Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.51 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: 0.36 Conformation dependent library (CDL) restraints added in 122.8 milliseconds Time building geometry restraints manager: 0.50 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: 537 0.91 - 1.17: 1108 1.17 - 1.43: 657 1.43 - 1.68: 821 1.68 - 1.94: 30 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.763 -0.237 1.14e-02 7.69e+03 4.32e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.236 1.494 -0.258 1.26e-02 6.30e+03 4.19e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.231 0.230 1.19e-02 7.06e+03 3.73e+02 bond pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.374 1.162 0.212 1.10e-02 8.26e+03 3.73e+02 bond pdb=" CA GLU A 116 " pdb=" C GLU A 116 " ideal model delta sigma weight residual 1.528 1.738 -0.210 1.25e-02 6.40e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.10: 2787 4.10 - 8.19: 1926 8.19 - 12.29: 811 12.29 - 16.38: 221 16.38 - 20.47: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 134.46 -12.96 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.36 108.72 10.64 8.40e-01 1.42e+00 1.60e+02 angle pdb=" CA SER A 161 " pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 117.07 131.07 -14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.83 108.26 12.57 1.07e+00 8.73e-01 1.38e+02 angle pdb=" O VAL A 186 " pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 122.57 107.93 14.64 1.25e+00 6.40e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 903 15.63 - 31.26: 141 31.26 - 46.88: 46 46.88 - 62.51: 18 62.51 - 78.14: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " 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=" CD1 PHE A 119 " pdb=" CE1 PHE A 119 " pdb=" CZ PHE A 119 " pdb=" HZ PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.243: 116 0.243 - 0.486: 76 0.486 - 0.728: 34 0.728 - 0.970: 16 0.970 - 1.212: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 29 " pdb=" N ALA A 29 " pdb=" C ALA A 29 " pdb=" CB ALA A 29 " both_signs ideal model delta sigma weight residual False 2.48 1.27 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 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 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.004 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.039 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG TYR A 141 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.087 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.074 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 791 2.28 - 2.86: 7857 2.86 - 3.44: 10640 3.44 - 4.02: 15198 4.02 - 4.60: 22153 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.799 1.816 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.831 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.836 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.877 1.850 ... (remaining 56634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_8230669_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= 0.2606 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788006 | | target function (ml) not normalized (work): 232257.622457 | | target function (ml) not normalized (free): 11788.552248 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2150 7.0006 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2425 0.1903 4.3568 4.368| | 3: 2.84 - 2.48 1.00 2833 165 0.2338 0.1705 4.1339 4.1704| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1475 3.8353 3.8318| | 5: 2.25 - 2.09 1.00 2756 127 0.2460 0.1683 3.801 3.831| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1678 3.4776 3.55| | 7: 1.97 - 1.87 1.00 2787 165 0.2576 0.1769 3.1307 3.1563| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1958 3.0551 3.1355| | 9: 1.79 - 1.72 1.00 2745 138 0.2456 0.1629 2.8959 2.8717| | 10: 1.72 - 1.66 1.00 2789 158 0.2382 0.2065 2.7952 2.8719| | 11: 1.66 - 1.61 1.00 2740 147 0.2541 0.1807 2.7606 2.7619| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.1885 2.6221 2.6638| | 13: 1.56 - 1.52 1.00 2745 130 0.2554 0.1746 2.5682 2.5737| | 14: 1.52 - 1.48 1.00 2803 134 0.2559 0.2036 2.5137 2.5721| | 15: 1.48 - 1.45 1.00 2738 128 0.2617 0.2048 2.4273 2.4557| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2165 2.3822 2.4394| | 17: 1.42 - 1.39 1.00 2785 139 0.2634 0.2114 2.3073 2.3301| | 18: 1.39 - 1.36 1.00 2741 179 0.2646 0.2170 2.2652 2.2956| | 19: 1.36 - 1.34 1.00 2807 134 0.2657 0.2483 2.2404 2.3304| | 20: 1.34 - 1.32 1.00 2696 147 0.2651 0.2191 2.1983 2.1779| | 21: 1.32 - 1.30 1.00 2785 112 0.2694 0.2281 2.1841 2.1939| | 22: 1.29 - 1.27 1.00 2704 152 0.2767 0.2435 2.1486 2.1602| | 23: 1.27 - 1.26 1.00 2802 156 0.2734 0.2456 2.0895 2.1965| | 24: 1.26 - 1.24 1.00 2744 132 0.2785 0.2620 2.0757 2.1977| | 25: 1.24 - 1.22 1.00 2734 148 0.2795 0.2680 2.0374 2.1094| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2132 2.0123 2.047| | 27: 1.21 - 1.19 1.00 2814 148 0.2934 0.2763 1.9936 2.037| | 28: 1.19 - 1.18 1.00 2671 147 0.3006 0.2563 1.9866 1.9643| | 29: 1.18 - 1.16 1.00 2800 134 0.2990 0.2564 1.9635 1.992| | 30: 1.16 - 1.15 1.00 2740 148 0.3065 0.2901 1.9286 1.9653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.06 0.76 0.23 1515.10| | 2: 3.57 - 2.84 2876 122 0.80 26.30 1.27 0.23 1515.10| | 3: 2.84 - 2.48 2833 165 0.74 32.21 1.24 0.23 1255.45| | 4: 2.47 - 2.25 2825 136 0.81 25.78 1.26 0.25 581.60| | 5: 2.25 - 2.09 2756 127 0.77 29.61 1.28 0.25 581.60| | 6: 2.09 - 1.97 2846 113 0.83 22.74 1.29 0.25 316.50| | 7: 1.97 - 1.87 2787 165 0.90 16.53 1.29 0.26 90.40| | 8: 1.87 - 1.79 2789 144 0.86 20.86 1.25 0.26 90.40| | 9: 1.79 - 1.72 2745 138 0.88 18.70 1.24 0.25 54.53| | 10: 1.72 - 1.66 2789 158 0.87 19.79 1.22 0.25 47.34| | 11: 1.66 - 1.61 2740 147 0.86 20.99 1.24 0.25 45.70| | 12: 1.61 - 1.56 2787 146 0.88 18.47 1.23 0.25 29.08| | 13: 1.56 - 1.52 2745 130 0.86 20.51 1.24 0.25 29.08| | 14: 1.52 - 1.48 2803 134 0.87 20.61 1.23 0.25 25.93| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.24 0.25 20.16| | 16: 1.45 - 1.42 2756 161 0.86 21.23 1.23 0.25 20.16| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.23 0.25 17.14| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.22 0.25 15.40| | 19: 1.36 - 1.34 2807 134 0.86 21.88 1.21 0.25 15.40| | 20: 1.34 - 1.32 2696 147 0.87 20.67 1.21 0.25 12.98| | 21: 1.32 - 1.30 2785 112 0.86 21.60 1.19 0.25 12.80| | 22: 1.29 - 1.27 2704 152 0.86 22.21 1.21 0.25 12.53| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.20 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 22.97 1.21 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.52 1.20 0.24 10.55| | 26: 1.22 - 1.21 2727 135 0.84 23.94 1.20 0.23 9.87| | 27: 1.21 - 1.19 2814 148 0.83 24.60 1.21 0.23 9.87| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.18 0.23 8.95| | 29: 1.18 - 1.16 2800 134 0.83 24.89 1.16 0.23 8.61| | 30: 1.16 - 1.15 2740 148 0.81 26.65 1.15 0.23 8.61| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.61 max = 1515.10 mean = 218.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.50| |phase err.(test): min = 0.00 max = 89.87 mean = 22.52| |-----------------------------------------------------------------------------| ----------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 0.259 1557 Z= 5.417 Angle : 5.274 17.862 2118 Z= 3.651 Chirality : 0.388 1.212 243 Planarity : 0.030 0.083 284 Dihedral : 13.735 78.136 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 29.73 % 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: -3.11 (0.45), residues: 224 helix: -2.67 (0.35), residues: 108 sheet: -1.30 (0.77), residues: 40 loop : -1.07 (0.57), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 28 TYR 0.072 0.025 TYR A 139 PHE 0.097 0.036 PHE A 119 HIS 0.079 0.024 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= 0.2606 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788006 | | target function (ml) not normalized (work): 232257.622457 | | target function (ml) not normalized (free): 11788.552248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2606 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2606 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1961 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2005 0.2008 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1772 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 0.3811 386.357 358.327 0.728 0.916 0.401 11.894-9.307 99.02 97 4 0.1812 613.709 593.358 1.010 0.917 0.380 9.237-7.194 100.00 213 7 0.2134 501.938 492.414 1.049 0.918 0.370 7.162-5.571 100.00 427 22 0.2267 376.677 363.512 1.018 0.918 0.282 5.546-4.326 100.00 867 58 0.1310 517.084 511.193 1.051 0.919 0.239 4.315-3.360 100.00 1859 96 0.1145 491.751 487.787 1.093 0.920 0.189 3.356-2.611 100.00 3867 181 0.1430 323.055 319.897 1.084 0.921 0.048 2.608-2.026 99.99 8198 413 0.1341 214.156 211.994 1.090 0.923 0.000 2.025-1.573 100.00 17313 902 0.1657 104.583 103.971 1.093 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.376 45.037 1.070 0.933 0.000 1.221-1.150 99.97 13689 708 0.2589 29.220 26.922 1.035 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0505 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1636 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.929463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2050.256697 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 0.1730 0.1844 0.0113 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1570 0.1708 0.0138 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1441 0.1607 0.0165 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1394 0.1585 0.0191 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1348 0.1551 0.0202 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1335 0.1534 0.0199 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1294 0.1510 0.0216 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1273 0.1501 0.0228 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1258 0.1490 0.0231 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1247 0.1481 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1239 0.1477 0.0237 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1238 0.1476 0.0238 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1235 0.1474 0.0239 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1230 0.1471 0.0241 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1228 0.1471 0.0243 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1472 0.0246 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1225 0.1471 0.0246 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1222 0.1477 0.0255 0.007 1.0 3.8 0.5 0.0 0 13.465 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1471 0.0243 0.006 0.9 3.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.71 2.43 3.013 19.079 2050.257 0.017 12.28 14.70 2.42 2.988 19.079 61.508 0.017 12.35 14.68 2.33 2.657 19.078 256.282 0.017 12.68 15.30 2.62 2.750 19.246 1025.128 0.016 12.56 15.52 2.96 3.353 19.669 2050.257 0.016 12.43 15.50 3.08 3.288 19.645 3075.385 0.015 12.26 15.36 3.10 3.234 19.599 4100.513 0.015 12.24 15.44 3.20 3.367 19.668 5125.642 0.015 12.23 15.43 3.20 3.396 19.669 6150.770 0.015 12.25 15.50 3.25 3.397 19.657 7175.898 0.015 12.17 15.41 3.24 3.347 19.620 8201.027 0.015 12.18 15.47 3.29 3.405 19.639 9226.155 0.015 12.19 15.52 3.33 3.314 19.573 10251.283 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 256.282 Accepted refinement result: 12.35 14.68 2.33 2.657 19.078 256.282 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.46 20.10 3.29 0 1785 Protein: 9.09 114.90 17.01 3.29 0 1519 Water: 11.47 119.46 38.25 N/A 0 258 Other: 19.77 26.62 22.09 N/A 0 8 Chain A: 9.09 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.17 227 31.17 - 42.20 125 42.20 - 53.24 94 53.24 - 64.28 42 64.28 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1468 r_work=0.1237 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1472 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 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= 0.1229 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016766 | | target function (ls_wunit_k1) not normalized (work): 1396.578138 | | target function (ls_wunit_k1) not normalized (free): 110.394644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1240 0.1229 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1678 0.1679 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1678 0.1679 0.1695 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1684 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1454 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 0.3522 300.892 280.969 0.649 1.003 0.376 11.894-9.307 99.02 97 4 0.1638 482.012 470.124 0.925 1.003 0.373 9.237-7.194 100.00 213 7 0.1877 394.227 388.913 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1790 295.845 290.502 0.938 1.003 0.263 5.546-4.326 100.00 867 58 0.0997 406.122 403.278 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0874 386.225 385.230 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1174 253.730 252.619 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1024 168.200 167.480 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.140 82.319 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.424 35.930 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.950 21.432 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0402 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1454 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=0.1229 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1454 | n_water=258 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1237 r_free=0.1451 | n_water=252 | time (s): 23.960 (total time: 26.000) Filter (q & B) r_work=0.1240 r_free=0.1451 | n_water=249 | time (s): 3.090 (total time: 29.090) Compute maps r_work=0.1240 r_free=0.1451 | n_water=249 | time (s): 1.060 (total time: 30.150) Filter (map) r_work=0.1259 r_free=0.1459 | n_water=225 | time (s): 2.850 (total time: 33.000) Find peaks r_work=0.1259 r_free=0.1459 | n_water=225 | time (s): 0.670 (total time: 33.670) Add new water r_work=0.1410 r_free=0.1643 | n_water=433 | time (s): 3.290 (total time: 36.960) Refine new water occ: r_work=0.1312 r_free=0.1511 adp: r_work=0.1229 r_free=0.1453 occ: r_work=0.1244 r_free=0.1444 adp: r_work=0.1208 r_free=0.1423 occ: r_work=0.1211 r_free=0.1414 adp: r_work=0.1201 r_free=0.1411 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1411 r_work=0.1201 r_free=0.1411 | n_water=433 | time (s): 95.020 (total time: 131.980) Filter (q & B) r_work=0.1202 r_free=0.1414 | n_water=423 | time (s): 2.770 (total time: 134.750) Filter (dist only) r_work=0.1203 r_free=0.1412 | n_water=422 | time (s): 35.750 (total time: 170.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.626272 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1472.662489 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 0.1658 0.1771 0.0113 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1497 0.1634 0.0138 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1365 0.1529 0.0164 0.001 0.5 6.7 0.0 0.0 0 0.500 0.1343 0.1508 0.0165 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1312 0.1488 0.0177 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1327 0.1502 0.0175 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1254 0.1447 0.0194 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1232 0.1438 0.0206 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1216 0.1428 0.0212 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1208 0.1425 0.0216 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1207 0.1426 0.0220 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1203 0.1428 0.0225 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1200 0.1423 0.0224 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1193 0.1412 0.0219 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1192 0.1415 0.0222 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1189 0.1412 0.0223 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1187 0.1414 0.0226 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1185 0.1408 0.0223 0.008 0.9 5.1 0.5 0.0 0 13.813 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1185 0.1408 0.0223 0.008 0.9 5.1 0.5 0.0 0 13.813 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 14.08 2.23 3.767 21.825 1472.662 0.016 11.85 14.08 2.23 3.767 21.825 44.180 0.016 11.85 14.08 2.23 3.767 21.825 184.083 0.016 12.04 14.47 2.43 3.630 21.826 736.331 0.015 11.99 14.79 2.80 3.467 21.999 1472.662 0.015 11.88 14.79 2.91 3.472 22.200 2208.994 0.014 11.75 14.69 2.94 3.475 22.150 2945.325 0.014 11.69 14.66 2.97 3.503 21.992 3681.656 0.014 11.73 14.77 3.04 3.509 22.182 4417.987 0.014 11.67 14.74 3.07 3.516 22.167 5154.319 0.014 11.66 14.75 3.09 3.533 22.180 5890.650 0.014 11.63 14.75 3.12 3.541 22.104 6626.981 0.014 11.65 14.81 3.16 3.569 22.208 7363.312 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 184.083 Accepted refinement result: 11.85 14.08 2.23 3.767 21.825 184.083 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 114.93 22.26 3.29 197 1752 Protein: 9.12 114.93 17.04 3.29 0 1519 Water: 11.50 76.69 41.04 N/A 197 225 Other: 19.80 26.65 22.12 N/A 0 8 Chain A: 9.12 114.93 19.47 N/A 0 1752 Chain S: 15.46 60.00 47.08 N/A 197 0 Histogram: Values Number of atoms 9.12 - 19.70 1260 19.70 - 30.28 245 30.28 - 40.86 161 40.86 - 51.44 134 51.44 - 62.02 127 62.02 - 72.60 10 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1408 r_work=0.1185 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1408 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1415 target_work(ls_wunit_k1) = 0.015 | | 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014773 | | target function (ls_wunit_k1) not normalized (work): 1230.523795 | | target function (ls_wunit_k1) not normalized (free): 101.094642 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1183 0.1415 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1583 0.1581 0.1654 n_refl.: 87592 remove outliers: r(all,work,free)=0.1583 0.1581 0.1654 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1584 0.1582 0.1655 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1405 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1405 n_refl.: 87590 ======================== 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 93.75 85 5 0.3293 299.772 274.385 0.599 1.002 0.350 11.894-9.307 99.02 97 4 0.1639 482.012 473.637 0.923 1.003 0.325 9.237-7.194 100.00 213 7 0.1668 394.227 393.870 0.989 1.003 0.270 7.162-5.571 100.00 427 22 0.1549 295.845 291.527 0.937 1.003 0.240 5.546-4.326 100.00 867 58 0.0860 406.122 403.414 0.963 1.003 0.215 4.315-3.360 100.00 1859 96 0.0761 386.225 385.591 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1078 253.730 252.821 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1013 168.200 167.619 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.140 82.362 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.424 35.953 1.026 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.950 21.461 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0051 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1405 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1179 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1407 | n_water=422 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1178 r_free=0.1404 | n_water=417 | time (s): 35.060 (total time: 36.840) Filter (q & B) r_work=0.1178 r_free=0.1405 | n_water=416 | time (s): 3.020 (total time: 39.860) Compute maps r_work=0.1178 r_free=0.1405 | n_water=416 | time (s): 1.500 (total time: 41.360) Filter (map) r_work=0.1223 r_free=0.1390 | n_water=287 | time (s): 2.610 (total time: 43.970) Find peaks r_work=0.1223 r_free=0.1390 | n_water=287 | time (s): 0.480 (total time: 44.450) Add new water r_work=0.1342 r_free=0.1538 | n_water=458 | time (s): 2.450 (total time: 46.900) Refine new water occ: r_work=0.1253 r_free=0.1456 adp: r_work=0.1254 r_free=0.1458 occ: r_work=0.1231 r_free=0.1430 adp: r_work=0.1230 r_free=0.1431 occ: r_work=0.1213 r_free=0.1409 adp: r_work=0.1208 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1406 r_work=0.1208 r_free=0.1406 | n_water=458 | time (s): 173.120 (total time: 220.020) Filter (q & B) r_work=0.1212 r_free=0.1410 | n_water=435 | time (s): 3.300 (total time: 223.320) Filter (dist only) r_work=0.1212 r_free=0.1409 | n_water=433 | time (s): 37.690 (total time: 261.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.781855 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.645025 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 0.1241 0.1376 0.0135 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1197 0.1342 0.0145 0.003 0.7 3.8 0.5 0.0 0 0.267 0.1178 0.1331 0.0152 0.004 0.8 3.5 0.5 0.0 0 0.535 0.1170 0.1328 0.0158 0.005 0.9 3.5 0.5 0.0 0 0.802 0.1167 0.1328 0.0161 0.006 1.0 3.8 0.5 0.0 0 1.069 0.1164 0.1327 0.0163 0.007 1.0 3.8 0.5 0.0 0 1.336 0.1162 0.1327 0.0165 0.007 1.1 3.8 0.5 0.0 0 1.604 0.1160 0.1326 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.871 0.1169 0.1330 0.0161 0.005 0.9 3.5 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1326 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.26 1.66 3.770 21.236 42.645 3.620 11.60 13.26 1.66 3.770 21.236 1.279 3.620 11.61 13.26 1.66 3.762 21.236 5.331 3.620 11.64 13.32 1.68 3.704 21.229 21.323 3.614 11.72 13.47 1.75 3.718 21.191 42.645 3.617 11.63 13.42 1.79 3.745 21.178 63.968 3.610 11.56 13.37 1.81 3.764 21.176 85.290 3.605 11.55 13.39 1.84 3.774 21.167 106.613 3.603 11.51 13.36 1.85 3.784 21.166 127.935 3.600 11.49 13.36 1.87 3.798 21.155 149.258 3.599 11.49 13.37 1.88 3.812 21.148 170.580 3.599 11.47 13.34 1.86 3.818 21.142 191.903 3.597 11.45 13.32 1.87 3.821 21.147 213.225 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.279 Accepted refinement result: 11.60 13.26 1.66 3.770 21.236 1.279 3.620 Individual atomic B min max mean iso aniso Overall: 9.12 114.93 21.18 3.29 213 1747 Protein: 9.12 114.93 17.04 3.29 0 1519 Water: 11.50 76.69 35.68 N/A 213 220 Other: 19.80 26.65 22.12 N/A 0 8 Chain A: 9.12 114.93 19.38 N/A 0 1747 Chain S: 15.46 60.00 35.92 N/A 213 0 Histogram: Values Number of atoms 9.12 - 19.70 1261 19.70 - 30.28 289 30.28 - 40.86 209 40.86 - 51.44 125 51.44 - 62.02 55 62.02 - 72.61 10 72.61 - 83.19 5 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1326 r_work=0.1160 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1326 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1310 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611654 | | target function (ml) not normalized (work): 300829.124132 | | target function (ml) not normalized (free): 15839.509131 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1150 0.1310 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1498 0.1499 0.1525 n_refl.: 87590 remove outliers: r(all,work,free)=0.1498 0.1499 0.1525 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1497 0.1524 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1306 n_refl.: 87590 remove outliers: r(all,work,free)=0.1149 0.1141 0.1306 n_refl.: 87580 ======================== 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 0.3563 292.781 267.910 0.505 1.000 0.320 11.894-9.307 98.04 96 4 0.2285 482.137 464.952 0.865 1.002 0.320 9.237-7.194 98.18 209 7 0.2281 385.715 385.707 0.947 1.002 0.206 7.162-5.571 100.00 427 22 0.2088 295.845 285.148 0.912 1.002 0.183 5.546-4.326 100.00 867 58 0.1118 406.122 401.376 0.954 1.002 0.170 4.315-3.360 100.00 1859 96 0.0940 386.225 383.872 0.994 1.002 0.160 3.356-2.611 100.00 3867 181 0.1128 253.730 251.663 0.997 1.002 0.034 2.608-2.026 99.99 8198 413 0.0935 168.200 167.372 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0898 82.140 82.438 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.424 36.012 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.950 21.498 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1306 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1145 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1307 | n_water=433 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1145 r_free=0.1307 | n_water=431 | time (s): 48.320 (total time: 50.750) Filter (q & B) r_work=0.1145 r_free=0.1307 | n_water=431 | time (s): 1.290 (total time: 52.040) Compute maps r_work=0.1145 r_free=0.1307 | n_water=431 | time (s): 1.760 (total time: 53.800) Filter (map) r_work=0.1173 r_free=0.1301 | n_water=318 | time (s): 3.610 (total time: 57.410) Find peaks r_work=0.1173 r_free=0.1301 | n_water=318 | time (s): 0.680 (total time: 58.090) Add new water r_work=0.1247 r_free=0.1393 | n_water=480 | time (s): 3.720 (total time: 61.810) Refine new water occ: r_work=0.1172 r_free=0.1332 adp: r_work=0.1172 r_free=0.1334 occ: r_work=0.1156 r_free=0.1314 adp: r_work=0.1155 r_free=0.1316 occ: r_work=0.1143 r_free=0.1295 adp: r_work=0.1139 r_free=0.1296 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1296 r_work=0.1139 r_free=0.1296 | n_water=480 | time (s): 303.530 (total time: 365.340) Filter (q & B) r_work=0.1145 r_free=0.1294 | n_water=445 | time (s): 4.020 (total time: 369.360) Filter (dist only) r_work=0.1146 r_free=0.1293 | n_water=444 | time (s): 46.950 (total time: 416.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.806699 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.786794 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 0.1203 0.1330 0.0126 0.002 0.6 4.2 0.5 0.0 0 0.090 0.1167 0.1308 0.0141 0.003 0.8 3.2 0.5 0.0 0 0.271 0.1153 0.1302 0.0149 0.005 0.9 3.8 0.5 0.0 0 0.542 0.1147 0.1299 0.0153 0.006 1.0 3.8 0.5 0.0 0 0.813 0.1143 0.1299 0.0156 0.007 1.0 3.5 0.5 0.0 0 1.084 0.1140 0.1299 0.0159 0.007 1.1 3.5 0.5 0.0 0 1.355 0.1138 0.1298 0.0160 0.008 1.1 3.8 0.5 0.0 0 1.626 0.1136 0.1294 0.0159 0.009 1.1 4.2 0.5 0.0 0 1.897 0.1145 0.1299 0.0154 0.006 1.0 3.8 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1294 0.0159 0.009 1.1 4.2 0.5 0.0 0 1.897 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.94 1.59 3.770 21.196 40.787 3.603 11.36 12.94 1.59 3.770 21.196 1.224 3.603 11.36 12.94 1.59 3.770 21.196 5.098 3.603 11.39 12.99 1.60 3.706 21.188 20.393 3.598 11.48 13.17 1.69 3.722 21.156 40.787 3.603 11.39 13.13 1.73 3.749 21.145 61.180 3.596 11.35 13.10 1.76 3.763 21.139 81.574 3.591 11.29 13.04 1.75 3.772 21.144 101.967 3.587 11.27 13.04 1.77 3.784 21.138 122.360 3.586 11.27 13.06 1.79 3.801 21.128 142.754 3.586 11.26 13.02 1.76 3.810 21.118 163.147 3.583 11.24 13.03 1.78 3.821 21.118 183.541 3.583 11.23 13.01 1.78 3.825 21.120 203.934 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.098 Accepted refinement result: 11.36 12.94 1.59 3.770 21.196 5.098 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 114.92 21.11 3.29 226 1745 Protein: 9.11 114.92 17.03 3.29 0 1519 Water: 11.49 76.68 35.05 N/A 226 218 Other: 19.79 26.65 22.12 N/A 0 8 Chain A: 9.11 114.92 19.37 N/A 0 1745 Chain S: 15.45 60.00 34.58 N/A 226 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.27 300 30.27 - 40.86 211 40.86 - 51.44 126 51.44 - 62.02 50 62.02 - 72.60 10 72.60 - 83.18 5 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1294 r_work=0.1136 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1294 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1290 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1290 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600782 | | target function (ml) not normalized (work): 299887.569568 | | target function (ml) not normalized (free): 15799.600553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1290 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1462 0.1462 0.1482 n_refl.: 87580 remove outliers: r(all,work,free)=0.1462 0.1462 0.1482 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1460 0.1461 0.1482 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1130 0.1289 n_refl.: 87580 remove outliers: r(all,work,free)=0.1137 0.1129 0.1289 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 88.54 80 5 0.3763 292.781 259.287 0.481 1.001 0.318 11.894-9.307 95.10 93 4 0.2217 485.480 460.222 0.864 1.002 0.310 9.237-7.194 98.18 209 7 0.2433 385.715 377.083 0.923 1.003 0.182 7.162-5.571 100.00 427 22 0.2120 295.845 285.149 0.913 1.003 0.153 5.546-4.326 100.00 867 58 0.1115 406.122 401.629 0.962 1.003 0.126 4.315-3.360 100.00 1859 96 0.0919 386.225 384.133 1.002 1.003 0.107 3.356-2.611 100.00 3867 181 0.1101 253.730 252.022 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0915 168.200 167.631 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.140 82.503 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.424 36.044 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.950 21.514 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0185 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1129 r_free=0.1289 After: r_work=0.1130 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1130 r_free=0.1289 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=0.1130 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1130 r_free=0.1289 | n_water=444 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1130 r_free=0.1289 | n_water=444 | time (s): 43.770 (total time: 46.140) Filter (q & B) r_work=0.1130 r_free=0.1289 | n_water=444 | time (s): 1.400 (total time: 47.540) Compute maps r_work=0.1130 r_free=0.1289 | n_water=444 | time (s): 1.840 (total time: 49.380) Filter (map) r_work=0.1152 r_free=0.1303 | n_water=348 | time (s): 3.890 (total time: 53.270) Find peaks r_work=0.1152 r_free=0.1303 | n_water=348 | time (s): 0.700 (total time: 53.970) Add new water r_work=0.1206 r_free=0.1361 | n_water=508 | time (s): 3.530 (total time: 57.500) Refine new water occ: r_work=0.1146 r_free=0.1302 adp: r_work=0.1146 r_free=0.1306 occ: r_work=0.1133 r_free=0.1284 adp: r_work=0.1132 r_free=0.1288 occ: r_work=0.1124 r_free=0.1271 adp: r_work=0.1121 r_free=0.1272 ADP+occupancy (water only), MIN, final r_work=0.1121 r_free=0.1272 r_work=0.1121 r_free=0.1272 | n_water=508 | time (s): 255.900 (total time: 313.400) Filter (q & B) r_work=0.1129 r_free=0.1277 | n_water=462 | time (s): 3.820 (total time: 317.220) Filter (dist only) r_work=0.1130 r_free=0.1276 | n_water=460 | time (s): 48.090 (total time: 365.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.659830 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.114610 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 0.1323 0.0117 0.004 0.7 6.4 0.0 0.0 0 0.083 0.1172 0.1301 0.0128 0.004 0.8 6.1 0.0 0.0 0 0.249 0.1152 0.1288 0.0136 0.005 0.9 5.4 0.5 0.0 0 0.498 0.1143 0.1282 0.0139 0.006 1.0 5.4 0.5 0.0 0 0.747 0.1137 0.1278 0.0141 0.006 1.1 5.1 0.5 0.0 0 0.996 0.1134 0.1277 0.0142 0.007 1.1 4.8 0.5 0.0 0 1.245 0.1132 0.1276 0.0144 0.008 1.1 4.8 0.5 0.0 0 1.494 0.1130 0.1275 0.0145 0.008 1.1 4.8 0.5 0.0 0 1.743 0.1141 0.1281 0.0139 0.006 1.0 5.1 0.5 0.0 0 0.830 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1275 0.0145 0.008 1.1 4.8 0.5 0.0 0 1.743 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.75 1.45 3.769 21.250 44.115 3.600 11.30 12.75 1.45 3.769 21.250 1.323 3.600 11.30 12.75 1.45 3.766 21.250 5.514 3.600 11.32 12.81 1.49 3.707 21.241 22.057 3.595 11.38 12.95 1.57 3.734 21.208 44.115 3.597 11.30 12.91 1.61 3.756 21.200 66.172 3.591 11.25 12.88 1.62 3.769 21.197 88.229 3.587 11.23 12.87 1.65 3.778 21.196 110.287 3.585 11.20 12.86 1.66 3.792 21.190 132.344 3.583 11.21 12.89 1.68 3.811 21.179 154.401 3.583 11.19 12.86 1.67 3.820 21.178 176.458 3.582 11.18 12.84 1.66 3.826 21.177 198.516 3.580 11.16 12.82 1.66 3.831 21.178 220.573 3.579 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.514 Accepted refinement result: 11.30 12.75 1.45 3.766 21.250 5.514 3.600 Individual atomic B min max mean iso aniso Overall: 9.11 114.88 21.22 3.28 242 1745 Protein: 9.11 114.88 17.03 3.28 0 1519 Water: 11.49 76.68 35.04 N/A 242 218 Other: 19.79 26.63 22.11 N/A 0 8 Chain A: 9.11 114.88 19.36 N/A 0 1745 Chain S: 15.45 60.00 34.59 N/A 242 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.26 312 30.26 - 40.84 213 40.84 - 51.42 125 51.42 - 61.99 54 61.99 - 72.57 10 72.57 - 83.15 5 83.15 - 93.72 4 93.72 - 104.30 0 104.30 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1275 r_work=0.1130 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1275 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1277 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599313 | | target function (ml) not normalized (work): 299754.415558 | | target function (ml) not normalized (free): 15780.812968 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1334 0.1317 5.669 5.5769| | 2: 3.57 - 2.84 1.00 2888 124 0.1052 0.1356 5.1423 5.1976| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1211 4.9218 4.9605| | 4: 2.47 - 2.25 1.00 2825 136 0.0892 0.0986 4.609 4.6334| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.0945 4.5538 4.6096| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.0961 4.2547 4.3414| | 7: 1.97 - 1.87 1.00 2787 165 0.0883 0.1130 3.9716 4.0843| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1090 3.8831 3.9904| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1190 3.6401 3.8189| | 10: 1.72 - 1.66 1.00 2831 160 0.0915 0.1165 3.5574 3.6982| | 11: 1.66 - 1.61 1.00 2712 147 0.0863 0.1029 3.4891 3.5658| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1178 3.3253 3.4792| | 13: 1.56 - 1.52 1.00 2745 130 0.0950 0.1046 3.3105 3.3963| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1042 3.2387 3.3215| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1236 3.1533 3.2689| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1227 3.1348 3.2277| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1296 3.1157 3.2241| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1315 3.1032 3.2322| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1559 3.1103 3.2634| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1460 3.1113 3.148| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1553 3.1117 3.1156| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1971 3.1207 3.2919| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1793 3.1316 3.198| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1840 3.1253 3.2335| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2131 3.1407 3.2573| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1758 3.1468 3.1985| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2150 3.1702 3.1597| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2296 3.1644 3.1713| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2386 3.1477 3.2278| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2450 3.1412 3.1679| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.05 1.00 0.97 5393.27| | 2: 3.57 - 2.84 2888 124 0.93 12.05 1.01 0.97 5393.27| | 3: 2.83 - 2.48 2820 163 0.90 16.04 0.99 0.97 4509.91| | 4: 2.47 - 2.25 2825 136 0.92 13.04 1.00 0.98 2232.00| | 5: 2.25 - 2.09 2756 127 0.91 15.16 1.01 0.98 2232.00| | 6: 2.09 - 1.97 2846 113 0.93 12.07 1.02 0.98 1297.73| | 7: 1.97 - 1.87 2787 165 0.95 9.23 1.02 0.97 500.92| | 8: 1.87 - 1.79 2789 144 0.93 12.52 1.00 0.97 500.92| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.97 285.51| | 10: 1.72 - 1.66 2831 160 0.94 11.10 0.98 0.97 242.37| | 11: 1.66 - 1.61 2712 147 0.93 11.70 0.98 0.97 232.31| | 12: 1.61 - 1.56 2773 144 0.95 8.90 0.99 0.97 137.52| | 13: 1.56 - 1.52 2745 130 0.95 10.45 1.02 0.97 137.52| | 14: 1.52 - 1.48 2803 134 0.94 10.77 1.02 0.97 123.26| | 15: 1.48 - 1.45 2738 128 0.95 9.88 1.02 0.98 97.16| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.16| | 17: 1.42 - 1.39 2785 139 0.95 10.85 1.01 0.98 88.49| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.47| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 83.47| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.66| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.39| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 79.82| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.02| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.02| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.00| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.19| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.19| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.92 89.79| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 91.14| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 91.14| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.39 max = 5393.27 mean = 840.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.35| |phase err.(test): min = 0.00 max = 89.56 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1129 0.1277 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1446 0.1447 0.1458 n_refl.: 87577 remove outliers: r(all,work,free)=0.1446 0.1447 0.1458 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1445 0.1446 0.1458 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1276 n_refl.: 87577 remove outliers: r(all,work,free)=0.1135 0.1128 0.1276 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 87.50 79 5 0.3976 288.017 253.092 0.453 1.002 0.313 11.894-9.307 94.12 92 4 0.2308 489.528 472.625 0.884 1.003 0.308 9.237-7.194 98.18 209 7 0.2443 385.715 377.355 0.917 1.003 0.150 7.162-5.571 100.00 427 22 0.2112 295.845 285.205 0.910 1.003 0.140 5.546-4.326 100.00 867 58 0.1128 406.122 402.022 0.961 1.003 0.099 4.315-3.360 100.00 1859 96 0.0913 386.225 384.017 1.002 1.003 0.083 3.356-2.611 100.00 3867 181 0.1097 253.730 251.785 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0904 168.200 167.566 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.140 82.479 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.424 36.028 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.950 21.500 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0156 ================= 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 : 0.2606 0.1961 0.082 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_weight: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1228 0.1471 0.006 0.876 9.1 119.5 20.1 258 0.136 1_adp: 0.1235 0.1468 0.006 0.876 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1237 0.1472 0.006 0.876 9.1 119.5 20.1 258 0.136 1_occ: 0.1229 0.1462 0.006 0.876 9.1 119.5 20.1 258 0.136 2_bss: 0.1227 0.1454 0.006 0.876 9.1 119.5 20.1 258 0.136 2_settarget: 0.1227 0.1454 0.006 0.876 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1227 0.1454 0.006 0.887 9.1 119.5 20.1 258 0.136 2_nqh: 0.1229 0.1454 0.006 0.887 9.1 119.5 20.1 258 0.139 2_sol: 0.1203 0.1412 0.006 0.887 9.1 114.9 22.3 422 n/a 2_weight: 0.1203 0.1412 0.006 0.887 9.1 114.9 22.3 422 n/a 2_xyzrec: 0.1185 0.1408 0.008 0.939 9.1 114.9 22.3 422 n/a 2_adp: 0.1185 0.1408 0.008 0.939 9.1 114.9 22.3 422 n/a 2_regHadp: 0.1185 0.1408 0.008 0.939 9.1 114.9 22.3 422 n/a 2_occ: 0.1183 0.1415 0.008 0.939 9.1 114.9 22.3 422 n/a 3_bss: 0.1178 0.1405 0.008 0.939 9.1 114.9 22.3 422 n/a 3_settarget: 0.1178 0.1405 0.008 0.939 9.1 114.9 22.3 422 n/a 3_updatecdl: 0.1178 0.1405 0.008 0.940 9.1 114.9 22.3 422 n/a 3_nqh: 0.1179 0.1407 0.008 0.940 9.1 114.9 22.3 422 n/a 3_sol: 0.1212 0.1409 0.008 0.940 9.1 114.9 21.2 433 n/a 3_weight: 0.1212 0.1409 0.008 0.940 9.1 114.9 21.2 433 n/a 3_xyzrec: 0.1160 0.1326 0.008 1.099 9.1 114.9 21.2 433 n/a 3_adp: 0.1160 0.1326 0.008 1.099 9.1 114.9 21.2 433 n/a 3_regHadp: 0.1160 0.1326 0.008 1.099 9.1 114.9 21.2 433 n/a 3_occ: 0.1150 0.1310 0.008 1.099 9.1 114.9 21.2 433 n/a 4_bss: 0.1141 0.1306 0.008 1.099 9.1 114.9 21.2 433 n/a 4_settarget: 0.1141 0.1306 0.008 1.099 9.1 114.9 21.2 433 n/a 4_updatecdl: 0.1141 0.1306 0.008 1.099 9.1 114.9 21.2 433 n/a 4_nqh: 0.1145 0.1307 0.008 1.099 9.1 114.9 21.2 433 n/a 4_sol: 0.1146 0.1293 0.008 1.099 9.1 114.9 21.1 444 n/a 4_weight: 0.1146 0.1293 0.008 1.099 9.1 114.9 21.1 444 n/a 4_xyzrec: 0.1136 0.1294 0.009 1.140 9.1 114.9 21.1 444 n/a 4_adp: 0.1136 0.1294 0.009 1.140 9.1 114.9 21.1 444 n/a 4_regHadp: 0.1136 0.1294 0.009 1.140 9.1 114.9 21.1 444 n/a 4_occ: 0.1132 0.1290 0.009 1.140 9.1 114.9 21.1 444 n/a 5_bss: 0.1129 0.1289 0.009 1.140 9.1 114.9 21.1 444 n/a 5_settarget: 0.1129 0.1289 0.009 1.140 9.1 114.9 21.1 444 n/a 5_updatecdl: 0.1129 0.1289 0.009 1.143 9.1 114.9 21.1 444 n/a 5_setrh: 0.1130 0.1289 0.009 1.143 9.1 114.9 21.1 444 n/a 5_nqh: 0.1130 0.1289 0.009 1.143 9.1 114.9 21.1 444 n/a 5_sol: 0.1130 0.1276 0.009 1.143 9.1 114.9 21.2 460 n/a 5_weight: 0.1130 0.1276 0.009 1.143 9.1 114.9 21.2 460 n/a 5_xyzrec: 0.1130 0.1275 0.008 1.147 9.1 114.9 21.2 460 n/a 5_adp: 0.1130 0.1275 0.008 1.147 9.1 114.9 21.2 460 n/a 5_regHadp: 0.1130 0.1275 0.008 1.147 9.1 114.9 21.2 460 n/a 5_occ: 0.1129 0.1277 0.008 1.147 9.1 114.9 21.2 460 n/a end: 0.1128 0.1276 0.008 1.147 9.1 114.9 21.2 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8230669_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8230669_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8900 Refinement macro-cycles (run) : 13409.7100 Write final files (write_after_run_outputs) : 91.8700 Total : 13505.4700 Total CPU time: 3.76 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:03:41 PST -0800 (1735365821.80 s) Start R-work = 0.1636, R-free = 0.1772 Final R-work = 0.1128, R-free = 0.1276 =============================================================================== Job complete usr+sys time: 13686.52 seconds wall clock time: 248 minutes 1.92 seconds (14881.92 seconds total)