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_7650209.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.72, per 1000 atoms: 0.51 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 206.2 milliseconds Time building geometry restraints manager: 0.76 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: 512 0.91 - 1.16: 1114 1.16 - 1.40: 601 1.40 - 1.65: 859 1.65 - 1.90: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.184 0.275 1.19e-02 7.06e+03 5.34e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.509 -0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.489 -0.157 8.60e-03 1.35e+04 3.33e+02 bond pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 1.526 1.751 -0.225 1.28e-02 6.10e+03 3.10e+02 bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.27e-02 6.20e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2849 4.17 - 8.35: 1898 8.35 - 12.52: 807 12.52 - 16.69: 201 16.69 - 20.86: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 122.99 137.39 -14.40 1.07e+00 8.73e-01 1.81e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 134.14 -13.84 1.07e+00 8.73e-01 1.67e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 110.15 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" C LEU A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 119.94 133.62 -13.68 1.11e+00 8.12e-01 1.52e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 109.53 13.74 1.13e+00 7.83e-01 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 914 16.41 - 32.81: 139 32.81 - 49.21: 37 49.21 - 65.62: 16 65.62 - 82.02: 5 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 157.03 22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CD1 PHE A 119 " pdb=" CG PHE A 119 " pdb=" CD2 PHE A 119 " pdb=" HD2 PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.215: 92 0.215 - 0.424: 79 0.424 - 0.634: 44 0.634 - 0.844: 22 0.844 - 1.053: 6 Chirality restraints: 243 Sorted by residual: 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 -1.54 -1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 7.83e-02 1.84e+02 pdb=" CG PHE A 119 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.066 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 139 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.119 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.005 2.00e-02 2.50e+03 5.59e-02 9.38e+01 pdb=" CG PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1035 2.32 - 2.89: 8049 2.89 - 3.46: 10545 3.46 - 4.03: 15207 4.03 - 4.60: 21803 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.748 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.846 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.857 1.850 nonbonded pdb=" O LEU A 92 " pdb=" H AGLU A 96 " model vdw 1.866 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.866 2.100 ... (remaining 56634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_7650209_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= 0.2611 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787888 | | target function (ml) not normalized (work): 232247.785032 | | target function (ml) not normalized (free): 11796.000060 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3036 0.2097 7.0688 4.9477| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1790 4.3464 4.3493| | 3: 2.84 - 2.48 1.00 2833 165 0.2375 0.1660 4.1269 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2310 0.1495 3.8262 3.8422| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1555 3.7965 3.8034| | 6: 2.09 - 1.97 1.00 2846 113 0.2572 0.1542 3.4678 3.5395| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1863 3.1228 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2471 0.1745 3.0453 3.0953| | 9: 1.79 - 1.72 1.00 2745 138 0.2454 0.1734 2.9136 2.8991| | 10: 1.72 - 1.66 1.00 2789 158 0.2448 0.2087 2.7994 2.9371| | 11: 1.66 - 1.61 1.00 2740 147 0.2452 0.1793 2.7327 2.7529| | 12: 1.61 - 1.56 1.00 2787 146 0.2527 0.2128 2.6104 2.6735| | 13: 1.56 - 1.52 1.00 2745 130 0.2541 0.1943 2.5625 2.626| | 14: 1.52 - 1.48 1.00 2803 134 0.2557 0.2132 2.4906 2.592| | 15: 1.48 - 1.45 1.00 2738 128 0.2564 0.2063 2.4456 2.484| | 16: 1.45 - 1.42 1.00 2756 161 0.2638 0.2161 2.3776 2.426| | 17: 1.42 - 1.39 1.00 2785 139 0.2679 0.2082 2.3369 2.3981| | 18: 1.39 - 1.36 1.00 2741 179 0.2706 0.2127 2.2797 2.2785| | 19: 1.36 - 1.34 1.00 2807 134 0.2672 0.2308 2.2681 2.3025| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2125 2.1907 2.175| | 21: 1.32 - 1.30 1.00 2785 112 0.2708 0.2135 2.1717 2.1369| | 22: 1.29 - 1.27 1.00 2704 152 0.2769 0.2689 2.1375 2.2172| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2288 2.0942 2.1301| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2597 2.0598 2.2234| | 25: 1.24 - 1.22 1.00 2734 148 0.2823 0.2372 2.0304 2.0366| | 26: 1.22 - 1.21 1.00 2727 135 0.2869 0.2514 2.0022 2.1492| | 27: 1.21 - 1.19 1.00 2814 148 0.2975 0.2423 1.9982 1.9834| | 28: 1.19 - 1.18 1.00 2671 147 0.3010 0.2523 1.9909 1.9215| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2541 1.9587 2.0079| | 30: 1.16 - 1.15 1.00 2740 148 0.3072 0.2869 1.9282 1.9809| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.93 0.76 0.23 1476.95| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1476.95| | 3: 2.84 - 2.48 2833 165 0.74 32.07 1.24 0.24 1223.23| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.25 0.25 564.79| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.28 0.25 564.79| | 6: 2.09 - 1.97 2846 113 0.84 22.43 1.30 0.25 306.31| | 7: 1.97 - 1.87 2787 165 0.90 16.03 1.28 0.26 85.86| | 8: 1.87 - 1.79 2789 144 0.86 20.34 1.25 0.26 85.86| | 9: 1.79 - 1.72 2745 138 0.89 17.99 1.24 0.25 53.18| | 10: 1.72 - 1.66 2789 158 0.87 19.78 1.23 0.25 46.63| | 11: 1.66 - 1.61 2740 147 0.86 20.92 1.24 0.25 45.09| | 12: 1.61 - 1.56 2787 146 0.88 18.55 1.24 0.25 29.42| | 13: 1.56 - 1.52 2745 130 0.86 20.52 1.24 0.25 29.42| | 14: 1.52 - 1.48 2803 134 0.86 20.94 1.24 0.25 26.42| | 15: 1.48 - 1.45 2738 128 0.87 20.11 1.22 0.25 20.94| | 16: 1.45 - 1.42 2756 161 0.86 21.66 1.24 0.25 20.94| | 17: 1.42 - 1.39 2785 139 0.86 20.94 1.23 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.44 1.23 0.25 15.81| | 19: 1.36 - 1.34 2807 134 0.86 21.88 1.21 0.25 15.81| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.21 0.24 12.82| | 21: 1.32 - 1.30 2785 112 0.86 21.68 1.20 0.24 12.61| | 22: 1.29 - 1.27 2704 152 0.86 22.11 1.22 0.24 12.34| | 23: 1.27 - 1.26 2802 156 0.86 21.77 1.22 0.24 10.95| | 24: 1.26 - 1.24 2744 132 0.85 22.88 1.21 0.24 10.95| | 25: 1.24 - 1.22 2734 148 0.84 23.43 1.20 0.24 10.29| | 26: 1.22 - 1.21 2727 135 0.85 23.39 1.21 0.24 9.55| | 27: 1.21 - 1.19 2814 148 0.84 24.05 1.21 0.24 9.55| | 28: 1.19 - 1.18 2671 147 0.84 23.97 1.18 0.23 8.58| | 29: 1.18 - 1.16 2800 134 0.84 24.19 1.17 0.23 8.22| | 30: 1.16 - 1.15 2740 148 0.83 25.56 1.16 0.23 8.22| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.22 max = 1476.95 mean = 213.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.31| |phase err.(test): min = 0.00 max = 89.65 mean = 22.11| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.275 1557 Z= 5.637 Angle : 5.171 17.906 2118 Z= 3.655 Chirality : 0.401 1.053 243 Planarity : 0.032 0.108 284 Dihedral : 14.076 82.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 34.59 % 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: -2.43 (0.46), residues: 224 helix: -2.39 (0.38), residues: 102 sheet: -0.74 (0.75), residues: 38 loop : -0.61 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.016 ARG A 156 TYR 0.061 0.025 TYR A 141 PHE 0.151 0.039 PHE A 119 HIS 0.088 0.044 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= 0.2611 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787888 | | target function (ml) not normalized (work): 232247.785032 | | target function (ml) not normalized (free): 11796.000060 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1982 0.1987 0.1927 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2005 0.2010 0.1938 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1751 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1751 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 0.3808 386.593 359.511 0.733 0.914 0.402 11.894-9.307 99.02 97 4 0.1872 614.084 595.938 1.018 0.916 0.380 9.237-7.194 100.00 213 7 0.2152 502.245 490.236 1.051 0.916 0.370 7.162-5.571 100.00 427 22 0.2198 376.907 364.878 1.024 0.917 0.340 5.546-4.326 100.00 867 58 0.1295 517.400 510.968 1.048 0.918 0.218 4.315-3.360 100.00 1859 96 0.1132 492.051 487.966 1.096 0.919 0.189 3.356-2.611 100.00 3867 181 0.1460 323.252 319.743 1.084 0.921 0.089 2.608-2.026 99.99 8198 413 0.1349 214.287 212.111 1.091 0.924 0.000 2.025-1.573 100.00 17313 902 0.1646 104.646 104.102 1.090 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.405 45.082 1.066 0.937 0.000 1.221-1.150 99.97 13689 708 0.2586 29.238 27.005 1.031 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0430 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1751 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1639 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.646446 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.874566 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 0.1685 0.1812 0.0126 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1568 0.1711 0.0143 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1460 0.1623 0.0163 0.001 0.4 3.8 0.0 0.0 0 0.500 0.1385 0.1575 0.0190 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1353 0.1548 0.0195 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1360 0.1561 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1295 0.1515 0.0220 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1265 0.1493 0.0228 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1257 0.1490 0.0233 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1248 0.1484 0.0235 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1243 0.1480 0.0237 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1239 0.1477 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1475 0.0241 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1471 0.0241 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1229 0.1470 0.0241 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1227 0.1475 0.0248 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1223 0.1470 0.0246 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1224 0.1474 0.0250 0.008 1.0 4.5 0.5 0.6 0 13.323 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1223 0.1470 0.0246 0.007 0.9 4.5 0.5 0.6 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 14.70 2.46 3.013 19.046 2021.875 0.017 12.23 14.69 2.46 2.989 19.046 60.656 0.017 12.30 14.67 2.37 2.666 19.046 252.734 0.017 12.71 15.38 2.67 2.950 19.373 1010.937 0.016 12.47 15.41 2.94 3.156 19.523 2021.875 0.016 12.40 15.40 3.00 3.328 19.637 3032.812 0.015 12.21 15.26 3.06 2.944 19.396 4043.749 0.015 12.16 15.31 3.15 3.323 19.628 5054.686 0.015 12.20 15.39 3.19 3.356 19.619 6065.624 0.015 12.16 15.38 3.22 3.386 19.632 7076.561 0.015 12.16 15.41 3.26 3.414 19.634 8087.498 0.015 12.15 15.46 3.31 3.534 19.689 9098.436 0.015 12.18 15.55 3.37 3.627 19.714 10109.373 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.734 Accepted refinement result: 12.30 14.67 2.37 2.666 19.046 252.734 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.07 3.31 0 1785 Protein: 9.06 114.96 16.98 3.31 0 1519 Water: 11.47 119.43 38.21 N/A 0 258 Other: 19.72 26.59 22.05 N/A 0 8 Chain A: 9.06 119.43 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.24 42 64.24 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1467 r_work=0.1232 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1471 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 = 0.1228 r_free = 0.1466 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1228 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016914 | | target function (ls_wunit_k1) not normalized (work): 1408.915473 | | target function (ls_wunit_k1) not normalized (free): 111.322591 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1466 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1674 0.1675 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1674 0.1675 0.1694 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1681 0.1682 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1226 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1237 0.1226 0.1457 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 0.3612 301.389 283.083 0.643 1.002 0.378 11.894-9.307 99.02 97 4 0.1729 482.808 469.060 0.919 1.003 0.368 9.237-7.194 100.00 213 7 0.1885 394.878 389.116 0.962 1.003 0.360 7.162-5.571 100.00 427 22 0.1846 296.334 290.032 0.935 1.003 0.263 5.546-4.326 100.00 867 58 0.1006 406.793 403.621 0.961 1.003 0.204 4.315-3.360 100.00 1859 96 0.0867 386.863 385.785 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1174 254.149 253.040 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1019 168.478 167.789 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1107 82.276 82.471 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.484 35.989 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.988 21.465 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0573 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1457 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1227 r_free=0.1458 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1458 | n_water=258 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1236 r_free=0.1456 | n_water=251 | time (s): 22.180 (total time: 24.000) Filter (q & B) r_work=0.1238 r_free=0.1457 | n_water=248 | time (s): 2.660 (total time: 26.660) Compute maps r_work=0.1238 r_free=0.1457 | n_water=248 | time (s): 1.520 (total time: 28.180) Filter (map) r_work=0.1255 r_free=0.1459 | n_water=225 | time (s): 2.880 (total time: 31.060) Find peaks r_work=0.1255 r_free=0.1459 | n_water=225 | time (s): 0.590 (total time: 31.650) Add new water r_work=0.1405 r_free=0.1640 | n_water=437 | time (s): 2.610 (total time: 34.260) Refine new water occ: r_work=0.1310 r_free=0.1485 adp: r_work=0.1225 r_free=0.1432 occ: r_work=0.1238 r_free=0.1412 adp: r_work=0.1204 r_free=0.1400 occ: r_work=0.1207 r_free=0.1383 adp: r_work=0.1196 r_free=0.1382 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1382 r_work=0.1196 r_free=0.1382 | n_water=437 | time (s): 62.840 (total time: 97.100) Filter (q & B) r_work=0.1200 r_free=0.1390 | n_water=418 | time (s): 3.000 (total time: 100.100) Filter (dist only) r_work=0.1200 r_free=0.1388 | n_water=417 | time (s): 36.250 (total time: 136.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.615365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1481.872150 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 0.1671 0.1777 0.0106 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1522 0.1652 0.0129 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1402 0.1556 0.0154 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1354 0.1524 0.0170 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1317 0.1500 0.0183 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1311 0.1494 0.0183 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1261 0.1469 0.0208 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1230 0.1440 0.0210 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1219 0.1437 0.0218 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1213 0.1430 0.0217 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1208 0.1430 0.0222 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1202 0.1422 0.0220 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1201 0.1426 0.0225 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1197 0.1419 0.0222 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1195 0.1420 0.0225 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1192 0.1428 0.0236 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1191 0.1421 0.0231 0.007 0.9 5.8 0.5 0.6 0 12.000 0.1188 0.1421 0.0233 0.008 0.9 5.8 0.5 0.6 0 13.808 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1419 0.0222 0.006 0.8 5.4 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 14.19 2.22 3.772 21.753 1481.872 0.016 11.97 14.19 2.22 3.772 21.753 44.456 0.016 11.97 14.19 2.22 3.772 21.753 185.234 0.016 12.15 14.64 2.49 3.631 21.758 740.936 0.016 12.21 15.00 2.80 3.509 22.127 1481.872 0.015 12.03 14.86 2.83 3.495 21.925 2222.808 0.015 11.90 14.77 2.88 3.518 21.902 2963.744 0.015 11.82 14.74 2.92 3.509 21.943 3704.680 0.014 11.84 14.84 3.00 3.517 22.135 4445.616 0.014 11.78 14.80 3.02 3.525 22.107 5186.553 0.014 11.78 14.84 3.07 3.554 22.170 5927.489 0.014 11.75 14.85 3.10 3.551 22.078 6668.425 0.014 11.76 14.89 3.13 3.598 22.196 7409.361 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: 44.456 Accepted refinement result: 11.97 14.19 2.22 3.772 21.753 44.456 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 22.15 3.31 192 1752 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.51 76.68 40.84 N/A 192 225 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.10 115.00 19.44 N/A 0 1752 Chain S: 14.97 60.00 46.91 N/A 192 0 Histogram: Values Number of atoms 9.10 - 19.69 1261 19.69 - 30.28 241 30.28 - 40.87 172 40.87 - 51.46 122 51.46 - 62.05 125 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=0.1197 r_free=0.1419 r_work=0.1197 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1419 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1415 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1198 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015425 | | target function (ls_wunit_k1) not normalized (work): 1284.847024 | | target function (ls_wunit_k1) not normalized (free): 103.282099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1198 0.1415 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1588 0.1587 0.1632 n_refl.: 87592 remove outliers: r(all,work,free)=0.1588 0.1587 0.1632 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1590 0.1589 0.1633 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1195 0.1412 n_refl.: 87592 remove outliers: r(all,work,free)=0.1204 0.1193 0.1412 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 0.3373 297.293 273.607 0.583 1.003 0.350 11.894-9.307 99.02 97 4 0.1687 482.808 475.007 0.911 1.003 0.337 9.237-7.194 100.00 213 7 0.1706 394.878 393.781 0.982 1.003 0.300 7.162-5.571 100.00 427 22 0.1645 296.334 291.791 0.932 1.003 0.260 5.546-4.326 100.00 867 58 0.0922 406.793 403.465 0.958 1.003 0.200 4.315-3.360 100.00 1859 96 0.0785 386.863 385.924 1.007 1.002 0.190 3.356-2.611 100.00 3867 181 0.1093 254.149 253.417 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1015 168.478 167.938 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.276 82.467 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.484 36.004 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 22.988 21.497 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0180 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1412 | n_water=417 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1193 r_free=0.1412 | n_water=413 | time (s): 36.300 (total time: 37.860) Filter (q & B) r_work=0.1193 r_free=0.1412 | n_water=413 | time (s): 1.040 (total time: 38.900) Compute maps r_work=0.1193 r_free=0.1412 | n_water=413 | time (s): 1.800 (total time: 40.700) Filter (map) r_work=0.1222 r_free=0.1404 | n_water=288 | time (s): 3.450 (total time: 44.150) Find peaks r_work=0.1222 r_free=0.1404 | n_water=288 | time (s): 0.680 (total time: 44.830) Add new water r_work=0.1335 r_free=0.1526 | n_water=458 | time (s): 3.100 (total time: 47.930) Refine new water occ: r_work=0.1249 r_free=0.1439 adp: r_work=0.1251 r_free=0.1440 occ: r_work=0.1229 r_free=0.1414 adp: r_work=0.1228 r_free=0.1416 occ: r_work=0.1213 r_free=0.1394 adp: r_work=0.1208 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1394 r_work=0.1208 r_free=0.1394 | n_water=458 | time (s): 176.410 (total time: 224.340) Filter (q & B) r_work=0.1212 r_free=0.1403 | n_water=426 | time (s): 2.760 (total time: 227.100) Filter (dist only) r_work=0.1212 r_free=0.1401 | n_water=425 | time (s): 37.750 (total time: 264.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.783373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.126424 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1370 0.0136 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1194 0.1338 0.0144 0.003 0.7 3.2 0.5 0.0 0 0.268 0.1176 0.1325 0.0149 0.004 0.8 2.9 0.5 0.0 0 0.535 0.1168 0.1320 0.0152 0.005 0.9 3.2 0.5 0.0 0 0.803 0.1165 0.1318 0.0154 0.006 1.0 2.9 0.5 0.0 0 1.070 0.1162 0.1318 0.0156 0.007 1.0 3.2 0.5 0.0 0 1.338 0.1159 0.1317 0.0158 0.007 1.1 3.2 0.5 0.0 0 1.605 0.1157 0.1315 0.0157 0.008 1.1 3.2 0.5 0.0 0 1.873 0.1165 0.1320 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1315 0.0157 0.008 1.1 3.2 0.5 0.0 0 1.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.15 1.57 3.776 21.190 46.126 3.621 11.57 13.15 1.57 3.776 21.190 1.384 3.621 11.58 13.15 1.57 3.766 21.190 5.766 3.621 11.63 13.26 1.62 3.709 21.176 23.063 3.616 11.64 13.33 1.68 3.728 21.143 46.126 3.614 11.55 13.29 1.74 3.757 21.135 69.190 3.608 11.53 13.27 1.74 3.767 21.126 92.253 3.605 11.49 13.25 1.76 3.781 21.122 115.316 3.601 11.45 13.22 1.77 3.789 21.122 138.379 3.598 11.46 13.28 1.82 3.810 21.103 161.442 3.599 11.46 13.25 1.80 3.820 21.095 184.506 3.598 11.44 13.24 1.80 3.828 21.094 207.569 3.596 11.43 13.23 1.80 3.834 21.095 230.632 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: 5.766 Accepted refinement result: 11.58 13.15 1.57 3.766 21.190 5.766 3.621 Individual atomic B min max mean iso aniso Overall: 9.12 114.89 21.11 3.27 201 1751 Protein: 9.12 114.89 17.03 3.28 0 1519 Water: 11.53 76.69 35.67 N/A 201 224 Other: 19.71 26.59 22.08 N/A 0 8 Chain A: 9.12 114.89 19.43 N/A 0 1751 Chain S: 14.96 60.01 35.74 N/A 201 0 Histogram: Values Number of atoms 9.12 - 19.69 1261 19.69 - 30.27 279 30.27 - 40.85 213 40.85 - 51.42 125 51.42 - 62.00 51 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.73 4 93.73 - 104.31 0 104.31 - 114.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1315 r_work=0.1158 r_free=0.1315 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1315 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1298 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1149 r_free= 0.1298 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612407 | | target function (ml) not normalized (work): 300888.218636 | | target function (ml) not normalized (free): 15830.677636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1149 0.1298 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1496 0.1497 0.1505 n_refl.: 87589 remove outliers: r(all,work,free)=0.1496 0.1497 0.1505 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1496 0.1504 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1291 n_refl.: 87589 remove outliers: r(all,work,free)=0.1149 0.1142 0.1291 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 92.71 84 5 0.3894 297.293 268.618 0.500 1.001 0.330 11.894-9.307 96.08 94 4 0.2145 478.638 463.640 0.879 1.002 0.330 9.237-7.194 98.64 210 7 0.2301 387.359 385.860 0.956 1.003 0.199 7.162-5.571 100.00 427 22 0.2133 296.334 285.072 0.919 1.003 0.180 5.546-4.326 100.00 867 58 0.1123 406.793 401.935 0.962 1.003 0.165 4.315-3.360 100.00 1859 96 0.0936 386.863 384.480 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1129 254.149 252.174 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0931 168.478 167.692 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.276 82.554 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.484 36.063 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.988 21.527 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1291 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=0.1142 r_free=0.1291 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1291 | n_water=425 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1144 r_free=0.1291 | n_water=421 | time (s): 44.010 (total time: 46.510) Filter (q & B) r_work=0.1145 r_free=0.1291 | n_water=420 | time (s): 3.810 (total time: 50.320) Compute maps r_work=0.1145 r_free=0.1291 | n_water=420 | time (s): 1.870 (total time: 52.190) Filter (map) r_work=0.1165 r_free=0.1296 | n_water=321 | time (s): 3.870 (total time: 56.060) Find peaks r_work=0.1165 r_free=0.1296 | n_water=321 | time (s): 0.690 (total time: 56.750) Add new water r_work=0.1235 r_free=0.1359 | n_water=484 | time (s): 3.820 (total time: 60.570) Refine new water occ: r_work=0.1164 r_free=0.1303 adp: r_work=0.1164 r_free=0.1306 occ: r_work=0.1149 r_free=0.1288 adp: r_work=0.1148 r_free=0.1290 occ: r_work=0.1138 r_free=0.1277 adp: r_work=0.1134 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1279 r_work=0.1134 r_free=0.1279 | n_water=484 | time (s): 281.780 (total time: 342.350) Filter (q & B) r_work=0.1139 r_free=0.1282 | n_water=446 | time (s): 3.950 (total time: 346.300) Filter (dist only) r_work=0.1139 r_free=0.1281 | n_water=444 | time (s): 46.890 (total time: 393.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.796047 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.182456 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 0.1207 0.1325 0.0118 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1165 0.1295 0.0130 0.003 0.7 3.2 0.5 0.0 0 0.269 0.1150 0.1290 0.0139 0.005 0.9 3.5 0.5 0.0 0 0.539 0.1144 0.1286 0.0142 0.006 0.9 3.2 0.5 0.0 0 0.808 0.1140 0.1284 0.0144 0.007 1.0 3.5 0.5 0.0 0 1.078 0.1137 0.1285 0.0148 0.007 1.1 3.8 0.5 0.0 0 1.347 0.1135 0.1285 0.0149 0.008 1.1 3.8 0.5 0.0 0 1.616 0.1134 0.1280 0.0146 0.009 1.1 4.2 0.5 0.0 0 1.886 0.1143 0.1285 0.0143 0.006 1.0 3.2 0.5 0.0 0 0.898 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1280 0.0146 0.009 1.1 4.2 0.5 0.0 0 1.886 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.80 1.46 3.762 21.225 45.182 3.604 11.34 12.80 1.46 3.762 21.225 1.355 3.604 11.34 12.80 1.46 3.762 21.225 5.648 3.604 11.36 12.86 1.50 3.701 21.216 22.591 3.598 11.40 12.98 1.58 3.730 21.187 45.182 3.601 11.34 12.94 1.60 3.749 21.173 67.774 3.595 11.29 12.91 1.62 3.761 21.171 90.365 3.590 11.27 12.90 1.63 3.772 21.164 112.956 3.588 11.26 12.91 1.66 3.785 21.159 135.547 3.587 11.25 12.91 1.67 3.799 21.147 158.139 3.585 11.23 12.91 1.68 3.804 21.154 180.730 3.585 11.22 12.90 1.68 3.816 21.145 203.321 3.584 11.21 12.89 1.68 3.820 21.146 225.912 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.648 Accepted refinement result: 11.34 12.80 1.46 3.762 21.225 5.648 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 114.88 21.18 3.27 222 1749 Protein: 9.11 114.88 17.02 3.28 0 1519 Water: 11.52 76.68 35.36 N/A 222 222 Other: 19.70 26.58 22.08 N/A 0 8 Chain A: 9.11 114.88 19.40 N/A 0 1749 Chain S: 14.96 60.01 35.15 N/A 222 0 Histogram: Values Number of atoms 9.11 - 19.69 1261 19.69 - 30.26 292 30.26 - 40.84 220 40.84 - 51.42 126 51.42 - 61.99 49 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.72 4 93.72 - 104.30 0 104.30 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1280 r_work=0.1134 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1280 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1279 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 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= 0.1129 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601486 | | target function (ml) not normalized (work): 299956.982967 | | target function (ml) not normalized (free): 15789.945181 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1129 0.1279 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1478 0.1478 0.1493 n_refl.: 87583 remove outliers: r(all,work,free)=0.1478 0.1478 0.1493 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1477 0.1478 0.1492 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1278 n_refl.: 87583 remove outliers: r(all,work,free)=0.1133 0.1125 0.1278 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3833 293.264 259.831 0.457 1.000 0.291 11.894-9.307 93.14 91 4 0.2307 476.108 460.472 0.855 1.002 0.278 9.237-7.194 98.18 209 7 0.2322 386.352 382.571 0.933 1.002 0.182 7.162-5.571 100.00 427 22 0.2152 296.334 285.681 0.915 1.002 0.170 5.546-4.326 100.00 867 58 0.1124 406.793 402.413 0.964 1.002 0.140 4.315-3.360 100.00 1859 96 0.0917 386.863 384.980 1.005 1.002 0.140 3.356-2.611 100.00 3867 181 0.1089 254.149 252.425 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0905 168.478 167.857 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.276 82.621 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.484 36.087 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.988 21.529 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1278 After: r_work=0.1127 r_free=0.1278 ================================== NQH flips ================================== r_work=0.1127 r_free=0.1278 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=0.1127 r_free=0.1278 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1127 r_free=0.1278 | n_water=444 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1127 r_free=0.1278 | n_water=444 | time (s): 43.330 (total time: 45.800) Filter (q & B) r_work=0.1127 r_free=0.1278 | n_water=444 | time (s): 1.320 (total time: 47.120) Compute maps r_work=0.1127 r_free=0.1278 | n_water=444 | time (s): 1.870 (total time: 48.990) Filter (map) r_work=0.1151 r_free=0.1293 | n_water=350 | time (s): 3.710 (total time: 52.700) Find peaks r_work=0.1151 r_free=0.1293 | n_water=350 | time (s): 0.650 (total time: 53.350) Add new water r_work=0.1201 r_free=0.1353 | n_water=492 | time (s): 3.710 (total time: 57.060) Refine new water occ: r_work=0.1147 r_free=0.1292 adp: r_work=0.1147 r_free=0.1296 occ: r_work=0.1136 r_free=0.1272 adp: r_work=0.1134 r_free=0.1277 occ: r_work=0.1128 r_free=0.1260 adp: r_work=0.1124 r_free=0.1262 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1262 r_work=0.1124 r_free=0.1262 | n_water=492 | time (s): 213.780 (total time: 270.840) Filter (q & B) r_work=0.1131 r_free=0.1268 | n_water=455 | time (s): 4.050 (total time: 274.890) Filter (dist only) r_work=0.1131 r_free=0.1268 | n_water=453 | time (s): 48.090 (total time: 322.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.725530 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.999950 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 0.1314 0.0105 0.004 0.7 4.8 0.0 0.0 0 0.086 0.1164 0.1284 0.0120 0.004 0.8 4.2 0.0 0.0 0 0.259 0.1147 0.1273 0.0127 0.005 1.0 3.8 0.5 0.0 0 0.518 0.1139 0.1269 0.0130 0.006 1.0 3.5 0.5 0.0 0 0.776 0.1136 0.1268 0.0132 0.007 1.1 3.5 0.5 0.0 0 1.035 0.1133 0.1267 0.0134 0.008 1.1 3.5 0.5 0.0 0 1.294 0.1131 0.1268 0.0136 0.009 1.1 3.5 0.5 0.0 0 1.553 0.1131 0.1268 0.0137 0.009 1.1 3.5 0.5 0.0 0 1.812 0.1138 0.1269 0.0131 0.006 1.1 3.5 0.5 0.0 0 0.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1267 0.0134 0.008 1.1 3.5 0.5 0.0 0 1.294 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.67 1.34 3.761 21.264 44.000 3.602 11.33 12.67 1.34 3.761 21.264 1.320 3.602 11.33 12.67 1.34 3.761 21.264 5.500 3.602 11.34 12.72 1.38 3.700 21.257 22.000 3.596 11.39 12.85 1.46 3.728 21.228 44.000 3.599 11.34 12.83 1.49 3.743 21.214 66.000 3.594 11.28 12.78 1.50 3.760 21.212 88.000 3.588 11.25 12.76 1.51 3.768 21.211 110.000 3.586 11.22 12.75 1.53 3.779 21.208 132.000 3.584 11.23 12.79 1.56 3.799 21.194 154.000 3.584 11.22 12.78 1.56 3.811 21.190 176.000 3.583 11.21 12.76 1.55 3.816 21.191 198.000 3.582 11.19 12.76 1.56 3.822 21.191 220.000 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.500 Accepted refinement result: 11.33 12.67 1.34 3.761 21.264 5.500 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 114.87 21.25 3.27 231 1749 Protein: 9.11 114.87 17.02 3.28 0 1519 Water: 11.52 76.68 35.43 N/A 231 222 Other: 19.70 26.58 22.07 N/A 0 8 Chain A: 9.11 114.87 19.40 N/A 0 1749 Chain S: 14.95 60.00 35.29 N/A 231 0 Histogram: Values Number of atoms 9.11 - 19.68 1262 19.68 - 30.26 292 30.26 - 40.84 229 40.84 - 51.41 124 51.41 - 61.99 50 61.99 - 72.57 11 72.57 - 83.14 6 83.14 - 93.72 4 93.72 - 104.30 0 104.30 - 114.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1267 r_work=0.1133 r_free=0.1267 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1267 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1264 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1264 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601142 | | target function (ml) not normalized (work): 299899.515060 | | target function (ml) not normalized (free): 15779.172343 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1329 0.1257 5.6619 5.5543| | 2: 3.57 - 2.84 1.00 2888 124 0.1054 0.1346 5.1336 5.1949| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1184 4.9156 4.9451| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.0991 4.5986 4.6291| | 5: 2.25 - 2.09 1.00 2756 127 0.0855 0.0951 4.5444 4.6019| | 6: 2.09 - 1.97 1.00 2846 113 0.0848 0.1021 4.2476 4.3606| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1114 3.9777 4.0823| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1089 3.8864 3.9864| | 9: 1.79 - 1.72 1.00 2745 138 0.0882 0.1186 3.6499 3.8314| | 10: 1.72 - 1.66 1.00 2831 160 0.0930 0.1190 3.5688 3.7135| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1031 3.4954 3.5672| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1116 3.333 3.4513| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1034 3.3117 3.3897| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1061 3.2429 3.3242| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1229 3.1543 3.2699| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1254 3.1366 3.245| | 17: 1.42 - 1.39 1.00 2785 139 0.1145 0.1286 3.1214 3.222| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1344 3.107 3.2411| | 19: 1.36 - 1.34 1.00 2807 134 0.1269 0.1557 3.116 3.2651| | 20: 1.34 - 1.32 1.00 2696 147 0.1374 0.1474 3.1147 3.1582| | 21: 1.32 - 1.30 1.00 2785 112 0.1481 0.1509 3.1176 3.1016| | 22: 1.29 - 1.27 1.00 2704 152 0.1568 0.1987 3.1264 3.295| | 23: 1.27 - 1.26 1.00 2802 156 0.1650 0.1786 3.1337 3.197| | 24: 1.26 - 1.24 1.00 2744 132 0.1714 0.1834 3.1294 3.2294| | 25: 1.24 - 1.22 1.00 2733 148 0.1889 0.2144 3.1446 3.2543| | 26: 1.22 - 1.21 1.00 2727 135 0.1913 0.1763 3.1498 3.1997| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2184 3.1732 3.164| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2295 3.1674 3.1737| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2394 3.1493 3.231| | 30: 1.16 - 1.15 1.00 2739 148 0.2453 0.2458 3.1449 3.1695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 7.83 1.00 0.97 5197.53| | 2: 3.57 - 2.84 2888 124 0.93 11.84 1.01 0.97 5197.53| | 3: 2.83 - 2.48 2820 163 0.90 15.63 0.99 0.97 4352.21| | 4: 2.47 - 2.25 2825 136 0.92 12.84 1.00 0.98 2172.41| | 5: 2.25 - 2.09 2756 127 0.91 14.88 1.01 0.98 2172.41| | 6: 2.09 - 1.97 2846 113 0.93 12.00 1.02 0.98 1273.19| | 7: 1.97 - 1.87 2787 165 0.95 9.22 1.02 0.98 506.28| | 8: 1.87 - 1.79 2789 144 0.93 12.56 0.99 0.98 506.28| | 9: 1.79 - 1.72 2745 138 0.94 10.05 0.98 0.97 288.54| | 10: 1.72 - 1.66 2831 160 0.94 11.09 0.98 0.97 244.93| | 11: 1.66 - 1.61 2712 147 0.94 11.71 0.98 0.97 234.58| | 12: 1.61 - 1.56 2773 144 0.96 8.87 0.99 0.97 136.96| | 13: 1.56 - 1.52 2745 130 0.95 10.34 1.03 0.97 136.96| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.98 122.86| | 15: 1.48 - 1.45 2738 128 0.95 9.81 1.02 0.98 97.04| | 16: 1.45 - 1.42 2756 161 0.94 11.04 1.02 0.98 97.04| | 17: 1.42 - 1.39 2785 139 0.95 10.87 1.01 0.98 88.63| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.75| | 19: 1.36 - 1.34 2807 134 0.94 11.86 0.99 0.98 83.75| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 79.97| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.70| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.12| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.26| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.94 82.26| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.28| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.52| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.52| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.93 90.43| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.92 91.90| | 30: 1.16 - 1.15 2739 148 0.86 22.12 0.97 0.92 91.90| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.70 max = 5197.53 mean = 817.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.91 mean = 13.30| |phase err.(test): min = 0.00 max = 89.49 mean = 13.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1130 0.1264 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1450 0.1450 0.1468 n_refl.: 87575 remove outliers: r(all,work,free)=0.1450 0.1450 0.1468 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1449 0.1449 0.1468 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1130 0.1266 n_refl.: 87575 remove outliers: r(all,work,free)=0.1135 0.1128 0.1266 n_refl.: 87571 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3932 288.493 259.717 0.460 1.001 0.292 11.894-9.307 91.18 89 4 0.2274 481.704 460.921 0.867 1.002 0.273 9.237-7.194 97.73 208 7 0.2309 385.872 380.746 0.924 1.002 0.184 7.162-5.571 100.00 427 22 0.2126 296.334 285.705 0.914 1.002 0.150 5.546-4.326 100.00 867 58 0.1128 406.793 402.557 0.962 1.002 0.113 4.315-3.360 100.00 1859 96 0.0918 386.863 384.826 1.004 1.002 0.093 3.356-2.611 100.00 3867 181 0.1095 254.149 252.418 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0904 168.478 167.873 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.276 82.624 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.484 36.090 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.988 21.533 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=-0.0114 ================= 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 : 0.2611 0.1926 0.084 5.171 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_weight: 0.1639 0.1751 0.084 5.171 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1223 0.1470 0.007 0.924 9.0 119.5 20.1 258 0.134 1_adp: 0.1230 0.1467 0.007 0.924 9.1 119.4 20.1 258 0.134 1_regHadp: 0.1232 0.1471 0.007 0.924 9.1 119.4 20.1 258 0.134 1_occ: 0.1228 0.1466 0.007 0.924 9.1 119.4 20.1 258 0.134 2_bss: 0.1226 0.1457 0.007 0.924 9.1 119.5 20.1 258 0.134 2_settarget: 0.1226 0.1457 0.007 0.924 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1226 0.1457 0.007 0.934 9.1 119.5 20.1 258 0.134 2_nqh: 0.1227 0.1458 0.007 0.934 9.1 119.5 20.1 258 0.137 2_sol: 0.1200 0.1388 0.007 0.934 9.1 115.0 22.1 417 n/a 2_weight: 0.1200 0.1388 0.007 0.934 9.1 115.0 22.1 417 n/a 2_xyzrec: 0.1197 0.1419 0.006 0.823 9.1 115.0 22.1 417 n/a 2_adp: 0.1197 0.1419 0.006 0.823 9.1 115.0 22.1 417 n/a 2_regHadp: 0.1197 0.1419 0.006 0.823 9.1 115.0 22.1 417 n/a 2_occ: 0.1198 0.1415 0.006 0.823 9.1 115.0 22.1 417 n/a 3_bss: 0.1193 0.1412 0.006 0.823 9.1 115.0 22.2 417 n/a 3_settarget: 0.1193 0.1412 0.006 0.823 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1193 0.1412 0.006 0.822 9.1 115.0 22.2 417 n/a 3_nqh: 0.1193 0.1412 0.006 0.822 9.1 115.0 22.2 417 n/a 3_sol: 0.1212 0.1401 0.006 0.822 9.1 115.0 21.1 425 n/a 3_weight: 0.1212 0.1401 0.006 0.822 9.1 115.0 21.1 425 n/a 3_xyzrec: 0.1157 0.1315 0.008 1.088 9.1 115.0 21.1 425 n/a 3_adp: 0.1158 0.1315 0.008 1.088 9.1 114.9 21.1 425 n/a 3_regHadp: 0.1158 0.1315 0.008 1.088 9.1 114.9 21.1 425 n/a 3_occ: 0.1149 0.1298 0.008 1.088 9.1 114.9 21.1 425 n/a 4_bss: 0.1142 0.1291 0.008 1.088 9.1 114.9 21.1 425 n/a 4_settarget: 0.1142 0.1291 0.008 1.088 9.1 114.9 21.1 425 n/a 4_updatecdl: 0.1142 0.1291 0.008 1.090 9.1 114.9 21.1 425 n/a 4_nqh: 0.1142 0.1291 0.008 1.090 9.1 114.9 21.1 425 n/a 4_sol: 0.1139 0.1281 0.008 1.090 9.1 114.9 21.2 444 n/a 4_weight: 0.1139 0.1281 0.008 1.090 9.1 114.9 21.2 444 n/a 4_xyzrec: 0.1134 0.1280 0.009 1.133 9.1 114.9 21.2 444 n/a 4_adp: 0.1134 0.1280 0.009 1.133 9.1 114.9 21.2 444 n/a 4_regHadp: 0.1134 0.1280 0.009 1.133 9.1 114.9 21.2 444 n/a 4_occ: 0.1129 0.1279 0.009 1.133 9.1 114.9 21.2 444 n/a 5_bss: 0.1125 0.1278 0.009 1.133 9.1 114.9 21.2 444 n/a 5_settarget: 0.1125 0.1278 0.009 1.133 9.1 114.9 21.2 444 n/a 5_updatecdl: 0.1125 0.1278 0.009 1.134 9.1 114.9 21.2 444 n/a 5_setrh: 0.1127 0.1278 0.009 1.134 9.1 114.9 21.2 444 n/a 5_nqh: 0.1127 0.1278 0.009 1.134 9.1 114.9 21.2 444 n/a 5_sol: 0.1131 0.1268 0.009 1.134 9.1 114.9 21.3 453 n/a 5_weight: 0.1131 0.1268 0.009 1.134 9.1 114.9 21.3 453 n/a 5_xyzrec: 0.1133 0.1267 0.008 1.115 9.1 114.9 21.3 453 n/a 5_adp: 0.1133 0.1267 0.008 1.115 9.1 114.9 21.3 453 n/a 5_regHadp: 0.1133 0.1267 0.008 1.115 9.1 114.9 21.3 453 n/a 5_occ: 0.1130 0.1264 0.008 1.115 9.1 114.9 21.3 453 n/a end: 0.1128 0.1266 0.008 1.115 9.1 114.9 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7650209_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7650209_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7200 Refinement macro-cycles (run) : 14114.1200 Write final files (write_after_run_outputs) : 76.9700 Total : 14194.8100 Total CPU time: 3.95 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:16:59 PST -0800 (1735366619.18 s) Start R-work = 0.1639, R-free = 0.1751 Final R-work = 0.1128, R-free = 0.1266 =============================================================================== Job complete usr+sys time: 14357.52 seconds wall clock time: 260 minutes 50.05 seconds (15650.05 seconds total)