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_1785239.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1785239.pdb" 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 1 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: 1.43, per 1000 atoms: 0.42 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: 0.55 Conformation dependent library (CDL) restraints added in 139.0 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.94: 678 0.94 - 1.18: 991 1.18 - 1.42: 612 1.42 - 1.66: 824 1.66 - 1.91: 48 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.335 1.112 0.223 1.25e-02 6.40e+03 3.18e+02 bond pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 1.236 1.048 0.188 1.15e-02 7.56e+03 2.67e+02 bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.047 0.189 1.16e-02 7.43e+03 2.66e+02 bond pdb=" C LYS A 148 " pdb=" O LYS A 148 " ideal model delta sigma weight residual 1.235 1.052 0.183 1.13e-02 7.83e+03 2.62e+02 bond pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 1.236 1.422 -0.185 1.15e-02 7.56e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.47: 3047 4.47 - 8.94: 1843 8.94 - 13.40: 705 13.40 - 17.87: 149 17.87 - 22.34: 33 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 107.03 12.17 9.00e-01 1.23e+00 1.83e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 108.05 15.05 1.17e+00 7.31e-01 1.65e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 117.15 103.15 14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 111.16 12.10 1.05e+00 9.07e-01 1.33e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N BGLN A 80 " ideal model delta sigma weight residual 122.07 133.82 -11.75 1.03e+00 9.43e-01 1.30e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.42: 940 17.42 - 34.83: 118 34.83 - 52.24: 39 52.24 - 69.65: 11 69.65 - 87.06: 3 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 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.245: 107 0.245 - 0.483: 77 0.483 - 0.722: 46 0.722 - 0.960: 12 0.960 - 1.199: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -3.83 1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" CA BPRO A 66 " pdb=" N BPRO A 66 " pdb=" C BPRO A 66 " pdb=" CB BPRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 3.66 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ATYR A 67 " pdb=" N ATYR A 67 " pdb=" C ATYR A 67 " pdb=" CB ATYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.104 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.022 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.097 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 6.11e-02 1.12e+02 pdb=" CG TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.098 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.038 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1110 2.33 - 2.90: 8216 2.90 - 3.47: 10433 3.47 - 4.03: 15222 4.03 - 4.60: 21585 Nonbonded interactions: 56566 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.794 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE1 GLU A 163 " model vdw 1.802 1.850 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.808 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.816 2.100 ... (remaining 56561 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_1785239_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788142 | | target function (ml) not normalized (work): 232268.962612 | | target function (ml) not normalized (free): 11808.401294 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2063 7.0951 4.9422| | 2: 3.57 - 2.84 1.00 2876 122 0.2444 0.1708 4.3471 4.323| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1699 4.1209 4.1518| | 4: 2.47 - 2.25 1.00 2825 136 0.2367 0.1382 3.8293 3.8216| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1594 3.7917 3.8128| | 6: 2.09 - 1.97 1.00 2846 113 0.2504 0.1874 3.454 3.6213| | 7: 1.97 - 1.87 1.00 2787 165 0.2523 0.1672 3.1283 3.1563| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1884 3.0475 3.0835| | 9: 1.79 - 1.72 1.00 2745 138 0.2473 0.1936 2.9108 2.9719| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1943 2.8139 2.9151| | 11: 1.66 - 1.61 1.00 2740 147 0.2521 0.1981 2.7485 2.7899| | 12: 1.61 - 1.56 1.00 2787 146 0.2464 0.1925 2.6176 2.655| | 13: 1.56 - 1.52 1.00 2745 130 0.2480 0.1804 2.5652 2.5996| | 14: 1.52 - 1.48 1.00 2803 134 0.2538 0.2004 2.4875 2.6071| | 15: 1.48 - 1.45 1.00 2738 128 0.2603 0.1908 2.4286 2.4103| | 16: 1.45 - 1.42 1.00 2756 161 0.2662 0.2062 2.3855 2.3818| | 17: 1.42 - 1.39 1.00 2785 139 0.2668 0.2013 2.3247 2.3635| | 18: 1.39 - 1.36 1.00 2741 179 0.2735 0.2254 2.267 2.3507| | 19: 1.36 - 1.34 1.00 2807 134 0.2673 0.2130 2.2328 2.2575| | 20: 1.34 - 1.32 1.00 2696 147 0.2670 0.2318 2.1899 2.2191| | 21: 1.32 - 1.30 1.00 2785 112 0.2677 0.2076 2.1446 2.139| | 22: 1.29 - 1.27 1.00 2704 152 0.2722 0.2330 2.1122 2.1499| | 23: 1.27 - 1.26 1.00 2802 156 0.2774 0.2490 2.1016 2.1578| | 24: 1.26 - 1.24 1.00 2744 132 0.2783 0.2732 2.0612 2.1993| | 25: 1.24 - 1.22 1.00 2734 148 0.2854 0.2723 2.0386 2.1507| | 26: 1.22 - 1.21 1.00 2727 135 0.2896 0.2567 2.031 2.1657| | 27: 1.21 - 1.19 1.00 2814 148 0.2960 0.2574 2.0149 2.0071| | 28: 1.19 - 1.18 1.00 2671 147 0.3034 0.2818 2.0042 2.01| | 29: 1.18 - 1.16 1.00 2800 134 0.2963 0.2405 1.9558 1.9565| | 30: 1.16 - 1.15 1.00 2740 148 0.3072 0.2814 1.9369 1.9489| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1451.34| | 2: 3.57 - 2.84 2876 122 0.81 25.88 1.27 0.23 1451.34| | 3: 2.84 - 2.48 2833 165 0.74 31.79 1.24 0.23 1203.72| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.26 0.25 561.08| | 5: 2.25 - 2.09 2756 127 0.77 29.11 1.28 0.25 561.08| | 6: 2.09 - 1.97 2846 113 0.84 22.44 1.29 0.25 307.52| | 7: 1.97 - 1.87 2787 165 0.90 16.35 1.28 0.26 91.27| | 8: 1.87 - 1.79 2789 144 0.86 21.11 1.25 0.26 91.27| | 9: 1.79 - 1.72 2745 138 0.88 18.49 1.24 0.26 55.04| | 10: 1.72 - 1.66 2789 158 0.87 20.14 1.22 0.26 47.78| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.24 0.25 46.12| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.22 0.25 29.22| | 13: 1.56 - 1.52 2745 130 0.87 20.26 1.23 0.25 29.22| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.23 0.25 25.97| | 15: 1.48 - 1.45 2738 128 0.87 19.68 1.23 0.25 20.02| | 16: 1.45 - 1.42 2756 161 0.86 21.36 1.24 0.25 20.02| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.23 0.25 16.86| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.24 0.25 15.04| | 19: 1.36 - 1.34 2807 134 0.86 21.55 1.22 0.25 15.04| | 20: 1.34 - 1.32 2696 147 0.87 20.33 1.21 0.25 12.56| | 21: 1.32 - 1.30 2785 112 0.86 21.40 1.21 0.25 12.39| | 22: 1.29 - 1.27 2704 152 0.86 21.84 1.21 0.24 12.17| | 23: 1.27 - 1.26 2802 156 0.85 22.27 1.20 0.24 11.04| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.21 0.24 11.04| | 25: 1.24 - 1.22 2734 148 0.84 23.55 1.21 0.24 10.55| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.20 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 24.65 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.93 1.18 0.23 9.17| | 29: 1.18 - 1.16 2800 134 0.83 25.17 1.17 0.23 8.85| | 30: 1.16 - 1.15 2740 148 0.81 26.85 1.15 0.23 8.85| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.85 max = 1451.34 mean = 210.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.40| |phase err.(test): min = 0.00 max = 89.72 mean = 22.22| |-----------------------------------------------------------------------------| ----------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 0.262 1557 Z= 5.552 Angle : 5.304 16.410 2118 Z= 3.719 Chirality : 0.393 1.199 243 Planarity : 0.031 0.096 284 Dihedral : 13.616 87.058 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % 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: -2.89 (0.48), residues: 224 helix: -2.45 (0.37), residues: 109 sheet: -1.32 (0.79), residues: 40 loop : -0.94 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.019 ARG A 27 TYR 0.081 0.038 TYR A 139 PHE 0.111 0.046 PHE A 119 HIS 0.059 0.027 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= 0.2609 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788142 | | target function (ml) not normalized (work): 232268.962612 | | target function (ml) not normalized (free): 11808.401294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2610 0.1920 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2610 0.1920 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1920 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2012 0.1935 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1634 0.1746 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1746 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3744 389.858 355.670 0.730 0.918 0.407 11.894-9.307 98.04 96 4 0.1703 616.565 591.273 1.008 0.919 0.380 9.237-7.194 100.00 213 7 0.2119 502.236 492.362 1.046 0.920 0.344 7.162-5.571 100.00 427 22 0.2174 376.900 363.940 1.013 0.920 0.320 5.546-4.326 100.00 867 58 0.1285 517.391 511.189 1.043 0.921 0.214 4.315-3.360 100.00 1859 96 0.1146 492.042 488.813 1.092 0.922 0.189 3.356-2.611 100.00 3867 181 0.1453 323.246 320.048 1.081 0.923 0.067 2.608-2.026 99.99 8198 413 0.1357 214.283 212.303 1.090 0.925 0.000 2.025-1.573 100.00 17313 902 0.1631 104.645 104.152 1.090 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.404 45.093 1.071 0.933 0.000 1.221-1.150 99.97 13689 708 0.2620 29.238 26.962 1.034 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0491 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1746 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1643 r_free=0.1758 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.554685 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2009.799467 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 0.1627 0.1749 0.0121 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1536 0.1675 0.0139 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1431 0.1593 0.0162 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1357 0.1537 0.0180 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1331 0.1522 0.0190 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1339 0.1530 0.0191 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1289 0.1504 0.0215 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1271 0.1498 0.0227 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1255 0.1484 0.0229 0.004 0.7 3.5 0.5 0.0 0 4.000 0.1245 0.1480 0.0235 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1238 0.1472 0.0234 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1233 0.1470 0.0237 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1234 0.1472 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1472 0.0240 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1229 0.1465 0.0236 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1225 0.1461 0.0236 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1224 0.1463 0.0238 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1225 0.1465 0.0240 0.008 1.0 2.9 0.5 0.0 0 13.777 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1461 0.0236 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.61 2.36 3.013 19.072 2009.799 0.017 12.25 14.60 2.35 2.989 19.072 60.294 0.017 12.32 14.59 2.27 2.665 19.072 251.225 0.017 12.69 15.38 2.69 2.935 19.398 1004.900 0.016 12.53 15.47 2.94 3.345 19.683 2009.799 0.016 12.38 15.41 3.02 3.197 19.596 3014.699 0.015 12.33 15.50 3.17 3.407 19.705 4019.599 0.015 12.21 15.44 3.22 3.447 19.736 5024.499 0.015 12.24 15.51 3.27 3.469 19.734 6029.398 0.015 12.19 15.43 3.24 3.299 19.621 7034.298 0.015 12.19 15.50 3.31 3.373 19.651 8039.198 0.015 12.14 15.45 3.31 3.424 19.673 9044.098 0.015 12.19 15.61 3.42 3.629 19.769 10048.997 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 251.225 Accepted refinement result: 12.32 14.59 2.27 2.665 19.072 251.225 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.10 3.30 0 1785 Protein: 9.07 114.97 17.01 3.31 0 1519 Water: 11.49 119.45 38.24 N/A 0 258 Other: 19.72 26.61 22.07 N/A 0 8 Chain A: 9.07 119.45 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 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 - 86.34 7 86.34 - 97.38 4 97.38 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1459 r_work=0.1233 r_free=0.1461 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1461 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 = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016607 | | target function (ls_wunit_k1) not normalized (work): 1383.285892 | | target function (ls_wunit_k1) not normalized (free): 109.043379 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1226 0.1460 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1671 0.1673 0.1687 n_refl.: 87591 remove outliers: r(all,work,free)=0.1671 0.1673 0.1687 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1676 0.1678 0.1691 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1455 n_refl.: 87591 remove outliers: r(all,work,free)=0.1236 0.1225 0.1455 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3468 305.918 285.466 0.670 1.002 0.395 11.894-9.307 98.04 96 4 0.1547 483.813 471.274 0.932 1.003 0.366 9.237-7.194 100.00 213 7 0.1880 394.100 388.483 0.966 1.003 0.349 7.162-5.571 100.00 427 22 0.1822 295.750 290.008 0.935 1.003 0.290 5.546-4.326 100.00 867 58 0.1001 405.992 402.608 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0870 386.101 385.129 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1173 253.648 252.470 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.146 167.429 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.114 82.312 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.413 35.919 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.942 21.430 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1455 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1225 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1454 | n_water=258 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1232 r_free=0.1456 | n_water=251 | time (s): 21.220 (total time: 23.220) Filter (q & B) r_work=0.1235 r_free=0.1455 | n_water=248 | time (s): 3.030 (total time: 26.250) Compute maps r_work=0.1235 r_free=0.1455 | n_water=248 | time (s): 1.710 (total time: 27.960) Filter (map) r_work=0.1252 r_free=0.1462 | n_water=225 | time (s): 3.140 (total time: 31.100) Find peaks r_work=0.1252 r_free=0.1462 | n_water=225 | time (s): 0.490 (total time: 31.590) Add new water r_work=0.1394 r_free=0.1622 | n_water=419 | time (s): 3.060 (total time: 34.650) Refine new water occ: r_work=0.1300 r_free=0.1491 adp: r_work=0.1224 r_free=0.1436 occ: r_work=0.1235 r_free=0.1424 adp: r_work=0.1204 r_free=0.1411 occ: r_work=0.1206 r_free=0.1401 adp: r_work=0.1196 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1399 r_work=0.1196 r_free=0.1399 | n_water=419 | time (s): 55.670 (total time: 90.320) Filter (q & B) r_work=0.1201 r_free=0.1399 | n_water=404 | time (s): 2.800 (total time: 93.120) Filter (dist only) r_work=0.1201 r_free=0.1399 | n_water=403 | time (s): 34.350 (total time: 127.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.418402 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1470.711791 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 0.1631 0.1745 0.0113 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1525 0.1655 0.0130 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1406 0.1559 0.0153 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1347 0.1512 0.0165 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1318 0.1491 0.0173 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1322 0.1500 0.0177 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1260 0.1454 0.0194 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1235 0.1440 0.0205 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1221 0.1434 0.0213 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1212 0.1427 0.0215 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1207 0.1426 0.0219 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1202 0.1424 0.0222 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1197 0.1422 0.0225 0.005 0.8 5.8 0.5 0.0 0 8.000 0.1195 0.1423 0.0228 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1190 0.1421 0.0231 0.006 0.8 5.4 0.5 0.0 0 10.000 0.1189 0.1422 0.0233 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1186 0.1420 0.0233 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1187 0.1420 0.0233 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1185 0.1423 0.0238 0.008 0.9 4.5 0.5 0.0 0 14.209 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1186 0.1420 0.0233 0.007 0.9 5.4 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.86 14.20 2.33 3.774 21.698 1470.712 0.016 11.86 14.20 2.33 3.774 21.698 44.121 0.016 11.86 14.20 2.33 3.774 21.698 183.839 0.016 12.02 14.58 2.56 3.632 21.702 735.356 0.015 12.04 14.92 2.88 3.458 21.880 1470.712 0.015 11.93 14.89 2.95 3.450 22.074 2206.068 0.014 11.79 14.80 3.01 3.484 21.862 2941.424 0.014 11.76 14.82 3.06 3.477 22.025 3676.779 0.014 11.66 14.67 3.01 3.505 21.931 4412.135 0.014 11.66 14.73 3.07 3.504 21.949 5147.491 0.014 11.70 14.90 3.20 3.560 22.070 5882.847 0.014 11.69 14.92 3.23 3.591 22.101 6618.203 0.014 11.69 15.02 3.32 3.634 22.169 7353.559 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: 44.121 Accepted refinement result: 11.86 14.20 2.33 3.774 21.698 44.121 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 22.03 3.30 178 1752 Protein: 9.10 115.00 17.04 3.31 0 1519 Water: 10.51 76.69 40.87 N/A 178 225 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.10 115.00 19.45 N/A 0 1752 Chain S: 10.51 60.00 47.48 N/A 178 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 239 30.28 - 40.87 163 40.87 - 51.46 125 51.46 - 62.05 121 62.05 - 72.64 12 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=0.1186 r_free=0.1420 r_work=0.1186 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1420 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 = 0.1185 r_free = 0.1418 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1185 r_free= 0.1418 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014900 | | target function (ls_wunit_k1) not normalized (work): 1241.107302 | | target function (ls_wunit_k1) not normalized (free): 106.216228 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1185 0.1418 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1594 0.1595 0.1615 n_refl.: 87591 remove outliers: r(all,work,free)=0.1594 0.1595 0.1615 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1595 0.1596 0.1616 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1183 0.1411 n_refl.: 87591 remove outliers: r(all,work,free)=0.1192 0.1181 0.1411 n_refl.: 87587 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3329 299.317 278.344 0.598 1.003 0.350 11.894-9.307 98.04 96 4 0.1549 483.813 475.538 0.931 1.003 0.337 9.237-7.194 100.00 213 7 0.1710 394.100 392.488 0.983 1.003 0.300 7.162-5.571 100.00 427 22 0.1612 295.750 291.575 0.936 1.003 0.250 5.546-4.326 100.00 867 58 0.0884 405.992 402.777 0.960 1.003 0.194 4.315-3.360 100.00 1859 96 0.0773 386.101 385.169 1.006 1.003 0.180 3.356-2.611 100.00 3867 181 0.1083 253.648 252.620 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.1002 168.146 167.612 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1100 82.114 82.335 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.413 35.943 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.942 21.457 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0098 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1411 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1181 r_free=0.1411 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1411 | n_water=403 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1181 r_free=0.1411 | n_water=400 | time (s): 36.480 (total time: 38.540) Filter (q & B) r_work=0.1181 r_free=0.1411 | n_water=400 | time (s): 1.060 (total time: 39.600) Compute maps r_work=0.1181 r_free=0.1411 | n_water=400 | time (s): 1.250 (total time: 40.850) Filter (map) r_work=0.1226 r_free=0.1410 | n_water=274 | time (s): 2.520 (total time: 43.370) Find peaks r_work=0.1226 r_free=0.1410 | n_water=274 | time (s): 0.530 (total time: 43.900) Add new water r_work=0.1344 r_free=0.1540 | n_water=459 | time (s): 3.310 (total time: 47.210) Refine new water occ: r_work=0.1248 r_free=0.1445 adp: r_work=0.1250 r_free=0.1447 occ: r_work=0.1226 r_free=0.1420 adp: r_work=0.1225 r_free=0.1422 occ: r_work=0.1207 r_free=0.1399 adp: r_work=0.1204 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1399 r_work=0.1204 r_free=0.1399 | n_water=459 | time (s): 179.160 (total time: 226.370) Filter (q & B) r_work=0.1208 r_free=0.1398 | n_water=428 | time (s): 3.180 (total time: 229.550) Filter (dist only) r_work=0.1208 r_free=0.1397 | n_water=427 | time (s): 36.010 (total time: 265.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.012233 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 0.1240 0.1385 0.0146 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1195 0.1346 0.0151 0.003 0.7 3.5 0.5 0.0 0 0.265 0.1182 0.1335 0.0153 0.004 0.8 3.5 0.5 0.0 0 0.530 0.1173 0.1326 0.0154 0.005 0.9 3.5 0.5 0.0 0 0.795 0.1170 0.1326 0.0156 0.006 1.0 3.5 0.5 0.0 0 1.061 0.1166 0.1326 0.0160 0.007 1.0 3.8 0.5 0.0 0 1.326 0.1163 0.1326 0.0162 0.007 1.1 4.5 0.5 0.0 0 1.591 0.1162 0.1323 0.0161 0.008 1.1 4.2 0.5 0.0 0 1.856 0.1172 0.1326 0.0154 0.005 0.9 3.2 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1323 0.0161 0.008 1.1 4.2 0.5 0.0 0 1.856 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.23 1.61 3.777 21.128 45.012 3.620 11.62 13.23 1.61 3.777 21.128 1.350 3.620 11.63 13.24 1.61 3.762 21.128 5.627 3.619 11.69 13.33 1.64 3.709 21.114 22.506 3.615 11.70 13.41 1.72 3.736 21.083 45.012 3.615 11.63 13.40 1.77 3.756 21.069 67.518 3.608 11.58 13.38 1.80 3.773 21.065 90.024 3.605 11.54 13.34 1.80 3.784 21.059 112.531 3.601 11.52 13.33 1.81 3.797 21.051 135.037 3.599 11.51 13.34 1.83 3.815 21.036 157.543 3.598 11.49 13.32 1.82 3.822 21.036 180.049 3.596 11.50 13.33 1.84 3.835 21.029 202.555 3.596 11.48 13.31 1.84 3.838 21.033 225.061 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.350 Accepted refinement result: 11.62 13.23 1.61 3.777 21.128 1.350 3.620 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 20.99 3.30 208 1746 Protein: 9.11 115.01 17.04 3.31 0 1519 Water: 10.52 76.70 35.00 N/A 208 219 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.01 19.34 N/A 0 1746 Chain S: 10.52 60.01 34.77 N/A 208 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 293 30.29 - 40.88 207 40.88 - 51.47 121 51.47 - 62.06 46 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1323 r_work=0.1162 r_free=0.1323 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1323 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1317 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1151 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611611 | | target function (ml) not normalized (work): 300814.731452 | | target function (ml) not normalized (free): 15845.698904 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1317 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1498 0.1499 0.1527 n_refl.: 87587 remove outliers: r(all,work,free)=0.1498 0.1499 0.1527 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1497 0.1526 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1309 n_refl.: 87587 remove outliers: r(all,work,free)=0.1151 0.1143 0.1309 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3851 299.317 269.297 0.485 1.001 0.330 11.894-9.307 97.06 95 4 0.2297 483.958 464.906 0.869 1.003 0.320 9.237-7.194 98.18 209 7 0.2354 385.591 385.969 0.940 1.003 0.240 7.162-5.571 100.00 427 22 0.2130 295.750 284.715 0.906 1.003 0.170 5.546-4.326 100.00 867 58 0.1119 405.992 401.124 0.954 1.003 0.150 4.315-3.360 100.00 1859 96 0.0934 386.101 383.569 0.994 1.003 0.150 3.356-2.611 100.00 3867 181 0.1142 253.648 251.333 0.998 1.002 0.053 2.608-2.026 99.99 8198 413 0.0931 168.146 167.416 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.114 82.424 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.413 36.001 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.942 21.491 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0214 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 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=0.1143 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1309 | n_water=427 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1146 r_free=0.1306 | n_water=424 | time (s): 46.970 (total time: 49.490) Filter (q & B) r_work=0.1147 r_free=0.1306 | n_water=422 | time (s): 3.880 (total time: 53.370) Compute maps r_work=0.1147 r_free=0.1306 | n_water=422 | time (s): 1.860 (total time: 55.230) Filter (map) r_work=0.1169 r_free=0.1300 | n_water=319 | time (s): 3.840 (total time: 59.070) Find peaks r_work=0.1169 r_free=0.1300 | n_water=319 | time (s): 0.700 (total time: 59.770) Add new water r_work=0.1238 r_free=0.1366 | n_water=476 | time (s): 3.830 (total time: 63.600) Refine new water occ: r_work=0.1167 r_free=0.1299 adp: r_work=0.1168 r_free=0.1300 occ: r_work=0.1151 r_free=0.1287 adp: r_work=0.1150 r_free=0.1287 occ: r_work=0.1138 r_free=0.1284 adp: r_work=0.1135 r_free=0.1282 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1282 r_work=0.1135 r_free=0.1282 | n_water=476 | time (s): 187.370 (total time: 250.970) Filter (q & B) r_work=0.1142 r_free=0.1290 | n_water=441 | time (s): 3.890 (total time: 254.860) Filter (dist only) r_work=0.1149 r_free=0.1288 | n_water=438 | time (s): 47.020 (total time: 301.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.710102 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.147384 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 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1178 0.1305 0.0126 0.003 0.7 3.5 0.5 0.0 0 0.257 0.1162 0.1300 0.0138 0.005 0.9 3.5 0.5 0.0 0 0.513 0.1156 0.1293 0.0137 0.006 0.9 3.8 0.5 0.0 0 0.770 0.1152 0.1294 0.0142 0.006 1.0 3.8 0.5 0.0 0 1.026 0.1149 0.1294 0.0145 0.007 1.0 3.8 0.5 0.0 0 1.283 0.1148 0.1294 0.0146 0.008 1.1 3.8 0.5 0.0 0 1.539 0.1146 0.1290 0.0144 0.008 1.1 4.2 0.5 0.0 0 1.796 0.1155 0.1300 0.0145 0.006 1.0 3.5 0.5 0.0 0 0.855 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1290 0.0144 0.008 1.1 4.2 0.5 0.0 0 1.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 12.90 1.44 3.777 21.141 41.147 3.606 11.46 12.90 1.44 3.777 21.141 1.234 3.606 11.46 12.90 1.44 3.777 21.141 5.143 3.606 11.50 12.95 1.45 3.710 21.134 20.574 3.601 11.60 13.14 1.54 3.727 21.103 41.147 3.606 11.51 13.09 1.58 3.753 21.091 61.721 3.600 11.45 13.04 1.59 3.769 21.087 82.295 3.595 11.44 13.05 1.61 3.778 21.083 102.868 3.593 11.38 12.98 1.60 3.784 21.087 123.442 3.589 11.40 13.06 1.65 3.806 21.070 144.016 3.590 11.37 13.02 1.65 3.809 21.075 164.590 3.588 11.37 13.03 1.66 3.823 21.062 185.163 3.587 11.36 13.03 1.67 3.833 21.060 205.737 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.234 Accepted refinement result: 11.46 12.90 1.44 3.777 21.141 1.234 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 21.02 3.30 221 1744 Protein: 9.10 115.00 17.03 3.31 0 1519 Water: 10.51 76.69 34.81 N/A 221 217 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.10 115.00 19.33 N/A 0 1744 Chain S: 10.51 60.00 34.33 N/A 221 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 297 30.28 - 40.87 214 40.87 - 51.46 123 51.46 - 62.05 44 62.05 - 72.64 12 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=0.1146 r_free=0.1290 r_work=0.1146 r_free=0.1290 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1290 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1293 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1141 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604404 | | target function (ml) not normalized (work): 300196.390894 | | target function (ml) not normalized (free): 15805.856003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1141 0.1293 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1492 0.1491 0.1529 n_refl.: 87582 remove outliers: r(all,work,free)=0.1492 0.1491 0.1529 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1490 0.1528 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1295 n_refl.: 87582 remove outliers: r(all,work,free)=0.1146 0.1138 0.1295 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3932 296.070 256.523 0.469 1.000 0.320 11.894-9.307 95.10 93 4 0.2292 477.183 467.738 0.880 1.002 0.268 9.237-7.194 98.18 209 7 0.2348 385.591 380.389 0.928 1.002 0.220 7.162-5.571 100.00 427 22 0.2164 295.750 285.665 0.909 1.002 0.156 5.546-4.326 100.00 867 58 0.1139 405.992 401.007 0.963 1.002 0.123 4.315-3.360 100.00 1859 96 0.0936 386.101 384.185 1.004 1.002 0.103 3.356-2.611 100.00 3867 181 0.1126 253.648 251.500 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0919 168.146 167.446 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.114 82.443 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.413 36.009 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.942 21.492 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0181 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1138 r_free=0.1295 After: r_work=0.1139 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1139 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=0.1139 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1295 | n_water=438 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1139 r_free=0.1295 | n_water=438 | time (s): 44.020 (total time: 46.500) Filter (q & B) r_work=0.1139 r_free=0.1295 | n_water=438 | time (s): 1.530 (total time: 48.030) Compute maps r_work=0.1139 r_free=0.1295 | n_water=438 | time (s): 1.920 (total time: 49.950) Filter (map) r_work=0.1163 r_free=0.1296 | n_water=346 | time (s): 3.990 (total time: 53.940) Find peaks r_work=0.1163 r_free=0.1296 | n_water=346 | time (s): 0.730 (total time: 54.670) Add new water r_work=0.1212 r_free=0.1350 | n_water=486 | time (s): 3.780 (total time: 58.450) Refine new water occ: r_work=0.1157 r_free=0.1295 adp: r_work=0.1158 r_free=0.1296 occ: r_work=0.1146 r_free=0.1284 adp: r_work=0.1145 r_free=0.1284 occ: r_work=0.1137 r_free=0.1276 adp: r_work=0.1134 r_free=0.1275 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1275 r_work=0.1134 r_free=0.1275 | n_water=486 | time (s): 187.040 (total time: 245.490) Filter (q & B) r_work=0.1142 r_free=0.1285 | n_water=446 | time (s): 3.940 (total time: 249.430) Filter (dist only) r_work=0.1142 r_free=0.1283 | n_water=444 | time (s): 47.760 (total time: 297.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.711659 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.410194 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 0.1230 0.1343 0.0113 0.004 0.7 5.4 0.0 0.0 0 0.086 0.1173 0.1302 0.0129 0.004 0.8 4.5 0.0 0.0 0 0.257 0.1158 0.1292 0.0134 0.005 0.9 4.2 0.5 0.0 0 0.513 0.1150 0.1287 0.0137 0.006 1.0 3.8 0.5 0.0 0 0.770 0.1146 0.1285 0.0138 0.007 1.1 3.8 0.5 0.0 0 1.027 0.1144 0.1284 0.0139 0.008 1.1 3.8 0.5 0.0 0 1.284 0.1143 0.1283 0.0140 0.008 1.1 4.2 0.5 0.0 0 1.540 0.1143 0.1283 0.0141 0.008 1.1 4.2 0.5 0.0 0 1.797 0.1149 0.1287 0.0137 0.006 1.1 3.8 0.5 0.0 0 0.856 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1283 0.0141 0.008 1.1 4.2 0.5 0.0 0 1.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.83 1.41 3.777 21.163 43.410 3.604 11.43 12.83 1.41 3.777 21.163 1.302 3.604 11.43 12.83 1.40 3.774 21.163 5.426 3.604 11.46 12.90 1.44 3.709 21.156 21.705 3.599 11.49 13.00 1.52 3.735 21.134 43.410 3.601 11.45 13.01 1.56 3.753 21.116 65.115 3.597 11.37 12.94 1.57 3.765 21.117 86.820 3.591 11.38 12.95 1.58 3.778 21.110 108.525 3.590 11.34 12.92 1.58 3.788 21.108 130.231 3.587 11.34 12.94 1.60 3.802 21.102 151.936 3.587 11.34 12.97 1.63 3.818 21.090 173.641 3.586 11.32 12.94 1.62 3.824 21.092 195.346 3.585 11.31 12.94 1.63 3.833 21.089 217.051 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.302 Accepted refinement result: 11.43 12.83 1.41 3.777 21.163 1.302 3.604 Individual atomic B min max mean iso aniso Overall: 9.09 114.99 21.06 3.30 227 1744 Protein: 9.09 114.99 17.03 3.31 0 1519 Water: 10.51 76.68 34.85 N/A 227 217 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.09 114.99 19.32 N/A 0 1744 Chain S: 10.51 60.00 34.43 N/A 227 0 Histogram: Values Number of atoms 9.09 - 19.68 1264 19.68 - 30.27 300 30.27 - 40.86 214 40.86 - 51.45 126 51.45 - 62.04 44 62.04 - 72.63 12 72.63 - 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=0.1143 r_free=0.1283 r_work=0.1143 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1283 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1280 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602794 | | target function (ml) not normalized (work): 300047.849762 | | target function (ml) not normalized (free): 15794.558409 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1343 0.1321 5.6415 5.5908| | 2: 3.57 - 2.84 1.00 2888 124 0.1088 0.1414 5.1684 5.2166| | 3: 2.83 - 2.48 1.00 2820 163 0.1106 0.1221 4.9393 4.9817| | 4: 2.47 - 2.25 1.00 2825 136 0.0900 0.0920 4.6276 4.6431| | 5: 2.25 - 2.09 1.00 2756 127 0.0868 0.0925 4.5731 4.6154| | 6: 2.09 - 1.97 1.00 2846 113 0.0861 0.0994 4.2671 4.3486| | 7: 1.97 - 1.87 1.00 2787 165 0.0894 0.1120 3.9829 4.1015| | 8: 1.87 - 1.79 1.00 2789 144 0.0920 0.1107 3.8895 3.991| | 9: 1.79 - 1.72 1.00 2745 138 0.0879 0.1161 3.6462 3.8075| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1190 3.5628 3.7231| | 11: 1.66 - 1.61 1.00 2712 147 0.0876 0.1038 3.4972 3.5728| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1135 3.3321 3.4445| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1068 3.3077 3.4193| | 14: 1.52 - 1.48 1.00 2803 134 0.0976 0.1038 3.2371 3.3133| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1242 3.1515 3.2632| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1249 3.1346 3.2339| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1326 3.1167 3.2445| | 18: 1.39 - 1.36 1.00 2741 179 0.1195 0.1328 3.1026 3.2315| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1564 3.1134 3.2625| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1452 3.1099 3.1517| | 21: 1.32 - 1.30 1.00 2785 112 0.1476 0.1516 3.1134 3.1077| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1968 3.1215 3.2866| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1800 3.1309 3.2005| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1824 3.1248 3.2251| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2131 3.1413 3.2481| | 26: 1.22 - 1.21 1.00 2727 135 0.1902 0.1758 3.1451 3.1988| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2157 3.1699 3.1597| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2284 3.1637 3.1711| | 29: 1.18 - 1.16 1.00 2800 134 0.2259 0.2390 3.1454 3.2284| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2452 3.1415 3.1662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.50 1.00 0.97 5665.38| | 2: 3.57 - 2.84 2888 124 0.93 12.50 1.01 0.97 5665.38| | 3: 2.83 - 2.48 2820 163 0.90 16.43 0.99 0.97 4733.41| | 4: 2.47 - 2.25 2825 136 0.92 13.39 1.00 0.98 2330.15| | 5: 2.25 - 2.09 2756 127 0.90 15.52 1.01 0.98 2330.15| | 6: 2.09 - 1.97 2846 113 0.93 12.30 1.02 0.98 1347.01| | 7: 1.97 - 1.87 2787 165 0.95 9.31 1.02 0.97 508.52| | 8: 1.87 - 1.79 2789 144 0.93 12.57 1.00 0.97 508.52| | 9: 1.79 - 1.72 2745 138 0.94 10.12 0.98 0.97 288.28| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.97 244.17| | 11: 1.66 - 1.61 2712 147 0.93 11.74 0.98 0.97 233.99| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.97 138.04| | 13: 1.56 - 1.52 2745 130 0.95 10.48 1.03 0.97 138.04| | 14: 1.52 - 1.48 2803 134 0.94 10.84 1.02 0.97 123.82| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.98 97.77| | 16: 1.45 - 1.42 2756 161 0.94 11.16 1.02 0.98 97.77| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.10| | 18: 1.39 - 1.36 2741 179 0.94 11.59 1.01 0.98 84.08| | 19: 1.36 - 1.34 2807 134 0.94 11.87 0.99 0.98 84.08| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.96 79.76| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.96 79.45| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 79.82| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 81.67| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.94 81.67| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 83.63| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.02 0.93 85.80| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 85.80| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.92 89.78| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 91.28| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.92 91.28| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.45 max = 5665.38 mean = 876.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.44| |phase err.(test): min = 0.00 max = 88.78 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1139 0.1280 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1469 0.1469 0.1498 n_refl.: 87578 remove outliers: r(all,work,free)=0.1469 0.1469 0.1498 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1468 0.1468 0.1497 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1281 n_refl.: 87578 remove outliers: r(all,work,free)=0.1145 0.1138 0.1281 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4022 292.687 257.534 0.464 1.000 0.307 11.894-9.307 95.10 93 4 0.2321 477.183 463.859 0.873 1.002 0.251 9.237-7.194 98.18 209 7 0.2382 385.591 379.996 0.925 1.002 0.200 7.162-5.571 100.00 427 22 0.2160 295.750 285.182 0.904 1.003 0.150 5.546-4.326 100.00 867 58 0.1145 405.992 400.939 0.962 1.003 0.130 4.315-3.360 100.00 1859 96 0.0930 386.101 384.156 1.005 1.003 0.130 3.356-2.611 100.00 3867 181 0.1124 253.648 251.583 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0912 168.146 167.472 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.114 82.456 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.413 36.015 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.942 21.497 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0134 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2609 0.1919 0.082 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1746 0.082 5.304 9.1 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1746 0.082 5.304 9.1 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1758 0.082 5.304 9.1 119.5 20.1 258 0.010 1_weight: 0.1643 0.1758 0.082 5.304 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1225 0.1461 0.007 0.910 9.1 119.5 20.1 258 0.137 1_adp: 0.1232 0.1459 0.007 0.910 9.1 119.5 20.1 258 0.137 1_regHadp: 0.1233 0.1461 0.007 0.910 9.1 119.5 20.1 258 0.137 1_occ: 0.1226 0.1460 0.007 0.910 9.1 119.5 20.1 258 0.137 2_bss: 0.1225 0.1455 0.007 0.910 9.1 119.5 20.1 258 0.137 2_settarget: 0.1225 0.1455 0.007 0.910 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1225 0.1455 0.007 0.916 9.1 119.5 20.1 258 0.137 2_nqh: 0.1225 0.1454 0.007 0.916 9.1 119.5 20.1 258 0.135 2_sol: 0.1201 0.1399 0.007 0.916 9.1 115.0 22.0 403 n/a 2_weight: 0.1201 0.1399 0.007 0.916 9.1 115.0 22.0 403 n/a 2_xyzrec: 0.1186 0.1420 0.007 0.895 9.1 115.0 22.0 403 n/a 2_adp: 0.1186 0.1420 0.007 0.895 9.1 115.0 22.0 403 n/a 2_regHadp: 0.1186 0.1420 0.007 0.895 9.1 115.0 22.0 403 n/a 2_occ: 0.1185 0.1418 0.007 0.895 9.1 115.0 22.0 403 n/a 3_bss: 0.1181 0.1411 0.007 0.895 9.1 115.0 22.0 403 n/a 3_settarget: 0.1181 0.1411 0.007 0.895 9.1 115.0 22.0 403 n/a 3_updatecdl: 0.1181 0.1411 0.007 0.897 9.1 115.0 22.0 403 n/a 3_nqh: 0.1181 0.1411 0.007 0.897 9.1 115.0 22.0 403 n/a 3_sol: 0.1208 0.1397 0.007 0.897 9.1 115.0 21.0 427 n/a 3_weight: 0.1208 0.1397 0.007 0.897 9.1 115.0 21.0 427 n/a 3_xyzrec: 0.1162 0.1323 0.008 1.088 9.1 115.0 21.0 427 n/a 3_adp: 0.1162 0.1323 0.008 1.088 9.1 115.0 21.0 427 n/a 3_regHadp: 0.1162 0.1323 0.008 1.088 9.1 115.0 21.0 427 n/a 3_occ: 0.1151 0.1317 0.008 1.088 9.1 115.0 21.0 427 n/a 4_bss: 0.1143 0.1309 0.008 1.088 9.1 115.0 21.0 427 n/a 4_settarget: 0.1143 0.1309 0.008 1.088 9.1 115.0 21.0 427 n/a 4_updatecdl: 0.1143 0.1309 0.008 1.089 9.1 115.0 21.0 427 n/a 4_nqh: 0.1143 0.1309 0.008 1.089 9.1 115.0 21.0 427 n/a 4_sol: 0.1149 0.1288 0.008 1.089 9.1 115.0 21.0 438 n/a 4_weight: 0.1149 0.1288 0.008 1.089 9.1 115.0 21.0 438 n/a 4_xyzrec: 0.1146 0.1290 0.008 1.125 9.1 115.0 21.0 438 n/a 4_adp: 0.1146 0.1290 0.008 1.125 9.1 115.0 21.0 438 n/a 4_regHadp: 0.1146 0.1290 0.008 1.125 9.1 115.0 21.0 438 n/a 4_occ: 0.1141 0.1293 0.008 1.125 9.1 115.0 21.0 438 n/a 5_bss: 0.1138 0.1295 0.008 1.125 9.1 115.0 21.0 438 n/a 5_settarget: 0.1138 0.1295 0.008 1.125 9.1 115.0 21.0 438 n/a 5_updatecdl: 0.1138 0.1295 0.008 1.124 9.1 115.0 21.0 438 n/a 5_setrh: 0.1139 0.1295 0.008 1.124 9.1 115.0 21.0 438 n/a 5_nqh: 0.1139 0.1295 0.008 1.124 9.1 115.0 21.0 438 n/a 5_sol: 0.1142 0.1283 0.008 1.124 9.1 115.0 21.1 444 n/a 5_weight: 0.1142 0.1283 0.008 1.124 9.1 115.0 21.1 444 n/a 5_xyzrec: 0.1143 0.1283 0.008 1.127 9.1 115.0 21.1 444 n/a 5_adp: 0.1143 0.1283 0.008 1.127 9.1 115.0 21.1 444 n/a 5_regHadp: 0.1143 0.1283 0.008 1.127 9.1 115.0 21.1 444 n/a 5_occ: 0.1139 0.1280 0.008 1.127 9.1 115.0 21.1 444 n/a end: 0.1138 0.1281 0.008 1.127 9.1 115.0 21.1 444 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1785239_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1785239_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9100 Refinement macro-cycles (run) : 13515.8900 Write final files (write_after_run_outputs) : 91.9900 Total : 13610.7900 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:21 PST -0800 (1735365981.30 s) Start R-work = 0.1632, R-free = 0.1746 Final R-work = 0.1138, R-free = 0.1281 =============================================================================== Job complete usr+sys time: 13789.06 seconds wall clock time: 250 minutes 33.30 seconds (15033.30 seconds total)