Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2ogu.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2ogu.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2ogu.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3448 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3448 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Time building chain proxies: 1.32, per 1000 atoms: 0.38 Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 338 8.00 N 305 7.00 C 1069 6.00 H 1729 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: 2.73 Conformation dependent library (CDL) restraints added in 570.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 2 sheets defined 39.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 127 through 130 No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 removed outlier: 4.449A pdb=" N LYS A 150 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 152 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.752A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.456A pdb=" N GLU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 280 through 283 No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 324 through 333 Processing sheet with id= A, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.277A pdb=" N VAL A 181 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 158 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA A 143 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 160 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.557A pdb=" N GLY A 320 " --> pdb=" O VAL A 265 " (cutoff:3.500A) 51 hydrogen bonds defined for protein. 135 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: 2.38 Time building geometry restraints manager: 1.71 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: 1726 1.15 - 1.31: 311 1.31 - 1.48: 654 1.48 - 1.65: 767 1.65 - 1.82: 11 Bond restraints: 3469 Sorted by residual: bond pdb=" CD GLU A 325 " pdb=" OE1 GLU A 325 " ideal model delta sigma weight residual 1.249 1.413 -0.164 1.90e-02 2.77e+03 7.49e+01 bond pdb=" N SER A 273 " pdb=" H SER A 273 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N SER A 235 " pdb=" H SER A 235 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 329 " pdb="HH22 ARG A 329 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASN A 174 " pdb=" H ASN A 174 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 96.85 - 107.61: 528 107.61 - 118.37: 4323 118.37 - 129.13: 1425 129.13 - 139.89: 9 139.89 - 150.65: 1 Bond angle restraints: 6286 Sorted by residual: angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 150.65 -39.35 2.30e+00 1.89e-01 2.93e+02 angle pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " pdb=" NE ARG A 213 " ideal model delta sigma weight residual 112.00 134.35 -22.35 2.20e+00 2.07e-01 1.03e+02 angle pdb=" N ASP A 202 " pdb=" CA ASP A 202 " pdb=" C ASP A 202 " ideal model delta sigma weight residual 107.32 118.69 -11.37 1.65e+00 3.67e-01 4.75e+01 angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 112.68 104.82 7.86 1.33e+00 5.65e-01 3.50e+01 angle pdb=" C VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta sigma weight residual 110.52 101.59 8.93 1.57e+00 4.06e-01 3.24e+01 ... (remaining 6281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1348 17.94 - 35.89: 149 35.89 - 53.83: 71 53.83 - 71.77: 28 71.77 - 89.72: 2 Dihedral angle restraints: 1598 sinusoidal: 909 harmonic: 689 Sorted by residual: dihedral pdb=" C THR A 261 " pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" CB THR A 261 " ideal model delta harmonic sigma weight residual -122.00 -133.67 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C VAL A 265 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.88e+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 122.80 132.91 -10.11 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 1595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 197 0.092 - 0.183: 58 0.183 - 0.275: 13 0.275 - 0.366: 2 0.366 - 0.458: 1 Chirality restraints: 271 Sorted by residual: 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 5.24e+00 chirality pdb=" CA THR A 261 " pdb=" N THR A 261 " pdb=" C THR A 261 " pdb=" CB THR A 261 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 268 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " 0.012 2.00e-02 2.50e+03 1.08e-02 3.52e+00 pdb=" CG PHE A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 232 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 232 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 232 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 232 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 232 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 333 " -0.019 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 333 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 333 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 333 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 333 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 333 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 333 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 333 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 333 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 333 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 247 " -0.002 2.00e-02 2.50e+03 7.99e-03 1.92e+00 pdb=" CG TYR A 247 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 247 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 247 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 247 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 247 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 247 " -0.001 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 100 1.82 - 2.51: 2854 2.51 - 3.21: 10924 3.21 - 3.90: 14901 3.90 - 4.60: 22721 Nonbonded interactions: 51500 Sorted by model distance: nonbonded pdb="HH11 ARG A 262 " pdb=" HB ILE A 304 " model vdw sym.op. 1.119 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb=" HB3 SER A 126 " pdb=" HD1 PHE A 232 " model vdw sym.op. 1.225 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb="HD22 LEU A 330 " pdb="HD11 ILE A 334 " model vdw 1.269 2.440 nonbonded pdb=" HB3 ASP A 202 " pdb="HG23 VAL A 205 " model vdw 1.288 2.440 nonbonded pdb=" HG3 GLU A 133 " pdb=" HG SER A 240 " model vdw sym.op. 1.307 2.270 -x+2,-x+y+1,-z+1 ... (remaining 51495 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 7 15.96 2 O 338 7.97 1 N 305 6.97 1 C 1069 5.97 2 H 1729 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: 1729 of 3448 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3448 n_use_u_iso = 3448 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 = 3448 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3448 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3448 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 127 through 130 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 132 through 134 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 146 through 155 helix_type = alpha pi *3_10 unknown } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 167 through 172 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 188 through 201 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 214 through 222 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 231 through 243 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 247 through 255 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 280 through 283 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 285 through 289 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 324 through 333 } sheet { first_strand = chain 'A' and resid 207 through 209 sheet_id = " A" strand { selection = chain 'A' and resid 180 through 183 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 181 and name N bond_start_previous = chain 'A' and resid 208 and name O } strand { selection = chain 'A' and resid 118 through 121 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 119 and name N bond_start_previous = chain 'A' and resid 180 and name O } strand { selection = chain 'A' and resid 139 through 143 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 140 and name N bond_start_previous = chain 'A' and resid 118 and name O } strand { selection = chain 'A' and resid 158 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 158 and name N bond_start_previous = chain 'A' and resid 141 and name O } } sheet { first_strand = chain 'A' and resid 263 through 268 sheet_id = " B" strand { selection = chain 'A' and resid 317 through 322 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 322 and name N bond_start_previous = chain 'A' and resid 263 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2ogu_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1729 occupancy sum: 1729.00 (% of total atoms 50.22) Rotatable: count: 500 occupancy sum: 500.00 (% of total atoms 14.52) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5099 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058324 | | target function (ml) not normalized (work): 38761.159679 | | target function (ml) not normalized (free): 1913.185558 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3212 159 0.4154 0.4599 6.5974 6.5063| | 2: 4.07 - 3.23 0.96 3186 160 0.6033 0.6527 5.5149 5.4918| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 28.61 - 4.07 3212 159 0.43 57.03 0.98 0.24 84005.03| | 2: 4.07 - 3.23 3186 160 0.53 49.94 1.93 0.59 9836.65| |alpha: min = 0.24 max = 0.59 mean = 0.42| |beta: min = 9836.65 max = 84005.03 mean = 47071.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.90 mean = 53.50| |phase err.(test): min = 2.39 max = 89.71 mean = 55.64| |-----------------------------------------------------------------------------| ----------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 : 0.013 0.164 1740 Z= 0.880 Angle : 1.793 39.348 2349 Z= 1.075 Chirality : 0.093 0.458 271 Planarity : 0.004 0.014 311 Dihedral : 20.776 89.715 667 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 3.20 % Allowed : 14.61 % Favored : 82.19 % Rotamer: Outliers : 20.63 % Allowed : 14.81 % Favored : 64.55 % Cbeta Deviations : 1.48 % 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: -5.26 (0.44), residues: 219 helix: -4.53 (0.27), residues: 89 sheet: -0.37 (0.86), residues: 42 loop : -3.82 (0.47), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 329 TYR 0.014 0.004 TYR A 247 PHE 0.020 0.003 PHE A 232 TRP 0.005 0.002 TRP A 123 HIS 0.003 0.001 HIS A 193 Individual atomic B min max mean iso aniso Overall: 91.32 163.00 123.43 0.77 1719 0 Protein: 91.32 163.00 123.43 0.77 1719 0 Chain A: 91.32 163.00 123.43 N/A 1719 0 Histogram: Values Number of atoms 91.32 - 98.49 108 98.49 - 105.66 221 105.66 - 112.82 174 112.82 - 119.99 133 119.99 - 127.16 184 127.16 - 134.33 354 134.33 - 141.50 450 141.50 - 148.66 70 148.66 - 155.83 17 155.83 - 163.00 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1 = 5 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5099 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058324 | | target function (ml) not normalized (work): 38761.159679 | | target function (ml) not normalized (free): 1913.185558 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4647 0.4624 0.5099 n_refl.: 6717 re-set all scales: r(all,work,free)=0.4647 0.4624 0.5099 n_refl.: 6717 remove outliers: r(all,work,free)=0.4639 0.4616 0.5099 n_refl.: 6712 overall B=-12.08 to atoms: r(all,work,free)=0.4399 0.4379 0.4756 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2973 0.2966 0.3135 n_refl.: 6712 remove outliers: r(all,work,free)=0.2973 0.2966 0.3135 n_refl.: 6712 ======================== 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 28.612-12.706 81.97 93 7 0.2705 2116.694 2050.380 1.316 0.964 0.337 12.682-10.260 91.59 95 3 0.1550 2500.151 2446.970 1.254 0.968 0.328 10.240-8.268 91.43 185 7 0.1279 2215.464 2168.706 1.217 0.969 0.301 8.239-6.652 93.16 358 10 0.2218 1353.840 1317.902 1.163 0.975 0.286 6.641-5.360 94.83 677 38 0.3037 820.100 772.991 0.955 0.983 0.240 5.359-4.320 95.50 1280 57 0.2894 759.011 710.060 0.881 0.992 0.160 4.319-3.481 96.04 2452 119 0.3937 427.822 388.084 0.990 1.009 0.052 3.480-3.231 96.10 1253 78 0.4479 240.887 203.131 1.029 1.019 0.026 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9878 b_overall=2.3997 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.745384 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163194 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3090 0.3369 0.0279 0.004 0.6 10.2 1.4 18.0 0 0.125 0.3068 0.3377 0.0309 0.003 0.6 10.2 1.4 18.0 0 0.250 0.3016 0.3315 0.0299 0.004 0.7 9.6 1.4 17.5 0 0.500 0.2949 0.3325 0.0376 0.005 0.7 12.2 0.9 18.0 0 1.000 0.2868 0.3335 0.0467 0.007 0.8 17.8 1.8 19.0 0 2.000 0.2817 0.3322 0.0505 0.009 0.9 21.0 2.3 19.0 0 3.000 0.2785 0.3360 0.0575 0.010 1.0 24.2 2.7 18.5 0 4.000 0.2764 0.3326 0.0562 0.012 1.1 26.2 2.3 20.1 0 5.000 0.2745 0.3309 0.0564 0.014 1.2 29.1 2.3 20.6 0 6.000 0.2726 0.3315 0.0589 0.015 1.3 30.9 2.7 20.6 0 7.000 0.2701 0.3348 0.0647 0.017 1.4 35.5 3.7 20.6 0 8.000 0.2687 0.3343 0.0656 0.018 1.5 36.7 5.0 21.2 0 9.000 0.2672 0.3328 0.0656 0.020 1.6 39.0 5.9 21.7 0 10.000 0.2720 0.3328 0.0608 0.015 1.3 32.3 3.2 20.6 0 6.873 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3016 0.3315 0.0299 0.004 0.7 9.6 1.4 17.5 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.16 33.15 2.99 0.548 111.307 0.163 0.083 30.11 33.16 3.06 1.656 111.361 0.005 0.083 29.66 32.95 3.29 1.822 111.400 0.020 0.080 28.84 32.62 3.78 3.292 111.633 0.082 0.076 27.53 32.30 4.76 8.031 112.895 0.163 0.069 27.21 32.22 5.01 9.582 113.362 0.245 0.068 27.00 32.14 5.14 10.712 113.698 0.326 0.067 26.86 32.13 5.26 11.571 113.955 0.408 0.066 26.70 32.11 5.41 12.552 114.286 0.490 0.065 26.54 32.13 5.58 13.514 114.622 0.571 0.064 26.52 32.10 5.58 13.773 114.674 0.653 0.064 26.12 32.22 6.10 16.443 115.690 0.734 0.062 26.06 32.23 6.17 17.012 115.868 0.816 0.062 max suggested for this run: 22.26 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.653 Accepted refinement result: 26.52 32.10 5.58 13.773 114.674 0.653 0.064 Individual atomic B min max mean iso aniso Overall: 74.49 171.81 118.11 11.77 1719 0 Protein: 74.49 171.81 118.11 11.77 1719 0 Chain A: 74.49 171.81 118.11 N/A 1719 0 Histogram: Values Number of atoms 74.49 - 84.23 49 84.23 - 93.96 136 93.96 - 103.69 172 103.69 - 113.42 274 113.42 - 123.15 466 123.15 - 132.89 295 132.89 - 142.62 185 142.62 - 152.35 92 152.35 - 162.08 33 162.08 - 171.81 17 =========================== Idealize ADP of riding H ========================== r_work=0.2652 r_free=0.3210 r_work=0.2625 r_free=0.3197 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2625 r_free= 0.3197 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ls_wunit_k1) (work): 0.063040 | | target function (ls_wunit_k1) not normalized (work): 403.014232 | | target function (ls_wunit_k1) not normalized (free): 31.168304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2650 0.2625 0.3197 n_refl.: 6712 re-set all scales: r(all,work,free)=0.4359 0.4332 0.4910 n_refl.: 6712 remove outliers: r(all,work,free)=0.4359 0.4332 0.4910 n_refl.: 6712 overall B=-0.65 to atoms: r(all,work,free)=0.4346 0.4319 0.4893 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2651 0.2625 0.3201 n_refl.: 6712 remove outliers: r(all,work,free)=0.2649 0.2624 0.3201 n_refl.: 6711 ======================== 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 28.612-12.706 81.97 93 7 0.2586 1251.372 1226.614 1.182 0.975 0.329 12.682-10.260 91.59 95 3 0.1316 1478.068 1442.271 1.171 0.979 0.320 10.240-8.268 91.00 185 7 0.1025 1309.764 1291.651 1.142 0.979 0.301 8.239-6.652 93.64 358 10 0.1727 800.379 793.227 1.082 0.981 0.281 6.641-5.360 94.83 677 38 0.2638 484.836 467.734 0.898 0.987 0.221 5.359-4.320 95.50 1280 57 0.2533 448.721 430.499 0.846 0.991 0.151 4.319-3.481 96.04 2451 119 0.3544 252.769 235.694 0.986 1.001 0.045 3.480-3.231 96.10 1253 78 0.4366 142.411 122.406 1.035 1.005 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.5361 ============================ 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 = 4.298114 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.028636 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2659 0.3267 0.0608 0.003 0.6 9.6 0.9 13.2 0 0.125 0.2598 0.3297 0.0700 0.003 0.6 12.5 0.9 13.2 0 0.250 0.2539 0.3313 0.0775 0.005 0.8 17.2 1.4 15.9 0 0.500 0.2487 0.3302 0.0815 0.008 0.9 21.8 2.3 16.4 0 1.000 0.2439 0.3328 0.0888 0.014 1.4 34.1 5.0 18.0 0 2.000 0.2409 0.3297 0.0888 0.019 1.7 37.6 6.8 19.0 0 3.000 0.2398 0.3321 0.0923 0.023 2.0 41.1 9.1 20.1 0 4.000 0.2376 0.3314 0.0938 0.027 2.2 50.4 11.4 22.2 0 5.000 0.2367 0.3325 0.0958 0.030 2.5 53.3 12.8 21.7 0 6.000 0.2352 0.3327 0.0975 0.034 2.7 53.9 13.2 22.2 0 7.000 0.2350 0.3317 0.0967 0.037 2.8 57.1 12.8 24.9 0 8.000 0.2348 0.3322 0.0973 0.040 3.1 62.6 12.8 28.0 0 9.000 0.2337 0.3310 0.0973 0.043 3.2 64.1 13.2 27.5 0 10.000 0.2441 0.3353 0.0913 0.015 1.4 35.8 6.4 19.0 0 2.149 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2659 0.3267 0.0608 0.003 0.6 9.6 0.9 13.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.59 32.67 6.08 18.911 129.769 0.029 6.180 30.70 35.30 4.59 13.022 138.232 0.001 6.237 29.92 34.53 4.61 13.564 137.342 0.004 6.215 28.23 32.99 4.76 16.622 134.593 0.014 6.172 27.12 32.19 5.07 17.255 133.307 0.029 6.146 26.62 31.73 5.11 17.739 132.774 0.043 6.132 26.37 31.60 5.23 18.204 132.812 0.057 6.124 26.22 31.57 5.35 18.663 132.978 0.072 6.119 26.15 31.50 5.35 19.252 133.389 0.086 6.113 26.10 31.49 5.40 19.898 133.775 0.100 6.110 26.06 31.46 5.40 20.533 134.112 0.115 6.107 25.80 31.14 5.35 20.169 133.600 0.129 6.104 25.71 31.17 5.46 19.731 133.029 0.143 6.106 max suggested for this run: 25.95 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.129 Accepted refinement result: 25.80 31.14 5.35 20.169 133.600 0.129 6.104 Individual atomic B min max mean iso aniso Overall: 69.89 194.32 125.14 18.70 1719 0 Protein: 69.89 194.32 125.14 18.70 1719 0 Chain A: 69.89 194.32 125.14 N/A 1719 0 Histogram: Values Number of atoms 69.89 - 82.33 27 82.33 - 94.78 88 94.78 - 107.22 245 107.22 - 119.66 397 119.66 - 132.10 365 132.10 - 144.55 282 144.55 - 156.99 156 156.99 - 169.43 98 169.43 - 181.87 51 181.87 - 194.32 10 =========================== Idealize ADP of riding H ========================== r_work=0.2580 r_free=0.3114 r_work=0.2587 r_free=0.3112 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2587 r_free= 0.3112 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 6.102040 | | target function (ml) not normalized (work): 39004.236573 | | target function (ml) not normalized (free): 1981.775848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2611 0.2587 0.3112 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4441 0.4414 0.5008 n_refl.: 6711 remove outliers: r(all,work,free)=0.4441 0.4414 0.5008 n_refl.: 6711 overall B=-11.11 to atoms: r(all,work,free)=0.4192 0.4167 0.4679 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2581 0.2559 0.3061 n_refl.: 6711 remove outliers: r(all,work,free)=0.2580 0.2558 0.3061 n_refl.: 6710 ======================== 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 28.612-12.706 81.97 93 7 0.2542 1251.372 1224.470 1.217 0.991 0.327 12.682-10.260 91.59 95 3 0.1325 1478.068 1445.860 1.208 0.992 0.317 10.240-8.268 91.00 185 7 0.1107 1309.764 1285.140 1.176 0.988 0.300 8.239-6.652 93.64 358 10 0.1921 800.379 786.264 1.119 0.987 0.284 6.641-5.360 94.83 677 38 0.2649 484.836 463.099 0.945 0.986 0.228 5.359-4.320 95.50 1280 57 0.2710 448.721 425.599 0.865 0.982 0.147 4.319-3.481 96.04 2451 119 0.3117 252.769 236.948 0.976 0.978 0.056 3.480-3.231 96.03 1252 78 0.3941 142.229 122.495 1.081 0.970 0.013 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=2.0353 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2558 r_free=0.3061 After: r_work=0.2558 r_free=0.3060 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.694064 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.030628 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2560 0.3075 0.0515 0.003 0.6 9.9 0.9 13.2 0 0.125 0.2556 0.3073 0.0517 0.003 0.6 9.9 0.9 13.2 0 0.250 0.2527 0.3045 0.0517 0.006 0.6 12.2 0.9 13.8 0 0.500 0.2457 0.3028 0.0571 0.011 1.2 19.2 0.9 13.2 0 1.000 0.2384 0.3047 0.0663 0.016 1.8 29.7 1.8 13.8 0 2.000 0.2346 0.3066 0.0719 0.021 2.1 39.0 3.7 13.8 0 3.000 0.2332 0.3063 0.0730 0.024 2.5 42.8 5.0 15.3 0 4.000 0.2316 0.3066 0.0750 0.027 2.7 45.2 5.9 18.0 0 5.000 0.2311 0.3082 0.0771 0.029 2.7 46.6 5.9 19.6 0 6.000 0.2319 0.3074 0.0755 0.029 2.7 47.2 6.4 20.1 0 7.000 0.2306 0.3058 0.0752 0.032 2.8 51.3 6.8 20.1 0 8.000 0.2287 0.3033 0.0746 0.033 2.8 45.4 5.0 18.5 0 9.000 0.2274 0.3041 0.0767 0.039 3.6 56.2 8.7 22.2 0 10.000 0.2372 0.3054 0.0681 0.018 1.9 32.9 2.7 13.2 0 2.347 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2556 0.3073 0.0517 0.003 0.6 9.9 0.9 13.2 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.56 30.73 5.17 22.417 127.147 0.031 6.110 31.72 36.20 4.49 16.172 138.950 0.001 6.229 30.41 34.91 4.50 16.143 136.978 0.004 6.211 27.98 32.72 4.74 17.747 132.434 0.015 6.168 26.90 31.99 5.09 18.704 130.680 0.031 6.141 26.37 31.72 5.36 19.195 130.149 0.046 6.126 26.04 31.66 5.63 19.401 129.989 0.061 6.117 25.94 31.87 5.93 19.827 130.646 0.077 6.113 25.50 31.45 5.95 19.986 129.604 0.092 6.103 25.34 31.38 6.03 20.358 129.505 0.107 6.098 25.25 31.39 6.14 20.662 129.692 0.123 6.095 25.15 31.27 6.12 20.987 129.491 0.138 6.093 25.08 31.22 6.13 21.242 129.482 0.153 6.091 max suggested for this run: 25.43 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.092 Accepted refinement result: 25.50 31.45 5.95 19.986 129.604 0.092 6.103 Individual atomic B min max mean iso aniso Overall: 54.91 192.37 118.96 16.04 1719 0 Protein: 54.91 192.37 118.96 16.04 1719 0 Chain A: 54.91 192.37 118.96 N/A 1719 0 Histogram: Values Number of atoms 54.91 - 68.66 8 68.66 - 82.41 49 82.41 - 96.15 170 96.15 - 109.90 368 109.90 - 123.64 476 123.64 - 137.39 340 137.39 - 151.14 180 151.14 - 164.88 92 164.88 - 178.63 26 178.63 - 192.37 10 =========================== Idealize ADP of riding H ========================== r_work=0.2550 r_free=0.3145 r_work=0.2553 r_free=0.3157 ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6710 (all), 4.75 % free)-------------| | | | r_work= 0.2553 r_free= 0.3157 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 6.104691 | | target function (ml) not normalized (work): 39015.078340 | | target function (ml) not normalized (free): 1986.844263 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3209 159 0.2327 0.2882 6.5245 6.63| | 2: 4.07 - 3.23 0.96 3182 160 0.3232 0.3939 5.6814 5.8292| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 28.61 - 4.07 3209 159 0.73 32.00 1.00 0.94 87221.94| | 2: 4.07 - 3.23 3182 160 0.62 42.27 1.05 0.98 19460.32| |alpha: min = 0.94 max = 0.98 mean = 0.96| |beta: min = 19460.32 max = 87221.94 mean = 53484.27| |figures of merit: min = 0.01 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.38 mean = 37.11| |phase err.(test): min = 0.00 max = 89.31 mean = 39.69| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2580 0.2553 0.3157 n_refl.: 6710 re-set all scales: r(all,work,free)=0.4300 0.4273 0.4898 n_refl.: 6710 remove outliers: r(all,work,free)=0.4300 0.4273 0.4898 n_refl.: 6710 overall B=-3.75 to atoms: r(all,work,free)=0.4217 0.4190 0.4788 n_refl.: 6710 bulk-solvent and scaling: r(all,work,free)=0.2555 0.2527 0.3142 n_refl.: 6710 remove outliers: r(all,work,free)=0.2555 0.2527 0.3142 n_refl.: 6710 ======================== 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 28.612-12.706 81.97 93 7 0.2562 1251.372 1218.432 1.211 0.986 0.324 12.682-10.260 91.59 95 3 0.1331 1478.068 1443.916 1.214 0.987 0.311 10.240-8.268 91.00 185 7 0.1110 1309.764 1284.717 1.185 0.984 0.292 8.239-6.652 93.64 358 10 0.1918 800.379 786.092 1.132 0.984 0.275 6.641-5.360 94.83 677 38 0.2659 484.836 464.124 0.969 0.984 0.226 5.359-4.320 95.50 1280 57 0.2675 448.721 426.534 0.882 0.981 0.136 4.319-3.481 96.04 2451 119 0.3068 252.769 237.871 1.016 0.980 0.060 3.480-3.231 96.03 1252 78 0.3763 142.229 124.702 1.133 0.975 0.011 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.5467 ================= 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 : 0.4624 0.5099 0.013 1.793 91.3 163.0 123.4 0 0.000 1_bss: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_settarget: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_weight: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_xyzrec: 0.3016 0.3315 0.004 0.656 79.2 150.9 111.4 0 0.198 1_adp: 0.2652 0.3210 0.004 0.656 74.5 171.8 118.1 0 0.198 1_regHadp: 0.2625 0.3197 0.004 0.656 74.5 171.8 118.1 0 0.198 2_bss: 0.2624 0.3201 0.004 0.656 73.8 171.2 117.5 0 0.198 2_settarget: 0.2624 0.3201 0.004 0.656 73.8 171.2 117.5 0 0.198 2_updatecdl: 0.2624 0.3201 0.004 0.724 73.8 171.2 117.5 0 0.198 2_weight: 0.2624 0.3201 0.004 0.724 73.8 171.2 117.5 0 0.198 2_xyzrec: 0.2659 0.3267 0.003 0.556 73.8 171.2 117.5 0 0.270 2_adp: 0.2580 0.3114 0.003 0.556 69.9 194.3 125.1 0 0.270 2_regHadp: 0.2587 0.3112 0.003 0.556 69.9 194.3 125.1 0 0.270 3_bss: 0.2558 0.3061 0.003 0.556 58.8 183.2 114.0 0 0.270 3_settarget: 0.2558 0.3061 0.003 0.556 58.8 183.2 114.0 0 0.270 3_updatecdl: 0.2558 0.3061 0.003 0.614 58.8 183.2 114.0 0 0.270 3_setrh: 0.2558 0.3060 0.003 0.614 58.8 183.2 114.0 0 0.270 3_weight: 0.2558 0.3060 0.003 0.614 58.8 183.2 114.0 0 0.270 3_xyzrec: 0.2556 0.3073 0.003 0.563 58.8 183.2 114.0 0 0.270 3_adp: 0.2550 0.3145 0.003 0.563 54.9 192.4 119.0 0 0.270 3_regHadp: 0.2553 0.3157 0.003 0.563 54.9 192.4 119.0 0 0.270 end: 0.2527 0.3142 0.003 0.563 51.2 188.6 115.2 0 0.270 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2ogu_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2ogu_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1000 Refinement macro-cycles (run) : 155.9200 Write final files (write_after_run_outputs) : 19.3700 Total : 180.3900 Total CPU time: 3.48 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:36 PDT -0700 (1716251496.97 s) Start R-work = 0.2966, R-free = 0.3135 Final R-work = 0.2527, R-free = 0.3142 =============================================================================== Job complete usr+sys time: 228.07 seconds wall clock time: 14 minutes 35.04 seconds (875.04 seconds total)