Starting phenix.refine on Sat Dec 28 21:06:33 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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 } 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 } } 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: 2.18, per 1000 atoms: 0.64 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: 0.56 Conformation dependent library (CDL) restraints added in 187.1 milliseconds Time building geometry restraints manager: 0.76 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 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 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 2.450 ... (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 } 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 } } 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 = 25.627694 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 0.1209 0.1463 0.0254 0.007 1.0 1.0 0.5 0.0 0 12.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.63 2.54 3.013 19.071 2028.628 0.017 12.35 15.33 2.98 3.158 19.546 2028.628 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.47 21.00 2.87 0 1785 Protein: 8.55 118.47 17.88 2.87 0 1519 Water: 11.10 114.51 39.12 N/A 0 258 Other: 22.84 35.97 29.00 N/A 0 8 Chain A: 8.55 118.47 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.55 1210 19.55 - 30.54 227 30.54 - 41.53 166 41.53 - 52.52 100 52.52 - 63.51 53 63.51 - 74.50 17 74.50 - 85.49 5 85.49 - 96.48 4 96.48 - 107.48 0 107.48 - 118.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1533 r_work=0.1240 r_free=0.1537 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1537 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1240 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 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= 0.1240 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015376 | | target function (ls_wunit_k1) not normalized (work): 1280.799055 | | target function (ls_wunit_k1) not normalized (free): 113.485610 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1254 0.1240 0.1540 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1774 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1774 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1723 0.1722 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1253 0.1239 0.1533 n_refl.: 87593 remove outliers: r(all,work,free)=0.1253 0.1239 0.1533 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 0.3610 298.004 277.012 0.636 1.002 0.380 11.894-9.307 99.02 97 4 0.1596 477.386 465.736 0.909 1.003 0.380 9.237-7.194 100.00 213 7 0.1818 390.443 385.161 0.949 1.003 0.330 7.162-5.571 100.00 427 22 0.1741 293.006 287.203 0.921 1.003 0.258 5.546-4.326 100.00 867 58 0.0933 402.225 399.427 0.948 1.003 0.209 4.315-3.360 100.00 1859 96 0.0780 382.519 381.551 0.994 1.002 0.190 3.356-2.611 100.00 3867 181 0.1024 251.295 250.576 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.0973 166.586 166.009 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1198 81.352 81.540 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1637 36.075 35.542 1.008 0.998 0.000 1.221-1.150 99.97 13689 708 0.2353 22.730 21.247 0.971 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0432 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1239 r_free=0.1533 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=0.1241 r_free=0.1535 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1241 r_free=0.1535 | n_water=258 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1250 r_free=0.1534 | n_water=252 | time (s): 25.920 (total time: 28.280) Filter (q & B) r_work=0.1253 r_free=0.1533 | n_water=249 | time (s): 3.680 (total time: 31.960) Compute maps r_work=0.1253 r_free=0.1533 | n_water=249 | time (s): 1.710 (total time: 33.670) Filter (map) r_work=0.1271 r_free=0.1538 | n_water=235 | time (s): 3.430 (total time: 37.100) Find peaks r_work=0.1271 r_free=0.1538 | n_water=235 | time (s): 0.660 (total time: 37.760) Add new water r_work=0.1427 r_free=0.1704 | n_water=458 | time (s): 3.820 (total time: 41.580) Refine new water occ: r_work=0.1334 r_free=0.1566 adp: r_work=0.1254 r_free=0.1517 occ: r_work=0.1269 r_free=0.1507 adp: r_work=0.1232 r_free=0.1494 occ: r_work=0.1236 r_free=0.1487 adp: r_work=0.1225 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1486 r_work=0.1225 r_free=0.1486 | n_water=458 | time (s): 71.420 (total time: 113.000) Filter (q & B) r_work=0.1231 r_free=0.1487 | n_water=433 | time (s): 3.890 (total time: 116.890) Filter (dist only) r_work=0.1231 r_free=0.1487 | n_water=433 | time (s): 40.370 (total time: 157.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.997127 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1518.494089 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 0.1226 0.1520 0.0294 0.007 0.9 1.9 0.5 0.0 0 12.999 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 15.20 2.94 3.783 23.182 1518.494 0.015 12.00 14.99 2.99 4.113 22.993 1518.494 0.015 Individual atomic B min max mean iso aniso Overall: 8.78 114.36 23.19 2.60 198 1762 Protein: 8.78 114.36 17.67 2.60 0 1519 Water: 11.02 73.74 42.46 N/A 198 235 Other: 25.43 36.88 30.31 N/A 0 8 Chain A: 8.78 114.36 20.36 N/A 0 1762 Chain S: 18.93 68.34 48.44 N/A 198 0 Histogram: Values Number of atoms 8.78 - 19.34 1209 19.34 - 29.90 248 29.90 - 40.45 187 40.45 - 51.01 143 51.01 - 61.57 118 61.57 - 72.13 44 72.13 - 82.69 5 82.69 - 93.25 3 93.25 - 103.80 1 103.80 - 114.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1499 r_work=0.1200 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1499 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1492 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.26 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= 0.1201 r_free= 0.1492 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014024 | | target function (ls_wunit_k1) not normalized (work): 1168.142540 | | target function (ls_wunit_k1) not normalized (free): 107.573458 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1492 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1597 0.1591 0.1745 n_refl.: 87592 remove outliers: r(all,work,free)=0.1597 0.1591 0.1745 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1603 0.1597 0.1749 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1487 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1196 0.1487 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 0.3402 293.955 268.562 0.628 0.941 0.368 11.894-9.307 99.02 97 4 0.1517 477.386 475.327 0.976 0.942 0.360 9.237-7.194 100.00 213 7 0.1704 390.443 389.324 1.039 0.942 0.290 7.162-5.571 100.00 427 22 0.1480 293.006 290.135 0.998 0.942 0.225 5.546-4.326 100.00 867 58 0.0832 402.225 399.512 1.019 0.942 0.213 4.315-3.360 100.00 1859 96 0.0722 382.519 381.278 1.065 0.943 0.206 3.356-2.611 100.00 3867 181 0.0953 251.295 250.578 1.071 0.943 0.072 2.608-2.026 99.99 8198 413 0.0964 166.586 166.223 1.080 0.944 0.000 2.025-1.573 100.00 17313 902 0.1174 81.352 81.536 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1610 36.075 35.574 1.071 0.948 0.000 1.221-1.150 99.97 13689 708 0.2338 22.730 21.282 1.027 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0553 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1487 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=0.1196 r_free=0.1487 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1487 | n_water=433 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1198 r_free=0.1486 | n_water=430 | time (s): 37.580 (total time: 39.320) Filter (q & B) r_work=0.1198 r_free=0.1486 | n_water=430 | time (s): 1.310 (total time: 40.630) Compute maps r_work=0.1198 r_free=0.1486 | n_water=430 | time (s): 1.550 (total time: 42.180) Filter (map) r_work=0.1239 r_free=0.1476 | n_water=285 | time (s): 3.390 (total time: 45.570) Find peaks r_work=0.1239 r_free=0.1476 | n_water=285 | time (s): 0.700 (total time: 46.270) Add new water r_work=0.1369 r_free=0.1626 | n_water=476 | time (s): 3.230 (total time: 49.500) Refine new water occ: r_work=0.1269 r_free=0.1541 adp: r_work=0.1270 r_free=0.1541 occ: r_work=0.1247 r_free=0.1520 adp: r_work=0.1245 r_free=0.1519 occ: r_work=0.1231 r_free=0.1501 adp: r_work=0.1224 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1498 r_work=0.1224 r_free=0.1498 | n_water=476 | time (s): 169.570 (total time: 219.070) Filter (q & B) r_work=0.1229 r_free=0.1491 | n_water=435 | time (s): 3.360 (total time: 222.430) Filter (dist only) r_work=0.1229 r_free=0.1489 | n_water=434 | time (s): 36.640 (total time: 259.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.018069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.860825 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 0.1232 0.1454 0.0222 0.006 0.9 2.2 0.5 0.0 0 1.009 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.54 2.22 3.624 22.112 40.861 3.721 12.28 14.21 1.93 4.142 21.905 40.861 3.657 Individual atomic B min max mean iso aniso Overall: 9.18 109.43 21.60 2.29 202 1759 Protein: 9.18 109.43 17.22 2.30 0 1519 Water: 11.55 72.74 36.80 N/A 202 232 Other: 21.41 32.99 27.42 N/A 0 8 Chain A: 9.18 109.43 19.87 N/A 0 1759 Chain S: 16.68 60.47 36.61 N/A 202 0 Histogram: Values Number of atoms 9.18 - 19.21 1233 19.21 - 29.23 270 29.23 - 39.26 215 39.26 - 49.28 127 49.28 - 59.31 81 59.31 - 69.33 22 69.33 - 79.36 7 79.36 - 89.38 3 89.38 - 99.41 1 99.41 - 109.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1421 r_work=0.1229 r_free=0.1421 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1421 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1421 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.22 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= 0.1225 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655192 | | target function (ml) not normalized (work): 304451.927420 | | target function (ml) not normalized (free): 16068.055665 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1225 0.1421 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1549 0.1547 0.1606 n_refl.: 87589 remove outliers: r(all,work,free)=0.1549 0.1547 0.1606 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1546 0.1545 0.1605 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1217 0.1392 n_refl.: 87589 remove outliers: r(all,work,free)=0.1223 0.1214 0.1392 n_refl.: 87582 ======================== 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 90.62 82 5 0.3876 290.715 259.345 0.472 1.000 0.295 11.894-9.307 97.06 95 4 0.2431 470.795 457.847 0.854 1.001 0.277 9.237-7.194 98.64 210 7 0.2390 383.009 381.387 0.941 1.002 0.170 7.162-5.571 100.00 427 22 0.2090 293.006 282.176 0.908 1.002 0.163 5.546-4.326 100.00 867 58 0.1100 402.225 397.999 0.953 1.002 0.159 4.315-3.360 100.00 1859 96 0.0960 382.519 379.641 0.993 1.002 0.156 3.356-2.611 100.00 3867 181 0.1176 251.295 249.417 1.000 1.001 0.062 2.608-2.026 99.99 8198 413 0.1062 166.586 165.573 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1031 81.352 81.484 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1302 36.075 35.643 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2135 22.730 21.337 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0337 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1214 r_free=0.1392 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=0.1214 r_free=0.1392 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1214 r_free=0.1392 | n_water=434 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1214 r_free=0.1392 | n_water=434 | time (s): 36.760 (total time: 38.940) Filter (q & B) r_work=0.1214 r_free=0.1392 | n_water=434 | time (s): 0.780 (total time: 39.720) Compute maps r_work=0.1214 r_free=0.1392 | n_water=434 | time (s): 1.290 (total time: 41.010) Filter (map) r_work=0.1234 r_free=0.1380 | n_water=309 | time (s): 2.720 (total time: 43.730) Find peaks r_work=0.1234 r_free=0.1380 | n_water=309 | time (s): 0.660 (total time: 44.390) Add new water r_work=0.1300 r_free=0.1445 | n_water=471 | time (s): 3.090 (total time: 47.480) Refine new water occ: r_work=0.1225 r_free=0.1387 adp: r_work=0.1225 r_free=0.1387 occ: r_work=0.1209 r_free=0.1375 adp: r_work=0.1208 r_free=0.1374 occ: r_work=0.1198 r_free=0.1369 adp: r_work=0.1195 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1365 r_work=0.1195 r_free=0.1365 | n_water=471 | time (s): 147.100 (total time: 194.580) Filter (q & B) r_work=0.1202 r_free=0.1372 | n_water=436 | time (s): 3.310 (total time: 197.890) Filter (dist only) r_work=0.1202 r_free=0.1371 | n_water=435 | time (s): 35.570 (total time: 233.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.948014 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.287309 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 0.1384 0.0179 0.006 1.0 1.9 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.84 1.79 3.418 21.492 50.287 3.642 11.84 13.69 1.86 3.831 21.356 50.287 3.622 Individual atomic B min max mean iso aniso Overall: 9.23 105.03 21.18 2.18 204 1758 Protein: 9.23 105.03 16.92 2.18 0 1519 Water: 11.28 71.47 36.00 N/A 204 231 Other: 21.57 30.46 26.17 N/A 0 8 Chain A: 9.23 105.03 19.51 N/A 0 1758 Chain S: 15.77 60.87 35.62 N/A 204 0 Histogram: Values Number of atoms 9.23 - 18.81 1231 18.81 - 28.39 272 28.39 - 37.97 204 37.97 - 47.55 140 47.55 - 57.13 78 57.13 - 66.71 22 66.71 - 76.29 10 76.29 - 85.87 2 85.87 - 95.45 1 95.45 - 105.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1369 r_work=0.1184 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1370 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1368 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1180 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620742 | | target function (ml) not normalized (work): 301557.113141 | | target function (ml) not normalized (free): 15928.337352 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1180 0.1368 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1499 0.1497 0.1569 n_refl.: 87582 remove outliers: r(all,work,free)=0.1499 0.1497 0.1569 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1495 0.1568 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1181 0.1370 n_refl.: 87582 remove outliers: r(all,work,free)=0.1188 0.1179 0.1370 n_refl.: 87577 ======================== 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 90.62 82 5 0.3974 290.715 255.799 0.453 1.000 0.308 11.894-9.307 94.12 92 4 0.2360 470.431 446.921 0.833 1.002 0.217 9.237-7.194 97.73 208 7 0.2480 383.282 376.933 0.912 1.002 0.136 7.162-5.571 100.00 427 22 0.2220 293.006 280.886 0.899 1.002 0.133 5.546-4.326 100.00 867 58 0.1146 402.225 398.085 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0943 382.519 380.162 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1148 251.295 249.512 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1017 166.586 165.793 1.013 1.000 0.000 2.025-1.573 100.00 17313 902 0.0965 81.352 81.610 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.075 35.700 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2126 22.730 21.354 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0227 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1370 After: r_work=0.1179 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.1179 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1374 | n_water=435 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1179 r_free=0.1374 | n_water=435 | time (s): 33.510 (total time: 35.550) Filter (q & B) r_work=0.1180 r_free=0.1373 | n_water=434 | time (s): 2.880 (total time: 38.430) Compute maps r_work=0.1180 r_free=0.1373 | n_water=434 | time (s): 1.110 (total time: 39.540) Filter (map) r_work=0.1207 r_free=0.1394 | n_water=322 | time (s): 2.940 (total time: 42.480) Find peaks r_work=0.1207 r_free=0.1394 | n_water=322 | time (s): 0.670 (total time: 43.150) Add new water r_work=0.1253 r_free=0.1431 | n_water=479 | time (s): 3.070 (total time: 46.220) Refine new water occ: r_work=0.1187 r_free=0.1361 adp: r_work=0.1187 r_free=0.1363 occ: r_work=0.1175 r_free=0.1350 adp: r_work=0.1174 r_free=0.1352 occ: r_work=0.1167 r_free=0.1345 adp: r_work=0.1164 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1345 r_work=0.1164 r_free=0.1345 | n_water=479 | time (s): 201.330 (total time: 247.550) Filter (q & B) r_work=0.1174 r_free=0.1354 | n_water=436 | time (s): 2.740 (total time: 250.290) Filter (dist only) r_work=0.1174 r_free=0.1353 | n_water=435 | time (s): 37.610 (total time: 287.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915709 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.597986 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 0.1213 0.1390 0.0177 0.007 1.0 6.7 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 13.90 1.77 3.298 21.054 48.598 3.633 12.15 13.91 1.77 3.444 21.007 48.598 3.625 Individual atomic B min max mean iso aniso Overall: 9.27 101.66 20.90 2.06 205 1757 Protein: 9.27 101.66 16.78 2.06 0 1519 Water: 11.33 70.91 35.21 N/A 205 230 Other: 21.49 30.04 26.03 N/A 0 8 Chain A: 9.27 101.66 19.35 N/A 0 1757 Chain S: 15.21 58.71 34.17 N/A 205 0 Histogram: Values Number of atoms 9.27 - 18.51 1222 18.51 - 27.75 284 27.75 - 36.99 211 36.99 - 46.23 131 46.23 - 55.46 70 55.46 - 64.70 28 64.70 - 73.94 11 73.94 - 83.18 2 83.18 - 92.42 1 92.42 - 101.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1391 r_work=0.1215 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1391 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1385 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1211 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623122 | | target function (ml) not normalized (work): 301737.236164 | | target function (ml) not normalized (free): 15945.933171 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1440 0.1401 5.7085 5.5994| | 2: 3.57 - 2.84 1.00 2888 124 0.1136 0.1462 5.2024 5.2754| | 3: 2.83 - 2.48 1.00 2820 163 0.1251 0.1350 5.0085 5.0479| | 4: 2.47 - 2.25 1.00 2825 136 0.1052 0.1226 4.71 4.7715| | 5: 2.25 - 2.09 1.00 2756 127 0.1018 0.1138 4.6504 4.7412| | 6: 2.09 - 1.97 1.00 2846 113 0.0989 0.1229 4.3586 4.4816| | 7: 1.97 - 1.87 1.00 2787 165 0.1011 0.1221 4.0897 4.1698| | 8: 1.87 - 1.79 1.00 2789 144 0.1037 0.1253 4.0041 4.0902| | 9: 1.79 - 1.72 1.00 2745 138 0.0968 0.1329 3.7282 3.9285| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1248 3.6395 3.7655| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1102 3.5734 3.6149| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1136 3.3448 3.4734| | 13: 1.56 - 1.52 1.00 2745 130 0.0984 0.1074 3.3348 3.4303| | 14: 1.52 - 1.48 1.00 2803 134 0.0994 0.1132 3.2581 3.3329| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1334 3.1644 3.314| | 16: 1.45 - 1.42 1.00 2756 161 0.1066 0.1285 3.1455 3.2394| | 17: 1.42 - 1.39 1.00 2785 139 0.1120 0.1272 3.11 3.2142| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1399 3.0824 3.2769| | 19: 1.36 - 1.34 1.00 2807 134 0.1211 0.1608 3.0874 3.2802| | 20: 1.34 - 1.32 1.00 2696 147 0.1318 0.1487 3.0862 3.1383| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1583 3.0845 3.1488| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1931 3.0845 3.2895| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1879 3.1018 3.2162| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1735 3.0927 3.182| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2336 3.106 3.3051| | 26: 1.22 - 1.21 1.00 2727 135 0.1868 0.1788 3.1236 3.1955| | 27: 1.21 - 1.19 1.00 2814 148 0.2016 0.2114 3.1409 3.157| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2312 3.1377 3.1686| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2364 3.1246 3.2208| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2526 3.1144 3.167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.96 1.00 0.97 6118.49| | 2: 3.57 - 2.84 2888 124 0.92 13.18 1.01 0.97 6118.49| | 3: 2.83 - 2.48 2820 163 0.89 17.41 0.99 0.97 5139.28| | 4: 2.47 - 2.25 2825 136 0.91 14.57 1.00 0.97 2614.21| | 5: 2.25 - 2.09 2756 127 0.89 16.83 1.01 0.97 2614.21| | 6: 2.09 - 1.97 2846 113 0.92 13.74 1.02 0.97 1552.95| | 7: 1.97 - 1.87 2787 165 0.94 11.13 1.02 0.97 647.84| | 8: 1.87 - 1.79 2789 144 0.91 14.72 1.00 0.97 647.84| | 9: 1.79 - 1.72 2745 138 0.93 11.66 0.98 0.97 348.66| | 10: 1.72 - 1.66 2831 160 0.93 12.50 0.98 0.97 288.75| | 11: 1.66 - 1.61 2712 147 0.93 13.11 0.98 0.97 275.24| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 147.87| | 13: 1.56 - 1.52 2745 130 0.94 11.21 1.02 0.97 147.87| | 14: 1.52 - 1.48 2803 134 0.94 11.27 1.02 0.97 131.82| | 15: 1.48 - 1.45 2738 128 0.95 10.37 1.02 0.98 102.42| | 16: 1.45 - 1.42 2756 161 0.94 11.58 1.02 0.98 102.42| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.98 92.55| | 18: 1.39 - 1.36 2741 179 0.94 11.69 1.01 0.98 86.84| | 19: 1.36 - 1.34 2807 134 0.94 12.29 1.00 0.98 86.84| | 20: 1.34 - 1.32 2696 147 0.94 12.44 0.99 0.96 82.15| | 21: 1.32 - 1.30 2785 112 0.93 13.40 0.99 0.96 81.82| | 22: 1.29 - 1.27 2704 152 0.93 13.95 0.98 0.96 82.05| | 23: 1.27 - 1.26 2802 156 0.92 14.99 0.98 0.94 83.21| | 24: 1.26 - 1.24 2744 132 0.92 15.01 0.97 0.94 83.21| | 25: 1.24 - 1.22 2733 148 0.91 16.45 0.96 0.94 84.85| | 26: 1.22 - 1.21 2727 135 0.90 18.23 1.02 0.93 86.68| | 27: 1.21 - 1.19 2814 148 0.89 18.87 1.02 0.93 86.68| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.05| | 29: 1.18 - 1.16 2800 134 0.88 20.68 0.99 0.92 91.31| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.31| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.82 max = 6118.49 mean = 963.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.91 mean = 14.11| |phase err.(test): min = 0.00 max = 88.91 mean = 14.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1211 0.1385 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1524 0.1523 0.1569 n_refl.: 87577 remove outliers: r(all,work,free)=0.1524 0.1523 0.1569 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1522 0.1521 0.1568 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1211 0.1384 n_refl.: 87577 remove outliers: r(all,work,free)=0.1218 0.1210 0.1384 n_refl.: 87574 ======================== 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 0.3886 289.971 252.901 0.450 1.002 0.308 11.894-9.307 94.12 92 4 0.2345 470.431 448.917 0.835 1.003 0.242 9.237-7.194 97.27 207 7 0.2493 384.365 375.765 0.907 1.003 0.162 7.162-5.571 100.00 427 22 0.2278 293.006 280.909 0.891 1.003 0.140 5.546-4.326 100.00 867 58 0.1221 402.225 397.814 0.953 1.003 0.140 4.315-3.360 100.00 1859 96 0.1016 382.519 379.966 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1209 251.295 249.321 1.000 1.002 0.048 2.608-2.026 99.99 8198 413 0.1063 166.586 165.603 1.013 1.000 0.000 2.025-1.573 100.00 17313 902 0.0987 81.352 81.591 1.028 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.075 35.710 1.023 0.995 0.000 1.221-1.150 99.97 13689 708 0.2116 22.730 21.371 0.982 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0272 ================= 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: 0.1209 0.1463 0.007 0.959 9.1 119.5 20.1 258 0.125 1_adp: 0.1235 0.1533 0.007 0.959 8.6 118.5 21.0 258 0.125 1_regHadp: 0.1240 0.1537 0.007 0.959 8.6 118.5 21.0 258 0.125 1_occ: 0.1240 0.1540 0.007 0.959 8.6 118.5 21.0 258 0.125 2_bss: 0.1239 0.1533 0.007 0.959 8.7 118.6 21.1 258 0.125 2_settarget: 0.1239 0.1533 0.007 0.959 8.7 118.6 21.1 258 0.125 2_updatecdl: 0.1239 0.1533 0.007 0.963 8.7 118.6 21.1 258 0.125 2_nqh: 0.1241 0.1535 0.007 0.963 8.7 118.6 21.1 258 0.125 2_sol: 0.1231 0.1487 0.007 0.963 8.7 118.6 23.5 433 n/a 2_weight: 0.1231 0.1487 0.007 0.963 8.7 118.6 23.5 433 n/a 2_xyzrec: 0.1226 0.1520 0.007 0.890 8.7 118.6 23.5 433 n/a 2_adp: 0.1201 0.1499 0.007 0.890 8.8 114.4 23.2 433 n/a 2_regHadp: 0.1200 0.1499 0.007 0.890 8.8 114.4 23.2 433 n/a 2_occ: 0.1201 0.1492 0.007 0.890 8.8 114.4 23.2 433 n/a 3_bss: 0.1196 0.1487 0.007 0.890 8.8 114.4 23.2 433 n/a 3_settarget: 0.1196 0.1487 0.007 0.890 8.8 114.4 23.2 433 n/a 3_updatecdl: 0.1196 0.1487 0.007 0.890 8.8 114.4 23.2 433 n/a 3_nqh: 0.1196 0.1487 0.007 0.890 8.8 114.4 23.2 433 n/a 3_sol: 0.1229 0.1489 0.007 0.890 8.8 114.4 22.0 434 n/a 3_weight: 0.1229 0.1489 0.007 0.890 8.8 114.4 22.0 434 n/a 3_xyzrec: 0.1232 0.1454 0.006 0.920 8.8 114.4 22.0 434 n/a 3_adp: 0.1228 0.1421 0.006 0.920 9.2 109.4 21.6 434 n/a 3_regHadp: 0.1229 0.1421 0.006 0.920 9.2 109.4 21.6 434 n/a 3_occ: 0.1225 0.1421 0.006 0.920 9.2 109.4 21.6 434 n/a 4_bss: 0.1214 0.1392 0.006 0.920 9.2 109.4 21.6 434 n/a 4_settarget: 0.1214 0.1392 0.006 0.920 9.2 109.4 21.6 434 n/a 4_updatecdl: 0.1214 0.1392 0.006 0.919 9.2 109.4 21.6 434 n/a 4_nqh: 0.1214 0.1392 0.006 0.919 9.2 109.4 21.6 434 n/a 4_sol: 0.1202 0.1371 0.006 0.919 9.2 109.4 21.4 435 n/a 4_weight: 0.1202 0.1371 0.006 0.919 9.2 109.4 21.4 435 n/a 4_xyzrec: 0.1206 0.1384 0.006 0.952 9.2 109.4 21.4 435 n/a 4_adp: 0.1184 0.1369 0.006 0.952 9.2 105.0 21.2 435 n/a 4_regHadp: 0.1184 0.1370 0.006 0.952 9.2 105.0 21.2 435 n/a 4_occ: 0.1180 0.1368 0.006 0.952 9.2 105.0 21.2 435 n/a 5_bss: 0.1179 0.1370 0.006 0.952 9.2 105.0 21.2 435 n/a 5_settarget: 0.1179 0.1370 0.006 0.952 9.2 105.0 21.2 435 n/a 5_updatecdl: 0.1179 0.1370 0.006 0.952 9.2 105.0 21.2 435 n/a 5_setrh: 0.1179 0.1370 0.006 0.952 9.2 105.0 21.2 435 n/a 5_nqh: 0.1179 0.1374 0.006 0.952 9.2 105.0 21.2 435 n/a 5_sol: 0.1174 0.1353 0.006 0.952 9.2 105.0 21.0 435 n/a 5_weight: 0.1174 0.1353 0.006 0.952 9.2 105.0 21.0 435 n/a 5_xyzrec: 0.1213 0.1390 0.007 1.038 9.2 105.0 21.0 435 n/a 5_adp: 0.1215 0.1391 0.007 1.038 9.3 101.7 20.9 435 n/a 5_regHadp: 0.1215 0.1391 0.007 1.038 9.3 101.7 20.9 435 n/a 5_occ: 0.1211 0.1385 0.007 1.038 9.3 101.7 20.9 435 n/a end: 0.1210 0.1384 0.007 1.038 9.3 101.6 20.9 435 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1821005_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1821005_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7100 Refinement macro-cycles (run) : 3370.4800 Write final files (write_after_run_outputs) : 74.7600 Total : 3449.9500 Total CPU time: 58.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:01 PST -0800 (1735452541.22 s) Start R-work = 0.1630, R-free = 0.1719 Final R-work = 0.1210, R-free = 0.1384 =============================================================================== Job complete usr+sys time: 3600.02 seconds wall clock time: 64 minutes 27.68 seconds (3867.68 seconds total)