Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 6M5H_complete.pdb Found miller_array, 6M5H.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_adp=true optimize_xyz=true hydrogens.refine=riding nproc=20 main.max_number_of_iterations=50 main.number_of_m=5 refine.adp.individual.aniso=not element H refine.adp.individual.iso=element H Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "6M5H.mtz" } default_miller_array = "6M5H.mtz" model { file = "6M5H_complete.pdb" } default_model = "6M5H_complete.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } 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: 6708 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 5565 Classifications: {'peptide': 361} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 341} Chain: "A" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 1143 Classifications: {'water': 381} Link IDs: {None: 380} Time building chain proxies: 1.13, per 1000 atoms: 0.17 Number of scatterers: 6708 At special positions: 0 Unit cell: (130.15, 59.98, 55.1, 90, 111.309, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 O 913 8.00 N 464 7.00 C 1769 6.00 H 3547 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: 2.17 Conformation dependent library (CDL) restraints added in 200.2 milliseconds Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 1369 1.04 - 1.24: 2472 1.24 - 1.43: 883 1.43 - 1.63: 1634 1.63 - 1.82: 30 Bond restraints: 6388 Sorted by residual: bond pdb=" N GLN A 78 " pdb=" H GLN A 78 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLY A 259 " pdb=" H GLY A 259 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASN A 319 " pdb=" H ASN A 319 " 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 178 " pdb=" H LEU A 178 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASN A 24 " pdb=" H ASN A 24 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6383 not shown) Histogram of bond angle deviations from ideal: 95.79 - 103.54: 70 103.54 - 111.29: 6507 111.29 - 119.04: 1752 119.04 - 126.79: 2221 126.79 - 134.55: 35 Bond angle restraints: 10585 Sorted by residual: angle pdb=" CA TYR A 202 " pdb=" CB TYR A 202 " pdb=" CG TYR A 202 " ideal model delta sigma weight residual 113.90 107.55 6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" N SER A 150 " pdb=" CA SER A 150 " pdb=" C SER A 150 " ideal model delta sigma weight residual 108.26 113.94 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" CD LYS A 224 " pdb=" CE LYS A 224 " pdb=" NZ LYS A 224 " ideal model delta sigma weight residual 111.90 101.00 10.90 3.20e+00 9.77e-02 1.16e+01 angle pdb=" CA TYR A 233 " pdb=" CB TYR A 233 " pdb=" CG TYR A 233 " ideal model delta sigma weight residual 113.90 119.37 -5.47 1.80e+00 3.09e-01 9.23e+00 angle pdb=" N SER A 344 " pdb=" CA SER A 344 " pdb=" C SER A 344 " ideal model delta sigma weight residual 110.35 114.28 -3.93 1.36e+00 5.41e-01 8.34e+00 ... (remaining 10580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 1820 16.78 - 33.56: 115 33.56 - 50.34: 39 50.34 - 67.12: 19 67.12 - 83.90: 4 Dihedral angle restraints: 1997 sinusoidal: 1456 harmonic: 541 Sorted by residual: dihedral pdb=" CA TYR A 187 " pdb=" C TYR A 187 " pdb=" N LEU A 188 " pdb=" CA LEU A 188 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE A 266 " pdb=" C ILE A 266 " pdb=" N THR A 267 " pdb=" CA THR A 267 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA MET A 28 " pdb=" C MET A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 1994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 271 0.076 - 0.152: 113 0.152 - 0.228: 44 0.228 - 0.304: 10 0.304 - 0.381: 3 Chirality restraints: 441 Sorted by residual: chirality pdb=" CG LEU A 177 " pdb=" CB LEU A 177 " pdb=" CD1 LEU A 177 " pdb=" CD2 LEU A 177 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA MET A 271 " pdb=" N MET A 271 " pdb=" C MET A 271 " pdb=" CB MET A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA PHE A 101 " pdb=" N PHE A 101 " pdb=" C PHE A 101 " pdb=" CB PHE A 101 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 438 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 233 " -0.100 2.00e-02 2.50e+03 3.98e-02 4.74e+01 pdb=" CG TYR A 233 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 233 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 233 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR A 233 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 233 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 233 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 233 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TYR A 233 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 TYR A 233 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TYR A 233 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 233 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 261 " -0.001 2.00e-02 2.50e+03 3.38e-02 3.43e+01 pdb=" CG PHE A 261 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 261 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 261 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 261 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 261 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 261 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 261 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A 261 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 261 " -0.057 2.00e-02 2.50e+03 pdb=" HE2 PHE A 261 " -0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 261 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 321 " -0.030 2.00e-02 2.50e+03 2.86e-02 2.45e+01 pdb=" CG PHE A 321 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 321 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 321 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 321 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 321 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 321 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 321 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 PHE A 321 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 321 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 PHE A 321 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 321 " 0.039 2.00e-02 2.50e+03 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.93: 285 1.93 - 2.60: 7905 2.60 - 3.27: 24252 3.27 - 3.93: 34437 3.93 - 4.60: 50900 Nonbonded interactions: 117779 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 262 " pdb=" O HOH A 404 " model vdw 1.267 1.850 nonbonded pdb=" H2 HIS A -1 " pdb=" O HOH A 405 " model vdw 1.296 1.850 nonbonded pdb=" OD2 ASP A 244 " pdb=" O HOH A 735 " model vdw sym.op. 1.389 2.200 -x,y,-z nonbonded pdb=" H SER A 84 " pdb=" HH TYR A 92 " model vdw 1.480 2.100 nonbonded pdb=" HB2 GLU A 95 " pdb=" HE2 MET A 131 " model vdw 1.509 2.440 ... (remaining 117774 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 15 15.96 2 O 913 7.97 2 N 464 6.97 2 C 1769 5.97 2 H 3547 1.00 2 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 ===================== n_use = 6708 n_use_u_iso = 6708 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 = 6708 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6708 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3547 aniso = 3161) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (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 { adp { individual { isotropic = element H anisotropic = not element H } } } main { number_of_macro_cycles = 5 max_number_of_iterations = 50 nproc = 20 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "6M5H_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3547 occupancy sum: 3547.00 (% of total atoms 52.88) Rotatable: count: 839 occupancy sum: 839.00 (% of total atoms 12.51) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.2443 r_free= 0.2753 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 5.401265 | | target function (ml) not normalized (work): 646072.312902 | | target function (ml) not normalized (free): 10745.605298 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.98 - 2.89 1.00 8821 149 0.2593 0.2936 7.2802 7.3344| | 2: 2.89 - 2.30 1.00 8697 147 0.1964 0.2287 6.6261 6.6129| | 3: 2.30 - 2.01 1.00 8687 140 0.2130 0.2735 5.9271 5.979| | 4: 2.01 - 1.82 1.00 8621 147 0.2215 0.2374 5.6712 5.7271| | 5: 1.82 - 1.69 0.99 8594 139 0.2362 0.2733 5.4432 5.4557| | 6: 1.69 - 1.59 0.99 8563 146 0.2451 0.2692 5.2969 5.2971| | 7: 1.59 - 1.51 0.99 8590 143 0.2562 0.3040 5.1794 5.1488| | 8: 1.51 - 1.45 0.99 8496 148 0.2567 0.2924 5.0517 5.0756| | 9: 1.45 - 1.39 0.98 8501 134 0.2716 0.2538 4.9526 4.8375| | 10: 1.39 - 1.34 0.98 8454 137 0.2816 0.2883 4.8954 4.7503| | 11: 1.34 - 1.30 0.98 8472 136 0.2981 0.3308 4.8591 4.9295| | 12: 1.30 - 1.26 0.98 8381 152 0.3023 0.3169 4.821 4.7874| | 13: 1.26 - 1.23 0.97 8381 125 0.3132 0.3420 4.7562 4.7497| | 14: 1.23 - 1.20 0.97 8357 148 0.3256 0.3400 4.7122 4.674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.98 - 2.89 8821 149 0.55 47.87 0.91 0.82 497576.51| | 2: 2.89 - 2.30 8697 147 0.63 41.93 1.09 1.28 184543.11| | 3: 2.30 - 2.01 8687 140 0.89 18.45 1.16 1.50 22304.00| | 4: 2.01 - 1.82 8621 147 0.88 19.24 1.16 1.54 12564.22| | 5: 1.82 - 1.69 8594 139 0.87 20.87 1.17 1.52 7966.56| | 6: 1.69 - 1.59 8563 146 0.86 21.43 1.19 1.52 5948.45| | 7: 1.59 - 1.51 8590 143 0.86 22.16 1.19 1.51 4661.52| | 8: 1.51 - 1.45 8496 148 0.86 22.14 1.17 1.49 3637.51| | 9: 1.45 - 1.39 8501 134 0.86 22.36 1.17 1.47 2793.53| | 10: 1.39 - 1.34 8454 137 0.86 22.33 1.17 1.49 2387.98| | 11: 1.34 - 1.30 8472 136 0.85 23.66 1.20 1.52 2334.68| | 12: 1.30 - 1.26 8381 152 0.84 24.19 1.21 1.54 2296.64| | 13: 1.26 - 1.23 8381 125 0.82 26.15 1.22 1.50 2214.27| | 14: 1.23 - 1.20 8357 148 0.81 27.73 1.23 1.46 2102.50| |alpha: min = 0.82 max = 1.54 mean = 1.44| |beta: min = 2102.50 max = 497576.51 mean = 55223.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.99 mean = 25.81| |phase err.(test): min = 0.00 max = 89.78 mean = 25.76| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.079 2841 Z= 0.471 Angle : 1.134 10.896 3863 Z= 0.645 Chirality : 0.099 0.381 441 Planarity : 0.008 0.052 495 Dihedral : 12.887 83.900 1040 Min Nonbonded Distance : 1.389 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.02 (0.42), residues: 359 helix: -0.19 (0.38), residues: 136 sheet: 0.87 (0.81), residues: 41 loop : 0.13 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.003 ARG A 147 TYR 0.088 0.010 TYR A 233 PHE 0.037 0.010 PHE A 101 TRP 0.028 0.008 TRP A 272 HIS 0.013 0.004 HIS A 210 Individual atomic B min max mean iso aniso Overall: 6.98 39.26 14.56 1.63 0 3161 Protein: 6.98 37.93 13.36 1.63 0 2780 Water: 7.51 39.26 23.35 N/A 0 381 Chain A: 6.98 39.26 14.56 N/A 0 3161 Histogram: Values Number of atoms 6.98 - 10.21 821 10.21 - 13.44 1005 13.44 - 16.66 521 16.66 - 19.89 254 19.89 - 23.12 183 23.12 - 26.35 144 26.35 - 29.58 125 29.58 - 32.80 67 32.80 - 36.03 34 36.03 - 39.26 7 |-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 5 ************************* |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.2443 r_free= 0.2753 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 5.401265 | | target function (ml) not normalized (work): 646072.312902 | | target function (ml) not normalized (free): 10745.605298 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2448 0.2443 0.2753 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2448 0.2443 0.2753 n_refl.: 121606 remove outliers: r(all,work,free)=0.2448 0.2443 0.2753 n_refl.: 121606 overall B=-0.79 to atoms: r(all,work,free)=0.2348 0.2344 0.2624 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1729 0.1729 0.1763 n_refl.: 121606 remove outliers: r(all,work,free)=0.1729 0.1729 0.1763 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2412 587.363 545.723 0.969 1.000 0.410 13.092-10.331 99.02 100 1 0.1623 721.546 707.712 0.943 1.000 0.411 10.310-8.156 100.00 206 5 0.1392 758.890 728.876 0.946 1.001 0.431 8.152-6.434 100.00 428 8 0.1777 575.746 552.308 0.959 1.001 0.435 6.433-5.079 100.00 828 13 0.1919 566.548 548.227 0.942 1.001 0.431 5.076-4.007 100.00 1696 28 0.1497 795.581 776.235 1.003 1.001 0.407 4.006-3.162 99.94 3432 56 0.1644 718.474 701.080 1.037 1.000 0.264 3.161-2.495 99.91 6892 117 0.1774 449.123 438.638 0.993 1.000 0.010 2.495-1.969 99.73 13973 228 0.1581 325.016 319.230 1.036 0.998 0.000 1.969-1.554 99.30 28180 467 0.1606 166.656 165.008 1.042 0.997 0.000 1.554-1.200 97.93 63783 1065 0.2028 81.432 78.023 1.010 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.2392 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1729 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 23 ASN A 38 ASN A 42 ASN A 235 GLN A 288 ASN A 313 ASN A 347 GLN Total number of N/Q/H flips: 8 r_work=0.1741 r_free=0.1785 ========================= Local real-space refinement ========================= Before: r_work=0.1741 r_free=0.1785 58 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.236 outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 1.3269 time to fit residues: 78.4684 After: r_work=0.1748 r_free=0.1775 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.253453 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1256.991534 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1721 0.1858 0.0137 0.009 1.0 2.3 0.0 0.7 0 10.627 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1721 r_free=0.1858 62 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.226 outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5046 time to fit residues: 1.3154 After: r_work=0.1749 r_free=0.1870 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 17.49 18.70 1.21 1.090 14.460 1256.992 0.032 17.62 19.06 1.44 1.214 14.494 37.710 0.032 16.11 18.02 1.91 2.877 15.022 157.124 0.026 15.07 17.53 2.46 4.911 15.589 628.496 0.023 14.91 17.82 2.91 5.680 15.898 1256.992 0.022 14.74 17.98 3.23 4.905 15.711 1885.487 0.022 14.69 17.99 3.30 5.126 15.774 2513.983 0.022 14.71 18.12 3.41 5.965 16.029 3142.479 0.021 14.67 18.21 3.54 5.820 15.986 3770.975 0.021 14.62 18.13 3.50 5.158 15.797 4399.470 0.021 14.72 18.46 3.75 6.446 16.171 5027.966 0.021 14.62 18.27 3.65 5.804 15.954 5656.462 0.021 14.63 18.28 3.65 5.992 15.980 6284.958 0.021 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 628.496 Accepted refinement result: 15.07 17.53 2.46 4.911 15.589 628.496 0.023 Individual atomic B min max mean iso aniso Overall: 5.47 73.50 16.16 1.39 0 3161 Protein: 6.83 53.16 13.83 1.39 0 2780 Water: 5.47 73.50 33.19 N/A 0 381 Chain A: 5.47 73.50 16.16 N/A 0 3161 Histogram: Values Number of atoms 5.47 - 12.27 1547 12.27 - 19.07 865 19.07 - 25.88 291 25.88 - 32.68 166 32.68 - 39.48 133 39.48 - 46.29 99 46.29 - 53.09 47 53.09 - 59.89 11 59.89 - 66.70 1 66.70 - 73.50 1 =========================== Idealize ADP of riding H ========================== r_work=0.1507 r_free=0.1753 r_work=0.1509 r_free=0.1755 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.1509 r_free= 0.1755 coordinate error (max.-lik. estimate): 0.13 A | | | | normalized target function (ls_wunit_k1) (work): 0.023182 | | target function (ls_wunit_k1) not normalized (work): 2772.936498 | | target function (ls_wunit_k1) not normalized (free): 68.003580 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1513 0.1509 0.1755 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2201 0.2193 0.2636 n_refl.: 121606 remove outliers: r(all,work,free)=0.2201 0.2193 0.2636 n_refl.: 121606 overall B=0.00 to atoms: r(all,work,free)=0.2201 0.2193 0.2636 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1506 0.1502 0.1753 n_refl.: 121606 remove outliers: r(all,work,free)=0.1506 0.1502 0.1753 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2478 533.640 496.589 0.885 1.001 0.400 13.092-10.331 99.02 100 1 0.1563 655.551 645.500 0.885 1.002 0.403 10.310-8.156 100.00 206 5 0.1355 689.479 665.118 0.905 1.002 0.420 8.152-6.434 100.00 428 8 0.1630 523.086 505.921 0.915 1.002 0.430 6.433-5.079 100.00 828 13 0.1683 514.729 501.969 0.898 1.002 0.430 5.076-4.007 100.00 1696 28 0.1187 722.814 711.766 0.964 1.002 0.410 4.006-3.162 99.94 3432 56 0.1203 652.759 644.594 1.018 1.001 0.200 3.161-2.495 99.91 6892 117 0.1297 408.044 403.396 0.986 1.001 0.000 2.495-1.969 99.73 13973 228 0.1259 295.289 292.508 1.030 0.999 0.000 1.969-1.554 99.30 28180 467 0.1504 151.413 150.742 1.017 0.998 0.000 1.554-1.200 97.93 63783 1065 0.2028 73.984 71.081 0.972 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0185 b_overall=0.4650 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1502 r_free=0.1753 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 51 GLN A 347 GLN Total number of N/Q/H flips: 3 r_work=0.1505 r_free=0.1749 ========================= Local real-space refinement ========================= Before: r_work=0.1505 r_free=0.1749 53 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.349 outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 1.8649 time to fit residues: 102.7197 After: r_work=0.1523 r_free=0.1752 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.334466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1814.976550 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1659 0.1829 0.0170 0.002 0.6 1.4 0.0 0.0 0 0.125 0.1651 0.1826 0.0175 0.002 0.6 1.4 0.0 0.0 0 0.250 0.1616 0.1803 0.0187 0.003 0.6 1.8 0.0 0.0 0 0.500 0.1590 0.1787 0.0197 0.003 0.6 2.0 0.0 0.0 0 0.750 0.1579 0.1780 0.0201 0.003 0.6 1.8 0.0 0.3 0 1.000 0.1579 0.1780 0.0201 0.003 0.6 1.8 0.0 0.3 0 1.000 0.1547 0.1761 0.0214 0.003 0.7 2.0 0.0 0.3 0 2.000 0.1537 0.1763 0.0226 0.004 0.7 2.0 0.0 0.3 0 3.000 0.1526 0.1764 0.0237 0.005 0.7 2.2 0.0 0.3 0 4.000 0.1519 0.1763 0.0244 0.005 0.8 2.2 0.0 0.3 0 5.000 0.1512 0.1763 0.0251 0.006 0.8 2.2 0.0 0.3 0 6.000 0.1504 0.1758 0.0254 0.006 0.8 2.2 0.0 0.3 0 7.000 0.1499 0.1756 0.0257 0.007 0.9 2.3 0.0 0.3 0 8.000 0.1496 0.1756 0.0260 0.007 0.9 2.3 0.0 0.3 0 9.000 0.1493 0.1758 0.0265 0.008 0.9 2.7 0.0 0.3 0 10.000 0.1491 0.1757 0.0267 0.008 1.0 2.7 0.0 0.3 0 11.000 0.1489 0.1757 0.0268 0.009 1.0 2.7 0.0 0.3 0 12.000 0.1486 0.1758 0.0272 0.009 1.0 2.5 0.0 0.3 0 13.167 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1496 0.1756 0.0260 0.007 0.9 2.3 0.0 0.3 0 9.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1496 r_free=0.1756 53 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.287 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3423 After: r_work=0.1496 r_free=0.1756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.96 17.56 2.60 3.351 19.281 1814.977 0.023 14.96 17.56 2.60 3.351 19.281 54.449 0.023 14.96 17.56 2.60 3.351 19.281 226.872 0.023 14.61 17.44 2.83 3.416 19.289 907.488 0.022 14.32 17.46 3.14 3.436 19.472 1814.977 0.020 14.18 17.52 3.33 3.462 19.478 2722.465 0.020 14.15 17.65 3.50 3.473 19.587 3629.953 0.020 14.11 17.71 3.59 3.518 19.591 4537.441 0.020 14.10 17.77 3.66 3.505 19.650 5444.930 0.019 14.08 17.81 3.73 3.544 19.652 6352.418 0.019 14.05 17.81 3.76 3.538 19.621 7259.906 0.019 14.04 17.84 3.79 3.556 19.627 8167.394 0.019 14.08 18.03 3.94 3.644 19.720 9074.883 0.019 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 907.488 Accepted refinement result: 14.61 17.44 2.83 3.416 19.289 907.488 0.022 Individual atomic B min max mean iso aniso Overall: 5.48 73.81 16.18 1.47 0 3161 Protein: 6.72 53.90 13.87 1.47 0 2780 Water: 5.48 73.81 33.08 N/A 0 381 Chain A: 5.48 73.81 16.18 N/A 0 3161 Histogram: Values Number of atoms 5.48 - 12.31 1548 12.31 - 19.14 874 19.14 - 25.98 284 25.98 - 32.81 163 32.81 - 39.64 141 39.64 - 46.48 96 46.48 - 53.31 41 53.31 - 60.14 12 60.14 - 66.98 1 66.98 - 73.81 1 =========================== Idealize ADP of riding H ========================== r_work=0.1461 r_free=0.1744 r_work=0.1461 r_free=0.1743 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.1461 r_free= 0.1743 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.021547 | | target function (ls_wunit_k1) not normalized (work): 2577.372468 | | target function (ls_wunit_k1) not normalized (free): 66.909709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1465 0.1461 0.1743 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2179 0.2171 0.2652 n_refl.: 121606 remove outliers: r(all,work,free)=0.2179 0.2171 0.2652 n_refl.: 121606 overall B=0.00 to atoms: r(all,work,free)=0.2179 0.2171 0.2652 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1465 0.1460 0.1743 n_refl.: 121606 remove outliers: r(all,work,free)=0.1465 0.1460 0.1743 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2413 533.640 498.719 0.884 1.002 0.400 13.092-10.331 99.02 100 1 0.1576 655.551 646.867 0.890 1.002 0.400 10.310-8.156 100.00 206 5 0.1331 689.479 664.487 0.901 1.002 0.400 8.152-6.434 100.00 428 8 0.1644 523.086 506.878 0.919 1.002 0.430 6.433-5.079 100.00 828 13 0.1662 514.729 502.401 0.899 1.002 0.430 5.076-4.007 100.00 1696 28 0.1151 722.814 712.828 0.965 1.002 0.410 4.006-3.162 99.94 3432 56 0.1166 652.759 645.348 1.024 1.001 0.200 3.161-2.495 99.91 6892 117 0.1249 408.044 404.285 0.995 1.001 0.000 2.495-1.969 99.73 13973 228 0.1212 295.289 292.997 1.040 0.999 0.000 1.969-1.554 99.30 28180 467 0.1447 151.413 150.878 1.027 0.997 0.000 1.554-1.200 97.93 63783 1065 0.2001 73.984 71.204 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.4527 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1460 r_free=0.1743 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 23 ASN A 51 GLN A 117 GLN A 251 GLN A 288 ASN A 313 ASN A 347 GLN Total number of N/Q/H flips: 8 r_work=0.1469 r_free=0.1744 ========================= Local real-space refinement ========================= Before: r_work=0.1469 r_free=0.1744 52 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.463 outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.9771 time to fit residues: 106.6596 After: r_work=0.1476 r_free=0.1746 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.999279 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 67.303168 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1520 0.1728 0.0208 0.003 0.6 2.0 0.0 0.3 0 0.100 0.1481 0.1713 0.0232 0.004 0.8 2.0 0.0 0.3 0 0.300 0.1463 0.1710 0.0247 0.005 0.9 2.7 0.0 0.3 0 0.600 0.1455 0.1714 0.0260 0.006 0.9 2.7 0.0 0.3 0 0.900 0.1450 0.1718 0.0268 0.007 1.0 2.7 0.0 0.3 0 1.200 0.1447 0.1720 0.0273 0.008 1.0 2.9 0.0 0.3 0 1.499 0.1443 0.1722 0.0279 0.009 1.0 3.1 0.0 0.3 0 1.799 0.1442 0.1725 0.0283 0.010 1.1 3.2 0.0 0.3 0 2.099 0.1452 0.1714 0.0262 0.007 0.9 2.7 0.0 0.3 0 1.000 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1463 0.1710 0.0247 0.005 0.9 2.7 0.0 0.3 0 0.600 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1463 r_free=0.1710 50 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.214 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.8413 time to fit residues: 1.0816 After: r_work=0.1463 r_free=0.1710 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.63 17.10 2.46 3.359 19.292 67.303 4.648 14.69 17.01 2.31 3.357 19.290 2.019 4.645 14.92 16.78 1.86 3.436 19.249 8.413 4.632 14.61 16.50 1.89 3.839 19.095 33.652 4.591 14.33 16.39 2.05 3.754 19.137 67.303 4.576 14.21 16.38 2.17 3.736 19.160 100.955 4.571 14.14 16.41 2.27 3.743 19.171 134.606 4.569 14.09 16.42 2.33 3.728 19.187 168.258 4.567 14.07 16.43 2.37 3.730 19.197 201.910 4.567 14.03 16.44 2.42 3.715 19.207 235.561 4.566 14.02 16.43 2.41 3.700 19.219 269.213 4.566 14.00 16.47 2.46 3.709 19.227 302.864 4.566 13.99 16.46 2.47 3.700 19.231 336.516 4.565 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 100.955 Accepted refinement result: 14.21 16.38 2.17 3.736 19.160 100.955 4.571 Individual atomic B min max mean iso aniso Overall: 6.18 74.35 15.90 1.61 0 3161 Protein: 6.76 53.71 13.61 1.61 0 2780 Water: 6.18 74.35 32.66 N/A 0 381 Chain A: 6.18 74.35 15.90 N/A 0 3161 Histogram: Values Number of atoms 6.18 - 13.00 1748 13.00 - 19.82 758 19.82 - 26.63 241 26.63 - 33.45 164 33.45 - 40.27 117 40.27 - 47.08 85 47.08 - 53.90 38 53.90 - 60.72 8 60.72 - 67.53 1 67.53 - 74.35 1 =========================== Idealize ADP of riding H ========================== r_work=0.1421 r_free=0.1638 r_work=0.1422 r_free=0.1636 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.1422 r_free= 0.1636 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.571295 | | target function (ml) not normalized (work): 546795.413652 | | target function (ml) not normalized (free): 9334.299528 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1426 0.1422 0.1636 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2135 0.2128 0.2552 n_refl.: 121606 remove outliers: r(all,work,free)=0.2135 0.2128 0.2552 n_refl.: 121606 overall B=0.00 to atoms: r(all,work,free)=0.2135 0.2128 0.2552 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1424 0.1421 0.1633 n_refl.: 121606 remove outliers: r(all,work,free)=0.1424 0.1421 0.1633 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2485 533.640 496.396 0.929 1.001 0.410 13.092-10.331 99.02 100 1 0.1652 655.551 622.605 0.875 1.001 0.410 10.310-8.156 100.00 206 5 0.1425 689.479 662.223 0.911 1.002 0.410 8.152-6.434 100.00 428 8 0.1783 523.086 504.611 0.933 1.002 0.440 6.433-5.079 100.00 828 13 0.1824 514.729 499.275 0.908 1.002 0.440 5.076-4.007 100.00 1696 28 0.1319 722.814 709.778 0.968 1.001 0.400 4.006-3.162 99.94 3432 56 0.1397 652.759 640.285 1.022 1.001 0.200 3.161-2.495 99.91 6892 117 0.1416 408.044 401.287 0.998 1.000 0.000 2.495-1.969 99.73 13973 228 0.1259 295.289 291.864 1.039 0.999 0.000 1.969-1.554 99.30 28180 467 0.1256 151.413 150.369 1.034 0.997 0.000 1.554-1.200 97.93 63783 1065 0.1683 73.984 71.781 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.3828 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1421 r_free=0.1633 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 117 GLN Total number of N/Q/H flips: 2 r_work=0.1422 r_free=0.1634 ========================= Local real-space refinement ========================= Before: r_work=0.1422 r_free=0.1634 61 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.203 outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 1.3578 time to fit residues: 86.0716 After: r_work=0.1441 r_free=0.1643 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.010400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 77.494110 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1462 0.1643 0.0181 0.003 0.6 2.0 0.0 0.0 0 0.125 0.1436 0.1631 0.0196 0.004 0.7 2.3 0.0 0.0 0 0.250 0.1418 0.1629 0.0211 0.005 0.8 2.5 0.0 0.0 0 0.500 0.1406 0.1627 0.0221 0.007 1.0 3.1 0.0 0.0 0 1.000 0.1396 0.1628 0.0233 0.009 1.1 3.2 0.0 0.0 0 2.000 0.1391 0.1629 0.0238 0.011 1.2 3.2 0.0 0.3 0 3.000 0.1387 0.1630 0.0243 0.013 1.2 3.2 0.0 0.3 0 4.000 0.1385 0.1632 0.0247 0.015 1.3 3.2 0.0 0.3 0 5.000 0.1382 0.1632 0.0250 0.016 1.3 3.2 0.0 0.3 0 6.000 0.1380 0.1633 0.0253 0.017 1.4 3.2 0.0 0.3 0 7.000 0.1379 0.1633 0.0254 0.018 1.4 3.4 0.0 0.3 0 8.000 0.1378 0.1634 0.0256 0.019 1.4 3.2 0.0 0.3 0 9.000 0.1377 0.1635 0.0258 0.020 1.5 3.1 0.0 0.3 0 10.000 0.1406 0.1626 0.0220 0.007 0.9 2.9 0.0 0.0 0 1.005 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1406 0.1626 0.0220 0.007 0.9 2.9 0.0 0.0 0 1.005 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1406 r_free=0.1626 61 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.233 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2123 After: r_work=0.1406 r_free=0.1626 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.06 16.26 2.20 3.340 18.978 77.494 4.561 14.06 16.26 2.20 3.340 18.978 2.325 4.561 14.06 16.26 2.20 3.340 18.978 9.687 4.561 14.08 16.26 2.18 3.348 18.965 38.747 4.560 14.02 16.24 2.22 3.427 18.920 77.494 4.556 13.91 16.20 2.29 3.517 18.905 116.241 4.550 13.83 16.21 2.39 3.586 18.902 154.988 4.547 13.78 16.20 2.42 3.577 18.914 193.735 4.545 13.76 16.20 2.44 3.563 18.922 232.482 4.544 13.74 16.23 2.50 3.569 18.930 271.229 4.544 13.72 16.25 2.53 3.581 18.934 309.976 4.544 13.71 16.26 2.55 3.589 18.940 348.723 4.544 13.69 16.29 2.60 3.615 18.948 387.471 4.544 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 193.735 Accepted refinement result: 13.78 16.20 2.42 3.577 18.914 193.735 4.545 Individual atomic B min max mean iso aniso Overall: 6.15 74.92 15.77 1.81 0 3161 Protein: 6.38 54.40 13.54 1.81 0 2780 Water: 6.15 74.92 31.98 N/A 0 381 Chain A: 6.15 74.92 15.77 N/A 0 3161 Histogram: Values Number of atoms 6.15 - 13.03 1771 13.03 - 19.90 745 19.90 - 26.78 244 26.78 - 33.66 158 33.66 - 40.53 122 40.53 - 47.41 78 47.41 - 54.29 33 54.29 - 61.16 8 61.16 - 68.04 1 68.04 - 74.92 1 =========================== Idealize ADP of riding H ========================== r_work=0.1378 r_free=0.1620 r_work=0.1378 r_free=0.1619 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.1378 r_free= 0.1619 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.544558 | | target function (ml) not normalized (work): 543597.250586 | | target function (ml) not normalized (free): 9309.334066 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1382 0.1378 0.1619 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2084 0.2078 0.2511 n_refl.: 121606 remove outliers: r(all,work,free)=0.2084 0.2078 0.2511 n_refl.: 121606 overall B=0.00 to atoms: r(all,work,free)=0.2084 0.2078 0.2511 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1380 0.1376 0.1617 n_refl.: 121606 remove outliers: r(all,work,free)=0.1380 0.1376 0.1617 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2481 533.640 494.949 0.916 1.002 0.410 13.092-10.331 99.02 100 1 0.1684 655.551 643.375 0.896 1.002 0.410 10.310-8.156 100.00 206 5 0.1430 689.479 660.020 0.900 1.003 0.410 8.152-6.434 100.00 428 8 0.1788 523.086 501.591 0.919 1.003 0.440 6.433-5.079 100.00 828 13 0.1821 514.729 499.095 0.899 1.003 0.440 5.076-4.007 100.00 1696 28 0.1329 722.814 708.207 0.958 1.002 0.410 4.006-3.162 99.94 3432 56 0.1398 652.759 640.102 1.010 1.001 0.200 3.161-2.495 99.91 6892 117 0.1392 408.044 401.492 0.988 1.000 0.000 2.495-1.969 99.73 13973 228 0.1202 295.289 292.089 1.026 0.998 0.000 1.969-1.554 99.30 28180 467 0.1168 151.413 150.963 1.025 0.995 0.000 1.554-1.200 97.93 63783 1065 0.1630 73.984 71.727 0.973 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0185 b_overall=0.4594 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1376 r_free=0.1617 After: r_work=0.1377 r_free=0.1617 ================================== NQH flips ================================== r_work=0.1377 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 117 GLN A 218 ASN A 288 ASN A 313 ASN Total number of N/Q/H flips: 5 r_work=0.1389 r_free=0.1626 ========================= Local real-space refinement ========================= Before: r_work=0.1389 r_free=0.1626 49 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.240 outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 1.2832 time to fit residues: 63.8672 After: r_work=0.1398 r_free=0.1635 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.954352 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 74.964759 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1431 0.1640 0.0210 0.004 0.8 3.4 0.0 0.3 0 0.098 0.1400 0.1626 0.0225 0.005 0.8 4.0 0.0 0.3 0 0.293 0.1388 0.1623 0.0235 0.005 0.9 3.6 0.0 0.3 0 0.586 0.1381 0.1622 0.0241 0.006 1.0 3.4 0.0 0.3 0 0.879 0.1377 0.1623 0.0246 0.007 1.0 3.4 0.0 0.3 0 1.173 0.1374 0.1624 0.0250 0.008 1.1 3.4 0.0 0.3 0 1.466 0.1372 0.1624 0.0253 0.009 1.1 3.4 0.0 0.3 0 1.759 0.1371 0.1625 0.0254 0.010 1.1 3.4 0.0 0.3 0 2.052 0.1379 0.1622 0.0243 0.007 1.0 3.4 0.0 0.3 0 0.977 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1381 0.1622 0.0241 0.006 1.0 3.4 0.0 0.3 0 0.879 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1381 r_free=0.1622 47 residues out of total 305 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.252 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.2052 After: r_work=0.1381 r_free=0.1622 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.81 16.22 2.41 3.356 18.816 74.965 4.547 13.81 16.22 2.41 3.356 18.816 2.249 4.547 13.81 16.22 2.41 3.356 18.816 9.371 4.547 13.82 16.21 2.39 3.357 18.812 37.482 4.547 13.83 16.20 2.37 3.366 18.796 74.965 4.546 13.82 16.20 2.37 3.380 18.782 112.447 4.545 13.80 16.19 2.38 3.397 18.778 149.930 4.544 13.80 16.21 2.41 3.414 18.771 187.412 4.544 13.81 16.24 2.43 3.477 18.762 224.894 4.543 13.79 16.27 2.48 3.512 18.765 262.377 4.543 13.76 16.26 2.50 3.508 18.775 299.859 4.542 13.75 16.28 2.53 3.510 18.784 337.341 4.542 13.74 16.29 2.55 3.513 18.792 374.824 4.542 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 149.930 Accepted refinement result: 13.80 16.19 2.38 3.397 18.778 149.930 4.544 Individual atomic B min max mean iso aniso Overall: 6.15 74.99 15.69 1.76 0 3161 Protein: 6.55 54.34 13.46 1.76 0 2780 Water: 6.15 74.99 31.89 N/A 0 381 Chain A: 6.15 74.99 15.69 N/A 0 3161 Histogram: Values Number of atoms 6.15 - 13.04 1788 13.04 - 19.92 739 19.92 - 26.80 235 26.80 - 33.69 158 33.69 - 40.57 121 40.57 - 47.45 79 47.45 - 54.34 31 54.34 - 61.22 8 61.22 - 68.10 1 68.10 - 74.99 1 =========================== Idealize ADP of riding H ========================== r_work=0.1380 r_free=0.1619 r_work=0.1380 r_free=0.1619 ----------X-ray data---------- |--(resolution: 1.20 - 32.98 A, n_refl.=121606 (all), 1.64 % free)-----------| | | | r_work= 0.1380 r_free= 0.1619 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.543870 | | target function (ml) not normalized (work): 543515.011240 | | target function (ml) not normalized (free): 9305.372957 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.98 - 2.89 1.00 8821 149 0.1477 0.1622 6.1003 6.1237| | 2: 2.89 - 2.30 1.00 8697 147 0.1342 0.1420 5.5755 5.6246| | 3: 2.30 - 2.01 1.00 8687 140 0.1151 0.1402 5.1711 5.2773| | 4: 2.01 - 1.82 1.00 8621 147 0.1164 0.1490 4.868 5.0703| | 5: 1.82 - 1.69 0.99 8594 139 0.1171 0.1429 4.5826 4.7549| | 6: 1.69 - 1.59 0.99 8563 146 0.1149 0.1419 4.3811 4.5306| | 7: 1.59 - 1.51 0.99 8590 143 0.1246 0.1686 4.2768 4.4466| | 8: 1.51 - 1.45 0.99 8496 148 0.1325 0.1733 4.1853 4.3713| | 9: 1.45 - 1.39 0.98 8501 134 0.1482 0.1872 4.1204 4.2549| | 10: 1.39 - 1.34 0.98 8454 137 0.1571 0.1979 4.0666 4.1827| | 11: 1.34 - 1.30 0.98 8472 136 0.1664 0.1909 4.0456 4.2201| | 12: 1.30 - 1.26 0.98 8381 152 0.1749 0.1998 4.0363 4.1288| | 13: 1.26 - 1.23 0.97 8381 125 0.1987 0.2727 4.0346 4.2004| | 14: 1.23 - 1.20 0.97 8357 148 0.2207 0.2644 4.0456 4.1014| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.98 - 2.89 8821 149 0.92 13.44 1.00 0.99 26314.67| | 2: 2.89 - 2.30 8697 147 0.90 16.48 0.99 1.00 13384.49| | 3: 2.30 - 2.01 8687 140 0.93 12.76 1.01 1.00 5525.54| | 4: 2.01 - 1.82 8621 147 0.92 13.74 1.01 0.99 3129.93| | 5: 1.82 - 1.69 8594 139 0.92 14.18 0.99 0.99 1872.36| | 6: 1.69 - 1.59 8563 146 0.93 13.60 0.99 0.99 1284.36| | 7: 1.59 - 1.51 8590 143 0.93 14.28 1.01 1.00 1009.93| | 8: 1.51 - 1.45 8496 148 0.92 15.14 1.03 0.99 852.39| | 9: 1.45 - 1.39 8501 134 0.91 16.29 1.00 0.97 744.90| | 10: 1.39 - 1.34 8454 137 0.91 16.64 0.99 0.97 665.32| | 11: 1.34 - 1.30 8472 136 0.91 17.47 0.98 0.96 636.08| | 12: 1.30 - 1.26 8381 152 0.90 18.17 0.97 0.94 627.53| | 13: 1.26 - 1.23 8381 125 0.88 20.43 0.95 0.90 639.65| | 14: 1.23 - 1.20 8357 148 0.86 22.53 0.94 0.87 656.63| |alpha: min = 0.87 max = 1.00 mean = 0.97| |beta: min = 627.53 max = 26314.67 mean = 4179.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.91 mean = 16.05| |phase err.(test): min = 0.00 max = 85.95 mean = 16.07| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1384 0.1380 0.1619 n_refl.: 121606 re-set all scales: r(all,work,free)=0.2069 0.2063 0.2493 n_refl.: 121606 remove outliers: r(all,work,free)=0.2069 0.2063 0.2493 n_refl.: 121606 overall B=0.00 to atoms: r(all,work,free)=0.2069 0.2063 0.2493 n_refl.: 121606 bulk-solvent and scaling: r(all,work,free)=0.1383 0.1379 0.1618 n_refl.: 121606 remove outliers: r(all,work,free)=0.1383 0.1379 0.1618 n_refl.: 121606 ======================== 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 32.981-13.145 97.09 97 3 0.2494 533.640 496.195 0.921 1.001 0.410 13.092-10.331 99.02 100 1 0.1688 655.551 622.362 0.871 1.002 0.410 10.310-8.156 100.00 206 5 0.1449 689.479 660.927 0.906 1.002 0.410 8.152-6.434 100.00 428 8 0.1802 523.086 503.779 0.926 1.002 0.440 6.433-5.079 100.00 828 13 0.1829 514.729 499.309 0.905 1.002 0.440 5.076-4.007 100.00 1696 28 0.1337 722.814 709.440 0.964 1.001 0.410 4.006-3.162 99.94 3432 56 0.1409 652.759 639.988 1.014 1.001 0.190 3.161-2.495 99.91 6892 117 0.1397 408.044 401.268 0.989 1.000 0.000 2.495-1.969 99.73 13973 228 0.1206 295.289 292.069 1.026 0.998 0.000 1.969-1.554 99.30 28180 467 0.1170 151.413 150.538 1.020 0.995 0.000 1.554-1.200 97.93 63783 1065 0.1626 73.984 71.956 0.971 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0185 b_overall=0.4676 ================= 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) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2443 0.2753 0.010 1.134 7.0 39.3 14.6 1143 0.000 1_bss: 0.1729 0.1763 0.010 1.134 6.2 38.5 13.8 1143 0.000 1_settarget: 0.1729 0.1763 0.010 1.134 6.2 38.5 13.8 1143 0.000 1_nqh: 0.1741 0.1785 0.010 1.134 6.2 38.5 13.8 1143 0.013 1_realsrl: 0.1748 0.1775 0.010 1.134 6.2 38.5 13.8 1143 0.021 1_weight: 0.1748 0.1775 0.010 1.134 6.2 38.5 13.8 1143 0.021 1_xyzrec: 0.1721 0.1858 0.009 0.983 6.2 38.5 13.8 1143 0.113 1_realsrl2: 0.1749 0.1870 0.009 0.983 6.2 38.5 13.8 1143 0.113 1_adp: 0.1507 0.1753 0.009 0.983 5.5 73.5 16.2 1143 0.113 1_regHadp: 0.1509 0.1755 0.009 0.983 5.5 73.5 16.2 1143 0.113 2_bss: 0.1502 0.1753 0.009 0.983 5.5 73.5 16.2 1143 0.113 2_settarget: 0.1502 0.1753 0.009 0.983 5.5 73.5 16.2 1143 0.113 2_updatecdl: 0.1502 0.1753 0.009 0.990 5.5 73.5 16.2 1143 0.113 2_nqh: 0.1505 0.1749 0.009 0.990 5.5 73.5 16.2 1143 0.112 2_realsrl: 0.1523 0.1752 0.009 0.990 5.5 73.5 16.2 1143 0.121 2_weight: 0.1523 0.1752 0.009 0.990 5.5 73.5 16.2 1143 0.121 2_xyzrec: 0.1496 0.1756 0.007 0.899 5.5 73.5 16.2 1143 0.130 2_realsrl2: 0.1496 0.1756 0.007 0.899 5.5 73.5 16.2 1143 0.130 2_adp: 0.1461 0.1744 0.007 0.899 5.5 73.8 16.2 1143 0.130 2_regHadp: 0.1461 0.1743 0.007 0.899 5.5 73.8 16.2 1143 0.130 3_bss: 0.1460 0.1743 0.007 0.899 5.5 73.8 16.2 1143 0.130 3_settarget: 0.1460 0.1743 0.007 0.899 5.5 73.8 16.2 1143 0.130 3_updatecdl: 0.1460 0.1743 0.007 0.901 5.5 73.8 16.2 1143 0.130 3_nqh: 0.1469 0.1744 0.007 0.901 5.5 73.8 16.2 1143 0.134 3_realsrl: 0.1476 0.1746 0.007 0.901 5.5 73.8 16.2 1143 0.133 3_weight: 0.1476 0.1746 0.007 0.901 5.5 73.8 16.2 1143 0.133 3_xyzrec: 0.1463 0.1710 0.005 0.852 5.5 73.8 16.2 1143 0.120 3_realsrl2: 0.1463 0.1710 0.005 0.852 5.5 73.8 16.2 1143 0.120 3_adp: 0.1421 0.1638 0.005 0.852 6.2 74.4 15.9 1143 0.120 3_regHadp: 0.1422 0.1636 0.005 0.852 6.2 74.4 15.9 1143 0.120 4_bss: 0.1421 0.1633 0.005 0.852 6.2 74.4 15.9 1143 0.120 4_settarget: 0.1421 0.1633 0.005 0.852 6.2 74.4 15.9 1143 0.120 4_updatecdl: 0.1421 0.1633 0.005 0.854 6.2 74.4 15.9 1143 0.120 4_nqh: 0.1422 0.1634 0.005 0.854 6.2 74.4 15.9 1143 0.120 4_realsrl: 0.1441 0.1643 0.005 0.854 6.2 74.4 15.9 1143 0.124 4_weight: 0.1441 0.1643 0.005 0.854 6.2 74.4 15.9 1143 0.124 4_xyzrec: 0.1406 0.1626 0.007 0.947 6.2 74.4 15.9 1143 0.121 4_realsrl2: 0.1406 0.1626 0.007 0.947 6.2 74.4 15.9 1143 0.121 4_adp: 0.1378 0.1620 0.007 0.947 6.1 74.9 15.8 1143 0.121 4_regHadp: 0.1378 0.1619 0.007 0.947 6.1 74.9 15.8 1143 0.121 5_bss: 0.1376 0.1617 0.007 0.947 6.1 74.9 15.8 1143 0.121 5_settarget: 0.1376 0.1617 0.007 0.947 6.1 74.9 15.8 1143 0.121 5_updatecdl: 0.1376 0.1617 0.007 0.948 6.1 74.9 15.8 1143 0.121 5_setrh: 0.1377 0.1617 0.007 0.948 6.1 74.9 15.8 1143 0.120 5_nqh: 0.1389 0.1626 0.007 0.948 6.1 74.9 15.8 1143 0.125 5_realsrl: 0.1398 0.1635 0.007 0.948 6.1 74.9 15.8 1143 0.125 5_weight: 0.1398 0.1635 0.007 0.948 6.1 74.9 15.8 1143 0.125 5_xyzrec: 0.1381 0.1622 0.006 0.982 6.1 74.9 15.8 1143 0.124 5_realsrl2: 0.1381 0.1622 0.006 0.982 6.1 74.9 15.8 1143 0.124 5_adp: 0.1380 0.1619 0.006 0.982 6.2 75.0 15.7 1143 0.124 5_regHadp: 0.1380 0.1619 0.006 0.982 6.2 75.0 15.7 1143 0.124 end: 0.1379 0.1618 0.006 0.982 6.2 75.0 15.7 1143 0.124 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6M5H_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/6M5H_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.4200 Refinement macro-cycles (run) : 1978.7200 Write final files (write_after_run_outputs) : 73.3700 Total : 2056.5100 Total CPU time: 34.70 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:44:58 PDT -0700 (1712792698.85 s) Start R-work = 0.1729, R-free = 0.1763 Final R-work = 0.1379, R-free = 0.1618 =============================================================================== Job complete usr+sys time: 2210.69 seconds wall clock time: 47 minutes 49.48 seconds (2869.48 seconds total)