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_8831905.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_8831905.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.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: 1.45, per 1000 atoms: 0.43 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: 0.28 Conformation dependent library (CDL) restraints added in 106.0 milliseconds Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 446 0.90 - 1.16: 1198 1.16 - 1.43: 666 1.43 - 1.69: 820 1.69 - 1.96: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.667 -0.130 5.00e-03 4.00e+04 6.81e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.521 1.750 -0.229 1.14e-02 7.69e+03 4.05e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.13e-02 7.83e+03 3.63e+02 bond pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta sigma weight residual 1.459 1.239 0.220 1.21e-02 6.83e+03 3.30e+02 bond pdb=" C SER A 47 " pdb=" O SER A 47 " ideal model delta sigma weight residual 1.236 1.031 0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 3102 4.56 - 9.11: 1867 9.11 - 13.67: 670 13.67 - 18.23: 122 18.23 - 22.79: 16 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.12 135.74 -13.62 1.06e+00 8.90e-01 1.65e+02 angle pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta sigma weight residual 103.52 115.46 -11.94 9.50e-01 1.11e+00 1.58e+02 angle pdb=" O TYR A 141 " pdb=" C TYR A 141 " pdb=" N SER A 142 " ideal model delta sigma weight residual 123.10 137.24 -14.14 1.15e+00 7.56e-01 1.51e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 133.58 -12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.82 133.15 -12.33 1.05e+00 9.07e-01 1.38e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 934 16.33 - 32.65: 116 32.65 - 48.97: 38 48.97 - 65.29: 20 65.29 - 81.62: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.209: 81 0.209 - 0.417: 91 0.417 - 0.626: 42 0.626 - 0.834: 20 0.834 - 1.042: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 142 " pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CB SER A 142 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CB VAL A 146 " pdb=" CA VAL A 146 " pdb=" CG1 VAL A 146 " pdb=" CG2 VAL A 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.153 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.041 2.00e-02 2.50e+03 6.27e-02 1.18e+02 pdb=" CG PHE A 119 " -0.177 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.021 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.91: 8328 2.91 - 3.48: 10416 3.48 - 4.04: 15153 4.04 - 4.60: 21502 Nonbonded interactions: 56665 Sorted by model distance: nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.792 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.836 1.850 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.847 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.858 1.850 ... (remaining 56660 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_8831905_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794496 | | target function (ml) not normalized (work): 232798.252770 | | target function (ml) not normalized (free): 11879.249091 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3023 0.2093 7.0152 4.9403| | 2: 3.57 - 2.84 1.00 2876 122 0.2426 0.1878 4.3546 4.3546| | 3: 2.84 - 2.48 1.00 2833 165 0.2351 0.1695 4.1341 4.1633| | 4: 2.47 - 2.25 1.00 2825 136 0.2366 0.1486 3.8423 3.8551| | 5: 2.25 - 2.09 1.00 2756 127 0.2466 0.1619 3.8027 3.8196| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1857 3.4712 3.612| | 7: 1.97 - 1.87 1.00 2787 165 0.2580 0.1843 3.1454 3.2449| | 8: 1.87 - 1.79 1.00 2789 144 0.2449 0.1910 3.0602 3.1348| | 9: 1.79 - 1.72 1.00 2745 138 0.2383 0.1825 2.8922 2.9833| | 10: 1.72 - 1.66 1.00 2789 158 0.2362 0.1786 2.8149 2.8441| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1940 2.7599 2.8281| | 12: 1.61 - 1.56 1.00 2787 146 0.2568 0.2151 2.6664 2.7039| | 13: 1.56 - 1.52 1.00 2745 130 0.2538 0.1981 2.5845 2.6558| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.1906 2.5171 2.5575| | 15: 1.48 - 1.45 1.00 2738 128 0.2634 0.2244 2.4488 2.5486| | 16: 1.45 - 1.42 1.00 2756 161 0.2583 0.2293 2.3893 2.4889| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.2296 2.3416 2.4379| | 18: 1.39 - 1.36 1.00 2741 179 0.2682 0.2216 2.2849 2.3345| | 19: 1.36 - 1.34 1.00 2807 134 0.2683 0.2201 2.2554 2.29| | 20: 1.34 - 1.32 1.00 2696 147 0.2723 0.2381 2.2139 2.2549| | 21: 1.32 - 1.30 1.00 2785 112 0.2721 0.2241 2.1564 2.1812| | 22: 1.29 - 1.27 1.00 2704 152 0.2733 0.2330 2.1311 2.1281| | 23: 1.27 - 1.26 1.00 2802 156 0.2755 0.2596 2.1046 2.2047| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2601 2.067 2.2274| | 25: 1.24 - 1.22 1.00 2734 148 0.2834 0.2282 2.0476 2.0257| | 26: 1.22 - 1.21 1.00 2727 135 0.2867 0.2396 2.0104 2.076| | 27: 1.21 - 1.19 1.00 2814 148 0.2969 0.2719 2.007 2.0407| | 28: 1.19 - 1.18 1.00 2671 147 0.3023 0.2687 1.9832 1.9596| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2696 1.9547 1.9849| | 30: 1.16 - 1.15 1.00 2740 148 0.3027 0.2903 1.9249 1.9496| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1497.92| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1497.92| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.24 0.23 1242.12| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 578.27| | 5: 2.25 - 2.09 2756 127 0.77 29.40 1.28 0.25 578.27| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 316.51| | 7: 1.97 - 1.87 2787 165 0.90 16.98 1.29 0.26 93.26| | 8: 1.87 - 1.79 2789 144 0.86 21.26 1.25 0.26 93.26| | 9: 1.79 - 1.72 2745 138 0.88 18.96 1.23 0.25 56.25| | 10: 1.72 - 1.66 2789 158 0.87 20.07 1.21 0.25 48.84| | 11: 1.66 - 1.61 2740 147 0.85 21.59 1.24 0.25 47.24| | 12: 1.61 - 1.56 2787 146 0.88 18.78 1.23 0.25 30.95| | 13: 1.56 - 1.52 2745 130 0.86 20.96 1.23 0.25 30.95| | 14: 1.52 - 1.48 2803 134 0.86 21.30 1.24 0.25 27.76| | 15: 1.48 - 1.45 2738 128 0.86 20.81 1.23 0.25 21.93| | 16: 1.45 - 1.42 2756 161 0.85 22.21 1.22 0.25 21.93| | 17: 1.42 - 1.39 2785 139 0.86 21.70 1.24 0.25 18.74| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.23 0.25 16.89| | 19: 1.36 - 1.34 2807 134 0.85 22.85 1.22 0.25 16.89| | 20: 1.34 - 1.32 2696 147 0.86 21.43 1.21 0.24 13.71| | 21: 1.32 - 1.30 2785 112 0.85 22.97 1.21 0.24 13.48| | 22: 1.29 - 1.27 2704 152 0.85 23.05 1.21 0.24 13.15| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.21 0.24 11.48| | 24: 1.26 - 1.24 2744 132 0.85 23.24 1.21 0.24 11.48| | 25: 1.24 - 1.22 2734 148 0.84 23.79 1.20 0.24 10.72| | 26: 1.22 - 1.21 2727 135 0.84 23.91 1.20 0.23 9.87| | 27: 1.21 - 1.19 2814 148 0.83 24.59 1.21 0.23 9.87| | 28: 1.19 - 1.18 2671 147 0.83 24.94 1.19 0.23 8.94| | 29: 1.18 - 1.16 2800 134 0.83 24.90 1.16 0.23 8.59| | 30: 1.16 - 1.15 2740 148 0.82 26.24 1.15 0.23 8.59| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.59 max = 1497.92 mean = 217.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.87| |phase err.(test): min = 0.00 max = 89.46 mean = 22.79| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.229 1557 Z= 5.677 Angle : 5.295 16.972 2118 Z= 3.642 Chirality : 0.407 1.042 243 Planarity : 0.030 0.077 284 Dihedral : 14.023 81.616 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % 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: -3.07 (0.46), residues: 224 helix: -2.72 (0.37), residues: 103 sheet: -0.98 (0.81), residues: 38 loop : -1.28 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.026 ARG A 156 TYR 0.084 0.045 TYR A 139 PHE 0.154 0.048 PHE A 119 HIS 0.060 0.034 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794496 | | target function (ml) not normalized (work): 232798.252770 | | target function (ml) not normalized (free): 11879.249091 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1971 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1971 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1971 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2008 0.1986 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1639 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1785 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3825 386.507 358.717 0.681 1.003 0.414 11.894-9.307 99.02 97 4 0.1817 613.947 594.136 0.928 1.004 0.386 9.237-7.194 100.00 213 7 0.2164 502.133 491.155 0.957 1.004 0.370 7.162-5.571 100.00 427 22 0.2188 376.823 363.704 0.930 1.004 0.287 5.546-4.326 100.00 867 58 0.1246 517.285 511.902 0.964 1.004 0.228 4.315-3.360 100.00 1859 96 0.1134 491.941 488.173 1.007 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.180 319.388 0.993 1.003 0.052 2.608-2.026 99.99 8198 413 0.1358 214.239 212.192 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1657 104.623 104.099 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2070 46.394 45.045 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2578 29.232 26.967 0.978 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1643 r_free=0.1792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.833758 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.527972 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 0.1647 0.1772 0.0125 0.002 0.5 5.1 0.0 0.0 0 0.125 0.1548 0.1692 0.0144 0.002 0.5 4.5 0.0 0.0 0 0.250 0.1445 0.1609 0.0164 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1384 0.1565 0.0181 0.002 0.5 4.2 0.0 0.0 0 0.750 0.1331 0.1521 0.0190 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1339 0.1531 0.0192 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1289 0.1500 0.0212 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1268 0.1488 0.0220 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1255 0.1483 0.0228 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1244 0.1477 0.0233 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1241 0.1477 0.0236 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1234 0.1468 0.0234 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1234 0.1472 0.0238 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1230 0.1468 0.0239 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1224 0.1463 0.0239 0.006 0.9 2.9 0.5 0.0 0 10.000 0.1229 0.1470 0.0241 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1225 0.1465 0.0240 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1224 0.1469 0.0245 0.008 1.0 4.2 0.5 0.6 0 13.917 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1463 0.0239 0.006 0.9 2.9 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.63 2.39 3.013 19.053 1996.528 0.017 12.24 14.62 2.38 2.989 19.053 59.896 0.017 12.30 14.59 2.29 2.689 19.052 249.566 0.017 12.67 15.29 2.63 2.771 19.244 998.264 0.017 12.52 15.45 2.93 3.175 19.518 1996.528 0.016 12.44 15.49 3.05 3.295 19.599 2994.792 0.015 12.36 15.50 3.14 3.446 19.676 3993.056 0.015 12.28 15.48 3.20 3.378 19.627 4991.320 0.015 12.25 15.49 3.24 3.282 19.571 5989.584 0.015 12.18 15.43 3.26 3.377 19.619 6987.848 0.015 12.22 15.49 3.27 3.315 19.565 7986.112 0.015 12.17 15.46 3.29 3.230 19.505 8984.376 0.015 12.16 15.49 3.32 3.542 19.672 9982.640 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: 249.566 Accepted refinement result: 12.30 14.59 2.29 2.689 19.052 249.566 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.35 0 1785 Protein: 9.07 115.19 16.99 3.36 0 1519 Water: 11.47 119.44 38.22 N/A 0 258 Other: 19.64 26.59 22.03 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1273 20.11 - 31.14 228 31.14 - 42.18 123 42.18 - 53.22 95 53.22 - 64.26 41 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1459 r_work=0.1232 r_free=0.1461 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 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 = 0.1225 r_free = 0.1458 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1225 r_free= 0.1458 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016902 | | target function (ls_wunit_k1) not normalized (work): 1407.867251 | | target function (ls_wunit_k1) not normalized (free): 110.308361 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1225 0.1458 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1669 0.1689 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1674 0.1675 0.1693 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1222 0.1449 n_refl.: 87593 remove outliers: r(all,work,free)=0.1233 0.1222 0.1449 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 96.88 88 5 0.3525 304.234 283.780 0.668 1.002 0.393 11.894-9.307 99.02 97 4 0.1645 483.260 471.150 0.923 1.003 0.380 9.237-7.194 100.00 213 7 0.1914 395.247 389.356 0.963 1.003 0.324 7.162-5.571 100.00 427 22 0.1847 296.611 290.887 0.937 1.003 0.263 5.546-4.326 100.00 867 58 0.1011 407.174 403.857 0.964 1.002 0.204 4.315-3.360 100.00 1859 96 0.0877 387.225 386.065 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1172 254.387 253.198 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.1011 168.635 167.912 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.353 82.567 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.519 36.030 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 23.009 21.495 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0538 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1449 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=0.1222 r_free=0.1449 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1449 | n_water=258 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1231 r_free=0.1443 | n_water=250 | time (s): 21.680 (total time: 23.300) Filter (q & B) r_work=0.1234 r_free=0.1443 | n_water=247 | time (s): 2.750 (total time: 26.050) Compute maps r_work=0.1234 r_free=0.1443 | n_water=247 | time (s): 1.360 (total time: 27.410) Filter (map) r_work=0.1246 r_free=0.1445 | n_water=229 | time (s): 3.170 (total time: 30.580) Find peaks r_work=0.1246 r_free=0.1445 | n_water=229 | time (s): 0.570 (total time: 31.150) Add new water r_work=0.1391 r_free=0.1620 | n_water=435 | time (s): 2.780 (total time: 33.930) Refine new water occ: r_work=0.1304 r_free=0.1481 adp: r_work=0.1218 r_free=0.1428 occ: r_work=0.1232 r_free=0.1412 adp: r_work=0.1197 r_free=0.1397 occ: r_work=0.1200 r_free=0.1385 adp: r_work=0.1192 r_free=0.1384 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1384 r_work=0.1192 r_free=0.1384 | n_water=435 | time (s): 60.370 (total time: 94.300) Filter (q & B) r_work=0.1196 r_free=0.1387 | n_water=420 | time (s): 2.710 (total time: 97.010) Filter (dist only) r_work=0.1196 r_free=0.1385 | n_water=419 | time (s): 33.770 (total time: 130.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.150033 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1471.396135 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 0.1613 0.1734 0.0120 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1526 0.1655 0.0129 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1386 0.1536 0.0150 0.002 0.4 6.4 0.0 0.0 0 0.500 0.1342 0.1502 0.0160 0.001 0.5 5.1 0.0 0.0 0 0.750 0.1323 0.1494 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1308 0.1479 0.0171 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1257 0.1450 0.0193 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1228 0.1432 0.0204 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1217 0.1425 0.0208 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1204 0.1411 0.0207 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1199 0.1413 0.0214 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1194 0.1412 0.0218 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1190 0.1414 0.0224 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1187 0.1414 0.0227 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1185 0.1413 0.0227 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1184 0.1413 0.0228 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1182 0.1404 0.0223 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1179 0.1404 0.0225 0.008 0.9 4.5 0.5 0.6 0 13.000 0.1175 0.1402 0.0227 0.008 0.9 4.5 0.5 0.6 0 14.075 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1175 0.1402 0.0227 0.008 0.9 4.5 0.5 0.6 0 14.075 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 14.02 2.27 3.793 21.783 1471.396 0.015 11.75 14.02 2.27 3.793 21.783 44.142 0.015 11.75 14.02 2.27 3.793 21.783 183.925 0.015 11.91 14.39 2.47 3.644 21.787 735.698 0.015 11.96 14.83 2.87 3.553 21.866 1471.396 0.014 11.86 14.85 3.00 3.459 22.165 2207.094 0.014 11.73 14.75 3.03 3.460 22.175 2942.792 0.014 11.64 14.73 3.09 3.500 21.994 3678.490 0.014 11.62 14.71 3.09 3.485 22.153 4414.188 0.014 11.60 14.74 3.14 3.500 22.170 5149.886 0.013 11.58 14.77 3.19 3.517 22.178 5885.585 0.013 11.57 14.80 3.23 3.533 22.182 6621.283 0.013 11.52 14.76 3.24 3.538 22.155 7356.981 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: 183.925 Accepted refinement result: 11.75 14.02 2.27 3.793 21.783 183.925 0.015 Individual atomic B min max mean iso aniso Overall: 9.11 115.23 22.20 3.35 190 1756 Protein: 9.11 115.23 17.02 3.36 0 1519 Water: 11.51 76.71 40.97 N/A 190 229 Other: 19.68 26.63 22.06 N/A 0 8 Chain A: 9.11 115.23 19.50 N/A 0 1756 Chain S: 13.58 60.00 47.09 N/A 190 0 Histogram: Values Number of atoms 9.11 - 19.72 1261 19.72 - 30.33 245 30.33 - 40.94 160 40.94 - 51.55 139 51.55 - 62.17 119 62.17 - 72.78 11 72.78 - 83.39 5 83.39 - 94.00 4 94.00 - 104.62 0 104.62 - 115.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1175 r_free=0.1402 r_work=0.1175 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1175 r_free = 0.1402 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1395 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1175 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014608 | | target function (ls_wunit_k1) not normalized (work): 1216.783149 | | target function (ls_wunit_k1) not normalized (free): 99.004118 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1175 0.1395 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1576 0.1575 0.1625 n_refl.: 87593 remove outliers: r(all,work,free)=0.1576 0.1575 0.1625 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1578 0.1577 0.1626 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1172 0.1391 n_refl.: 87593 remove outliers: r(all,work,free)=0.1181 0.1170 0.1391 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 0.3333 297.572 277.079 0.613 1.003 0.364 11.894-9.307 99.02 97 4 0.1604 483.260 477.085 0.925 1.003 0.360 9.237-7.194 100.00 213 7 0.1616 395.247 396.350 0.985 1.003 0.259 7.162-5.571 100.00 427 22 0.1576 296.611 292.186 0.938 1.003 0.230 5.546-4.326 100.00 867 58 0.0864 407.174 404.181 0.961 1.003 0.204 4.315-3.360 100.00 1859 96 0.0767 387.225 386.602 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1068 254.387 253.476 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1003 168.635 168.113 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.353 82.586 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1428 36.519 36.067 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2239 23.009 21.524 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0161 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1170 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1170 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1170 r_free=0.1391 | n_water=419 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1171 r_free=0.1391 | n_water=416 | time (s): 34.260 (total time: 36.100) Filter (q & B) r_work=0.1171 r_free=0.1391 | n_water=416 | time (s): 1.030 (total time: 37.130) Compute maps r_work=0.1171 r_free=0.1391 | n_water=416 | time (s): 1.770 (total time: 38.900) Filter (map) r_work=0.1215 r_free=0.1382 | n_water=286 | time (s): 3.070 (total time: 41.970) Find peaks r_work=0.1215 r_free=0.1382 | n_water=286 | time (s): 0.480 (total time: 42.450) Add new water r_work=0.1338 r_free=0.1503 | n_water=473 | time (s): 2.700 (total time: 45.150) Refine new water occ: r_work=0.1241 r_free=0.1429 adp: r_work=0.1242 r_free=0.1429 occ: r_work=0.1217 r_free=0.1411 adp: r_work=0.1215 r_free=0.1410 occ: r_work=0.1198 r_free=0.1399 adp: r_work=0.1192 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1394 r_work=0.1192 r_free=0.1394 | n_water=473 | time (s): 185.550 (total time: 230.700) Filter (q & B) r_work=0.1196 r_free=0.1405 | n_water=444 | time (s): 3.700 (total time: 234.400) Filter (dist only) r_work=0.1196 r_free=0.1404 | n_water=442 | time (s): 37.660 (total time: 272.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.775951 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.262776 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 0.1228 0.1372 0.0144 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1184 0.1342 0.0158 0.003 0.7 3.5 0.5 0.0 0 0.266 0.1170 0.1334 0.0164 0.004 0.8 3.2 0.5 0.0 0 0.533 0.1161 0.1329 0.0168 0.005 0.9 3.2 0.5 0.0 0 0.799 0.1157 0.1327 0.0170 0.006 1.0 2.9 0.5 0.0 0 1.066 0.1154 0.1328 0.0174 0.007 1.0 3.2 0.5 0.0 0 1.332 0.1153 0.1328 0.0175 0.007 1.1 2.9 0.5 0.6 0 1.598 0.1150 0.1327 0.0177 0.008 1.1 3.2 0.5 0.6 0 1.865 0.1159 0.1328 0.0169 0.005 0.9 3.2 0.5 0.0 0 0.888 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1150 0.1327 0.0177 0.008 1.1 3.2 0.5 0.6 0 1.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 13.27 1.77 3.797 21.340 46.263 3.618 11.50 13.27 1.77 3.797 21.340 1.388 3.618 11.51 13.27 1.76 3.782 21.340 5.783 3.618 11.59 13.37 1.78 3.722 21.327 23.131 3.614 11.56 13.41 1.85 3.747 21.308 46.263 3.613 11.54 13.42 1.88 3.759 21.286 69.394 3.609 11.50 13.40 1.90 3.775 21.280 92.526 3.606 11.46 13.38 1.92 3.787 21.277 115.657 3.603 11.44 13.39 1.95 3.799 21.270 138.788 3.601 11.40 13.34 1.94 3.803 21.272 161.920 3.598 11.40 13.37 1.96 3.819 21.259 185.051 3.598 11.40 13.36 1.96 3.830 21.248 208.182 3.597 11.38 13.34 1.96 3.834 21.252 231.314 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.388 Accepted refinement result: 11.50 13.27 1.77 3.797 21.340 1.388 3.618 Individual atomic B min max mean iso aniso Overall: 9.12 115.24 21.38 3.35 220 1749 Protein: 9.12 115.24 17.03 3.36 0 1519 Water: 11.52 76.72 36.31 N/A 220 222 Other: 19.69 26.64 22.07 N/A 0 8 Chain A: 9.12 115.24 19.40 N/A 0 1749 Chain S: 13.59 60.01 37.12 N/A 220 0 Histogram: Values Number of atoms 9.12 - 19.73 1264 19.73 - 30.34 283 30.34 - 40.95 208 40.95 - 51.56 134 51.56 - 62.18 58 62.18 - 72.79 11 72.79 - 83.40 5 83.40 - 94.01 4 94.01 - 104.63 0 104.63 - 115.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1327 r_work=0.1151 r_free=0.1327 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1327 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1324 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1141 r_free= 0.1324 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612083 | | target function (ml) not normalized (work): 300861.189890 | | target function (ml) not normalized (free): 15854.170556 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1141 0.1324 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1476 0.1476 0.1519 n_refl.: 87589 remove outliers: r(all,work,free)=0.1476 0.1476 0.1519 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1475 0.1475 0.1518 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1315 n_refl.: 87589 remove outliers: r(all,work,free)=0.1143 0.1134 0.1315 n_refl.: 87585 ======================== 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 0.3963 292.117 265.229 0.502 1.000 0.330 11.894-9.307 98.04 96 4 0.2153 483.385 469.100 0.889 1.001 0.330 9.237-7.194 99.09 211 7 0.2192 390.355 389.878 0.963 1.001 0.207 7.162-5.571 100.00 427 22 0.2030 296.611 286.228 0.915 1.002 0.175 5.546-4.326 100.00 867 58 0.1100 407.174 402.563 0.967 1.002 0.162 4.315-3.360 100.00 1859 96 0.0932 387.225 384.976 1.005 1.001 0.143 3.356-2.611 100.00 3867 181 0.1131 254.387 252.255 1.008 1.001 0.043 2.608-2.026 99.99 8198 413 0.0929 168.635 167.835 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.353 82.645 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.519 36.108 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2161 23.009 21.554 0.988 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1134 r_free=0.1315 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=0.1134 r_free=0.1315 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1315 | n_water=442 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1134 r_free=0.1316 | n_water=440 | time (s): 48.880 (total time: 51.310) Filter (q & B) r_work=0.1134 r_free=0.1317 | n_water=438 | time (s): 3.920 (total time: 55.230) Compute maps r_work=0.1134 r_free=0.1317 | n_water=438 | time (s): 1.840 (total time: 57.070) Filter (map) r_work=0.1156 r_free=0.1298 | n_water=339 | time (s): 3.770 (total time: 60.840) Find peaks r_work=0.1156 r_free=0.1298 | n_water=339 | time (s): 0.710 (total time: 61.550) Add new water r_work=0.1229 r_free=0.1375 | n_water=503 | time (s): 4.010 (total time: 65.560) Refine new water occ: r_work=0.1159 r_free=0.1325 adp: r_work=0.1159 r_free=0.1326 occ: r_work=0.1143 r_free=0.1309 adp: r_work=0.1142 r_free=0.1310 occ: r_work=0.1132 r_free=0.1296 adp: r_work=0.1128 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1295 r_work=0.1128 r_free=0.1295 | n_water=503 | time (s): 181.480 (total time: 247.040) Filter (q & B) r_work=0.1136 r_free=0.1306 | n_water=466 | time (s): 3.830 (total time: 250.870) Filter (dist only) r_work=0.1142 r_free=0.1304 | n_water=464 | time (s): 47.230 (total time: 298.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.787121 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.711139 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 0.1204 0.1341 0.0137 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1166 0.1315 0.0149 0.003 0.8 3.2 0.5 0.0 0 0.268 0.1154 0.1310 0.0156 0.005 0.9 3.5 0.5 0.0 0 0.536 0.1148 0.1308 0.0160 0.006 0.9 3.5 0.5 0.0 0 0.804 0.1144 0.1306 0.0162 0.006 1.0 3.2 0.5 0.0 0 1.072 0.1141 0.1305 0.0164 0.007 1.1 3.5 0.5 0.6 0 1.340 0.1140 0.1303 0.0163 0.008 1.1 4.2 0.5 0.6 0 1.608 0.1138 0.1302 0.0164 0.009 1.1 4.2 0.5 0.6 0 1.876 0.1146 0.1305 0.0159 0.006 1.0 3.2 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1302 0.0164 0.009 1.1 4.2 0.5 0.6 0 1.876 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 13.02 1.64 3.798 21.312 44.711 3.608 11.38 13.02 1.64 3.798 21.312 1.341 3.608 11.38 13.02 1.64 3.798 21.312 5.589 3.608 11.41 13.06 1.65 3.727 21.305 22.356 3.604 11.45 13.18 1.73 3.748 21.284 44.711 3.606 11.42 13.21 1.79 3.762 21.267 67.067 3.603 11.36 13.18 1.81 3.778 21.265 89.422 3.598 11.32 13.13 1.81 3.786 21.265 111.778 3.594 11.29 13.12 1.83 3.794 21.264 134.133 3.592 11.31 13.19 1.88 3.815 21.249 156.489 3.593 11.30 13.18 1.88 3.824 21.245 178.845 3.592 11.29 13.17 1.88 3.831 21.242 201.200 3.591 11.28 13.16 1.88 3.837 21.241 223.556 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.589 Accepted refinement result: 11.38 13.02 1.64 3.798 21.312 5.589 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 115.23 21.33 3.35 246 1745 Protein: 9.11 115.23 17.03 3.36 0 1519 Water: 11.51 76.71 35.41 N/A 246 218 Other: 19.68 26.63 22.07 N/A 0 8 Chain A: 9.11 115.23 19.35 N/A 0 1745 Chain S: 13.58 60.00 35.38 N/A 246 0 Histogram: Values Number of atoms 9.11 - 19.72 1266 19.72 - 30.33 295 30.33 - 40.95 222 40.95 - 51.56 136 51.56 - 62.17 50 62.17 - 72.78 11 72.78 - 83.40 5 83.40 - 94.01 4 94.01 - 104.62 0 104.62 - 115.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1138 r_free=0.1302 r_work=0.1138 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1302 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1303 target_work(ml) = 3.606 | | 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.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1135 r_free= 0.1303 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606419 | | target function (ml) not normalized (work): 300375.030050 | | target function (ml) not normalized (free): 15829.990816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1135 0.1303 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1467 0.1466 0.1521 n_refl.: 87585 remove outliers: r(all,work,free)=0.1467 0.1466 0.1521 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1466 0.1465 0.1520 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1133 0.1304 n_refl.: 87585 remove outliers: r(all,work,free)=0.1139 0.1131 0.1304 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4095 281.459 249.836 0.447 1.001 0.314 11.894-9.307 97.06 95 4 0.2304 484.588 466.690 0.871 1.002 0.310 9.237-7.194 98.18 209 7 0.2268 386.714 384.763 0.941 1.003 0.170 7.162-5.571 100.00 427 22 0.2077 296.611 286.874 0.907 1.003 0.150 5.546-4.326 100.00 867 58 0.1128 407.174 402.745 0.964 1.003 0.130 4.315-3.360 100.00 1859 96 0.0923 387.225 384.802 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1119 254.387 252.457 1.009 1.002 0.038 2.608-2.026 99.99 8198 413 0.0920 168.635 167.964 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.353 82.667 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.519 36.116 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 23.009 21.555 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0145 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1304 After: r_work=0.1132 r_free=0.1304 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1304 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1136 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1306 | n_water=464 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1136 r_free=0.1306 | n_water=464 | time (s): 47.510 (total time: 50.000) Filter (q & B) r_work=0.1136 r_free=0.1306 | n_water=464 | time (s): 1.400 (total time: 51.400) Compute maps r_work=0.1136 r_free=0.1306 | n_water=464 | time (s): 1.910 (total time: 53.310) Filter (map) r_work=0.1159 r_free=0.1291 | n_water=361 | time (s): 3.960 (total time: 57.270) Find peaks r_work=0.1159 r_free=0.1291 | n_water=361 | time (s): 0.700 (total time: 57.970) Add new water r_work=0.1212 r_free=0.1345 | n_water=510 | time (s): 3.800 (total time: 61.770) Refine new water occ: r_work=0.1154 r_free=0.1296 adp: r_work=0.1155 r_free=0.1298 occ: r_work=0.1143 r_free=0.1285 adp: r_work=0.1141 r_free=0.1286 occ: r_work=0.1134 r_free=0.1277 adp: r_work=0.1131 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1276 r_work=0.1131 r_free=0.1276 | n_water=510 | time (s): 271.540 (total time: 333.310) Filter (q & B) r_work=0.1139 r_free=0.1281 | n_water=466 | time (s): 4.310 (total time: 337.620) Filter (dist only) r_work=0.1139 r_free=0.1280 | n_water=465 | time (s): 49.000 (total time: 386.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.809905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.631451 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 0.1222 0.1332 0.0110 0.004 0.7 6.1 0.0 0.0 0 0.090 0.1175 0.1301 0.0126 0.004 0.8 5.8 0.0 0.6 0 0.271 0.1155 0.1289 0.0133 0.005 0.9 5.1 0.5 0.6 0 0.543 0.1150 0.1286 0.0137 0.006 1.0 5.1 0.5 0.6 0 0.814 0.1144 0.1282 0.0138 0.006 1.0 4.8 0.5 0.6 0 1.086 0.1140 0.1280 0.0140 0.007 1.1 4.8 0.5 0.6 0 1.357 0.1138 0.1279 0.0141 0.008 1.1 4.8 0.5 0.6 0 1.629 0.1136 0.1279 0.0142 0.009 1.2 4.8 0.5 0.6 0 1.900 0.1147 0.1284 0.0137 0.006 1.0 5.1 0.5 0.6 0 0.905 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1279 0.0142 0.009 1.2 4.8 0.5 0.6 0 1.900 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.79 1.42 3.797 21.257 43.631 3.604 11.36 12.79 1.42 3.797 21.257 1.309 3.604 11.37 12.78 1.42 3.787 21.257 5.454 3.604 11.38 12.82 1.44 3.725 21.251 21.816 3.599 11.41 12.92 1.50 3.744 21.231 43.631 3.601 11.37 12.94 1.57 3.761 21.216 65.447 3.597 11.32 12.92 1.60 3.775 21.212 87.263 3.592 11.29 12.90 1.61 3.782 21.211 109.079 3.589 11.27 12.91 1.64 3.794 21.204 130.894 3.588 11.25 12.89 1.64 3.803 21.204 152.710 3.587 11.26 12.93 1.66 3.815 21.196 174.526 3.587 11.25 12.92 1.67 3.824 21.195 196.342 3.586 11.22 12.89 1.67 3.830 21.197 218.157 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: 5.454 Accepted refinement result: 11.37 12.78 1.42 3.787 21.257 5.454 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.11 21.24 3.32 247 1745 Protein: 9.11 115.11 17.02 3.32 0 1519 Water: 11.51 76.70 34.99 N/A 247 218 Other: 19.66 26.59 22.06 N/A 0 8 Chain A: 9.11 115.11 19.34 N/A 0 1745 Chain S: 13.56 60.00 34.60 N/A 247 0 Histogram: Values Number of atoms 9.11 - 19.71 1266 19.71 - 30.31 305 30.31 - 40.91 218 40.91 - 51.51 135 51.51 - 62.11 46 62.11 - 72.71 11 72.71 - 83.31 5 83.31 - 93.91 4 93.91 - 104.51 0 104.51 - 115.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1278 r_work=0.1137 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1279 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1277 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601788 | | target function (ml) not normalized (work): 299967.741716 | | target function (ml) not normalized (free): 15799.590479 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1332 0.1317 5.6536 5.6132| | 2: 3.57 - 2.84 1.00 2888 124 0.1076 0.1349 5.165 5.2004| | 3: 2.83 - 2.48 1.00 2820 163 0.1100 0.1212 4.9392 4.978| | 4: 2.47 - 2.25 1.00 2825 136 0.0910 0.1014 4.6298 4.6667| | 5: 2.25 - 2.09 1.00 2756 127 0.0870 0.0967 4.5756 4.619| | 6: 2.09 - 1.97 1.00 2846 113 0.0862 0.0994 4.2661 4.3616| | 7: 1.97 - 1.87 1.00 2787 165 0.0873 0.1112 3.9719 4.0922| | 8: 1.87 - 1.79 1.00 2789 144 0.0909 0.1088 3.8859 3.9816| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1173 3.6397 3.8105| | 10: 1.72 - 1.66 1.00 2831 160 0.0909 0.1170 3.5601 3.706| | 11: 1.66 - 1.61 1.00 2712 147 0.0861 0.1004 3.489 3.5698| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1152 3.3298 3.4679| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1014 3.304 3.3843| | 14: 1.52 - 1.48 1.00 2803 134 0.0972 0.1039 3.235 3.3281| | 15: 1.48 - 1.45 1.00 2738 128 0.0996 0.1244 3.1517 3.2641| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1257 3.132 3.2397| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1291 3.1169 3.2231| | 18: 1.39 - 1.36 1.00 2741 179 0.1191 0.1317 3.1001 3.2358| | 19: 1.36 - 1.34 1.00 2807 134 0.1253 0.1545 3.1088 3.256| | 20: 1.34 - 1.32 1.00 2696 147 0.1360 0.1482 3.1091 3.166| | 21: 1.32 - 1.30 1.00 2785 112 0.1463 0.1525 3.1114 3.1134| | 22: 1.29 - 1.27 1.00 2704 152 0.1548 0.1973 3.118 3.2939| | 23: 1.27 - 1.26 1.00 2802 156 0.1640 0.1780 3.1324 3.2005| | 24: 1.26 - 1.24 1.00 2744 132 0.1703 0.1821 3.1256 3.2243| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2127 3.1423 3.2575| | 26: 1.22 - 1.21 1.00 2727 135 0.1902 0.1764 3.1465 3.201| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2165 3.1712 3.1615| | 28: 1.19 - 1.18 1.00 2671 147 0.2196 0.2290 3.1651 3.17| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2370 3.1482 3.2255| | 30: 1.16 - 1.15 1.00 2739 148 0.2443 0.2444 3.1433 3.1684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.56 1.00 0.97 5687.81| | 2: 3.57 - 2.84 2888 124 0.93 12.49 1.01 0.97 5687.81| | 3: 2.83 - 2.48 2820 163 0.90 16.45 0.99 0.97 4751.77| | 4: 2.47 - 2.25 2825 136 0.92 13.37 1.00 0.98 2338.01| | 5: 2.25 - 2.09 2756 127 0.90 15.47 1.01 0.98 2338.01| | 6: 2.09 - 1.97 2846 113 0.92 12.32 1.02 0.98 1350.55| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.98 508.37| | 8: 1.87 - 1.79 2789 144 0.93 12.55 1.00 0.98 508.37| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.98 286.87| | 10: 1.72 - 1.66 2831 160 0.94 11.02 0.98 0.98 242.52| | 11: 1.66 - 1.61 2712 147 0.94 11.68 0.98 0.98 232.44| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.97 137.45| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.02 0.97 137.45| | 14: 1.52 - 1.48 2803 134 0.94 10.72 1.02 0.98 123.42| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.98 97.72| | 16: 1.45 - 1.42 2756 161 0.94 11.04 1.02 0.98 97.72| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.98 89.01| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.97| | 19: 1.36 - 1.34 2807 134 0.94 11.87 1.00 0.98 83.97| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.97 80.03| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 79.75| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 80.14| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 82.12| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.95 82.12| | 25: 1.24 - 1.22 2733 148 0.91 16.26 0.96 0.94 84.03| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.03 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.29 1.01 0.93 89.66| | 29: 1.18 - 1.16 2800 134 0.88 20.39 0.99 0.93 90.98| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.93 90.98| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.75 max = 5687.81 mean = 878.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.40| |phase err.(test): min = 0.00 max = 89.38 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1277 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1462 0.1462 0.1481 n_refl.: 87579 remove outliers: r(all,work,free)=0.1462 0.1462 0.1481 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1461 0.1461 0.1480 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1275 n_refl.: 87579 remove outliers: r(all,work,free)=0.1136 0.1129 0.1275 n_refl.: 87573 ======================== 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 0.4154 284.008 240.391 0.429 1.001 0.314 11.894-9.307 92.16 90 4 0.2234 477.438 457.125 0.879 1.003 0.232 9.237-7.194 98.18 209 7 0.2334 386.714 380.569 0.925 1.003 0.160 7.162-5.571 100.00 427 22 0.2064 296.611 286.765 0.906 1.003 0.150 5.546-4.326 100.00 867 58 0.1137 407.174 402.628 0.964 1.003 0.120 4.315-3.360 100.00 1859 96 0.0913 387.225 385.186 1.003 1.003 0.110 3.356-2.611 100.00 3867 181 0.1120 254.387 252.481 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0915 168.635 168.007 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.353 82.700 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.519 36.129 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.009 21.563 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0148 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1971 0.083 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1785 0.083 5.295 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1785 0.083 5.295 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1792 0.083 5.295 9.0 119.5 20.1 258 0.007 1_weight: 0.1643 0.1792 0.083 5.295 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1224 0.1463 0.006 0.897 9.0 119.5 20.1 258 0.129 1_adp: 0.1230 0.1459 0.006 0.897 9.1 119.4 20.1 258 0.129 1_regHadp: 0.1232 0.1461 0.006 0.897 9.1 119.4 20.1 258 0.129 1_occ: 0.1225 0.1458 0.006 0.897 9.1 119.4 20.1 258 0.129 2_bss: 0.1222 0.1449 0.006 0.897 9.1 119.5 20.1 258 0.129 2_settarget: 0.1222 0.1449 0.006 0.897 9.1 119.5 20.1 258 0.129 2_updatecdl: 0.1222 0.1449 0.006 0.900 9.1 119.5 20.1 258 0.129 2_nqh: 0.1222 0.1449 0.006 0.900 9.1 119.5 20.1 258 0.129 2_sol: 0.1196 0.1385 0.006 0.900 9.1 115.2 22.2 419 n/a 2_weight: 0.1196 0.1385 0.006 0.900 9.1 115.2 22.2 419 n/a 2_xyzrec: 0.1175 0.1402 0.008 0.949 9.1 115.2 22.2 419 n/a 2_adp: 0.1175 0.1402 0.008 0.949 9.1 115.2 22.2 419 n/a 2_regHadp: 0.1175 0.1402 0.008 0.949 9.1 115.2 22.2 419 n/a 2_occ: 0.1175 0.1395 0.008 0.949 9.1 115.2 22.2 419 n/a 3_bss: 0.1170 0.1391 0.008 0.949 9.1 115.2 22.2 419 n/a 3_settarget: 0.1170 0.1391 0.008 0.949 9.1 115.2 22.2 419 n/a 3_updatecdl: 0.1170 0.1391 0.008 0.950 9.1 115.2 22.2 419 n/a 3_nqh: 0.1170 0.1391 0.008 0.950 9.1 115.2 22.2 419 n/a 3_sol: 0.1196 0.1404 0.008 0.950 9.1 115.2 21.4 442 n/a 3_weight: 0.1196 0.1404 0.008 0.950 9.1 115.2 21.4 442 n/a 3_xyzrec: 0.1150 0.1327 0.008 1.093 9.1 115.2 21.4 442 n/a 3_adp: 0.1150 0.1327 0.008 1.093 9.1 115.2 21.4 442 n/a 3_regHadp: 0.1151 0.1327 0.008 1.093 9.1 115.2 21.4 442 n/a 3_occ: 0.1141 0.1324 0.008 1.093 9.1 115.2 21.4 442 n/a 4_bss: 0.1134 0.1315 0.008 1.093 9.1 115.2 21.4 442 n/a 4_settarget: 0.1134 0.1315 0.008 1.093 9.1 115.2 21.4 442 n/a 4_updatecdl: 0.1134 0.1315 0.008 1.093 9.1 115.2 21.4 442 n/a 4_nqh: 0.1134 0.1315 0.008 1.093 9.1 115.2 21.4 442 n/a 4_sol: 0.1142 0.1304 0.008 1.093 9.1 115.2 21.3 464 n/a 4_weight: 0.1142 0.1304 0.008 1.093 9.1 115.2 21.3 464 n/a 4_xyzrec: 0.1138 0.1302 0.009 1.127 9.1 115.2 21.3 464 n/a 4_adp: 0.1138 0.1302 0.009 1.127 9.1 115.2 21.3 464 n/a 4_regHadp: 0.1138 0.1302 0.009 1.127 9.1 115.2 21.3 464 n/a 4_occ: 0.1135 0.1303 0.009 1.127 9.1 115.2 21.3 464 n/a 5_bss: 0.1131 0.1304 0.009 1.127 9.1 115.2 21.3 464 n/a 5_settarget: 0.1131 0.1304 0.009 1.127 9.1 115.2 21.3 464 n/a 5_updatecdl: 0.1131 0.1304 0.009 1.128 9.1 115.2 21.3 464 n/a 5_setrh: 0.1132 0.1304 0.009 1.128 9.1 115.2 21.3 464 n/a 5_nqh: 0.1136 0.1306 0.009 1.128 9.1 115.2 21.3 464 n/a 5_sol: 0.1139 0.1280 0.009 1.128 9.1 115.2 21.2 465 n/a 5_weight: 0.1139 0.1280 0.009 1.128 9.1 115.2 21.2 465 n/a 5_xyzrec: 0.1136 0.1279 0.009 1.172 9.1 115.2 21.2 465 n/a 5_adp: 0.1137 0.1278 0.009 1.172 9.1 115.1 21.2 465 n/a 5_regHadp: 0.1137 0.1279 0.009 1.172 9.1 115.1 21.2 465 n/a 5_occ: 0.1132 0.1277 0.009 1.172 9.1 115.1 21.2 465 n/a end: 0.1129 0.1275 0.009 1.172 9.1 115.1 21.2 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8831905_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8831905_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7900 Refinement macro-cycles (run) : 14369.1700 Write final files (write_after_run_outputs) : 73.1000 Total : 14446.0600 Total CPU time: 4.02 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:28 PST -0800 (1735366828.57 s) Start R-work = 0.1638, R-free = 0.1785 Final R-work = 0.1129, R-free = 0.1275 =============================================================================== Job complete usr+sys time: 14584.36 seconds wall clock time: 263 minutes 57.73 seconds (15837.73 seconds total)