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_5431713.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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 3 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: 1.51, per 1000 atoms: 0.45 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 136.7 milliseconds Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 481 0.90 - 1.16: 1143 1.16 - 1.41: 623 1.41 - 1.67: 871 1.67 - 1.92: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 8 " pdb=" O VAL A 8 " ideal model delta sigma weight residual 1.237 1.004 0.233 1.08e-02 8.57e+03 4.67e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.706 -0.247 1.20e-02 6.94e+03 4.23e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.526 -0.205 1.00e-02 1.00e+04 4.20e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.123 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.460 1.266 0.194 1.10e-02 8.26e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3189 4.76 - 9.52: 1851 9.52 - 14.29: 626 14.29 - 19.05: 104 19.05 - 23.81: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BASN A 97 " pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 122.12 137.77 -15.65 1.06e+00 8.90e-01 2.18e+02 angle pdb=" N MET A 26 " pdb=" CA MET A 26 " pdb=" C MET A 26 " ideal model delta sigma weight residual 111.28 125.26 -13.98 1.09e+00 8.42e-01 1.64e+02 angle pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" O LEU A 101 " ideal model delta sigma weight residual 121.05 135.61 -14.56 1.14e+00 7.69e-01 1.63e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 111.03 8.26 6.50e-01 2.37e+00 1.62e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.43 -10.20 8.10e-01 1.52e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 935 17.00 - 34.00: 119 34.00 - 51.00: 40 51.00 - 68.00: 16 68.00 - 85.00: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.239: 107 0.239 - 0.476: 85 0.476 - 0.712: 34 0.712 - 0.949: 14 0.949 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA ASP A 55 " pdb=" N ASP A 55 " pdb=" C ASP A 55 " pdb=" CB ASP A 55 " both_signs ideal model delta sigma weight residual False 2.51 3.50 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.003 2.00e-02 2.50e+03 6.39e-02 1.23e+02 pdb=" CG ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.124 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.132 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.032 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.021 2.00e-02 2.50e+03 5.13e-02 7.88e+01 pdb=" CG PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1083 2.33 - 2.90: 8181 2.90 - 3.46: 10442 3.46 - 4.03: 15295 4.03 - 4.60: 21653 Nonbonded interactions: 56654 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.759 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.794 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 1.850 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.839 1.850 ... (remaining 56649 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_5431713_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789921 | | target function (ml) not normalized (work): 232417.117616 | | target function (ml) not normalized (free): 11754.765529 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3019 0.2068 7.0713 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1746 4.3468 4.3305| | 3: 2.84 - 2.48 1.00 2833 165 0.2354 0.1621 4.1284 4.1435| | 4: 2.47 - 2.25 1.00 2825 136 0.2318 0.1395 3.8294 3.8196| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1522 3.7975 3.8208| | 6: 2.09 - 1.97 1.00 2846 113 0.2576 0.1924 3.4525 3.556| | 7: 1.97 - 1.87 1.00 2787 165 0.2536 0.1834 3.1264 3.2336| | 8: 1.87 - 1.79 1.00 2789 144 0.2514 0.1890 3.0761 3.1099| | 9: 1.79 - 1.72 1.00 2745 138 0.2417 0.1839 2.9133 2.9507| | 10: 1.72 - 1.66 1.00 2789 158 0.2457 0.1957 2.8133 2.9293| | 11: 1.66 - 1.61 1.00 2740 147 0.2451 0.1655 2.7486 2.7321| | 12: 1.61 - 1.56 1.00 2787 146 0.2532 0.1802 2.629 2.571| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1851 2.546 2.5733| | 14: 1.52 - 1.48 1.00 2803 134 0.2558 0.2099 2.4861 2.5753| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.1891 2.415 2.4317| | 16: 1.45 - 1.42 1.00 2756 161 0.2635 0.1982 2.3799 2.3806| | 17: 1.42 - 1.39 1.00 2785 139 0.2701 0.2124 2.3411 2.3793| | 18: 1.39 - 1.36 1.00 2741 179 0.2715 0.2242 2.2745 2.3336| | 19: 1.36 - 1.34 1.00 2807 134 0.2629 0.2152 2.238 2.2853| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2129 2.2027 2.1826| | 21: 1.32 - 1.30 1.00 2785 112 0.2691 0.1981 2.1762 2.0672| | 22: 1.29 - 1.27 1.00 2704 152 0.2740 0.2486 2.1403 2.1873| | 23: 1.27 - 1.26 1.00 2802 156 0.2831 0.2375 2.098 2.1705| | 24: 1.26 - 1.24 1.00 2744 132 0.2844 0.2324 2.0776 2.0903| | 25: 1.24 - 1.22 1.00 2734 148 0.2889 0.2597 2.0503 2.0507| | 26: 1.22 - 1.21 1.00 2727 135 0.2882 0.2319 2.0183 2.087| | 27: 1.21 - 1.19 1.00 2814 148 0.2923 0.2864 1.9981 2.0828| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2737 1.9826 1.9603| | 29: 1.18 - 1.16 1.00 2800 134 0.2966 0.2698 1.9544 2.0017| | 30: 1.16 - 1.15 1.00 2740 148 0.3078 0.2717 1.9302 1.9176| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.79 0.76 0.23 1474.03| | 2: 3.57 - 2.84 2876 122 0.81 25.97 1.27 0.23 1474.03| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.24 1223.05| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.26 0.25 571.69| | 5: 2.25 - 2.09 2756 127 0.77 29.22 1.28 0.25 571.69| | 6: 2.09 - 1.97 2846 113 0.83 22.91 1.30 0.25 313.70| | 7: 1.97 - 1.87 2787 165 0.90 16.84 1.28 0.26 93.67| | 8: 1.87 - 1.79 2789 144 0.85 21.34 1.25 0.26 93.67| | 9: 1.79 - 1.72 2745 138 0.88 18.43 1.23 0.26 55.28| | 10: 1.72 - 1.66 2789 158 0.87 19.72 1.23 0.26 47.59| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.23 0.26 45.82| | 12: 1.61 - 1.56 2787 146 0.89 17.95 1.23 0.25 27.84| | 13: 1.56 - 1.52 2745 130 0.87 19.86 1.23 0.25 27.84| | 14: 1.52 - 1.48 2803 134 0.87 19.93 1.24 0.25 24.76| | 15: 1.48 - 1.45 2738 128 0.88 19.18 1.24 0.25 19.12| | 16: 1.45 - 1.42 2756 161 0.86 20.75 1.23 0.25 19.12| | 17: 1.42 - 1.39 2785 139 0.88 19.80 1.23 0.25 16.32| | 18: 1.39 - 1.36 2741 179 0.87 20.16 1.24 0.25 14.70| | 19: 1.36 - 1.34 2807 134 0.86 21.12 1.21 0.25 14.70| | 20: 1.34 - 1.32 2696 147 0.88 19.94 1.21 0.25 12.21| | 21: 1.32 - 1.30 2785 112 0.87 20.82 1.19 0.25 12.03| | 22: 1.29 - 1.27 2704 152 0.86 21.58 1.20 0.25 11.80| | 23: 1.27 - 1.26 2802 156 0.86 21.72 1.23 0.24 10.65| | 24: 1.26 - 1.24 2744 132 0.86 22.06 1.22 0.24 10.65| | 25: 1.24 - 1.22 2734 148 0.85 22.85 1.21 0.24 10.12| | 26: 1.22 - 1.21 2727 135 0.85 23.14 1.20 0.24 9.53| | 27: 1.21 - 1.19 2814 148 0.84 23.84 1.20 0.24 9.53| | 28: 1.19 - 1.18 2671 147 0.84 24.34 1.19 0.23 8.68| | 29: 1.18 - 1.16 2800 134 0.84 24.23 1.16 0.23 8.36| | 30: 1.16 - 1.15 2740 148 0.82 25.94 1.16 0.23 8.36| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 8.36 max = 1474.03 mean = 213.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.03| |phase err.(test): min = 0.00 max = 89.73 mean = 21.97| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 1557 Z= 5.412 Angle : 5.242 17.749 2118 Z= 3.615 Chirality : 0.385 1.185 243 Planarity : 0.031 0.077 284 Dihedral : 13.529 84.996 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 29.19 % 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: -3.03 (0.46), residues: 224 helix: -3.13 (0.35), residues: 102 sheet: -0.48 (0.95), residues: 28 loop : -0.87 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.017 ARG A 27 TYR 0.110 0.034 TYR A 141 PHE 0.102 0.042 PHE A 162 HIS 0.067 0.029 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= 0.2608 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789921 | | target function (ml) not normalized (work): 232417.117616 | | target function (ml) not normalized (free): 11754.765529 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2609 0.1905 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2609 0.1905 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1905 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2001 0.2007 0.1919 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1632 0.1735 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1630 0.1735 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3820 386.475 356.575 0.666 1.002 0.401 11.894-9.307 98.04 96 4 0.1716 616.389 589.810 0.916 1.003 0.380 9.237-7.194 100.00 213 7 0.2134 502.092 491.291 0.956 1.004 0.340 7.162-5.571 100.00 427 22 0.2188 376.792 365.014 0.933 1.004 0.320 5.546-4.326 100.00 867 58 0.1289 517.243 511.756 0.960 1.004 0.225 4.315-3.360 100.00 1859 96 0.1115 491.902 488.121 1.001 1.003 0.209 3.356-2.611 100.00 3867 181 0.1448 323.154 320.338 0.997 1.003 0.119 2.608-2.026 99.99 8198 413 0.1324 214.222 212.164 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1656 104.615 104.048 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.390 45.018 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2589 29.229 26.958 0.976 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0475 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1735 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** A 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1635 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.490367 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2047.957730 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 0.1752 0.1857 0.0104 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1545 0.1677 0.0132 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1449 0.1607 0.0159 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1386 0.1570 0.0185 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1359 0.1557 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1346 0.1547 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1295 0.1510 0.0215 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1279 0.1503 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1266 0.1496 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1254 0.1481 0.0228 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1245 0.1475 0.0230 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1243 0.1474 0.0230 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1237 0.1469 0.0232 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1235 0.1467 0.0232 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1232 0.1467 0.0235 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1229 0.1464 0.0235 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1227 0.1465 0.0238 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1226 0.1473 0.0248 0.008 1.0 3.5 0.5 0.6 0 13.245 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1464 0.0235 0.007 0.9 3.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.64 2.35 3.013 19.066 2047.958 0.017 12.29 14.63 2.34 2.989 19.066 61.439 0.017 12.36 14.59 2.23 2.657 19.066 255.995 0.017 12.66 15.20 2.54 2.743 19.243 1023.979 0.016 12.44 15.30 2.86 3.128 19.542 2047.958 0.015 12.41 15.38 2.97 3.354 19.680 3071.937 0.015 12.35 15.38 3.03 3.384 19.681 4095.915 0.015 12.22 15.27 3.05 3.268 19.619 5119.894 0.015 12.21 15.33 3.12 3.432 19.701 6143.873 0.015 12.16 15.29 3.13 3.374 19.665 7167.852 0.015 12.18 15.38 3.20 3.306 19.611 8191.831 0.015 12.16 15.36 3.20 3.440 19.681 9215.810 0.015 12.18 15.43 3.26 3.507 19.708 10239.789 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: 255.995 Accepted refinement result: 12.36 14.59 2.23 2.657 19.066 255.995 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.09 3.29 0 1785 Protein: 9.08 114.88 17.00 3.29 0 1519 Water: 11.48 119.45 38.23 N/A 0 258 Other: 19.75 26.62 22.08 N/A 0 8 Chain A: 9.08 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1271 20.12 - 31.16 228 31.16 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1459 r_work=0.1237 r_free=0.1463 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1463 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 = 0.1231 r_free = 0.1456 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1231 r_free= 0.1456 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016695 | | target function (ls_wunit_k1) not normalized (work): 1390.640643 | | target function (ls_wunit_k1) not normalized (free): 108.805717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1456 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1674 0.1675 0.1692 n_refl.: 87592 remove outliers: r(all,work,free)=0.1674 0.1675 0.1692 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1679 0.1681 0.1696 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1229 0.1450 n_refl.: 87592 remove outliers: r(all,work,free)=0.1238 0.1228 0.1450 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3438 302.815 279.977 0.632 1.003 0.370 11.894-9.307 98.04 96 4 0.1611 483.843 471.926 0.927 1.003 0.363 9.237-7.194 100.00 213 7 0.1884 394.125 388.346 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1819 295.769 289.874 0.940 1.003 0.290 5.546-4.326 100.00 867 58 0.1001 406.017 403.050 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0864 386.125 385.075 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1173 253.664 252.549 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1025 168.156 167.461 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.119 82.324 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.415 35.921 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.944 21.431 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0460 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1450 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1226 r_free=0.1448 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1448 | n_water=258 | time (s): 1.510 (total time: 1.510) Filter (dist) r_work=0.1235 r_free=0.1447 | n_water=251 | time (s): 22.380 (total time: 23.890) Filter (q & B) r_work=0.1237 r_free=0.1447 | n_water=248 | time (s): 2.480 (total time: 26.370) Compute maps r_work=0.1237 r_free=0.1447 | n_water=248 | time (s): 1.320 (total time: 27.690) Filter (map) r_work=0.1250 r_free=0.1450 | n_water=227 | time (s): 2.450 (total time: 30.140) Find peaks r_work=0.1250 r_free=0.1450 | n_water=227 | time (s): 0.460 (total time: 30.600) Add new water r_work=0.1396 r_free=0.1624 | n_water=428 | time (s): 2.670 (total time: 33.270) Refine new water occ: r_work=0.1301 r_free=0.1488 adp: r_work=0.1222 r_free=0.1433 occ: r_work=0.1234 r_free=0.1422 adp: r_work=0.1201 r_free=0.1405 occ: r_work=0.1203 r_free=0.1400 adp: r_work=0.1194 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1397 r_work=0.1194 r_free=0.1397 | n_water=428 | time (s): 54.210 (total time: 87.480) Filter (q & B) r_work=0.1197 r_free=0.1403 | n_water=414 | time (s): 2.690 (total time: 90.170) Filter (dist only) r_work=0.1197 r_free=0.1402 | n_water=413 | time (s): 32.390 (total time: 122.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.205182 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.669754 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 0.1605 0.1729 0.0124 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1549 0.1678 0.0129 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1412 0.1568 0.0156 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1363 0.1534 0.0171 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1319 0.1498 0.0179 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1317 0.1497 0.0180 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1266 0.1464 0.0198 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1234 0.1440 0.0206 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1221 0.1434 0.0213 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1216 0.1430 0.0214 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1208 0.1422 0.0215 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1202 0.1418 0.0217 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1201 0.1420 0.0219 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1197 0.1415 0.0218 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1192 0.1417 0.0224 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1191 0.1417 0.0226 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1191 0.1419 0.0228 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1187 0.1416 0.0228 0.007 0.9 5.4 0.5 0.6 0 13.000 0.1185 0.1417 0.0232 0.008 0.9 6.1 0.5 0.6 0 14.103 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1415 0.0218 0.006 0.8 6.1 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 14.15 2.18 3.766 21.716 1485.670 0.016 11.97 14.15 2.18 3.766 21.716 44.570 0.016 11.97 14.15 2.18 3.766 21.716 185.709 0.016 12.15 14.61 2.46 3.627 21.717 742.835 0.016 12.14 14.95 2.81 3.465 21.896 1485.670 0.015 12.03 14.99 2.96 3.501 21.848 2228.505 0.015 11.89 14.81 2.92 3.467 22.002 2971.340 0.014 11.77 14.81 3.04 3.526 21.849 3714.174 0.014 11.79 14.79 2.99 3.509 21.984 4457.009 0.014 11.79 14.84 3.05 3.535 22.031 5199.844 0.014 11.73 14.84 3.11 3.530 21.956 5942.679 0.014 11.68 14.77 3.09 3.550 21.996 6685.514 0.014 11.73 14.88 3.15 3.593 22.106 7428.349 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: 44.570 Accepted refinement result: 11.97 14.15 2.18 3.766 21.716 44.570 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 22.07 3.29 186 1754 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.51 76.69 40.60 N/A 186 227 Other: 19.78 26.65 22.11 N/A 0 8 Chain A: 9.11 114.91 19.48 N/A 0 1754 Chain S: 13.84 60.00 46.49 N/A 186 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.27 245 30.27 - 40.85 165 40.85 - 51.43 129 51.43 - 62.01 116 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1415 r_work=0.1197 r_free=0.1415 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1415 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 = 0.1194 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1194 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015168 | | target function (ls_wunit_k1) not normalized (work): 1263.433392 | | target function (ls_wunit_k1) not normalized (free): 103.697605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1194 0.1412 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1545 0.1543 0.1602 n_refl.: 87590 remove outliers: r(all,work,free)=0.1545 0.1543 0.1602 n_refl.: 87590 overall B=0.01 to atoms: r(all,work,free)=0.1546 0.1544 0.1603 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1190 0.1407 n_refl.: 87590 remove outliers: r(all,work,free)=0.1200 0.1189 0.1407 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 93.75 85 5 0.3389 299.694 283.091 0.600 1.003 0.350 11.894-9.307 98.04 96 4 0.1581 483.843 477.228 0.924 1.003 0.350 9.237-7.194 100.00 213 7 0.1726 394.125 393.513 0.983 1.003 0.290 7.162-5.571 100.00 427 22 0.1599 295.769 290.561 0.935 1.003 0.240 5.546-4.326 100.00 867 58 0.0902 406.017 402.681 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0781 386.125 384.980 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1085 253.664 252.746 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.1014 168.156 167.609 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.119 82.314 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.415 35.936 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2254 22.944 21.457 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1407 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1407 | n_water=413 | time (s): 2.110 (total time: 2.110) Filter (dist) r_work=0.1189 r_free=0.1407 | n_water=410 | time (s): 33.060 (total time: 35.170) Filter (q & B) r_work=0.1189 r_free=0.1407 | n_water=410 | time (s): 0.950 (total time: 36.120) Compute maps r_work=0.1189 r_free=0.1407 | n_water=410 | time (s): 1.450 (total time: 37.570) Filter (map) r_work=0.1224 r_free=0.1399 | n_water=288 | time (s): 2.790 (total time: 40.360) Find peaks r_work=0.1224 r_free=0.1399 | n_water=288 | time (s): 0.500 (total time: 40.860) Add new water r_work=0.1342 r_free=0.1517 | n_water=468 | time (s): 3.030 (total time: 43.890) Refine new water occ: r_work=0.1250 r_free=0.1433 adp: r_work=0.1252 r_free=0.1434 occ: r_work=0.1228 r_free=0.1414 adp: r_work=0.1227 r_free=0.1414 occ: r_work=0.1210 r_free=0.1397 adp: r_work=0.1204 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1393 r_work=0.1204 r_free=0.1393 | n_water=468 | time (s): 183.170 (total time: 227.060) Filter (q & B) r_work=0.1209 r_free=0.1397 | n_water=437 | time (s): 3.420 (total time: 230.480) Filter (dist only) r_work=0.1209 r_free=0.1396 | n_water=435 | time (s): 36.840 (total time: 267.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.703660 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.029662 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 0.1236 0.1371 0.0135 0.002 0.6 4.8 0.5 0.0 0 0.085 0.1189 0.1337 0.0148 0.003 0.7 3.5 0.5 0.0 0 0.256 0.1172 0.1327 0.0155 0.004 0.8 3.2 0.5 0.0 0 0.511 0.1165 0.1324 0.0159 0.005 0.9 3.5 0.5 0.0 0 0.767 0.1162 0.1322 0.0160 0.006 1.0 3.2 0.5 0.0 0 1.022 0.1159 0.1321 0.0162 0.007 1.0 2.9 0.5 0.0 0 1.278 0.1157 0.1320 0.0163 0.007 1.0 3.8 0.5 0.0 0 1.533 0.1155 0.1318 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.789 0.1165 0.1325 0.0159 0.005 0.9 2.9 0.5 0.0 0 0.852 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1155 0.1318 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 13.18 1.64 3.769 21.286 51.030 3.617 11.55 13.18 1.64 3.769 21.286 1.531 3.617 11.56 13.19 1.63 3.752 21.286 6.379 3.617 11.56 13.23 1.68 3.715 21.278 25.515 3.609 11.63 13.33 1.70 3.734 21.233 51.030 3.611 11.52 13.27 1.75 3.759 21.226 76.544 3.602 11.49 13.28 1.79 3.773 21.219 102.059 3.599 11.45 13.27 1.82 3.788 21.212 127.574 3.597 11.46 13.29 1.83 3.810 21.190 153.089 3.596 11.43 13.28 1.85 3.821 21.191 178.604 3.595 11.41 13.26 1.84 3.828 21.188 204.119 3.593 11.39 13.24 1.85 3.831 21.191 229.633 3.591 11.40 13.26 1.86 3.844 21.184 255.148 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.531 Accepted refinement result: 11.55 13.18 1.64 3.769 21.286 1.531 3.617 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.28 3.29 211 1751 Protein: 9.12 114.92 17.04 3.29 0 1519 Water: 11.52 76.69 36.05 N/A 211 224 Other: 19.79 26.65 22.12 N/A 0 8 Chain A: 9.12 114.92 19.45 N/A 0 1751 Chain S: 13.85 60.01 36.46 N/A 211 0 Histogram: Values Number of atoms 9.12 - 19.70 1264 19.70 - 30.28 287 30.28 - 40.86 197 40.86 - 51.44 134 51.44 - 62.02 57 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1318 r_work=0.1155 r_free=0.1318 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1318 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1319 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.13 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= 0.1147 r_free= 0.1319 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610553 | | target function (ml) not normalized (work): 300733.764026 | | target function (ml) not normalized (free): 15837.391399 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1147 0.1319 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1499 0.1499 0.1536 n_refl.: 87589 remove outliers: r(all,work,free)=0.1499 0.1499 0.1536 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1497 0.1535 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1143 0.1312 n_refl.: 87589 remove outliers: r(all,work,free)=0.1148 0.1139 0.1312 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3897 296.068 265.751 0.509 1.002 0.330 11.894-9.307 97.06 95 4 0.2053 483.961 469.765 0.900 1.003 0.330 9.237-7.194 97.73 208 7 0.2116 386.697 386.390 0.960 1.003 0.216 7.162-5.571 100.00 427 22 0.1982 295.769 285.867 0.927 1.003 0.193 5.546-4.326 100.00 867 58 0.1121 406.017 401.272 0.966 1.003 0.184 4.315-3.360 100.00 1859 96 0.0933 386.125 383.851 1.004 1.002 0.170 3.356-2.611 100.00 3867 181 0.1144 253.664 251.320 1.007 1.002 0.048 2.608-2.026 99.99 8198 413 0.0941 168.156 167.331 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.119 82.416 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.415 36.002 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.944 21.496 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1312 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1140 r_free=0.1311 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1311 | n_water=435 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1142 r_free=0.1315 | n_water=433 | time (s): 44.010 (total time: 46.260) Filter (q & B) r_work=0.1143 r_free=0.1315 | n_water=431 | time (s): 3.800 (total time: 50.060) Compute maps r_work=0.1143 r_free=0.1315 | n_water=431 | time (s): 1.890 (total time: 51.950) Filter (map) r_work=0.1157 r_free=0.1299 | n_water=332 | time (s): 3.870 (total time: 55.820) Find peaks r_work=0.1157 r_free=0.1299 | n_water=332 | time (s): 0.650 (total time: 56.470) Add new water r_work=0.1230 r_free=0.1386 | n_water=484 | time (s): 3.500 (total time: 59.970) Refine new water occ: r_work=0.1165 r_free=0.1323 adp: r_work=0.1166 r_free=0.1324 occ: r_work=0.1151 r_free=0.1308 adp: r_work=0.1150 r_free=0.1307 occ: r_work=0.1139 r_free=0.1295 adp: r_work=0.1136 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1291 r_work=0.1136 r_free=0.1291 | n_water=484 | time (s): 243.260 (total time: 303.230) Filter (q & B) r_work=0.1142 r_free=0.1297 | n_water=447 | time (s): 4.050 (total time: 307.280) Filter (dist only) r_work=0.1142 r_free=0.1295 | n_water=446 | time (s): 45.200 (total time: 352.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.801222 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.236659 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 0.1201 0.1334 0.0133 0.002 0.6 3.8 0.5 0.0 0 0.090 0.1167 0.1311 0.0143 0.003 0.8 2.9 0.5 0.0 0 0.270 0.1153 0.1303 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.540 0.1147 0.1302 0.0155 0.006 0.9 3.2 0.5 0.0 0 0.811 0.1143 0.1300 0.0157 0.007 1.0 3.2 0.5 0.0 0 1.081 0.1141 0.1300 0.0159 0.007 1.1 3.5 0.5 0.0 0 1.351 0.1138 0.1300 0.0162 0.008 1.1 3.5 0.5 0.0 0 1.621 0.1137 0.1300 0.0163 0.009 1.1 3.5 0.5 0.0 0 1.891 0.1145 0.1300 0.0154 0.006 1.0 3.5 0.5 0.0 0 0.901 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1300 0.0154 0.006 1.0 3.5 0.5 0.0 0 0.901 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 13.00 1.54 3.769 21.239 40.237 3.610 11.45 13.00 1.54 3.769 21.239 1.207 3.610 11.45 13.00 1.54 3.769 21.239 5.030 3.610 11.49 13.07 1.58 3.704 21.231 20.118 3.606 11.56 13.21 1.66 3.728 21.205 40.237 3.609 11.49 13.18 1.69 3.746 21.193 60.355 3.603 11.43 13.14 1.71 3.761 21.189 80.473 3.598 11.41 13.14 1.73 3.770 21.185 100.592 3.596 11.37 13.09 1.72 3.780 21.186 120.710 3.593 11.38 13.16 1.78 3.800 21.172 140.828 3.593 11.37 13.16 1.79 3.811 21.167 160.947 3.592 11.36 13.15 1.79 3.817 21.166 181.065 3.591 11.34 13.14 1.79 3.825 21.165 201.183 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: 5.030 Accepted refinement result: 11.45 13.00 1.54 3.769 21.239 5.030 3.610 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.19 3.29 223 1750 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.51 76.69 35.36 N/A 223 223 Other: 19.78 26.65 22.11 N/A 0 8 Chain A: 9.11 114.91 19.44 N/A 0 1750 Chain S: 13.84 60.00 35.00 N/A 223 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.27 295 30.27 - 40.85 213 40.85 - 51.43 131 51.43 - 62.01 48 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1300 r_work=0.1145 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1300 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1297 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1297 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608263 | | target function (ml) not normalized (work): 300510.569697 | | target function (ml) not normalized (free): 15823.305859 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1147 0.1139 0.1297 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1479 0.1478 0.1527 n_refl.: 87580 remove outliers: r(all,work,free)=0.1479 0.1478 0.1527 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1478 0.1477 0.1526 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1137 0.1295 n_refl.: 87580 remove outliers: r(all,work,free)=0.1142 0.1135 0.1295 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 0.3655 292.705 259.280 0.465 1.000 0.292 11.894-9.307 94.12 92 4 0.2306 477.784 467.291 0.870 1.002 0.273 9.237-7.194 97.73 208 7 0.2260 386.697 380.848 0.936 1.002 0.170 7.162-5.571 100.00 427 22 0.2129 295.769 285.941 0.923 1.002 0.170 5.546-4.326 100.00 867 58 0.1138 406.017 401.247 0.967 1.002 0.140 4.315-3.360 100.00 1859 96 0.0908 386.125 384.170 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1111 253.664 251.668 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0922 168.156 167.463 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.119 82.443 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.415 36.019 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.944 21.494 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=-0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1135 r_free=0.1295 After: r_work=0.1135 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1295 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1135 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1295 | n_water=446 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1135 r_free=0.1295 | n_water=446 | time (s): 43.470 (total time: 45.740) Filter (q & B) r_work=0.1135 r_free=0.1295 | n_water=445 | time (s): 3.800 (total time: 49.540) Compute maps r_work=0.1135 r_free=0.1295 | n_water=445 | time (s): 1.770 (total time: 51.310) Filter (map) r_work=0.1161 r_free=0.1299 | n_water=354 | time (s): 3.730 (total time: 55.040) Find peaks r_work=0.1161 r_free=0.1299 | n_water=354 | time (s): 0.690 (total time: 55.730) Add new water r_work=0.1208 r_free=0.1357 | n_water=487 | time (s): 3.490 (total time: 59.220) Refine new water occ: r_work=0.1157 r_free=0.1296 adp: r_work=0.1158 r_free=0.1299 occ: r_work=0.1146 r_free=0.1280 adp: r_work=0.1145 r_free=0.1282 occ: r_work=0.1138 r_free=0.1268 adp: r_work=0.1134 r_free=0.1268 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1268 r_work=0.1134 r_free=0.1268 | n_water=487 | time (s): 302.990 (total time: 362.210) Filter (q & B) r_work=0.1141 r_free=0.1283 | n_water=450 | time (s): 3.760 (total time: 365.970) Filter (dist only) r_work=0.1141 r_free=0.1282 | n_water=448 | time (s): 47.210 (total time: 413.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.781462 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.782584 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1217 0.1331 0.0114 0.003 0.7 5.4 0.0 0.0 0 0.089 0.1168 0.1298 0.0129 0.004 0.8 4.8 0.0 0.0 0 0.267 0.1150 0.1284 0.0135 0.005 0.9 4.2 0.5 0.0 0 0.534 0.1142 0.1281 0.0139 0.006 1.0 3.8 0.5 0.0 0 0.802 0.1140 0.1281 0.0141 0.006 1.0 3.5 0.5 0.0 0 1.069 0.1139 0.1281 0.0142 0.007 1.0 3.5 0.5 0.0 0 1.336 0.1137 0.1279 0.0142 0.008 1.1 3.5 0.5 0.0 0 1.603 0.1136 0.1279 0.0143 0.009 1.1 3.5 0.5 0.0 0 1.871 0.1141 0.1281 0.0140 0.006 1.0 3.5 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1279 0.0143 0.009 1.1 3.5 0.5 0.0 0 1.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.79 1.43 3.769 21.257 38.783 3.602 11.36 12.79 1.43 3.769 21.257 1.163 3.602 11.36 12.79 1.43 3.769 21.257 4.848 3.602 11.40 12.83 1.44 3.703 21.248 19.391 3.598 11.41 12.94 1.52 3.727 21.226 38.783 3.597 11.41 12.97 1.56 3.745 21.208 58.174 3.596 11.34 12.92 1.58 3.761 21.205 77.565 3.591 11.29 12.89 1.60 3.769 21.205 96.956 3.587 11.28 12.88 1.60 3.778 21.204 116.348 3.586 11.27 12.90 1.63 3.793 21.195 135.739 3.585 11.28 12.92 1.64 3.808 21.185 155.130 3.585 11.25 12.89 1.64 3.813 21.186 174.522 3.583 11.24 12.89 1.65 3.821 21.186 193.913 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: 4.848 Accepted refinement result: 11.36 12.79 1.43 3.769 21.257 4.848 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.23 3.29 225 1750 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.51 76.68 35.48 N/A 225 223 Other: 19.78 26.64 22.10 N/A 0 8 Chain A: 9.11 114.91 19.43 N/A 0 1750 Chain S: 13.84 59.99 35.26 N/A 225 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.27 298 30.27 - 40.85 209 40.85 - 51.43 128 51.43 - 62.01 53 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1279 r_work=0.1136 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1279 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1275 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1275 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600229 | | target function (ml) not normalized (work): 299823.497907 | | target function (ml) not normalized (free): 15785.510645 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1321 0.1265 5.6511 5.5544| | 2: 3.57 - 2.84 1.00 2888 124 0.1065 0.1375 5.1435 5.2066| | 3: 2.83 - 2.48 1.00 2820 163 0.1097 0.1239 4.9188 4.9704| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.1005 4.6073 4.6321| | 5: 2.25 - 2.09 1.00 2756 127 0.0878 0.0957 4.5545 4.6051| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.1025 4.2565 4.3565| | 7: 1.97 - 1.87 1.00 2787 165 0.0892 0.1107 3.9826 4.0814| | 8: 1.87 - 1.79 1.00 2789 144 0.0922 0.1124 3.8928 4.0082| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1145 3.6438 3.8083| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1152 3.562 3.6877| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1039 3.496 3.5801| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1167 3.3321 3.4688| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1056 3.3121 3.4063| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1059 3.243 3.3178| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1229 3.1526 3.2659| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1235 3.1358 3.2425| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1299 3.1185 3.2293| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1332 3.1024 3.2427| | 19: 1.36 - 1.34 1.00 2807 134 0.1265 0.1561 3.1113 3.2649| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1479 3.1101 3.1582| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1516 3.1136 3.1097| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1994 3.1228 3.2984| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1785 3.1308 3.1953| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1837 3.1255 3.2274| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2131 3.1418 3.2587| | 26: 1.22 - 1.21 1.00 2727 135 0.1902 0.1762 3.145 3.1965| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2160 3.1685 3.1577| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2281 3.164 3.169| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2381 3.1464 3.2284| | 30: 1.16 - 1.15 1.00 2739 148 0.2440 0.2450 3.1401 3.166| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.13 1.00 0.96 5292.11| | 2: 3.57 - 2.84 2888 124 0.93 11.99 1.01 0.96 5292.11| | 3: 2.83 - 2.48 2820 163 0.90 15.90 0.99 0.97 4431.56| | 4: 2.47 - 2.25 2825 136 0.92 12.99 1.00 0.98 2212.49| | 5: 2.25 - 2.09 2756 127 0.91 15.09 1.01 0.98 2212.49| | 6: 2.09 - 1.97 2846 113 0.93 12.15 1.02 0.97 1296.84| | 7: 1.97 - 1.87 2787 165 0.95 9.41 1.02 0.97 515.93| | 8: 1.87 - 1.79 2789 144 0.93 12.73 1.00 0.97 515.93| | 9: 1.79 - 1.72 2745 138 0.94 10.12 0.98 0.97 290.72| | 10: 1.72 - 1.66 2831 160 0.94 11.17 0.98 0.97 245.61| | 11: 1.66 - 1.61 2712 147 0.93 11.79 0.98 0.97 235.38| | 12: 1.61 - 1.56 2773 144 0.95 8.96 0.99 0.97 138.90| | 13: 1.56 - 1.52 2745 130 0.95 10.51 1.03 0.97 138.90| | 14: 1.52 - 1.48 2803 134 0.94 10.86 1.02 0.97 124.44| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 97.95| | 16: 1.45 - 1.42 2756 161 0.94 11.15 1.02 0.98 97.95| | 17: 1.42 - 1.39 2785 139 0.95 10.99 1.01 0.98 89.28| | 18: 1.39 - 1.36 2741 179 0.94 11.60 1.01 0.98 84.26| | 19: 1.36 - 1.34 2807 134 0.94 11.93 1.00 0.98 84.26| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.96 80.09| | 21: 1.32 - 1.30 2785 112 0.94 13.13 0.98 0.96 79.79| | 22: 1.29 - 1.27 2704 152 0.93 13.70 0.98 0.96 80.18| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 82.17| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.94 82.17| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.02| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.93 86.08| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.08| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 89.66| | 29: 1.18 - 1.16 2800 134 0.88 20.48 0.99 0.92 91.00| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.92 91.00| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.79 max = 5292.11 mean = 830.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.39| |phase err.(test): min = 0.00 max = 88.73 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1275 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1456 0.1455 0.1497 n_refl.: 87575 remove outliers: r(all,work,free)=0.1456 0.1455 0.1497 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1455 0.1454 0.1496 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1277 n_refl.: 87575 remove outliers: r(all,work,free)=0.1138 0.1131 0.1277 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 0.3883 287.943 253.713 0.463 1.000 0.314 11.894-9.307 93.14 91 4 0.2157 481.794 468.068 0.869 1.002 0.237 9.237-7.194 97.73 208 7 0.2291 386.697 379.729 0.931 1.002 0.170 7.162-5.571 100.00 427 22 0.2128 295.769 285.126 0.914 1.002 0.137 5.546-4.326 100.00 867 58 0.1144 406.017 401.217 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0910 386.125 384.104 1.002 1.002 0.097 3.356-2.611 100.00 3867 181 0.1114 253.664 251.830 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0911 168.156 167.517 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.119 82.455 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.415 36.014 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.944 21.491 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0138 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1904 0.082 5.242 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1735 0.082 5.242 9.1 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1735 0.082 5.242 9.1 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1739 0.082 5.242 9.1 119.5 20.1 258 0.010 1_weight: 0.1635 0.1739 0.082 5.242 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1229 0.1464 0.007 0.900 9.1 119.5 20.1 258 0.142 1_adp: 0.1236 0.1459 0.007 0.900 9.1 119.4 20.1 258 0.142 1_regHadp: 0.1237 0.1463 0.007 0.900 9.1 119.4 20.1 258 0.142 1_occ: 0.1231 0.1456 0.007 0.900 9.1 119.4 20.1 258 0.142 2_bss: 0.1228 0.1450 0.007 0.900 9.1 119.5 20.1 258 0.142 2_settarget: 0.1228 0.1450 0.007 0.900 9.1 119.5 20.1 258 0.142 2_updatecdl: 0.1228 0.1450 0.007 0.917 9.1 119.5 20.1 258 0.142 2_nqh: 0.1226 0.1448 0.007 0.917 9.1 119.5 20.1 258 0.136 2_sol: 0.1197 0.1402 0.007 0.917 9.1 114.9 22.1 413 n/a 2_weight: 0.1197 0.1402 0.007 0.917 9.1 114.9 22.1 413 n/a 2_xyzrec: 0.1197 0.1415 0.006 0.828 9.1 114.9 22.1 413 n/a 2_adp: 0.1197 0.1415 0.006 0.828 9.1 114.9 22.1 413 n/a 2_regHadp: 0.1197 0.1415 0.006 0.828 9.1 114.9 22.1 413 n/a 2_occ: 0.1194 0.1412 0.006 0.828 9.1 114.9 22.1 413 n/a 3_bss: 0.1189 0.1407 0.006 0.828 9.1 114.9 22.1 413 n/a 3_settarget: 0.1189 0.1407 0.006 0.828 9.1 114.9 22.1 413 n/a 3_updatecdl: 0.1189 0.1407 0.006 0.828 9.1 114.9 22.1 413 n/a 3_nqh: 0.1189 0.1407 0.006 0.828 9.1 114.9 22.1 413 n/a 3_sol: 0.1209 0.1396 0.006 0.828 9.1 114.9 21.3 435 n/a 3_weight: 0.1209 0.1396 0.006 0.828 9.1 114.9 21.3 435 n/a 3_xyzrec: 0.1155 0.1318 0.008 1.081 9.1 114.9 21.3 435 n/a 3_adp: 0.1155 0.1318 0.008 1.081 9.1 114.9 21.3 435 n/a 3_regHadp: 0.1155 0.1318 0.008 1.081 9.1 114.9 21.3 435 n/a 3_occ: 0.1147 0.1319 0.008 1.081 9.1 114.9 21.3 435 n/a 4_bss: 0.1139 0.1312 0.008 1.081 9.1 114.9 21.3 435 n/a 4_settarget: 0.1139 0.1312 0.008 1.081 9.1 114.9 21.3 435 n/a 4_updatecdl: 0.1139 0.1312 0.008 1.083 9.1 114.9 21.3 435 n/a 4_nqh: 0.1140 0.1311 0.008 1.083 9.1 114.9 21.3 435 n/a 4_sol: 0.1142 0.1295 0.008 1.083 9.1 114.9 21.2 446 n/a 4_weight: 0.1142 0.1295 0.008 1.083 9.1 114.9 21.2 446 n/a 4_xyzrec: 0.1145 0.1300 0.006 0.973 9.1 114.9 21.2 446 n/a 4_adp: 0.1145 0.1300 0.006 0.973 9.1 114.9 21.2 446 n/a 4_regHadp: 0.1145 0.1300 0.006 0.973 9.1 114.9 21.2 446 n/a 4_occ: 0.1139 0.1297 0.006 0.973 9.1 114.9 21.2 446 n/a 5_bss: 0.1135 0.1295 0.006 0.973 9.1 114.9 21.2 446 n/a 5_settarget: 0.1135 0.1295 0.006 0.973 9.1 114.9 21.2 446 n/a 5_updatecdl: 0.1135 0.1295 0.006 0.975 9.1 114.9 21.2 446 n/a 5_setrh: 0.1135 0.1295 0.006 0.975 9.1 114.9 21.2 446 n/a 5_nqh: 0.1135 0.1295 0.006 0.975 9.1 114.9 21.2 446 n/a 5_sol: 0.1141 0.1282 0.006 0.975 9.1 114.9 21.2 448 n/a 5_weight: 0.1141 0.1282 0.006 0.975 9.1 114.9 21.2 448 n/a 5_xyzrec: 0.1136 0.1279 0.009 1.113 9.1 114.9 21.2 448 n/a 5_adp: 0.1136 0.1279 0.009 1.113 9.1 114.9 21.2 448 n/a 5_regHadp: 0.1136 0.1279 0.009 1.113 9.1 114.9 21.2 448 n/a 5_occ: 0.1132 0.1275 0.009 1.113 9.1 114.9 21.2 448 n/a end: 0.1131 0.1277 0.009 1.113 9.1 114.9 21.2 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5431713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5431713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9800 Refinement macro-cycles (run) : 13287.8700 Write final files (write_after_run_outputs) : 95.1400 Total : 13386.9900 Total CPU time: 3.73 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:02:23 PST -0800 (1735365743.02 s) Start R-work = 0.1630, R-free = 0.1735 Final R-work = 0.1131, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 13558.65 seconds wall clock time: 246 minutes 42.66 seconds (14802.66 seconds total)