Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 2FMA_complete.pdb Found miller_array, 2FMA.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 = "2FMA.mtz" } default_miller_array = "2FMA.mtz" model { file = "2FMA_complete.pdb" } default_model = "2FMA_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 Residue "A GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 1283 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 924 Classifications: {'peptide': 59} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 359 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1, 'water': 115} Link IDs: {None: 115} Time building chain proxies: 0.36, per 1000 atoms: 0.28 Number of scatterers: 1283 At special positions: 0 Unit cell: (31.289, 32.488, 50.088, 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 8 16.00 O 205 8.00 N 82 7.00 C 301 6.00 H 687 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 187 " distance=2.07 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 158 " - pdb=" SG CYS A 186 " distance=2.03 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: 0.56 Conformation dependent library (CDL) restraints added in 30.0 milliseconds Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.05: 331 1.05 - 1.24: 406 1.24 - 1.44: 190 1.44 - 1.64: 242 1.64 - 1.84: 10 Bond restraints: 1179 Sorted by residual: bond pdb=" C LEU A 189 " pdb=" OXT LEU A 189 " ideal model delta sigma weight residual 1.231 1.459 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" CG HIS A 151 " pdb=" CD2 HIS A 151 " ideal model delta sigma weight residual 1.354 1.263 0.091 1.10e-02 8.26e+03 6.85e+01 bond pdb=" N ALA A 154 " pdb=" H ALA A 154 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N TRP A 150 " pdb=" H TRP A 150 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER A 159 " pdb=" H SER A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 1174 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.10: 146 105.10 - 112.68: 1066 112.68 - 120.26: 311 120.26 - 127.84: 295 127.84 - 135.41: 9 Bond angle restraints: 1827 Sorted by residual: angle pdb=" CB ASN A 164 " pdb=" CG ASN A 164 " pdb=" ND2 ASN A 164 " ideal model delta sigma weight residual 116.40 107.56 8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" ND1 HIS A 147 " pdb=" CE1 HIS A 147 " pdb=" NE2 HIS A 147 " ideal model delta sigma weight residual 108.40 113.73 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CD2 HIS A 147 " pdb=" NE2 HIS A 147 " pdb=" CE1 HIS A 147 " ideal model delta sigma weight residual 109.00 103.70 5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" CA ILE A 176 " pdb=" C ILE A 176 " pdb=" N ASP A 177 " ideal model delta sigma weight residual 118.36 123.00 -4.64 9.70e-01 1.06e+00 2.29e+01 angle pdb=" CG LYS A 155 " pdb=" CD LYS A 155 " pdb=" CE LYS A 155 " ideal model delta sigma weight residual 111.30 121.92 -10.62 2.30e+00 1.89e-01 2.13e+01 ... (remaining 1822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.27: 313 18.27 - 36.55: 17 36.55 - 54.82: 8 54.82 - 73.09: 2 73.09 - 91.37: 1 Dihedral angle restraints: 341 sinusoidal: 242 harmonic: 99 Sorted by residual: dihedral pdb=" CA LEU A 171 " pdb=" C LEU A 171 " pdb=" N LEU A 172 " pdb=" CA LEU A 172 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA VAL A 182 " pdb=" C VAL A 182 " pdb=" N GLU A 183 " pdb=" CA GLU A 183 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CB GLU A 139 " pdb=" CG GLU A 139 " pdb=" CD GLU A 139 " pdb=" OE1 GLU A 139 " ideal model delta sinusoidal sigma weight residual 0.00 -91.37 91.37 1 3.00e+01 1.11e-03 1.09e+01 ... (remaining 338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 42 0.072 - 0.143: 19 0.143 - 0.214: 5 0.214 - 0.286: 3 0.286 - 0.357: 2 Chirality restraints: 71 Sorted by residual: chirality pdb=" CB ILE A 176 " pdb=" CA ILE A 176 " pdb=" CG1 ILE A 176 " pdb=" CG2 ILE A 176 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA HIS A 166 " pdb=" N HIS A 166 " pdb=" C HIS A 166 " pdb=" CB HIS A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA CYS A 174 " pdb=" N CYS A 174 " pdb=" C CYS A 174 " pdb=" CB CYS A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 68 not shown) Planarity restraints: 140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 140 " 0.107 9.50e-02 1.11e+02 4.03e-02 8.96e+00 pdb=" NE ARG A 140 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 140 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG A 140 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 140 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 140 " 0.029 2.00e-02 2.50e+03 pdb="HH12 ARG A 140 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 140 " 0.030 2.00e-02 2.50e+03 pdb="HH22 ARG A 140 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 167 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C ASP A 167 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP A 167 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 168 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 167 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" CG ASP A 167 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP A 167 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 167 " -0.016 2.00e-02 2.50e+03 ... (remaining 137 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 141 2.06 - 2.69: 2194 2.69 - 3.33: 4861 3.33 - 3.96: 7465 3.96 - 4.60: 11053 Nonbonded interactions: 25714 Sorted by model distance: nonbonded pdb=" HD1 HIS A 149 " pdb=" H GLY A 175 " model vdw sym.op. 1.421 2.100 x-1/2,-y+3/2,-z nonbonded pdb=" HB3 HIS A 147 " pdb=" HO3 GOL A1001 " model vdw 1.467 2.270 nonbonded pdb=" HZ2 LYS A 134 " pdb=" O HOH A2053 " model vdw 1.555 1.850 nonbonded pdb=" HB3 CYS A 158 " pdb=" HG1 THR A 163 " model vdw 1.645 2.270 nonbonded pdb=" HE2 HIS A 147 " pdb=" OH TYR A 168 " model vdw 1.668 1.850 ... (remaining 25709 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 8 15.96 3 O 205 7.98 3 N 82 6.98 3 C 301 5.99 3 H 687 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 = 1283 n_use_u_iso = 687 n_use_u_aniso = 596 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 = 1283 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (1283 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 687 aniso = 596) 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 = "2FMA_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 687 occupancy sum: 687.00 (% of total atoms 53.55) Rotatable: count: 115 occupancy sum: 115.00 (% of total atoms 8.96) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.85 - 13.85 A, n_refl.=41365 (all), 5.09 % free)------------| | | | r_work= 0.2824 r_free= 0.2935 coordinate error (max.-lik. estimate): 0.02 A | | | | normalized target function (ml) (work): 3.093710 | | target function (ml) not normalized (work): 121452.866395 | | target function (ml) not normalized (free): 6602.847946 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 13.85 - 2.09 0.93 2862 160 0.2489 0.2488 4.967 5.0164| | 2: 2.09 - 1.66 1.00 2960 151 0.1738 0.2148 4.2646 4.2991| | 3: 1.66 - 1.45 1.00 2919 174 0.2269 0.2206 3.6774 3.6869| | 4: 1.45 - 1.32 1.00 2902 152 0.2724 0.2986 3.4082 3.413| | 5: 1.32 - 1.23 1.00 2860 176 0.3065 0.3233 3.2287 3.3178| | 6: 1.22 - 1.15 1.00 2889 150 0.3447 0.3603 3.1148 3.2157| | 7: 1.15 - 1.10 0.99 2868 152 0.3700 0.3674 2.9954 2.9685| | 8: 1.10 - 1.05 0.98 2790 138 0.3811 0.3741 2.804 2.7957| | 9: 1.05 - 1.01 0.96 2764 151 0.3911 0.3986 2.6852 2.7041| | 10: 1.01 - 0.97 0.94 2704 147 0.3957 0.3891 2.5418 2.5718| | 11: 0.97 - 0.94 0.93 2647 138 0.4033 0.4260 2.4418 2.5091| | 12: 0.94 - 0.92 0.90 2578 133 0.4040 0.3894 2.3446 2.2904| | 13: 0.92 - 0.89 0.83 2357 124 0.4061 0.3997 2.2749 2.2601| | 14: 0.89 - 0.87 0.68 1922 102 0.4052 0.4142 2.2994 2.2863| | 15: 0.87 - 0.85 0.43 1236 59 0.4008 0.4049 2.2318 2.3179| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 13.85 - 2.09 2862 160 0.82 23.12 0.87 0.89 2865.50| | 2: 2.09 - 1.66 2960 151 0.83 22.78 1.12 1.10 1168.55| | 3: 1.66 - 1.45 2919 174 0.91 14.63 1.25 1.25 255.82| | 4: 1.45 - 1.32 2902 152 0.92 13.74 1.34 1.36 146.55| | 5: 1.32 - 1.23 2860 176 0.92 13.65 1.41 1.45 100.33| | 6: 1.22 - 1.15 2889 150 0.93 12.37 1.50 1.53 78.15| | 7: 1.15 - 1.10 2868 152 0.93 12.32 1.57 1.59 59.59| | 8: 1.10 - 1.05 2790 138 0.92 13.86 1.59 1.63 44.83| | 9: 1.05 - 1.01 2764 151 0.91 14.81 1.61 1.66 33.11| | 10: 1.01 - 0.97 2704 147 0.90 16.38 1.62 1.68 26.73| | 11: 0.97 - 0.94 2647 138 0.90 16.59 1.63 1.71 21.56| | 12: 0.94 - 0.92 2578 133 0.89 18.04 1.62 1.70 17.53| | 13: 0.92 - 0.89 2357 124 0.89 18.78 1.60 1.69 14.45| | 14: 0.89 - 0.87 1922 102 0.88 20.53 1.56 1.63 13.93| | 15: 0.87 - 0.85 1236 59 0.84 24.60 1.54 1.60 15.43| |alpha: min = 0.89 max = 1.71 mean = 1.48| |beta: min = 13.93 max = 2865.50 mean = 356.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.90| |phase err.(work): min = 0.00 max = 89.98 mean = 16.68| |phase err.(test): min = 0.00 max = 88.67 mean = 16.51| |-----------------------------------------------------------------------------| ----------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 : 0.032 0.228 492 Z= 2.030 Angle : 2.163 10.617 662 Z= 1.353 Chirality : 0.107 0.357 71 Planarity : 0.011 0.058 84 Dihedral : 13.389 91.368 179 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.51 (0.99), residues: 57 helix: 0.67 (1.14), residues: 17 sheet: -1.05 (0.95), residues: 20 loop : -2.32 (1.31), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.005 ARG A 140 TYR 0.001 0.000 TYR A 168 PHE 0.003 0.001 PHE A 184 TRP 0.000 0.000 TRP A 150 HIS 0.001 0.000 HIS A 149 Individual atomic B min max mean iso aniso Overall: 6.73 53.62 13.29 1.89 0 596 Protein: 6.73 29.36 10.37 1.89 0 475 Water: 8.37 53.62 25.28 N/A 0 115 Other: 11.01 16.27 14.10 N/A 0 6 Chain A: 6.73 53.62 13.29 N/A 0 596 Histogram: Values Number of atoms 6.73 - 11.42 366 11.42 - 16.11 104 16.11 - 20.80 41 20.80 - 25.48 25 25.48 - 30.17 28 30.17 - 34.86 15 34.86 - 39.55 8 39.55 - 44.24 3 44.24 - 48.93 1 48.93 - 53.62 5 |-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: 0.85 - 13.85 A, n_refl.=41365 (all), 5.09 % free)------------| | | | r_work= 0.2824 r_free= 0.2935 coordinate error (max.-lik. estimate): 0.02 A | | | | normalized target function (ml) (work): 3.093710 | | target function (ml) not normalized (work): 121452.866395 | | target function (ml) not normalized (free): 6602.847946 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2830 0.2824 0.2935 n_refl.: 41365 re-set all scales: r(all,work,free)=0.2830 0.2824 0.2935 n_refl.: 41365 remove outliers: r(all,work,free)=0.2829 0.2823 0.2935 n_refl.: 41358 overall B=-1.76 to atoms: r(all,work,free)=0.1969 0.1962 0.2092 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1591 0.1583 0.1741 n_refl.: 41358 remove outliers: r(all,work,free)=0.1591 0.1583 0.1741 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.3008 98.523 92.311 0.745 0.997 0.341 6.147-4.946 75.19 97 3 0.2363 123.492 117.917 0.780 1.000 0.335 4.941-3.976 72.22 154 15 0.2457 158.722 147.208 0.772 0.996 0.276 3.966-3.193 82.44 356 15 0.1786 174.228 169.449 0.857 0.995 0.125 3.191-2.566 97.65 782 48 0.1956 127.574 126.782 0.822 0.991 0.030 2.565-2.063 99.94 1509 79 0.1932 102.252 101.616 0.840 0.985 0.000 2.062-1.658 99.97 2875 153 0.1368 78.012 77.077 0.991 0.975 0.000 1.658-1.333 100.00 5434 308 0.1315 49.286 48.697 1.062 0.959 0.000 1.332-1.071 99.44 10311 550 0.1280 32.905 32.550 1.132 0.934 0.000 1.071-0.850 82.07 17636 933 0.1897 13.720 13.679 1.112 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9274 b_overall=-0.3744 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1586 r_free=0.1741 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1586 r_free=0.1741 ========================= Local real-space refinement ========================= Before: r_work=0.1586 r_free=0.1741 5 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.044 outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.7106 time to fit residues: 3.6522 After: r_work=0.1590 r_free=0.1750 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 10.823784 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 60.345478 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 0.1904 0.2052 0.0148 0.002 0.6 1.1 0.0 0.0 0 0.125 0.1817 0.1976 0.0159 0.002 0.6 2.1 0.0 0.0 0 0.250 0.1740 0.1909 0.0169 0.003 0.6 1.1 0.0 0.0 0 0.500 0.1671 0.1847 0.0176 0.003 0.7 1.1 0.0 0.0 0 1.000 0.1618 0.1803 0.0185 0.005 0.8 1.1 0.0 0.0 0 2.000 0.1596 0.1793 0.0197 0.006 0.9 1.1 0.0 0.0 0 3.000 0.1588 0.1792 0.0204 0.007 0.9 1.1 0.0 0.0 0 4.000 0.1577 0.1782 0.0205 0.008 0.9 1.1 0.0 0.0 0 5.000 0.1572 0.1785 0.0212 0.009 1.0 1.1 0.0 0.0 0 6.000 0.1565 0.1777 0.0213 0.010 1.0 1.1 0.0 0.0 0 7.000 0.1560 0.1775 0.0215 0.011 1.1 1.1 0.0 0.0 0 8.000 0.1556 0.1773 0.0217 0.012 1.1 1.1 0.0 0.0 0 9.000 0.1554 0.1775 0.0222 0.013 1.1 1.1 0.0 0.0 0 10.000 0.1577 0.1785 0.0208 0.009 1.0 1.1 0.0 0.0 0 5.412 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1556 0.1773 0.0217 0.012 1.1 1.1 0.0 0.0 0 9.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1556 r_free=0.1773 6 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.044 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0400 After: r_work=0.1556 r_free=0.1773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.56 17.73 2.17 1.221 12.926 60.345 0.031 15.54 17.68 2.14 0.969 12.928 1.810 0.031 15.32 17.48 2.16 0.941 12.929 7.543 0.030 15.25 17.59 2.34 0.998 12.931 30.173 0.029 15.45 17.97 2.53 1.580 13.109 60.345 0.027 15.28 18.10 2.82 1.820 13.196 90.518 0.026 15.33 18.29 2.96 2.507 13.399 120.691 0.026 15.16 18.15 2.99 2.732 13.469 150.864 0.025 15.00 17.98 2.98 2.620 13.450 181.036 0.025 14.97 18.01 3.04 2.634 13.448 211.209 0.025 14.91 18.00 3.10 2.809 13.494 241.382 0.025 14.77 17.79 3.01 2.599 13.441 271.555 0.024 14.74 17.78 3.04 2.525 13.420 301.727 0.024 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 7.543 Accepted refinement result: 15.32 17.48 2.16 0.941 12.929 7.543 0.030 Individual atomic B min max mean iso aniso Overall: 5.11 51.86 11.54 1.29 0 596 Protein: 5.11 25.43 8.62 1.29 0 475 Water: 6.58 51.86 23.54 N/A 0 115 Other: 10.00 14.06 12.38 N/A 0 6 Chain A: 5.11 51.86 11.54 N/A 0 596 Histogram: Values Number of atoms 5.11 - 9.79 368 9.79 - 14.46 107 14.46 - 19.14 36 19.14 - 23.81 26 23.81 - 28.49 27 28.49 - 33.16 15 33.16 - 37.84 8 37.84 - 42.51 3 42.51 - 47.19 1 47.19 - 51.86 5 =========================== Idealize ADP of riding H ========================== r_work=0.1532 r_free=0.1748 r_work=0.1526 r_free=0.1733 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.85 - 13.85 A, n_refl.=41358 (all), 5.09 % free)------------| | | | r_work= 0.1526 r_free= 0.1733 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ls_wunit_k1) (work): 0.029827 | | target function (ls_wunit_k1) not normalized (work): 1170.740249 | | target function (ls_wunit_k1) not normalized (free): 97.235705 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1536 0.1526 0.1733 n_refl.: 41358 re-set all scales: r(all,work,free)=0.1964 0.1953 0.2169 n_refl.: 41358 remove outliers: r(all,work,free)=0.1964 0.1953 0.2169 n_refl.: 41358 overall B=-0.18 to atoms: r(all,work,free)=0.1895 0.1884 0.2098 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1535 0.1524 0.1724 n_refl.: 41358 remove outliers: r(all,work,free)=0.1535 0.1524 0.1724 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.2872 89.072 84.290 0.760 0.989 0.357 6.147-4.946 75.19 97 3 0.1982 111.646 108.201 0.775 0.993 0.356 4.941-3.976 72.22 154 15 0.2009 143.497 136.964 0.776 0.990 0.345 3.966-3.193 82.44 356 15 0.1405 157.516 155.199 0.859 0.990 0.150 3.191-2.566 97.65 782 48 0.1703 115.337 115.322 0.818 0.990 0.034 2.565-2.063 99.94 1509 79 0.1774 92.444 92.405 0.830 0.988 0.000 2.062-1.658 99.97 2875 153 0.1325 70.529 69.758 0.965 0.984 0.000 1.658-1.333 100.00 5434 308 0.1304 44.558 43.993 1.013 0.979 0.000 1.332-1.071 99.44 10311 550 0.1291 29.749 29.391 1.066 0.971 0.000 1.071-0.850 82.07 17636 933 0.1958 12.404 12.373 1.014 0.961 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.3234 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1525 r_free=0.1724 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1525 r_free=0.1724 ========================= Local real-space refinement ========================= Before: r_work=0.1525 r_free=0.1724 10 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.048 outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 1.0904 time to fit residues: 11.0659 After: r_work=0.1528 r_free=0.1731 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 11.624873 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.319560 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 0.1909 0.2043 0.0134 0.002 0.5 0.0 0.0 0.0 0 0.125 0.1789 0.1935 0.0147 0.002 0.5 0.0 0.0 0.0 0 0.250 0.1717 0.1876 0.0159 0.002 0.6 1.1 0.0 0.0 0 0.500 0.1632 0.1802 0.0170 0.003 0.7 1.1 0.0 0.0 0 1.000 0.1581 0.1761 0.0180 0.004 0.8 1.1 0.0 0.0 0 2.000 0.1556 0.1743 0.0187 0.005 0.8 1.1 0.0 0.0 0 3.000 0.1541 0.1733 0.0192 0.006 0.9 1.1 0.0 0.0 0 4.000 0.1531 0.1725 0.0194 0.008 0.9 1.1 0.0 0.0 0 5.000 0.1525 0.1723 0.0199 0.009 1.0 1.1 0.0 0.0 0 6.000 0.1519 0.1723 0.0204 0.010 1.0 1.1 0.0 0.0 0 7.000 0.1517 0.1723 0.0206 0.011 1.0 1.1 0.0 0.0 0 8.000 0.1514 0.1723 0.0209 0.012 1.1 1.1 0.0 0.0 0 9.000 0.1512 0.1724 0.0213 0.013 1.1 1.1 0.0 0.0 0 10.000 0.1526 0.1723 0.0198 0.008 1.0 1.1 0.0 0.0 0 5.812 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1514 0.1723 0.0209 0.012 1.1 1.1 0.0 0.0 0 9.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1514 r_free=0.1723 10 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.048 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0416 After: r_work=0.1514 r_free=0.1723 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.14 17.23 2.09 2.729 14.214 50.320 0.029 15.14 17.23 2.09 2.729 14.214 1.510 0.029 15.14 17.22 2.08 2.726 14.214 6.290 0.029 15.23 17.51 2.29 2.734 14.218 25.160 0.028 15.40 18.06 2.65 2.612 14.407 50.320 0.027 14.98 17.72 2.74 2.520 14.497 75.479 0.026 14.90 17.72 2.81 2.479 14.601 100.639 0.025 14.80 17.71 2.91 2.471 14.632 125.799 0.025 14.76 17.70 2.94 2.481 14.667 150.959 0.024 14.67 17.67 3.00 2.461 14.661 176.118 0.024 14.56 17.56 3.00 2.435 14.670 201.278 0.024 14.64 17.89 3.25 2.535 14.760 226.438 0.024 14.58 17.81 3.23 2.486 14.725 251.598 0.023 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.290 Accepted refinement result: 15.14 17.22 2.08 2.726 14.214 6.290 0.029 Individual atomic B min max mean iso aniso Overall: 4.94 51.68 11.35 1.25 0 596 Protein: 4.94 25.12 8.43 1.25 0 475 Water: 6.39 51.68 23.36 N/A 0 115 Other: 9.88 13.83 12.19 N/A 0 6 Chain A: 4.94 51.68 11.35 N/A 0 596 Histogram: Values Number of atoms 4.94 - 9.61 369 9.61 - 14.28 108 14.28 - 18.96 34 18.96 - 23.63 26 23.63 - 28.31 27 28.31 - 32.98 15 32.98 - 37.65 8 37.65 - 42.33 3 42.33 - 47.00 1 47.00 - 51.68 5 =========================== Idealize ADP of riding H ========================== r_work=0.1514 r_free=0.1722 r_work=0.1514 r_free=0.1722 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.85 - 13.85 A, n_refl.=41358 (all), 5.09 % free)------------| | | | r_work= 0.1514 r_free= 0.1722 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.029173 | | target function (ls_wunit_k1) not normalized (work): 1145.065607 | | target function (ls_wunit_k1) not normalized (free): 96.552423 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1525 0.1514 0.1722 n_refl.: 41358 re-set all scales: r(all,work,free)=0.1890 0.1880 0.2085 n_refl.: 41358 remove outliers: r(all,work,free)=0.1890 0.1880 0.2085 n_refl.: 41358 overall B=-0.08 to atoms: r(all,work,free)=0.1864 0.1854 0.2058 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1527 0.1516 0.1724 n_refl.: 41358 remove outliers: r(all,work,free)=0.1527 0.1516 0.1724 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.2823 89.072 85.018 0.793 0.994 0.370 6.147-4.946 75.19 97 3 0.1995 111.646 108.998 0.803 0.997 0.366 4.941-3.976 72.22 154 15 0.1973 143.497 137.414 0.807 0.994 0.337 3.966-3.193 82.44 356 15 0.1399 157.516 155.447 0.893 0.993 0.147 3.191-2.566 97.65 782 48 0.1707 115.337 115.416 0.850 0.992 0.048 2.565-2.063 99.94 1509 79 0.1764 92.444 92.464 0.863 0.989 0.000 2.062-1.658 99.97 2875 153 0.1315 70.529 69.779 1.004 0.984 0.000 1.658-1.333 100.00 5434 308 0.1289 44.558 44.012 1.054 0.975 0.000 1.332-1.071 99.44 10311 550 0.1279 29.749 29.396 1.110 0.963 0.000 1.071-0.850 82.07 17636 933 0.1964 12.404 12.372 1.058 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.2707 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1516 r_free=0.1724 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1516 r_free=0.1724 ========================= Local real-space refinement ========================= Before: r_work=0.1516 r_free=0.1724 10 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.045 outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 1.0222 time to fit residues: 10.3670 After: r_work=0.1525 r_free=0.1743 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.479255 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.304349 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 0.1585 0.1722 0.0136 0.003 0.7 1.1 0.0 0.0 0 0.074 0.1531 0.1663 0.0132 0.004 0.9 1.1 0.0 0.0 0 0.222 0.1514 0.1643 0.0129 0.005 0.9 2.1 0.0 0.0 0 0.444 0.1506 0.1640 0.0134 0.006 1.0 2.1 0.0 0.0 0 0.666 0.1502 0.1639 0.0137 0.007 1.0 2.1 0.0 0.0 0 0.888 0.1499 0.1640 0.0141 0.008 1.1 2.1 0.0 0.0 0 1.109 0.1497 0.1639 0.0142 0.009 1.1 2.1 0.0 0.0 0 1.331 0.1494 0.1638 0.0144 0.010 1.1 1.1 0.0 0.0 0 1.553 0.1501 0.1639 0.0138 0.007 1.0 2.1 0.0 0.0 0 0.740 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1494 0.1638 0.0144 0.010 1.1 1.1 0.0 0.0 0 1.553 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1494 r_free=0.1638 11 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.073 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0719 After: r_work=0.1494 r_free=0.1638 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.94 16.38 1.44 2.698 14.117 2.304 2.915 14.96 16.38 1.42 2.696 14.118 0.069 2.916 15.01 16.39 1.37 2.700 14.124 0.288 2.907 15.00 16.41 1.41 2.776 14.115 1.152 2.884 14.64 16.11 1.47 2.827 14.084 2.304 2.858 14.43 15.95 1.51 2.821 14.082 3.457 2.843 14.44 15.91 1.47 2.890 14.061 4.609 2.834 14.40 15.87 1.47 2.923 14.050 5.761 2.828 14.37 15.82 1.45 2.955 14.035 6.913 2.824 14.33 15.82 1.49 2.977 14.031 8.065 2.820 14.26 15.74 1.48 2.938 14.043 9.217 2.816 14.28 15.80 1.51 2.980 14.032 10.370 2.816 14.25 15.75 1.50 2.954 14.041 11.522 2.814 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 9.217 Accepted refinement result: 14.26 15.74 1.48 2.938 14.043 9.217 2.816 Individual atomic B min max mean iso aniso Overall: 4.98 51.54 11.11 1.13 0 596 Protein: 4.98 22.88 8.25 1.13 0 475 Water: 6.34 51.54 22.97 N/A 0 115 Other: 8.71 11.72 10.73 N/A 0 6 Chain A: 4.98 51.54 11.11 N/A 0 596 Histogram: Values Number of atoms 4.98 - 9.63 380 9.63 - 14.29 105 14.29 - 18.95 33 18.95 - 23.60 24 23.60 - 28.26 22 28.26 - 32.92 15 32.92 - 37.57 8 37.57 - 42.23 3 42.23 - 46.89 1 46.89 - 51.54 5 =========================== Idealize ADP of riding H ========================== r_work=0.1426 r_free=0.1574 r_work=0.1426 r_free=0.1576 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.85 - 13.85 A, n_refl.=41358 (all), 5.09 % free)------------| | | | r_work= 0.1426 r_free= 0.1576 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 2.816337 | | target function (ml) not normalized (work): 110544.057013 | | target function (ml) not normalized (free): 6097.723870 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1434 0.1426 0.1576 n_refl.: 41358 re-set all scales: r(all,work,free)=0.1873 0.1870 0.1931 n_refl.: 41358 remove outliers: r(all,work,free)=0.1873 0.1870 0.1931 n_refl.: 41358 overall B=-0.08 to atoms: r(all,work,free)=0.1839 0.1836 0.1900 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1434 0.1426 0.1572 n_refl.: 41358 remove outliers: r(all,work,free)=0.1434 0.1426 0.1572 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.2951 89.072 84.296 0.757 0.985 0.350 6.147-4.946 75.19 97 3 0.2245 111.646 107.406 0.791 0.989 0.353 4.941-3.976 72.22 154 15 0.2263 143.497 135.179 0.785 0.987 0.319 3.966-3.193 82.44 356 15 0.1696 157.516 153.980 0.867 0.989 0.159 3.191-2.566 97.65 782 48 0.1927 115.337 114.829 0.820 0.990 0.038 2.565-2.063 99.94 1509 79 0.1947 92.444 91.998 0.828 0.991 0.000 2.062-1.658 99.97 2875 153 0.1372 70.529 69.611 0.963 0.993 0.000 1.658-1.333 100.00 5434 308 0.1148 44.558 44.154 1.005 0.995 0.000 1.332-1.071 99.44 10311 550 0.0976 29.749 29.510 1.047 0.997 0.000 1.071-0.850 82.07 17636 933 0.1628 12.404 12.449 0.982 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.3663 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1427 r_free=0.1572 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1431 r_free=0.1567 ========================= Local real-space refinement ========================= Before: r_work=0.1431 r_free=0.1567 13 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.088 outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 2.3459 time to fit residues: 30.7742 After: r_work=0.1434 r_free=0.1582 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.334776 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.965556 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 0.1503 0.1623 0.0120 0.003 0.7 2.1 0.0 0.0 0 0.067 0.1458 0.1579 0.0122 0.004 0.9 2.1 0.0 0.0 0 0.200 0.1439 0.1575 0.0136 0.006 1.0 1.1 0.0 0.0 0 0.400 0.1433 0.1566 0.0133 0.007 1.0 1.1 0.0 0.0 0 0.601 0.1429 0.1567 0.0138 0.008 1.1 1.1 0.0 0.0 0 0.801 0.1425 0.1563 0.0139 0.009 1.1 1.1 0.0 0.0 0 1.001 0.1424 0.1564 0.0140 0.010 1.1 1.1 0.0 0.0 0 1.201 0.1419 0.1562 0.0143 0.012 1.2 1.1 0.0 0.0 0 1.402 0.1431 0.1565 0.0134 0.008 1.0 1.1 0.0 0.0 0 0.667 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1419 0.1562 0.0143 0.012 1.2 1.1 0.0 0.0 0 1.402 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1419 r_free=0.1562 12 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.085 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0708 After: r_work=0.1419 r_free=0.1562 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.19 15.62 1.43 2.630 13.805 1.966 2.812 14.19 15.62 1.43 2.630 13.805 0.059 2.812 14.19 15.62 1.43 2.630 13.805 0.246 2.812 14.19 15.63 1.44 2.629 13.806 0.983 2.813 14.20 15.65 1.46 2.628 13.810 1.966 2.814 14.21 15.68 1.47 2.626 13.815 2.948 2.813 14.21 15.69 1.47 2.627 13.816 3.931 2.812 14.24 15.73 1.48 2.628 13.821 4.914 2.812 14.24 15.73 1.49 2.686 13.796 5.897 2.811 14.23 15.75 1.52 2.769 13.764 6.879 2.808 14.19 15.71 1.53 2.743 13.778 7.862 2.805 14.18 15.74 1.56 2.791 13.764 8.845 2.803 14.17 15.73 1.56 2.809 13.759 9.828 2.802 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.059 Accepted refinement result: 14.19 15.62 1.43 2.630 13.805 0.059 2.812 Individual atomic B min max mean iso aniso Overall: 4.89 51.46 11.03 1.13 0 596 Protein: 4.89 22.79 8.17 1.13 0 475 Water: 6.26 51.46 22.89 N/A 0 115 Other: 8.63 11.64 10.65 N/A 0 6 Chain A: 4.89 51.46 11.03 N/A 0 596 Histogram: Values Number of atoms 4.89 - 9.55 380 9.55 - 14.21 105 14.21 - 18.86 33 18.86 - 23.52 24 23.52 - 28.18 22 28.18 - 32.83 15 32.83 - 37.49 8 37.49 - 42.15 3 42.15 - 46.80 1 46.80 - 51.46 5 =========================== Idealize ADP of riding H ========================== r_work=0.1419 r_free=0.1562 r_work=0.1419 r_free=0.1562 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.85 - 13.85 A, n_refl.=41358 (all), 5.09 % free)------------| | | | r_work= 0.1419 r_free= 0.1562 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 2.812328 | | target function (ml) not normalized (work): 110386.696986 | | target function (ml) not normalized (free): 6088.320005 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1426 0.1419 0.1562 n_refl.: 41358 re-set all scales: r(all,work,free)=0.1834 0.1831 0.1889 n_refl.: 41358 remove outliers: r(all,work,free)=0.1834 0.1831 0.1889 n_refl.: 41358 overall B=-0.07 to atoms: r(all,work,free)=0.1807 0.1804 0.1865 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1428 0.1420 0.1561 n_refl.: 41358 remove outliers: r(all,work,free)=0.1428 0.1420 0.1561 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.3053 89.072 83.610 0.764 0.974 0.360 6.147-4.946 75.19 97 3 0.2349 111.646 106.717 0.799 0.979 0.360 4.941-3.976 72.22 154 15 0.2284 143.497 134.770 0.798 0.977 0.360 3.966-3.193 82.44 356 15 0.1736 157.516 153.697 0.874 0.978 0.146 3.191-2.566 97.65 782 48 0.1938 115.337 114.823 0.829 0.979 0.019 2.565-2.063 99.94 1509 79 0.1941 92.444 91.955 0.836 0.980 0.000 2.062-1.658 99.97 2875 153 0.1356 70.529 69.626 0.972 0.980 0.000 1.658-1.333 100.00 5434 308 0.1130 44.558 44.177 1.013 0.980 0.000 1.332-1.071 99.44 10311 550 0.0963 29.749 29.520 1.052 0.981 0.000 1.071-0.850 82.07 17636 933 0.1622 12.404 12.450 0.985 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.3050 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1420 r_free=0.1561 After: r_work=0.1422 r_free=0.1562 ================================== NQH flips ================================== r_work=0.1422 r_free=0.1562 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1422 r_free=0.1562 ========================= Local real-space refinement ========================= Before: r_work=0.1422 r_free=0.1562 12 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.080 outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 1.8738 time to fit residues: 22.7590 After: r_work=0.1428 r_free=0.1574 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.302463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.832471 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 0.1512 0.1631 0.0120 0.004 0.8 2.1 0.0 0.0 0 0.065 0.1465 0.1593 0.0128 0.005 0.9 2.1 0.0 0.0 0 0.195 0.1452 0.1584 0.0132 0.005 1.0 2.1 0.0 0.0 0 0.391 0.1444 0.1580 0.0136 0.006 1.0 2.1 0.0 0.0 0 0.586 0.1438 0.1574 0.0137 0.008 1.1 2.1 0.0 0.0 0 0.781 0.1431 0.1571 0.0139 0.010 1.1 1.1 0.0 0.0 0 0.977 0.1428 0.1569 0.0141 0.011 1.2 1.1 0.0 0.0 0 1.172 0.1426 0.1568 0.0143 0.012 1.2 1.1 0.0 0.0 0 1.368 0.1441 0.1577 0.0136 0.007 1.1 2.1 0.0 0.0 0 0.651 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1426 0.1568 0.0143 0.012 1.2 1.1 0.0 0.0 0 1.368 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1426 r_free=0.1568 12 residues out of total 48 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.079 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0604 After: r_work=0.1426 r_free=0.1568 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 14.26 15.68 1.43 2.620 13.728 1.832 2.816 14.26 15.68 1.43 2.620 13.728 0.055 2.816 14.26 15.68 1.43 2.620 13.728 0.229 2.816 14.26 15.69 1.43 2.619 13.730 0.916 2.817 14.26 15.71 1.45 2.618 13.734 1.832 2.818 14.27 15.74 1.46 2.617 13.737 2.749 2.817 14.29 15.76 1.47 2.617 13.740 3.665 2.816 14.32 15.79 1.47 2.619 13.744 4.581 2.816 14.31 15.79 1.48 2.644 13.734 5.497 2.816 14.31 15.81 1.50 2.714 13.706 6.414 2.814 14.28 15.79 1.51 2.738 13.698 7.330 2.810 14.29 15.84 1.54 2.798 13.682 8.246 2.809 14.23 15.78 1.55 2.749 13.701 9.162 2.806 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.055 Accepted refinement result: 14.26 15.68 1.43 2.620 13.728 0.055 2.816 Individual atomic B min max mean iso aniso Overall: 4.83 51.39 10.97 1.13 0 596 Protein: 4.83 22.73 8.10 1.13 0 475 Water: 6.19 51.39 22.82 N/A 0 115 Other: 8.56 11.57 10.58 N/A 0 6 Chain A: 4.83 51.39 10.97 N/A 0 596 Histogram: Values Number of atoms 4.83 - 9.48 380 9.48 - 14.14 105 14.14 - 18.80 33 18.80 - 23.45 24 23.45 - 28.11 22 28.11 - 32.77 15 32.77 - 37.42 8 37.42 - 42.08 3 42.08 - 46.74 1 46.74 - 51.39 5 =========================== Idealize ADP of riding H ========================== r_work=0.1426 r_free=0.1568 r_work=0.1426 r_free=0.1568 ----------X-ray data---------- |--(resolution: 0.85 - 13.85 A, n_refl.=41358 (all), 5.09 % free)------------| | | | r_work= 0.1426 r_free= 0.1568 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 2.816191 | | target function (ml) not normalized (work): 110538.330243 | | target function (ml) not normalized (free): 6096.899343 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 13.85 - 2.09 0.93 2862 160 0.1987 0.2091 4.7464 4.8695| | 2: 2.09 - 1.66 1.00 2960 151 0.1391 0.1604 4.1228 4.1202| | 3: 1.66 - 1.45 1.00 2919 174 0.1184 0.1380 3.4445 3.5025| | 4: 1.45 - 1.32 1.00 2902 152 0.1067 0.1231 3.118 3.1806| | 5: 1.32 - 1.23 1.00 2860 176 0.1033 0.1205 2.896 3.0297| | 6: 1.22 - 1.15 1.00 2889 150 0.0936 0.1067 2.7356 2.7813| | 7: 1.15 - 1.10 0.99 2868 152 0.0896 0.1074 2.5893 2.6587| | 8: 1.10 - 1.05 0.98 2790 138 0.1146 0.1176 2.5198 2.5834| | 9: 1.05 - 1.01 0.96 2763 151 0.1264 0.1351 2.3587 2.4469| | 10: 1.01 - 0.97 0.94 2704 147 0.1245 0.1330 2.2275 2.3253| | 11: 0.97 - 0.94 0.93 2647 138 0.1363 0.1378 2.1763 2.2441| | 12: 0.94 - 0.92 0.90 2577 133 0.1631 0.1635 2.0703 2.0848| | 13: 0.92 - 0.89 0.83 2356 124 0.2208 0.2077 2.071 2.0647| | 14: 0.89 - 0.87 0.68 1920 102 0.2952 0.2705 2.0763 2.1018| | 15: 0.87 - 0.85 0.43 1234 59 0.3787 0.3717 2.0291 2.0847| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 13.85 - 2.09 2862 160 0.83 22.26 1.00 0.93 2179.04| | 2: 2.09 - 1.66 2960 151 0.85 21.25 1.01 0.95 873.31| | 3: 1.66 - 1.45 2919 174 0.93 12.76 1.00 0.97 174.13| | 4: 1.45 - 1.32 2902 152 0.94 11.49 1.00 0.96 91.97| | 5: 1.32 - 1.23 2860 176 0.94 10.66 1.01 0.97 57.90| | 6: 1.22 - 1.15 2889 150 0.95 8.93 1.01 0.98 40.57| | 7: 1.15 - 1.10 2868 152 0.96 8.57 1.00 0.98 30.15| | 8: 1.10 - 1.05 2790 138 0.94 10.69 1.02 0.98 23.84| | 9: 1.05 - 1.01 2763 151 0.93 12.17 1.07 1.00 19.08| | 10: 1.01 - 0.97 2704 147 0.93 13.16 1.03 1.01 15.61| | 11: 0.97 - 0.94 2647 138 0.93 13.04 0.99 1.00 12.50| | 12: 0.94 - 0.92 2577 133 0.93 14.23 0.94 0.95 10.10| | 13: 0.92 - 0.89 2356 124 0.92 14.82 0.88 0.90 8.45| | 14: 0.89 - 0.87 1920 102 0.92 16.36 0.81 0.82 8.29| | 15: 0.87 - 0.85 1234 59 0.88 20.27 0.75 0.74 9.19| |alpha: min = 0.74 max = 1.01 mean = 0.95| |beta: min = 8.29 max = 2179.04 mean = 260.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.75| |phase err.(test): min = 0.00 max = 89.97 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1433 0.1426 0.1568 n_refl.: 41358 re-set all scales: r(all,work,free)=0.1811 0.1808 0.1872 n_refl.: 41358 remove outliers: r(all,work,free)=0.1811 0.1808 0.1872 n_refl.: 41358 overall B=-0.07 to atoms: r(all,work,free)=0.1785 0.1781 0.1848 n_refl.: 41358 bulk-solvent and scaling: r(all,work,free)=0.1436 0.1428 0.1572 n_refl.: 41358 remove outliers: r(all,work,free)=0.1436 0.1428 0.1572 n_refl.: 41358 ======================== 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 13.854-6.148 73.53 97 3 0.3048 89.072 83.813 0.794 0.974 0.346 6.147-4.946 75.19 97 3 0.2383 111.646 106.659 0.830 0.979 0.343 4.941-3.976 72.22 154 15 0.2310 143.497 134.784 0.827 0.977 0.320 3.966-3.193 82.44 356 15 0.1751 157.516 153.705 0.910 0.978 0.122 3.191-2.566 97.65 782 48 0.1946 115.337 114.845 0.862 0.979 0.010 2.565-2.063 99.94 1509 79 0.1942 92.444 91.983 0.870 0.980 0.000 2.062-1.658 99.97 2875 153 0.1365 70.529 69.623 1.009 0.981 0.000 1.658-1.333 100.00 5434 308 0.1136 44.558 44.177 1.048 0.982 0.000 1.332-1.071 99.44 10311 550 0.0968 29.749 29.514 1.083 0.983 0.000 1.071-0.850 82.07 17636 933 0.1634 12.404 12.450 1.007 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.2470 ================= 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 : 0.2824 0.2935 0.032 2.163 6.7 53.6 13.3 345 0.000 1_bss: 0.1586 0.1741 0.032 2.163 5.0 51.9 11.5 345 0.000 1_settarget: 0.1586 0.1741 0.032 2.163 5.0 51.9 11.5 345 0.000 1_nqh: 0.1586 0.1741 0.032 2.163 5.0 51.9 11.5 345 0.000 1_realsrl: 0.1590 0.1750 0.032 2.163 5.0 51.9 11.5 345 0.001 1_weight: 0.1590 0.1750 0.032 2.163 5.0 51.9 11.5 345 0.001 1_xyzrec: 0.1556 0.1773 0.012 1.084 5.0 51.9 11.5 345 0.117 1_realsrl2: 0.1556 0.1773 0.012 1.084 5.0 51.9 11.5 345 0.117 1_adp: 0.1532 0.1748 0.012 1.084 5.1 51.9 11.5 345 0.117 1_regHadp: 0.1526 0.1733 0.012 1.084 5.1 51.9 11.5 345 0.117 2_bss: 0.1525 0.1724 0.012 1.084 4.9 51.7 11.4 345 0.117 2_settarget: 0.1525 0.1724 0.012 1.084 4.9 51.7 11.4 345 0.117 2_updatecdl: 0.1525 0.1724 0.012 1.086 4.9 51.7 11.4 345 0.117 2_nqh: 0.1525 0.1724 0.012 1.086 4.9 51.7 11.4 345 0.117 2_realsrl: 0.1528 0.1731 0.012 1.086 4.9 51.7 11.4 345 0.118 2_weight: 0.1528 0.1731 0.012 1.086 4.9 51.7 11.4 345 0.118 2_xyzrec: 0.1514 0.1723 0.012 1.065 4.9 51.7 11.4 345 0.138 2_realsrl2: 0.1514 0.1723 0.012 1.065 4.9 51.7 11.4 345 0.138 2_adp: 0.1514 0.1722 0.012 1.065 4.9 51.7 11.4 345 0.138 2_regHadp: 0.1514 0.1722 0.012 1.065 4.9 51.7 11.4 345 0.138 3_bss: 0.1516 0.1724 0.012 1.065 4.9 51.6 11.3 345 0.138 3_settarget: 0.1516 0.1724 0.012 1.065 4.9 51.6 11.3 345 0.138 3_updatecdl: 0.1516 0.1724 0.012 1.065 4.9 51.6 11.3 345 0.138 3_nqh: 0.1516 0.1724 0.012 1.065 4.9 51.6 11.3 345 0.138 3_realsrl: 0.1525 0.1743 0.012 1.065 4.9 51.6 11.3 345 0.138 3_weight: 0.1525 0.1743 0.012 1.065 4.9 51.6 11.3 345 0.138 3_xyzrec: 0.1494 0.1638 0.010 1.137 4.9 51.6 11.3 345 0.127 3_realsrl2: 0.1494 0.1638 0.010 1.137 4.9 51.6 11.3 345 0.127 3_adp: 0.1426 0.1574 0.010 1.137 5.0 51.5 11.1 345 0.127 3_regHadp: 0.1426 0.1576 0.010 1.137 5.0 51.5 11.1 345 0.127 4_bss: 0.1427 0.1572 0.010 1.137 4.9 51.5 11.0 345 0.127 4_settarget: 0.1427 0.1572 0.010 1.137 4.9 51.5 11.0 345 0.127 4_updatecdl: 0.1427 0.1572 0.010 1.134 4.9 51.5 11.0 345 0.127 4_nqh: 0.1431 0.1567 0.010 1.134 4.9 51.5 11.0 345 0.135 4_realsrl: 0.1434 0.1582 0.010 1.134 4.9 51.5 11.0 345 0.135 4_weight: 0.1434 0.1582 0.010 1.134 4.9 51.5 11.0 345 0.135 4_xyzrec: 0.1419 0.1562 0.012 1.156 4.9 51.5 11.0 345 0.133 4_realsrl2: 0.1419 0.1562 0.012 1.156 4.9 51.5 11.0 345 0.133 4_adp: 0.1419 0.1562 0.012 1.156 4.9 51.5 11.0 345 0.133 4_regHadp: 0.1419 0.1562 0.012 1.156 4.9 51.5 11.0 345 0.133 5_bss: 0.1420 0.1561 0.012 1.156 4.8 51.4 11.0 345 0.133 5_settarget: 0.1420 0.1561 0.012 1.156 4.8 51.4 11.0 345 0.133 5_updatecdl: 0.1420 0.1561 0.012 1.158 4.8 51.4 11.0 345 0.133 5_setrh: 0.1422 0.1562 0.012 1.158 4.8 51.4 11.0 345 0.133 5_nqh: 0.1422 0.1562 0.012 1.158 4.8 51.4 11.0 345 0.133 5_realsrl: 0.1428 0.1574 0.012 1.158 4.8 51.4 11.0 345 0.133 5_weight: 0.1428 0.1574 0.012 1.158 4.8 51.4 11.0 345 0.133 5_xyzrec: 0.1426 0.1568 0.012 1.186 4.8 51.4 11.0 345 0.133 5_realsrl2: 0.1426 0.1568 0.012 1.186 4.8 51.4 11.0 345 0.133 5_adp: 0.1426 0.1568 0.012 1.186 4.8 51.4 11.0 345 0.133 5_regHadp: 0.1426 0.1568 0.012 1.186 4.8 51.4 11.0 345 0.133 end: 0.1428 0.1572 0.012 1.186 4.8 51.3 10.9 345 0.133 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/2FMA_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/2FMA_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 0.8700 Refinement macro-cycles (run) : 599.6500 Write final files (write_after_run_outputs) : 38.4200 Total : 638.9400 Total CPU time: 10.83 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:15:36 PDT -0700 (1712790936.74 s) Start R-work = 0.1586, R-free = 0.1741 Final R-work = 0.1428, R-free = 0.1572 =============================================================================== Job complete usr+sys time: 708.61 seconds wall clock time: 17 minutes 17.75 seconds (1037.75 seconds total)