Starting phenix.refine on Mon May 20 17:16:28 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=False main.nqh_flips=False 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 { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { 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: 0.81 Conformation dependent library (CDL) restraints added in 185.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Time building geometry restraints manager: 0.94 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: 110 1.82 - 2.51: 2893 2.51 - 3.21: 10969 3.21 - 3.90: 14997 3.90 - 4.60: 22785 Nonbonded interactions: 51754 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 51749 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 { 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= 0.742 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 = 13.545854 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 0.3094 0.3335 0.0242 0.003 0.6 8.4 1.4 17.5 0 0.125 0.3053 0.3293 0.0240 0.003 0.6 9.9 1.4 18.0 0 0.250 0.3021 0.3307 0.0286 0.004 0.6 7.9 1.4 17.5 0 0.500 0.2941 0.3306 0.0364 0.005 0.7 12.2 0.9 18.5 0 1.000 0.2861 0.3283 0.0422 0.007 0.8 16.9 2.3 20.1 0 2.000 0.2812 0.3283 0.0471 0.009 0.9 20.7 2.7 19.6 0 3.000 0.2781 0.3281 0.0500 0.010 1.0 23.9 2.3 19.6 0 4.000 0.2755 0.3267 0.0512 0.012 1.1 26.8 2.7 20.1 0 5.000 0.2740 0.3307 0.0567 0.014 1.3 32.6 4.1 20.6 0 6.000 0.2714 0.3328 0.0613 0.015 1.3 35.5 5.5 20.6 0 7.000 0.2693 0.3309 0.0616 0.017 1.4 38.7 4.6 20.6 0 8.000 0.2673 0.3337 0.0664 0.018 1.5 40.2 4.6 21.2 0 9.000 0.2663 0.3291 0.0628 0.020 1.5 38.7 3.7 21.2 0 10.000 0.2721 0.3323 0.0602 0.015 1.3 34.1 5.5 20.6 0 6.773 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3021 0.3307 0.0286 0.004 0.6 7.9 1.4 17.5 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.21 33.07 2.86 0.548 111.307 0.163 0.083 30.16 33.11 2.95 1.651 111.363 0.005 0.083 29.70 32.85 3.15 1.817 111.405 0.020 0.080 28.87 32.44 3.57 3.292 111.644 0.082 0.076 27.55 32.02 4.46 8.070 112.908 0.163 0.069 27.23 31.91 4.68 9.627 113.361 0.245 0.068 27.03 31.84 4.81 10.787 113.697 0.326 0.067 26.89 31.78 4.89 11.663 113.949 0.408 0.066 26.70 31.72 5.02 12.777 114.334 0.490 0.065 26.53 31.70 5.16 13.792 114.685 0.571 0.064 26.54 31.68 5.14 13.906 114.674 0.653 0.064 26.13 31.77 5.64 16.633 115.706 0.734 0.062 26.07 31.78 5.70 17.147 115.857 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: 26.54 31.68 5.14 13.906 114.674 0.653 0.064 Individual atomic B min max mean iso aniso Overall: 74.49 172.04 118.11 11.95 1719 0 Protein: 74.49 172.04 118.11 11.95 1719 0 Chain A: 74.49 172.04 118.11 N/A 1719 0 Histogram: Values Number of atoms 74.49 - 84.25 47 84.25 - 94.00 135 94.00 - 103.76 173 103.76 - 113.51 280 113.51 - 123.27 448 123.27 - 133.02 305 133.02 - 142.78 192 142.78 - 152.53 92 152.53 - 162.29 32 162.29 - 172.04 15 =========================== Idealize ADP of riding H ========================== r_work=0.2654 r_free=0.3168 r_work=0.2626 r_free=0.3164 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2626 r_free= 0.3164 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ls_wunit_k1) (work): 0.063076 | | target function (ls_wunit_k1) not normalized (work): 403.243024 | | target function (ls_wunit_k1) not normalized (free): 30.448729 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2651 0.2626 0.3164 n_refl.: 6712 re-set all scales: r(all,work,free)=0.4355 0.4328 0.4933 n_refl.: 6712 remove outliers: r(all,work,free)=0.4355 0.4328 0.4933 n_refl.: 6712 overall B=-0.85 to atoms: r(all,work,free)=0.4338 0.4311 0.4910 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2648 0.2625 0.3157 n_refl.: 6712 remove outliers: r(all,work,free)=0.2647 0.2623 0.3157 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 0.2469 1253.422 1220.465 1.227 0.973 0.335 12.682-10.260 91.59 95 3 0.1328 1480.490 1444.947 1.176 0.977 0.323 10.240-8.268 91.00 185 7 0.1059 1311.910 1291.585 1.144 0.977 0.297 8.239-6.652 93.64 358 10 0.1771 801.690 794.821 1.089 0.980 0.281 6.641-5.360 94.83 677 38 0.2620 485.630 468.241 0.898 0.986 0.221 5.359-4.320 95.50 1280 57 0.2552 449.456 430.717 0.843 0.991 0.141 4.319-3.481 96.04 2451 119 0.3542 253.183 236.055 0.988 1.001 0.043 3.480-3.231 96.10 1253 78 0.4290 142.644 123.072 1.040 1.005 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.7032 ============================ 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 = 4.033569 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.029577 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 0.2636 0.3208 0.0571 0.003 0.5 8.2 0.9 13.8 0 0.125 0.2571 0.3187 0.0616 0.003 0.6 11.4 0.9 14.3 0 0.250 0.2529 0.3204 0.0675 0.005 0.7 14.9 1.8 15.9 0 0.500 0.2482 0.3227 0.0746 0.008 0.9 21.3 2.3 15.9 0 1.000 0.2431 0.3301 0.0869 0.014 1.4 32.3 5.0 18.5 0 2.000 0.2400 0.3299 0.0899 0.019 1.7 36.1 6.8 20.1 0 3.000 0.2382 0.3300 0.0918 0.023 2.0 43.7 8.7 20.6 0 4.000 0.2372 0.3300 0.0928 0.027 2.2 49.2 11.9 22.2 0 5.000 0.2359 0.3295 0.0935 0.030 2.5 51.8 12.8 22.2 0 6.000 0.2359 0.3323 0.0964 0.035 2.7 58.0 13.2 23.8 0 7.000 0.2351 0.3304 0.0952 0.037 2.9 59.1 13.2 25.4 0 8.000 0.2337 0.3273 0.0936 0.040 3.1 62.6 13.7 25.9 0 9.000 0.2334 0.3279 0.0945 0.044 3.3 65.8 14.6 27.0 0 10.000 0.2424 0.3294 0.0870 0.014 1.3 31.5 4.1 18.0 0 2.017 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2636 0.3208 0.0571 0.003 0.5 8.2 0.9 13.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.36 32.08 5.71 18.991 129.665 0.030 6.172 30.52 34.78 4.26 13.137 138.080 0.001 6.228 29.68 33.83 4.15 13.765 137.079 0.004 6.206 27.92 32.43 4.51 16.791 134.393 0.015 6.165 26.86 31.53 4.67 17.307 133.054 0.030 6.137 26.42 31.13 4.71 17.908 132.828 0.044 6.123 26.18 30.98 4.80 18.382 132.765 0.059 6.115 26.06 30.91 4.85 18.884 133.052 0.074 6.109 25.98 30.88 4.90 19.509 133.481 0.089 6.104 25.93 30.87 4.94 20.171 133.871 0.104 6.101 25.68 30.65 4.97 20.042 133.495 0.118 6.097 25.60 30.69 5.09 19.287 132.417 0.133 6.102 25.56 30.68 5.12 19.475 132.531 0.148 6.101 max suggested for this run: 25.93 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.118 Accepted refinement result: 25.68 30.65 4.97 20.042 133.495 0.118 6.097 Individual atomic B min max mean iso aniso Overall: 69.69 195.11 124.94 18.54 1719 0 Protein: 69.69 195.11 124.94 18.54 1719 0 Chain A: 69.69 195.11 124.94 N/A 1719 0 Histogram: Values Number of atoms 69.69 - 82.23 23 82.23 - 94.78 88 94.78 - 107.32 253 107.32 - 119.86 407 119.86 - 132.40 346 132.40 - 144.94 310 144.94 - 157.48 140 157.48 - 170.02 99 170.02 - 182.57 45 182.57 - 195.11 8 =========================== Idealize ADP of riding H ========================== r_work=0.2568 r_free=0.3065 r_work=0.2576 r_free=0.3058 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2576 r_free= 0.3058 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 6.095038 | | target function (ml) not normalized (work): 38959.483206 | | target function (ml) not normalized (free): 1979.027366 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2598 0.2576 0.3058 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4430 0.4402 0.5019 n_refl.: 6711 remove outliers: r(all,work,free)=0.4430 0.4402 0.5019 n_refl.: 6711 overall B=-14.92 to atoms: r(all,work,free)=0.4099 0.4075 0.4600 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2576 0.2554 0.3051 n_refl.: 6711 remove outliers: r(all,work,free)=0.2576 0.2554 0.3051 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 0.2495 1253.422 1221.823 1.476 0.904 0.334 12.682-10.260 91.59 95 3 0.1358 1480.490 1443.930 1.437 0.905 0.330 10.240-8.268 91.00 185 7 0.1137 1311.910 1282.075 1.369 0.903 0.304 8.239-6.652 93.64 358 10 0.1906 801.690 785.891 1.284 0.903 0.290 6.641-5.360 94.83 677 38 0.2675 485.630 463.078 1.068 0.904 0.234 5.359-4.320 95.50 1280 57 0.2710 449.456 426.073 0.966 0.903 0.154 4.319-3.481 96.04 2451 119 0.3106 253.183 237.132 1.066 0.903 0.030 3.480-3.231 96.10 1253 78 0.3862 142.644 124.086 1.156 0.900 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=5.2068 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2554 r_free=0.3051 After: r_work=0.2554 r_free=0.3051 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.770426 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.030703 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 0.2554 0.3049 0.0495 0.003 0.5 8.7 0.9 13.8 0 0.125 0.2551 0.3048 0.0497 0.003 0.5 8.7 0.9 13.8 0 0.250 0.2528 0.3029 0.0500 0.006 0.6 11.7 0.9 13.8 0 0.500 0.2456 0.2988 0.0533 0.011 1.1 18.9 0.9 13.8 0 1.000 0.2403 0.3038 0.0635 0.015 1.6 32.3 2.7 13.8 0 2.000 0.2369 0.3037 0.0669 0.020 2.1 36.7 4.1 13.8 0 3.000 0.2343 0.3018 0.0674 0.025 2.4 39.6 4.6 14.8 0 4.000 0.2329 0.3035 0.0706 0.027 2.7 44.6 4.6 16.4 0 5.000 0.2309 0.3035 0.0726 0.031 2.9 48.6 6.4 18.0 0 6.000 0.2303 0.3051 0.0749 0.030 2.9 47.2 6.8 18.0 0 7.000 0.2293 0.3078 0.0784 0.034 3.1 50.1 8.2 19.6 0 8.000 0.2280 0.3079 0.0799 0.038 3.4 57.4 8.2 20.6 0 9.000 0.2271 0.3073 0.0802 0.040 3.7 60.6 9.6 21.7 0 10.000 0.2390 0.3025 0.0634 0.017 1.8 32.6 2.7 13.8 0 2.385 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2551 0.3048 0.0497 0.003 0.5 8.7 0.9 13.8 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.51 30.48 4.97 22.309 123.060 0.031 6.106 31.57 35.52 3.94 15.667 134.418 0.001 6.220 30.36 34.31 3.94 15.538 132.832 0.004 6.202 27.90 32.40 4.50 17.473 128.586 0.015 6.164 26.76 31.51 4.76 18.382 126.720 0.031 6.135 26.21 31.30 5.08 18.822 126.166 0.046 6.120 25.88 31.19 5.31 19.087 126.023 0.061 6.112 25.70 31.18 5.48 19.396 126.384 0.077 6.106 25.38 30.81 5.43 19.659 125.911 0.092 6.096 25.21 30.73 5.51 20.080 125.659 0.107 6.092 25.11 30.66 5.55 20.429 125.639 0.123 6.089 25.03 30.64 5.61 20.735 125.737 0.138 6.086 24.98 30.59 5.61 21.028 125.514 0.154 6.085 max suggested for this run: 24.61 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.154 Accepted refinement result: 24.98 30.59 5.61 21.028 125.514 0.154 6.085 Individual atomic B min max mean iso aniso Overall: 51.37 192.88 114.94 19.93 1719 0 Protein: 51.37 192.88 114.94 19.93 1719 0 Chain A: 51.37 192.88 114.94 N/A 1719 0 Histogram: Values Number of atoms 51.37 - 65.52 11 65.52 - 79.67 63 79.67 - 93.82 231 93.82 - 107.97 370 107.97 - 122.12 454 122.12 - 136.27 306 136.27 - 150.42 157 150.42 - 164.58 89 164.58 - 178.73 34 178.73 - 192.88 4 =========================== Idealize ADP of riding H ========================== r_work=0.2498 r_free=0.3059 r_work=0.2494 r_free=0.3061 ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2494 r_free= 0.3061 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 6.084554 | | target function (ml) not normalized (work): 38892.466991 | | target function (ml) not normalized (free): 1984.731507 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2299 0.2800 6.521 6.6396| | 2: 4.07 - 3.23 0.96 3183 160 0.3082 0.3806 5.6445 5.8064| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.74 31.85 1.00 0.88 87371.82| | 2: 4.07 - 3.23 3183 160 0.63 41.71 1.06 0.90 18659.84| |alpha: min = 0.88 max = 0.90 mean = 0.89| |beta: min = 18659.84 max = 87371.82 mean = 53155.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.99 mean = 36.76| |phase err.(test): min = 0.00 max = 89.16 mean = 39.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2520 0.2494 0.3061 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4173 0.4145 0.4761 n_refl.: 6711 remove outliers: r(all,work,free)=0.4173 0.4145 0.4761 n_refl.: 6711 overall B=-0.19 to atoms: r(all,work,free)=0.4168 0.4141 0.4756 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2502 0.2475 0.3074 n_refl.: 6711 remove outliers: r(all,work,free)=0.2502 0.2475 0.3074 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 0.2498 1253.422 1220.995 1.260 0.987 0.329 12.682-10.260 91.59 95 3 0.1335 1480.490 1444.455 1.240 0.988 0.320 10.240-8.268 91.00 185 7 0.1123 1311.910 1281.493 1.202 0.985 0.300 8.239-6.652 93.64 358 10 0.1898 801.690 787.736 1.134 0.984 0.280 6.641-5.360 94.83 677 38 0.2616 485.630 464.869 0.968 0.984 0.230 5.359-4.320 95.50 1280 57 0.2640 449.456 427.088 0.879 0.979 0.140 4.319-3.481 96.04 2451 119 0.2964 253.183 238.593 1.018 0.976 0.019 3.480-3.231 96.10 1253 78 0.3639 142.644 125.834 1.147 0.970 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.6840 ================= 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: 0.3021 0.3307 0.004 0.618 79.2 150.9 111.4 0 0.197 1_adp: 0.2654 0.3168 0.004 0.618 74.5 172.0 118.1 0 0.197 1_regHadp: 0.2626 0.3164 0.004 0.618 74.5 172.0 118.1 0 0.197 2_bss: 0.2623 0.3157 0.004 0.618 73.6 171.2 117.3 0 0.197 2_settarget: 0.2623 0.3157 0.004 0.618 73.6 171.2 117.3 0 0.197 2_updatecdl: 0.2623 0.3157 0.004 0.690 73.6 171.2 117.3 0 0.197 2_weight: 0.2623 0.3157 0.004 0.690 73.6 171.2 117.3 0 0.197 2_xyzrec: 0.2636 0.3208 0.003 0.531 73.6 171.2 117.3 0 0.260 2_adp: 0.2568 0.3065 0.003 0.531 69.7 195.1 124.9 0 0.260 2_regHadp: 0.2576 0.3058 0.003 0.531 69.7 195.1 124.9 0 0.260 3_bss: 0.2554 0.3051 0.003 0.531 54.8 180.2 110.0 0 0.260 3_settarget: 0.2554 0.3051 0.003 0.531 54.8 180.2 110.0 0 0.260 3_updatecdl: 0.2554 0.3051 0.003 0.585 54.8 180.2 110.0 0 0.260 3_setrh: 0.2554 0.3051 0.003 0.585 54.8 180.2 110.0 0 0.260 3_weight: 0.2554 0.3051 0.003 0.585 54.8 180.2 110.0 0 0.260 3_xyzrec: 0.2551 0.3048 0.003 0.539 54.8 180.2 110.0 0 0.260 3_adp: 0.2498 0.3059 0.003 0.539 51.4 192.9 114.9 0 0.260 3_regHadp: 0.2494 0.3061 0.003 0.539 51.4 192.9 114.9 0 0.260 end: 0.2475 0.3074 0.003 0.539 51.2 192.7 114.7 0 0.260 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2ogu_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2ogu_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3900 Refinement macro-cycles (run) : 156.7400 Write final files (write_after_run_outputs) : 20.4200 Total : 181.5500 Total CPU time: 3.33 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:29:29 PDT -0700 (1716251369.75 s) Start R-work = 0.2966, R-free = 0.3135 Final R-work = 0.2475, R-free = 0.3074 =============================================================================== Job complete usr+sys time: 220.04 seconds wall clock time: 13 minutes 43.51 seconds (823.51 seconds total)