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/1xgo.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.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/1xgo.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1xgo.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.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: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Time building chain proxies: 0.94, per 1000 atoms: 0.20 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 1.17 Conformation dependent library (CDL) restraints added in 237.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2407 1.16 - 1.34: 725 1.34 - 1.52: 904 1.52 - 1.70: 706 1.70 - 1.88: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" N GLU A 257 " pdb=" H GLU A 257 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 123 " pdb="HH11 ARG A 123 " 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 A 25 " pdb=" HE ARG A 25 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 7 " pdb=" H MET A 7 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 215 " pdb="HH11 ARG A 215 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.31: 128 103.31 - 110.98: 4961 110.98 - 118.66: 1711 118.66 - 126.34: 1854 126.34 - 134.02: 35 Bond angle restraints: 8689 Sorted by residual: angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 114.48 102.68 11.80 1.19e+00 7.06e-01 9.84e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.03 100.14 10.89 1.11e+00 8.12e-01 9.62e+01 angle pdb=" N TYR A 237 " pdb=" CA TYR A 237 " pdb=" C TYR A 237 " ideal model delta sigma weight residual 111.36 101.53 9.83 1.09e+00 8.42e-01 8.13e+01 angle pdb=" N THR A 64 " pdb=" CA THR A 64 " pdb=" C THR A 64 " ideal model delta sigma weight residual 110.14 96.77 13.37 1.51e+00 4.39e-01 7.84e+01 angle pdb=" N ASP A 182 " pdb=" CA ASP A 182 " pdb=" C ASP A 182 " ideal model delta sigma weight residual 110.23 97.58 12.65 1.45e+00 4.76e-01 7.61e+01 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1843 17.47 - 34.93: 215 34.93 - 52.40: 90 52.40 - 69.86: 38 69.86 - 87.33: 12 Dihedral angle restraints: 2198 sinusoidal: 1234 harmonic: 964 Sorted by residual: dihedral pdb=" C HIS A 86 " pdb=" N HIS A 86 " pdb=" CA HIS A 86 " pdb=" CB HIS A 86 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C LEU A 150 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C LEU A 131 " pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " ideal model delta harmonic sigma weight residual -122.60 -112.34 -10.26 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 200 0.107 - 0.215: 103 0.215 - 0.322: 47 0.322 - 0.429: 11 0.429 - 0.536: 4 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ASN A 53 " pdb=" N ASN A 53 " pdb=" C ASN A 53 " pdb=" CB ASN A 53 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU A 150 " pdb=" N LEU A 150 " pdb=" C LEU A 150 " pdb=" CB LEU A 150 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.157 2.00e-02 2.50e+03 6.46e-02 1.25e+02 pdb=" CG TYR A 78 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.125 2.00e-02 2.50e+03 pdb=" HD1 TYR A 78 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 78 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR A 78 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 78 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 265 " -0.144 2.00e-02 2.50e+03 5.64e-02 9.54e+01 pdb=" CG TYR A 265 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 265 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 265 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 265 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 265 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 265 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR A 265 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 265 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR A 265 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 265 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.131 2.00e-02 2.50e+03 5.19e-02 8.08e+01 pdb=" CG TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR A 170 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 170 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 170 " -0.016 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 207 1.80 - 2.50: 4384 2.50 - 3.20: 16080 3.20 - 3.90: 22187 3.90 - 4.60: 33487 Nonbonded interactions: 76345 Sorted by model distance: nonbonded pdb=" HE2 PHE A 221 " pdb=" HB3 LYS A 258 " model vdw sym.op. 1.102 2.270 -y+1,x-y,z-1/3 nonbonded pdb=" HA VAL A 285 " pdb="HG12 VAL A 290 " model vdw 1.137 2.440 nonbonded pdb="HH12 ARG A 123 " pdb=" HA ASP A 288 " model vdw 1.169 2.270 nonbonded pdb=" H GLY A 27 " pdb="HG13 VAL A 72 " model vdw 1.177 2.270 nonbonded pdb=" HB2 ALA A 60 " pdb="HG21 VAL A 197 " model vdw 1.192 2.440 ... (remaining 76340 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 9 15.91 1 O 423 7.97 1 N 390 6.97 1 C 1490 5.97 1 H 2407 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: 2407 of 4719 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4719 n_use_u_iso = 4719 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 = 4719 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4719 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4719 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 = "1xgo_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2407 occupancy sum: 2407.00 (% of total atoms 51.01) Rotatable: count: 742 occupancy sum: 742.00 (% of total atoms 15.72) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3043 r_free= 0.2973 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775446 | | target function (ml) not normalized (work): 18934.094254 | | target function (ml) not normalized (free): 2088.341598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1619 177 0.3308 0.3084 3.393 3.3877| | 2: 6.00 - 4.77 0.93 1498 166 0.2497 0.2533 2.7716 2.7743| | 3: 4.77 - 4.16 0.89 1443 156 0.2701 0.2738 2.6018 2.67| | 4: 4.16 - 3.78 0.76 1216 130 0.3199 0.3113 2.4611 2.5682| | 5: 3.78 - 3.51 0.66 1046 120 0.3548 0.3588 2.4301 2.3149| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1619 177 0.62 42.01 0.85 0.01 129.62| | 2: 6.00 - 4.77 1498 166 0.55 48.28 1.19 0.01 106.43| | 3: 4.77 - 4.16 1443 156 0.78 30.68 1.27 0.02 57.82| | 4: 4.16 - 3.78 1216 130 0.86 22.43 1.34 0.02 31.93| | 5: 3.78 - 3.51 1046 120 0.93 16.40 1.42 0.02 18.56| |alpha: min = 0.01 max = 0.02 mean = 0.02| |beta: min = 18.56 max = 129.62 mean = 74.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.99 mean = 33.57| |phase err.(test): min = 0.00 max = 85.41 mean = 33.49| |-----------------------------------------------------------------------------| ----------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 : 0.016 0.079 2353 Z= 0.953 Angle : 2.306 13.371 3178 Z= 1.460 Chirality : 0.158 0.536 365 Planarity : 0.016 0.129 405 Dihedral : 20.740 87.330 901 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 83.28 Ramachandran Plot: Outliers : 8.19 % Allowed : 22.18 % Favored : 69.62 % Rotamer: Outliers : 27.16 % Allowed : 18.52 % Favored : 54.32 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 7.14 % 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: -6.45 (0.33), residues: 293 helix: -4.64 (0.26), residues: 96 sheet: -3.34 (0.65), residues: 50 loop : -4.43 (0.36), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 25 TYR 0.131 0.025 TYR A 78 PHE 0.083 0.011 PHE A 221 TRP 0.019 0.007 TRP A 239 HIS 0.006 0.001 HIS A 281 Individual atomic B min max mean iso aniso Overall: 2.00 107.66 31.50 4.99 2312 0 Protein: 2.00 107.66 31.50 4.99 2312 0 Chain A: 2.00 107.66 31.50 N/A 2312 0 Histogram: Values Number of atoms 2.00 - 12.57 417 12.57 - 23.13 473 23.13 - 33.70 490 33.70 - 44.26 393 44.26 - 54.83 220 54.83 - 65.40 164 65.40 - 75.96 98 75.96 - 86.53 29 86.53 - 97.09 20 97.09 - 107.66 8 |-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: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3043 r_free= 0.2973 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775446 | | target function (ml) not normalized (work): 18934.094254 | | target function (ml) not normalized (free): 2088.341598 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7571 re-set all scales: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7571 remove outliers: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7570 overall B=3.64 to atoms: r(all,work,free)=0.3166 0.3173 0.3101 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1932 0.1925 0.1997 n_refl.: 7570 remove outliers: r(all,work,free)=0.1932 0.1925 0.1997 n_refl.: 7570 ======================== 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 47.029-15.950 98.06 89 12 0.3007 1414.453 1341.492 1.574 0.993 0.369 15.935-12.710 100.00 89 10 0.1574 1569.136 1549.736 1.335 0.993 0.254 12.669-10.064 98.05 182 19 0.1369 1430.329 1407.075 1.246 0.994 0.228 10.054-8.008 99.48 344 37 0.1287 1203.527 1188.791 1.191 0.995 0.227 7.993-6.350 95.81 662 70 0.1846 763.345 742.669 1.113 0.996 0.216 6.344-5.045 94.08 1288 142 0.2012 645.629 615.645 0.984 0.996 0.155 5.041-4.007 88.08 2360 262 0.1884 666.989 633.520 0.957 0.995 0.067 4.004-3.512 68.80 1807 197 0.2244 609.358 569.198 1.052 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.3659 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.378205 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.524469 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 0.1864 0.2329 0.0465 0.015 1.6 64.4 9.9 25.9 0 9.189 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.64 23.29 4.65 3.509 35.115 0.524 0.044 19.49 24.22 4.73 4.292 35.648 0.016 0.048 19.32 24.20 4.88 4.257 35.658 0.066 0.047 18.78 24.13 5.35 4.548 35.753 0.262 0.045 18.30 24.07 5.77 5.331 35.873 0.524 0.042 17.98 24.03 6.05 6.274 36.053 0.787 0.041 17.73 24.03 6.31 7.416 36.339 1.049 0.040 17.58 23.99 6.42 8.094 36.471 1.311 0.039 17.47 23.98 6.51 8.628 36.578 1.573 0.039 17.38 23.96 6.58 9.085 36.673 1.836 0.039 17.30 23.93 6.64 9.602 36.798 2.098 0.038 17.26 23.92 6.66 9.830 36.832 2.360 0.038 17.20 23.90 6.70 10.266 36.941 2.622 0.038 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.524 Accepted refinement result: 18.30 24.07 5.77 5.331 35.873 0.524 0.042 Individual atomic B min max mean iso aniso Overall: 8.08 107.94 36.68 5.69 2312 0 Protein: 8.08 107.94 36.68 5.69 2312 0 Chain A: 8.08 107.94 36.68 N/A 2312 0 Histogram: Values Number of atoms 8.08 - 18.07 300 18.07 - 28.06 568 28.06 - 38.04 534 38.04 - 48.03 371 48.03 - 58.01 225 58.01 - 68.00 158 68.00 - 77.99 97 77.99 - 87.97 28 87.97 - 97.96 20 97.96 - 107.94 11 =========================== Idealize ADP of riding H ========================== r_work=0.1830 r_free=0.2407 r_work=0.1821 r_free=0.2407 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1821 r_free= 0.2407 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ls_wunit_k1) (work): 0.042042 | | target function (ls_wunit_k1) not normalized (work): 286.766855 | | target function (ls_wunit_k1) not normalized (free): 54.563759 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1881 0.1821 0.2407 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3195 0.3173 0.3390 n_refl.: 7570 remove outliers: r(all,work,free)=0.3195 0.3173 0.3390 n_refl.: 7570 overall B=1.39 to atoms: r(all,work,free)=0.3246 0.3224 0.3431 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1861 0.1801 0.2378 n_refl.: 7570 remove outliers: r(all,work,free)=0.1861 0.1801 0.2378 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.2231 978.679 957.297 1.817 0.995 0.380 15.935-12.710 100.00 89 10 0.1215 1085.707 1084.532 1.352 0.995 0.270 12.669-10.064 99.01 182 19 0.1125 989.664 977.072 1.278 0.995 0.249 10.054-8.008 99.48 344 37 0.1185 832.737 825.751 1.215 0.996 0.249 7.993-6.350 96.06 662 70 0.1673 528.169 516.144 1.124 0.996 0.248 6.344-5.045 94.20 1288 142 0.1911 446.719 425.940 0.974 0.995 0.188 5.041-4.007 88.19 2360 262 0.1830 461.499 438.546 0.937 0.993 0.054 4.004-3.512 68.84 1807 197 0.2151 421.623 394.941 1.089 0.985 0.029 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2424 ============================ 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 = 4.104779 wxc_scale = 0.165 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169439 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 0.2159 0.2474 0.0315 0.004 0.8 17.4 5.1 22.6 0 0.068 0.2056 0.2452 0.0396 0.004 0.8 20.8 5.5 23.9 0 0.203 0.1995 0.2467 0.0472 0.005 0.9 24.2 6.1 24.3 0 0.405 0.1936 0.2477 0.0541 0.007 1.0 32.4 7.8 25.1 0 0.608 0.1899 0.2485 0.0586 0.008 1.1 37.7 8.9 26.7 0 0.811 0.1874 0.2484 0.0610 0.010 1.2 42.0 9.9 27.6 0 1.014 0.1855 0.2494 0.0639 0.011 1.3 45.8 9.9 29.2 0 1.216 0.1834 0.2482 0.0648 0.012 1.4 49.0 10.9 30.5 0 1.419 0.1935 0.2482 0.0547 0.007 1.0 32.4 8.2 25.1 0 0.676 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2159 0.2474 0.0315 0.004 0.8 17.4 5.1 22.6 0 0.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.59 24.74 3.15 7.121 42.261 0.169 6.279 22.92 25.27 2.35 7.951 43.774 0.005 6.314 22.44 25.10 2.66 7.619 43.713 0.021 6.300 21.06 24.70 3.63 7.901 43.819 0.085 6.262 20.48 24.56 4.08 8.878 43.690 0.169 6.247 20.15 24.58 4.43 10.217 44.058 0.254 6.240 19.95 24.61 4.66 11.422 44.390 0.339 6.236 19.80 24.65 4.85 12.594 44.716 0.424 6.233 19.67 24.69 5.02 13.801 45.072 0.508 6.231 19.60 24.72 5.11 14.544 45.289 0.593 6.230 19.55 24.74 5.18 15.184 45.475 0.678 6.229 19.59 24.68 5.09 14.544 45.294 0.762 6.229 19.55 24.69 5.14 15.014 45.436 0.847 6.229 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.169 Accepted refinement result: 20.48 24.56 4.08 8.878 43.690 0.169 6.247 Individual atomic B min max mean iso aniso Overall: 6.21 113.96 40.99 9.67 2312 0 Protein: 6.21 113.96 40.99 9.67 2312 0 Chain A: 6.21 113.96 40.99 N/A 2312 0 Histogram: Values Number of atoms 6.21 - 16.99 182 16.99 - 27.76 445 27.76 - 38.54 587 38.54 - 49.31 449 49.31 - 60.09 257 60.09 - 70.86 188 70.86 - 81.64 105 81.64 - 92.41 64 92.41 - 103.19 26 103.19 - 113.96 9 =========================== Idealize ADP of riding H ========================== r_work=0.2048 r_free=0.2456 r_work=0.2035 r_free=0.2453 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.2035 r_free= 0.2453 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ml) (work): 6.243438 | | target function (ml) not normalized (work): 42586.490729 | | target function (ml) not normalized (free): 4775.705740 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2077 0.2035 0.2453 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3379 0.3366 0.3496 n_refl.: 7570 remove outliers: r(all,work,free)=0.3379 0.3366 0.3496 n_refl.: 7570 overall B=7.09 to atoms: r(all,work,free)=0.3638 0.3628 0.3717 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.2046 0.2004 0.2427 n_refl.: 7570 remove outliers: r(all,work,free)=0.2046 0.2004 0.2427 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.1986 978.679 967.482 1.833 1.001 0.378 15.935-12.710 100.00 89 10 0.1286 1085.707 1086.441 1.465 1.000 0.307 12.669-10.064 99.01 182 19 0.1232 989.664 977.457 1.307 1.000 0.271 10.054-8.008 99.48 344 37 0.1389 832.737 823.800 1.229 1.000 0.264 7.993-6.350 96.06 662 70 0.1833 528.169 513.587 1.123 0.999 0.251 6.344-5.045 94.20 1288 142 0.2135 446.719 418.488 0.976 0.996 0.208 5.041-4.007 88.19 2360 262 0.2037 461.499 430.548 0.924 0.991 0.073 4.004-3.512 68.84 1807 197 0.2441 421.623 383.900 1.121 0.979 0.026 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.9089 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2004 r_free=0.2427 After: r_work=0.2004 r_free=0.2427 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.404454 wxc_scale = 0.027 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.142759 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 0.2008 0.2428 0.0419 0.003 0.8 18.6 5.1 22.2 0 0.012 0.2008 0.2428 0.0420 0.003 0.8 18.6 5.1 22.2 0 0.035 0.2007 0.2428 0.0421 0.003 0.8 18.6 5.1 22.2 0 0.070 0.2006 0.2428 0.0422 0.003 0.8 18.4 5.1 22.2 0 0.106 0.2005 0.2427 0.0422 0.004 0.8 18.6 5.1 22.2 0 0.141 0.2004 0.2426 0.0422 0.004 0.8 18.6 5.1 22.2 0 0.176 0.2003 0.2426 0.0423 0.004 0.8 18.6 5.1 22.2 0 0.211 0.2001 0.2426 0.0424 0.004 0.8 18.6 5.1 22.2 0 0.246 0.2005 0.2427 0.0422 0.003 0.8 18.6 5.1 22.2 0 0.117 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2006 0.2428 0.0422 0.003 0.8 18.4 5.1 22.2 0 0.106 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.06 24.28 4.22 9.483 53.104 0.143 6.233 22.49 25.10 2.61 9.573 55.859 0.004 6.286 21.94 24.85 2.91 9.267 55.218 0.018 6.275 20.61 24.56 3.95 9.260 53.546 0.071 6.248 19.77 24.36 4.59 9.914 53.676 0.143 6.228 19.37 24.33 4.96 11.061 53.866 0.214 6.219 19.22 24.36 5.14 11.814 54.018 0.286 6.216 19.11 24.39 5.28 12.555 54.275 0.357 6.214 19.02 24.42 5.40 13.358 54.580 0.428 6.212 18.98 24.43 5.45 13.775 54.730 0.500 6.212 18.94 24.45 5.51 14.282 54.920 0.571 6.211 18.91 24.47 5.56 14.724 55.087 0.642 6.210 18.88 24.48 5.59 15.124 55.236 0.714 6.210 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.214 Accepted refinement result: 19.37 24.33 4.96 11.061 53.866 0.214 6.219 Individual atomic B min max mean iso aniso Overall: 8.30 135.22 49.64 13.29 2312 0 Protein: 8.30 135.22 49.64 13.29 2312 0 Chain A: 8.30 135.22 49.64 N/A 2312 0 Histogram: Values Number of atoms 8.30 - 20.99 156 20.99 - 33.69 434 33.69 - 46.38 564 46.38 - 59.07 504 59.07 - 71.76 278 71.76 - 84.45 182 84.45 - 97.14 116 97.14 - 109.83 51 109.83 - 122.53 22 122.53 - 135.22 5 =========================== Idealize ADP of riding H ========================== r_work=0.1937 r_free=0.2433 r_work=0.1927 r_free=0.2435 ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1927 r_free= 0.2435 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.216942 | | target function (ml) not normalized (work): 42405.760132 | | target function (ml) not normalized (free): 4768.533640 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1618 177 0.1568 0.1885 6.33 6.4923| | 2: 6.00 - 4.77 0.93 1498 166 0.2025 0.2396 6.1684 6.2555| | 3: 4.77 - 4.16 0.89 1443 156 0.1925 0.2647 6.1717 6.4215| | 4: 4.16 - 3.78 0.76 1216 130 0.2229 0.2993 6.1821 6.356| | 5: 3.78 - 3.51 0.66 1046 120 0.2342 0.2885 6.2146 6.2746| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1618 177 0.91 15.91 1.00 1.10 51007.65| | 2: 6.00 - 4.77 1498 166 0.86 22.23 0.99 1.08 52501.72| | 3: 4.77 - 4.16 1443 156 0.88 21.50 0.99 1.03 55631.85| | 4: 4.16 - 3.78 1216 130 0.84 24.99 1.00 0.99 59543.41| | 5: 3.78 - 3.51 1046 120 0.83 26.21 1.02 0.97 61562.60| |alpha: min = 0.97 max = 1.10 mean = 1.04| |beta: min = 51007.65 max = 61562.60 mean = 55454.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.82 mean = 21.68| |phase err.(test): min = 0.00 max = 89.11 mean = 22.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1978 0.1927 0.2435 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3623 0.3610 0.3727 n_refl.: 7570 remove outliers: r(all,work,free)=0.3623 0.3610 0.3727 n_refl.: 7570 overall B=0.00 to atoms: r(all,work,free)=0.3623 0.3610 0.3727 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1977 0.1925 0.2439 n_refl.: 7570 remove outliers: r(all,work,free)=0.1977 0.1925 0.2439 n_refl.: 7570 ======================== 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 47.029-15.950 98.06 89 12 0.1950 865.891 852.211 1.859 0.994 0.380 15.935-12.710 100.00 89 10 0.1266 960.584 958.658 1.476 0.995 0.310 12.669-10.064 98.05 182 19 0.1192 875.610 863.343 1.313 0.995 0.275 10.054-8.008 99.48 344 37 0.1320 736.768 727.649 1.241 0.996 0.270 7.993-6.350 95.81 662 70 0.1737 467.300 453.409 1.143 0.996 0.270 6.344-5.045 94.08 1288 142 0.2062 395.237 370.791 0.968 0.996 0.210 5.041-4.007 88.08 2360 262 0.1959 408.313 382.431 0.918 0.994 0.090 4.004-3.512 68.80 1807 197 0.2339 373.033 343.030 1.117 0.988 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8542 ================= 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 : 0.3043 0.2973 0.016 2.306 2.0 107.7 31.5 0 0.000 1_bss: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_settarget: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_weight: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_xyzrec: 0.1864 0.2329 0.015 1.626 5.6 111.3 35.1 0 0.220 1_adp: 0.1830 0.2407 0.015 1.626 8.1 107.9 36.7 0 0.220 1_regHadp: 0.1821 0.2407 0.015 1.626 8.1 107.9 36.7 0 0.220 2_bss: 0.1801 0.2378 0.015 1.626 9.5 109.3 38.1 0 0.220 2_settarget: 0.1801 0.2378 0.015 1.626 9.5 109.3 38.1 0 0.220 2_updatecdl: 0.1801 0.2378 0.015 1.651 9.5 109.3 38.1 0 0.220 2_weight: 0.1801 0.2378 0.015 1.651 9.5 109.3 38.1 0 0.220 2_xyzrec: 0.2159 0.2474 0.004 0.822 9.5 109.3 38.1 0 0.298 2_adp: 0.2048 0.2456 0.004 0.822 6.2 114.0 41.0 0 0.298 2_regHadp: 0.2035 0.2453 0.004 0.822 6.2 114.0 41.0 0 0.298 3_bss: 0.2004 0.2427 0.004 0.822 13.3 121.1 48.1 0 0.298 3_settarget: 0.2004 0.2427 0.004 0.822 13.3 121.1 48.1 0 0.298 3_updatecdl: 0.2004 0.2427 0.004 0.887 13.3 121.1 48.1 0 0.298 3_setrh: 0.2004 0.2427 0.004 0.887 13.3 121.1 48.1 0 0.297 3_weight: 0.2004 0.2427 0.004 0.887 13.3 121.1 48.1 0 0.297 3_xyzrec: 0.2006 0.2428 0.003 0.831 13.3 121.1 48.1 0 0.297 3_adp: 0.1937 0.2433 0.003 0.831 8.3 135.2 49.6 0 0.297 3_regHadp: 0.1927 0.2435 0.003 0.831 8.3 135.2 49.6 0 0.297 end: 0.1925 0.2439 0.003 0.831 8.3 135.2 49.6 0 0.297 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1xgo_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1xgo_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 209.1500 Write final files (write_after_run_outputs) : 22.2700 Total : 236.2400 Total CPU time: 4.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:29:24 PDT -0700 (1716251364.87 s) Start R-work = 0.1925, R-free = 0.1997 Final R-work = 0.1925, R-free = 0.2439 =============================================================================== Job complete usr+sys time: 278.43 seconds wall clock time: 13 minutes 44.02 seconds (824.02 seconds total)