Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 2PND_complete.pdb Found miller_array, 2PND.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 = "2PND.mtz" } default_miller_array = "2PND.mtz" model { file = "2PND_complete.pdb" } default_model = "2PND_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: 2659 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1948 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 711 Classifications: {'water': 237} Link IDs: {None: 236} Time building chain proxies: 0.53, per 1000 atoms: 0.20 Number of scatterers: 2659 At special positions: 0 Unit cell: (31.334, 50.684, 62.809, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 414 8.00 N 182 7.00 C 606 6.00 H 1454 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 54.8 milliseconds Time building geometry restraints manager: 1.20 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: 717 1.04 - 1.24: 817 1.24 - 1.43: 330 1.43 - 1.62: 574 1.62 - 1.82: 4 Bond restraints: 2442 Sorted by residual: bond pdb=" N VAL A 116 " pdb=" H VAL A 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N THR A 6 " pdb=" H THR A 6 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N CYS A 22 " pdb=" H CYS A 22 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 69 " pdb=" H VAL A 69 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" NH1 ARG A 51 " pdb="HH11 ARG A 51 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2437 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.25: 284 105.25 - 112.39: 2229 112.39 - 119.52: 519 119.52 - 126.66: 744 126.66 - 133.79: 20 Bond angle restraints: 3796 Sorted by residual: angle pdb=" CA ASN A 82 " pdb=" CB ASN A 82 " pdb=" CG ASN A 82 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" N GLN A 59 " pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 111.82 115.60 -3.78 1.16e+00 7.43e-01 1.06e+01 angle pdb=" C ARG A 66 " pdb=" CA ARG A 66 " pdb=" CB ARG A 66 " ideal model delta sigma weight residual 109.38 104.04 5.34 1.68e+00 3.54e-01 1.01e+01 angle pdb=" CA ASP A 109 " pdb=" CB ASP A 109 " pdb=" CG ASP A 109 " ideal model delta sigma weight residual 112.60 115.66 -3.06 1.00e+00 1.00e+00 9.36e+00 angle pdb=" CA GLN A 59 " pdb=" CB GLN A 59 " pdb=" CG GLN A 59 " ideal model delta sigma weight residual 114.10 119.59 -5.49 2.00e+00 2.50e-01 7.53e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 618 17.58 - 35.17: 47 35.17 - 52.75: 18 52.75 - 70.34: 4 70.34 - 87.92: 2 Dihedral angle restraints: 689 sinusoidal: 513 harmonic: 176 Sorted by residual: dihedral pdb=" CA LYS A 36 " pdb=" C LYS A 36 " pdb=" N TRP A 37 " pdb=" CA TRP A 37 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TRP A 98 " pdb=" C TRP A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CB GLU A 95 " pdb=" CG GLU A 95 " pdb=" CD GLU A 95 " pdb=" OE1 GLU A 95 " ideal model delta sinusoidal sigma weight residual 0.00 -87.92 87.92 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 686 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.086: 90 0.086 - 0.171: 42 0.171 - 0.256: 12 0.256 - 0.341: 3 0.341 - 0.425: 2 Chirality restraints: 149 Sorted by residual: chirality pdb=" CA GLN A 59 " pdb=" N GLN A 59 " pdb=" C GLN A 59 " pdb=" CB GLN A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL A 106 " pdb=" CA VAL A 106 " pdb=" CG1 VAL A 106 " pdb=" CG2 VAL A 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 146 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " -0.056 2.00e-02 2.50e+03 2.79e-02 2.34e+01 pdb=" CG TYR A 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR A 92 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR A 92 " 0.010 2.00e-02 2.50e+03 pdb=" HE1 TYR A 92 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 92 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " -0.058 2.00e-02 2.50e+03 2.67e-02 2.14e+01 pdb=" CG TYR A 24 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR A 24 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 TYR A 24 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 24 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 24 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 82 " -0.011 2.00e-02 2.50e+03 3.41e-02 1.75e+01 pdb=" CG ASN A 82 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 82 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 82 " -0.006 2.00e-02 2.50e+03 pdb="HD21 ASN A 82 " -0.028 2.00e-02 2.50e+03 pdb="HD22 ASN A 82 " 0.044 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 359 2.05 - 2.69: 4686 2.69 - 3.32: 10370 3.32 - 3.96: 15832 3.96 - 4.60: 23006 Nonbonded interactions: 54253 Sorted by model distance: nonbonded pdb=" H2 GLY A 0 " pdb=" O HOH A 297 " model vdw 1.409 1.850 nonbonded pdb=" HZ3 LYS A 19 " pdb=" HG SER A 43 " model vdw sym.op. 1.424 2.100 x+1,y,z nonbonded pdb=" HZ3 LYS A 19 " pdb=" OG SER A 43 " model vdw sym.op. 1.541 1.850 x+1,y,z nonbonded pdb=" HE2 HIS A 91 " pdb=" O HOH A 305 " model vdw sym.op. 1.583 1.850 x-1/2,-y+1/2,-z nonbonded pdb=" HZ1 LYS A 15 " pdb=" O HOH A 147 " model vdw 1.671 1.850 ... (remaining 54248 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 3 15.96 2 O 414 7.97 2 N 182 6.98 3 C 606 5.99 3 H 1454 1.00 3 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 = 2659 n_use_u_iso = 1454 n_use_u_aniso = 1205 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 = 2659 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2659 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1454 aniso = 1205) 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 = "2PND_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1454 occupancy sum: 1454.00 (% of total atoms 54.68) Rotatable: count: 262 occupancy sum: 262.00 (% of total atoms 9.85) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.97 - 31.40 A, n_refl.=51757 (all), 4.99 % free)------------| | | | r_work= 0.2059 r_free= 0.2353 coordinate error (max.-lik. estimate): 0.02 A | | | | normalized target function (ml) (work): 4.233637 | | target function (ml) not normalized (work): 208193.338507 | | target function (ml) not normalized (free): 11000.363199 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 31.40 - 2.54 0.97 3313 162 0.2027 0.2479 5.7744 5.9549| | 2: 2.54 - 2.02 1.00 3248 160 0.1632 0.1856 5.2206 5.2448| | 3: 2.02 - 1.76 1.00 3218 165 0.1605 0.1876 4.624 4.704| | 4: 1.76 - 1.60 1.00 3176 168 0.1773 0.1985 4.3456 4.2939| | 5: 1.60 - 1.49 1.00 3181 169 0.1823 0.2219 4.1717 4.2464| | 6: 1.49 - 1.40 1.00 3172 162 0.1972 0.1985 4.072 4.1002| | 7: 1.40 - 1.33 1.00 3173 148 0.2115 0.2478 4.0352 4.1398| | 8: 1.33 - 1.27 1.00 3130 173 0.2291 0.2553 4.0273 4.1149| | 9: 1.27 - 1.22 1.00 3146 172 0.2423 0.2907 4.0513 4.1584| | 10: 1.22 - 1.18 1.00 3148 170 0.2484 0.2581 4.0406 4.0769| | 11: 1.18 - 1.14 1.00 3120 176 0.2545 0.2879 4.0216 4.0209| | 12: 1.14 - 1.11 0.99 3080 163 0.2783 0.2880 4.0367 4.0262| | 13: 1.11 - 1.08 0.93 2860 151 0.2906 0.3116 3.9869 4.0137| | 14: 1.08 - 1.06 0.83 2615 151 0.2766 0.2834 3.8179 3.7797| | 15: 1.06 - 1.03 0.73 2281 103 0.2761 0.2992 3.6858 3.7849| | 16: 1.03 - 1.01 0.53 1632 92 0.2685 0.3002 3.5535 3.5816| | 17: 1.01 - 0.99 0.36 1118 60 0.2693 0.2773 3.44 3.3609| | 18: 0.99 - 0.97 0.18 565 36 0.2961 0.3345 3.4418 3.4006| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 31.40 - 2.54 3313 162 0.75 30.41 0.96 0.96 23165.28| | 2: 2.54 - 2.02 3248 160 0.78 28.52 1.02 1.06 9318.85| | 3: 2.02 - 1.76 3218 165 0.88 17.99 1.05 1.12 1884.07| | 4: 1.76 - 1.60 3176 168 0.89 17.31 1.04 1.15 945.86| | 5: 1.60 - 1.49 3181 169 0.88 18.15 1.06 1.15 689.98| | 6: 1.49 - 1.40 3172 162 0.87 19.67 1.06 1.14 566.49| | 7: 1.40 - 1.33 3173 148 0.87 20.46 1.08 1.16 509.83| | 8: 1.33 - 1.27 3130 173 0.86 21.13 1.08 1.16 486.96| | 9: 1.27 - 1.22 3146 172 0.84 22.77 1.09 1.17 490.19| | 10: 1.22 - 1.18 3148 170 0.83 24.01 1.09 1.13 484.71| | 11: 1.18 - 1.14 3120 176 0.83 24.13 1.07 1.13 474.02| | 12: 1.14 - 1.11 3080 163 0.81 26.10 1.09 1.13 452.23| | 13: 1.11 - 1.08 2860 151 0.78 28.45 1.09 1.13 431.51| | 14: 1.08 - 1.06 2615 151 0.76 30.78 1.11 1.13 399.25| | 15: 1.06 - 1.03 2281 103 0.75 31.94 1.12 1.11 344.48| | 16: 1.03 - 1.01 1632 92 0.76 30.49 1.16 1.15 280.95| | 17: 1.01 - 0.99 1118 60 0.79 28.38 1.17 1.17 208.01| | 18: 0.99 - 0.97 565 36 0.83 24.22 1.18 1.18 142.77| |alpha: min = 0.96 max = 1.18 mean = 1.12| |beta: min = 142.77 max = 23165.28 mean = 2704.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.98 mean = 24.20| |phase err.(test): min = 0.00 max = 89.83 mean = 24.28| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.072 988 Z= 0.705 Angle : 1.242 5.488 1338 Z= 0.762 Chirality : 0.115 0.425 149 Planarity : 0.009 0.044 171 Dihedral : 15.038 87.924 376 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.92 % Allowed : 3.67 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.80), residues: 117 helix: None (None), residues: 0 sheet: 1.22 (0.71), residues: 55 loop : 0.22 (0.84), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 31 TYR 0.043 0.016 TYR A 92 PHE 0.014 0.008 PHE A 49 TRP 0.023 0.010 TRP A 37 HIS 0.013 0.005 HIS A 91 Individual atomic B min max mean iso aniso Overall: 4.61 83.25 12.44 2.08 0 1205 Protein: 4.61 37.52 9.56 2.08 0 968 Water: 6.13 83.25 24.19 N/A 0 237 Chain A: 4.61 83.25 12.44 N/A 0 1205 Histogram: Values Number of atoms 4.61 - 12.48 843 12.48 - 20.34 178 20.34 - 28.20 89 28.20 - 36.07 57 36.07 - 43.93 14 43.93 - 51.79 9 51.79 - 59.66 8 59.66 - 67.52 2 67.52 - 75.38 3 75.38 - 83.25 2 |-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: 0.97 - 31.40 A, n_refl.=51757 (all), 4.99 % free)------------| | | | r_work= 0.2059 r_free= 0.2353 coordinate error (max.-lik. estimate): 0.02 A | | | | normalized target function (ml) (work): 4.233637 | | target function (ml) not normalized (work): 208193.338507 | | target function (ml) not normalized (free): 11000.363199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2072 0.2059 0.2353 n_refl.: 51757 re-set all scales: r(all,work,free)=0.2072 0.2059 0.2353 n_refl.: 51757 remove outliers: r(all,work,free)=0.2072 0.2059 0.2353 n_refl.: 51754 overall B=-0.55 to atoms: r(all,work,free)=0.2020 0.2008 0.2287 n_refl.: 51754 bulk-solvent and scaling: r(all,work,free)=0.1471 0.1465 0.1594 n_refl.: 51754 remove outliers: r(all,work,free)=0.1471 0.1465 0.1594 n_refl.: 51752 ======================== 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 31.404-8.345 81.30 92 8 0.3217 203.210 184.591 0.954 1.010 0.491 8.232-6.663 94.34 95 5 0.2796 212.307 203.967 0.920 1.010 0.453 6.647-5.377 96.24 173 6 0.2343 246.089 234.513 0.982 1.010 0.445 5.365-4.336 90.25 312 12 0.1816 313.119 301.471 1.014 1.009 0.443 4.332-3.500 96.43 585 36 0.1573 340.596 334.654 0.983 1.008 0.205 3.499-2.826 99.83 1156 52 0.1572 271.876 265.583 0.965 1.006 0.152 2.825-2.282 100.00 2146 114 0.1635 188.375 184.791 0.968 1.003 0.000 2.281-1.842 100.00 4019 190 0.1325 150.633 148.702 0.989 0.999 0.000 1.842-1.488 100.00 7536 401 0.1282 83.766 82.356 0.994 0.991 0.000 1.488-1.201 100.00 14170 731 0.1264 53.989 53.029 1.005 0.979 0.000 1.201-0.970 71.03 18887 1026 0.1603 37.460 36.942 0.950 1.042 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.0799 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1464 r_free=0.1593 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 r_work=0.1463 r_free=0.1593 ========================= Local real-space refinement ========================= Before: r_work=0.1463 r_free=0.1593 28 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.090 revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 1.4700 time to fit residues: 41.8147 After: r_work=0.1489 r_free=0.1651 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.237340 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 212.567042 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 0.1783 0.1900 0.0117 0.003 0.6 2.6 0.0 0.9 0 0.125 0.1731 0.1860 0.0129 0.003 0.6 2.1 0.0 0.9 0 0.250 0.1671 0.1818 0.0147 0.003 0.6 2.6 0.0 0.9 0 0.500 0.1612 0.1779 0.0167 0.004 0.6 2.1 0.0 0.9 0 1.000 0.1578 0.1787 0.0209 0.005 0.7 2.6 0.0 0.9 0 2.000 0.1554 0.1784 0.0229 0.006 0.8 2.6 0.0 0.9 0 3.000 0.1535 0.1773 0.0238 0.007 0.8 2.6 0.0 0.9 0 4.000 0.1520 0.1758 0.0238 0.008 0.9 3.1 0.0 0.9 0 5.000 0.1514 0.1759 0.0245 0.009 0.9 3.6 0.0 0.9 0 6.000 0.1512 0.1761 0.0249 0.010 1.0 4.6 0.0 0.9 0 7.000 0.1503 0.1756 0.0253 0.011 1.0 5.1 0.0 0.9 0 8.000 0.1498 0.1758 0.0259 0.011 1.0 5.1 0.0 0.9 0 9.000 0.1493 0.1756 0.0263 0.012 1.1 4.6 0.0 0.9 0 10.000 0.1510 0.1754 0.0244 0.009 1.0 4.1 0.0 0.9 0 6.619 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1510 0.1754 0.0244 0.009 1.0 4.1 0.0 0.9 0 6.619 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1510 r_free=0.1754 33 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.126 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.0876 After: r_work=0.1510 r_free=0.1754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.10 17.54 2.44 1.322 13.216 212.567 0.027 15.10 17.54 2.44 1.322 13.216 6.377 0.027 15.06 17.25 2.19 1.118 13.215 26.571 0.027 14.36 17.10 2.73 5.234 14.541 106.284 0.022 13.62 16.75 3.13 4.144 14.288 212.567 0.020 13.24 16.45 3.21 4.635 14.455 318.851 0.019 13.14 16.55 3.42 4.407 14.427 425.134 0.018 13.09 16.58 3.49 4.774 14.534 531.418 0.018 13.05 16.57 3.52 4.757 14.535 637.701 0.018 12.85 16.44 3.58 4.295 14.399 743.985 0.018 12.84 16.54 3.70 4.632 14.508 850.268 0.017 12.80 16.50 3.70 4.730 14.539 956.552 0.017 12.78 16.44 3.67 4.087 14.343 1062.835 0.017 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 743.985 Accepted refinement result: 12.85 16.44 3.58 4.295 14.399 743.985 0.018 Individual atomic B min max mean iso aniso Overall: 3.70 84.80 14.50 2.30 0 1205 Protein: 3.70 44.49 10.90 2.30 0 968 Water: 5.60 84.80 29.22 N/A 0 237 Chain A: 3.70 84.80 14.50 N/A 0 1205 Histogram: Values Number of atoms 3.70 - 11.81 742 11.81 - 19.92 173 19.92 - 28.03 107 28.03 - 36.14 88 36.14 - 44.25 66 44.25 - 52.36 18 52.36 - 60.47 4 60.47 - 68.58 2 68.58 - 76.69 1 76.69 - 84.80 4 =========================== Idealize ADP of riding H ========================== r_work=0.1286 r_free=0.1644 r_work=0.1278 r_free=0.1634 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.97 - 31.40 A, n_refl.=51752 (all), 4.99 % free)------------| | | | r_work= 0.1278 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ls_wunit_k1) (work): 0.017293 | | target function (ls_wunit_k1) not normalized (work): 850.320874 | | target function (ls_wunit_k1) not normalized (free): 87.192337 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1634 n_refl.: 51752 re-set all scales: r(all,work,free)=0.1832 0.1811 0.2252 n_refl.: 51752 remove outliers: r(all,work,free)=0.1832 0.1811 0.2252 n_refl.: 51752 overall B=0.05 to atoms: r(all,work,free)=0.1834 0.1813 0.2256 n_refl.: 51752 bulk-solvent and scaling: r(all,work,free)=0.1284 0.1267 0.1620 n_refl.: 51752 remove outliers: r(all,work,free)=0.1284 0.1267 0.1620 n_refl.: 51752 ======================== 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 31.404-8.345 81.30 92 8 0.3286 174.280 162.237 0.962 0.965 0.480 8.232-6.663 94.34 95 5 0.2232 182.082 177.247 0.927 0.965 0.418 6.647-5.377 96.24 173 6 0.1897 211.054 206.087 0.986 0.965 0.400 5.365-4.336 90.25 312 12 0.1188 268.541 264.438 1.020 0.964 0.370 4.332-3.500 96.43 585 36 0.0934 292.107 290.609 1.006 0.963 0.149 3.499-2.826 99.83 1156 52 0.0937 233.170 231.033 1.005 0.962 0.120 2.825-2.282 100.00 2146 114 0.1051 161.557 159.893 1.019 0.959 0.000 2.281-1.842 100.00 4019 190 0.1023 129.188 128.154 1.042 0.956 0.000 1.842-1.488 100.00 7536 401 0.1241 71.841 70.840 1.026 0.950 0.000 1.488-1.201 100.00 14170 731 0.1379 46.303 45.389 1.037 0.940 0.000 1.201-0.970 71.03 18887 1026 0.1632 32.127 31.715 0.972 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=0.0069 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1267 r_free=0.1620 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 82 ASN A 91 HIS Total number of N/Q/H flips: 3 r_work=0.1277 r_free=0.1630 ========================= Local real-space refinement ========================= Before: r_work=0.1277 r_free=0.1630 17 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.086 revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.8628 time to fit residues: 32.0796 After: r_work=0.1281 r_free=0.1637 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.302875 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 298.803559 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 0.1605 0.1886 0.0281 0.002 0.5 3.1 0.0 0.0 0 0.125 0.1515 0.1815 0.0300 0.002 0.5 3.1 0.0 0.0 0 0.250 0.1443 0.1763 0.0319 0.002 0.6 2.6 0.0 0.0 0 0.500 0.1370 0.1706 0.0336 0.003 0.6 2.6 0.0 0.0 0 1.000 0.1312 0.1665 0.0353 0.004 0.7 2.6 0.0 0.0 0 2.000 0.1286 0.1647 0.0361 0.005 0.7 3.6 0.0 0.0 0 3.000 0.1272 0.1639 0.0368 0.006 0.8 3.6 0.0 0.0 0 4.000 0.1263 0.1636 0.0373 0.007 0.8 3.6 0.0 0.0 0 5.000 0.1257 0.1634 0.0377 0.007 0.9 3.6 0.0 0.0 0 6.000 0.1252 0.1636 0.0384 0.008 0.9 3.6 0.0 0.9 0 7.000 0.1250 0.1636 0.0386 0.009 0.9 3.6 0.0 0.9 0 8.000 0.1246 0.1634 0.0388 0.009 1.0 3.1 0.0 0.9 0 9.000 0.1243 0.1635 0.0392 0.010 1.0 3.6 0.0 0.9 0 10.000 0.1251 0.1636 0.0385 0.009 0.9 3.6 0.0 0.9 0 7.651 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1634 0.0377 0.007 0.9 3.6 0.0 0.0 0 6.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1257 r_free=0.1634 15 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.094 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0863 After: r_work=0.1257 r_free=0.1634 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 16.34 3.77 3.721 18.127 298.804 0.017 12.57 16.34 3.77 3.721 18.127 8.964 0.017 12.57 16.34 3.77 3.721 18.127 37.350 0.017 12.57 16.34 3.77 3.721 18.127 149.402 0.017 12.52 16.24 3.72 3.712 18.131 298.804 0.017 12.44 16.17 3.72 3.512 18.153 448.205 0.016 12.33 16.13 3.80 3.231 18.284 597.607 0.016 12.24 16.10 3.86 3.148 18.337 747.009 0.016 12.18 16.11 3.93 3.107 18.383 896.411 0.015 12.12 16.11 4.00 3.143 18.381 1045.812 0.015 12.08 16.13 4.05 3.070 18.449 1195.214 0.015 12.05 16.14 4.09 3.193 18.401 1344.616 0.015 12.02 16.15 4.13 3.077 18.505 1494.018 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 747.009 Accepted refinement result: 12.24 16.10 3.86 3.148 18.337 747.009 0.016 Individual atomic B min max mean iso aniso Overall: 3.75 87.12 15.01 2.29 0 1205 Protein: 3.75 49.24 11.03 2.29 0 968 Water: 5.73 87.12 31.28 N/A 0 237 Chain A: 3.75 87.12 15.01 N/A 0 1205 Histogram: Values Number of atoms 3.75 - 12.09 759 12.09 - 20.43 169 20.43 - 28.76 91 28.76 - 37.10 71 37.10 - 45.44 70 45.44 - 53.78 28 53.78 - 62.11 9 62.11 - 70.45 2 70.45 - 78.79 2 78.79 - 87.12 4 =========================== Idealize ADP of riding H ========================== r_work=0.1225 r_free=0.1610 r_work=0.1224 r_free=0.1609 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.97 - 31.40 A, n_refl.=51752 (all), 4.99 % free)------------| | | | r_work= 0.1224 r_free= 0.1609 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.015695 | | target function (ls_wunit_k1) not normalized (work): 771.749823 | | target function (ls_wunit_k1) not normalized (free): 82.617962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1224 0.1609 n_refl.: 51752 re-set all scales: r(all,work,free)=0.1794 0.1771 0.2244 n_refl.: 51752 remove outliers: r(all,work,free)=0.1794 0.1771 0.2244 n_refl.: 51752 overall B=-0.00 to atoms: r(all,work,free)=0.1794 0.1771 0.2243 n_refl.: 51752 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1224 0.1608 n_refl.: 51752 remove outliers: r(all,work,free)=0.1243 0.1224 0.1608 n_refl.: 51752 ======================== 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 31.404-8.345 81.30 92 8 0.3319 174.280 163.163 0.959 0.971 0.480 8.232-6.663 94.34 95 5 0.2034 182.082 178.906 0.916 0.971 0.407 6.647-5.377 96.24 173 6 0.1687 211.054 207.564 0.978 0.971 0.377 5.365-4.336 90.25 312 12 0.1063 268.541 265.562 1.006 0.970 0.300 4.332-3.500 96.43 585 36 0.0882 292.107 291.229 0.995 0.969 0.124 3.499-2.826 99.83 1156 52 0.0910 233.170 231.319 1.000 0.968 0.110 2.825-2.282 100.00 2146 114 0.1012 161.557 160.232 1.014 0.965 0.000 2.281-1.842 100.00 4019 190 0.1003 129.188 128.382 1.037 0.962 0.000 1.842-1.488 100.00 7536 401 0.1192 71.841 70.901 1.020 0.955 0.000 1.488-1.201 100.00 14170 731 0.1344 46.303 45.428 1.034 0.945 0.000 1.201-0.970 71.03 18887 1026 0.1584 32.127 31.745 0.970 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.0056 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1608 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN Total number of N/Q/H flips: 1 r_work=0.1225 r_free=0.1609 ========================= Local real-space refinement ========================= Before: r_work=0.1225 r_free=0.1609 17 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.184 revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 3.9292 time to fit residues: 67.5900 After: r_work=0.1238 r_free=0.1620 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519542 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 9.374849 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 0.1307 0.1636 0.0329 0.003 0.6 3.1 0.0 0.0 0 0.076 0.1251 0.1587 0.0336 0.004 0.7 3.1 0.0 0.0 0 0.228 0.1227 0.1569 0.0342 0.006 0.9 4.1 0.0 0.0 0 0.456 0.1220 0.1561 0.0341 0.007 0.9 3.6 0.0 0.9 0 0.684 0.1215 0.1556 0.0341 0.008 1.0 3.1 0.0 0.9 0 0.912 0.1209 0.1551 0.0342 0.008 1.0 3.1 0.0 0.9 0 1.140 0.1206 0.1550 0.0344 0.009 1.0 3.6 0.0 0.9 0 1.368 0.1205 0.1550 0.0345 0.010 1.1 3.6 0.0 0.9 0 1.596 0.1218 0.1559 0.0341 0.007 0.9 3.1 0.0 0.9 0 0.760 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1550 0.0344 0.009 1.0 3.6 0.0 0.9 0 1.368 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1206 r_free=0.1550 18 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.170 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1279 After: r_work=0.1206 r_free=0.1550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 15.50 3.44 3.911 18.784 9.375 3.592 12.13 15.41 3.28 3.904 18.785 0.281 3.592 12.15 15.36 3.21 3.903 18.787 1.172 3.587 12.54 15.17 2.64 3.948 18.775 4.687 3.573 12.57 15.08 2.51 4.303 18.615 9.375 3.547 12.38 14.91 2.53 4.379 18.583 14.062 3.526 12.29 14.80 2.51 4.445 18.563 18.750 3.514 12.19 14.77 2.58 4.367 18.597 23.437 3.510 12.10 14.73 2.63 4.337 18.613 28.125 3.506 12.04 14.72 2.67 4.315 18.624 32.812 3.503 12.03 14.71 2.69 4.319 18.628 37.499 3.501 12.00 14.69 2.69 4.327 18.627 42.187 3.499 11.97 14.69 2.72 4.296 18.645 46.874 3.498 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 46.874 Accepted refinement result: 11.97 14.69 2.72 4.296 18.645 46.874 3.498 Individual atomic B min max mean iso aniso Overall: 3.90 87.21 14.70 2.14 0 1205 Protein: 3.90 47.00 10.84 2.14 0 968 Water: 5.98 87.21 30.48 N/A 0 237 Chain A: 3.90 87.21 14.70 N/A 0 1205 Histogram: Values Number of atoms 3.90 - 12.23 776 12.23 - 20.56 175 20.56 - 28.89 85 28.89 - 37.22 56 37.22 - 45.56 70 45.56 - 53.89 26 53.89 - 62.22 9 62.22 - 70.55 2 70.55 - 78.88 2 78.88 - 87.21 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1470 r_work=0.1201 r_free=0.1472 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.97 - 31.40 A, n_refl.=51752 (all), 4.99 % free)------------| | | | r_work= 0.1201 r_free= 0.1472 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 3.499775 | | target function (ml) not normalized (work): 172087.432637 | | target function (ml) not normalized (free): 9336.195763 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1201 0.1472 n_refl.: 51752 re-set all scales: r(all,work,free)=0.1751 0.1733 0.2131 n_refl.: 51752 remove outliers: r(all,work,free)=0.1751 0.1733 0.2131 n_refl.: 51752 overall B=-0.05 to atoms: r(all,work,free)=0.1746 0.1728 0.2124 n_refl.: 51752 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1188 0.1468 n_refl.: 51752 remove outliers: r(all,work,free)=0.1201 0.1187 0.1468 n_refl.: 51750 ======================== 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 31.404-8.345 81.30 92 8 0.3435 174.280 162.039 0.985 0.952 0.470 8.232-6.663 94.34 95 5 0.2399 182.082 176.796 0.930 0.952 0.404 6.647-5.377 96.24 173 6 0.1960 211.054 204.993 0.997 0.952 0.380 5.365-4.336 90.25 312 12 0.1313 268.541 262.695 1.028 0.950 0.320 4.332-3.500 96.43 585 36 0.1160 292.107 288.976 1.018 0.950 0.160 3.499-2.826 99.83 1156 52 0.1172 233.170 229.678 1.014 0.948 0.140 2.825-2.282 100.00 2146 114 0.1273 161.557 159.179 1.032 0.945 0.000 2.281-1.842 100.00 4019 190 0.1121 129.188 127.807 1.058 0.941 0.000 1.842-1.488 100.00 7536 401 0.1107 71.841 70.783 1.054 0.934 0.000 1.488-1.201 100.00 14170 731 0.1058 46.303 45.540 1.081 0.923 0.000 1.201-0.970 71.02 18885 1026 0.1263 32.125 31.822 1.026 0.977 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9548 b_overall=-0.1670 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1468 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 r_work=0.1188 r_free=0.1468 ========================= Local real-space refinement ========================= Before: r_work=0.1188 r_free=0.1468 33 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.094 revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 2.0165 time to fit residues: 67.5897 After: r_work=0.1229 r_free=0.1504 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.292818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 5.913214 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 0.1282 0.1533 0.0252 0.003 0.7 2.6 0.0 0.0 0 0.065 0.1233 0.1491 0.0257 0.005 0.8 2.1 0.0 0.9 0 0.194 0.1212 0.1473 0.0262 0.006 0.9 2.6 0.0 0.9 0 0.388 0.1203 0.1465 0.0262 0.007 0.9 2.1 0.0 0.9 0 0.582 0.1198 0.1461 0.0263 0.008 1.0 2.1 0.0 0.9 0 0.776 0.1193 0.1459 0.0266 0.009 1.0 3.1 0.0 0.9 0 0.970 0.1191 0.1458 0.0267 0.009 1.0 3.1 0.0 0.9 0 1.164 0.1188 0.1457 0.0269 0.010 1.1 3.1 0.0 0.9 0 1.357 0.1201 0.1463 0.0262 0.007 0.9 1.5 0.0 0.9 0 0.646 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1188 0.1457 0.0269 0.010 1.1 3.1 0.0 0.9 0 1.357 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1188 r_free=0.1457 34 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.122 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.0885 After: r_work=0.1188 r_free=0.1457 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 14.57 2.69 3.810 18.299 5.913 3.492 11.88 14.57 2.69 3.810 18.299 0.177 3.492 11.88 14.56 2.68 3.810 18.299 0.739 3.492 11.91 14.52 2.61 3.806 18.304 2.957 3.492 11.91 14.52 2.61 3.805 18.308 5.913 3.491 11.90 14.52 2.61 3.806 18.310 8.870 3.490 11.92 14.53 2.60 3.805 18.316 11.826 3.490 11.95 14.53 2.57 3.814 18.314 14.783 3.489 11.97 14.51 2.55 3.835 18.304 17.740 3.487 11.98 14.55 2.57 3.908 18.268 20.696 3.486 11.97 14.51 2.54 3.974 18.241 23.653 3.483 11.98 14.49 2.51 4.099 18.189 26.609 3.478 11.94 14.46 2.52 4.075 18.202 29.566 3.475 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 29.566 Accepted refinement result: 11.94 14.46 2.52 4.075 18.202 29.566 3.475 Individual atomic B min max mean iso aniso Overall: 4.04 87.25 14.44 1.95 0 1205 Protein: 4.04 45.29 10.64 1.95 0 968 Water: 6.01 87.25 29.98 N/A 0 237 Chain A: 4.04 87.25 14.44 N/A 0 1205 Histogram: Values Number of atoms 4.04 - 12.36 787 12.36 - 20.68 176 20.68 - 29.00 79 29.00 - 37.32 58 37.32 - 45.64 66 45.64 - 53.96 22 53.96 - 62.28 9 62.28 - 70.60 2 70.60 - 78.92 2 78.92 - 87.25 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1446 r_work=0.1195 r_free=0.1447 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.97 - 31.40 A, n_refl.=51750 (all), 4.99 % free)------------| | | | r_work= 0.1195 r_free= 0.1447 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 3.475911 | | target function (ml) not normalized (work): 170907.082592 | | target function (ml) not normalized (free): 9270.863594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1195 0.1447 n_refl.: 51750 re-set all scales: r(all,work,free)=0.1729 0.1711 0.2105 n_refl.: 51750 remove outliers: r(all,work,free)=0.1729 0.1711 0.2105 n_refl.: 51750 overall B=-0.14 to atoms: r(all,work,free)=0.1711 0.1694 0.2081 n_refl.: 51750 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1201 0.1458 n_refl.: 51750 remove outliers: r(all,work,free)=0.1214 0.1201 0.1458 n_refl.: 51750 ======================== 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 31.404-8.345 81.30 92 8 0.3359 174.280 162.075 0.949 1.010 0.470 8.232-6.663 94.34 95 5 0.2479 182.082 176.425 0.885 1.010 0.417 6.647-5.377 96.24 173 6 0.2046 211.054 204.806 0.947 1.009 0.394 5.365-4.336 90.25 312 12 0.1404 268.541 262.404 0.977 1.008 0.331 4.332-3.500 96.43 585 36 0.1223 292.107 289.287 0.967 1.006 0.160 3.499-2.826 99.83 1156 52 0.1230 233.170 229.943 0.962 1.003 0.141 2.825-2.282 100.00 2146 114 0.1345 161.557 159.138 0.978 0.999 0.000 2.281-1.842 100.00 4019 190 0.1152 129.188 127.786 1.006 0.992 0.000 1.842-1.488 100.00 7536 401 0.1095 71.841 70.771 1.008 0.980 0.000 1.488-1.201 100.00 14170 731 0.1009 46.303 45.500 1.037 0.963 0.000 1.201-0.970 71.02 18885 1026 0.1269 32.125 31.738 0.994 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.1836 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1201 r_free=0.1458 After: r_work=0.1203 r_free=0.1458 ================================== NQH flips ================================== r_work=0.1203 r_free=0.1458 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 85 GLN Total number of N/Q/H flips: 2 r_work=0.1204 r_free=0.1462 ========================= Local real-space refinement ========================= Before: r_work=0.1204 r_free=0.1462 37 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.124 revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 1.8037 time to fit residues: 67.7817 After: r_work=0.1237 r_free=0.1491 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.282886 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 7.974716 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 0.1299 0.1531 0.0232 0.005 0.8 5.6 0.0 0.0 0 0.064 0.1244 0.1487 0.0243 0.006 0.8 6.2 0.0 0.9 0 0.192 0.1224 0.1476 0.0252 0.007 0.9 5.6 0.0 0.9 0 0.385 0.1218 0.1471 0.0253 0.007 1.0 5.1 0.0 0.9 0 0.577 0.1212 0.1467 0.0256 0.008 1.0 4.1 0.0 0.9 0 0.770 0.1208 0.1467 0.0258 0.009 1.1 4.1 0.0 0.9 0 0.962 0.1206 0.1466 0.0260 0.010 1.1 4.1 0.0 0.9 0 1.155 0.1204 0.1464 0.0260 0.011 1.1 4.1 0.0 0.9 0 1.347 0.1216 0.1470 0.0254 0.008 1.0 5.1 0.0 0.9 0 0.641 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1464 0.0260 0.011 1.1 4.1 0.0 0.9 0 1.347 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1204 r_free=0.1464 37 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.106 outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.1559 After: r_work=0.1204 r_free=0.1464 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 14.64 2.60 3.711 17.861 7.975 3.487 12.04 14.64 2.60 3.711 17.861 0.239 3.487 12.04 14.64 2.60 3.710 17.861 0.997 3.488 12.06 14.62 2.55 3.707 17.868 3.987 3.488 12.13 14.63 2.51 3.703 17.882 7.975 3.489 12.11 14.63 2.52 3.706 17.881 11.962 3.488 12.11 14.62 2.52 3.710 17.881 15.949 3.486 12.16 14.66 2.50 3.788 17.849 19.937 3.484 12.19 14.60 2.41 3.947 17.789 23.924 3.479 12.15 14.58 2.42 3.956 17.795 27.912 3.475 12.09 14.56 2.47 3.919 17.813 31.899 3.473 12.05 14.56 2.51 3.891 17.828 35.886 3.472 12.03 14.56 2.53 3.873 17.838 39.874 3.471 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 35.886 Accepted refinement result: 12.05 14.56 2.51 3.891 17.828 35.886 3.472 Individual atomic B min max mean iso aniso Overall: 4.00 87.19 14.23 1.95 0 1205 Protein: 4.00 43.80 10.49 1.95 0 968 Water: 5.99 87.19 29.48 N/A 0 237 Chain A: 4.00 87.19 14.23 N/A 0 1205 Histogram: Values Number of atoms 4.00 - 12.32 783 12.32 - 20.64 191 20.64 - 28.95 76 28.95 - 37.27 57 37.27 - 45.59 60 45.59 - 53.91 22 53.91 - 62.23 8 62.23 - 70.55 2 70.55 - 78.87 2 78.87 - 87.19 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1456 r_work=0.1206 r_free=0.1457 ----------X-ray data---------- |--(resolution: 0.97 - 31.40 A, n_refl.=51750 (all), 4.99 % free)------------| | | | r_work= 0.1206 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 3.472475 | | target function (ml) not normalized (work): 170738.137718 | | target function (ml) not normalized (free): 9281.290166 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 31.40 - 2.54 0.97 3313 162 0.1429 0.1765 5.1671 5.3331| | 2: 2.54 - 2.02 1.00 3248 160 0.1287 0.1444 4.6891 4.7479| | 3: 2.02 - 1.76 1.00 3218 165 0.1117 0.1382 4.1653 4.3194| | 4: 1.76 - 1.60 1.00 3176 168 0.1098 0.1398 3.799 3.9163| | 5: 1.60 - 1.49 1.00 3181 169 0.1044 0.1241 3.5585 3.647| | 6: 1.49 - 1.40 1.00 3172 162 0.1010 0.1134 3.3603 3.472| | 7: 1.40 - 1.33 1.00 3173 148 0.0980 0.1111 3.2421 3.4091| | 8: 1.33 - 1.27 1.00 3130 173 0.1001 0.1225 3.1691 3.317| | 9: 1.27 - 1.22 1.00 3146 172 0.0983 0.1244 3.0991 3.2631| | 10: 1.22 - 1.18 1.00 3148 170 0.1051 0.1337 3.0895 3.2968| | 11: 1.18 - 1.14 1.00 3120 176 0.1123 0.1395 3.0252 3.2153| | 12: 1.14 - 1.11 0.99 3078 163 0.1097 0.1274 2.968 3.0659| | 13: 1.11 - 1.08 0.93 2860 151 0.1115 0.1332 2.9798 3.077| | 14: 1.08 - 1.06 0.83 2613 151 0.1161 0.1608 2.9286 3.106| | 15: 1.06 - 1.03 0.73 2281 103 0.1353 0.1437 2.9332 3.0477| | 16: 1.03 - 1.01 0.53 1631 92 0.1707 0.2125 2.9933 3.225| | 17: 1.01 - 0.99 0.35 1117 60 0.2019 0.2758 2.9294 3.1528| | 18: 0.99 - 0.97 0.18 564 36 0.2403 0.2936 2.9541 3.0293| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 31.40 - 2.54 3313 162 0.89 16.19 1.00 0.99 5535.92| | 2: 2.54 - 2.02 3248 160 0.89 16.80 1.00 0.99 2531.23| | 3: 2.02 - 1.76 3218 165 0.92 13.08 1.00 1.00 796.57| | 4: 1.76 - 1.60 3176 168 0.93 12.17 1.00 1.00 378.10| | 5: 1.60 - 1.49 3181 169 0.94 11.51 1.01 1.01 235.11| | 6: 1.49 - 1.40 3172 162 0.93 11.63 1.02 1.01 166.76| | 7: 1.40 - 1.33 3173 148 0.94 11.34 1.02 1.01 132.43| | 8: 1.33 - 1.27 3130 173 0.95 10.63 1.01 1.01 108.68| | 9: 1.27 - 1.22 3146 172 0.94 10.83 1.00 1.00 94.59| | 10: 1.22 - 1.18 3148 170 0.94 10.88 1.03 1.00 84.31| | 11: 1.18 - 1.14 3120 176 0.94 10.88 1.06 1.02 79.30| | 12: 1.14 - 1.11 3078 163 0.94 11.23 1.05 1.04 73.43| | 13: 1.11 - 1.08 2860 151 0.94 11.65 1.03 1.06 66.82| | 14: 1.08 - 1.06 2613 151 0.94 12.29 1.00 1.03 59.93| | 15: 1.06 - 1.03 2281 103 0.94 12.73 0.95 1.00 56.22| | 16: 1.03 - 1.01 1631 92 0.94 13.34 0.91 0.97 57.28| | 17: 1.01 - 0.99 1117 60 0.92 15.26 0.88 0.91 59.23| | 18: 0.99 - 0.97 564 36 0.91 16.90 0.85 0.83 61.27| |alpha: min = 0.83 max = 1.06 mean = 1.01| |beta: min = 56.22 max = 5535.92 mean = 692.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 12.43| |phase err.(test): min = 0.00 max = 88.02 mean = 12.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1206 0.1457 n_refl.: 51750 re-set all scales: r(all,work,free)=0.1702 0.1683 0.2086 n_refl.: 51750 remove outliers: r(all,work,free)=0.1702 0.1683 0.2086 n_refl.: 51750 overall B=-0.07 to atoms: r(all,work,free)=0.1693 0.1675 0.2074 n_refl.: 51750 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1202 0.1459 n_refl.: 51750 remove outliers: r(all,work,free)=0.1215 0.1202 0.1459 n_refl.: 51750 ======================== 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 31.404-8.345 81.30 92 8 0.3372 174.280 162.203 0.950 1.009 0.470 8.232-6.663 94.34 95 5 0.2518 182.082 176.332 0.888 1.009 0.425 6.647-5.377 96.24 173 6 0.2088 211.054 205.308 0.948 1.009 0.406 5.365-4.336 90.25 312 12 0.1444 268.541 261.989 0.980 1.007 0.360 4.332-3.500 96.43 585 36 0.1259 292.107 289.151 0.966 1.005 0.170 3.499-2.826 99.83 1156 52 0.1263 233.170 229.680 0.962 1.003 0.160 2.825-2.282 100.00 2146 114 0.1388 161.557 159.018 0.978 0.998 0.000 2.281-1.842 100.00 4019 190 0.1169 129.188 127.726 1.008 0.992 0.000 1.842-1.488 100.00 7536 401 0.1093 71.841 70.770 1.014 0.980 0.000 1.488-1.201 100.00 14170 731 0.0981 46.303 45.531 1.045 0.963 0.000 1.201-0.970 71.02 18885 1026 0.1235 32.125 31.758 1.006 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.2377 ================= 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 : 0.2059 0.2353 0.013 1.242 4.6 83.2 12.4 711 0.000 1_bss: 0.1464 0.1593 0.013 1.242 4.1 82.7 11.9 711 0.000 1_settarget: 0.1464 0.1593 0.013 1.242 4.1 82.7 11.9 711 0.000 1_nqh: 0.1463 0.1593 0.013 1.242 4.1 82.7 11.9 711 0.006 1_realsrl: 0.1489 0.1651 0.013 1.242 4.1 82.7 11.9 711 0.049 1_weight: 0.1489 0.1651 0.013 1.242 4.1 82.7 11.9 711 0.049 1_xyzrec: 0.1510 0.1754 0.009 0.964 4.1 82.7 11.9 711 0.154 1_realsrl2: 0.1510 0.1754 0.009 0.964 4.1 82.7 11.9 711 0.154 1_adp: 0.1286 0.1644 0.009 0.964 3.7 84.8 14.5 711 0.154 1_regHadp: 0.1278 0.1634 0.009 0.964 3.7 84.8 14.5 711 0.154 2_bss: 0.1267 0.1620 0.009 0.964 3.7 84.9 14.5 711 0.154 2_settarget: 0.1267 0.1620 0.009 0.964 3.7 84.9 14.5 711 0.154 2_updatecdl: 0.1267 0.1620 0.009 0.968 3.7 84.9 14.5 711 0.154 2_nqh: 0.1277 0.1630 0.009 0.968 3.7 84.9 14.5 711 0.159 2_realsrl: 0.1281 0.1637 0.009 0.968 3.7 84.9 14.5 711 0.175 2_weight: 0.1281 0.1637 0.009 0.968 3.7 84.9 14.5 711 0.175 2_xyzrec: 0.1257 0.1634 0.007 0.870 3.7 84.9 14.5 711 0.184 2_realsrl2: 0.1257 0.1634 0.007 0.870 3.7 84.9 14.5 711 0.184 2_adp: 0.1225 0.1610 0.007 0.870 3.8 87.1 15.0 711 0.184 2_regHadp: 0.1224 0.1609 0.007 0.870 3.8 87.1 15.0 711 0.184 3_bss: 0.1224 0.1608 0.007 0.870 3.8 87.1 15.0 711 0.184 3_settarget: 0.1224 0.1608 0.007 0.870 3.8 87.1 15.0 711 0.184 3_updatecdl: 0.1224 0.1608 0.007 0.871 3.8 87.1 15.0 711 0.184 3_nqh: 0.1225 0.1609 0.007 0.871 3.8 87.1 15.0 711 0.180 3_realsrl: 0.1238 0.1620 0.007 0.871 3.8 87.1 15.0 711 0.197 3_weight: 0.1238 0.1620 0.007 0.871 3.8 87.1 15.0 711 0.197 3_xyzrec: 0.1206 0.1550 0.009 1.033 3.8 87.1 15.0 711 0.178 3_realsrl2: 0.1206 0.1550 0.009 1.033 3.8 87.1 15.0 711 0.178 3_adp: 0.1198 0.1470 0.009 1.033 3.9 87.2 14.7 711 0.178 3_regHadp: 0.1201 0.1472 0.009 1.033 3.9 87.2 14.7 711 0.178 4_bss: 0.1188 0.1468 0.009 1.033 3.9 87.2 14.7 711 0.178 4_settarget: 0.1188 0.1468 0.009 1.033 3.9 87.2 14.7 711 0.178 4_updatecdl: 0.1188 0.1468 0.009 1.035 3.9 87.2 14.7 711 0.178 4_nqh: 0.1188 0.1468 0.009 1.035 3.9 87.2 14.7 711 0.173 4_realsrl: 0.1229 0.1504 0.009 1.035 3.9 87.2 14.7 711 0.182 4_weight: 0.1229 0.1504 0.009 1.035 3.9 87.2 14.7 711 0.182 4_xyzrec: 0.1188 0.1457 0.010 1.075 3.9 87.2 14.7 711 0.178 4_realsrl2: 0.1188 0.1457 0.010 1.075 3.9 87.2 14.7 711 0.178 4_adp: 0.1194 0.1446 0.010 1.075 4.0 87.2 14.4 711 0.178 4_regHadp: 0.1195 0.1447 0.010 1.075 4.0 87.2 14.4 711 0.178 5_bss: 0.1201 0.1458 0.010 1.075 3.9 87.1 14.3 711 0.178 5_settarget: 0.1201 0.1458 0.010 1.075 3.9 87.1 14.3 711 0.178 5_updatecdl: 0.1201 0.1458 0.010 1.075 3.9 87.1 14.3 711 0.178 5_setrh: 0.1203 0.1458 0.010 1.075 3.9 87.1 14.3 711 0.177 5_nqh: 0.1204 0.1462 0.010 1.075 3.9 87.1 14.3 711 0.170 5_realsrl: 0.1237 0.1491 0.010 1.075 3.9 87.1 14.3 711 0.178 5_weight: 0.1237 0.1491 0.010 1.075 3.9 87.1 14.3 711 0.178 5_xyzrec: 0.1204 0.1464 0.011 1.128 3.9 87.1 14.3 711 0.176 5_realsrl2: 0.1204 0.1464 0.011 1.128 3.9 87.1 14.3 711 0.176 5_adp: 0.1206 0.1456 0.011 1.128 4.0 87.2 14.2 711 0.176 5_regHadp: 0.1206 0.1457 0.011 1.128 4.0 87.2 14.2 711 0.176 end: 0.1202 0.1459 0.011 1.128 3.9 87.1 14.2 711 0.176 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/2PND_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/2PND_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.6900 Refinement macro-cycles (run) : 1026.5000 Write final files (write_after_run_outputs) : 33.9300 Total : 1062.1200 Total CPU time: 17.94 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:24:51 PDT -0700 (1712791491.09 s) Start R-work = 0.1464, R-free = 0.1593 Final R-work = 0.1202, R-free = 0.1459 =============================================================================== Job complete usr+sys time: 1132.29 seconds wall clock time: 26 minutes 29.02 seconds (1589.02 seconds total)