Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s 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: 2.50, per 1000 atoms: 0.74 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: 0.98 Conformation dependent library (CDL) restraints added in 413.1 milliseconds Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.90: 449 0.90 - 1.18: 1237 1.18 - 1.47: 788 1.47 - 1.75: 667 1.75 - 2.03: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.512 -0.183 1.00e-02 1.00e+04 3.34e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.186 0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 1.236 1.458 -0.222 1.29e-02 6.01e+03 2.97e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.329 1.562 -0.232 1.36e-02 5.41e+03 2.92e+02 bond pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 1.330 1.551 -0.221 1.30e-02 5.92e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 3122 4.39 - 8.78: 1743 8.78 - 13.17: 714 13.17 - 17.56: 173 17.56 - 21.95: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 137.65 -14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" CA ASN A 144 " pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 121.47 136.75 -15.28 1.15e+00 7.56e-01 1.76e+02 angle pdb=" CA ASP A 42 " pdb=" C ASP A 42 " pdb=" O ASP A 42 " ideal model delta sigma weight residual 120.96 134.69 -13.73 1.09e+00 8.42e-01 1.59e+02 angle pdb=" CA VAL A 44 " pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 120.39 133.57 -13.18 1.05e+00 9.07e-01 1.58e+02 angle pdb=" O ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.12 109.26 12.86 1.06e+00 8.90e-01 1.47e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 913 15.93 - 31.86: 140 31.86 - 47.79: 35 47.79 - 63.71: 20 63.71 - 79.64: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CG BTYR A 67 " pdb=" CD1BTYR A 67 " pdb=" CE1BTYR A 67 " pdb=" HE1BTYR A 67 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.173: 85 0.173 - 0.345: 59 0.345 - 0.517: 53 0.517 - 0.688: 32 0.688 - 0.860: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BGLN A 80 " pdb=" N BGLN A 80 " pdb=" C BGLN A 80 " pdb=" CB BGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.79 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 7.08e-02 1.50e+02 pdb=" CG PHE A 164 " 0.171 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.111 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.046 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.005 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.051 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.043 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 783 2.28 - 2.86: 7873 2.86 - 3.44: 10542 3.44 - 4.02: 15323 4.02 - 4.60: 22055 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.698 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.750 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.776 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.794 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 ... (remaining 56571 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_8555406_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= 0.2605 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791195 | | target function (ml) not normalized (work): 232523.290880 | | target function (ml) not normalized (free): 11856.192874 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 6.9997 4.9525| | 2: 3.57 - 2.84 1.00 2876 122 0.2430 0.1892 4.3542 4.3533| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1796 4.1422 4.1745| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1496 3.8488 3.8493| | 5: 2.25 - 2.09 1.00 2756 127 0.2466 0.1644 3.8135 3.8493| | 6: 2.09 - 1.97 1.00 2846 113 0.2549 0.1945 3.4667 3.5887| | 7: 1.97 - 1.87 1.00 2787 165 0.2542 0.1866 3.1371 3.2476| | 8: 1.87 - 1.79 1.00 2789 144 0.2448 0.2003 3.0778 3.1247| | 9: 1.79 - 1.72 1.00 2745 138 0.2451 0.1909 2.9232 2.946| | 10: 1.72 - 1.66 1.00 2789 158 0.2395 0.1775 2.8199 2.8223| | 11: 1.66 - 1.61 1.00 2740 147 0.2455 0.1865 2.7552 2.7757| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2127 2.6416 2.6955| | 13: 1.56 - 1.52 1.00 2745 130 0.2578 0.1798 2.5727 2.5536| | 14: 1.52 - 1.48 1.00 2803 134 0.2624 0.2076 2.4995 2.5895| | 15: 1.48 - 1.45 1.00 2738 128 0.2631 0.2176 2.4184 2.5369| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.1990 2.3769 2.3775| | 17: 1.42 - 1.39 1.00 2785 139 0.2631 0.1869 2.314 2.3006| | 18: 1.39 - 1.36 1.00 2741 179 0.2663 0.2207 2.2622 2.3405| | 19: 1.36 - 1.34 1.00 2807 134 0.2641 0.2528 2.2248 2.3406| | 20: 1.34 - 1.32 1.00 2696 147 0.2728 0.2197 2.2178 2.2372| | 21: 1.32 - 1.30 1.00 2785 112 0.2719 0.2245 2.1658 2.1439| | 22: 1.29 - 1.27 1.00 2704 152 0.2752 0.2782 2.1294 2.2742| | 23: 1.27 - 1.26 1.00 2802 156 0.2760 0.2750 2.0963 2.3019| | 24: 1.26 - 1.24 1.00 2744 132 0.2741 0.2584 2.0755 2.1645| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2400 2.0323 2.0412| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2114 2.0193 2.0407| | 27: 1.21 - 1.19 1.00 2814 148 0.2953 0.2313 2.0054 1.9489| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2685 1.984 2.0153| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2857 1.9714 2.0937| | 30: 1.16 - 1.15 1.00 2740 148 0.3004 0.2772 1.9376 1.9629| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.10 0.76 0.23 1524.45| | 2: 3.57 - 2.84 2876 122 0.80 26.41 1.27 0.23 1524.45| | 3: 2.84 - 2.48 2833 165 0.74 32.24 1.24 0.24 1265.33| | 4: 2.47 - 2.25 2825 136 0.81 25.96 1.26 0.25 592.87| | 5: 2.25 - 2.09 2756 127 0.77 29.69 1.28 0.25 592.87| | 6: 2.09 - 1.97 2846 113 0.83 23.40 1.29 0.25 326.08| | 7: 1.97 - 1.87 2787 165 0.89 17.37 1.28 0.26 98.55| | 8: 1.87 - 1.79 2789 144 0.85 21.92 1.24 0.26 98.55| | 9: 1.79 - 1.72 2745 138 0.88 18.94 1.23 0.26 57.67| | 10: 1.72 - 1.66 2789 158 0.86 20.35 1.22 0.26 49.49| | 11: 1.66 - 1.61 2740 147 0.86 21.35 1.24 0.25 47.67| | 12: 1.61 - 1.56 2787 146 0.88 18.38 1.23 0.25 29.29| | 13: 1.56 - 1.52 2745 130 0.87 20.43 1.24 0.25 29.29| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.25 0.25 26.18| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.24 0.25 20.47| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 20.47| | 17: 1.42 - 1.39 2785 139 0.87 20.71 1.23 0.25 17.55| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.22 0.25 15.86| | 19: 1.36 - 1.34 2807 134 0.85 22.02 1.23 0.25 15.86| | 20: 1.34 - 1.32 2696 147 0.87 21.03 1.21 0.25 13.34| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.25 13.16| | 22: 1.29 - 1.27 2704 152 0.85 22.45 1.22 0.25 12.89| | 23: 1.27 - 1.26 2802 156 0.85 22.50 1.21 0.24 11.49| | 24: 1.26 - 1.24 2744 132 0.85 22.86 1.20 0.24 11.49| | 25: 1.24 - 1.22 2734 148 0.84 24.23 1.20 0.24 10.90| | 26: 1.22 - 1.21 2727 135 0.84 24.31 1.19 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.83 25.29 1.20 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.81 26.52 1.18 0.22 9.89| | 29: 1.18 - 1.16 2800 134 0.81 26.85 1.15 0.22 9.76| | 30: 1.16 - 1.15 2740 148 0.80 28.16 1.14 0.22 9.76| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.76 max = 1524.45 mean = 221.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.94| |phase err.(test): min = 0.00 max = 89.96 mean = 22.75| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.232 1557 Z= 5.531 Angle : 5.263 16.495 2118 Z= 3.759 Chirality : 0.374 0.860 243 Planarity : 0.033 0.105 284 Dihedral : 13.785 79.642 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 34.05 % 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: -2.11 (0.48), residues: 224 helix: -2.32 (0.40), residues: 103 sheet: -0.82 (0.75), residues: 28 loop : -0.13 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.014 ARG A 48 TYR 0.090 0.055 TYR A 141 PHE 0.147 0.050 PHE A 164 HIS 0.077 0.033 HIS A 126 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= 0.2605 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791195 | | target function (ml) not normalized (work): 232523.290880 | | target function (ml) not normalized (free): 11856.192874 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1989 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1989 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1982 0.1989 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2005 0.2008 0.2005 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1642 0.1634 0.1806 n_refl.: 87594 remove outliers: r(all,work,free)=0.1641 0.1633 0.1806 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 98.94 88 5 0.3877 386.375 358.573 0.732 0.913 0.407 11.894-9.307 98.04 96 4 0.1698 616.229 588.682 1.017 0.914 0.374 9.237-7.194 100.00 213 7 0.2157 501.963 491.969 1.050 0.915 0.360 7.162-5.571 100.00 427 22 0.2182 376.695 365.110 1.019 0.915 0.320 5.546-4.326 100.00 867 58 0.1293 517.109 511.043 1.050 0.916 0.233 4.315-3.360 100.00 1859 96 0.1124 491.775 488.169 1.100 0.917 0.217 3.356-2.611 100.00 3867 181 0.1437 323.070 319.877 1.085 0.919 0.043 2.608-2.026 99.99 8198 413 0.1359 214.166 212.291 1.093 0.922 0.000 2.025-1.573 100.00 17313 902 0.1649 104.588 103.914 1.088 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.378 45.128 1.072 0.935 0.000 1.221-1.150 99.97 13689 708 0.2591 29.222 26.999 1.027 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1806 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=0.1633 r_free=0.1806 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.660739 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2000.946103 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 0.1208 0.1458 0.0250 0.007 0.9 1.3 0.5 0.0 0 12.830 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.58 2.50 3.013 19.066 2000.946 0.017 12.41 15.42 3.01 3.267 19.597 2000.946 0.015 Individual atomic B min max mean iso aniso Overall: 8.63 118.81 21.10 2.86 0 1785 Protein: 8.63 118.81 17.97 2.86 0 1519 Water: 11.09 114.65 39.28 N/A 0 258 Other: 22.98 36.61 29.44 N/A 0 8 Chain A: 8.63 118.81 21.10 N/A 0 1785 Histogram: Values Number of atoms 8.63 - 19.64 1205 19.64 - 30.66 228 30.66 - 41.68 169 41.68 - 52.70 101 52.70 - 63.72 53 63.72 - 74.74 16 74.74 - 85.75 6 85.75 - 96.77 4 96.77 - 107.79 0 107.79 - 118.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1542 r_work=0.1246 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1546 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 = 0.1246 r_free = 0.1550 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015290 | | target function (ls_wunit_k1) not normalized (work): 1273.567046 | | target function (ls_wunit_k1) not normalized (free): 113.508101 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1246 0.1550 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1713 0.1712 0.1775 n_refl.: 87592 remove outliers: r(all,work,free)=0.1713 0.1712 0.1775 n_refl.: 87592 overall B=0.10 to atoms: r(all,work,free)=0.1730 0.1730 0.1787 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1244 0.1543 n_refl.: 87592 remove outliers: r(all,work,free)=0.1258 0.1243 0.1543 n_refl.: 87591 ======================== 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 0.3584 297.694 278.600 0.687 0.924 0.380 11.894-9.307 98.04 96 4 0.1551 478.825 467.792 0.992 0.924 0.372 9.237-7.194 100.00 213 7 0.1808 390.037 384.777 1.029 0.925 0.350 7.162-5.571 100.00 427 22 0.1726 292.701 287.213 1.001 0.925 0.290 5.546-4.326 100.00 867 58 0.0916 401.807 398.979 1.026 0.926 0.209 4.315-3.360 100.00 1859 96 0.0770 382.121 381.069 1.077 0.927 0.190 3.356-2.611 100.00 3867 181 0.1018 251.034 250.299 1.078 0.928 0.048 2.608-2.026 99.99 8198 413 0.0978 166.412 165.853 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1213 81.267 81.435 1.088 0.935 0.000 1.573-1.221 100.00 36679 1900 0.1653 36.037 35.507 1.068 0.942 0.000 1.221-1.150 99.97 13689 708 0.2365 22.706 21.242 1.021 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0404 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1543 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** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1544 | n_water=258 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1254 r_free=0.1544 | n_water=252 | time (s): 26.020 (total time: 28.410) Filter (q & B) r_work=0.1257 r_free=0.1543 | n_water=249 | time (s): 3.890 (total time: 32.300) Compute maps r_work=0.1257 r_free=0.1543 | n_water=249 | time (s): 1.930 (total time: 34.230) Filter (map) r_work=0.1274 r_free=0.1550 | n_water=235 | time (s): 3.980 (total time: 38.210) Find peaks r_work=0.1274 r_free=0.1550 | n_water=235 | time (s): 0.820 (total time: 39.030) Add new water r_work=0.1432 r_free=0.1702 | n_water=456 | time (s): 3.910 (total time: 42.940) Refine new water occ: r_work=0.1340 r_free=0.1560 adp: r_work=0.1259 r_free=0.1514 occ: r_work=0.1271 r_free=0.1504 adp: r_work=0.1236 r_free=0.1492 occ: r_work=0.1239 r_free=0.1479 adp: r_work=0.1229 r_free=0.1478 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1478 r_work=0.1229 r_free=0.1478 | n_water=456 | time (s): 108.420 (total time: 151.360) Filter (q & B) r_work=0.1235 r_free=0.1485 | n_water=434 | time (s): 3.890 (total time: 155.250) Filter (dist only) r_work=0.1235 r_free=0.1484 | n_water=433 | time (s): 45.230 (total time: 200.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.962241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1630.262841 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 0.1235 0.1517 0.0282 0.007 0.9 1.9 0.5 0.0 0 12.481 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 15.17 2.82 3.800 23.259 1630.263 0.016 12.01 14.85 2.84 4.293 23.057 1630.263 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.19 23.21 2.64 198 1762 Protein: 8.70 114.19 17.68 2.64 0 1519 Water: 11.08 72.13 42.56 N/A 198 235 Other: 21.31 33.07 26.49 N/A 0 8 Chain A: 8.70 114.19 20.38 N/A 0 1762 Chain S: 14.22 70.92 48.44 N/A 198 0 Histogram: Values Number of atoms 8.70 - 19.25 1208 19.25 - 29.80 246 29.80 - 40.35 187 40.35 - 50.90 142 50.90 - 61.44 108 61.44 - 71.99 57 71.99 - 82.54 6 82.54 - 93.09 3 93.09 - 103.64 1 103.64 - 114.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1485 r_work=0.1200 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1484 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1481 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014075 | | target function (ls_wunit_k1) not normalized (work): 1172.354077 | | target function (ls_wunit_k1) not normalized (free): 104.815739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1201 0.1481 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1606 0.1603 0.1704 n_refl.: 87591 remove outliers: r(all,work,free)=0.1606 0.1603 0.1704 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1612 0.1609 0.1708 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1476 n_refl.: 87591 remove outliers: r(all,work,free)=0.1210 0.1196 0.1476 n_refl.: 87587 ======================== 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 0.3420 290.422 270.087 0.612 0.938 0.350 11.894-9.307 98.04 96 4 0.1449 478.825 477.876 0.985 0.938 0.331 9.237-7.194 100.00 213 7 0.1717 390.037 390.436 1.044 0.939 0.280 7.162-5.571 100.00 427 22 0.1540 292.701 288.958 0.999 0.939 0.233 5.546-4.326 100.00 867 58 0.0841 401.807 398.937 1.020 0.939 0.210 4.315-3.360 100.00 1859 96 0.0705 382.121 381.026 1.068 0.939 0.200 3.356-2.611 100.00 3867 181 0.0957 251.034 250.332 1.076 0.940 0.062 2.608-2.026 99.99 8198 413 0.0955 166.412 166.022 1.082 0.941 0.000 2.025-1.573 100.00 17313 902 0.1183 81.267 81.454 1.089 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1608 36.037 35.538 1.073 0.947 0.000 1.221-1.150 99.97 13689 708 0.2338 22.706 21.257 1.026 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0577 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1476 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1476 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1476 | n_water=433 | time (s): 1.570 (total time: 1.570) Filter (dist) r_work=0.1196 r_free=0.1477 | n_water=431 | time (s): 37.680 (total time: 39.250) Filter (q & B) r_work=0.1196 r_free=0.1477 | n_water=431 | time (s): 0.900 (total time: 40.150) Compute maps r_work=0.1196 r_free=0.1477 | n_water=431 | time (s): 1.230 (total time: 41.380) Filter (map) r_work=0.1239 r_free=0.1479 | n_water=296 | time (s): 3.200 (total time: 44.580) Find peaks r_work=0.1239 r_free=0.1479 | n_water=296 | time (s): 0.730 (total time: 45.310) Add new water r_work=0.1368 r_free=0.1589 | n_water=488 | time (s): 3.400 (total time: 48.710) Refine new water occ: r_work=0.1264 r_free=0.1509 adp: r_work=0.1265 r_free=0.1509 occ: r_work=0.1241 r_free=0.1492 adp: r_work=0.1239 r_free=0.1491 occ: r_work=0.1226 r_free=0.1482 adp: r_work=0.1219 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1477 r_work=0.1219 r_free=0.1477 | n_water=488 | time (s): 154.280 (total time: 202.990) Filter (q & B) r_work=0.1220 r_free=0.1479 | n_water=457 | time (s): 3.650 (total time: 206.640) Filter (dist only) r_work=0.1220 r_free=0.1479 | n_water=457 | time (s): 37.670 (total time: 244.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.049492 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.552312 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 0.1225 0.1448 0.0223 0.006 0.9 2.2 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.48 2.23 3.635 22.144 43.552 3.718 12.15 14.07 1.92 4.160 21.962 43.552 3.651 Individual atomic B min max mean iso aniso Overall: 9.27 109.28 21.76 2.31 225 1759 Protein: 9.27 109.28 17.23 2.31 0 1519 Water: 11.52 70.93 36.75 N/A 225 232 Other: 19.23 29.49 24.28 N/A 0 8 Chain A: 9.27 109.28 19.88 N/A 0 1759 Chain S: 16.43 67.72 36.45 N/A 225 0 Histogram: Values Number of atoms 9.27 - 19.28 1233 19.28 - 29.28 277 29.28 - 39.28 231 39.28 - 49.28 134 49.28 - 59.28 74 59.28 - 69.28 21 69.28 - 79.28 8 79.28 - 89.28 3 89.28 - 99.28 1 99.28 - 109.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1407 r_work=0.1216 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1408 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1405 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648138 | | target function (ml) not normalized (work): 303857.053058 | | target function (ml) not normalized (free): 16049.662850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1210 0.1405 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1537 0.1536 0.1584 n_refl.: 87587 remove outliers: r(all,work,free)=0.1537 0.1536 0.1584 n_refl.: 87587 overall B=-0.02 to atoms: r(all,work,free)=0.1534 0.1533 0.1582 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1375 n_refl.: 87587 remove outliers: r(all,work,free)=0.1206 0.1198 0.1375 n_refl.: 87578 ======================== 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 0.4009 282.385 253.967 0.458 1.000 0.314 11.894-9.307 97.06 95 4 0.2297 472.136 464.854 0.870 1.002 0.269 9.237-7.194 97.73 208 7 0.2267 382.687 383.610 0.941 1.002 0.202 7.162-5.571 100.00 427 22 0.2022 292.701 283.431 0.917 1.002 0.177 5.546-4.326 100.00 867 58 0.1089 401.807 397.781 0.951 1.002 0.156 4.315-3.360 100.00 1859 96 0.0928 382.121 379.162 0.992 1.002 0.147 3.356-2.611 100.00 3867 181 0.1151 251.034 249.127 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1057 166.412 165.349 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1016 81.267 81.402 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1296 36.037 35.602 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2133 22.706 21.322 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0447 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1375 | n_water=457 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1198 r_free=0.1373 | n_water=454 | time (s): 40.960 (total time: 43.040) Filter (q & B) r_work=0.1198 r_free=0.1373 | n_water=454 | time (s): 0.910 (total time: 43.950) Compute maps r_work=0.1198 r_free=0.1373 | n_water=454 | time (s): 1.490 (total time: 45.440) Filter (map) r_work=0.1220 r_free=0.1380 | n_water=316 | time (s): 3.460 (total time: 48.900) Find peaks r_work=0.1220 r_free=0.1380 | n_water=316 | time (s): 0.510 (total time: 49.410) Add new water r_work=0.1290 r_free=0.1450 | n_water=489 | time (s): 3.300 (total time: 52.710) Refine new water occ: r_work=0.1218 r_free=0.1379 adp: r_work=0.1219 r_free=0.1381 occ: r_work=0.1202 r_free=0.1366 adp: r_work=0.1202 r_free=0.1366 occ: r_work=0.1191 r_free=0.1359 adp: r_work=0.1187 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1356 r_work=0.1187 r_free=0.1356 | n_water=489 | time (s): 155.150 (total time: 207.860) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=454 | time (s): 2.750 (total time: 210.610) Filter (dist only) r_work=0.1192 r_free=0.1356 | n_water=453 | time (s): 38.220 (total time: 248.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.998417 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.621305 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 0.1199 0.1364 0.0164 0.006 0.9 2.9 0.5 0.0 0 0.999 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.64 1.64 3.417 21.480 48.621 3.636 11.82 13.58 1.76 3.827 21.357 48.621 3.616 Individual atomic B min max mean iso aniso Overall: 9.26 105.29 21.22 2.17 223 1757 Protein: 9.26 105.29 16.94 2.17 0 1519 Water: 11.54 69.46 35.54 N/A 223 230 Other: 19.09 26.56 22.57 N/A 0 8 Chain A: 9.26 105.29 19.51 N/A 0 1757 Chain S: 15.37 58.02 34.67 N/A 223 0 Histogram: Values Number of atoms 9.26 - 18.86 1229 18.86 - 28.47 284 28.47 - 38.07 221 38.07 - 47.67 136 47.67 - 57.28 71 57.28 - 66.88 25 66.88 - 76.48 9 76.48 - 86.09 2 86.09 - 95.69 1 95.69 - 105.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1358 r_work=0.1182 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1358 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1356 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1179 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615471 | | target function (ml) not normalized (work): 301103.669518 | | target function (ml) not normalized (free): 15919.518802 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1179 0.1356 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1505 0.1506 0.1540 n_refl.: 87578 remove outliers: r(all,work,free)=0.1505 0.1506 0.1540 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1503 0.1538 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1177 0.1356 n_refl.: 87578 remove outliers: r(all,work,free)=0.1185 0.1176 0.1356 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 0.4182 282.385 246.907 0.429 1.001 0.310 11.894-9.307 94.12 92 4 0.2354 469.942 454.002 0.839 1.002 0.246 9.237-7.194 97.73 208 7 0.2426 382.687 375.789 0.908 1.002 0.162 7.162-5.571 100.00 427 22 0.2185 292.701 282.152 0.906 1.002 0.133 5.546-4.326 100.00 867 58 0.1142 401.807 397.416 0.951 1.002 0.120 4.315-3.360 100.00 1859 96 0.0955 382.121 379.462 0.992 1.002 0.120 3.356-2.611 100.00 3867 181 0.1142 251.034 249.115 1.002 1.002 0.100 2.608-2.026 99.99 8198 413 0.1024 166.412 165.565 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0954 81.267 81.547 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.037 35.661 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.706 21.334 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0410 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1176 r_free=0.1356 After: r_work=0.1177 r_free=0.1356 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1356 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=0.1177 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1356 | n_water=453 | time (s): 1.530 (total time: 1.530) Filter (dist) r_work=0.1177 r_free=0.1356 | n_water=453 | time (s): 35.740 (total time: 37.270) Filter (q & B) r_work=0.1177 r_free=0.1357 | n_water=451 | time (s): 2.500 (total time: 39.770) Compute maps r_work=0.1177 r_free=0.1357 | n_water=451 | time (s): 1.490 (total time: 41.260) Filter (map) r_work=0.1204 r_free=0.1368 | n_water=337 | time (s): 3.160 (total time: 44.420) Find peaks r_work=0.1204 r_free=0.1368 | n_water=337 | time (s): 0.470 (total time: 44.890) Add new water r_work=0.1249 r_free=0.1406 | n_water=489 | time (s): 2.480 (total time: 47.370) Refine new water occ: r_work=0.1186 r_free=0.1357 adp: r_work=0.1187 r_free=0.1359 occ: r_work=0.1175 r_free=0.1346 adp: r_work=0.1175 r_free=0.1348 occ: r_work=0.1167 r_free=0.1338 adp: r_work=0.1164 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1339 r_work=0.1164 r_free=0.1339 | n_water=489 | time (s): 210.600 (total time: 257.970) Filter (q & B) r_work=0.1172 r_free=0.1338 | n_water=446 | time (s): 3.200 (total time: 261.170) Filter (dist only) r_work=0.1172 r_free=0.1339 | n_water=445 | time (s): 37.330 (total time: 298.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915655 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.297331 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 0.1201 0.1375 0.0174 0.007 1.1 4.2 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.75 1.74 3.289 21.085 47.297 3.626 12.04 13.77 1.73 3.451 21.027 47.297 3.620 Individual atomic B min max mean iso aniso Overall: 9.27 101.62 20.97 2.05 215 1757 Protein: 9.27 101.62 16.78 2.05 0 1519 Water: 11.56 68.78 35.26 N/A 215 230 Other: 18.97 26.52 22.61 N/A 0 8 Chain A: 9.27 101.62 19.34 N/A 0 1757 Chain S: 14.37 54.51 34.29 N/A 215 0 Histogram: Values Number of atoms 9.27 - 18.50 1216 18.50 - 27.74 281 27.74 - 36.97 228 36.97 - 46.21 130 46.21 - 55.44 75 55.44 - 64.68 26 64.68 - 73.91 11 73.91 - 83.15 2 83.15 - 92.38 1 92.38 - 101.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1377 r_work=0.1204 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1376 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1374 target_work(ml) = 3.619 | | 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= 0.1201 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618699 | | target function (ml) not normalized (work): 301361.667147 | | target function (ml) not normalized (free): 15939.966449 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1435 0.1430 5.6834 5.6373| | 2: 3.57 - 2.84 1.00 2888 124 0.1127 0.1416 5.199 5.2498| | 3: 2.83 - 2.48 1.00 2820 163 0.1224 0.1273 5.0033 5.0186| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1153 4.7069 4.7552| | 5: 2.25 - 2.09 1.00 2756 127 0.0990 0.1102 4.6446 4.7041| | 6: 2.09 - 1.97 1.00 2846 113 0.0978 0.1191 4.3543 4.4713| | 7: 1.97 - 1.87 1.00 2787 165 0.0996 0.1255 4.0777 4.2029| | 8: 1.87 - 1.79 1.00 2789 144 0.1013 0.1277 3.9915 4.0891| | 9: 1.79 - 1.72 1.00 2745 138 0.0959 0.1336 3.7162 3.9137| | 10: 1.72 - 1.66 1.00 2831 160 0.1004 0.1286 3.6325 3.7755| | 11: 1.66 - 1.61 1.00 2712 147 0.0971 0.1078 3.5703 3.6036| | 12: 1.61 - 1.56 1.00 2773 144 0.0919 0.1163 3.3442 3.463| | 13: 1.56 - 1.52 1.00 2745 130 0.0980 0.1090 3.3336 3.4527| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1108 3.2553 3.3428| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1339 3.1614 3.3134| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1272 3.1462 3.2461| | 17: 1.42 - 1.39 1.00 2785 139 0.1116 0.1302 3.1115 3.229| | 18: 1.39 - 1.36 1.00 2741 179 0.1147 0.1409 3.0805 3.275| | 19: 1.36 - 1.34 1.00 2807 134 0.1217 0.1613 3.0914 3.2806| | 20: 1.34 - 1.32 1.00 2696 147 0.1313 0.1482 3.0827 3.1408| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1648 3.0842 3.1675| | 22: 1.29 - 1.27 1.00 2704 152 0.1459 0.1924 3.0776 3.2772| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1830 3.0995 3.2039| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1793 3.0929 3.2073| | 25: 1.24 - 1.22 1.00 2733 148 0.1788 0.2303 3.1056 3.2822| | 26: 1.22 - 1.21 1.00 2727 135 0.1863 0.1765 3.1186 3.1923| | 27: 1.21 - 1.19 1.00 2814 148 0.2001 0.2120 3.1334 3.1523| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2313 3.135 3.1619| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2379 3.1228 3.2183| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2484 3.1113 3.1585| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.11 1.00 0.97 6197.39| | 2: 3.57 - 2.84 2888 124 0.92 13.28 1.01 0.97 6197.39| | 3: 2.83 - 2.48 2820 163 0.89 17.47 0.98 0.97 5199.17| | 4: 2.47 - 2.25 2825 136 0.91 14.67 1.00 0.97 2625.08| | 5: 2.25 - 2.09 2756 127 0.89 16.85 1.01 0.97 2625.08| | 6: 2.09 - 1.97 2846 113 0.92 13.74 1.02 0.97 1549.12| | 7: 1.97 - 1.87 2787 165 0.94 10.93 1.02 0.97 631.47| | 8: 1.87 - 1.79 2789 144 0.91 14.56 1.00 0.97 631.47| | 9: 1.79 - 1.72 2745 138 0.93 11.52 0.98 0.97 341.87| | 10: 1.72 - 1.66 2831 160 0.93 12.36 0.98 0.97 283.88| | 11: 1.66 - 1.61 2712 147 0.93 13.03 0.98 0.97 270.80| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 147.44| | 13: 1.56 - 1.52 2745 130 0.94 11.16 1.02 0.97 147.44| | 14: 1.52 - 1.48 2803 134 0.94 11.29 1.02 0.97 131.90| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.02 0.98 103.45| | 16: 1.45 - 1.42 2756 161 0.94 11.66 1.02 0.98 103.45| | 17: 1.42 - 1.39 2785 139 0.94 11.53 1.01 0.98 93.62| | 18: 1.39 - 1.36 2741 179 0.94 11.88 1.01 0.98 87.94| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.98 87.94| | 20: 1.34 - 1.32 2696 147 0.94 12.55 0.99 0.96 82.94| | 21: 1.32 - 1.30 2785 112 0.93 13.50 0.99 0.96 82.59| | 22: 1.29 - 1.27 2704 152 0.93 14.02 0.99 0.96 82.67| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.98 0.95 83.05| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.05| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.96 0.94 84.34| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 85.78| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 85.78| | 28: 1.19 - 1.18 2671 147 0.88 20.20 1.01 0.93 88.66| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 89.75| | 30: 1.16 - 1.15 2739 148 0.86 21.91 0.98 0.92 89.75| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.59 max = 6197.39 mean = 969.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.11| |phase err.(test): min = 0.00 max = 89.83 mean = 14.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1201 0.1374 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1524 0.1524 0.1567 n_refl.: 87575 remove outliers: r(all,work,free)=0.1524 0.1524 0.1567 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1521 0.1521 0.1565 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1373 n_refl.: 87575 remove outliers: r(all,work,free)=0.1209 0.1201 0.1373 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 0.4261 282.385 246.521 0.430 1.000 0.304 11.894-9.307 93.14 91 4 0.2419 469.969 450.090 0.846 1.001 0.246 9.237-7.194 97.73 208 7 0.2540 382.687 375.329 0.907 1.001 0.163 7.162-5.571 100.00 427 22 0.2291 292.701 282.013 0.901 1.002 0.133 5.546-4.326 100.00 867 58 0.1220 401.807 396.914 0.954 1.002 0.110 4.315-3.360 100.00 1859 96 0.0999 382.121 379.151 0.993 1.002 0.100 3.356-2.611 100.00 3867 181 0.1182 251.034 249.217 1.002 1.002 0.043 2.608-2.026 99.99 8198 413 0.1046 166.412 165.441 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0979 81.267 81.549 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1224 36.037 35.680 1.021 1.000 0.000 1.221-1.150 99.97 13689 708 0.2115 22.706 21.316 0.976 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0417 ================= 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 : 0.2605 0.1988 0.082 5.263 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_weight: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1208 0.1458 0.007 0.948 9.1 119.5 20.1 258 0.123 1_adp: 0.1242 0.1542 0.007 0.948 8.6 118.8 21.1 258 0.123 1_regHadp: 0.1246 0.1546 0.007 0.948 8.6 118.8 21.1 258 0.123 1_occ: 0.1246 0.1550 0.007 0.948 8.6 118.8 21.1 258 0.123 2_bss: 0.1243 0.1543 0.007 0.948 8.7 118.9 21.2 258 0.123 2_settarget: 0.1243 0.1543 0.007 0.948 8.7 118.9 21.2 258 0.123 2_updatecdl: 0.1243 0.1543 0.007 0.965 8.7 118.9 21.2 258 0.123 2_nqh: 0.1245 0.1544 0.007 0.965 8.7 118.9 21.2 258 0.126 2_sol: 0.1235 0.1484 0.007 0.965 8.7 118.9 23.6 433 n/a 2_weight: 0.1235 0.1484 0.007 0.965 8.7 118.9 23.6 433 n/a 2_xyzrec: 0.1235 0.1517 0.007 0.876 8.7 118.9 23.6 433 n/a 2_adp: 0.1201 0.1485 0.007 0.876 8.7 114.2 23.2 433 n/a 2_regHadp: 0.1200 0.1484 0.007 0.876 8.7 114.2 23.2 433 n/a 2_occ: 0.1201 0.1481 0.007 0.876 8.7 114.2 23.2 433 n/a 3_bss: 0.1196 0.1476 0.007 0.876 8.7 114.2 23.2 433 n/a 3_settarget: 0.1196 0.1476 0.007 0.876 8.7 114.2 23.2 433 n/a 3_updatecdl: 0.1196 0.1476 0.007 0.874 8.7 114.2 23.2 433 n/a 3_nqh: 0.1196 0.1476 0.007 0.874 8.7 114.2 23.2 433 n/a 3_sol: 0.1220 0.1479 0.007 0.874 8.7 114.2 22.1 457 n/a 3_weight: 0.1220 0.1479 0.007 0.874 8.7 114.2 22.1 457 n/a 3_xyzrec: 0.1225 0.1448 0.006 0.927 8.7 114.2 22.1 457 n/a 3_adp: 0.1215 0.1407 0.006 0.927 9.3 109.3 21.8 457 n/a 3_regHadp: 0.1216 0.1408 0.006 0.927 9.3 109.3 21.8 457 n/a 3_occ: 0.1210 0.1405 0.006 0.927 9.3 109.3 21.8 457 n/a 4_bss: 0.1198 0.1375 0.006 0.927 9.3 109.3 21.7 457 n/a 4_settarget: 0.1198 0.1375 0.006 0.927 9.3 109.3 21.7 457 n/a 4_updatecdl: 0.1198 0.1375 0.006 0.925 9.3 109.3 21.7 457 n/a 4_nqh: 0.1198 0.1375 0.006 0.925 9.3 109.3 21.7 457 n/a 4_sol: 0.1192 0.1356 0.006 0.925 9.3 109.3 21.4 453 n/a 4_weight: 0.1192 0.1356 0.006 0.925 9.3 109.3 21.4 453 n/a 4_xyzrec: 0.1199 0.1364 0.006 0.949 9.3 109.3 21.4 453 n/a 4_adp: 0.1182 0.1358 0.006 0.949 9.3 105.3 21.2 453 n/a 4_regHadp: 0.1182 0.1358 0.006 0.949 9.3 105.3 21.2 453 n/a 4_occ: 0.1179 0.1356 0.006 0.949 9.3 105.3 21.2 453 n/a 5_bss: 0.1176 0.1356 0.006 0.949 9.2 105.3 21.2 453 n/a 5_settarget: 0.1176 0.1356 0.006 0.949 9.2 105.3 21.2 453 n/a 5_updatecdl: 0.1176 0.1356 0.006 0.950 9.2 105.3 21.2 453 n/a 5_setrh: 0.1177 0.1356 0.006 0.950 9.2 105.3 21.2 453 n/a 5_nqh: 0.1177 0.1356 0.006 0.950 9.2 105.3 21.2 453 n/a 5_sol: 0.1172 0.1339 0.006 0.950 9.2 105.3 21.1 445 n/a 5_weight: 0.1172 0.1339 0.006 0.950 9.2 105.3 21.1 445 n/a 5_xyzrec: 0.1201 0.1375 0.007 1.089 9.2 105.3 21.1 445 n/a 5_adp: 0.1204 0.1377 0.007 1.089 9.3 101.6 21.0 445 n/a 5_regHadp: 0.1204 0.1376 0.007 1.089 9.3 101.6 21.0 445 n/a 5_occ: 0.1201 0.1374 0.007 1.089 9.3 101.6 21.0 445 n/a end: 0.1201 0.1373 0.007 1.089 9.3 101.6 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8555406_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8555406_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9900 Refinement macro-cycles (run) : 3483.4200 Write final files (write_after_run_outputs) : 70.5800 Total : 3558.9900 Total CPU time: 59.96 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:29 PST -0800 (1735452689.06 s) Start R-work = 0.1633, R-free = 0.1806 Final R-work = 0.1201, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 3700.40 seconds wall clock time: 66 minutes 44.31 seconds (4004.31 seconds total)