Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1821005.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.25, per 1000 atoms: 0.37 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 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 - 3.00 Amino acid : True - 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: 0.33 Conformation dependent library (CDL) restraints added in 127.9 milliseconds Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 527 0.91 - 1.17: 1108 1.17 - 1.42: 653 1.42 - 1.67: 828 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.582 -0.228 1.10e-02 8.26e+03 4.30e+02 bond pdb=" CA ALA A 178 " pdb=" C ALA A 178 " ideal model delta sigma weight residual 1.523 1.279 0.245 1.30e-02 5.92e+03 3.54e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.237 1.443 -0.206 1.17e-02 7.31e+03 3.11e+02 bond pdb=" CA ALA A 6 " pdb=" C ALA A 6 " ideal model delta sigma weight residual 1.522 1.313 0.209 1.22e-02 6.72e+03 2.93e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.25e-02 6.40e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 3031 4.44 - 8.87: 1883 8.87 - 13.30: 696 13.30 - 17.74: 146 17.74 - 22.17: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.59 -13.39 9.00e-01 1.23e+00 2.21e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 130.80 -12.17 9.20e-01 1.18e+00 1.75e+02 angle pdb=" O MET A 26 " pdb=" C MET A 26 " pdb=" N ARG A 27 " ideal model delta sigma weight residual 122.07 109.91 12.16 1.03e+00 9.43e-01 1.39e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 118.86 -11.66 1.00e+00 1.00e+00 1.36e+02 angle pdb=" C PRO A 43 " pdb=" N VAL A 44 " pdb=" CA VAL A 44 " ideal model delta sigma weight residual 123.14 107.94 15.20 1.31e+00 5.83e-01 1.35e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 931 16.71 - 33.42: 121 33.42 - 50.13: 45 50.13 - 66.84: 10 66.84 - 83.55: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.212: 95 0.212 - 0.416: 71 0.416 - 0.620: 51 0.620 - 0.823: 15 0.823 - 1.027: 11 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.51 1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.54 1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 8.37e-02 2.10e+02 pdb=" CG PHE A 119 " -0.178 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.037 2.00e-02 2.50e+03 5.39e-02 8.72e+01 pdb=" CG TYR A 139 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.116 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.093 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 57 " -0.046 2.00e-02 2.50e+03 8.74e-02 7.65e+01 pdb=" C SER A 57 " 0.151 2.00e-02 2.50e+03 pdb=" O SER A 57 " -0.060 2.00e-02 2.50e+03 pdb=" N LEU A 58 " -0.045 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1092 2.33 - 2.89: 8109 2.89 - 3.46: 10462 3.46 - 4.03: 15214 4.03 - 4.60: 21740 Nonbonded interactions: 56617 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.808 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.824 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.855 1.850 ... (remaining 56612 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: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_1821005_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1900 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785494 | | target function (ml) not normalized (work): 232048.343155 | | target function (ml) not normalized (free): 11786.481203 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3027 0.2070 7.1455 4.9341| | 2: 3.57 - 2.84 1.00 2876 122 0.2434 0.1790 4.339 4.3348| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1520 4.1149 4.1261| | 4: 2.47 - 2.25 1.00 2825 136 0.2375 0.1414 3.8212 3.8176| | 5: 2.25 - 2.09 1.00 2756 127 0.2457 0.1433 3.7858 3.8036| | 6: 2.09 - 1.97 1.00 2846 113 0.2548 0.1573 3.4563 3.5032| | 7: 1.97 - 1.87 1.00 2787 165 0.2559 0.1731 3.1189 3.1962| | 8: 1.87 - 1.79 1.00 2789 144 0.2470 0.1863 3.029 3.0894| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1762 2.8819 2.9265| | 10: 1.72 - 1.66 1.00 2789 158 0.2388 0.1912 2.7973 2.8482| | 11: 1.66 - 1.61 1.00 2740 147 0.2518 0.1881 2.7339 2.7714| | 12: 1.61 - 1.56 1.00 2787 146 0.2508 0.2048 2.6462 2.6574| | 13: 1.56 - 1.52 1.00 2745 130 0.2587 0.1842 2.5774 2.5639| | 14: 1.52 - 1.48 1.00 2803 134 0.2557 0.2139 2.4991 2.5916| | 15: 1.48 - 1.45 1.00 2738 128 0.2599 0.2267 2.4118 2.5217| | 16: 1.45 - 1.42 1.00 2756 161 0.2627 0.2181 2.3803 2.4352| | 17: 1.42 - 1.39 1.00 2785 139 0.2699 0.2266 2.3372 2.428| | 18: 1.39 - 1.36 1.00 2741 179 0.2656 0.2099 2.2582 2.3232| | 19: 1.36 - 1.34 1.00 2807 134 0.2656 0.2349 2.232 2.3091| | 20: 1.34 - 1.32 1.00 2696 147 0.2710 0.2193 2.1942 2.1853| | 21: 1.32 - 1.30 1.00 2785 112 0.2693 0.2254 2.1558 2.1868| | 22: 1.29 - 1.27 1.00 2704 152 0.2696 0.2807 2.1139 2.2784| | 23: 1.27 - 1.26 1.00 2802 156 0.2852 0.2492 2.103 2.185| | 24: 1.26 - 1.24 1.00 2744 132 0.2829 0.2685 2.0842 2.1909| | 25: 1.24 - 1.22 1.00 2734 148 0.2800 0.2657 2.0376 2.1091| | 26: 1.22 - 1.21 1.00 2727 135 0.2826 0.2221 1.9994 2.019| | 27: 1.21 - 1.19 1.00 2814 148 0.2944 0.2477 1.986 1.9813| | 28: 1.19 - 1.18 1.00 2671 147 0.3022 0.2724 1.9865 1.9767| | 29: 1.18 - 1.16 1.00 2800 134 0.2956 0.2263 1.9547 1.8989| | 30: 1.16 - 1.15 1.00 2740 148 0.3005 0.2780 1.9227 1.958| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.58 2941 171 0.87 18.52 0.76 0.23 1435.76| | 2: 3.57 - 2.84 2876 122 0.81 25.65 1.27 0.23 1435.76| | 3: 2.84 - 2.48 2833 165 0.74 31.50 1.25 0.24 1189.25| | 4: 2.47 - 2.25 2825 136 0.82 25.16 1.26 0.25 549.53| | 5: 2.25 - 2.09 2756 127 0.78 28.70 1.28 0.25 549.53| | 6: 2.09 - 1.97 2846 113 0.84 22.03 1.29 0.25 298.42| | 7: 1.97 - 1.87 2787 165 0.90 15.97 1.29 0.25 84.27| | 8: 1.87 - 1.79 2789 144 0.86 20.49 1.25 0.25 84.27| | 9: 1.79 - 1.72 2745 138 0.88 18.22 1.23 0.25 52.21| | 10: 1.72 - 1.66 2789 158 0.87 19.54 1.22 0.25 45.79| | 11: 1.66 - 1.61 2740 147 0.86 20.93 1.25 0.25 44.33| | 12: 1.61 - 1.56 2787 146 0.89 18.27 1.23 0.25 29.49| | 13: 1.56 - 1.52 2745 130 0.86 20.50 1.24 0.25 29.49| | 14: 1.52 - 1.48 2803 134 0.86 20.80 1.24 0.25 26.61| | 15: 1.48 - 1.45 2738 128 0.86 20.78 1.24 0.25 21.33| | 16: 1.45 - 1.42 2756 161 0.85 22.20 1.23 0.25 21.33| | 17: 1.42 - 1.39 2785 139 0.86 21.01 1.24 0.25 18.26| | 18: 1.39 - 1.36 2741 179 0.86 21.67 1.23 0.25 16.49| | 19: 1.36 - 1.34 2807 134 0.85 22.52 1.23 0.25 16.49| | 20: 1.34 - 1.32 2696 147 0.86 21.35 1.22 0.25 13.45| | 21: 1.32 - 1.30 2785 112 0.85 22.38 1.20 0.25 13.23| | 22: 1.29 - 1.27 2704 152 0.85 22.65 1.21 0.24 12.91| | 23: 1.27 - 1.26 2802 156 0.85 22.54 1.22 0.24 11.25| | 24: 1.26 - 1.24 2744 132 0.85 23.11 1.21 0.24 11.25| | 25: 1.24 - 1.22 2734 148 0.84 23.44 1.20 0.24 10.44| | 26: 1.22 - 1.21 2727 135 0.85 23.32 1.20 0.24 9.53| | 27: 1.21 - 1.19 2814 148 0.84 24.05 1.21 0.24 9.53| | 28: 1.19 - 1.18 2671 147 0.84 23.80 1.19 0.23 8.37| | 29: 1.18 - 1.16 2800 134 0.85 23.65 1.16 0.23 7.94| | 30: 1.16 - 1.15 2740 148 0.83 24.92 1.15 0.23 7.94| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 7.94 max = 1435.76 mean = 207.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.32| |phase err.(test): min = 0.00 max = 89.55 mean = 22.19| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.245 1557 Z= 5.298 Angle : 5.247 19.084 2118 Z= 3.703 Chirality : 0.399 1.027 243 Planarity : 0.032 0.090 284 Dihedral : 13.708 83.547 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % 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: -2.52 (0.47), residues: 224 helix: -2.00 (0.41), residues: 107 sheet: -1.54 (0.67), residues: 38 loop : -0.83 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.084 0.018 ARG A 27 TYR 0.085 0.034 TYR A 141 PHE 0.170 0.041 PHE A 119 HIS 0.028 0.017 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1900 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785494 | | target function (ml) not normalized (work): 232048.343155 | | target function (ml) not normalized (free): 11786.481203 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2610 0.1900 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2610 0.1900 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1982 0.1900 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2002 0.2009 0.1916 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1631 0.1719 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1630 0.1719 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3821 386.500 358.413 0.730 0.917 0.407 11.894-9.307 99.02 97 4 0.1832 613.936 595.788 1.014 0.918 0.390 9.237-7.194 100.00 213 7 0.2129 502.124 491.276 1.038 0.918 0.353 7.162-5.571 100.00 427 22 0.2169 376.816 364.512 1.017 0.918 0.320 5.546-4.326 100.00 867 58 0.1312 517.276 511.300 1.046 0.919 0.239 4.315-3.360 100.00 1859 96 0.1154 491.933 487.694 1.093 0.920 0.199 3.356-2.611 100.00 3867 181 0.1425 323.174 319.880 1.084 0.921 0.048 2.608-2.026 99.99 8198 413 0.1353 214.235 212.454 1.094 0.922 0.000 2.025-1.573 100.00 17313 902 0.1638 104.621 103.908 1.092 0.925 0.000 1.573-1.221 100.00 36679 1900 0.2046 46.393 45.036 1.076 0.929 0.000 1.221-1.150 99.97 13689 708 0.2563 29.231 26.971 1.039 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1719 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1632 r_free=0.1724 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.670464 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2028.628373 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 0.1206 0.1455 0.0249 0.007 1.0 3.8 0.5 0.0 0 13.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 14.55 2.49 3.013 19.071 2028.628 0.017 12.06 14.55 2.48 3.008 19.071 60.859 0.017 12.13 14.52 2.40 2.695 19.070 253.579 0.017 12.49 15.22 2.73 2.734 19.231 1014.314 0.016 12.30 15.29 2.99 3.045 19.462 2028.628 0.015 12.25 15.39 3.14 3.309 19.631 3042.943 0.015 12.09 15.20 3.11 2.924 19.397 4057.257 0.015 12.16 15.38 3.22 3.305 19.604 5071.571 0.015 12.02 15.22 3.20 3.285 19.580 6085.885 0.015 12.10 15.42 3.32 3.099 19.452 7100.199 0.015 12.04 15.36 3.32 3.417 19.649 8114.513 0.015 12.02 15.36 3.34 3.502 19.687 9128.828 0.014 12.00 15.37 3.37 3.540 19.694 10143.142 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 253.579 Accepted refinement result: 12.13 14.52 2.40 2.695 19.070 253.579 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.47 20.10 3.36 0 1785 Protein: 9.09 115.27 17.00 3.37 0 1519 Water: 11.50 119.47 38.24 N/A 0 258 Other: 19.69 26.63 22.05 N/A 0 8 Chain A: 9.09 119.47 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1273 20.13 - 31.17 227 31.17 - 42.20 126 42.20 - 53.24 93 53.24 - 64.28 41 64.28 - 75.32 11 75.32 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1213 r_free=0.1452 r_work=0.1214 r_free=0.1456 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1214 r_free = 0.1456 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1452 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1452 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016401 | | target function (ls_wunit_k1) not normalized (work): 1366.189865 | | target function (ls_wunit_k1) not normalized (free): 109.376802 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1207 0.1452 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1665 0.1666 0.1684 n_refl.: 87593 remove outliers: r(all,work,free)=0.1665 0.1666 0.1684 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1670 0.1671 0.1687 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1206 0.1444 n_refl.: 87593 remove outliers: r(all,work,free)=0.1217 0.1206 0.1444 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3576 300.863 280.809 0.647 1.002 0.380 11.894-9.307 99.02 97 4 0.1642 481.966 469.166 0.924 1.003 0.380 9.237-7.194 100.00 213 7 0.1874 394.189 389.587 0.963 1.003 0.324 7.162-5.571 100.00 427 22 0.1852 295.817 289.716 0.934 1.003 0.269 5.546-4.326 100.00 867 58 0.1005 406.083 402.758 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0864 386.188 384.956 1.007 1.002 0.180 3.356-2.611 100.00 3867 181 0.1143 253.706 252.583 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.0993 168.184 167.502 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1081 82.132 82.345 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1430 36.421 35.936 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2245 22.948 21.433 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0424 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1444 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1207 r_free=0.1444 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1444 | n_water=258 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1214 r_free=0.1443 | n_water=252 | time (s): 22.920 (total time: 24.580) Filter (q & B) r_work=0.1217 r_free=0.1442 | n_water=249 | time (s): 2.490 (total time: 27.070) Compute maps r_work=0.1217 r_free=0.1442 | n_water=249 | time (s): 1.150 (total time: 28.220) Filter (map) r_work=0.1229 r_free=0.1450 | n_water=235 | time (s): 3.340 (total time: 31.560) Find peaks r_work=0.1229 r_free=0.1450 | n_water=235 | time (s): 0.560 (total time: 32.120) Add new water r_work=0.1374 r_free=0.1617 | n_water=446 | time (s): 3.330 (total time: 35.450) Refine new water occ: r_work=0.1281 r_free=0.1478 adp: r_work=0.1202 r_free=0.1423 occ: r_work=0.1218 r_free=0.1412 adp: r_work=0.1182 r_free=0.1393 occ: r_work=0.1185 r_free=0.1393 adp: r_work=0.1175 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1387 r_work=0.1175 r_free=0.1387 | n_water=446 | time (s): 58.400 (total time: 93.850) Filter (q & B) r_work=0.1180 r_free=0.1391 | n_water=429 | time (s): 2.660 (total time: 96.510) Filter (dist only) r_work=0.1180 r_free=0.1389 | n_water=428 | time (s): 35.970 (total time: 132.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.189632 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.196590 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 0.1649 0.1772 0.0122 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1509 0.1648 0.0139 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1373 0.1538 0.0164 0.002 0.5 5.4 0.0 0.0 0 0.500 0.1343 0.1515 0.0173 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1293 0.1474 0.0181 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1322 0.1498 0.0176 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1248 0.1447 0.0199 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1223 0.1429 0.0206 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1210 0.1417 0.0207 0.003 0.6 4.5 0.5 0.0 0 4.000 0.1200 0.1413 0.0213 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1197 0.1414 0.0217 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1190 0.1414 0.0224 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1189 0.1416 0.0227 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1187 0.1422 0.0235 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1186 0.1416 0.0231 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1184 0.1420 0.0237 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1181 0.1419 0.0238 0.007 0.9 5.1 0.5 0.6 0 12.000 0.1176 0.1409 0.0233 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1175 0.1412 0.0237 0.008 0.9 4.8 0.5 0.6 0 14.095 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1176 0.1409 0.0233 0.008 0.9 5.4 0.5 0.6 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 14.09 2.33 3.800 21.892 1483.197 0.015 11.76 14.09 2.33 3.800 21.892 44.496 0.015 11.76 14.09 2.33 3.800 21.892 185.400 0.015 11.92 14.43 2.52 3.652 21.890 741.598 0.015 11.96 14.81 2.85 3.454 22.133 1483.197 0.014 11.80 14.71 2.91 3.455 22.228 2224.795 0.014 11.76 14.77 3.01 3.483 22.241 2966.393 0.014 11.65 14.69 3.04 3.476 22.204 3707.991 0.014 11.62 14.78 3.16 3.484 22.123 4449.590 0.014 11.64 14.86 3.22 3.520 22.310 5191.188 0.014 11.59 14.76 3.17 3.520 22.259 5932.786 0.013 11.55 14.77 3.22 3.523 22.193 6674.385 0.013 11.55 14.79 3.24 3.542 22.245 7415.983 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: 185.400 Accepted refinement result: 11.76 14.09 2.33 3.800 21.892 185.400 0.015 Individual atomic B min max mean iso aniso Overall: 9.12 115.29 22.38 3.36 193 1762 Protein: 9.12 115.29 17.03 3.37 0 1519 Water: 11.52 76.71 41.38 N/A 193 235 Other: 19.72 26.66 22.07 N/A 0 8 Chain A: 9.12 115.29 19.62 N/A 0 1762 Chain S: 12.86 60.00 47.60 N/A 193 0 Histogram: Values Number of atoms 9.12 - 19.74 1260 19.74 - 30.35 246 30.35 - 40.97 161 40.97 - 51.59 139 51.59 - 62.21 125 62.21 - 72.82 13 72.82 - 83.44 5 83.44 - 94.06 4 94.06 - 104.68 0 104.68 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1409 r_work=0.1177 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1177 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1405 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1177 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014689 | | target function (ls_wunit_k1) not normalized (work): 1223.548889 | | target function (ls_wunit_k1) not normalized (free): 99.232942 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1177 0.1405 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1570 0.1568 0.1640 n_refl.: 87592 remove outliers: r(all,work,free)=0.1570 0.1568 0.1640 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1571 0.1569 0.1640 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1173 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1183 0.1171 0.1402 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3325 296.775 273.145 0.601 1.002 0.360 11.894-9.307 99.02 97 4 0.1584 481.966 472.976 0.917 1.003 0.350 9.237-7.194 100.00 213 7 0.1633 394.189 394.723 0.989 1.003 0.251 7.162-5.571 100.00 427 22 0.1540 295.817 292.445 0.939 1.003 0.218 5.546-4.326 100.00 867 58 0.0890 406.083 403.320 0.960 1.003 0.203 4.315-3.360 100.00 1859 96 0.0776 386.188 384.949 1.004 1.003 0.180 3.356-2.611 100.00 3867 181 0.1065 253.706 252.832 1.008 1.002 0.120 2.608-2.026 99.99 8198 413 0.1000 168.184 167.707 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1085 82.132 82.356 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1434 36.421 35.971 1.026 0.997 0.000 1.221-1.150 99.97 13689 708 0.2243 22.948 21.471 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0071 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1171 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1171 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1402 | n_water=428 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1171 r_free=0.1401 | n_water=422 | time (s): 35.040 (total time: 37.240) Filter (q & B) r_work=0.1171 r_free=0.1401 | n_water=422 | time (s): 0.960 (total time: 38.200) Compute maps r_work=0.1171 r_free=0.1401 | n_water=422 | time (s): 1.500 (total time: 39.700) Filter (map) r_work=0.1209 r_free=0.1379 | n_water=293 | time (s): 3.390 (total time: 43.090) Find peaks r_work=0.1209 r_free=0.1379 | n_water=293 | time (s): 0.660 (total time: 43.750) Add new water r_work=0.1318 r_free=0.1491 | n_water=482 | time (s): 3.200 (total time: 46.950) Refine new water occ: r_work=0.1230 r_free=0.1416 adp: r_work=0.1231 r_free=0.1418 occ: r_work=0.1208 r_free=0.1397 adp: r_work=0.1207 r_free=0.1397 occ: r_work=0.1192 r_free=0.1383 adp: r_work=0.1187 r_free=0.1381 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1381 r_work=0.1187 r_free=0.1381 | n_water=482 | time (s): 179.320 (total time: 226.270) Filter (q & B) r_work=0.1192 r_free=0.1380 | n_water=451 | time (s): 2.760 (total time: 229.030) Filter (dist only) r_work=0.1192 r_free=0.1378 | n_water=450 | time (s): 39.670 (total time: 268.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.734540 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.776460 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 0.1222 0.1354 0.0132 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1183 0.1317 0.0135 0.003 0.7 3.5 0.5 0.0 0 0.260 0.1165 0.1305 0.0140 0.004 0.8 3.2 0.5 0.0 0 0.520 0.1159 0.1305 0.0146 0.005 0.9 3.5 0.5 0.0 0 0.781 0.1153 0.1305 0.0151 0.006 1.0 3.2 0.5 0.0 0 1.041 0.1152 0.1308 0.0157 0.007 1.0 3.2 0.5 0.0 0 1.301 0.1149 0.1309 0.0160 0.007 1.1 3.5 0.5 0.0 0 1.561 0.1149 0.1306 0.0158 0.008 1.1 3.2 0.5 0.0 0 1.821 0.1158 0.1305 0.0147 0.005 0.9 3.5 0.5 0.0 0 0.867 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1305 0.0151 0.006 1.0 3.2 0.5 0.0 0 1.041 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 13.05 1.51 3.803 21.378 42.776 3.617 11.53 13.04 1.51 3.803 21.378 1.283 3.617 11.54 13.05 1.51 3.791 21.378 5.347 3.617 11.60 13.14 1.54 3.722 21.366 21.388 3.613 11.60 13.18 1.58 3.744 21.350 42.776 3.613 11.54 13.17 1.63 3.760 21.336 64.165 3.608 11.49 13.14 1.64 3.772 21.331 85.553 3.603 11.47 13.12 1.65 3.779 21.325 106.941 3.600 11.44 13.10 1.66 3.790 21.322 128.329 3.598 11.43 13.13 1.70 3.803 21.313 149.718 3.597 11.42 13.13 1.70 3.814 21.306 171.106 3.597 11.41 13.10 1.69 3.820 21.302 192.494 3.595 11.40 13.10 1.70 3.827 21.301 213.882 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.283 Accepted refinement result: 11.53 13.04 1.51 3.803 21.378 1.283 3.617 Individual atomic B min max mean iso aniso Overall: 9.12 115.30 21.44 3.36 218 1759 Protein: 9.12 115.30 17.04 3.37 0 1519 Water: 11.53 76.71 36.30 N/A 218 232 Other: 19.72 26.66 22.08 N/A 0 8 Chain A: 9.12 115.30 19.56 N/A 0 1759 Chain S: 12.87 60.00 36.58 N/A 218 0 Histogram: Values Number of atoms 9.12 - 19.74 1263 19.74 - 30.36 288 30.36 - 40.98 214 40.98 - 51.59 130 51.59 - 62.21 58 62.21 - 72.83 13 72.83 - 83.44 5 83.44 - 94.06 4 94.06 - 104.68 0 104.68 - 115.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1304 r_work=0.1153 r_free=0.1305 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1305 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1308 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1146 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611552 | | target function (ml) not normalized (work): 300816.971136 | | target function (ml) not normalized (free): 15837.669636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1308 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1484 0.1483 0.1531 n_refl.: 87589 remove outliers: r(all,work,free)=0.1484 0.1483 0.1531 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1483 0.1482 0.1530 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1142 0.1302 n_refl.: 87589 remove outliers: r(all,work,free)=0.1148 0.1140 0.1302 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3961 291.334 266.256 0.494 1.000 0.320 11.894-9.307 97.06 95 4 0.2325 482.189 458.978 0.868 1.002 0.277 9.237-7.194 98.64 210 7 0.2283 386.684 385.517 0.956 1.002 0.194 7.162-5.571 100.00 427 22 0.2082 295.817 285.098 0.914 1.002 0.163 5.546-4.326 100.00 867 58 0.1105 406.083 401.554 0.966 1.002 0.160 4.315-3.360 100.00 1859 96 0.0928 386.188 383.798 1.004 1.002 0.160 3.356-2.611 100.00 3867 181 0.1122 253.706 251.685 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0926 168.184 167.392 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.132 82.423 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.421 36.009 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.948 21.486 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1302 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1140 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1302 | n_water=450 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1140 r_free=0.1301 | n_water=448 | time (s): 35.450 (total time: 37.790) Filter (q & B) r_work=0.1141 r_free=0.1302 | n_water=447 | time (s): 2.830 (total time: 40.620) Compute maps r_work=0.1141 r_free=0.1302 | n_water=447 | time (s): 1.330 (total time: 41.950) Filter (map) r_work=0.1161 r_free=0.1295 | n_water=342 | time (s): 3.320 (total time: 45.270) Find peaks r_work=0.1161 r_free=0.1295 | n_water=342 | time (s): 0.620 (total time: 45.890) Add new water r_work=0.1220 r_free=0.1352 | n_water=500 | time (s): 2.970 (total time: 48.860) Refine new water occ: r_work=0.1154 r_free=0.1298 adp: r_work=0.1154 r_free=0.1299 occ: r_work=0.1141 r_free=0.1288 adp: r_work=0.1139 r_free=0.1289 occ: r_work=0.1131 r_free=0.1283 adp: r_work=0.1127 r_free=0.1282 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1282 r_work=0.1127 r_free=0.1282 | n_water=500 | time (s): 192.080 (total time: 240.940) Filter (q & B) r_work=0.1131 r_free=0.1290 | n_water=468 | time (s): 3.330 (total time: 244.270) Filter (dist only) r_work=0.1132 r_free=0.1289 | n_water=467 | time (s): 38.240 (total time: 282.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.803042 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.581899 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 0.1188 0.1324 0.0136 0.002 0.6 4.2 0.5 0.0 0 0.090 0.1151 0.1297 0.0146 0.003 0.8 3.5 0.5 0.0 0 0.270 0.1137 0.1290 0.0152 0.005 0.9 4.2 0.5 0.0 0 0.541 0.1131 0.1288 0.0157 0.006 1.0 4.2 0.5 0.0 0 0.811 0.1128 0.1288 0.0160 0.007 1.0 3.8 0.5 0.0 0 1.082 0.1125 0.1288 0.0163 0.007 1.1 3.8 0.5 0.0 0 1.352 0.1123 0.1287 0.0164 0.008 1.1 4.5 0.5 0.0 0 1.623 0.1121 0.1285 0.0164 0.009 1.1 5.1 0.5 0.0 0 1.893 0.1130 0.1287 0.0157 0.006 1.0 3.8 0.5 0.0 0 0.902 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1285 0.0164 0.009 1.1 5.1 0.5 0.0 0 1.893 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 12.85 1.64 3.803 21.364 35.582 3.598 11.21 12.85 1.64 3.803 21.364 1.067 3.598 11.21 12.85 1.64 3.803 21.364 4.448 3.598 11.26 12.90 1.64 3.724 21.359 17.791 3.594 11.30 12.98 1.69 3.739 21.344 35.582 3.596 11.26 13.00 1.74 3.756 21.328 53.373 3.593 11.23 13.00 1.76 3.767 21.319 71.164 3.589 11.19 12.96 1.77 3.776 21.317 88.955 3.586 11.16 12.93 1.77 3.784 21.318 106.746 3.583 11.16 12.95 1.80 3.792 21.309 124.537 3.582 11.14 12.94 1.81 3.800 21.308 142.328 3.581 11.12 12.95 1.82 3.809 21.305 160.119 3.580 11.14 12.96 1.82 3.818 21.294 177.909 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.067 Accepted refinement result: 11.21 12.85 1.64 3.803 21.364 1.067 3.598 Individual atomic B min max mean iso aniso Overall: 9.12 115.29 21.42 3.36 235 1759 Protein: 9.12 115.29 17.03 3.37 0 1519 Water: 11.52 76.71 35.68 N/A 235 232 Other: 19.71 26.65 22.07 N/A 0 8 Chain A: 9.12 115.29 19.56 N/A 0 1759 Chain S: 12.86 60.00 35.35 N/A 235 0 Histogram: Values Number of atoms 9.12 - 19.74 1266 19.74 - 30.35 303 30.35 - 40.97 217 40.97 - 51.59 129 51.59 - 62.20 55 62.20 - 72.82 13 72.82 - 83.44 5 83.44 - 94.06 4 94.06 - 104.67 0 104.67 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1121 r_free=0.1285 r_work=0.1121 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1121 r_free = 0.1285 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1282 target_work(ml) = 3.595 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1116 r_free= 0.1282 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.594982 | | target function (ml) not normalized (work): 299415.264762 | | target function (ml) not normalized (free): 15790.750340 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1116 0.1282 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1453 0.1452 0.1499 n_refl.: 87583 remove outliers: r(all,work,free)=0.1453 0.1452 0.1499 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1452 0.1451 0.1499 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1115 0.1284 n_refl.: 87583 remove outliers: r(all,work,free)=0.1120 0.1111 0.1284 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3971 285.391 250.989 0.442 0.999 0.291 11.894-9.307 93.14 91 4 0.2306 469.168 465.515 0.872 1.001 0.213 9.237-7.194 98.18 209 7 0.2285 385.678 380.597 0.938 1.002 0.160 7.162-5.571 100.00 427 22 0.2080 295.817 286.481 0.913 1.002 0.150 5.546-4.326 100.00 867 58 0.1071 406.083 401.906 0.968 1.002 0.150 4.315-3.360 100.00 1859 96 0.0895 386.188 384.116 1.002 1.002 0.130 3.356-2.611 100.00 3867 181 0.1080 253.706 251.872 1.009 1.002 0.050 2.608-2.026 99.99 8198 413 0.0897 168.184 167.511 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0871 82.132 82.438 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.421 36.015 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.948 21.492 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0153 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1111 r_free=0.1284 After: r_work=0.1113 r_free=0.1284 ================================== NQH flips ================================== r_work=0.1113 r_free=0.1284 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1113 r_free=0.1284 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1113 r_free=0.1284 | n_water=467 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1113 r_free=0.1285 | n_water=466 | time (s): 51.980 (total time: 54.440) Filter (q & B) r_work=0.1113 r_free=0.1285 | n_water=465 | time (s): 4.000 (total time: 58.440) Compute maps r_work=0.1113 r_free=0.1285 | n_water=465 | time (s): 1.830 (total time: 60.270) Filter (map) r_work=0.1135 r_free=0.1276 | n_water=377 | time (s): 3.920 (total time: 64.190) Find peaks r_work=0.1135 r_free=0.1276 | n_water=377 | time (s): 0.720 (total time: 64.910) Add new water r_work=0.1181 r_free=0.1316 | n_water=508 | time (s): 3.880 (total time: 68.790) Refine new water occ: r_work=0.1134 r_free=0.1281 adp: r_work=0.1134 r_free=0.1281 occ: r_work=0.1123 r_free=0.1273 adp: r_work=0.1121 r_free=0.1272 occ: r_work=0.1115 r_free=0.1268 adp: r_work=0.1112 r_free=0.1266 ADP+occupancy (water only), MIN, final r_work=0.1112 r_free=0.1266 r_work=0.1112 r_free=0.1266 | n_water=508 | time (s): 225.940 (total time: 294.730) Filter (q & B) r_work=0.1119 r_free=0.1276 | n_water=472 | time (s): 3.720 (total time: 298.450) Filter (dist only) r_work=0.1120 r_free=0.1276 | n_water=471 | time (s): 50.460 (total time: 348.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.762168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 30.588803 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 0.1215 0.1335 0.0120 0.004 0.7 6.7 0.0 0.0 0 0.088 0.1162 0.1299 0.0137 0.004 0.8 5.4 0.0 0.0 0 0.264 0.1141 0.1287 0.0145 0.005 0.9 6.1 0.5 0.0 0 0.529 0.1135 0.1283 0.0148 0.006 1.0 5.8 0.5 0.0 0 0.793 0.1127 0.1278 0.0151 0.006 1.1 5.8 0.5 0.0 0 1.057 0.1124 0.1277 0.0152 0.007 1.1 6.1 0.5 0.0 0 1.322 0.1121 0.1276 0.0155 0.008 1.1 6.1 0.5 0.0 0 1.586 0.1120 0.1275 0.0156 0.009 1.1 6.1 0.5 0.0 0 1.850 0.1131 0.1281 0.0149 0.006 1.0 5.4 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1275 0.0156 0.009 1.1 6.1 0.5 0.0 0 1.850 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 12.75 1.56 3.802 21.401 30.589 3.595 11.20 12.75 1.56 3.802 21.401 0.918 3.595 11.20 12.75 1.56 3.802 21.401 3.824 3.595 11.21 12.76 1.55 3.750 21.400 15.294 3.592 11.31 12.90 1.59 3.731 21.379 30.589 3.596 11.23 12.85 1.62 3.747 21.377 45.883 3.590 11.26 12.93 1.67 3.751 21.360 61.178 3.590 11.17 12.87 1.69 3.770 21.362 76.472 3.585 11.18 12.87 1.69 3.779 21.354 91.766 3.584 11.14 12.85 1.71 3.786 21.355 107.061 3.582 11.16 12.88 1.72 3.790 21.346 122.355 3.582 11.13 12.84 1.71 3.798 21.349 137.650 3.580 11.11 12.82 1.72 3.803 21.350 152.944 3.578 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 3.824 Accepted refinement result: 11.20 12.75 1.56 3.802 21.401 3.824 3.595 Individual atomic B min max mean iso aniso Overall: 9.11 115.29 21.49 3.36 240 1758 Protein: 9.11 115.29 17.03 3.37 0 1519 Water: 11.52 76.70 35.88 N/A 240 231 Other: 19.71 26.65 22.07 N/A 0 8 Chain A: 9.11 115.29 19.54 N/A 0 1758 Chain S: 12.86 60.00 35.81 N/A 240 0 Histogram: Values Number of atoms 9.11 - 19.73 1265 19.73 - 30.35 300 30.35 - 40.96 219 40.96 - 51.58 133 51.58 - 62.20 57 62.20 - 72.82 13 72.82 - 83.43 5 83.43 - 94.05 4 94.05 - 104.67 0 104.67 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1120 r_free=0.1275 r_work=0.1120 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1120 r_free = 0.1275 target_work(ml) = 3.595 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1117 r_free = 0.1275 target_work(ml) = 3.594 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1117 r_free= 0.1275 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.594173 | | target function (ml) not normalized (work): 299319.158779 | | target function (ml) not normalized (free): 15783.587048 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1298 0.1312 5.6096 5.5842| | 2: 3.57 - 2.84 1.00 2888 124 0.1045 0.1306 5.1351 5.1797| | 3: 2.83 - 2.48 1.00 2820 163 0.1080 0.1187 4.9207 4.944| | 4: 2.47 - 2.25 1.00 2825 136 0.0883 0.0989 4.6077 4.6387| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.1001 4.5552 4.6297| | 6: 2.09 - 1.97 1.00 2846 113 0.0844 0.1075 4.2493 4.3675| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1068 3.9723 4.0737| | 8: 1.87 - 1.79 1.00 2789 144 0.0903 0.1116 3.8816 3.9966| | 9: 1.79 - 1.72 1.00 2745 138 0.0861 0.1184 3.6361 3.8349| | 10: 1.72 - 1.66 1.00 2831 160 0.0908 0.1202 3.5571 3.705| | 11: 1.66 - 1.61 1.00 2712 147 0.0859 0.1013 3.4881 3.5588| | 12: 1.61 - 1.56 1.00 2773 144 0.0894 0.1143 3.3194 3.4685| | 13: 1.56 - 1.52 1.00 2745 130 0.0937 0.1029 3.2975 3.3813| | 14: 1.52 - 1.48 1.00 2803 134 0.0969 0.1038 3.2303 3.3097| | 15: 1.48 - 1.45 1.00 2738 128 0.0990 0.1193 3.143 3.2538| | 16: 1.45 - 1.42 1.00 2756 161 0.1046 0.1243 3.1266 3.2395| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1314 3.1134 3.2387| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1318 3.0989 3.2292| | 19: 1.36 - 1.34 1.00 2807 134 0.1255 0.1573 3.1062 3.2738| | 20: 1.34 - 1.32 1.00 2696 147 0.1360 0.1482 3.1075 3.1542| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1499 3.1114 3.1033| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1991 3.1207 3.2956| | 23: 1.27 - 1.26 1.00 2802 156 0.1640 0.1800 3.1294 3.2062| | 24: 1.26 - 1.24 1.00 2744 132 0.1705 0.1842 3.1252 3.2323| | 25: 1.24 - 1.22 1.00 2733 148 0.1876 0.2152 3.1389 3.2562| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1752 3.146 3.1968| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2169 3.1685 3.1637| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2297 3.1641 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2379 3.1451 3.2265| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2453 3.1409 3.1647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 7.99 1.00 0.97 5390.75| | 2: 3.57 - 2.84 2888 124 0.93 12.01 1.01 0.97 5390.75| | 3: 2.83 - 2.48 2820 163 0.90 16.02 0.99 0.97 4510.52| | 4: 2.47 - 2.25 2825 136 0.92 13.06 1.00 0.98 2240.68| | 5: 2.25 - 2.09 2756 127 0.91 15.17 1.01 0.98 2240.68| | 6: 2.09 - 1.97 2846 113 0.93 12.16 1.02 0.98 1306.58| | 7: 1.97 - 1.87 2787 165 0.95 9.30 1.02 0.97 509.91| | 8: 1.87 - 1.79 2789 144 0.93 12.65 1.00 0.97 509.91| | 9: 1.79 - 1.72 2745 138 0.94 10.04 0.98 0.97 288.32| | 10: 1.72 - 1.66 2831 160 0.94 11.17 0.98 0.97 243.95| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.97 233.61| | 12: 1.61 - 1.56 2773 144 0.96 8.86 0.99 0.97 136.09| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.03 0.97 136.09| | 14: 1.52 - 1.48 2803 134 0.94 10.70 1.02 0.98 122.03| | 15: 1.48 - 1.45 2738 128 0.95 9.82 1.02 0.98 96.28| | 16: 1.45 - 1.42 2756 161 0.94 10.99 1.02 0.98 96.28| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.98 88.11| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.38| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.98 83.38| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.96 79.91| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.96 79.67| | 22: 1.29 - 1.27 2704 152 0.93 13.70 0.98 0.96 80.11| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.34| | 24: 1.26 - 1.24 2744 132 0.92 14.90 0.96 0.94 82.34| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.23| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.32| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.32| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 89.82| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.92 91.14| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.92 91.14| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.67 max = 5390.75 mean = 841.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.35| |phase err.(test): min = 0.00 max = 89.08 mean = 13.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1117 0.1275 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1516 n_refl.: 87575 remove outliers: r(all,work,free)=0.1439 0.1436 0.1516 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1438 0.1435 0.1515 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1116 0.1276 n_refl.: 87575 remove outliers: r(all,work,free)=0.1123 0.1115 0.1276 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3945 282.826 255.343 0.437 0.999 0.277 11.894-9.307 93.14 91 4 0.2427 469.168 453.033 0.853 1.001 0.253 9.237-7.194 97.73 208 7 0.2252 386.760 378.739 0.932 1.001 0.140 7.162-5.571 100.00 427 22 0.2066 295.817 286.274 0.911 1.002 0.120 5.546-4.326 100.00 867 58 0.1087 406.083 401.793 0.966 1.002 0.120 4.315-3.360 100.00 1859 96 0.0901 386.188 384.282 1.002 1.002 0.100 3.356-2.611 100.00 3867 181 0.1087 253.706 251.924 1.010 1.001 0.050 2.608-2.026 99.99 8198 413 0.0897 168.184 167.573 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.132 82.478 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.421 36.035 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.948 21.506 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0173 ================= 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_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1900 0.081 5.247 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1719 0.081 5.247 9.1 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1719 0.081 5.247 9.1 119.5 20.1 258 0.000 1_nqh: 0.1632 0.1724 0.081 5.247 9.1 119.5 20.1 258 0.003 1_weight: 0.1632 0.1724 0.081 5.247 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1206 0.1455 0.007 0.954 9.1 119.5 20.1 258 0.130 1_adp: 0.1213 0.1452 0.007 0.954 9.1 119.5 20.1 258 0.130 1_regHadp: 0.1214 0.1456 0.007 0.954 9.1 119.5 20.1 258 0.130 1_occ: 0.1207 0.1452 0.007 0.954 9.1 119.5 20.1 258 0.130 2_bss: 0.1206 0.1444 0.007 0.954 9.1 119.5 20.1 258 0.130 2_settarget: 0.1206 0.1444 0.007 0.954 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1206 0.1444 0.007 0.957 9.1 119.5 20.1 258 0.130 2_nqh: 0.1207 0.1444 0.007 0.957 9.1 119.5 20.1 258 0.130 2_sol: 0.1180 0.1389 0.007 0.957 9.1 115.3 22.4 428 n/a 2_weight: 0.1180 0.1389 0.007 0.957 9.1 115.3 22.4 428 n/a 2_xyzrec: 0.1176 0.1409 0.008 0.919 9.1 115.3 22.4 428 n/a 2_adp: 0.1176 0.1409 0.008 0.919 9.1 115.3 22.4 428 n/a 2_regHadp: 0.1177 0.1409 0.008 0.919 9.1 115.3 22.4 428 n/a 2_occ: 0.1177 0.1405 0.008 0.919 9.1 115.3 22.4 428 n/a 3_bss: 0.1171 0.1402 0.008 0.919 9.1 115.3 22.4 428 n/a 3_settarget: 0.1171 0.1402 0.008 0.919 9.1 115.3 22.4 428 n/a 3_updatecdl: 0.1171 0.1402 0.008 0.919 9.1 115.3 22.4 428 n/a 3_nqh: 0.1171 0.1402 0.008 0.919 9.1 115.3 22.4 428 n/a 3_sol: 0.1192 0.1378 0.008 0.919 9.1 115.3 21.4 450 n/a 3_weight: 0.1192 0.1378 0.008 0.919 9.1 115.3 21.4 450 n/a 3_xyzrec: 0.1153 0.1305 0.006 0.971 9.1 115.3 21.4 450 n/a 3_adp: 0.1153 0.1304 0.006 0.971 9.1 115.3 21.4 450 n/a 3_regHadp: 0.1153 0.1305 0.006 0.971 9.1 115.3 21.4 450 n/a 3_occ: 0.1146 0.1308 0.006 0.971 9.1 115.3 21.4 450 n/a 4_bss: 0.1140 0.1302 0.006 0.971 9.1 115.3 21.4 450 n/a 4_settarget: 0.1140 0.1302 0.006 0.971 9.1 115.3 21.4 450 n/a 4_updatecdl: 0.1140 0.1302 0.006 0.973 9.1 115.3 21.4 450 n/a 4_nqh: 0.1140 0.1302 0.006 0.973 9.1 115.3 21.4 450 n/a 4_sol: 0.1132 0.1289 0.006 0.973 9.1 115.3 21.4 467 n/a 4_weight: 0.1132 0.1289 0.006 0.973 9.1 115.3 21.4 467 n/a 4_xyzrec: 0.1121 0.1285 0.009 1.128 9.1 115.3 21.4 467 n/a 4_adp: 0.1121 0.1285 0.009 1.128 9.1 115.3 21.4 467 n/a 4_regHadp: 0.1121 0.1285 0.009 1.128 9.1 115.3 21.4 467 n/a 4_occ: 0.1116 0.1282 0.009 1.128 9.1 115.3 21.4 467 n/a 5_bss: 0.1111 0.1284 0.009 1.128 9.1 115.3 21.4 467 n/a 5_settarget: 0.1111 0.1284 0.009 1.128 9.1 115.3 21.4 467 n/a 5_updatecdl: 0.1111 0.1284 0.009 1.129 9.1 115.3 21.4 467 n/a 5_setrh: 0.1113 0.1284 0.009 1.129 9.1 115.3 21.4 467 n/a 5_nqh: 0.1113 0.1284 0.009 1.129 9.1 115.3 21.4 467 n/a 5_sol: 0.1120 0.1276 0.009 1.129 9.1 115.3 21.5 471 n/a 5_weight: 0.1120 0.1276 0.009 1.129 9.1 115.3 21.5 471 n/a 5_xyzrec: 0.1120 0.1275 0.009 1.137 9.1 115.3 21.5 471 n/a 5_adp: 0.1120 0.1275 0.009 1.137 9.1 115.3 21.5 471 n/a 5_regHadp: 0.1120 0.1275 0.009 1.137 9.1 115.3 21.5 471 n/a 5_occ: 0.1117 0.1275 0.009 1.137 9.1 115.3 21.5 471 n/a end: 0.1115 0.1276 0.009 1.137 9.1 115.3 21.5 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1821005_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1821005_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0200 Refinement macro-cycles (run) : 11080.9800 Write final files (write_after_run_outputs) : 92.1600 Total : 11176.1600 Total CPU time: 3.11 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:21:29 PST -0800 (1735363289.41 s) Start R-work = 0.1630, R-free = 0.1719 Final R-work = 0.1115, R-free = 0.1276 =============================================================================== Job complete usr+sys time: 11348.69 seconds wall clock time: 206 minutes 4.91 seconds (12364.91 seconds total)