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_6218374.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.86, per 1000 atoms: 0.55 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: 0.68 Conformation dependent library (CDL) restraints added in 225.6 milliseconds Time building geometry restraints manager: 0.89 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: 534 0.91 - 1.17: 1108 1.17 - 1.42: 643 1.42 - 1.68: 837 1.68 - 1.94: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.686 -0.227 1.25e-02 6.40e+03 3.31e+02 bond pdb=" C PRO A 73 " pdb=" O PRO A 73 " ideal model delta sigma weight residual 1.232 0.999 0.232 1.31e-02 5.83e+03 3.14e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.049 0.187 1.08e-02 8.57e+03 2.99e+02 bond pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 1.537 1.745 -0.208 1.26e-02 6.30e+03 2.72e+02 bond pdb=" N ALA A 6 " pdb=" CA ALA A 6 " ideal model delta sigma weight residual 1.455 1.657 -0.202 1.25e-02 6.40e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 3130 4.60 - 9.21: 1832 9.21 - 13.81: 657 13.81 - 18.41: 147 18.41 - 23.02: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.15 15.62 1.00e+00 1.00e+00 2.44e+02 angle pdb=" O THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " ideal model delta sigma weight residual 122.92 106.88 16.04 1.17e+00 7.31e-01 1.88e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 128.25 -13.50 9.90e-01 1.02e+00 1.86e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.15 137.42 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" CA GLY A 100 " pdb=" C GLY A 100 " pdb=" O GLY A 100 " ideal model delta sigma weight residual 121.23 135.40 -14.17 1.08e+00 8.57e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 930 16.69 - 33.37: 123 33.37 - 50.05: 40 50.05 - 66.73: 15 66.73 - 83.41: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 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 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.270: 112 0.270 - 0.538: 96 0.538 - 0.806: 26 0.806 - 1.074: 7 1.074 - 1.342: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.78 -1.34 2.00e-01 2.50e+01 4.50e+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 -1.45 -1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA GLU A 176 " pdb=" N GLU A 176 " pdb=" C GLU A 176 " pdb=" CB GLU A 176 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.037 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.066 2.00e-02 2.50e+03 5.74e-02 9.88e+01 pdb=" CG PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.120 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.065 2.00e-02 2.50e+03 4.96e-02 7.37e+01 pdb=" CG TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 952 2.31 - 2.88: 8002 2.88 - 3.45: 10574 3.45 - 4.03: 15252 4.03 - 4.60: 21810 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.828 1.850 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.834 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.834 1.850 nonbonded pdb=" HD3 ARG A 28 " pdb="HH11 ARG A 28 " model vdw 1.837 2.270 ... (remaining 56585 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_6218374_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= 0.1966 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788164 | | target function (ml) not normalized (work): 232270.773334 | | target function (ml) not normalized (free): 11796.557822 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3016 0.2145 6.9974 4.9515| | 2: 3.57 - 2.84 1.00 2876 122 0.2462 0.1819 4.3578 4.3437| | 3: 2.84 - 2.48 1.00 2833 165 0.2329 0.1822 4.1376 4.1862| | 4: 2.47 - 2.25 1.00 2825 136 0.2364 0.1435 3.8416 3.8287| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1482 3.8106 3.8152| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1723 3.4625 3.5781| | 7: 1.97 - 1.87 1.00 2787 165 0.2546 0.1747 3.146 3.2049| | 8: 1.87 - 1.79 1.00 2789 144 0.2452 0.1989 3.0554 3.1335| | 9: 1.79 - 1.72 1.00 2745 138 0.2376 0.2041 2.9098 2.9973| | 10: 1.72 - 1.66 1.00 2789 158 0.2385 0.1931 2.7937 2.8511| | 11: 1.66 - 1.61 1.00 2740 147 0.2516 0.1953 2.7536 2.7618| | 12: 1.61 - 1.56 1.00 2787 146 0.2502 0.1946 2.6255 2.6039| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1839 2.5856 2.5926| | 14: 1.52 - 1.48 1.00 2803 134 0.2553 0.1863 2.4918 2.5103| | 15: 1.48 - 1.45 1.00 2738 128 0.2604 0.2197 2.4076 2.4698| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2196 2.3787 2.4215| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.1947 2.3277 2.3273| | 18: 1.39 - 1.36 1.00 2741 179 0.2708 0.2128 2.2954 2.2801| | 19: 1.36 - 1.34 1.00 2807 134 0.2699 0.2323 2.2518 2.2739| | 20: 1.34 - 1.32 1.00 2696 147 0.2673 0.2445 2.1811 2.2617| | 21: 1.32 - 1.30 1.00 2785 112 0.2702 0.1982 2.1393 2.0954| | 22: 1.29 - 1.27 1.00 2704 152 0.2741 0.2700 2.1239 2.1927| | 23: 1.27 - 1.26 1.00 2802 156 0.2717 0.2352 2.0875 2.1451| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2505 2.0745 2.1127| | 25: 1.24 - 1.22 1.00 2734 148 0.2893 0.2609 2.0558 2.1359| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2271 2.011 2.0853| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2792 2.0064 2.0471| | 28: 1.19 - 1.18 1.00 2671 147 0.2991 0.2826 1.9809 1.9903| | 29: 1.18 - 1.16 1.00 2800 134 0.2977 0.2830 1.9549 2.0665| | 30: 1.16 - 1.15 1.00 2740 148 0.3104 0.2822 1.9466 1.9565| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.98 0.76 0.23 1517.78| | 2: 3.57 - 2.84 2876 122 0.80 26.51 1.28 0.23 1517.78| | 3: 2.84 - 2.48 2833 165 0.74 32.29 1.24 0.23 1258.41| | 4: 2.47 - 2.25 2825 136 0.81 25.97 1.26 0.25 585.32| | 5: 2.25 - 2.09 2756 127 0.77 29.67 1.28 0.25 585.32| | 6: 2.09 - 1.97 2846 113 0.83 23.05 1.29 0.25 319.65| | 7: 1.97 - 1.87 2787 165 0.90 16.60 1.28 0.26 93.08| | 8: 1.87 - 1.79 2789 144 0.85 21.37 1.25 0.26 93.08| | 9: 1.79 - 1.72 2745 138 0.88 18.44 1.23 0.26 55.44| | 10: 1.72 - 1.66 2789 158 0.87 19.97 1.22 0.26 47.90| | 11: 1.66 - 1.61 2740 147 0.86 21.16 1.24 0.26 46.18| | 12: 1.61 - 1.56 2787 146 0.89 18.15 1.23 0.25 28.70| | 13: 1.56 - 1.52 2745 130 0.87 19.82 1.23 0.25 28.70| | 14: 1.52 - 1.48 2803 134 0.87 20.00 1.23 0.25 25.56| | 15: 1.48 - 1.45 2738 128 0.88 19.57 1.23 0.25 19.82| | 16: 1.45 - 1.42 2756 161 0.86 20.95 1.24 0.25 19.82| | 17: 1.42 - 1.39 2785 139 0.87 20.11 1.23 0.25 16.75| | 18: 1.39 - 1.36 2741 179 0.87 20.42 1.22 0.25 14.97| | 19: 1.36 - 1.34 2807 134 0.86 21.14 1.22 0.25 14.97| | 20: 1.34 - 1.32 2696 147 0.87 20.94 1.21 0.25 12.67| | 21: 1.32 - 1.30 2785 112 0.86 21.93 1.21 0.25 12.51| | 22: 1.29 - 1.27 2704 152 0.86 22.12 1.21 0.24 12.27| | 23: 1.27 - 1.26 2802 156 0.86 21.76 1.22 0.24 11.03| | 24: 1.26 - 1.24 2744 132 0.85 22.77 1.21 0.24 11.03| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.21 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 24.35 1.20 0.23 10.10| | 27: 1.21 - 1.19 2814 148 0.83 24.93 1.20 0.23 10.10| | 28: 1.19 - 1.18 2671 147 0.82 25.59 1.19 0.23 9.57| | 29: 1.18 - 1.16 2800 134 0.82 25.76 1.17 0.23 9.37| | 30: 1.16 - 1.15 2740 148 0.80 27.43 1.16 0.23 9.37| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.37 max = 1517.78 mean = 219.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.52| |phase err.(test): min = 0.00 max = 89.85 mean = 22.56| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.239 1557 Z= 5.325 Angle : 5.304 16.901 2118 Z= 3.669 Chirality : 0.395 1.342 243 Planarity : 0.032 0.089 284 Dihedral : 13.779 83.411 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % 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: -2.32 (0.48), residues: 224 helix: -2.65 (0.40), residues: 103 sheet: 0.21 (0.88), residues: 28 loop : -0.45 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.020 ARG A 48 TYR 0.089 0.035 TYR A 139 PHE 0.077 0.029 PHE A 162 HIS 0.060 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1966 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788164 | | target function (ml) not normalized (work): 232270.773334 | | target function (ml) not normalized (free): 11796.557822 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1967 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1967 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1967 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2009 0.1981 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1639 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1639 0.1785 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 0.3817 386.399 360.761 0.680 1.002 0.408 11.894-9.307 99.02 97 4 0.1799 613.776 593.996 0.926 1.003 0.390 9.237-7.194 100.00 213 7 0.2183 501.993 491.615 0.957 1.003 0.350 7.162-5.571 100.00 427 22 0.2213 376.718 364.077 0.940 1.003 0.320 5.546-4.326 100.00 867 58 0.1306 517.141 511.256 0.958 1.003 0.214 4.315-3.360 100.00 1859 96 0.1159 491.804 487.639 1.005 1.003 0.158 3.356-2.611 100.00 3867 181 0.1438 323.090 320.012 0.998 1.002 0.119 2.608-2.026 99.99 8198 413 0.1356 214.179 212.045 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.594 104.029 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.381 45.044 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2586 29.223 26.931 0.979 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1785 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=0.1639 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.283677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2030.263708 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 0.1622 0.1744 0.0122 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1504 0.1649 0.0145 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1412 0.1574 0.0162 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1387 0.1566 0.0178 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1347 0.1540 0.0193 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1354 0.1546 0.0192 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1305 0.1526 0.0221 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1272 0.1501 0.0229 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1258 0.1489 0.0231 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1486 0.0239 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1245 0.1482 0.0237 0.005 0.8 2.9 0.5 0.0 0 6.000 0.1239 0.1481 0.0242 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1235 0.1476 0.0241 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1232 0.1475 0.0242 0.006 0.9 2.9 0.5 0.0 0 9.000 0.1232 0.1477 0.0245 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1229 0.1472 0.0243 0.007 0.9 2.9 0.5 0.6 0 11.000 0.1229 0.1475 0.0246 0.007 0.9 3.2 0.5 0.6 0 12.000 0.1224 0.1469 0.0245 0.008 1.0 3.5 0.5 0.6 0 13.642 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1469 0.0245 0.008 1.0 3.5 0.5 0.6 0 13.642 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.69 2.45 3.013 19.055 2030.264 0.017 12.24 14.69 2.45 3.008 19.055 60.908 0.017 12.31 14.67 2.36 2.665 19.054 253.783 0.017 12.63 15.30 2.67 2.736 19.215 1015.132 0.016 12.51 15.48 2.96 3.378 19.675 2030.264 0.016 12.42 15.52 3.10 3.337 19.655 3045.396 0.015 12.29 15.48 3.19 3.371 19.664 4060.527 0.015 12.23 15.46 3.23 3.367 19.653 5075.659 0.015 12.24 15.52 3.28 3.387 19.639 6090.791 0.015 12.27 15.63 3.37 3.525 19.704 7105.923 0.015 12.27 15.72 3.44 3.535 19.695 8121.055 0.015 12.19 15.60 3.41 3.574 19.717 9136.187 0.015 12.21 15.69 3.47 3.551 19.685 10151.319 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: 253.783 Accepted refinement result: 12.31 14.67 2.36 2.665 19.054 253.783 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.30 0 1785 Protein: 9.07 114.96 16.99 3.31 0 1519 Water: 11.47 119.44 38.22 N/A 0 258 Other: 19.71 26.62 22.06 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 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=0.1231 r_free=0.1467 r_work=0.1232 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1470 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 = 0.1226 r_free = 0.1465 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1226 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016637 | | target function (ls_wunit_k1) not normalized (work): 1385.811399 | | target function (ls_wunit_k1) not normalized (free): 109.037333 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1226 0.1465 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1696 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1676 0.1677 0.1700 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1455 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 0.3455 301.611 282.219 0.655 1.002 0.380 11.894-9.307 99.02 97 4 0.1673 483.164 471.098 0.922 1.003 0.357 9.237-7.194 100.00 213 7 0.1838 395.169 390.706 0.964 1.003 0.345 7.162-5.571 100.00 427 22 0.1795 296.552 290.953 0.940 1.003 0.263 5.546-4.326 100.00 867 58 0.0998 407.093 404.215 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0866 387.148 386.226 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1169 254.336 253.226 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 168.602 167.876 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.336 82.525 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.511 36.014 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 23.005 21.484 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0522 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1455 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=0.1224 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1455 | n_water=258 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1234 r_free=0.1454 | n_water=251 | time (s): 22.980 (total time: 25.200) Filter (q & B) r_work=0.1236 r_free=0.1453 | n_water=248 | time (s): 2.610 (total time: 27.810) Compute maps r_work=0.1236 r_free=0.1453 | n_water=248 | time (s): 1.370 (total time: 29.180) Filter (map) r_work=0.1259 r_free=0.1464 | n_water=221 | time (s): 3.020 (total time: 32.200) Find peaks r_work=0.1259 r_free=0.1464 | n_water=221 | time (s): 0.680 (total time: 32.880) Add new water r_work=0.1406 r_free=0.1632 | n_water=427 | time (s): 3.000 (total time: 35.880) Refine new water occ: r_work=0.1303 r_free=0.1491 adp: r_work=0.1222 r_free=0.1439 occ: r_work=0.1234 r_free=0.1423 adp: r_work=0.1202 r_free=0.1409 occ: r_work=0.1205 r_free=0.1393 adp: r_work=0.1195 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1394 r_work=0.1195 r_free=0.1394 | n_water=427 | time (s): 66.420 (total time: 102.300) Filter (q & B) r_work=0.1199 r_free=0.1397 | n_water=414 | time (s): 2.780 (total time: 105.080) Filter (dist only) r_work=0.1199 r_free=0.1396 | n_water=413 | time (s): 34.750 (total time: 139.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.536465 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1492.747835 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 0.1653 0.1764 0.0110 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1535 0.1662 0.0127 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1429 0.1576 0.0147 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1363 0.1525 0.0162 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1322 0.1497 0.0175 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1318 0.1492 0.0174 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1258 0.1458 0.0200 0.002 0.5 5.1 0.5 0.0 0 2.000 0.1225 0.1434 0.0208 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1222 0.1434 0.0212 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1214 0.1429 0.0215 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1206 0.1426 0.0221 0.004 0.7 5.4 0.5 0.0 0 6.000 0.1204 0.1426 0.0222 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1198 0.1425 0.0227 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1196 0.1419 0.0223 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1193 0.1420 0.0227 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1192 0.1418 0.0226 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1190 0.1412 0.0222 0.007 0.9 6.4 0.5 0.6 0 12.000 0.1188 0.1411 0.0223 0.008 0.9 6.1 0.5 0.6 0 13.000 0.1187 0.1409 0.0223 0.008 1.0 5.8 0.5 0.6 0 14.268 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1409 0.0223 0.008 1.0 5.8 0.5 0.6 0 14.268 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.09 2.23 3.772 21.742 1492.748 0.016 11.87 14.09 2.23 3.772 21.742 44.782 0.016 11.87 14.09 2.23 3.772 21.742 186.593 0.016 12.01 14.48 2.47 3.637 21.738 746.374 0.015 12.06 14.86 2.81 3.556 21.798 1492.748 0.015 11.88 14.81 2.93 3.460 21.951 2239.122 0.014 11.82 14.74 2.92 3.478 22.071 2985.496 0.014 11.77 14.78 3.01 3.491 22.097 3731.870 0.014 11.73 14.79 3.06 3.501 22.021 4478.244 0.014 11.70 14.80 3.10 3.526 22.067 5224.617 0.014 11.71 14.91 3.21 3.546 22.057 5970.991 0.014 11.66 14.84 3.18 3.551 22.055 6717.365 0.014 11.64 14.85 3.21 3.568 22.072 7463.739 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: 186.593 Accepted refinement result: 11.87 14.09 2.23 3.772 21.742 186.593 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 22.12 3.30 192 1748 Protein: 9.10 114.99 17.02 3.31 0 1519 Water: 11.51 76.68 40.89 N/A 192 221 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.10 114.99 19.40 N/A 0 1748 Chain S: 17.41 60.00 46.92 N/A 192 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 248 30.28 - 40.87 167 40.87 - 51.46 122 51.46 - 62.05 121 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1409 r_work=0.1187 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1409 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 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= 0.1187 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014896 | | target function (ls_wunit_k1) not normalized (work): 1240.755466 | | target function (ls_wunit_k1) not normalized (free): 98.281021 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1187 0.1409 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1589 0.1587 0.1644 n_refl.: 87592 remove outliers: r(all,work,free)=0.1589 0.1587 0.1644 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1589 0.1646 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1184 0.1403 n_refl.: 87592 remove outliers: r(all,work,free)=0.1194 0.1183 0.1403 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3202 296.955 279.604 0.596 1.002 0.350 11.894-9.307 99.02 97 4 0.1616 483.164 476.891 0.916 1.003 0.326 9.237-7.194 100.00 213 7 0.1685 395.169 395.423 0.985 1.003 0.267 7.162-5.571 100.00 427 22 0.1595 296.552 291.869 0.940 1.003 0.224 5.546-4.326 100.00 867 58 0.0860 407.093 404.170 0.960 1.003 0.205 4.315-3.360 100.00 1859 96 0.0774 387.148 386.071 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1079 254.336 253.436 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1020 168.602 168.081 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.336 82.554 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.511 36.048 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2249 23.005 21.514 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0153 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1403 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** Total number of N/Q/H flips: 1 r_work=0.1183 r_free=0.1404 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1404 | n_water=413 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1183 r_free=0.1401 | n_water=410 | time (s): 36.530 (total time: 38.190) Filter (q & B) r_work=0.1183 r_free=0.1401 | n_water=410 | time (s): 1.120 (total time: 39.310) Compute maps r_work=0.1183 r_free=0.1401 | n_water=410 | time (s): 1.760 (total time: 41.070) Filter (map) r_work=0.1221 r_free=0.1404 | n_water=290 | time (s): 3.290 (total time: 44.360) Find peaks r_work=0.1221 r_free=0.1404 | n_water=290 | time (s): 0.690 (total time: 45.050) Add new water r_work=0.1345 r_free=0.1537 | n_water=475 | time (s): 3.370 (total time: 48.420) Refine new water occ: r_work=0.1247 r_free=0.1443 adp: r_work=0.1248 r_free=0.1447 occ: r_work=0.1223 r_free=0.1414 adp: r_work=0.1222 r_free=0.1417 occ: r_work=0.1205 r_free=0.1393 adp: r_work=0.1200 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1394 r_work=0.1200 r_free=0.1394 | n_water=475 | time (s): 221.280 (total time: 269.700) Filter (q & B) r_work=0.1205 r_free=0.1397 | n_water=448 | time (s): 2.830 (total time: 272.530) Filter (dist only) r_work=0.1205 r_free=0.1397 | n_water=446 | time (s): 36.150 (total time: 308.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.742215 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.882527 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 0.1243 0.1368 0.0125 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1196 0.1333 0.0137 0.003 0.7 3.8 0.5 0.0 0 0.261 0.1175 0.1321 0.0147 0.004 0.8 3.2 0.5 0.0 0 0.523 0.1167 0.1317 0.0150 0.005 0.9 3.8 0.5 0.0 0 0.784 0.1164 0.1318 0.0154 0.006 1.0 4.2 0.5 0.0 0 1.045 0.1161 0.1318 0.0157 0.007 1.0 3.8 0.5 0.0 0 1.307 0.1158 0.1318 0.0160 0.007 1.1 3.8 0.5 0.0 0 1.568 0.1157 0.1317 0.0161 0.008 1.1 3.8 0.5 0.6 0 1.829 0.1166 0.1318 0.0153 0.005 0.9 3.8 0.5 0.0 0 0.871 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1167 0.1317 0.0150 0.005 0.9 3.8 0.5 0.0 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 13.17 1.50 3.775 21.320 55.883 3.626 11.67 13.17 1.50 3.775 21.320 1.676 3.626 11.70 13.18 1.48 3.734 21.320 6.985 3.626 11.74 13.30 1.56 3.713 21.303 27.941 3.621 11.72 13.37 1.65 3.732 21.272 55.883 3.618 11.64 13.31 1.68 3.759 21.264 83.824 3.612 11.60 13.31 1.70 3.776 21.257 111.765 3.608 11.57 13.29 1.72 3.792 21.248 139.706 3.606 11.57 13.33 1.76 3.811 21.236 167.648 3.606 11.54 13.28 1.74 3.818 21.235 195.589 3.603 11.51 13.23 1.73 3.820 21.240 223.530 3.601 11.51 13.26 1.75 3.833 21.233 251.471 3.600 11.49 13.24 1.74 3.834 21.238 279.413 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: 1.676 Accepted refinement result: 11.67 13.17 1.50 3.775 21.320 1.676 3.626 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.34 3.30 227 1746 Protein: 9.11 115.00 17.03 3.31 0 1519 Water: 11.52 76.69 36.01 N/A 227 219 Other: 19.76 26.66 22.10 N/A 0 8 Chain A: 9.11 115.00 19.38 N/A 0 1746 Chain S: 16.25 60.01 36.40 N/A 227 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 290 30.29 - 40.88 210 40.88 - 51.47 125 51.47 - 62.06 61 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=0.1167 r_free=0.1317 r_work=0.1167 r_free=0.1317 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1317 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1159 r_free = 0.1312 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1159 r_free= 0.1312 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619045 | | target function (ml) not normalized (work): 301441.131912 | | target function (ml) not normalized (free): 15842.145040 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1159 0.1312 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1498 0.1499 0.1520 n_refl.: 87589 remove outliers: r(all,work,free)=0.1498 0.1499 0.1520 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1498 0.1520 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1155 0.1309 n_refl.: 87589 remove outliers: r(all,work,free)=0.1160 0.1153 0.1309 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3865 294.243 269.973 0.494 1.000 0.320 11.894-9.307 97.06 95 4 0.2276 483.388 462.333 0.875 1.002 0.283 9.237-7.194 98.64 210 7 0.2277 389.599 387.675 0.961 1.002 0.212 7.162-5.571 100.00 427 22 0.2112 296.552 286.046 0.924 1.003 0.183 5.546-4.326 100.00 867 58 0.1129 407.093 402.351 0.962 1.003 0.150 4.315-3.360 100.00 1859 96 0.0928 387.148 385.041 1.005 1.002 0.150 3.356-2.611 100.00 3867 181 0.1136 254.336 252.113 1.007 1.002 0.100 2.608-2.026 99.99 8198 413 0.0940 168.602 167.898 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0919 82.336 82.654 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1273 36.511 36.118 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 23.005 21.556 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=-0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1153 r_free=0.1309 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=0.1153 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1153 r_free=0.1309 | n_water=446 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1153 r_free=0.1309 | n_water=446 | time (s): 46.090 (total time: 48.650) Filter (q & B) r_work=0.1153 r_free=0.1310 | n_water=445 | time (s): 3.870 (total time: 52.520) Compute maps r_work=0.1153 r_free=0.1310 | n_water=445 | time (s): 1.780 (total time: 54.300) Filter (map) r_work=0.1179 r_free=0.1318 | n_water=328 | time (s): 3.720 (total time: 58.020) Find peaks r_work=0.1179 r_free=0.1318 | n_water=328 | time (s): 0.680 (total time: 58.700) Add new water r_work=0.1249 r_free=0.1384 | n_water=484 | time (s): 3.750 (total time: 62.450) Refine new water occ: r_work=0.1177 r_free=0.1324 adp: r_work=0.1177 r_free=0.1327 occ: r_work=0.1162 r_free=0.1309 adp: r_work=0.1161 r_free=0.1311 occ: r_work=0.1150 r_free=0.1300 adp: r_work=0.1146 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1300 r_work=0.1146 r_free=0.1300 | n_water=484 | time (s): 203.870 (total time: 266.320) Filter (q & B) r_work=0.1151 r_free=0.1302 | n_water=451 | time (s): 4.080 (total time: 270.400) Filter (dist only) r_work=0.1152 r_free=0.1301 | n_water=450 | time (s): 47.340 (total time: 317.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.754269 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.228542 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1341 0.0132 0.002 0.6 5.1 0.5 0.0 0 0.088 0.1170 0.1314 0.0144 0.003 0.7 3.8 0.5 0.0 0 0.263 0.1156 0.1307 0.0151 0.004 0.9 4.2 0.5 0.0 0 0.526 0.1149 0.1303 0.0154 0.006 0.9 3.8 0.5 0.0 0 0.789 0.1146 0.1303 0.0157 0.006 1.0 4.2 0.5 0.0 0 1.053 0.1143 0.1303 0.0160 0.007 1.1 4.2 0.5 0.0 0 1.316 0.1141 0.1303 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.579 0.1139 0.1302 0.0163 0.008 1.1 4.8 0.5 0.0 0 1.842 0.1148 0.1304 0.0156 0.006 1.0 3.8 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1302 0.0163 0.008 1.1 4.8 0.5 0.0 0 1.842 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 13.02 1.63 3.776 21.186 46.229 3.608 11.39 13.02 1.63 3.776 21.186 1.387 3.608 11.39 13.03 1.63 3.766 21.186 5.779 3.608 11.41 13.07 1.65 3.712 21.178 23.114 3.603 11.47 13.23 1.77 3.736 21.147 46.229 3.606 11.39 13.20 1.80 3.759 21.138 69.343 3.600 11.35 13.16 1.81 3.771 21.135 92.457 3.596 11.32 13.15 1.83 3.782 21.131 115.571 3.593 11.31 13.16 1.85 3.797 21.125 138.686 3.592 11.30 13.17 1.87 3.811 21.117 161.800 3.591 11.30 13.18 1.88 3.824 21.109 184.914 3.591 11.28 13.15 1.87 3.829 21.110 208.028 3.589 11.27 13.14 1.87 3.835 21.109 231.143 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.387 Accepted refinement result: 11.39 13.02 1.63 3.776 21.186 1.387 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.10 3.30 233 1744 Protein: 9.11 115.00 17.03 3.31 0 1519 Water: 11.51 76.68 34.84 N/A 233 217 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.11 115.00 19.34 N/A 0 1744 Chain S: 16.83 60.00 34.26 N/A 233 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 304 30.29 - 40.87 218 40.87 - 51.46 120 51.46 - 62.05 47 62.05 - 72.64 11 72.64 - 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=0.1139 r_free=0.1302 r_work=0.1139 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1302 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1299 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605180 | | target function (ml) not normalized (work): 300264.617071 | | target function (ml) not normalized (free): 15821.262560 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1134 0.1299 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1470 0.1470 0.1504 n_refl.: 87583 remove outliers: r(all,work,free)=0.1470 0.1470 0.1504 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1469 0.1469 0.1504 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1133 0.1302 n_refl.: 87583 remove outliers: r(all,work,free)=0.1139 0.1131 0.1302 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 0.4067 288.689 257.084 0.456 1.000 0.314 11.894-9.307 95.10 93 4 0.2437 470.296 464.639 0.874 1.001 0.233 9.237-7.194 98.18 209 7 0.2396 386.637 382.784 0.935 1.002 0.160 7.162-5.571 100.00 427 22 0.2101 296.552 285.452 0.917 1.002 0.157 5.546-4.326 100.00 867 58 0.1128 407.093 402.668 0.962 1.002 0.119 4.315-3.360 100.00 1859 96 0.0915 387.148 384.756 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1110 254.336 252.153 1.010 1.002 0.060 2.608-2.026 99.99 8198 413 0.0915 168.602 167.889 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.336 82.650 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.511 36.109 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.005 21.544 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0146 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1302 After: r_work=0.1133 r_free=0.1302 ================================== NQH flips ================================== r_work=0.1133 r_free=0.1302 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** Total number of N/Q/H flips: 1 r_work=0.1137 r_free=0.1303 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1303 | n_water=450 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1137 r_free=0.1303 | n_water=450 | time (s): 43.450 (total time: 45.940) Filter (q & B) r_work=0.1138 r_free=0.1304 | n_water=447 | time (s): 3.930 (total time: 49.870) Compute maps r_work=0.1138 r_free=0.1304 | n_water=447 | time (s): 1.690 (total time: 51.560) Filter (map) r_work=0.1165 r_free=0.1309 | n_water=347 | time (s): 3.620 (total time: 55.180) Find peaks r_work=0.1165 r_free=0.1309 | n_water=347 | time (s): 0.690 (total time: 55.870) Add new water r_work=0.1210 r_free=0.1358 | n_water=496 | time (s): 3.710 (total time: 59.580) Refine new water occ: r_work=0.1155 r_free=0.1304 adp: r_work=0.1156 r_free=0.1306 occ: r_work=0.1145 r_free=0.1290 adp: r_work=0.1143 r_free=0.1292 occ: r_work=0.1137 r_free=0.1282 adp: r_work=0.1134 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1281 r_work=0.1134 r_free=0.1281 | n_water=496 | time (s): 196.070 (total time: 255.650) Filter (q & B) r_work=0.1141 r_free=0.1283 | n_water=454 | time (s): 3.850 (total time: 259.500) Filter (dist only) r_work=0.1141 r_free=0.1283 | n_water=453 | time (s): 48.960 (total time: 308.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784808 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.090694 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 0.1217 0.1330 0.0113 0.004 0.7 5.4 0.0 0.0 0 0.089 0.1167 0.1296 0.0129 0.004 0.8 4.5 0.5 0.0 0 0.268 0.1153 0.1288 0.0135 0.005 0.9 4.2 0.5 0.0 0 0.535 0.1147 0.1285 0.0137 0.006 1.0 4.2 0.5 0.0 0 0.803 0.1143 0.1282 0.0139 0.007 1.1 4.2 0.5 0.0 0 1.071 0.1141 0.1281 0.0141 0.007 1.1 4.2 0.5 0.0 0 1.339 0.1139 0.1280 0.0141 0.008 1.1 4.2 0.5 0.0 0 1.606 0.1137 0.1280 0.0143 0.009 1.2 4.2 0.5 0.0 0 1.874 0.1145 0.1283 0.0138 0.006 1.0 4.2 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1280 0.0143 0.009 1.2 4.2 0.5 0.0 0 1.874 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.80 1.43 3.776 21.220 45.091 3.605 11.37 12.80 1.43 3.776 21.220 1.353 3.605 11.37 12.80 1.43 3.776 21.220 5.636 3.605 11.40 12.85 1.45 3.710 21.212 22.545 3.600 11.45 13.04 1.59 3.729 21.181 45.091 3.603 11.37 13.01 1.64 3.757 21.172 67.636 3.598 11.32 12.96 1.64 3.770 21.170 90.181 3.593 11.31 12.96 1.65 3.782 21.164 112.727 3.591 11.29 12.98 1.68 3.799 21.158 135.272 3.591 11.27 12.96 1.69 3.808 21.156 157.817 3.589 11.27 12.97 1.70 3.819 21.150 180.363 3.588 11.25 12.95 1.70 3.828 21.149 202.908 3.586 11.23 12.93 1.70 3.833 21.150 225.453 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.353 Accepted refinement result: 11.37 12.80 1.43 3.776 21.220 1.353 3.605 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 21.17 3.30 236 1744 Protein: 9.10 114.99 17.02 3.31 0 1519 Water: 11.51 76.68 35.06 N/A 236 217 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.10 114.99 19.34 N/A 0 1744 Chain S: 16.83 60.00 34.69 N/A 236 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 305 30.28 - 40.87 217 40.87 - 51.46 122 51.46 - 62.05 50 62.05 - 72.64 11 72.64 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1280 r_work=0.1137 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1280 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1277 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603359 | | target function (ml) not normalized (work): 300098.552185 | | target function (ml) not normalized (free): 15803.134527 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1336 0.1287 5.6661 5.575| | 2: 3.57 - 2.84 1.00 2888 124 0.1057 0.1362 5.1478 5.2125| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1201 4.9319 4.967| | 4: 2.47 - 2.25 1.00 2825 136 0.0908 0.1030 4.6194 4.6534| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0964 4.5639 4.6149| | 6: 2.09 - 1.97 1.00 2846 113 0.0860 0.0970 4.2603 4.3441| | 7: 1.97 - 1.87 1.00 2787 165 0.0887 0.1111 3.9737 4.075| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1094 3.8858 3.993| | 9: 1.79 - 1.72 1.00 2745 138 0.0874 0.1185 3.6446 3.8199| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1200 3.5619 3.72| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1059 3.4958 3.5738| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1169 3.3318 3.4818| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1037 3.3116 3.3956| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1040 3.2425 3.3216| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1212 3.1548 3.2695| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1243 3.1365 3.2431| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1304 3.1186 3.2308| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1326 3.1072 3.2405| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1560 3.1129 3.2719| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1456 3.1147 3.1515| | 21: 1.32 - 1.30 1.00 2785 112 0.1475 0.1512 3.1171 3.106| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.2003 3.1252 3.3065| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1803 3.1333 3.2075| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1832 3.1299 3.2313| | 25: 1.24 - 1.22 1.00 2733 148 0.1882 0.2166 3.1437 3.2645| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1753 3.1496 3.1978| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2155 3.1728 3.163| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2315 3.1677 3.1772| | 29: 1.18 - 1.16 1.00 2800 134 0.2272 0.2388 3.1502 3.2275| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2469 3.1442 3.1736| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.21 1.00 0.97 5503.40| | 2: 3.57 - 2.84 2888 124 0.93 12.14 1.01 0.97 5503.40| | 3: 2.83 - 2.48 2820 163 0.90 16.13 0.99 0.98 4600.32| | 4: 2.47 - 2.25 2825 136 0.92 13.15 1.00 0.98 2271.57| | 5: 2.25 - 2.09 2756 127 0.91 15.27 1.01 0.98 2271.57| | 6: 2.09 - 1.97 2846 113 0.93 12.17 1.02 0.98 1317.80| | 7: 1.97 - 1.87 2787 165 0.95 9.19 1.02 0.98 504.36| | 8: 1.87 - 1.79 2789 144 0.93 12.51 1.00 0.98 504.36| | 9: 1.79 - 1.72 2745 138 0.94 10.04 0.98 0.97 288.63| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.97 245.43| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.97 235.20| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.97 138.73| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.03 0.97 138.73| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.98 124.35| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.98 98.01| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 98.01| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 89.33| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.30| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 84.30| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.97 80.40| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.96 80.12| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.56| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.97 0.94 82.79| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.96 0.94 82.79| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.78| | 26: 1.22 - 1.21 2727 135 0.90 18.18 1.02 0.93 86.99| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.99| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.93 90.72| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.92 92.12| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 92.12| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.12 max = 5503.40 mean = 855.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.83 mean = 13.40| |phase err.(test): min = 0.00 max = 89.62 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1133 0.1277 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1468 0.1469 0.1487 n_refl.: 87579 remove outliers: r(all,work,free)=0.1468 0.1469 0.1487 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1467 0.1468 0.1486 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1277 n_refl.: 87579 remove outliers: r(all,work,free)=0.1139 0.1132 0.1277 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4155 286.519 247.000 0.432 1.000 0.304 11.894-9.307 93.14 91 4 0.2438 475.340 452.117 0.850 1.002 0.252 9.237-7.194 97.73 208 7 0.2373 387.722 379.947 0.923 1.002 0.177 7.162-5.571 100.00 427 22 0.2175 296.552 285.283 0.913 1.002 0.148 5.546-4.326 100.00 867 58 0.1124 407.093 402.811 0.962 1.002 0.115 4.315-3.360 100.00 1859 96 0.0901 387.148 385.268 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1101 254.336 252.532 1.010 1.002 0.038 2.608-2.026 99.99 8198 413 0.0916 168.602 167.969 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.336 82.712 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.511 36.131 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 23.005 21.553 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0099 ================= 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 0.1966 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1785 0.080 5.304 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1785 0.080 5.304 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1786 0.080 5.304 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1786 0.080 5.304 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1224 0.1469 0.008 0.966 9.0 119.5 20.1 258 0.137 1_adp: 0.1231 0.1467 0.008 0.966 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1232 0.1470 0.008 0.966 9.1 119.4 20.1 258 0.137 1_occ: 0.1226 0.1465 0.008 0.966 9.1 119.4 20.1 258 0.137 2_bss: 0.1224 0.1455 0.008 0.966 9.1 119.5 20.1 258 0.137 2_settarget: 0.1224 0.1455 0.008 0.966 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1224 0.1455 0.008 0.978 9.1 119.5 20.1 258 0.137 2_nqh: 0.1224 0.1455 0.008 0.978 9.1 119.5 20.1 258 0.137 2_sol: 0.1199 0.1396 0.008 0.978 9.1 115.0 22.1 413 n/a 2_weight: 0.1199 0.1396 0.008 0.978 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1187 0.1409 0.008 0.953 9.1 115.0 22.1 413 n/a 2_adp: 0.1187 0.1409 0.008 0.953 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1187 0.1409 0.008 0.953 9.1 115.0 22.1 413 n/a 2_occ: 0.1187 0.1409 0.008 0.953 9.1 115.0 22.1 413 n/a 3_bss: 0.1183 0.1403 0.008 0.953 9.1 115.0 22.1 413 n/a 3_settarget: 0.1183 0.1403 0.008 0.953 9.1 115.0 22.1 413 n/a 3_updatecdl: 0.1183 0.1403 0.008 0.955 9.1 115.0 22.1 413 n/a 3_nqh: 0.1183 0.1404 0.008 0.955 9.1 115.0 22.1 413 n/a 3_sol: 0.1205 0.1397 0.008 0.955 9.1 115.0 21.3 446 n/a 3_weight: 0.1205 0.1397 0.008 0.955 9.1 115.0 21.3 446 n/a 3_xyzrec: 0.1167 0.1317 0.005 0.913 9.1 115.0 21.3 446 n/a 3_adp: 0.1167 0.1317 0.005 0.913 9.1 115.0 21.3 446 n/a 3_regHadp: 0.1167 0.1317 0.005 0.913 9.1 115.0 21.3 446 n/a 3_occ: 0.1159 0.1312 0.005 0.913 9.1 115.0 21.3 446 n/a 4_bss: 0.1153 0.1309 0.005 0.913 9.1 115.0 21.3 446 n/a 4_settarget: 0.1153 0.1309 0.005 0.913 9.1 115.0 21.3 446 n/a 4_updatecdl: 0.1153 0.1309 0.005 0.912 9.1 115.0 21.3 446 n/a 4_nqh: 0.1153 0.1309 0.005 0.912 9.1 115.0 21.3 446 n/a 4_sol: 0.1152 0.1301 0.005 0.912 9.1 115.0 21.1 450 n/a 4_weight: 0.1152 0.1301 0.005 0.912 9.1 115.0 21.1 450 n/a 4_xyzrec: 0.1139 0.1302 0.008 1.122 9.1 115.0 21.1 450 n/a 4_adp: 0.1139 0.1302 0.008 1.122 9.1 115.0 21.1 450 n/a 4_regHadp: 0.1139 0.1302 0.008 1.122 9.1 115.0 21.1 450 n/a 4_occ: 0.1134 0.1299 0.008 1.122 9.1 115.0 21.1 450 n/a 5_bss: 0.1131 0.1302 0.008 1.122 9.1 115.0 21.1 450 n/a 5_settarget: 0.1131 0.1302 0.008 1.122 9.1 115.0 21.1 450 n/a 5_updatecdl: 0.1131 0.1302 0.008 1.123 9.1 115.0 21.1 450 n/a 5_setrh: 0.1133 0.1302 0.008 1.123 9.1 115.0 21.1 450 n/a 5_nqh: 0.1137 0.1303 0.008 1.123 9.1 115.0 21.1 450 n/a 5_sol: 0.1141 0.1283 0.008 1.123 9.1 115.0 21.2 453 n/a 5_weight: 0.1141 0.1283 0.008 1.123 9.1 115.0 21.2 453 n/a 5_xyzrec: 0.1137 0.1280 0.009 1.161 9.1 115.0 21.2 453 n/a 5_adp: 0.1137 0.1280 0.009 1.161 9.1 115.0 21.2 453 n/a 5_regHadp: 0.1137 0.1280 0.009 1.161 9.1 115.0 21.2 453 n/a 5_occ: 0.1133 0.1277 0.009 1.161 9.1 115.0 21.2 453 n/a end: 0.1132 0.1277 0.009 1.161 9.1 115.0 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6218374_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6218374_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7700 Refinement macro-cycles (run) : 13662.8300 Write final files (write_after_run_outputs) : 91.7700 Total : 13758.3700 Total CPU time: 3.83 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:09:47 PST -0800 (1735366187.07 s) Start R-work = 0.1639, R-free = 0.1785 Final R-work = 0.1132, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 13933.57 seconds wall clock time: 253 minutes 53.30 seconds (15233.30 seconds total)