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_8960824.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.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 =============================================================================== Symmetric amino acids flipped. Time to flip 4 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: 1.35, per 1000 atoms: 0.40 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: 0.37 Conformation dependent library (CDL) restraints added in 123.2 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: 0.63 - 0.89: 431 0.89 - 1.16: 1194 1.16 - 1.42: 654 1.42 - 1.68: 837 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 1.459 1.687 -0.229 1.16e-02 7.43e+03 3.89e+02 bond pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.335 1.593 -0.258 1.35e-02 5.49e+03 3.65e+02 bond pdb=" N LEU A 101 " pdb=" CA LEU A 101 " ideal model delta sigma weight residual 1.456 1.673 -0.217 1.22e-02 6.72e+03 3.17e+02 bond pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.84e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.338 0.188 1.13e-02 7.83e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3126 4.69 - 9.38: 1925 9.38 - 14.07: 595 14.07 - 18.76: 114 18.76 - 23.44: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 131.10 -11.78 7.40e-01 1.83e+00 2.53e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 137.01 -16.46 1.06e+00 8.90e-01 2.41e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 135.28 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 108.76 12.74 1.00e+00 1.00e+00 1.62e+02 angle pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" O ALA A 107 " ideal model delta sigma weight residual 119.18 134.20 -15.02 1.19e+00 7.06e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 19.06: 950 19.06 - 38.11: 114 38.11 - 57.16: 39 57.16 - 76.20: 7 76.20 - 95.25: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.182: 80 0.182 - 0.362: 69 0.362 - 0.543: 54 0.543 - 0.724: 21 0.724 - 0.905: 19 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.53 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.055 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" CG TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.058 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.141 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1020 2.32 - 2.89: 8040 2.89 - 3.46: 10588 3.46 - 4.03: 15216 4.03 - 4.60: 21742 Nonbonded interactions: 56606 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.812 1.850 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.831 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.832 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.839 1.850 ... (remaining 56601 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_8960824_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= 0.2608 r_free= 0.1979 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791094 | | target function (ml) not normalized (work): 232514.855436 | | target function (ml) not normalized (free): 11859.384229 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2204 6.967 4.9604| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1772 4.3586 4.3555| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1720 4.143 4.1849| | 4: 2.47 - 2.25 1.00 2825 136 0.2303 0.1588 3.8393 3.859| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1505 3.81 3.8173| | 6: 2.09 - 1.97 1.00 2846 113 0.2569 0.1620 3.4804 3.5259| | 7: 1.97 - 1.87 1.00 2787 165 0.2552 0.1813 3.1301 3.1646| | 8: 1.87 - 1.79 1.00 2789 144 0.2542 0.2047 3.0619 3.1751| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1892 2.8952 2.9807| | 10: 1.72 - 1.66 1.00 2789 158 0.2408 0.1893 2.8157 2.888| | 11: 1.66 - 1.61 1.00 2740 147 0.2447 0.1985 2.7562 2.8262| | 12: 1.61 - 1.56 1.00 2787 146 0.2502 0.2055 2.6118 2.6586| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1634 2.5773 2.511| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.1895 2.5006 2.5211| | 15: 1.48 - 1.45 1.00 2738 128 0.2605 0.2093 2.4176 2.4592| | 16: 1.45 - 1.42 1.00 2756 161 0.2684 0.2222 2.3884 2.4846| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.1842 2.3205 2.2904| | 18: 1.39 - 1.36 1.00 2741 179 0.2737 0.2223 2.2818 2.3042| | 19: 1.36 - 1.34 1.00 2807 134 0.2630 0.2416 2.2417 2.3402| | 20: 1.34 - 1.32 1.00 2696 147 0.2724 0.2350 2.2177 2.2521| | 21: 1.32 - 1.30 1.00 2785 112 0.2709 0.2572 2.1543 2.2731| | 22: 1.29 - 1.27 1.00 2704 152 0.2757 0.2765 2.1417 2.2328| | 23: 1.27 - 1.26 1.00 2802 156 0.2771 0.2554 2.1181 2.1831| | 24: 1.26 - 1.24 1.00 2744 132 0.2835 0.2425 2.0934 2.1486| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2609 2.0383 2.1217| | 26: 1.22 - 1.21 1.00 2727 135 0.2896 0.2355 2.0265 2.0668| | 27: 1.21 - 1.19 1.00 2814 148 0.2950 0.2667 2.0144 2.0235| | 28: 1.19 - 1.18 1.00 2671 147 0.2998 0.3050 1.9977 2.0625| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2762 1.9594 2.0212| | 30: 1.16 - 1.15 1.00 2740 148 0.3044 0.2858 1.924 1.9691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.16 0.76 0.23 1538.90| | 2: 3.57 - 2.84 2876 122 0.80 26.57 1.27 0.23 1538.90| | 3: 2.84 - 2.48 2833 165 0.74 32.38 1.24 0.24 1274.70| | 4: 2.47 - 2.25 2825 136 0.81 25.93 1.25 0.25 589.05| | 5: 2.25 - 2.09 2756 127 0.77 29.65 1.28 0.25 589.05| | 6: 2.09 - 1.97 2846 113 0.83 22.83 1.30 0.25 319.81| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.28 0.26 90.18| | 8: 1.87 - 1.79 2789 144 0.86 20.98 1.26 0.26 90.18| | 9: 1.79 - 1.72 2745 138 0.88 18.71 1.23 0.25 55.70| | 10: 1.72 - 1.66 2789 158 0.87 20.01 1.22 0.25 48.79| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.23 0.25 47.06| | 12: 1.61 - 1.56 2787 146 0.88 18.54 1.24 0.25 29.46| | 13: 1.56 - 1.52 2745 130 0.87 20.39 1.23 0.25 29.46| | 14: 1.52 - 1.48 2803 134 0.86 20.67 1.23 0.25 26.29| | 15: 1.48 - 1.45 2738 128 0.87 20.26 1.24 0.25 20.49| | 16: 1.45 - 1.42 2756 161 0.86 21.63 1.24 0.25 20.49| | 17: 1.42 - 1.39 2785 139 0.87 20.79 1.24 0.25 17.62| | 18: 1.39 - 1.36 2741 179 0.86 21.58 1.23 0.25 15.95| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.21 0.25 15.95| | 20: 1.34 - 1.32 2696 147 0.86 21.53 1.20 0.25 13.79| | 21: 1.32 - 1.30 2785 112 0.85 22.55 1.21 0.25 13.64| | 22: 1.29 - 1.27 2704 152 0.84 23.33 1.21 0.24 13.37| | 23: 1.27 - 1.26 2802 156 0.85 22.84 1.21 0.24 11.99| | 24: 1.26 - 1.24 2744 132 0.84 23.78 1.21 0.24 11.99| | 25: 1.24 - 1.22 2734 148 0.83 24.71 1.21 0.24 11.40| | 26: 1.22 - 1.21 2727 135 0.83 25.10 1.20 0.23 10.74| | 27: 1.21 - 1.19 2814 148 0.82 25.65 1.21 0.23 10.74| | 28: 1.19 - 1.18 2671 147 0.82 26.33 1.17 0.23 10.10| | 29: 1.18 - 1.16 2800 134 0.81 27.33 1.16 0.22 9.86| | 30: 1.16 - 1.15 2740 148 0.79 28.63 1.16 0.22 9.86| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.86 max = 1538.90 mean = 222.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.96 mean = 23.06| |phase err.(test): min = 0.00 max = 89.32 mean = 22.94| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.430 Angle : 5.342 16.459 2118 Z= 3.797 Chirality : 0.396 0.905 243 Planarity : 0.033 0.105 284 Dihedral : 14.246 95.252 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.43 % 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: -2.97 (0.45), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -1.10 (0.76), residues: 38 loop : -0.48 (0.58), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.012 ARG A 28 TYR 0.112 0.051 TYR A 141 PHE 0.123 0.054 PHE A 164 HIS 0.063 0.030 HIS A 138 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= 0.2608 r_free= 0.1979 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791094 | | target function (ml) not normalized (work): 232514.855436 | | target function (ml) not normalized (free): 11859.384229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1979 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1979 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1980 0.1979 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2002 0.2005 0.1992 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1632 0.1800 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1631 0.1800 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 0.3774 386.567 359.431 0.675 1.002 0.407 11.894-9.307 98.04 96 4 0.1677 616.536 588.445 0.924 1.003 0.390 9.237-7.194 100.00 213 7 0.2144 502.212 491.733 0.959 1.003 0.380 7.162-5.571 100.00 427 22 0.2212 376.882 364.703 0.924 1.003 0.292 5.546-4.326 100.00 867 58 0.1267 517.366 511.396 0.960 1.003 0.214 4.315-3.360 100.00 1859 96 0.1134 492.019 488.711 1.002 1.003 0.189 3.356-2.611 100.00 3867 181 0.1445 323.231 319.717 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.1335 214.273 212.116 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.640 104.103 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.401 45.086 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2585 29.236 26.968 0.974 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1631 r_free=0.1800 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.486770 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2019.594547 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 0.1720 0.1834 0.0114 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1558 0.1695 0.0137 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1442 0.1613 0.0171 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1405 0.1590 0.0185 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1366 0.1567 0.0200 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1366 0.1562 0.0196 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1292 0.1507 0.0215 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1265 0.1486 0.0221 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1258 0.1482 0.0225 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1249 0.1477 0.0228 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1240 0.1469 0.0229 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1237 0.1471 0.0234 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1234 0.1468 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1467 0.0235 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1230 0.1468 0.0238 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1473 0.0244 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1226 0.1469 0.0243 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1224 0.1475 0.0251 0.008 1.0 4.2 0.5 0.6 0 13.243 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1467 0.0235 0.006 0.8 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.67 2.35 3.013 19.057 2019.595 0.017 12.32 14.66 2.35 2.989 19.057 60.588 0.017 12.38 14.65 2.26 2.666 19.057 252.449 0.017 12.77 15.36 2.59 2.885 19.352 1009.797 0.016 12.54 15.42 2.88 3.197 19.577 2019.595 0.016 12.48 15.50 3.03 3.414 19.710 3029.392 0.015 12.32 15.34 3.02 3.310 19.648 4039.189 0.015 12.31 15.44 3.13 3.431 19.700 5048.986 0.015 12.25 15.41 3.16 3.417 19.688 6058.784 0.015 12.25 15.49 3.23 3.509 19.723 7068.581 0.015 12.25 15.51 3.26 3.490 19.692 8078.378 0.015 12.18 15.42 3.24 3.457 19.667 9088.175 0.015 12.20 15.45 3.24 3.520 19.686 10097.973 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: 252.449 Accepted refinement result: 12.38 14.65 2.26 2.666 19.057 252.449 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.44 20.08 3.31 0 1785 Protein: 9.08 114.97 16.99 3.31 0 1519 Water: 11.45 119.44 38.23 N/A 0 258 Other: 19.71 26.61 22.06 N/A 0 8 Chain A: 9.08 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1465 r_work=0.1239 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1468 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 = 0.1234 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1234 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016836 | | target function (ls_wunit_k1) not normalized (work): 1402.351394 | | target function (ls_wunit_k1) not normalized (free): 110.290484 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1462 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1691 n_refl.: 87592 remove outliers: r(all,work,free)=0.1675 0.1676 0.1691 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1695 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1232 0.1455 n_refl.: 87592 remove outliers: r(all,work,free)=0.1242 0.1231 0.1455 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 94.79 86 5 0.3376 303.131 279.170 0.637 1.003 0.370 11.894-9.307 98.04 96 4 0.1538 484.349 473.745 0.934 1.003 0.369 9.237-7.194 100.00 213 7 0.1882 394.536 388.821 0.967 1.003 0.350 7.162-5.571 100.00 427 22 0.1811 296.078 290.323 0.936 1.003 0.254 5.546-4.326 100.00 867 58 0.1000 406.441 403.722 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0877 386.529 385.462 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1180 253.929 252.756 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1032 168.332 167.617 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1118 82.205 82.385 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.453 35.957 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 22.968 21.452 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1455 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1232 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1455 | n_water=258 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1240 r_free=0.1452 | n_water=252 | time (s): 20.050 (total time: 21.760) Filter (q & B) r_work=0.1242 r_free=0.1452 | n_water=249 | time (s): 2.580 (total time: 24.340) Compute maps r_work=0.1242 r_free=0.1452 | n_water=249 | time (s): 1.350 (total time: 25.690) Filter (map) r_work=0.1254 r_free=0.1453 | n_water=229 | time (s): 3.310 (total time: 29.000) Find peaks r_work=0.1254 r_free=0.1453 | n_water=229 | time (s): 0.520 (total time: 29.520) Add new water r_work=0.1396 r_free=0.1630 | n_water=438 | time (s): 3.270 (total time: 32.790) Refine new water occ: r_work=0.1301 r_free=0.1485 adp: r_work=0.1224 r_free=0.1439 occ: r_work=0.1236 r_free=0.1426 adp: r_work=0.1203 r_free=0.1415 occ: r_work=0.1206 r_free=0.1401 adp: r_work=0.1196 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1402 r_work=0.1196 r_free=0.1402 | n_water=438 | time (s): 52.020 (total time: 84.810) Filter (q & B) r_work=0.1202 r_free=0.1407 | n_water=419 | time (s): 2.670 (total time: 87.480) Filter (dist only) r_work=0.1202 r_free=0.1406 | n_water=418 | time (s): 36.080 (total time: 123.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.737640 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1475.690385 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 0.1677 0.1799 0.0122 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1541 0.1679 0.0138 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1390 0.1551 0.0161 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1358 0.1527 0.0170 0.002 0.4 5.1 0.0 0.0 0 0.750 0.1308 0.1487 0.0179 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1309 0.1481 0.0172 0.002 0.5 6.4 0.0 0.0 0 1.000 0.1248 0.1432 0.0184 0.002 0.6 5.8 0.5 0.0 0 2.000 0.1221 0.1426 0.0205 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1211 0.1419 0.0208 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1203 0.1421 0.0218 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1200 0.1417 0.0216 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1196 0.1419 0.0223 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1193 0.1417 0.0224 0.005 0.8 6.1 0.5 0.0 0 8.000 0.1189 0.1410 0.0222 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1185 0.1408 0.0223 0.006 0.9 5.8 0.5 0.0 0 10.000 0.1183 0.1406 0.0223 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1184 0.1414 0.0230 0.007 0.9 5.8 0.5 0.0 0 12.000 0.1183 0.1413 0.0231 0.008 0.9 5.8 0.5 0.6 0 13.869 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1183 0.1406 0.0223 0.007 0.9 5.4 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 14.06 2.23 3.774 21.791 1475.690 0.016 11.83 14.06 2.23 3.774 21.791 44.271 0.016 11.83 14.06 2.23 3.774 21.791 184.461 0.016 12.06 14.49 2.43 3.618 21.802 737.845 0.015 11.99 14.78 2.79 3.440 22.096 1475.690 0.015 11.83 14.71 2.88 3.436 22.079 2213.536 0.014 11.77 14.72 2.95 3.468 22.154 2951.381 0.014 11.76 14.88 3.12 3.504 22.232 3689.226 0.014 11.71 14.85 3.14 3.510 22.224 4427.071 0.014 11.67 14.87 3.20 3.509 22.251 5164.916 0.014 11.60 14.78 3.18 3.526 22.215 5902.762 0.013 11.61 14.83 3.22 3.534 22.165 6640.607 0.013 11.61 14.87 3.26 3.583 22.283 7378.452 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.271 Accepted refinement result: 11.83 14.06 2.23 3.774 21.791 44.271 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 22.21 3.31 189 1756 Protein: 9.11 115.00 17.02 3.31 0 1519 Water: 11.26 76.68 41.07 N/A 189 229 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.11 115.00 19.51 N/A 0 1756 Chain S: 11.26 60.00 47.29 N/A 189 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 245 30.29 - 40.88 162 40.88 - 51.47 132 51.47 - 62.06 124 62.06 - 72.65 12 72.65 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1406 r_work=0.1183 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1406 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1181 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014756 | | target function (ls_wunit_k1) not normalized (work): 1229.118552 | | target function (ls_wunit_k1) not normalized (free): 104.305310 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1181 0.1409 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1531 0.1528 0.1618 n_refl.: 87590 remove outliers: r(all,work,free)=0.1531 0.1528 0.1618 n_refl.: 87590 overall B=0.01 to atoms: r(all,work,free)=0.1533 0.1529 0.1619 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1179 0.1402 n_refl.: 87590 remove outliers: r(all,work,free)=0.1189 0.1179 0.1402 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 94.79 86 5 0.3354 303.131 281.279 0.607 1.003 0.350 11.894-9.307 98.04 96 4 0.1562 484.349 477.053 0.930 1.003 0.333 9.237-7.194 100.00 213 7 0.1741 394.536 394.738 0.981 1.003 0.280 7.162-5.571 100.00 427 22 0.1593 296.078 291.317 0.935 1.003 0.225 5.546-4.326 100.00 867 58 0.0878 406.441 403.305 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0777 386.529 385.503 1.004 1.002 0.180 3.356-2.611 100.00 3867 181 0.1082 253.929 252.876 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.0997 168.332 167.809 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.205 82.399 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1440 36.453 35.982 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2249 22.968 21.476 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0146 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1179 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1179 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1402 | n_water=418 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1180 r_free=0.1401 | n_water=414 | time (s): 34.390 (total time: 36.090) Filter (q & B) r_work=0.1180 r_free=0.1401 | n_water=414 | time (s): 0.960 (total time: 37.050) Compute maps r_work=0.1180 r_free=0.1401 | n_water=414 | time (s): 1.590 (total time: 38.640) Filter (map) r_work=0.1220 r_free=0.1398 | n_water=291 | time (s): 2.850 (total time: 41.490) Find peaks r_work=0.1220 r_free=0.1398 | n_water=291 | time (s): 0.680 (total time: 42.170) Add new water r_work=0.1338 r_free=0.1520 | n_water=481 | time (s): 3.020 (total time: 45.190) Refine new water occ: r_work=0.1246 r_free=0.1436 adp: r_work=0.1247 r_free=0.1439 occ: r_work=0.1224 r_free=0.1413 adp: r_work=0.1224 r_free=0.1415 occ: r_work=0.1206 r_free=0.1394 adp: r_work=0.1201 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1395 r_work=0.1201 r_free=0.1395 | n_water=481 | time (s): 178.320 (total time: 223.510) Filter (q & B) r_work=0.1205 r_free=0.1398 | n_water=447 | time (s): 2.810 (total time: 226.320) Filter (dist only) r_work=0.1206 r_free=0.1397 | n_water=446 | time (s): 36.370 (total time: 262.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.719380 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.104589 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 0.1238 0.1382 0.0143 0.002 0.6 4.2 0.5 0.0 0 0.086 0.1196 0.1348 0.0152 0.003 0.7 3.8 0.5 0.0 0 0.258 0.1180 0.1337 0.0157 0.004 0.8 3.2 0.5 0.0 0 0.516 0.1173 0.1332 0.0160 0.005 0.9 3.2 0.5 0.0 0 0.774 0.1168 0.1333 0.0164 0.006 1.0 2.9 0.5 0.0 0 1.032 0.1163 0.1329 0.0165 0.007 1.0 3.2 0.5 0.0 0 1.290 0.1161 0.1328 0.0167 0.007 1.0 3.2 0.5 0.0 0 1.547 0.1161 0.1329 0.0168 0.008 1.1 3.2 0.5 0.0 0 1.805 0.1170 0.1332 0.0161 0.005 0.9 3.2 0.5 0.0 0 0.860 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1328 0.0167 0.007 1.0 3.2 0.5 0.0 0 1.547 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.28 1.67 3.777 21.343 44.105 3.623 11.61 13.28 1.67 3.777 21.343 1.323 3.623 11.61 13.28 1.67 3.774 21.343 5.513 3.623 11.64 13.33 1.69 3.709 21.335 22.052 3.617 11.73 13.50 1.77 3.714 21.302 44.105 3.619 11.62 13.43 1.81 3.752 21.291 66.157 3.612 11.58 13.42 1.84 3.765 21.281 88.209 3.608 11.54 13.39 1.85 3.777 21.282 110.261 3.605 11.52 13.41 1.89 3.794 21.270 132.314 3.604 11.52 13.41 1.90 3.808 21.258 154.366 3.603 11.49 13.38 1.89 3.816 21.257 176.418 3.601 11.48 13.35 1.87 3.823 21.252 198.471 3.599 11.47 13.35 1.88 3.832 21.251 220.523 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.513 Accepted refinement result: 11.61 13.28 1.67 3.774 21.343 5.513 3.623 Individual atomic B min max mean iso aniso Overall: 9.12 114.98 21.38 3.30 220 1753 Protein: 9.12 114.98 17.03 3.30 0 1519 Water: 11.27 76.69 36.19 N/A 220 226 Other: 19.74 26.64 22.10 N/A 0 8 Chain A: 9.12 114.98 19.48 N/A 0 1753 Chain S: 11.27 60.01 36.59 N/A 220 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.29 286 30.29 - 40.88 206 40.88 - 51.47 138 51.47 - 62.05 57 62.05 - 72.64 12 72.64 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1328 r_work=0.1161 r_free=0.1328 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1328 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1324 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.21 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= 0.1152 r_free= 0.1324 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615754 | | target function (ml) not normalized (work): 301170.591525 | | target function (ml) not normalized (free): 15858.764396 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1152 0.1324 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1494 0.1493 0.1534 n_refl.: 87590 remove outliers: r(all,work,free)=0.1494 0.1493 0.1534 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1493 0.1533 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1312 n_refl.: 87590 remove outliers: r(all,work,free)=0.1154 0.1146 0.1312 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3863 297.036 274.147 0.505 0.999 0.320 11.894-9.307 96.08 94 4 0.2325 484.615 463.202 0.892 1.000 0.283 9.237-7.194 99.09 211 7 0.2222 389.038 387.717 0.958 1.001 0.200 7.162-5.571 100.00 427 22 0.2094 296.078 285.531 0.926 1.001 0.200 5.546-4.326 100.00 867 58 0.1114 406.441 402.030 0.964 1.001 0.160 4.315-3.360 100.00 1859 96 0.0937 386.529 383.959 1.003 1.001 0.150 3.356-2.611 100.00 3867 181 0.1137 253.929 251.898 1.006 1.001 0.080 2.608-2.026 99.99 8198 413 0.0940 168.332 167.595 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0903 82.205 82.549 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.453 36.049 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 22.968 21.442 0.981 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0090 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1312 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=0.1146 r_free=0.1312 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1312 | n_water=446 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1149 r_free=0.1314 | n_water=443 | time (s): 48.470 (total time: 50.840) Filter (q & B) r_work=0.1149 r_free=0.1314 | n_water=443 | time (s): 1.310 (total time: 52.150) Compute maps r_work=0.1149 r_free=0.1314 | n_water=443 | time (s): 1.840 (total time: 53.990) Filter (map) r_work=0.1166 r_free=0.1310 | n_water=341 | time (s): 3.830 (total time: 57.820) Find peaks r_work=0.1166 r_free=0.1310 | n_water=341 | time (s): 0.730 (total time: 58.550) Add new water r_work=0.1229 r_free=0.1388 | n_water=495 | time (s): 3.760 (total time: 62.310) Refine new water occ: r_work=0.1162 r_free=0.1316 adp: r_work=0.1163 r_free=0.1320 occ: r_work=0.1149 r_free=0.1300 adp: r_work=0.1148 r_free=0.1303 occ: r_work=0.1139 r_free=0.1290 adp: r_work=0.1135 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1290 r_work=0.1135 r_free=0.1290 | n_water=495 | time (s): 213.750 (total time: 276.060) Filter (q & B) r_work=0.1141 r_free=0.1296 | n_water=461 | time (s): 3.880 (total time: 279.940) Filter (dist only) r_work=0.1141 r_free=0.1295 | n_water=460 | time (s): 47.380 (total time: 327.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.785660 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.989418 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 0.1205 0.1330 0.0125 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1167 0.1308 0.0141 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1151 0.1305 0.0154 0.005 0.9 3.8 0.5 0.0 0 0.536 0.1145 0.1299 0.0155 0.006 1.0 3.8 0.5 0.0 0 0.804 0.1141 0.1299 0.0158 0.007 1.0 3.5 0.5 0.0 0 1.071 0.1138 0.1302 0.0164 0.007 1.0 3.5 0.5 0.0 0 1.339 0.1136 0.1305 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.607 0.1134 0.1303 0.0168 0.009 1.1 3.8 0.5 0.0 0 1.875 0.1143 0.1308 0.0165 0.006 1.0 3.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1299 0.0158 0.007 1.0 3.5 0.5 0.0 0 1.071 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.99 1.58 3.774 21.301 41.989 3.611 11.41 12.99 1.58 3.774 21.301 1.260 3.611 11.41 12.99 1.58 3.774 21.301 5.249 3.611 11.43 13.03 1.60 3.708 21.294 20.995 3.606 11.52 13.19 1.67 3.721 21.268 41.989 3.611 11.43 13.15 1.72 3.747 21.259 62.984 3.603 11.35 13.09 1.74 3.762 21.257 83.979 3.598 11.35 13.10 1.75 3.772 21.252 104.974 3.596 11.32 13.08 1.77 3.784 21.249 125.968 3.594 11.30 13.07 1.77 3.794 21.246 146.963 3.592 11.30 13.10 1.79 3.811 21.236 167.958 3.592 11.29 13.08 1.79 3.818 21.235 188.952 3.591 11.27 13.06 1.79 3.825 21.234 209.947 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.249 Accepted refinement result: 11.41 12.99 1.58 3.774 21.301 5.249 3.611 Individual atomic B min max mean iso aniso Overall: 9.12 114.98 21.31 3.30 236 1751 Protein: 9.12 114.98 17.03 3.30 0 1519 Water: 11.26 76.69 35.43 N/A 236 224 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.12 114.98 19.47 N/A 0 1751 Chain S: 11.26 60.01 35.00 N/A 236 0 Histogram: Values Number of atoms 9.12 - 19.71 1266 19.71 - 30.29 292 30.29 - 40.88 223 40.88 - 51.46 134 51.46 - 62.05 49 62.05 - 72.64 12 72.64 - 83.22 5 83.22 - 93.81 4 93.81 - 104.39 0 104.39 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1299 r_work=0.1141 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1299 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1292 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1135 r_free= 0.1292 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608180 | | target function (ml) not normalized (work): 300518.103227 | | target function (ml) not normalized (free): 15821.326875 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1135 0.1292 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1467 0.1466 0.1521 n_refl.: 87584 remove outliers: r(all,work,free)=0.1467 0.1466 0.1521 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1467 0.1465 0.1520 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1133 0.1296 n_refl.: 87584 remove outliers: r(all,work,free)=0.1139 0.1131 0.1296 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4097 293.763 253.133 0.449 1.000 0.304 11.894-9.307 95.10 93 4 0.2359 477.711 469.185 0.885 1.002 0.242 9.237-7.194 98.18 209 7 0.2265 386.018 383.802 0.935 1.002 0.168 7.162-5.571 100.00 427 22 0.2098 296.078 285.738 0.918 1.002 0.141 5.546-4.326 100.00 867 58 0.1097 406.441 402.896 0.963 1.002 0.121 4.315-3.360 100.00 1859 96 0.0912 386.529 384.420 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1100 253.929 251.903 1.010 1.001 0.080 2.608-2.026 99.99 8198 413 0.0915 168.332 167.633 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.205 82.519 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.453 36.037 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 22.968 21.498 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0133 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1296 After: r_work=0.1132 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1295 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=0.1132 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1295 | n_water=460 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1132 r_free=0.1297 | n_water=459 | time (s): 46.940 (total time: 49.270) Filter (q & B) r_work=0.1132 r_free=0.1296 | n_water=457 | time (s): 3.790 (total time: 53.060) Compute maps r_work=0.1132 r_free=0.1296 | n_water=457 | time (s): 1.720 (total time: 54.780) Filter (map) r_work=0.1158 r_free=0.1308 | n_water=354 | time (s): 3.790 (total time: 58.570) Find peaks r_work=0.1158 r_free=0.1308 | n_water=354 | time (s): 0.680 (total time: 59.250) Add new water r_work=0.1202 r_free=0.1354 | n_water=495 | time (s): 3.630 (total time: 62.880) Refine new water occ: r_work=0.1150 r_free=0.1297 adp: r_work=0.1150 r_free=0.1301 occ: r_work=0.1140 r_free=0.1284 adp: r_work=0.1138 r_free=0.1287 occ: r_work=0.1132 r_free=0.1278 adp: r_work=0.1129 r_free=0.1278 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1278 r_work=0.1129 r_free=0.1278 | n_water=495 | time (s): 245.200 (total time: 308.080) Filter (q & B) r_work=0.1135 r_free=0.1280 | n_water=455 | time (s): 3.830 (total time: 311.910) Filter (dist only) r_work=0.1142 r_free=0.1282 | n_water=452 | time (s): 47.560 (total time: 359.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.806423 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.426938 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1329 0.0110 0.004 0.7 5.1 0.0 0.0 0 0.090 0.1174 0.1302 0.0128 0.004 0.8 5.1 0.0 0.0 0 0.271 0.1154 0.1289 0.0135 0.005 0.9 4.5 0.5 0.0 0 0.542 0.1145 0.1283 0.0138 0.006 1.0 4.2 0.5 0.0 0 0.813 0.1142 0.1282 0.0140 0.007 1.0 4.2 0.5 0.0 0 1.084 0.1141 0.1281 0.0140 0.007 1.0 3.8 0.5 0.0 0 1.355 0.1139 0.1281 0.0142 0.008 1.1 4.2 0.5 0.0 0 1.626 0.1139 0.1281 0.0143 0.008 1.1 3.8 0.5 0.0 0 1.897 0.1143 0.1282 0.0139 0.006 1.0 4.2 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1281 0.0140 0.007 1.0 3.8 0.5 0.0 0 1.355 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.81 1.40 3.773 21.244 41.427 3.607 11.41 12.81 1.40 3.773 21.244 1.243 3.607 11.41 12.81 1.40 3.773 21.244 5.178 3.607 11.43 12.86 1.42 3.706 21.238 20.713 3.602 11.50 13.02 1.52 3.728 21.212 41.427 3.607 11.43 13.01 1.58 3.747 21.199 62.140 3.600 11.39 12.99 1.60 3.761 21.196 82.854 3.596 11.34 12.94 1.60 3.772 21.196 103.567 3.592 11.32 12.94 1.62 3.782 21.193 124.281 3.591 11.31 12.94 1.63 3.794 21.187 144.994 3.589 11.30 12.94 1.64 3.806 21.181 165.708 3.589 11.29 12.94 1.65 3.815 21.178 186.421 3.588 11.27 12.92 1.64 3.819 21.179 207.135 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.243 Accepted refinement result: 11.41 12.81 1.40 3.773 21.244 1.243 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 114.97 21.21 3.30 230 1749 Protein: 9.11 114.97 17.03 3.30 0 1519 Water: 11.26 76.68 35.26 N/A 230 222 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.11 114.97 19.44 N/A 0 1749 Chain S: 11.26 60.00 34.67 N/A 230 0 Histogram: Values Number of atoms 9.11 - 19.70 1268 19.70 - 30.29 294 30.29 - 40.87 216 40.87 - 51.46 129 51.46 - 62.04 49 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.80 4 93.80 - 104.39 0 104.39 - 114.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1281 r_work=0.1141 r_free=0.1281 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1281 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1278 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606101 | | target function (ml) not normalized (work): 300326.902535 | | target function (ml) not normalized (free): 15800.726970 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1338 0.1311 5.6672 5.5982| | 2: 3.57 - 2.84 1.00 2888 124 0.1063 0.1327 5.1529 5.1843| | 3: 2.83 - 2.48 1.00 2820 163 0.1103 0.1208 4.9325 4.9636| | 4: 2.47 - 2.25 1.00 2825 136 0.0907 0.0998 4.6227 4.6557| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0976 4.5644 4.6241| | 6: 2.09 - 1.97 1.00 2846 113 0.0866 0.0988 4.268 4.3496| | 7: 1.97 - 1.87 1.00 2787 165 0.0894 0.1075 3.9859 4.0747| | 8: 1.87 - 1.79 1.00 2789 144 0.0925 0.1165 3.8963 4.0202| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1162 3.6547 3.8182| | 10: 1.72 - 1.66 1.00 2831 160 0.0936 0.1204 3.5744 3.7312| | 11: 1.66 - 1.61 1.00 2712 147 0.0879 0.1034 3.5043 3.5716| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1142 3.3362 3.4559| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1065 3.3143 3.3984| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1036 3.2461 3.3233| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1220 3.1551 3.2577| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1272 3.1385 3.246| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1308 3.1197 3.2325| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1331 3.1061 3.2373| | 19: 1.36 - 1.34 1.00 2807 134 0.1271 0.1561 3.1161 3.2611| | 20: 1.34 - 1.32 1.00 2696 147 0.1375 0.1480 3.1157 3.1545| | 21: 1.32 - 1.30 1.00 2785 112 0.1480 0.1522 3.116 3.1119| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.1992 3.1249 3.2975| | 23: 1.27 - 1.26 1.00 2802 156 0.1655 0.1786 3.1341 3.1981| | 24: 1.26 - 1.24 1.00 2744 132 0.1714 0.1835 3.1285 3.2301| | 25: 1.24 - 1.22 1.00 2733 148 0.1888 0.2163 3.1446 3.2617| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1772 3.1484 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2193 3.1713 3.1649| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2288 3.1661 3.1707| | 29: 1.18 - 1.16 1.00 2800 134 0.2270 0.2396 3.1485 3.2286| | 30: 1.16 - 1.15 1.00 2739 148 0.2454 0.2451 3.1439 3.1664| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.20 1.00 0.97 5496.35| | 2: 3.57 - 2.84 2888 124 0.93 12.21 1.01 0.97 5496.35| | 3: 2.83 - 2.48 2820 163 0.90 16.17 0.99 0.97 4597.90| | 4: 2.47 - 2.25 2825 136 0.92 13.21 1.00 0.98 2281.09| | 5: 2.25 - 2.09 2756 127 0.91 15.34 1.01 0.98 2281.09| | 6: 2.09 - 1.97 2846 113 0.93 12.28 1.02 0.98 1328.97| | 7: 1.97 - 1.87 2787 165 0.95 9.40 1.02 0.97 516.93| | 8: 1.87 - 1.79 2789 144 0.93 12.68 1.00 0.97 516.93| | 9: 1.79 - 1.72 2745 138 0.94 10.20 0.98 0.97 294.90| | 10: 1.72 - 1.66 2831 160 0.94 11.33 0.98 0.97 250.43| | 11: 1.66 - 1.61 2712 147 0.93 11.94 0.98 0.97 239.78| | 12: 1.61 - 1.56 2773 144 0.95 9.02 0.99 0.97 139.32| | 13: 1.56 - 1.52 2745 130 0.95 10.50 1.03 0.97 139.32| | 14: 1.52 - 1.48 2803 134 0.94 10.86 1.02 0.98 124.68| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.98 97.88| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.98 97.88| | 17: 1.42 - 1.39 2785 139 0.95 10.97 1.01 0.98 89.04| | 18: 1.39 - 1.36 2741 179 0.94 11.57 1.01 0.98 83.92| | 19: 1.36 - 1.34 2807 134 0.94 11.90 1.00 0.98 83.92| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.97 80.12| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 79.86| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.29| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.97 0.94 82.46| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.96 0.94 82.46| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.39| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.93 86.53| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.53| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 89.98| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 91.27| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.92 91.27| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.86 max = 5496.35 mean = 857.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.45| |phase err.(test): min = 0.00 max = 89.16 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1138 0.1278 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1460 0.1458 0.1513 n_refl.: 87579 remove outliers: r(all,work,free)=0.1460 0.1458 0.1513 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1459 0.1457 0.1512 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1137 0.1279 n_refl.: 87579 remove outliers: r(all,work,free)=0.1141 0.1134 0.1279 n_refl.: 87572 ======================== 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 0.3897 287.706 250.345 0.450 0.999 0.296 11.894-9.307 92.16 90 4 0.2290 479.138 460.606 0.874 1.001 0.216 9.237-7.194 97.73 208 7 0.2276 387.111 380.187 0.922 1.002 0.160 7.162-5.571 100.00 427 22 0.2121 296.078 285.510 0.911 1.002 0.144 5.546-4.326 100.00 867 58 0.1136 406.441 402.550 0.965 1.002 0.130 4.315-3.360 100.00 1859 96 0.0917 386.529 384.428 1.005 1.002 0.120 3.356-2.611 100.00 3867 181 0.1107 253.929 252.169 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0916 168.332 167.727 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.205 82.559 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.453 36.060 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.968 21.516 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0105 ================= 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 : 0.2608 0.1979 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_weight: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1232 0.1467 0.006 0.848 9.0 119.5 20.1 258 0.136 1_adp: 0.1238 0.1465 0.006 0.848 9.1 119.4 20.1 258 0.136 1_regHadp: 0.1239 0.1468 0.006 0.848 9.1 119.4 20.1 258 0.136 1_occ: 0.1234 0.1462 0.006 0.848 9.1 119.4 20.1 258 0.136 2_bss: 0.1231 0.1455 0.006 0.848 9.1 119.5 20.1 258 0.136 2_settarget: 0.1231 0.1455 0.006 0.848 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1231 0.1455 0.006 0.861 9.1 119.5 20.1 258 0.136 2_nqh: 0.1232 0.1455 0.006 0.861 9.1 119.5 20.1 258 0.139 2_sol: 0.1202 0.1406 0.006 0.861 9.1 115.0 22.2 418 n/a 2_weight: 0.1202 0.1406 0.006 0.861 9.1 115.0 22.2 418 n/a 2_xyzrec: 0.1183 0.1406 0.007 0.876 9.1 115.0 22.2 418 n/a 2_adp: 0.1183 0.1406 0.007 0.876 9.1 115.0 22.2 418 n/a 2_regHadp: 0.1183 0.1406 0.007 0.876 9.1 115.0 22.2 418 n/a 2_occ: 0.1181 0.1409 0.007 0.876 9.1 115.0 22.2 418 n/a 3_bss: 0.1179 0.1402 0.007 0.876 9.1 115.0 22.2 418 n/a 3_settarget: 0.1179 0.1402 0.007 0.876 9.1 115.0 22.2 418 n/a 3_updatecdl: 0.1179 0.1402 0.007 0.875 9.1 115.0 22.2 418 n/a 3_nqh: 0.1179 0.1402 0.007 0.875 9.1 115.0 22.2 418 n/a 3_sol: 0.1206 0.1397 0.007 0.875 9.1 115.0 21.4 446 n/a 3_weight: 0.1206 0.1397 0.007 0.875 9.1 115.0 21.4 446 n/a 3_xyzrec: 0.1161 0.1328 0.007 1.045 9.1 115.0 21.4 446 n/a 3_adp: 0.1161 0.1328 0.007 1.045 9.1 115.0 21.4 446 n/a 3_regHadp: 0.1161 0.1328 0.007 1.045 9.1 115.0 21.4 446 n/a 3_occ: 0.1152 0.1324 0.007 1.045 9.1 115.0 21.4 446 n/a 4_bss: 0.1146 0.1312 0.007 1.045 9.1 115.0 21.4 446 n/a 4_settarget: 0.1146 0.1312 0.007 1.045 9.1 115.0 21.4 446 n/a 4_updatecdl: 0.1146 0.1312 0.007 1.046 9.1 115.0 21.4 446 n/a 4_nqh: 0.1146 0.1312 0.007 1.046 9.1 115.0 21.4 446 n/a 4_sol: 0.1141 0.1295 0.007 1.046 9.1 115.0 21.3 460 n/a 4_weight: 0.1141 0.1295 0.007 1.046 9.1 115.0 21.3 460 n/a 4_xyzrec: 0.1141 0.1299 0.007 1.007 9.1 115.0 21.3 460 n/a 4_adp: 0.1141 0.1299 0.007 1.007 9.1 115.0 21.3 460 n/a 4_regHadp: 0.1141 0.1299 0.007 1.007 9.1 115.0 21.3 460 n/a 4_occ: 0.1135 0.1292 0.007 1.007 9.1 115.0 21.3 460 n/a 5_bss: 0.1131 0.1296 0.007 1.007 9.1 115.0 21.3 460 n/a 5_settarget: 0.1131 0.1296 0.007 1.007 9.1 115.0 21.3 460 n/a 5_updatecdl: 0.1131 0.1296 0.007 1.010 9.1 115.0 21.3 460 n/a 5_setrh: 0.1132 0.1295 0.007 1.010 9.1 115.0 21.3 460 n/a 5_nqh: 0.1132 0.1295 0.007 1.010 9.1 115.0 21.3 460 n/a 5_sol: 0.1142 0.1282 0.007 1.010 9.1 115.0 21.2 452 n/a 5_weight: 0.1142 0.1282 0.007 1.010 9.1 115.0 21.2 452 n/a 5_xyzrec: 0.1141 0.1281 0.007 1.035 9.1 115.0 21.2 452 n/a 5_adp: 0.1141 0.1281 0.007 1.035 9.1 115.0 21.2 452 n/a 5_regHadp: 0.1141 0.1281 0.007 1.035 9.1 115.0 21.2 452 n/a 5_occ: 0.1138 0.1278 0.007 1.035 9.1 115.0 21.2 452 n/a end: 0.1134 0.1279 0.007 1.035 9.1 115.0 21.2 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8960824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8960824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0800 Refinement macro-cycles (run) : 13189.6100 Write final files (write_after_run_outputs) : 94.3300 Total : 13287.0200 Total CPU time: 3.70 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:59:38 PST -0800 (1735365578.61 s) Start R-work = 0.1631, R-free = 0.1800 Final R-work = 0.1134, R-free = 0.1279 =============================================================================== Job complete usr+sys time: 13462.88 seconds wall clock time: 243 minutes 59.72 seconds (14639.72 seconds total)