 9561 remove outliers: r(all,work,free)=0.2461 0.2442 0.2786 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 0.3804 514.674 522.628 1.395 1.021 0.420 16.951-13.495 94.17 95 2 0.2693 741.689 741.879 1.012 1.023 0.365 13.466-10.728 99.01 188 12 0.2140 916.836 908.665 1.115 1.017 0.360 10.715-8.517 98.92 348 19 0.1754 865.813 856.976 1.114 1.014 0.349 8.515-6.766 98.37 689 37 0.2245 576.266 557.918 1.044 1.004 0.349 6.761-5.374 96.29 1294 80 0.2848 361.155 342.590 0.920 0.989 0.289 5.373-4.268 96.39 2549 123 0.2236 401.661 384.486 0.963 0.964 0.219 4.267-3.500 89.96 3807 225 0.2699 284.955 267.062 1.080 0.939 0.109 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.1096 ================= 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_updatephipsi: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_nqh: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_realsrl: 0.2591 0.2903 0.005 1.323 44.8 123.8 79.6 0 0.013 1_weight: 0.2591 0.2903 0.005 1.323 44.8 123.8 79.6 0 0.013 1_xyzrec: 0.2512 0.2802 0.003 0.528 44.8 123.8 79.6 0 0.221 1_realsrl2: 0.2538 0.2793 0.003 0.528 44.8 123.8 79.6 0 0.223 1_adp: 0.2501 0.2768 0.003 0.528 51.3 122.4 79.9 0 0.223 1_regHadp: 0.2489 0.2757 0.003 0.528 51.3 122.4 79.9 0 0.223 2_bss: 0.2505 0.2800 0.003 0.528 51.2 122.3 79.7 0 0.223 2_settarget: 0.2505 0.2800 0.003 0.528 51.2 122.3 79.7 0 0.223 2_updatephipsi: 0.2505 0.2800 0.003 0.528 51.2 122.3 79.7 0 0.223 2_updatecdl: 0.2505 0.2800 0.003 0.565 51.2 122.3 79.7 0 0.223 2_nqh: 0.2506 0.2792 0.003 0.565 51.2 122.3 79.7 0 0.230 2_realsrl: 0.2506 0.2792 0.003 0.565 51.2 122.3 79.7 0 0.230 2_weight: 0.2506 0.2792 0.003 0.565 51.2 122.3 79.7 0 0.230 2_xyzrec: 0.2479 0.2811 0.002 0.417 51.2 122.3 79.7 0 0.295 2_realsrl2: 0.2479 0.2811 0.002 0.417 51.2 122.3 79.7 0 0.295 2_adp: 0.2463 0.2803 0.002 0.417 51.3 123.0 79.6 0 0.295 2_regHadp: 0.2462 0.2802 0.002 0.417 51.3 123.0 79.6 0 0.295 3_bss: 0.2458 0.2784 0.002 0.417 52.5 124.2 80.8 0 0.295 3_settarget: 0.2458 0.2784 0.002 0.417 52.5 124.2 80.8 0 0.295 3_updatephipsi: 0.2458 0.2784 0.002 0.417 52.5 124.2 80.8 0 0.295 3_updatecdl: 0.2458 0.2784 0.002 0.435 52.5 124.2 80.8 0 0.295 3_setrh: 0.2458 0.2784 0.002 0.435 52.5 124.2 80.8 0 0.295 3_nqh: 0.2458 0.2784 0.002 0.435 52.5 124.2 80.8 0 0.299 3_realsrl: 0.2459 0.2790 0.002 0.435 52.5 124.2 80.8 0 0.297 3_weight: 0.2459 0.2790 0.002 0.435 52.5 124.2 80.8 0 0.297 3_xyzrec: 0.2460 0.2788 0.002 0.410 52.5 124.2 80.8 0 0.298 3_realsrl2: 0.2460 0.2788 0.002 0.410 52.5 124.2 80.8 0 0.298 3_adp: 0.2445 0.2784 0.002 0.410 51.8 125.4 80.7 0 0.298 3_regHadp: 0.2444 0.2783 0.002 0.410 51.8 125.4 80.7 0 0.298 end: 0.2442 0.2786 0.002 0.410 52.4 126.0 81.3 0 0.298 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1wl3_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1wl3_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1400 Refinement macro-cycles (run) : 406.5900 Write final files (write_after_run_outputs) : 20.5000 Total : 434.2300 Total CPU time: 7.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:16 PDT -0700 (1716251716.98 s) Start R-work = 0.2579, R-free = 0.2869 Final R-work = 0.2442, R-free = 0.2786 =============================================================================== Job complete usr+sys time: 481.57 seconds wall clock time: 20 minutes 10.41 seconds (1210.41 seconds total)