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/1wl3.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { 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: 8905 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4443 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 1.60, per 1000 atoms: 0.18 Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 291.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4496 1.15 - 1.31: 769 1.31 - 1.48: 1661 1.48 - 1.64: 2002 1.64 - 1.81: 46 Bond restraints: 8974 Sorted by residual: bond pdb=" N GLY B 56 " pdb=" H GLY B 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 22 " pdb=" H GLN A 22 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG B 88 " pdb=" HE ARG B 88 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 144 " pdb=" H LEU A 144 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B 118 " pdb=" HE2 HIS B 118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8969 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.54: 115 104.54 - 111.91: 10297 111.91 - 119.29: 2244 119.29 - 126.66: 3608 126.66 - 134.03: 30 Bond angle restraints: 16294 Sorted by residual: angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 111.11 124.42 -13.31 1.20e+00 6.94e-01 1.23e+02 angle pdb=" N GLU B 14 " pdb=" CA GLU B 14 " pdb=" C GLU B 14 " ideal model delta sigma weight residual 112.23 102.63 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" N ARG B 286 " pdb=" CA ARG B 286 " pdb=" C ARG B 286 " ideal model delta sigma weight residual 112.87 104.22 8.65 1.20e+00 6.94e-01 5.20e+01 angle pdb=" N ARG A 286 " pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 112.83 120.50 -7.67 1.22e+00 6.72e-01 3.96e+01 ... (remaining 16289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3699 15.89 - 31.78: 227 31.78 - 47.67: 111 47.67 - 63.56: 81 63.56 - 79.45: 14 Dihedral angle restraints: 4132 sinusoidal: 2289 harmonic: 1843 Sorted by residual: dihedral pdb=" C ASP A 287 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 131.25 -8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual -180.00 -137.85 -42.15 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 495 0.097 - 0.194: 152 0.194 - 0.291: 22 0.291 - 0.388: 1 0.388 - 0.485: 3 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ARG A 286 " pdb=" N ARG A 286 " pdb=" C ARG A 286 " pdb=" CB ARG A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " -0.140 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG PHE A 171 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 171 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 171 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 171 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 171 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " 0.084 2.00e-02 2.50e+03 2.57e-02 2.63e+01 pdb=" CG TRP B 251 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 251 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP B 251 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 251 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 251 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 251 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 11 " 0.072 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 11 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 11 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 11 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 11 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 11 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 11 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.75: 107 1.75 - 2.46: 5136 2.46 - 3.17: 29832 3.17 - 3.89: 39137 3.89 - 4.60: 59445 Nonbonded interactions: 133657 Sorted by model distance: nonbonded pdb=" HD2 PHE A 171 " pdb=" HA2 GLY A 197 " model vdw 1.033 2.270 nonbonded pdb=" HH TYR B 11 " pdb=" HG2 LYS B 15 " model vdw sym.op. 1.245 2.270 -y+1,-x+1,-z+1 nonbonded pdb=" HE3 LYS A 93 " pdb="HH22 ARG B 259 " model vdw sym.op. 1.356 2.270 y+1/2,-x+1/2,z nonbonded pdb=" O LEU A 170 " pdb=" H LEU A 173 " model vdw 1.370 1.850 nonbonded pdb=" H GLU A 157 " pdb=" HG3 GLU A 157 " model vdw 1.448 2.270 ... (remaining 133652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 24 15.91 1 O 823 7.97 1 N 729 6.97 1 C 2831 5.97 1 H 4498 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 4498 of 8905 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8905 n_use_u_iso = 8905 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 8905 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8905 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8905 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1wl3_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4498 occupancy sum: 4498.00 (% of total atoms 50.51) Rotatable: count: 1300 occupancy sum: 1300.00 (% of total atoms 14.60) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.98 2477 144 0.4989 0.4770 4.495 5.1259| | 2: 5.55 - 4.41 0.96 2311 121 0.3871 0.4311 3.6506 3.6312| | 3: 4.41 - 3.85 0.93 2220 112 0.4708 0.5130 3.3519 3.4414| | 4: 3.85 - 3.50 0.88 2062 132 0.4868 0.5658 3.1476 3.3492| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 41.75 - 5.55 2477 144 0.45 54.77 0.83 0.03 995.04| | 2: 5.55 - 4.41 2311 121 0.46 55.10 1.34 0.02 444.27| | 3: 4.41 - 3.85 2220 112 0.63 41.12 1.62 0.03 154.61| | 4: 3.85 - 3.50 2062 132 0.56 47.24 1.53 0.03 126.03| |alpha: min = 0.02 max = 0.03 mean = 0.03| |beta: min = 126.03 max = 995.04 mean = 451.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.52| |phase err.(work): min = 0.00 max = 89.98 mean = 49.80| |phase err.(test): min = 0.00 max = 89.87 mean = 48.86| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 4476 Z= 0.328 Angle : 1.323 14.340 6012 Z= 0.928 Chirality : 0.095 0.485 673 Planarity : 0.005 0.053 772 Dihedral : 15.841 79.450 1703 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 2.36 % Allowed : 5.26 % Favored : 92.38 % Rotamer: Outliers : 3.40 % Allowed : 7.43 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.27), residues: 551 helix: -2.44 (0.18), residues: 445 sheet: None (None), residues: 0 loop : -2.62 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 TYR 0.056 0.011 TYR A 11 PHE 0.085 0.007 PHE A 171 TRP 0.056 0.008 TRP B 251 HIS 0.001 0.000 HIS B 118 Individual atomic B min max mean iso aniso Overall: 21.36 100.34 56.13 1.48 4407 0 Protein: 21.36 100.34 56.13 1.48 4407 0 Chain A: 24.53 91.36 59.78 N/A 2198 0 Chain B: 21.36 100.34 52.50 N/A 2209 0 Histogram: Values Number of atoms 21.36 - 29.26 126 29.26 - 37.16 321 37.16 - 45.05 629 45.05 - 52.95 817 52.95 - 60.85 833 60.85 - 68.75 769 68.75 - 76.65 497 76.65 - 84.54 290 84.54 - 92.44 121 92.44 - 100.34 4 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 re-set all scales: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 remove outliers: r(all,work,free)=0.4621 0.4602 0.4849 n_refl.: 9561 overall B=23.46 to atoms: r(all,work,free)=0.5303 0.5276 0.5612 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 remove outliers: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 41.747-17.006 86.11 84 9 0.4381 1220.303 1224.065 1.165 1.112 0.405 16.951-13.495 94.17 95 2 0.3095 1758.562 1726.307 0.965 1.108 0.377 13.466-10.728 99.01 188 12 0.2313 2173.838 2118.815 1.052 1.095 0.368 10.715-8.517 98.92 348 19 0.1972 2052.862 2022.519 1.059 1.081 0.351 8.515-6.766 98.37 689 37 0.2427 1366.340 1306.911 0.994 1.051 0.326 6.761-5.374 96.29 1294 80 0.2758 856.308 812.122 0.876 1.007 0.279 5.373-4.268 96.39 2549 123 0.2287 952.347 913.140 0.992 0.935 0.223 4.267-3.500 89.96 3807 225 0.2939 675.635 628.033 1.221 0.844 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.4189 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.332842 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168723 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2544 0.2811 0.0267 0.002 0.5 1.2 1.1 2.5 0 0.125 0.2502 0.2791 0.0289 0.002 0.5 1.9 1.1 2.5 0 0.250 0.2449 0.2781 0.0332 0.003 0.5 2.8 0.9 2.5 0 0.500 0.2391 0.2802 0.0411 0.005 0.7 3.7 0.9 2.8 0 1.000 0.2324 0.2831 0.0507 0.008 0.9 6.9 0.9 2.8 0 2.000 0.2190 0.2901 0.0711 0.007 0.8 7.0 1.1 3.2 0 3.000 0.2164 0.2969 0.0805 0.008 0.9 8.9 1.6 3.2 0 4.000 0.2140 0.2990 0.0849 0.010 1.0 11.1 2.2 3.8 0 5.000 0.2124 0.2979 0.0854 0.011 1.1 12.0 2.4 3.8 0 6.000 0.2113 0.2996 0.0883 0.012 1.1 13.1 2.5 4.2 0 7.000 0.2101 0.3026 0.0925 0.013 1.2 14.6 3.1 4.9 0 8.000 0.2089 0.3018 0.0929 0.014 1.3 15.4 3.3 4.9 0 9.000 0.2080 0.3020 0.0940 0.016 1.4 17.2 3.6 5.5 0 10.000 0.2120 0.3006 0.0885 0.011 1.1 13.0 2.4 4.0 0 6.166 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2544 0.2811 0.0267 0.002 0.5 1.2 1.1 2.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.44 28.11 2.67 1.044 79.246 0.169 0.073 25.45 27.88 2.44 2.174 79.344 0.005 0.073 25.06 27.90 2.85 2.296 79.390 0.021 0.071 23.72 27.98 4.26 5.209 79.894 0.084 0.063 23.05 28.11 5.06 7.179 80.385 0.169 0.060 22.71 28.19 5.48 8.548 80.760 0.253 0.059 22.53 28.27 5.74 9.407 80.979 0.337 0.058 22.22 28.37 6.16 10.959 81.513 0.422 0.056 22.10 28.44 6.34 11.645 81.705 0.506 0.056 21.97 28.49 6.52 12.369 81.925 0.591 0.055 21.85 28.55 6.71 13.205 82.189 0.675 0.054 21.78 28.59 6.81 13.668 82.321 0.759 0.054 21.73 28.62 6.89 14.079 82.436 0.844 0.054 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 25.45 27.88 2.44 2.174 79.344 0.005 0.073 Individual atomic B min max mean iso aniso Overall: 50.67 120.75 79.79 1.50 4407 0 Protein: 50.67 120.75 79.79 1.50 4407 0 Chain A: 53.37 112.51 83.28 N/A 2198 0 Chain B: 50.67 120.75 76.31 N/A 2209 0 Histogram: Values Number of atoms 50.67 - 57.68 172 57.68 - 64.69 412 64.69 - 71.69 743 71.69 - 78.70 830 78.70 - 85.71 804 85.71 - 92.72 645 92.72 - 99.73 447 99.73 - 106.74 244 106.74 - 113.75 106 113.75 - 120.75 4 =========================== Idealize ADP of riding H ========================== r_work=0.2545 r_free=0.2788 r_work=0.2533 r_free=0.2785 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2533 r_free= 0.2785 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.072187 | | target function (ls_wunit_k1) not normalized (work): 653.580452 | | target function (ls_wunit_k1) not normalized (free): 44.075454 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2546 0.2533 0.2785 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5274 0.5245 0.5604 n_refl.: 9561 remove outliers: r(all,work,free)=0.5274 0.5245 0.5604 n_refl.: 9561 overall B=2.74 to atoms: r(all,work,free)=0.5359 0.5330 0.5692 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2540 0.2526 0.2794 n_refl.: 9561 remove outliers: r(all,work,free)=0.2540 0.2526 0.2794 n_refl.: 9561 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 41.747-17.006 86.11 84 9 0.3862 515.768 510.377 1.239 1.093 0.409 16.951-13.495 94.17 95 2 0.2892 743.266 733.028 0.969 1.089 0.370 13.466-10.728 99.01 188 12 0.2240 918.785 899.280 1.060 1.077 0.360 10.715-8.517 98.92 348 19 0.1849 867.654 856.875 1.074 1.065 0.353 8.515-6.766 98.37 689 37 0.2283 577.492 555.071 1.004 1.039 0.346 6.761-5.374 96.29 1294 80 0.2696 361.924 345.702 0.902 1.001 0.294 5.373-4.268 96.39 2549 123 0.2309 402.515 386.297 0.984 0.938 0.223 4.267-3.500 89.96 3807 225 0.2902 285.561 266.113 1.200 0.860 0.127 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.3248 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.176811 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044546 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2602 0.2788 0.0186 0.002 0.3 1.5 0.9 1.7 0 0.007 0.2536 0.2789 0.0253 0.002 0.4 1.7 1.1 1.9 0 0.022 0.2459 0.2771 0.0312 0.002 0.4 1.1 1.1 1.9 0 0.043 0.2406 0.2772 0.0366 0.002 0.4 1.8 1.1 1.9 0 0.065 0.2361 0.2775 0.0414 0.002 0.4 2.0 1.1 1.9 0 0.086 0.2336 0.2782 0.0446 0.002 0.4 1.9 0.9 1.9 0 0.108 0.2317 0.2784 0.0467 0.002 0.4 1.9 0.9 1.9 0 0.130 0.2311 0.2779 0.0469 0.003 0.5 2.0 1.1 1.9 0 0.151 0.2388 0.2770 0.0381 0.002 0.4 1.9 1.1 1.9 0 0.072 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2459 0.2771 0.0312 0.002 0.4 1.1 1.1 1.9 0 0.043 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.59 27.71 3.12 11.426 90.259 0.045 6.149 25.03 27.96 2.93 11.664 91.130 0.001 6.161 24.05 27.62 3.57 11.720 90.803 0.006 6.128 22.59 27.61 5.01 11.933 91.378 0.022 6.083 22.13 27.84 5.71 12.887 91.962 0.045 6.071 21.85 28.02 6.17 14.234 92.618 0.067 6.064 21.76 27.97 6.21 14.250 92.570 0.089 6.062 21.66 28.04 6.39 14.960 92.845 0.111 6.060 21.71 28.01 6.31 14.650 92.659 0.134 6.061 21.68 28.04 6.36 14.891 92.743 0.156 6.060 21.65 28.06 6.41 15.130 92.831 0.178 6.060 21.61 28.10 6.49 15.530 92.986 0.200 6.059 21.56 28.15 6.59 16.040 93.180 0.223 6.058 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.022 Accepted refinement result: 22.59 27.61 5.01 11.933 91.378 0.022 6.083 Individual atomic B min max mean iso aniso Overall: 50.65 155.25 84.79 6.61 4407 0 Protein: 50.65 155.25 84.79 6.61 4407 0 Chain A: 51.50 140.88 87.81 N/A 2198 0 Chain B: 50.65 155.25 81.79 N/A 2209 0 Histogram: Values Number of atoms 50.65 - 61.11 122 61.11 - 71.57 784 71.57 - 82.03 1228 82.03 - 92.49 1026 92.49 - 102.95 667 102.95 - 113.41 352 113.41 - 123.87 171 123.87 - 134.33 47 134.33 - 144.79 7 144.79 - 155.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.2259 r_free=0.2761 r_work=0.2244 r_free=0.2764 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2244 r_free= 0.2764 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.079435 | | target function (ml) not normalized (work): 55043.207340 | | target function (ml) not normalized (free): 3156.392137 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2272 0.2244 0.2764 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5343 0.5307 0.5757 n_refl.: 9561 remove outliers: r(all,work,free)=0.5343 0.5307 0.5757 n_refl.: 9561 overall B=1.12 to atoms: r(all,work,free)=0.5380 0.5344 0.5793 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2265 0.2238 0.2738 n_refl.: 9561 remove outliers: r(all,work,free)=0.2265 0.2238 0.2738 n_refl.: 9561 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 41.747-17.006 86.11 84 9 0.3724 515.768 502.147 1.177 1.131 0.408 16.951-13.495 94.17 95 2 0.2674 743.266 738.792 0.947 1.125 0.374 13.466-10.728 99.01 188 12 0.2131 918.785 902.575 1.013 1.110 0.362 10.715-8.517 98.92 348 19 0.1746 867.654 855.325 1.011 1.092 0.337 8.515-6.766 98.37 689 37 0.2150 577.492 557.467 0.965 1.058 0.321 6.761-5.374 96.29 1294 80 0.2676 361.924 346.427 0.914 1.006 0.288 5.373-4.268 96.39 2549 123 0.2055 402.515 388.373 1.004 0.921 0.217 4.267-3.500 89.96 3807 225 0.2321 285.561 270.674 1.264 0.811 0.108 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.2039 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2238 r_free=0.2738 After: r_work=0.2238 r_free=0.2738 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.986366 wxc_scale = 0.027 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045798 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2241 0.2738 0.0497 0.002 0.4 1.5 1.1 1.9 0 0.011 0.2240 0.2738 0.0498 0.002 0.4 1.5 1.1 1.9 0 0.032 0.2238 0.2737 0.0499 0.002 0.4 1.5 1.1 1.9 0 0.065 0.2236 0.2741 0.0504 0.002 0.4 1.5 1.1 1.9 0 0.097 0.2234 0.2739 0.0505 0.002 0.4 1.5 1.1 1.9 0 0.129 0.2232 0.2739 0.0507 0.002 0.4 1.6 1.1 1.9 0 0.161 0.2225 0.2742 0.0517 0.003 0.4 1.7 1.1 1.9 0 0.194 0.2218 0.2744 0.0526 0.003 0.4 1.7 1.1 1.9 0 0.226 0.2236 0.2741 0.0505 0.002 0.4 1.5 1.1 1.9 0 0.108 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2240 0.2738 0.0498 0.002 0.4 1.5 1.1 1.9 0 0.032 0.2238 0.2737 0.0499 0.002 0.4 1.5 1.1 1.9 0 0.065 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.40 27.38 4.98 13.081 94.504 0.046 6.079 25.25 28.68 3.43 10.012 99.587 0.001 6.148 24.07 28.09 4.02 11.241 97.557 0.006 6.124 22.25 27.36 5.11 13.152 94.474 0.023 6.075 21.23 27.75 6.51 13.638 95.776 0.046 6.049 21.01 27.83 6.82 14.329 95.952 0.069 6.044 20.91 27.89 6.98 14.945 96.174 0.092 6.042 20.91 27.91 7.00 15.057 96.095 0.114 6.043 20.87 27.96 7.09 15.363 96.239 0.137 6.042 20.84 27.98 7.13 15.576 96.329 0.160 6.042 20.78 28.06 7.27 16.023 96.574 0.183 6.041 20.78 28.08 7.30 16.155 96.626 0.206 6.041 20.76 28.10 7.34 16.363 96.725 0.229 6.041 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.023 Accepted refinement result: 22.25 27.36 5.11 13.152 94.474 0.023 6.075 Individual atomic B min max mean iso aniso Overall: 50.81 156.30 85.85 6.54 4407 0 Protein: 50.81 156.30 85.85 6.54 4407 0 Chain A: 50.88 140.16 88.85 N/A 2198 0 Chain B: 50.81 156.30 82.87 N/A 2209 0 Histogram: Values Number of atoms 50.81 - 61.36 105 61.36 - 71.91 748 71.91 - 82.46 1213 82.46 - 93.01 1058 93.01 - 103.56 683 103.56 - 114.10 364 114.10 - 124.65 178 124.65 - 135.20 48 135.20 - 145.75 7 145.75 - 156.30 3 =========================== Idealize ADP of riding H ========================== r_work=0.2225 r_free=0.2736 r_work=0.2224 r_free=0.2737 ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2224 r_free= 0.2737 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 6.074507 | | target function (ml) not normalized (work): 54998.583896 | | target function (ml) not normalized (free): 3155.248577 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.97 2463 143 0.2314 0.2749 6.5056 6.6192| | 2: 5.55 - 4.41 0.96 2310 121 0.2112 0.2509 6.1328 6.2055| | 3: 4.41 - 3.85 0.93 2220 112 0.2069 0.2788 5.8891 6.1095| | 4: 3.85 - 3.50 0.88 2061 131 0.2413 0.2965 5.6938 5.9051| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 41.75 - 5.55 2463 143 0.73 30.55 1.00 1.00 80653.26| | 2: 5.55 - 4.41 2310 121 0.77 28.37 1.00 1.02 46763.05| | 3: 4.41 - 3.85 2220 112 0.80 25.95 1.03 1.01 26149.59| | 4: 3.85 - 3.50 2061 131 0.76 29.86 0.96 0.95 18812.89| |alpha: min = 0.95 max = 1.02 mean = 1.00| |beta: min = 18812.89 max = 80653.26 mean = 44565.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.97 mean = 28.71| |phase err.(test): min = 0.00 max = 87.51 mean = 28.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2251 0.2224 0.2737 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5378 0.5342 0.5792 n_refl.: 9561 remove outliers: r(all,work,free)=0.5378 0.5342 0.5792 n_refl.: 9561 overall B=-0.15 to atoms: r(all,work,free)=0.5373 0.5338 0.5787 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2262 0.2233 0.2775 n_refl.: 9561 remove outliers: r(all,work,free)=0.2262 0.2233 0.2775 n_refl.: 9561 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 41.747-17.006 86.11 84 9 0.3754 515.768 517.158 1.309 1.085 0.419 16.951-13.495 94.17 95 2 0.2681 743.266 739.147 0.994 1.083 0.376 13.466-10.728 99.01 188 12 0.2129 918.785 903.950 1.051 1.072 0.362 10.715-8.517 98.92 348 19 0.1751 867.654 855.412 1.045 1.060 0.337 8.515-6.766 98.37 689 37 0.2154 577.492 557.718 0.991 1.035 0.322 6.761-5.374 96.29 1294 80 0.2679 361.924 346.186 0.928 0.998 0.290 5.373-4.268 96.39 2549 123 0.2048 402.515 387.467 0.988 0.936 0.220 4.267-3.500 89.96 3807 225 0.2304 285.561 270.601 1.195 0.860 0.109 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.5103 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4622 0.4889 0.005 1.323 21.4 100.3 56.1 0 0.000 1_bss: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_settarget: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_weight: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_xyzrec: 0.2544 0.2811 0.002 0.469 44.8 123.8 79.6 0 0.148 1_adp: 0.2545 0.2788 0.002 0.469 50.7 120.8 79.8 0 0.148 1_regHadp: 0.2533 0.2785 0.002 0.469 50.7 120.8 79.8 0 0.148 2_bss: 0.2526 0.2794 0.002 0.469 53.4 123.5 82.5 0 0.148 2_settarget: 0.2526 0.2794 0.002 0.469 53.4 123.5 82.5 0 0.148 2_updatecdl: 0.2526 0.2794 0.002 0.509 53.4 123.5 82.5 0 0.148 2_weight: 0.2526 0.2794 0.002 0.509 53.4 123.5 82.5 0 0.148 2_xyzrec: 0.2459 0.2771 0.002 0.373 53.4 123.5 82.5 0 0.234 2_adp: 0.2259 0.2761 0.002 0.373 50.7 155.2 84.8 0 0.234 2_regHadp: 0.2244 0.2764 0.002 0.373 50.7 155.2 84.8 0 0.234 3_bss: 0.2238 0.2738 0.002 0.373 51.8 156.4 85.9 0 0.234 3_settarget: 0.2238 0.2738 0.002 0.373 51.8 156.4 85.9 0 0.234 3_updatecdl: 0.2238 0.2738 0.002 0.430 51.8 156.4 85.9 0 0.234 3_setrh: 0.2238 0.2738 0.002 0.430 51.8 156.4 85.9 0 0.234 3_weight: 0.2238 0.2738 0.002 0.430 51.8 156.4 85.9 0 0.234 3_xyzrec: 0.2240 0.2738 0.002 0.379 51.8 156.4 85.9 0 0.234 3_adp: 0.2225 0.2736 0.002 0.379 50.8 156.3 85.9 0 0.234 3_regHadp: 0.2224 0.2737 0.002 0.379 50.8 156.3 85.9 0 0.234 end: 0.2233 0.2775 0.002 0.379 50.7 156.2 85.7 0 0.234 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1wl3_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1wl3_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.5800 Refinement macro-cycles (run) : 294.4500 Write final files (write_after_run_outputs) : 27.7900 Total : 333.8200 Total CPU time: 6.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:35 PDT -0700 (1716251675.07 s) Start R-work = 0.2579, R-free = 0.2869 Final R-work = 0.2233, R-free = 0.2775 =============================================================================== Job complete usr+sys time: 392.33 seconds wall clock time: 18 minutes 35.53 seconds (1115.53 seconds total)