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/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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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: 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: 0.70, per 1000 atoms: 0.20 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: 0.79 Conformation dependent library (CDL) restraints added in 162.4 milliseconds 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. 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: 0.28 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: 0.74 Time building geometry restraints manager: 0.90 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2966 r_free=0.3135 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2966 r_free=0.3135 ========================= Local real-space refinement ========================= Before: r_work=0.2966 r_free=0.3135 131 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 0.159 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 39 average time/residue: 0.1739 time to fit residues: 8.9853 After: r_work=0.2997 r_free=0.3272 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.556650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162276 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 0.3093 0.3395 0.0303 0.003 0.7 9.3 0.0 12.2 0 0.125 0.3057 0.3362 0.0305 0.004 0.7 9.6 0.0 12.2 0 0.250 0.3017 0.3330 0.0313 0.004 0.7 11.9 0.0 11.6 0 0.500 0.2955 0.3321 0.0367 0.005 0.8 11.7 0.0 12.2 0 1.000 0.2890 0.3323 0.0433 0.007 0.9 16.6 0.0 13.2 0 2.000 0.2839 0.3326 0.0487 0.009 1.0 19.8 0.0 13.8 0 3.000 0.2805 0.3345 0.0540 0.011 1.1 23.6 0.0 14.3 0 4.000 0.2783 0.3284 0.0501 0.012 1.2 24.8 0.0 14.8 0 5.000 0.2746 0.3316 0.0569 0.014 1.3 28.5 0.0 15.9 0 6.000 0.2734 0.3296 0.0562 0.015 1.4 29.1 0.0 15.9 0 7.000 0.2714 0.3287 0.0574 0.017 1.5 33.2 0.0 15.3 0 8.000 0.2701 0.3300 0.0599 0.018 1.6 35.0 0.0 15.9 0 9.000 0.2691 0.3294 0.0603 0.020 1.7 37.3 0.5 16.4 0 10.000 0.2728 0.3299 0.0571 0.015 1.4 31.2 0.0 15.9 0 7.278 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3093 0.3395 0.0303 0.003 0.7 9.3 0.0 12.2 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.3093 r_free=0.3395 117 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.274 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 4 residues processed: 23 average time/residue: 0.1166 time to fit residues: 4.3803 After: r_work=0.3176 r_free=0.3435 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 31.76 34.35 2.60 0.548 111.307 0.162 0.095 31.69 34.34 2.66 1.660 111.356 0.005 0.094 31.25 34.15 2.90 1.846 111.381 0.020 0.091 30.38 33.74 3.36 3.584 111.616 0.081 0.086 29.75 33.56 3.81 5.606 112.104 0.162 0.083 29.23 33.38 4.14 7.676 112.757 0.243 0.080 28.19 32.96 4.77 14.690 114.654 0.325 0.074 28.05 32.90 4.85 16.085 115.068 0.406 0.073 27.94 32.85 4.90 17.151 115.379 0.487 0.073 27.75 32.84 5.09 18.529 115.868 0.568 0.072 27.69 32.83 5.14 19.291 116.098 0.649 0.072 27.64 32.83 5.18 19.935 116.291 0.730 0.071 27.34 32.87 5.53 22.092 117.080 0.811 0.070 max suggested for this run: 22.26 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.730 Accepted refinement result: 27.64 32.83 5.18 19.935 116.291 0.730 0.071 Individual atomic B min max mean iso aniso Overall: 74.49 217.67 121.35 16.62 1719 0 Protein: 74.49 217.67 121.35 16.62 1719 0 Chain A: 74.49 217.67 121.35 N/A 1719 0 Histogram: Values Number of atoms 74.49 - 88.81 106 88.81 - 103.13 208 103.13 - 117.45 437 117.45 - 131.77 511 131.77 - 146.08 240 146.08 - 160.40 145 160.40 - 174.72 43 174.72 - 189.04 23 189.04 - 203.36 3 203.36 - 217.67 3 =========================== Idealize ADP of riding H ========================== r_work=0.2764 r_free=0.3283 r_work=0.2739 r_free=0.3260 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2739 r_free= 0.3260 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.070080 | | target function (ls_wunit_k1) not normalized (work): 448.019901 | | target function (ls_wunit_k1) not normalized (free): 32.843448 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2762 0.2739 0.3260 n_refl.: 6712 re-set all scales: r(all,work,free)=0.4408 0.4380 0.5022 n_refl.: 6712 remove outliers: r(all,work,free)=0.4408 0.4380 0.5022 n_refl.: 6712 overall B=-2.85 to atoms: r(all,work,free)=0.4351 0.4324 0.4940 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2750 0.2725 0.3279 n_refl.: 6712 remove outliers: r(all,work,free)=0.2748 0.2723 0.3279 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 0.2724 1242.303 1215.134 1.257 0.975 0.330 12.682-10.260 91.59 95 3 0.1488 1467.357 1435.207 1.232 0.978 0.322 10.240-8.268 91.00 185 7 0.1260 1300.272 1280.613 1.185 0.978 0.293 8.239-6.652 93.64 358 10 0.1993 794.578 785.474 1.111 0.981 0.271 6.641-5.360 94.83 677 38 0.2564 481.322 467.161 0.927 0.986 0.214 5.359-4.320 95.50 1280 57 0.2594 445.469 424.985 0.873 0.990 0.134 4.319-3.481 96.04 2451 119 0.3624 250.937 233.283 1.025 0.999 0.039 3.480-3.231 96.03 1252 78 0.4439 141.198 119.537 1.058 1.002 0.021 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=0.2637 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2723 r_free=0.3279 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2723 r_free=0.3279 ========================= Local real-space refinement ========================= Before: r_work=0.2723 r_free=0.3279 99 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.565 revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.4061 time to fit residues: 2.8987 After: r_work=0.2728 r_free=0.3265 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.163063 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.030106 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 0.2670 0.3238 0.0568 0.003 0.5 9.9 0.0 3.2 0 0.125 0.2612 0.3235 0.0622 0.003 0.6 11.7 0.0 3.2 0 0.250 0.2551 0.3227 0.0676 0.005 0.7 16.0 0.0 4.8 0 0.500 0.2483 0.3188 0.0705 0.008 0.9 18.6 0.0 9.0 0 1.000 0.2422 0.3212 0.0790 0.013 1.3 24.8 0.0 12.2 0 2.000 0.2385 0.3250 0.0865 0.018 1.7 35.0 0.0 13.8 0 3.000 0.2374 0.3292 0.0919 0.022 1.9 40.2 0.5 16.9 0 4.000 0.2360 0.3265 0.0905 0.026 2.1 42.8 0.5 20.6 0 5.000 0.2353 0.3293 0.0940 0.030 2.4 44.9 0.9 24.9 0 6.000 0.2341 0.3310 0.0969 0.033 2.6 50.4 1.4 25.4 0 7.000 0.2333 0.3344 0.1012 0.036 2.8 54.5 2.7 28.0 0 8.000 0.2320 0.3343 0.1023 0.040 3.0 56.5 3.2 28.6 0 9.000 0.2314 0.3330 0.1016 0.043 3.1 60.6 3.2 31.2 0 10.000 0.2418 0.3220 0.0802 0.014 1.4 27.4 0.0 13.2 0 2.082 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2670 0.3238 0.0568 0.003 0.5 9.9 0.0 3.2 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2670 r_free=0.3238 99 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.633 outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2849 time to fit residues: 3.7383 After: r_work=0.2689 r_free=0.3274 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.89 32.74 5.85 21.200 131.632 0.030 6.180 31.95 36.82 4.87 16.069 142.605 0.001 6.236 30.16 35.24 5.08 16.353 139.636 0.004 6.208 28.15 33.74 5.59 18.287 137.024 0.015 6.165 27.12 32.88 5.76 19.198 135.291 0.030 6.140 26.80 32.39 5.60 19.900 135.213 0.045 6.128 26.56 32.15 5.59 20.234 134.824 0.060 6.121 26.44 32.07 5.63 20.609 134.861 0.075 6.117 26.35 32.05 5.70 20.911 134.858 0.090 6.114 26.32 32.04 5.72 21.289 135.079 0.105 6.112 26.27 32.02 5.75 21.648 135.278 0.120 6.109 26.25 32.02 5.77 22.013 135.483 0.135 6.108 26.22 32.00 5.78 22.354 135.658 0.151 6.106 max suggested for this run: 26.33 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.151 Accepted refinement result: 26.22 32.00 5.78 22.354 135.658 0.151 6.106 Individual atomic B min max mean iso aniso Overall: 67.70 209.83 126.58 21.08 1719 0 Protein: 67.70 209.83 126.58 21.08 1719 0 Chain A: 67.70 209.83 126.58 N/A 1719 0 Histogram: Values Number of atoms 67.70 - 81.91 29 81.91 - 96.12 109 96.12 - 110.33 317 110.33 - 124.55 406 124.55 - 138.76 346 138.76 - 152.97 279 152.97 - 167.19 133 167.19 - 181.40 73 181.40 - 195.61 22 195.61 - 209.83 5 =========================== Idealize ADP of riding H ========================== r_work=0.2622 r_free=0.3200 r_work=0.2628 r_free=0.3195 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6710 (all), 4.75 % free)-------------| | | | r_work= 0.2628 r_free= 0.3195 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 6.105044 | | target function (ml) not normalized (work): 39017.335537 | | target function (ml) not normalized (free): 1984.203522 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2654 0.2628 0.3195 n_refl.: 6710 re-set all scales: r(all,work,free)=0.4453 0.4421 0.5126 n_refl.: 6710 remove outliers: r(all,work,free)=0.4453 0.4421 0.5126 n_refl.: 6710 overall B=-15.73 to atoms: r(all,work,free)=0.4109 0.4082 0.4685 n_refl.: 6710 bulk-solvent and scaling: r(all,work,free)=0.2623 0.2599 0.3139 n_refl.: 6710 remove outliers: r(all,work,free)=0.2623 0.2599 0.3139 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 0.2580 1242.303 1210.550 1.369 0.970 0.328 12.682-10.260 91.59 95 3 0.1336 1467.357 1436.425 1.334 0.972 0.320 10.240-8.268 91.00 185 7 0.1178 1300.272 1271.971 1.283 0.971 0.294 8.239-6.652 93.64 358 10 0.2024 794.578 775.970 1.158 0.972 0.252 6.641-5.360 94.83 677 38 0.2687 481.322 460.235 1.003 0.976 0.235 5.359-4.320 95.50 1280 57 0.2756 445.469 421.583 0.889 0.978 0.131 4.319-3.481 96.04 2451 119 0.3139 250.937 234.611 0.975 0.985 0.024 3.480-3.231 96.03 1252 78 0.3923 141.198 121.759 1.041 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=5.4888 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2599 r_free=0.3139 After: r_work=0.2599 r_free=0.3140 ================================== NQH flips ================================== r_work=0.2599 r_free=0.3140 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2599 r_free=0.3140 ========================= Local real-space refinement ========================= Before: r_work=0.2599 r_free=0.3140 92 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.042 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2353 After: r_work=0.2599 r_free=0.3140 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.921960 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.032594 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 0.2591 0.3122 0.0531 0.003 0.5 12.8 0.0 0.0 0 0.125 0.2587 0.3119 0.0532 0.003 0.5 12.8 0.0 0.0 0 0.250 0.2571 0.3111 0.0540 0.004 0.6 12.2 0.0 0.0 0 0.500 0.2505 0.3074 0.0569 0.011 0.9 12.5 0.0 0.0 0 1.000 0.2410 0.3025 0.0615 0.013 1.4 26.5 0.0 2.6 0 2.000 0.2379 0.3021 0.0641 0.016 1.7 28.5 0.0 4.2 0 3.000 0.2351 0.3018 0.0666 0.024 2.3 35.8 0.5 5.3 0 4.000 0.2326 0.3028 0.0702 0.027 2.5 41.4 0.5 6.9 0 5.000 0.2315 0.3030 0.0715 0.029 2.8 43.7 0.5 8.5 0 6.000 0.2302 0.3015 0.0713 0.031 2.9 43.4 0.5 7.9 0 7.000 0.2287 0.3038 0.0750 0.033 3.1 51.8 2.3 11.1 0 8.000 0.2274 0.3038 0.0765 0.036 3.2 55.3 1.8 13.2 1 9.000 0.2263 0.3048 0.0785 0.038 3.5 58.8 2.3 12.7 0 10.000 0.2390 0.3019 0.0629 0.016 1.6 29.7 0.0 4.2 0 2.461 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2571 0.3111 0.0540 0.004 0.6 12.2 0.0 0.0 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2571 r_free=0.3111 91 residues out of total 189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.679 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6731 After: r_work=0.2571 r_free=0.3111 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.71 31.11 5.40 23.654 124.191 0.033 6.107 32.38 36.37 3.99 17.111 136.843 0.001 6.218 31.10 35.16 4.07 16.801 135.139 0.004 6.202 28.41 33.59 5.18 18.773 130.323 0.016 6.169 27.17 32.47 5.30 19.797 128.290 0.033 6.141 26.50 31.84 5.34 20.332 127.488 0.049 6.124 26.16 31.52 5.36 20.724 127.407 0.065 6.114 25.73 31.06 5.33 20.768 126.716 0.081 6.102 25.56 30.97 5.41 21.081 126.901 0.098 6.097 25.37 30.90 5.53 21.399 126.522 0.114 6.092 25.25 30.78 5.53 21.697 126.396 0.130 6.088 25.18 30.77 5.59 21.953 126.577 0.147 6.086 25.11 30.68 5.57 22.212 126.302 0.163 6.084 max suggested for this run: 24.84 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.163 Accepted refinement result: 25.11 30.68 5.57 22.212 126.302 0.163 6.084 Individual atomic B min max mean iso aniso Overall: 48.10 197.83 115.09 21.00 1719 0 Protein: 48.10 197.83 115.09 21.00 1719 0 Chain A: 48.10 197.83 115.09 N/A 1719 0 Histogram: Values Number of atoms 48.10 - 63.07 10 63.07 - 78.04 64 78.04 - 93.02 250 93.02 - 107.99 377 107.99 - 122.96 421 122.96 - 137.94 303 137.94 - 152.91 170 152.91 - 167.89 86 167.89 - 182.86 28 182.86 - 197.83 10 =========================== Idealize ADP of riding H ========================== r_work=0.2511 r_free=0.3068 r_work=0.2508 r_free=0.3067 ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6710 (all), 4.75 % free)-------------| | | | r_work= 0.2508 r_free= 0.3067 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 6.083511 | | target function (ml) not normalized (work): 38879.719913 | | target function (ml) not normalized (free): 1981.271746 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2300 0.2772 6.5036 6.5865| | 2: 4.07 - 3.23 0.96 3182 160 0.3135 0.3908 5.6599 5.8376| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.75 30.94 1.00 0.85 79735.92| | 2: 4.07 - 3.23 3182 160 0.60 43.41 1.05 0.87 20018.82| |alpha: min = 0.85 max = 0.87 mean = 0.86| |beta: min = 20018.82 max = 79735.92 mean = 50003.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.88 mean = 37.15| |phase err.(test): min = 0.00 max = 89.81 mean = 39.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2533 0.2508 0.3067 n_refl.: 6710 re-set all scales: r(all,work,free)=0.4164 0.4136 0.4788 n_refl.: 6710 remove outliers: r(all,work,free)=0.4164 0.4136 0.4788 n_refl.: 6710 overall B=0.81 to atoms: r(all,work,free)=0.4181 0.4153 0.4811 n_refl.: 6710 bulk-solvent and scaling: r(all,work,free)=0.2526 0.2501 0.3060 n_refl.: 6710 remove outliers: r(all,work,free)=0.2526 0.2501 0.3060 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 0.2563 1242.303 1205.013 1.263 0.990 0.329 12.682-10.260 91.59 95 3 0.1288 1467.357 1433.796 1.241 0.989 0.319 10.240-8.268 91.00 185 7 0.1112 1300.272 1276.866 1.197 0.987 0.288 8.239-6.652 93.64 358 10 0.1952 794.578 779.814 1.093 0.986 0.244 6.641-5.360 94.83 677 38 0.2622 481.322 461.329 0.970 0.986 0.229 5.359-4.320 95.50 1280 57 0.2671 445.469 422.564 0.879 0.982 0.129 4.319-3.481 96.04 2451 119 0.2993 250.937 235.412 1.012 0.980 0.021 3.480-3.231 96.03 1252 78 0.3721 141.198 123.241 1.125 0.974 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.2536 ================= 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_updatephipsi: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_nqh: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_realsrl: 0.2997 0.3272 0.013 1.793 79.2 150.9 111.4 0 0.039 1_weight: 0.2997 0.3272 0.013 1.793 79.2 150.9 111.4 0 0.039 1_xyzrec: 0.3093 0.3395 0.003 0.665 79.2 150.9 111.4 0 0.223 1_realsrl2: 0.3176 0.3435 0.003 0.665 79.2 150.9 111.4 0 0.265 1_adp: 0.2764 0.3283 0.003 0.665 74.5 217.7 121.4 0 0.265 1_regHadp: 0.2739 0.3260 0.003 0.665 74.5 217.7 121.4 0 0.265 2_bss: 0.2723 0.3279 0.003 0.665 71.6 214.8 118.5 0 0.265 2_settarget: 0.2723 0.3279 0.003 0.665 71.6 214.8 118.5 0 0.265 2_updatephipsi: 0.2723 0.3279 0.003 0.665 71.6 214.8 118.5 0 0.265 2_updatecdl: 0.2723 0.3279 0.004 0.726 71.6 214.8 118.5 0 0.265 2_nqh: 0.2723 0.3279 0.004 0.726 71.6 214.8 118.5 0 0.265 2_realsrl: 0.2728 0.3265 0.004 0.726 71.6 214.8 118.5 0 0.267 2_weight: 0.2728 0.3265 0.004 0.726 71.6 214.8 118.5 0 0.267 2_xyzrec: 0.2670 0.3238 0.003 0.517 71.6 214.8 118.5 0 0.333 2_realsrl2: 0.2689 0.3274 0.003 0.517 71.6 214.8 118.5 0 0.342 2_adp: 0.2622 0.3200 0.003 0.517 67.7 209.8 126.6 0 0.342 2_regHadp: 0.2628 0.3195 0.003 0.517 67.7 209.8 126.6 0 0.342 3_bss: 0.2599 0.3139 0.003 0.517 52.0 194.1 110.9 0 0.342 3_settarget: 0.2599 0.3139 0.003 0.517 52.0 194.1 110.9 0 0.342 3_updatephipsi: 0.2599 0.3139 0.003 0.517 52.0 194.1 110.9 0 0.342 3_updatecdl: 0.2599 0.3139 0.003 0.549 52.0 194.1 110.9 0 0.342 3_setrh: 0.2599 0.3140 0.003 0.549 52.0 194.1 110.9 0 0.343 3_nqh: 0.2599 0.3140 0.003 0.549 52.0 194.1 110.9 0 0.343 3_realsrl: 0.2599 0.3140 0.003 0.549 52.0 194.1 110.9 0 0.343 3_weight: 0.2599 0.3140 0.003 0.549 52.0 194.1 110.9 0 0.343 3_xyzrec: 0.2571 0.3111 0.004 0.577 52.0 194.1 110.9 0 0.343 3_realsrl2: 0.2571 0.3111 0.004 0.577 52.0 194.1 110.9 0 0.343 3_adp: 0.2511 0.3068 0.004 0.577 48.1 197.8 115.1 0 0.343 3_regHadp: 0.2508 0.3067 0.004 0.577 48.1 197.8 115.1 0 0.343 end: 0.2501 0.3060 0.004 0.577 48.9 198.6 115.9 0 0.343 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2ogu_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2ogu_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.6300 Refinement macro-cycles (run) : 203.5900 Write final files (write_after_run_outputs) : 19.8400 Total : 226.0600 Total CPU time: 4.05 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:23 PDT -0700 (1716251303.20 s) Start R-work = 0.2966, R-free = 0.3135 Final R-work = 0.2501, R-free = 0.3060 =============================================================================== Job complete usr+sys time: 261.74 seconds wall clock time: 13 minutes 47.31 seconds (827.31 seconds total)