Starting phenix.refine on Mon May 20 17:17:05 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=True 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 { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 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: 1.64, per 1000 atoms: 0.35 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: 2.87 Conformation dependent library (CDL) restraints added in 614.0 milliseconds 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Time building geometry restraints manager: 2.41 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.506395 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 0.1896 0.2256 0.0361 0.016 1.7 61.7 1.7 26.7 0 8.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.96 22.56 3.61 3.509 35.115 0.524 0.046 19.76 23.33 3.57 4.304 35.651 0.016 0.049 19.58 23.31 3.73 4.279 35.666 0.066 0.049 19.03 23.27 4.25 4.618 35.781 0.262 0.046 18.53 23.26 4.72 5.403 35.892 0.524 0.044 18.20 23.27 5.08 6.438 36.102 0.787 0.042 17.93 23.29 5.36 7.585 36.393 1.049 0.041 17.78 23.29 5.50 8.255 36.520 1.311 0.041 17.67 23.28 5.60 8.811 36.629 1.573 0.040 17.58 23.28 5.70 9.408 36.770 1.836 0.040 17.51 23.28 5.77 9.807 36.850 2.098 0.040 17.45 23.28 5.83 10.254 36.956 2.360 0.039 17.39 23.29 5.90 10.837 37.113 2.622 0.039 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: 18.53 23.26 4.72 5.403 35.892 0.524 0.044 Individual atomic B min max mean iso aniso Overall: 8.02 107.45 36.72 5.70 2312 0 Protein: 8.02 107.45 36.72 5.70 2312 0 Chain A: 8.02 107.45 36.72 N/A 2312 0 Histogram: Values Number of atoms 8.02 - 17.96 294 17.96 - 27.90 569 27.90 - 37.85 524 37.85 - 47.79 382 47.79 - 57.73 227 57.73 - 67.68 153 67.68 - 77.62 103 77.62 - 87.56 28 87.56 - 97.50 21 97.50 - 107.45 11 =========================== Idealize ADP of riding H ========================== r_work=0.1853 r_free=0.2326 r_work=0.1842 r_free=0.2327 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1842 r_free= 0.2327 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ls_wunit_k1) (work): 0.043324 | | target function (ls_wunit_k1) not normalized (work): 295.511839 | | target function (ls_wunit_k1) not normalized (free): 51.205336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1891 0.1842 0.2327 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3205 0.3189 0.3338 n_refl.: 7570 remove outliers: r(all,work,free)=0.3205 0.3189 0.3338 n_refl.: 7570 overall B=1.40 to atoms: r(all,work,free)=0.3256 0.3241 0.3382 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1871 0.1822 0.2303 n_refl.: 7570 remove outliers: r(all,work,free)=0.1871 0.1822 0.2303 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 0.2295 977.051 958.239 1.822 0.989 0.380 15.935-12.710 100.00 89 10 0.1226 1083.900 1081.253 1.398 0.989 0.280 12.669-10.064 99.01 182 19 0.1136 988.017 974.447 1.309 0.990 0.259 10.054-8.008 99.48 344 37 0.1220 831.351 824.516 1.227 0.990 0.252 7.993-6.350 96.06 662 70 0.1691 527.290 515.777 1.113 0.991 0.228 6.344-5.045 94.20 1288 142 0.1943 445.976 424.691 0.974 0.992 0.188 5.041-4.007 88.19 2360 262 0.1846 460.731 437.393 0.939 0.993 0.079 4.004-3.512 68.84 1807 197 0.2166 420.922 394.311 1.082 0.989 0.029 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2823 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.972531 wxc_scale = 0.143 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157225 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 0.2134 0.2392 0.0258 0.004 1.0 19.1 0.7 24.7 0 0.057 0.2094 0.2415 0.0321 0.004 0.9 20.3 0.7 23.0 0 0.170 0.2023 0.2426 0.0404 0.005 0.9 23.5 0.7 24.3 0 0.340 0.1976 0.2437 0.0461 0.006 1.0 28.0 0.7 25.5 0 0.510 0.1933 0.2429 0.0496 0.008 1.1 34.8 0.7 26.3 0 0.680 0.1903 0.2441 0.0538 0.009 1.2 35.2 0.7 28.4 0 0.850 0.1882 0.2446 0.0564 0.010 1.3 38.8 1.0 30.0 0 1.020 0.1860 0.2435 0.0575 0.011 1.4 41.7 1.4 30.0 0 1.190 0.1960 0.2442 0.0481 0.007 1.1 31.4 0.7 26.3 0 0.567 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2094 0.2415 0.0321 0.004 0.9 20.3 0.7 23.0 0 0.170 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.94 24.15 3.21 7.144 42.399 0.157 6.255 22.43 24.69 2.26 7.990 44.189 0.005 6.294 21.90 24.59 2.68 7.662 44.058 0.020 6.280 20.49 24.31 3.82 7.756 43.976 0.079 6.243 19.86 24.17 4.30 8.772 43.871 0.157 6.226 19.53 24.16 4.64 10.059 44.183 0.236 6.219 19.34 24.17 4.83 11.129 44.457 0.314 6.214 19.22 24.18 4.96 12.019 44.695 0.393 6.212 19.12 24.19 5.07 12.932 44.948 0.472 6.210 19.03 24.21 5.18 13.856 45.214 0.550 6.208 18.96 24.22 5.26 14.647 45.461 0.629 6.206 18.91 24.23 5.32 15.275 45.647 0.708 6.205 18.87 24.26 5.39 15.936 45.839 0.786 6.204 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.236 Accepted refinement result: 19.53 24.16 4.64 10.059 44.183 0.236 6.219 Individual atomic B min max mean iso aniso Overall: 4.41 118.43 41.76 11.43 2312 0 Protein: 4.41 118.43 41.76 11.43 2312 0 Chain A: 4.41 118.43 41.76 N/A 2312 0 Histogram: Values Number of atoms 4.41 - 15.81 176 15.81 - 27.22 431 27.22 - 38.62 557 38.62 - 50.02 473 50.02 - 61.42 279 61.42 - 72.82 186 72.82 - 84.22 117 84.22 - 95.62 57 95.62 - 107.03 30 107.03 - 118.43 6 =========================== Idealize ADP of riding H ========================== r_work=0.1953 r_free=0.2416 r_work=0.1937 r_free=0.2415 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1937 r_free= 0.2415 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.214667 | | target function (ml) not normalized (work): 42390.243078 | | target function (ml) not normalized (free): 4763.321037 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1986 0.1937 0.2415 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3350 0.3336 0.3471 n_refl.: 7570 remove outliers: r(all,work,free)=0.3350 0.3336 0.3471 n_refl.: 7570 overall B=4.13 to atoms: r(all,work,free)=0.3503 0.3491 0.3605 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1965 0.1917 0.2392 n_refl.: 7570 remove outliers: r(all,work,free)=0.1965 0.1917 0.2392 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 0.2001 977.051 968.222 1.840 1.004 0.379 15.935-12.710 100.00 89 10 0.1258 1083.900 1082.527 1.463 1.004 0.308 12.669-10.064 99.01 182 19 0.1199 988.017 973.459 1.285 1.003 0.268 10.054-8.008 99.48 344 37 0.1298 831.351 823.049 1.227 1.002 0.266 7.993-6.350 96.06 662 70 0.1758 527.290 511.689 1.106 1.001 0.242 6.344-5.045 94.20 1288 142 0.2062 445.976 418.587 0.959 0.997 0.193 5.041-4.007 88.19 2360 262 0.1951 460.731 431.280 0.915 0.991 0.085 4.004-3.512 68.84 1807 197 0.2307 420.922 387.380 1.090 0.980 0.028 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.2251 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1917 r_free=0.2392 After: r_work=0.1918 r_free=0.2392 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.789074 wxc_scale = 0.033 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.146348 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 0.1921 0.2392 0.0470 0.004 0.9 21.0 0.7 23.0 0 0.016 0.1921 0.2393 0.0472 0.004 0.9 20.6 0.7 23.0 0 0.048 0.1920 0.2393 0.0473 0.004 0.9 20.8 0.7 23.0 0 0.095 0.1919 0.2393 0.0473 0.004 0.9 20.8 0.7 23.0 0 0.143 0.1919 0.2393 0.0474 0.004 0.9 20.8 0.7 23.0 0 0.191 0.1918 0.2392 0.0474 0.004 0.9 20.6 0.7 23.0 0 0.239 0.1917 0.2392 0.0476 0.004 0.9 20.6 0.7 23.0 0 0.286 0.1916 0.2393 0.0477 0.004 0.9 21.0 0.7 23.0 0 0.334 0.1919 0.2393 0.0473 0.004 0.9 20.8 0.7 23.0 0 0.159 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1918 0.2392 0.0474 0.004 0.9 20.6 0.7 23.0 0 0.239 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.18 23.92 4.74 10.548 51.248 0.146 6.206 21.78 24.51 2.72 10.298 54.168 0.004 6.258 21.31 24.32 3.00 10.025 53.682 0.018 6.248 20.08 24.08 4.00 9.969 52.055 0.073 6.225 19.29 24.01 4.72 10.193 51.803 0.146 6.208 18.88 23.97 5.09 11.055 51.930 0.220 6.199 18.62 23.97 5.35 12.009 52.135 0.293 6.194 18.49 23.99 5.50 12.797 52.316 0.366 6.192 18.40 24.02 5.61 13.432 52.487 0.439 6.191 18.35 24.03 5.68 13.963 52.654 0.512 6.190 18.30 24.05 5.75 14.493 52.837 0.585 6.189 18.27 24.07 5.80 14.920 52.982 0.659 6.189 18.26 24.07 5.81 15.156 53.060 0.732 6.188 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.220 Accepted refinement result: 18.88 23.97 5.09 11.055 51.930 0.220 6.199 Individual atomic B min max mean iso aniso Overall: 6.55 138.24 47.28 12.98 2312 0 Protein: 6.55 138.24 47.28 12.98 2312 0 Chain A: 6.55 138.24 47.28 N/A 2312 0 Histogram: Values Number of atoms 6.55 - 19.72 158 19.72 - 32.89 481 32.89 - 46.06 628 46.06 - 59.22 473 59.22 - 72.39 246 72.39 - 85.56 176 85.56 - 98.73 82 98.73 - 111.90 49 111.90 - 125.07 17 125.07 - 138.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1888 r_free=0.2397 r_work=0.1883 r_free=0.2397 ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1883 r_free= 0.2397 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.198020 | | target function (ml) not normalized (work): 42276.691713 | | target function (ml) not normalized (free): 4757.290457 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1515 0.1894 6.3066 6.4776| | 2: 6.00 - 4.77 0.93 1498 166 0.1983 0.2314 6.1528 6.2345| | 3: 4.77 - 4.16 0.89 1443 156 0.1883 0.2637 6.1518 6.414| | 4: 4.16 - 3.78 0.76 1216 130 0.2177 0.2871 6.1639 6.3347| | 5: 3.78 - 3.51 0.66 1046 120 0.2325 0.2859 6.1983 6.2646| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 15.59 1.00 1.09 49749.96| | 2: 6.00 - 4.77 1498 166 0.87 21.86 0.99 1.07 50946.04| | 3: 4.77 - 4.16 1443 156 0.88 20.94 0.99 1.02 53451.88| | 4: 4.16 - 3.78 1216 130 0.85 24.02 1.00 0.99 56799.28| | 5: 3.78 - 3.51 1046 120 0.84 25.07 1.02 0.97 58527.24| |alpha: min = 0.97 max = 1.09 mean = 1.04| |beta: min = 49749.96 max = 58527.24 mean = 53398.49| |figures of merit: min = 0.01 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 88.96 mean = 21.06| |phase err.(test): min = 0.00 max = 84.43 mean = 21.70| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1935 0.1883 0.2397 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3515 0.3502 0.3631 n_refl.: 7570 remove outliers: r(all,work,free)=0.3515 0.3502 0.3631 n_refl.: 7570 overall B=1.45 to atoms: r(all,work,free)=0.3571 0.3559 0.3681 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1933 0.1881 0.2401 n_refl.: 7570 remove outliers: r(all,work,free)=0.1933 0.1881 0.2401 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 0.1966 877.531 862.251 1.824 0.999 0.380 15.935-12.710 100.00 89 10 0.1224 973.497 970.009 1.502 1.000 0.319 12.669-10.064 98.05 182 19 0.1163 887.381 876.918 1.282 1.000 0.269 10.054-8.008 99.48 344 37 0.1257 746.672 738.889 1.230 1.000 0.269 7.993-6.350 95.81 662 70 0.1663 473.582 459.563 1.131 1.000 0.268 6.344-5.045 94.08 1288 142 0.2011 400.550 377.862 0.959 0.998 0.198 5.041-4.007 88.08 2360 262 0.1923 413.802 388.870 0.916 0.996 0.098 4.004-3.512 68.80 1807 197 0.2297 378.048 345.506 1.096 0.988 0.039 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.5237 ================= 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_updatephipsi: 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: 0.1896 0.2256 0.016 1.750 5.6 111.3 35.1 0 0.160 1_adp: 0.1853 0.2326 0.016 1.750 8.0 107.4 36.7 0 0.160 1_regHadp: 0.1842 0.2327 0.016 1.750 8.0 107.4 36.7 0 0.160 2_bss: 0.1822 0.2303 0.016 1.750 9.4 108.8 38.1 0 0.160 2_settarget: 0.1822 0.2303 0.016 1.750 9.4 108.8 38.1 0 0.160 2_updatephipsi: 0.1822 0.2303 0.016 1.750 9.4 108.8 38.1 0 0.160 2_updatecdl: 0.1822 0.2303 0.016 1.766 9.4 108.8 38.1 0 0.160 2_weight: 0.1822 0.2303 0.016 1.766 9.4 108.8 38.1 0 0.160 2_xyzrec: 0.2094 0.2415 0.004 0.853 9.4 108.8 38.1 0 0.292 2_adp: 0.1953 0.2416 0.004 0.853 4.4 118.4 41.8 0 0.292 2_regHadp: 0.1937 0.2415 0.004 0.853 4.4 118.4 41.8 0 0.292 3_bss: 0.1917 0.2392 0.004 0.853 8.5 122.6 45.9 0 0.292 3_settarget: 0.1917 0.2392 0.004 0.853 8.5 122.6 45.9 0 0.292 3_updatephipsi: 0.1917 0.2392 0.004 0.853 8.5 122.6 45.9 0 0.292 3_updatecdl: 0.1917 0.2392 0.004 0.884 8.5 122.6 45.9 0 0.292 3_setrh: 0.1918 0.2392 0.004 0.884 8.5 122.6 45.9 0 0.291 3_weight: 0.1918 0.2392 0.004 0.884 8.5 122.6 45.9 0 0.291 3_xyzrec: 0.1918 0.2392 0.004 0.855 8.5 122.6 45.9 0 0.291 3_adp: 0.1888 0.2397 0.004 0.855 6.6 138.2 47.3 0 0.291 3_regHadp: 0.1883 0.2397 0.004 0.855 6.6 138.2 47.3 0 0.291 end: 0.1881 0.2401 0.004 0.855 8.0 139.7 48.7 0 0.291 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1xgo_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1xgo_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0300 Refinement macro-cycles (run) : 220.6400 Write final files (write_after_run_outputs) : 21.6900 Total : 249.3600 Total CPU time: 4.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:34 PDT -0700 (1716251494.81 s) Start R-work = 0.1925, R-free = 0.1997 Final R-work = 0.1881, R-free = 0.2401 =============================================================================== Job complete usr+sys time: 303.79 seconds wall clock time: 15 minutes 5.22 seconds (905.22 seconds total)