Starting phenix.refine on Wed Apr 10 15:59:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4O8H_complete.pdb Found miller_array, 4O8H.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 = "4O8H.mtz" } default_miller_array = "4O8H.mtz" model { file = "4O8H_complete.pdb" } default_model = "4O8H_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 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3428 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2473 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 955 Unusual residues: {'1PE': 1, 'PEG': 1} Classifications: {'undetermined': 2, 'water': 300} Link IDs: {None: 301} Time building chain proxies: 0.72, per 1000 atoms: 0.21 Number of scatterers: 3428 At special positions: 0 Unit cell: (57.02, 57.02, 87.159, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 541 8.00 N 216 7.00 C 799 6.00 H 1865 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: 1.52 Conformation dependent library (CDL) restraints added in 117.9 milliseconds Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.06: 886 1.06 - 1.26: 1176 1.26 - 1.47: 534 1.47 - 1.68: 547 1.68 - 1.88: 10 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLN A 163 " pdb=" H GLN A 163 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" ND2 ASN A 106 " pdb="HD21 ASN A 106 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 5 " pdb=" H LEU A 5 " 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 40 " pdb=" H CYS A 40 " 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 77 " pdb=" H SER A 77 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 91.29 - 99.90: 1 99.90 - 108.51: 1139 108.51 - 117.12: 2584 117.12 - 125.73: 1149 125.73 - 134.35: 38 Bond angle restraints: 4911 Sorted by residual: angle pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " pdb=" CG ASP A 11 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " ideal model delta sigma weight residual 112.00 125.32 -13.32 2.20e+00 2.07e-01 3.67e+01 angle pdb=" CB ARG A 151 " pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " ideal model delta sigma weight residual 111.30 100.62 10.68 2.30e+00 1.89e-01 2.16e+01 angle pdb=" C ASP A 11 " pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " ideal model delta sigma weight residual 109.80 102.42 7.38 1.65e+00 3.67e-01 2.00e+01 angle pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sigma weight residual 100.90 91.29 9.61 2.20e+00 2.07e-01 1.91e+01 ... (remaining 4906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.30: 871 26.30 - 52.59: 29 52.59 - 78.89: 13 78.89 - 105.18: 0 105.18 - 131.48: 1 Dihedral angle restraints: 914 sinusoidal: 659 harmonic: 255 Sorted by residual: dihedral pdb=" CA THR A 52 " pdb=" C THR A 52 " pdb=" N PHE A 53 " pdb=" CA PHE A 53 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" OH4 1PE A 202 " pdb=" C14 1PE A 202 " pdb=" C24 1PE A 202 " pdb=" OH5 1PE A 202 " ideal model delta sinusoidal sigma weight residual -65.42 66.06 -131.48 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" CA SER A 51 " pdb=" C SER A 51 " pdb=" N THR A 52 " pdb=" CA THR A 52 " ideal model delta harmonic sigma weight residual 180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 92 0.071 - 0.142: 57 0.142 - 0.213: 25 0.213 - 0.284: 11 0.284 - 0.354: 1 Chirality restraints: 186 Sorted by residual: chirality pdb=" CA GLU A 134 " pdb=" N GLU A 134 " pdb=" C GLU A 134 " pdb=" CB GLU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA ASN A 71 " pdb=" N ASN A 71 " pdb=" C ASN A 71 " pdb=" CB ASN A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 183 not shown) Planarity restraints: 379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 112 " 0.067 2.00e-02 2.50e+03 3.06e-02 2.81e+01 pdb=" CG PHE A 112 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 112 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 112 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 112 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE A 112 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 PHE A 112 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 PHE A 112 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 112 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 112 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 121 " 0.003 2.00e-02 2.50e+03 2.61e-02 2.71e+01 pdb=" CG TRP A 121 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 121 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 121 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP A 121 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 121 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A 121 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 121 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 121 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP A 121 " -0.065 2.00e-02 2.50e+03 pdb=" HE1 TRP A 121 " 0.013 2.00e-02 2.50e+03 pdb=" HE3 TRP A 121 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 121 " 0.017 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 121 " -0.027 2.00e-02 2.50e+03 pdb=" HH2 TRP A 121 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " -0.053 2.00e-02 2.50e+03 2.67e-02 2.15e+01 pdb=" CG PHE A 113 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 113 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 113 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 113 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 PHE A 113 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 113 " -0.019 2.00e-02 2.50e+03 ... (remaining 376 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.58: 9 1.58 - 2.34: 1533 2.34 - 3.09: 12504 3.09 - 3.85: 19771 3.85 - 4.60: 31689 Warning: very small nonbonded interaction distances. Nonbonded interactions: 65506 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 148 " pdb=" O HOH A 362 " model vdw sym.op. 0.827 1.850 x+1/2,-y+3/2,-z-1/4 nonbonded pdb=" HG1 THR A 68 " pdb=" H GLY A 75 " model vdw 1.142 2.100 nonbonded pdb=" HZ3 LYS A 155 " pdb=" O HOH A 503 " model vdw sym.op. 1.209 1.850 x-1/2,-y+3/2,-z-1/4 nonbonded pdb="HH22 ARG A 151 " pdb=" O HOH A 493 " model vdw 1.271 1.850 nonbonded pdb=" NZ LYS A 148 " pdb=" O HOH A 362 " model vdw sym.op. 1.461 2.350 x+1/2,-y+3/2,-z-1/4 ... (remaining 65501 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 7 15.96 3 O 541 7.98 3 N 216 6.98 3 C 799 5.99 3 H 1865 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 = 3428 n_use_u_iso = 1880 n_use_u_aniso = 1548 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 = 3428 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3428 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1865 aniso = 1563) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (8 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 = "4O8H_complete_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1865 occupancy sum: 1865.00 (% of total atoms 54.52) Rotatable: count: 339 occupancy sum: 339.00 (% of total atoms 9.91) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.85 - 47.72 A, n_refl.=123342 (all), 5.02 % free)-----------| | | | r_work= 0.1433 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 3.667788 | | target function (ml) not normalized (work): 429692.329452 | | target function (ml) not normalized (free): 23112.693462 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.72 - 2.64 1.00 4357 226 0.2202 0.2120 6.2114 6.0775| | 2: 2.64 - 2.10 1.00 4125 240 0.1520 0.1445 5.3376 5.3554| | 3: 2.10 - 1.83 1.00 4086 198 0.1450 0.1491 4.9089 5.0119| | 4: 1.83 - 1.66 1.00 4080 214 0.1376 0.1454 4.5628 4.6494| | 5: 1.66 - 1.54 1.00 4021 220 0.1296 0.1264 4.2956 4.359| | 6: 1.54 - 1.45 1.00 4016 219 0.1230 0.1227 4.1026 4.2005| | 7: 1.45 - 1.38 1.00 3973 250 0.1188 0.1064 3.9562 3.9746| | 8: 1.38 - 1.32 1.00 4018 191 0.1158 0.0949 3.8291 3.882| | 9: 1.32 - 1.27 1.00 4006 221 0.1138 0.0985 3.7474 3.8245| | 10: 1.27 - 1.23 1.00 4000 193 0.1061 0.0999 3.6654 3.7467| | 11: 1.23 - 1.19 1.00 3996 189 0.1055 0.0991 3.6103 3.6908| | 12: 1.19 - 1.15 1.00 4003 231 0.0988 0.0988 3.5421 3.7226| | 13: 1.15 - 1.12 1.00 3975 211 0.0999 0.0881 3.4754 3.5224| | 14: 1.12 - 1.10 1.00 3925 227 0.0945 0.0782 3.3744 3.386| | 15: 1.10 - 1.07 1.00 3981 204 0.1002 0.0854 3.3188 3.3878| | 16: 1.07 - 1.05 1.00 3991 188 0.1005 0.0976 3.2492 3.3171| | 17: 1.05 - 1.03 1.00 3994 208 0.1060 0.1019 3.1965 3.2893| | 18: 1.03 - 1.01 1.00 3947 201 0.1080 0.1101 3.1518 3.2329| | 19: 1.01 - 0.99 1.00 3960 204 0.1115 0.1135 3.1182 3.2208| | 20: 0.99 - 0.97 1.00 3968 182 0.1197 0.1197 3.1032 3.2194| | 21: 0.97 - 0.96 1.00 3969 215 0.1244 0.1289 3.068 3.2215| | 22: 0.96 - 0.94 1.00 3943 213 0.1321 0.1199 3.0625 3.1275| | 23: 0.94 - 0.93 1.00 3926 223 0.1364 0.1273 3.0807 3.1347| | 24: 0.93 - 0.92 1.00 3965 208 0.1465 0.1308 3.1262 3.1668| | 25: 0.92 - 0.90 1.00 3938 197 0.1466 0.1364 3.0997 3.1746| | 26: 0.90 - 0.89 1.00 3926 218 0.1544 0.1548 3.0927 3.1995| | 27: 0.89 - 0.88 1.00 3964 216 0.1626 0.1605 3.1301 3.1406| | 28: 0.88 - 0.87 0.97 3828 200 0.1964 0.2041 3.2468 3.2125| | 29: 0.87 - 0.86 0.84 3308 174 0.2359 0.2665 3.3621 3.4757| | 30: 0.86 - 0.85 0.50 1964 108 0.2724 0.2927 3.3856 3.3159| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 47.72 - 2.64 4357 226 0.85 20.41 0.92 0.86 29110.14| | 2: 2.64 - 2.10 4125 240 0.89 16.64 1.05 0.89 9301.52| | 3: 2.10 - 1.83 4086 198 0.93 11.72 1.09 0.90 2970.18| | 4: 1.83 - 1.66 4080 214 0.93 11.82 1.07 0.91 1588.13| | 5: 1.66 - 1.54 4021 220 0.94 10.53 1.08 0.91 923.81| | 6: 1.54 - 1.45 4016 219 0.95 8.80 1.08 0.92 579.90| | 7: 1.45 - 1.38 3973 250 0.96 7.96 1.07 0.91 420.13| | 8: 1.38 - 1.32 4018 191 0.96 7.19 1.07 0.91 308.00| | 9: 1.32 - 1.27 4006 221 0.96 7.43 1.07 0.91 268.24| | 10: 1.27 - 1.23 4000 193 0.97 6.47 1.07 0.90 233.35| | 11: 1.23 - 1.19 3996 189 0.97 6.30 1.07 0.91 207.32| | 12: 1.19 - 1.15 4003 231 0.97 6.09 1.06 0.91 190.29| | 13: 1.15 - 1.12 3975 211 0.97 5.77 1.07 0.90 160.03| | 14: 1.12 - 1.10 3925 227 0.97 5.39 1.06 0.90 128.25| | 15: 1.10 - 1.07 3981 204 0.97 5.43 1.06 0.90 105.83| | 16: 1.07 - 1.05 3991 188 0.97 5.74 1.06 0.91 98.09| | 17: 1.05 - 1.03 3994 208 0.97 6.19 1.07 0.91 90.89| | 18: 1.03 - 1.01 3947 201 0.97 6.46 1.07 0.91 84.41| | 19: 1.01 - 0.99 3960 204 0.97 7.23 1.07 0.91 81.38| | 20: 0.99 - 0.97 3968 182 0.96 8.02 1.08 0.92 81.05| | 21: 0.97 - 0.96 3969 215 0.96 8.25 1.09 0.92 77.25| | 22: 0.96 - 0.94 3943 213 0.96 8.54 1.09 0.92 69.80| | 23: 0.94 - 0.93 3926 223 0.96 8.73 1.08 0.92 67.54| | 24: 0.93 - 0.92 3965 208 0.96 9.74 1.07 0.92 69.09| | 25: 0.92 - 0.90 3938 197 0.95 10.38 1.07 0.91 70.13| | 26: 0.90 - 0.89 3926 218 0.95 11.77 1.06 0.89 71.57| | 27: 0.89 - 0.88 3964 216 0.94 12.30 1.06 0.88 72.53| | 28: 0.88 - 0.87 3828 200 0.93 14.23 1.03 0.85 78.88| | 29: 0.87 - 0.86 3308 174 0.90 18.16 0.99 0.83 109.99| | 30: 0.86 - 0.85 1964 108 0.84 24.14 0.98 0.77 140.20| |alpha: min = 0.75 max = 0.92 mean = 0.90| |beta: min = 67.12 max = 34685.38 mean = 1729.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.97 mean = 9.68| |phase err.(test): min = 0.00 max = 89.77 mean = 9.85| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.163 1288 Z= 0.678 Angle : 1.432 13.324 1727 Z= 0.863 Chirality : 0.111 0.354 186 Planarity : 0.010 0.055 223 Dihedral : 12.618 131.480 475 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.04 (0.69), residues: 162 helix: -1.06 (0.84), residues: 25 sheet: 1.57 (1.01), residues: 33 loop : -0.17 (0.66), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG A 151 TYR 0.025 0.009 TYR A 48 PHE 0.030 0.009 PHE A 113 TRP 0.038 0.015 TRP A 121 HIS 0.007 0.003 HIS A 70 Individual atomic B min max mean iso aniso Overall: 2.84 30.32 8.13 0.74 0 1563 Protein: 2.84 18.08 5.77 0.73 0 1240 Water: 4.23 30.32 17.52 N/A 0 300 Other: 8.27 19.43 12.75 N/A 0 23 Chain A: 2.84 30.32 8.13 N/A 0 1563 Histogram: Values Number of atoms 2.84 - 5.59 715 5.59 - 8.34 443 8.34 - 11.09 122 11.09 - 13.84 61 13.84 - 16.58 68 16.58 - 19.33 40 19.33 - 22.08 15 22.08 - 24.83 35 24.83 - 27.58 31 27.58 - 30.32 33 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.85 - 47.72 A, n_refl.=123342 (all), 5.02 % free)-----------| | | | r_work= 0.1433 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 3.667788 | | target function (ml) not normalized (work): 429692.329452 | | target function (ml) not normalized (free): 23112.693462 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1427 0.1433 0.1378 n_refl.: 123342 re-set all scales: r(all,work,free)=0.1427 0.1433 0.1378 n_refl.: 123342 remove outliers: r(all,work,free)=0.1419 0.1425 0.1378 n_refl.: 123340 overall B=0.00 to atoms: r(all,work,free)=0.1420 0.1426 0.1378 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1181 0.1176 0.1283 n_refl.: 123340 remove outliers: r(all,work,free)=0.1181 0.1176 0.1283 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.2049 506.188 475.405 1.112 0.893 0.395 10.177-7.930 100.00 91 9 0.1755 483.674 469.623 1.123 0.895 0.400 7.929-6.185 100.00 198 10 0.2017 371.468 366.241 1.156 0.895 0.413 6.173-4.813 100.00 395 17 0.1653 439.682 427.016 1.136 0.895 0.420 4.812-3.754 100.00 805 46 0.1346 587.760 579.896 1.166 0.896 0.417 3.748-2.922 100.00 1685 76 0.1511 513.885 503.964 1.151 0.896 0.300 2.922-2.277 100.00 3410 183 0.1565 337.419 329.807 1.098 0.896 0.000 2.276-1.774 99.99 7110 384 0.1264 253.911 248.601 1.145 0.896 0.000 1.774-1.382 100.00 14808 836 0.1086 142.533 139.874 1.140 0.896 0.000 1.382-1.077 99.96 31030 1619 0.0870 96.149 94.493 1.130 0.895 0.000 1.077-0.850 95.46 57526 3003 0.1143 47.085 46.070 1.134 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0021 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1176 r_free=0.1283 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1283 ========================= Local real-space refinement ========================= Before: r_work=0.1176 r_free=0.1283 36 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.125 outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.4793 time to fit residues: 54.6929 After: r_work=0.1191 r_free=0.1290 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.768341 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 211.799843 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 0.1219 0.1355 0.0136 0.007 0.9 0.8 0.0 0.0 0 8.384 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1219 r_free=0.1355 37 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.122 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1209 After: r_work=0.1219 r_free=0.1355 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 13.55 1.36 0.474 9.114 211.800 0.020 12.19 13.55 1.36 0.474 9.114 6.354 0.020 12.19 13.55 1.36 0.474 9.114 26.475 0.020 12.11 13.83 1.73 2.432 9.515 105.900 0.017 11.77 13.60 1.83 2.513 9.566 211.800 0.016 11.70 13.57 1.88 2.897 9.656 317.700 0.016 11.59 13.51 1.92 2.763 9.645 423.600 0.016 11.53 13.47 1.94 2.773 9.650 529.500 0.015 11.52 13.51 1.98 2.837 9.676 635.400 0.015 11.48 13.46 1.97 3.016 9.709 741.299 0.015 11.50 13.50 2.00 3.045 9.720 847.199 0.015 11.51 13.51 2.00 3.239 9.757 953.099 0.015 11.48 13.56 2.08 3.124 9.744 1058.999 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: 741.299 Accepted refinement result: 11.48 13.46 1.97 3.016 9.709 741.299 0.015 Individual atomic B min max mean iso aniso Overall: 2.70 50.61 9.43 1.11 0 1563 Protein: 2.70 25.03 6.26 1.08 0 1240 Water: 4.44 50.61 22.10 N/A 0 300 Other: 9.14 25.06 15.02 N/A 0 23 Chain A: 2.70 50.61 9.43 N/A 0 1563 Histogram: Values Number of atoms 2.70 - 7.49 994 7.49 - 12.28 240 12.28 - 17.07 89 17.07 - 21.87 63 21.87 - 26.66 73 26.66 - 31.45 65 31.45 - 36.24 32 36.24 - 41.03 5 41.03 - 45.82 0 45.82 - 50.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1346 r_work=0.1141 r_free=0.1338 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1338 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1339 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.85 - 29.60 A, n_refl.=123340 (all), 5.02 % free)-----------| | | | r_work= 0.1140 r_free= 0.1339 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.014743 | | target function (ls_wunit_k1) not normalized (work): 1727.193359 | | target function (ls_wunit_k1) not normalized (free): 145.453199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1140 0.1339 n_refl.: 123340 re-set all scales: r(all,work,free)=0.1392 0.1393 0.1437 n_refl.: 123340 remove outliers: r(all,work,free)=0.1392 0.1393 0.1437 n_refl.: 123340 overall B=0.00 to atoms: r(all,work,free)=0.1392 0.1393 0.1437 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1135 0.1335 n_refl.: 123340 remove outliers: r(all,work,free)=0.1145 0.1135 0.1335 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.1752 506.188 479.239 1.107 0.903 0.398 10.177-7.930 100.00 91 9 0.1559 483.674 473.253 1.109 0.904 0.401 7.929-6.185 100.00 198 10 0.1576 371.468 369.062 1.135 0.904 0.420 6.173-4.813 100.00 395 17 0.1344 439.682 429.720 1.106 0.904 0.440 4.812-3.754 100.00 805 46 0.0980 587.760 584.421 1.148 0.904 0.440 3.748-2.922 100.00 1685 76 0.1065 513.885 509.196 1.159 0.904 0.260 2.922-2.277 100.00 3410 183 0.1086 337.419 333.244 1.121 0.904 0.000 2.276-1.774 99.99 7110 384 0.0987 253.911 250.798 1.168 0.904 0.000 1.774-1.382 100.00 14808 836 0.1044 142.533 140.077 1.146 0.903 0.000 1.382-1.077 99.96 31030 1619 0.1052 96.149 94.219 1.133 0.901 0.000 1.077-0.850 95.46 57526 3003 0.1420 47.085 45.815 1.126 0.899 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=0.0897 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1335 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1135 r_free=0.1335 ========================= Local real-space refinement ========================= Before: r_work=0.1135 r_free=0.1335 16 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.189 outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 2.7660 time to fit residues: 45.3458 After: r_work=0.1152 r_free=0.1349 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.271262 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 235.783445 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 0.1540 0.1688 0.0149 0.002 0.5 0.4 0.0 0.0 0 0.125 0.1433 0.1592 0.0159 0.002 0.5 0.4 0.0 0.0 0 0.250 0.1323 0.1493 0.0171 0.002 0.5 0.4 0.0 0.0 0 0.500 0.1243 0.1424 0.0181 0.003 0.6 0.4 0.0 0.0 0 1.000 0.1185 0.1378 0.0193 0.003 0.7 0.4 0.0 0.0 0 2.000 0.1160 0.1355 0.0195 0.004 0.7 0.4 0.0 0.0 0 3.000 0.1147 0.1346 0.0199 0.004 0.8 0.0 0.0 0.0 0 4.000 0.1139 0.1338 0.0199 0.005 0.8 0.0 0.0 0.0 0 5.000 0.1134 0.1335 0.0201 0.005 0.8 0.0 0.0 0.0 0 6.000 0.1131 0.1333 0.0202 0.005 0.8 0.0 0.0 0.0 0 7.000 0.1128 0.1332 0.0204 0.006 0.9 0.0 0.0 0.0 0 8.000 0.1125 0.1331 0.0206 0.006 0.9 0.0 0.0 0.0 0 9.000 0.1122 0.1329 0.0207 0.007 0.9 0.0 0.0 0.0 0 10.000 0.1126 0.1331 0.0205 0.006 0.9 0.0 0.0 0.0 0 8.636 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1122 0.1329 0.0207 0.007 0.9 0.0 0.0 0.0 0 10.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1122 r_free=0.1329 18 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.236 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2519 After: r_work=0.1122 r_free=0.1329 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 13.29 2.07 2.421 12.088 235.783 0.014 11.22 13.29 2.07 2.421 12.088 7.074 0.014 11.22 13.29 2.07 2.421 12.088 29.473 0.014 11.22 13.29 2.07 2.421 12.088 117.892 0.014 11.22 13.28 2.06 2.420 12.088 235.783 0.014 11.22 13.27 2.05 2.420 12.088 353.675 0.014 11.11 13.20 2.09 2.413 12.062 471.567 0.014 11.02 13.13 2.11 2.277 12.112 589.459 0.014 11.01 13.15 2.14 2.261 12.119 707.350 0.014 10.96 13.14 2.17 2.205 12.143 825.242 0.014 10.94 13.13 2.19 2.181 12.149 943.134 0.013 10.93 13.16 2.23 2.146 12.168 1061.026 0.013 10.92 13.17 2.25 2.110 12.185 1178.917 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 943.134 Accepted refinement result: 10.94 13.13 2.19 2.181 12.149 943.134 0.013 Individual atomic B min max mean iso aniso Overall: 2.73 56.51 9.56 1.12 0 1563 Protein: 2.73 26.12 6.23 1.09 0 1240 Water: 4.37 56.51 22.96 N/A 0 300 Other: 8.67 23.91 14.49 N/A 0 23 Chain A: 2.73 56.51 9.56 N/A 0 1563 Histogram: Values Number of atoms 2.73 - 8.11 1064 8.11 - 13.49 204 13.49 - 18.87 80 18.87 - 24.24 70 24.24 - 29.62 55 29.62 - 35.00 65 35.00 - 40.38 19 40.38 - 45.75 4 45.75 - 51.13 0 51.13 - 56.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1094 r_free=0.1313 r_work=0.1094 r_free=0.1312 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1094 r_free = 0.1312 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1094 r_free = 0.1314 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.85 - 29.60 A, n_refl.=123340 (all), 5.02 % free)-----------| | | | r_work= 0.1094 r_free= 0.1314 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ls_wunit_k1) (work): 0.013435 | | target function (ls_wunit_k1) not normalized (work): 1573.920480 | | target function (ls_wunit_k1) not normalized (free): 138.529926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1105 0.1094 0.1314 n_refl.: 123340 re-set all scales: r(all,work,free)=0.1351 0.1352 0.1410 n_refl.: 123340 remove outliers: r(all,work,free)=0.1351 0.1352 0.1410 n_refl.: 123340 overall B=0.00 to atoms: r(all,work,free)=0.1351 0.1352 0.1410 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1105 0.1094 0.1315 n_refl.: 123340 remove outliers: r(all,work,free)=0.1105 0.1094 0.1315 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.1754 506.188 478.651 1.086 0.908 0.400 10.177-7.930 100.00 91 9 0.1598 483.674 474.494 1.086 0.909 0.410 7.929-6.185 100.00 198 10 0.1566 371.468 370.506 1.107 0.909 0.410 6.173-4.813 100.00 395 17 0.1283 439.682 430.885 1.083 0.909 0.430 4.812-3.754 100.00 805 46 0.0931 587.760 584.993 1.121 0.909 0.430 3.748-2.922 100.00 1685 76 0.1000 513.885 509.952 1.134 0.909 0.240 2.922-2.277 100.00 3410 183 0.1042 337.419 333.793 1.100 0.909 0.000 2.276-1.774 99.99 7110 384 0.0945 253.911 251.178 1.144 0.909 0.000 1.774-1.382 100.00 14808 836 0.1003 142.533 140.179 1.121 0.908 0.000 1.382-1.077 99.96 31030 1619 0.1008 96.149 94.294 1.107 0.907 0.000 1.077-0.850 95.46 57526 3003 0.1392 47.085 45.823 1.099 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.0950 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1094 r_free=0.1315 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1094 r_free=0.1315 ========================= Local real-space refinement ========================= Before: r_work=0.1094 r_free=0.1315 16 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.164 outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 2.4349 time to fit residues: 39.7975 After: r_work=0.1099 r_free=0.1320 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.206089 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 4.890260 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 0.1131 0.1310 0.0179 0.003 0.7 0.0 0.0 0.0 0 0.060 0.1095 0.1273 0.0178 0.004 0.8 0.0 0.0 0.0 0 0.181 0.1082 0.1258 0.0176 0.005 0.9 0.0 0.0 0.0 0 0.362 0.1077 0.1252 0.0175 0.005 1.0 0.0 0.0 0.0 0 0.543 0.1074 0.1249 0.0175 0.006 1.0 0.0 0.0 0.0 0 0.724 0.1073 0.1247 0.0174 0.006 1.1 0.0 0.0 0.0 0 0.905 0.1070 0.1245 0.0175 0.007 1.1 0.0 0.0 0.0 0 1.085 0.1069 0.1244 0.0175 0.007 1.1 0.0 0.0 0.0 0 1.266 0.1075 0.1252 0.0178 0.006 1.0 0.0 0.0 0.0 0 0.603 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1069 0.1244 0.0175 0.007 1.1 0.0 0.0 0.0 0 1.266 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1069 r_free=0.1244 14 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.234 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2171 After: r_work=0.1069 r_free=0.1244 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.69 12.44 1.75 2.507 12.309 4.890 3.820 10.72 12.43 1.71 2.505 12.309 0.147 3.820 10.72 12.41 1.69 2.506 12.308 0.611 3.817 10.77 12.28 1.50 2.515 12.305 2.445 3.803 10.89 12.11 1.23 2.979 12.130 4.890 3.762 10.71 11.99 1.28 2.883 12.160 7.335 3.746 10.62 11.93 1.31 2.850 12.171 9.781 3.739 10.57 11.88 1.32 2.827 12.178 12.226 3.734 10.53 11.86 1.33 2.805 12.186 14.671 3.731 10.50 11.84 1.34 2.791 12.191 17.116 3.729 10.47 11.83 1.36 2.772 12.198 19.561 3.727 10.45 11.81 1.35 2.793 12.195 22.006 3.724 10.43 11.79 1.36 2.778 12.201 24.451 3.723 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 24.451 Accepted refinement result: 10.43 11.79 1.36 2.778 12.201 24.451 3.723 Individual atomic B min max mean iso aniso Overall: 2.90 56.54 9.33 1.03 0 1563 Protein: 2.90 25.01 6.09 1.00 0 1240 Water: 4.23 56.54 22.42 N/A 0 300 Other: 6.95 22.68 13.09 N/A 0 23 Chain A: 2.90 56.54 9.33 N/A 0 1563 Histogram: Values Number of atoms 2.90 - 8.27 1109 8.27 - 13.63 182 13.63 - 19.00 71 19.00 - 24.36 67 24.36 - 29.72 47 29.72 - 35.09 63 35.09 - 40.45 18 40.45 - 45.82 4 45.82 - 51.18 0 51.18 - 56.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1044 r_free=0.1180 r_work=0.1045 r_free=0.1181 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1045 r_free = 0.1181 target_work(ml) = 3.724 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1045 r_free = 0.1180 target_work(ml) = 3.723 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.85 - 29.60 A, n_refl.=123340 (all), 5.02 % free)-----------| | | | r_work= 0.1045 r_free= 0.1180 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 3.723246 | | target function (ml) not normalized (work): 436181.997389 | | target function (ml) not normalized (free): 23587.989346 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1045 0.1180 n_refl.: 123340 re-set all scales: r(all,work,free)=0.1305 0.1310 0.1279 n_refl.: 123340 remove outliers: r(all,work,free)=0.1305 0.1310 0.1279 n_refl.: 123340 overall B=0.00 to atoms: r(all,work,free)=0.1307 0.1312 0.1280 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1040 0.1175 n_refl.: 123340 remove outliers: r(all,work,free)=0.1047 0.1040 0.1175 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.1912 506.188 474.699 1.095 0.899 0.400 10.177-7.930 100.00 91 9 0.1721 483.674 471.814 1.098 0.900 0.400 7.929-6.185 100.00 198 10 0.1778 371.468 368.973 1.121 0.900 0.400 6.173-4.813 100.00 395 17 0.1411 439.682 430.018 1.102 0.900 0.440 4.812-3.754 100.00 805 46 0.1084 587.760 583.160 1.137 0.900 0.440 3.748-2.922 100.00 1685 76 0.1180 513.885 507.437 1.141 0.900 0.220 2.922-2.277 100.00 3410 183 0.1235 337.419 332.097 1.104 0.900 0.000 2.276-1.774 99.99 7110 384 0.1049 253.911 249.970 1.150 0.900 0.000 1.774-1.382 100.00 14808 836 0.0974 142.533 140.074 1.131 0.900 0.000 1.382-1.077 99.96 31030 1619 0.0834 96.149 94.445 1.124 0.899 0.000 1.077-0.850 95.46 57526 3003 0.1107 47.085 46.024 1.129 0.897 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0051 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1040 r_free=0.1175 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1040 r_free=0.1175 ========================= Local real-space refinement ========================= Before: r_work=0.1040 r_free=0.1175 36 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.113 outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.4245 time to fit residues: 52.6377 After: r_work=0.1059 r_free=0.1193 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.136164 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 3.810121 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 0.1095 0.1221 0.0126 0.003 0.7 0.0 0.0 0.0 0 0.057 0.1063 0.1193 0.0130 0.004 0.9 0.0 0.0 0.0 0 0.170 0.1050 0.1181 0.0130 0.005 1.0 0.0 0.0 0.0 0 0.341 0.1045 0.1177 0.0132 0.006 1.0 0.0 0.0 0.0 0 0.511 0.1043 0.1175 0.0133 0.007 1.1 0.0 0.0 0.0 0 0.682 0.1041 0.1174 0.0133 0.007 1.1 0.0 0.0 0.0 0 0.852 0.1040 0.1173 0.0134 0.008 1.1 0.0 0.0 0.0 0 1.023 0.1039 0.1172 0.0133 0.008 1.2 0.0 0.0 0.0 0 1.193 0.1044 0.1177 0.0133 0.006 1.0 0.0 0.0 0.0 0 0.568 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1039 0.1172 0.0133 0.008 1.2 0.0 0.0 0.0 0 1.193 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1039 r_free=0.1172 36 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.168 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1484 After: r_work=0.1039 r_free=0.1172 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.39 11.72 1.33 2.442 12.001 3.810 3.719 10.39 11.72 1.33 2.442 12.001 0.114 3.719 10.39 11.72 1.33 2.442 12.001 0.476 3.719 10.39 11.72 1.33 2.442 12.001 1.905 3.719 10.39 11.72 1.33 2.442 12.001 3.810 3.719 10.41 11.73 1.32 2.444 12.002 5.715 3.719 10.41 11.72 1.31 2.446 12.002 7.620 3.719 10.44 11.74 1.30 2.462 11.995 9.525 3.719 10.45 11.73 1.28 2.635 11.939 11.430 3.711 10.45 11.73 1.28 2.714 11.919 13.335 3.707 10.42 11.71 1.28 2.691 11.926 15.240 3.705 10.40 11.69 1.29 2.693 11.928 17.146 3.703 10.39 11.68 1.29 2.675 11.934 19.051 3.702 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 19.051 Accepted refinement result: 10.39 11.68 1.29 2.675 11.934 19.051 3.702 Individual atomic B min max mean iso aniso Overall: 2.90 56.58 9.18 0.95 0 1563 Protein: 2.90 23.78 6.04 0.93 0 1240 Water: 4.25 56.58 21.93 N/A 0 300 Other: 6.97 21.64 12.25 N/A 0 23 Chain A: 2.90 56.58 9.18 N/A 0 1563 Histogram: Values Number of atoms 2.90 - 8.27 1116 8.27 - 13.63 182 13.63 - 19.00 76 19.00 - 24.37 64 24.37 - 29.74 42 29.74 - 35.11 60 35.11 - 40.48 17 40.48 - 45.85 4 45.85 - 51.21 0 51.21 - 56.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1039 r_free=0.1169 r_work=0.1040 r_free=0.1170 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1040 r_free = 0.1170 target_work(ml) = 3.703 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1040 r_free = 0.1170 target_work(ml) = 3.703 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.85 - 29.60 A, n_refl.=123340 (all), 5.02 % free)-----------| | | | r_work= 0.1040 r_free= 0.1170 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 3.702846 | | target function (ml) not normalized (work): 433792.069351 | | target function (ml) not normalized (free): 23477.466520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1040 0.1170 n_refl.: 123340 re-set all scales: r(all,work,free)=0.1314 0.1319 0.1278 n_refl.: 123340 remove outliers: r(all,work,free)=0.1314 0.1319 0.1278 n_refl.: 123340 overall B=-0.05 to atoms: r(all,work,free)=0.1294 0.1299 0.1272 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1045 0.1038 0.1167 n_refl.: 123340 remove outliers: r(all,work,free)=0.1045 0.1038 0.1167 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.1950 506.188 475.442 1.078 0.899 0.400 10.177-7.930 100.00 91 9 0.1742 483.674 470.532 1.075 0.900 0.400 7.929-6.185 100.00 198 10 0.1798 371.468 368.192 1.101 0.900 0.410 6.173-4.813 100.00 395 17 0.1436 439.682 429.674 1.082 0.900 0.450 4.812-3.754 100.00 805 46 0.1106 587.760 582.758 1.115 0.901 0.450 3.748-2.922 100.00 1685 76 0.1211 513.885 506.939 1.115 0.901 0.240 2.922-2.277 100.00 3410 183 0.1278 337.419 331.669 1.076 0.901 0.000 2.276-1.774 99.99 7110 384 0.1074 253.911 249.747 1.121 0.900 0.000 1.774-1.382 100.00 14808 836 0.0981 142.533 140.108 1.103 0.900 0.000 1.382-1.077 99.96 31030 1619 0.0806 96.149 94.570 1.095 0.899 0.000 1.077-0.850 95.46 57526 3003 0.1072 47.085 46.160 1.101 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0115 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1038 r_free=0.1167 After: r_work=0.1039 r_free=0.1167 ================================== NQH flips ================================== r_work=0.1039 r_free=0.1167 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1039 r_free=0.1167 ========================= Local real-space refinement ========================= Before: r_work=0.1039 r_free=0.1167 36 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.111 outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 1.3177 time to fit residues: 48.6679 After: r_work=0.1059 r_free=0.1187 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.047242 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 3.774412 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 0.1102 0.1222 0.0120 0.004 0.8 0.0 0.0 0.0 0 0.052 0.1072 0.1197 0.0125 0.004 0.9 0.0 0.0 0.0 0 0.157 0.1059 0.1186 0.0127 0.005 1.0 0.0 0.0 0.0 0 0.314 0.1052 0.1180 0.0128 0.006 1.0 0.0 0.0 0.0 0 0.471 0.1049 0.1177 0.0128 0.007 1.1 0.0 0.0 0.0 0 0.628 0.1046 0.1174 0.0128 0.007 1.1 0.0 0.0 0.0 0 0.785 0.1045 0.1173 0.0128 0.008 1.1 0.0 0.0 0.0 0 0.943 0.1044 0.1172 0.0128 0.008 1.2 0.0 0.0 0.0 0 1.100 0.1051 0.1179 0.0128 0.006 1.1 0.0 0.0 0.0 0 0.524 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1044 0.1172 0.0128 0.008 1.2 0.0 0.0 0.0 0 1.100 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1044 r_free=0.1172 35 residues out of total 135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.111 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1081 After: r_work=0.1044 r_free=0.1172 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.44 11.72 1.28 2.387 11.728 3.774 3.709 10.44 11.72 1.28 2.387 11.728 0.113 3.709 10.44 11.72 1.28 2.387 11.728 0.472 3.709 10.44 11.72 1.28 2.387 11.728 1.887 3.709 10.44 11.72 1.28 2.387 11.728 3.774 3.709 10.45 11.72 1.27 2.387 11.729 5.662 3.709 10.46 11.72 1.26 2.388 11.730 7.549 3.709 10.47 11.72 1.24 2.399 11.726 9.436 3.709 10.49 11.72 1.23 2.568 11.678 11.323 3.704 10.47 11.71 1.24 2.591 11.675 13.210 3.700 10.44 11.68 1.24 2.574 11.681 15.098 3.698 10.42 11.66 1.25 2.568 11.684 16.985 3.696 10.40 11.66 1.25 2.553 11.690 18.872 3.695 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 18.872 Accepted refinement result: 10.40 11.66 1.25 2.553 11.690 18.872 3.695 Individual atomic B min max mean iso aniso Overall: 2.87 56.57 9.05 0.94 0 1563 Protein: 2.87 22.62 5.98 0.91 0 1240 Water: 4.19 56.57 21.50 N/A 0 300 Other: 6.90 20.54 11.82 N/A 0 23 Chain A: 2.87 56.57 9.05 N/A 0 1563 Histogram: Values Number of atoms 2.87 - 8.24 1119 8.24 - 13.61 189 13.61 - 18.98 75 18.98 - 24.35 58 24.35 - 29.72 45 29.72 - 35.09 54 35.09 - 40.46 17 40.46 - 45.83 4 45.83 - 51.20 0 51.20 - 56.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1041 r_free=0.1166 r_work=0.1041 r_free=0.1167 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1041 r_free = 0.1167 target_work(ml) = 3.696 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1041 r_free = 0.1167 target_work(ml) = 3.696 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.85 - 29.60 A, n_refl.=123340 (all), 5.02 % free)-----------| | | | r_work= 0.1041 r_free= 0.1167 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 3.695504 | | target function (ml) not normalized (work): 432932.014026 | | target function (ml) not normalized (free): 23421.504268 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.60 - 2.64 1.00 4357 226 0.1290 0.1471 5.7437 5.8486| | 2: 2.64 - 2.10 1.00 4126 240 0.1210 0.1337 5.2894 5.3563| | 3: 2.10 - 1.83 1.00 4085 198 0.1084 0.1298 4.9261 5.0421| | 4: 1.83 - 1.66 1.00 4079 214 0.1075 0.1192 4.594 4.6549| | 5: 1.66 - 1.54 1.00 4021 220 0.0995 0.1101 4.3425 4.3824| | 6: 1.54 - 1.45 1.00 4017 219 0.0931 0.1019 4.1537 4.2405| | 7: 1.45 - 1.38 1.00 3973 250 0.0942 0.0992 4.0444 4.0694| | 8: 1.38 - 1.32 1.00 4019 192 0.0905 0.0922 3.9201 3.9533| | 9: 1.32 - 1.27 1.00 4006 220 0.0903 0.0978 3.8451 3.9639| | 10: 1.27 - 1.23 1.00 3999 193 0.0827 0.0871 3.7579 3.8213| | 11: 1.23 - 1.19 1.00 3996 189 0.0792 0.0849 3.6833 3.7628| | 12: 1.19 - 1.15 1.00 4002 231 0.0743 0.0872 3.605 3.73| | 13: 1.15 - 1.12 1.00 3978 211 0.0737 0.0771 3.5273 3.5588| | 14: 1.12 - 1.10 1.00 3923 227 0.0692 0.0719 3.4121 3.4739| | 15: 1.10 - 1.07 1.00 3981 204 0.0713 0.0760 3.3403 3.4284| | 16: 1.07 - 1.05 1.00 3990 188 0.0737 0.0920 3.2849 3.4236| | 17: 1.05 - 1.03 1.00 3994 208 0.0769 0.1021 3.2461 3.3729| | 18: 1.03 - 1.01 1.00 3947 201 0.0763 0.0952 3.1809 3.2941| | 19: 1.01 - 0.99 1.00 3960 204 0.0812 0.0992 3.149 3.2618| | 20: 0.99 - 0.97 1.00 3968 182 0.0870 0.1026 3.1273 3.2127| | 21: 0.97 - 0.96 1.00 3970 217 0.0911 0.1046 3.1034 3.2402| | 22: 0.96 - 0.94 1.00 3941 211 0.0968 0.1085 3.1001 3.2051| | 23: 0.94 - 0.93 1.00 3927 223 0.1013 0.1182 3.1147 3.2085| | 24: 0.93 - 0.92 1.00 3966 208 0.1167 0.1182 3.1668 3.238| | 25: 0.92 - 0.90 1.00 3938 197 0.1177 0.1257 3.1351 3.222| | 26: 0.90 - 0.89 1.00 3924 218 0.1287 0.1451 3.1409 3.2986| | 27: 0.89 - 0.88 1.00 3965 216 0.1394 0.1595 3.181 3.2464| | 28: 0.88 - 0.87 0.97 3827 200 0.1774 0.1848 3.2975 3.2746| | 29: 0.87 - 0.86 0.84 3308 174 0.2248 0.2536 3.4378 3.5802| | 30: 0.86 - 0.85 0.50 1964 108 0.2691 0.2915 3.4867 3.431| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.60 - 2.64 4357 226 0.93 11.21 1.00 1.09 13878.62| | 2: 2.64 - 2.10 4126 240 0.93 11.89 1.00 1.07 6867.72| | 3: 2.10 - 1.83 4085 198 0.95 9.59 1.00 1.07 3065.23| | 4: 1.83 - 1.66 4079 214 0.95 9.50 1.00 1.07 1600.85| | 5: 1.66 - 1.54 4021 220 0.95 8.61 1.00 1.08 942.50| | 6: 1.54 - 1.45 4017 219 0.96 7.41 1.00 1.08 625.57| | 7: 1.45 - 1.38 3973 250 0.97 6.91 1.00 1.08 482.22| | 8: 1.38 - 1.32 4019 192 0.97 6.67 1.01 1.08 380.90| | 9: 1.32 - 1.27 4006 220 0.97 6.70 1.00 1.09 330.17| | 10: 1.27 - 1.23 3999 193 0.97 5.77 1.00 1.08 277.60| | 11: 1.23 - 1.19 3996 189 0.97 5.39 1.00 1.09 236.96| | 12: 1.19 - 1.15 4002 231 0.98 4.97 1.00 1.09 207.27| | 13: 1.15 - 1.12 3978 211 0.98 4.68 1.00 1.08 172.88| | 14: 1.12 - 1.10 3923 227 0.98 4.45 1.00 1.08 142.77| | 15: 1.10 - 1.07 3981 204 0.98 4.50 1.00 1.08 119.87| | 16: 1.07 - 1.05 3990 188 0.98 4.84 1.00 1.09 111.46| | 17: 1.05 - 1.03 3994 208 0.98 5.39 1.01 1.10 106.94| | 18: 1.03 - 1.01 3947 201 0.98 5.55 1.01 1.10 98.27| | 19: 1.01 - 0.99 3960 204 0.97 5.90 1.01 1.10 87.00| | 20: 0.99 - 0.97 3968 182 0.97 6.18 1.02 1.10 81.20| | 21: 0.97 - 0.96 3970 217 0.97 6.40 1.02 1.10 78.59| | 22: 0.96 - 0.94 3941 211 0.97 7.13 1.02 1.10 76.44| | 23: 0.94 - 0.93 3927 223 0.97 7.42 1.02 1.10 76.63| | 24: 0.93 - 0.92 3966 208 0.97 8.28 1.00 1.10 76.83| | 25: 0.92 - 0.90 3938 197 0.97 8.70 1.00 1.08 76.72| | 26: 0.90 - 0.89 3924 218 0.96 10.30 0.99 1.07 80.99| | 27: 0.89 - 0.88 3965 216 0.95 11.07 0.98 1.04 85.52| | 28: 0.88 - 0.87 3827 200 0.94 12.94 0.96 1.02 93.47| | 29: 0.87 - 0.86 3308 174 0.91 16.36 0.92 0.99 128.05| | 30: 0.86 - 0.85 1964 108 0.86 22.39 0.90 0.92 167.45| |alpha: min = 0.89 max = 1.10 mean = 1.08| |beta: min = 75.75 max = 15716.73 mean = 1099.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.96| |phase err.(work): min = 0.00 max = 89.93 mean = 7.96| |phase err.(test): min = 0.00 max = 89.52 mean = 8.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1041 0.1167 n_refl.: 123340 re-set all scales: r(all,work,free)=0.1301 0.1306 0.1270 n_refl.: 123340 remove outliers: r(all,work,free)=0.1301 0.1306 0.1270 n_refl.: 123340 overall B=0.00 to atoms: r(all,work,free)=0.1301 0.1306 0.1270 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1041 0.1167 n_refl.: 123340 remove outliers: r(all,work,free)=0.1047 0.1041 0.1167 n_refl.: 123340 ======================== 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 29.596-10.246 100.00 93 6 0.1940 506.188 475.350 1.104 0.899 0.400 10.177-7.930 100.00 91 9 0.1747 483.674 471.256 1.106 0.900 0.400 7.929-6.185 100.00 198 10 0.1813 371.468 367.811 1.132 0.900 0.410 6.173-4.813 100.00 395 17 0.1445 439.682 429.413 1.109 0.900 0.440 4.812-3.754 100.00 805 46 0.1124 587.760 582.821 1.144 0.900 0.440 3.748-2.922 100.00 1685 76 0.1231 513.885 507.162 1.144 0.900 0.260 2.922-2.277 100.00 3410 183 0.1302 337.419 331.621 1.102 0.900 0.000 2.276-1.774 99.99 7110 384 0.1091 253.911 249.675 1.149 0.900 0.000 1.774-1.382 100.00 14808 836 0.0981 142.533 140.068 1.131 0.900 0.000 1.382-1.077 99.96 31030 1619 0.0794 96.149 94.489 1.124 0.899 0.000 1.077-0.850 95.46 57526 3003 0.1064 47.085 46.080 1.131 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0006 ================= 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 : 0.1433 0.1378 0.014 1.432 2.8 30.3 8.1 900 0.000 1_bss: 0.1176 0.1283 0.014 1.432 2.8 30.3 8.1 900 0.000 1_settarget: 0.1176 0.1283 0.014 1.432 2.8 30.3 8.1 900 0.000 1_nqh: 0.1176 0.1283 0.014 1.432 2.8 30.3 8.1 900 0.000 1_realsrl: 0.1191 0.1290 0.014 1.432 2.8 30.3 8.1 900 0.039 1_weight: 0.1191 0.1290 0.014 1.432 2.8 30.3 8.1 900 0.039 1_xyzrec: 0.1219 0.1355 0.007 0.892 2.8 30.3 8.1 900 0.131 1_realsrl2: 0.1219 0.1355 0.007 0.892 2.8 30.3 8.1 900 0.131 1_adp: 0.1149 0.1346 0.007 0.892 2.7 50.6 9.4 900 0.131 1_regHadp: 0.1141 0.1338 0.007 0.892 2.7 50.6 9.4 900 0.131 1_occ: 0.1140 0.1339 0.007 0.892 2.7 50.6 9.4 900 0.131 2_bss: 0.1135 0.1335 0.007 0.892 2.7 50.6 9.4 900 0.131 2_settarget: 0.1135 0.1335 0.007 0.892 2.7 50.6 9.4 900 0.131 2_updatecdl: 0.1135 0.1335 0.007 0.896 2.7 50.6 9.4 900 0.131 2_nqh: 0.1135 0.1335 0.007 0.896 2.7 50.6 9.4 900 0.131 2_realsrl: 0.1152 0.1349 0.007 0.896 2.7 50.6 9.4 900 0.129 2_weight: 0.1152 0.1349 0.007 0.896 2.7 50.6 9.4 900 0.129 2_xyzrec: 0.1122 0.1329 0.007 0.905 2.7 50.6 9.4 900 0.140 2_realsrl2: 0.1122 0.1329 0.007 0.905 2.7 50.6 9.4 900 0.140 2_adp: 0.1094 0.1313 0.007 0.905 2.7 56.5 9.6 900 0.140 2_regHadp: 0.1094 0.1312 0.007 0.905 2.7 56.5 9.6 900 0.140 2_occ: 0.1094 0.1314 0.007 0.905 2.7 56.5 9.6 900 0.140 3_bss: 0.1094 0.1315 0.007 0.905 2.7 56.5 9.6 900 0.140 3_settarget: 0.1094 0.1315 0.007 0.905 2.7 56.5 9.6 900 0.140 3_updatecdl: 0.1094 0.1315 0.007 0.904 2.7 56.5 9.6 900 0.140 3_nqh: 0.1094 0.1315 0.007 0.904 2.7 56.5 9.6 900 0.140 3_realsrl: 0.1099 0.1320 0.007 0.904 2.7 56.5 9.6 900 0.141 3_weight: 0.1099 0.1320 0.007 0.904 2.7 56.5 9.6 900 0.141 3_xyzrec: 0.1069 0.1244 0.007 1.108 2.7 56.5 9.6 900 0.126 3_realsrl2: 0.1069 0.1244 0.007 1.108 2.7 56.5 9.6 900 0.126 3_adp: 0.1044 0.1180 0.007 1.108 2.9 56.5 9.3 900 0.126 3_regHadp: 0.1045 0.1181 0.007 1.108 2.9 56.5 9.3 900 0.126 3_occ: 0.1045 0.1180 0.007 1.108 2.9 56.5 9.3 900 0.126 4_bss: 0.1040 0.1175 0.007 1.108 2.9 56.5 9.3 900 0.126 4_settarget: 0.1040 0.1175 0.007 1.108 2.9 56.5 9.3 900 0.126 4_updatecdl: 0.1040 0.1175 0.007 1.110 2.9 56.5 9.3 900 0.126 4_nqh: 0.1040 0.1175 0.007 1.110 2.9 56.5 9.3 900 0.126 4_realsrl: 0.1059 0.1193 0.007 1.110 2.9 56.5 9.3 900 0.126 4_weight: 0.1059 0.1193 0.007 1.110 2.9 56.5 9.3 900 0.126 4_xyzrec: 0.1039 0.1172 0.008 1.152 2.9 56.5 9.3 900 0.122 4_realsrl2: 0.1039 0.1172 0.008 1.152 2.9 56.5 9.3 900 0.122 4_adp: 0.1039 0.1169 0.008 1.152 2.9 56.6 9.2 900 0.122 4_regHadp: 0.1040 0.1170 0.008 1.152 2.9 56.6 9.2 900 0.122 4_occ: 0.1040 0.1170 0.008 1.152 2.9 56.6 9.2 900 0.122 5_bss: 0.1038 0.1167 0.008 1.152 2.8 56.5 9.1 900 0.122 5_settarget: 0.1038 0.1167 0.008 1.152 2.8 56.5 9.1 900 0.122 5_updatecdl: 0.1038 0.1167 0.008 1.152 2.8 56.5 9.1 900 0.122 5_setrh: 0.1039 0.1167 0.008 1.152 2.8 56.5 9.1 900 0.122 5_nqh: 0.1039 0.1167 0.008 1.152 2.8 56.5 9.1 900 0.122 5_realsrl: 0.1059 0.1187 0.008 1.152 2.8 56.5 9.1 900 0.124 5_weight: 0.1059 0.1187 0.008 1.152 2.8 56.5 9.1 900 0.124 5_xyzrec: 0.1044 0.1172 0.008 1.170 2.8 56.5 9.1 900 0.123 5_realsrl2: 0.1044 0.1172 0.008 1.170 2.8 56.5 9.1 900 0.123 5_adp: 0.1041 0.1166 0.008 1.170 2.9 56.6 9.0 900 0.123 5_regHadp: 0.1041 0.1167 0.008 1.170 2.9 56.6 9.0 900 0.123 5_occ: 0.1041 0.1167 0.008 1.170 2.9 56.6 9.0 900 0.123 end: 0.1041 0.1167 0.008 1.170 2.9 56.6 9.0 900 0.123 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4O8H_complete_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/highres/finalised/4O8H_complete_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.1900 Refinement macro-cycles (run) : 1678.4800 Write final files (write_after_run_outputs) : 62.9100 Total : 1743.5800 Total CPU time: 29.40 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-10 Time 16:41:34 PDT -0700 (1712792494.97 s) Start R-work = 0.1176, R-free = 0.1283 Final R-work = 0.1041, R-free = 0.1167 =============================================================================== Job complete usr+sys time: 1867.87 seconds wall clock time: 44 minutes 1.13 seconds (2641.13 seconds total)