Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.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_4279219.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.73, per 1000 atoms: 0.51 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 111.4 milliseconds Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 540 0.91 - 1.18: 1116 1.18 - 1.44: 680 1.44 - 1.70: 797 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.109 0.265 1.10e-02 8.26e+03 5.80e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.674 -0.140 6.80e-03 2.16e+04 4.22e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.031 0.206 1.13e-02 7.83e+03 3.32e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.02e+02 bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.351 0.167 1.00e-02 1.00e+04 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3244 4.79 - 9.58: 1845 9.58 - 14.36: 584 14.36 - 19.15: 98 19.15 - 23.94: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.71 -12.48 8.10e-01 1.52e+00 2.38e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.03 107.07 15.96 1.11e+00 8.12e-01 2.07e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.25 9.04 6.50e-01 2.37e+00 1.93e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 112.85 9.60 7.20e-01 1.93e+00 1.78e+02 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 112.04 125.10 -13.06 1.02e+00 9.61e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 918 16.41 - 32.82: 129 32.82 - 49.22: 42 49.22 - 65.63: 18 65.63 - 82.04: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 89 0.198 - 0.396: 95 0.396 - 0.593: 35 0.593 - 0.791: 15 0.791 - 0.989: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.60 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.070 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.036 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.054 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.045 9.50e-02 1.11e+02 6.26e-02 8.32e+01 pdb=" NE ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.093 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.108 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1297 2.36 - 2.92: 8286 2.92 - 3.48: 10469 3.48 - 4.04: 15144 4.04 - 4.60: 21483 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 1.850 nonbonded pdb="HH12 ARG A 5 " pdb=" O BGLU A 64 " model vdw 1.829 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.833 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.833 2.100 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.850 1.850 ... (remaining 56674 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_4279219_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= 0.2603 r_free= 0.1921 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788322 | | target function (ml) not normalized (work): 232283.981254 | | target function (ml) not normalized (free): 11788.859775 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3043 0.2084 7.0855 4.9399| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1731 4.345 4.3458| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1604 4.1238 4.1494| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1376 3.8264 3.8243| | 5: 2.25 - 2.09 1.00 2756 127 0.2454 0.1672 3.7944 3.8097| | 6: 2.09 - 1.97 1.00 2846 113 0.2522 0.1878 3.4514 3.5562| | 7: 1.97 - 1.87 1.00 2787 165 0.2546 0.1756 3.1293 3.18| | 8: 1.87 - 1.79 1.00 2789 144 0.2426 0.1785 3.0726 3.1082| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1828 2.9138 2.8897| | 10: 1.72 - 1.66 1.00 2789 158 0.2410 0.2112 2.7975 2.9304| | 11: 1.66 - 1.61 1.00 2740 147 0.2516 0.1631 2.7277 2.7015| | 12: 1.61 - 1.56 1.00 2787 146 0.2530 0.2150 2.6278 2.7164| | 13: 1.56 - 1.52 1.00 2745 130 0.2551 0.1786 2.5624 2.5672| | 14: 1.52 - 1.48 1.00 2803 134 0.2581 0.1767 2.5012 2.5316| | 15: 1.48 - 1.45 1.00 2738 128 0.2575 0.1945 2.4003 2.4255| | 16: 1.45 - 1.42 1.00 2756 161 0.2619 0.2123 2.375 2.4462| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.2116 2.333 2.3484| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2399 2.2619 2.4263| | 19: 1.36 - 1.34 1.00 2807 134 0.2684 0.2450 2.257 2.2736| | 20: 1.34 - 1.32 1.00 2696 147 0.2663 0.2338 2.1829 2.236| | 21: 1.32 - 1.30 1.00 2785 112 0.2780 0.2278 2.1664 2.1883| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2591 2.1264 2.2209| | 23: 1.27 - 1.26 1.00 2802 156 0.2775 0.2308 2.1092 2.1277| | 24: 1.26 - 1.24 1.00 2744 132 0.2783 0.2422 2.0776 2.1359| | 25: 1.24 - 1.22 1.00 2734 148 0.2831 0.2487 2.047 2.0583| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2337 2.0093 2.0521| | 27: 1.21 - 1.19 1.00 2814 148 0.2960 0.2778 2.0071 2.0615| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2667 1.9882 1.9678| | 29: 1.18 - 1.16 1.00 2800 134 0.2938 0.2611 1.9623 1.9711| | 30: 1.16 - 1.15 1.00 2740 148 0.3068 0.2723 1.9289 1.9438| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.72 0.76 0.23 1459.89| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1459.89| | 3: 2.84 - 2.48 2833 165 0.74 31.80 1.24 0.23 1211.35| | 4: 2.47 - 2.25 2825 136 0.81 25.49 1.26 0.25 566.37| | 5: 2.25 - 2.09 2756 127 0.77 29.14 1.28 0.25 566.37| | 6: 2.09 - 1.97 2846 113 0.83 22.71 1.29 0.25 311.07| | 7: 1.97 - 1.87 2787 165 0.90 16.83 1.28 0.26 93.34| | 8: 1.87 - 1.79 2789 144 0.86 21.10 1.24 0.26 93.34| | 9: 1.79 - 1.72 2745 138 0.88 18.23 1.23 0.26 54.93| | 10: 1.72 - 1.66 2789 158 0.87 19.92 1.22 0.26 47.23| | 11: 1.66 - 1.61 2740 147 0.86 21.21 1.25 0.26 45.55| | 12: 1.61 - 1.56 2787 146 0.89 17.99 1.23 0.25 28.46| | 13: 1.56 - 1.52 2745 130 0.87 20.08 1.24 0.25 28.46| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.24 0.25 25.48| | 15: 1.48 - 1.45 2738 128 0.87 19.87 1.23 0.25 20.01| | 16: 1.45 - 1.42 2756 161 0.86 21.03 1.24 0.25 20.01| | 17: 1.42 - 1.39 2785 139 0.87 20.68 1.23 0.25 17.44| | 18: 1.39 - 1.36 2741 179 0.86 21.46 1.23 0.25 15.95| | 19: 1.36 - 1.34 2807 134 0.85 22.10 1.22 0.25 15.95| | 20: 1.34 - 1.32 2696 147 0.87 21.17 1.21 0.24 13.36| | 21: 1.32 - 1.30 2785 112 0.85 22.70 1.22 0.24 13.18| | 22: 1.29 - 1.27 2704 152 0.85 22.60 1.22 0.24 12.85| | 23: 1.27 - 1.26 2802 156 0.86 22.19 1.21 0.24 11.19| | 24: 1.26 - 1.24 2744 132 0.85 23.14 1.20 0.24 11.19| | 25: 1.24 - 1.22 2734 148 0.84 23.72 1.20 0.23 10.44| | 26: 1.22 - 1.21 2727 135 0.85 23.45 1.19 0.23 9.62| | 27: 1.21 - 1.19 2814 148 0.84 24.39 1.20 0.23 9.62| | 28: 1.19 - 1.18 2671 147 0.84 24.39 1.18 0.23 8.78| | 29: 1.18 - 1.16 2800 134 0.84 24.31 1.16 0.23 8.47| | 30: 1.16 - 1.15 2740 148 0.82 26.25 1.16 0.23 8.47| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.47 max = 1459.89 mean = 212.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.44| |phase err.(test): min = 0.00 max = 89.78 mean = 22.39| |-----------------------------------------------------------------------------| ----------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 0.265 1557 Z= 5.480 Angle : 5.250 16.235 2118 Z= 3.755 Chirality : 0.363 0.989 243 Planarity : 0.033 0.112 284 Dihedral : 13.970 82.037 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % 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: -2.70 (0.47), residues: 224 helix: -2.63 (0.39), residues: 102 sheet: -0.96 (0.92), residues: 28 loop : -0.76 (0.53), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.013 ARG A 27 TYR 0.078 0.033 TYR A 141 PHE 0.088 0.037 PHE A 162 HIS 0.088 0.049 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1921 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788322 | | target function (ml) not normalized (work): 232283.981254 | | target function (ml) not normalized (free): 11788.859775 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1970 0.1975 0.1921 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1995 0.2000 0.1935 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1630 0.1734 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1629 0.1734 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 0.3849 386.345 357.073 0.739 0.912 0.402 11.894-9.307 99.02 97 4 0.1820 613.690 593.376 1.020 0.912 0.385 9.237-7.194 100.00 213 7 0.2069 501.923 491.061 1.045 0.913 0.380 7.162-5.571 100.00 427 22 0.2241 376.665 364.213 1.022 0.914 0.288 5.546-4.326 100.00 867 58 0.1296 517.069 511.973 1.057 0.915 0.218 4.315-3.360 100.00 1859 96 0.1131 491.736 487.866 1.102 0.916 0.189 3.356-2.611 100.00 3867 181 0.1440 323.045 319.930 1.086 0.918 0.109 2.608-2.026 99.99 8198 413 0.1347 214.149 211.823 1.091 0.922 0.000 2.025-1.573 100.00 17313 902 0.1626 104.579 103.945 1.088 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.375 45.128 1.066 0.940 0.000 1.221-1.150 99.97 13689 708 0.2599 29.219 26.983 1.020 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1734 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=0.1633 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.636742 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2008.762726 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 0.1670 0.1781 0.0111 0.001 0.5 4.5 0.0 0.0 0 0.125 0.1567 0.1698 0.0132 0.001 0.5 4.5 0.0 0.0 0 0.250 0.1441 0.1603 0.0162 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1382 0.1564 0.0182 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1547 0.0193 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1352 0.1546 0.0194 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1299 0.1519 0.0220 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1266 0.1487 0.0221 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1250 0.1480 0.0230 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1243 0.1475 0.0232 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1476 0.0235 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1235 0.1471 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1233 0.1471 0.0237 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1232 0.1474 0.0242 0.006 0.9 4.5 0.5 0.0 0 9.000 0.1231 0.1473 0.0242 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1226 0.1468 0.0242 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1226 0.1473 0.0247 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1222 0.1470 0.0247 0.007 1.0 3.8 0.5 0.6 0 13.318 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1468 0.0242 0.007 0.9 4.5 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.68 2.42 3.013 19.064 2008.763 0.017 12.26 14.68 2.42 3.013 19.064 60.263 0.017 12.32 14.65 2.33 2.675 19.063 251.095 0.017 12.65 15.28 2.63 2.730 19.219 1004.381 0.016 12.59 15.56 2.98 3.279 19.596 2008.763 0.016 12.44 15.48 3.04 3.325 19.644 3013.144 0.015 12.38 15.51 3.13 3.423 19.675 4017.525 0.015 12.24 15.38 3.15 3.011 19.440 5021.907 0.015 12.17 15.36 3.19 3.363 19.648 6026.288 0.015 12.19 15.43 3.23 3.436 19.674 7030.670 0.015 12.16 15.42 3.26 3.406 19.642 8035.051 0.015 12.12 15.39 3.27 3.410 19.634 9039.432 0.015 12.14 15.45 3.30 3.467 19.658 10043.814 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: 251.095 Accepted refinement result: 12.32 14.65 2.33 2.675 19.063 251.095 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.45 20.09 3.32 0 1785 Protein: 9.06 115.07 17.00 3.33 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.69 26.60 22.05 N/A 0 8 Chain A: 9.06 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1273 20.10 - 31.14 226 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1465 r_work=0.1234 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1463 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= 0.1226 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016820 | | target function (ls_wunit_k1) not normalized (work): 1401.049413 | | target function (ls_wunit_k1) not normalized (free): 109.848585 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1226 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1670 0.1690 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1675 0.1676 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1455 n_refl.: 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 0.3544 303.926 284.418 0.667 1.003 0.393 11.894-9.307 99.02 97 4 0.1631 482.771 471.085 0.922 1.003 0.380 9.237-7.194 100.00 213 7 0.1893 394.847 388.948 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1831 296.311 290.270 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.1005 406.762 403.721 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0870 386.833 385.777 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1172 254.129 252.998 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.1018 168.465 167.739 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.269 82.478 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.482 35.984 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2245 22.986 21.471 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0511 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1455 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1224 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1455 | n_water=258 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1234 r_free=0.1455 | n_water=251 | time (s): 20.410 (total time: 22.630) Filter (q & B) r_work=0.1236 r_free=0.1454 | n_water=248 | time (s): 3.030 (total time: 25.660) Compute maps r_work=0.1236 r_free=0.1454 | n_water=248 | time (s): 1.340 (total time: 27.000) Filter (map) r_work=0.1253 r_free=0.1458 | n_water=223 | time (s): 2.470 (total time: 29.470) Find peaks r_work=0.1253 r_free=0.1458 | n_water=223 | time (s): 0.580 (total time: 30.050) Add new water r_work=0.1401 r_free=0.1624 | n_water=420 | time (s): 2.650 (total time: 32.700) Refine new water occ: r_work=0.1307 r_free=0.1484 adp: r_work=0.1225 r_free=0.1430 occ: r_work=0.1236 r_free=0.1415 adp: r_work=0.1204 r_free=0.1402 occ: r_work=0.1207 r_free=0.1386 adp: r_work=0.1198 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1387 r_work=0.1198 r_free=0.1387 | n_water=420 | time (s): 61.170 (total time: 93.870) Filter (q & B) r_work=0.1200 r_free=0.1387 | n_water=410 | time (s): 2.690 (total time: 96.560) Filter (dist only) r_work=0.1200 r_free=0.1387 | n_water=409 | time (s): 35.760 (total time: 132.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.537921 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1486.616007 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 0.1668 0.1775 0.0107 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1540 0.1664 0.0123 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1419 0.1566 0.0147 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1354 0.1516 0.0162 0.001 0.4 5.8 0.0 0.0 0 0.750 0.1313 0.1483 0.0170 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1319 0.1486 0.0167 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1257 0.1444 0.0187 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1226 0.1421 0.0195 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1216 0.1420 0.0204 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1211 0.1418 0.0207 0.004 0.7 5.1 0.5 0.0 0 5.000 0.1206 0.1417 0.0212 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1201 0.1414 0.0212 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1199 0.1415 0.0216 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1192 0.1408 0.0216 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1191 0.1415 0.0224 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1190 0.1414 0.0223 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1186 0.1413 0.0227 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1186 0.1413 0.0227 0.008 0.9 5.1 0.5 0.0 0 13.769 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1408 0.0216 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 14.08 2.16 3.782 21.726 1486.616 0.016 11.92 14.08 2.16 3.782 21.726 44.598 0.016 11.92 14.08 2.16 3.782 21.726 185.827 0.016 12.14 14.53 2.39 3.614 21.739 743.308 0.015 12.12 14.78 2.66 3.542 21.800 1486.616 0.015 11.97 14.84 2.87 3.484 21.885 2229.924 0.014 11.84 14.77 2.92 3.456 21.939 2973.232 0.014 11.77 14.76 2.99 3.502 21.886 3716.540 0.014 11.82 14.74 2.92 3.497 22.095 4459.848 0.014 11.84 14.90 3.07 3.531 22.153 5203.156 0.014 11.74 14.80 3.06 3.525 22.115 5946.464 0.014 11.77 14.92 3.15 3.547 22.076 6689.772 0.014 11.71 14.83 3.12 3.556 22.119 7433.080 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: 44.598 Accepted refinement result: 11.92 14.08 2.16 3.782 21.726 44.598 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.11 22.09 3.32 186 1750 Protein: 9.10 115.11 17.03 3.33 0 1519 Water: 11.51 76.70 40.88 N/A 186 223 Other: 19.72 26.64 22.09 N/A 0 8 Chain A: 9.10 115.11 19.41 N/A 0 1750 Chain S: 14.13 60.00 47.30 N/A 186 0 Histogram: Values Number of atoms 9.10 - 19.70 1260 19.70 - 30.30 244 30.30 - 40.90 159 40.90 - 51.50 138 51.50 - 62.10 112 62.10 - 72.70 12 72.70 - 83.30 5 83.30 - 93.90 4 93.90 - 104.51 0 104.51 - 115.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1408 r_work=0.1192 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1408 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1399 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1194 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015250 | | target function (ls_wunit_k1) not normalized (work): 1270.273879 | | target function (ls_wunit_k1) not normalized (free): 103.101657 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1194 0.1399 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1594 0.1594 0.1625 n_refl.: 87593 remove outliers: r(all,work,free)=0.1594 0.1594 0.1625 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1596 0.1596 0.1627 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1190 0.1397 n_refl.: 87593 remove outliers: r(all,work,free)=0.1199 0.1189 0.1397 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 93.75 85 5 0.3385 299.914 275.520 0.608 1.003 0.360 11.894-9.307 99.02 97 4 0.1634 482.771 475.621 0.924 1.003 0.353 9.237-7.194 100.00 213 7 0.1708 394.847 394.922 0.987 1.003 0.280 7.162-5.571 100.00 427 22 0.1643 296.311 290.967 0.936 1.003 0.224 5.546-4.326 100.00 867 58 0.0883 406.762 403.854 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0789 386.833 385.784 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1090 254.129 253.095 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1019 168.465 167.868 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.269 82.480 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.482 36.004 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.986 21.495 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1397 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1398 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1398 | n_water=409 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1190 r_free=0.1399 | n_water=405 | time (s): 33.180 (total time: 34.940) Filter (q & B) r_work=0.1190 r_free=0.1399 | n_water=405 | time (s): 0.910 (total time: 35.850) Compute maps r_work=0.1190 r_free=0.1399 | n_water=405 | time (s): 1.640 (total time: 37.490) Filter (map) r_work=0.1234 r_free=0.1402 | n_water=283 | time (s): 3.220 (total time: 40.710) Find peaks r_work=0.1234 r_free=0.1402 | n_water=283 | time (s): 0.490 (total time: 41.200) Add new water r_work=0.1355 r_free=0.1543 | n_water=464 | time (s): 2.340 (total time: 43.540) Refine new water occ: r_work=0.1256 r_free=0.1445 adp: r_work=0.1258 r_free=0.1447 occ: r_work=0.1233 r_free=0.1421 adp: r_work=0.1233 r_free=0.1421 occ: r_work=0.1214 r_free=0.1398 adp: r_work=0.1210 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1210 r_free=0.1397 r_work=0.1210 r_free=0.1397 | n_water=464 | time (s): 176.900 (total time: 220.440) Filter (q & B) r_work=0.1214 r_free=0.1400 | n_water=438 | time (s): 2.570 (total time: 223.010) Filter (dist only) r_work=0.1214 r_free=0.1398 | n_water=436 | time (s): 37.290 (total time: 260.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.840061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.322118 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1367 0.0132 0.002 0.6 5.1 0.5 0.0 0 0.092 0.1189 0.1335 0.0146 0.003 0.7 3.5 0.5 0.0 0 0.276 0.1173 0.1326 0.0152 0.004 0.8 3.5 0.5 0.0 0 0.552 0.1168 0.1325 0.0157 0.005 0.9 3.2 0.5 0.0 0 0.828 0.1163 0.1321 0.0158 0.006 1.0 3.2 0.5 0.0 0 1.104 0.1161 0.1325 0.0164 0.007 1.0 3.8 0.5 0.0 0 1.380 0.1158 0.1323 0.0165 0.007 1.1 3.8 0.5 0.0 0 1.656 0.1156 0.1320 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.932 0.1165 0.1322 0.0157 0.006 0.9 3.2 0.5 0.0 0 0.920 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1320 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.932 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.20 1.64 3.786 21.231 48.322 3.617 11.56 13.20 1.64 3.786 21.231 1.450 3.617 11.57 13.20 1.64 3.772 21.231 6.040 3.617 11.64 13.31 1.67 3.717 21.215 24.161 3.613 11.61 13.35 1.74 3.745 21.188 48.322 3.611 11.57 13.35 1.78 3.758 21.171 72.483 3.606 11.52 13.32 1.80 3.775 21.169 96.644 3.602 11.49 13.30 1.81 3.789 21.158 120.805 3.599 11.46 13.29 1.83 3.803 21.151 144.966 3.597 11.46 13.30 1.84 3.819 21.137 169.127 3.596 11.45 13.30 1.85 3.828 21.133 193.288 3.595 11.43 13.28 1.85 3.834 21.134 217.450 3.593 11.42 13.28 1.86 3.842 21.134 241.611 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.450 Accepted refinement result: 11.56 13.20 1.64 3.786 21.231 1.450 3.617 Individual atomic B min max mean iso aniso Overall: 9.11 115.12 21.17 3.32 217 1746 Protein: 9.11 115.12 17.04 3.33 0 1519 Water: 11.52 76.71 35.55 N/A 217 219 Other: 19.73 26.65 22.10 N/A 0 8 Chain A: 9.11 115.12 19.36 N/A 0 1746 Chain S: 14.14 60.01 35.76 N/A 217 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.31 292 30.31 - 40.91 204 40.91 - 51.51 129 51.51 - 62.11 51 62.11 - 72.71 12 72.71 - 83.31 5 83.31 - 93.91 4 93.91 - 104.51 0 104.51 - 115.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1320 r_work=0.1156 r_free=0.1320 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1320 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1318 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1146 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610432 | | target function (ml) not normalized (work): 300727.332370 | | target function (ml) not normalized (free): 15843.463231 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1146 0.1318 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1488 0.1487 0.1529 n_refl.: 87590 remove outliers: r(all,work,free)=0.1488 0.1487 0.1529 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1487 0.1486 0.1528 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1316 n_refl.: 87590 remove outliers: r(all,work,free)=0.1146 0.1137 0.1316 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3825 294.403 265.135 0.497 1.000 0.318 11.894-9.307 97.06 95 4 0.2122 476.106 465.806 0.873 1.001 0.310 9.237-7.194 98.64 210 7 0.2337 387.330 387.011 0.959 1.002 0.195 7.162-5.571 100.00 427 22 0.2065 296.311 286.260 0.922 1.002 0.170 5.546-4.326 100.00 867 58 0.1109 406.762 402.182 0.964 1.002 0.154 4.315-3.360 100.00 1859 96 0.0941 386.833 384.287 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1127 254.129 252.022 1.008 1.002 0.090 2.608-2.026 99.99 8198 413 0.0928 168.465 167.671 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.269 82.548 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.482 36.063 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2163 22.986 21.522 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0174 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1316 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=0.1137 r_free=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1316 | n_water=436 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1138 r_free=0.1316 | n_water=435 | time (s): 46.850 (total time: 49.390) Filter (q & B) r_work=0.1138 r_free=0.1316 | n_water=435 | time (s): 1.340 (total time: 50.730) Compute maps r_work=0.1138 r_free=0.1316 | n_water=435 | time (s): 1.800 (total time: 52.530) Filter (map) r_work=0.1163 r_free=0.1298 | n_water=325 | time (s): 3.950 (total time: 56.480) Find peaks r_work=0.1163 r_free=0.1298 | n_water=325 | time (s): 0.680 (total time: 57.160) Add new water r_work=0.1236 r_free=0.1359 | n_water=490 | time (s): 3.850 (total time: 61.010) Refine new water occ: r_work=0.1164 r_free=0.1306 adp: r_work=0.1164 r_free=0.1309 occ: r_work=0.1147 r_free=0.1292 adp: r_work=0.1145 r_free=0.1293 occ: r_work=0.1134 r_free=0.1287 adp: r_work=0.1129 r_free=0.1285 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1285 r_work=0.1129 r_free=0.1285 | n_water=490 | time (s): 321.810 (total time: 382.820) Filter (q & B) r_work=0.1135 r_free=0.1295 | n_water=457 | time (s): 3.840 (total time: 386.660) Filter (dist only) r_work=0.1142 r_free=0.1295 | n_water=454 | time (s): 47.980 (total time: 434.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.853475 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.563773 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 0.1337 0.0133 0.002 0.6 4.8 0.5 0.0 0 0.093 0.1164 0.1309 0.0145 0.004 0.8 4.8 0.5 0.0 0 0.278 0.1154 0.1306 0.0151 0.005 0.9 4.2 0.5 0.0 0 0.556 0.1148 0.1300 0.0152 0.006 1.0 4.8 0.5 0.0 0 0.834 0.1145 0.1303 0.0158 0.007 1.0 4.2 0.5 0.0 0 1.112 0.1142 0.1301 0.0159 0.007 1.1 4.2 0.5 0.0 0 1.390 0.1141 0.1302 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.668 0.1139 0.1300 0.0161 0.009 1.1 4.2 0.5 0.0 0 1.946 0.1147 0.1302 0.0155 0.006 1.0 4.2 0.5 0.0 0 0.927 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1300 0.0161 0.009 1.1 4.2 0.5 0.0 0 1.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 13.00 1.61 3.786 21.226 43.564 3.606 11.39 13.00 1.61 3.786 21.226 1.307 3.606 11.39 13.00 1.61 3.782 21.226 5.445 3.606 11.42 13.04 1.61 3.719 21.218 21.782 3.602 11.46 13.15 1.69 3.743 21.195 43.564 3.604 11.43 13.17 1.74 3.757 21.177 65.346 3.600 11.37 13.13 1.76 3.774 21.173 87.128 3.595 11.35 13.13 1.78 3.784 21.170 108.909 3.593 11.31 13.11 1.80 3.794 21.168 130.691 3.590 11.33 13.16 1.83 3.812 21.152 152.473 3.591 11.31 13.14 1.83 3.822 21.151 174.255 3.589 11.28 13.12 1.83 3.825 21.154 196.037 3.588 11.28 13.11 1.83 3.836 21.149 217.819 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.307 Accepted refinement result: 11.39 13.00 1.61 3.786 21.226 1.307 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 115.11 21.17 3.32 237 1744 Protein: 9.10 115.11 17.03 3.33 0 1519 Water: 11.51 76.70 34.99 N/A 237 217 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.10 115.11 19.33 N/A 0 1744 Chain S: 14.13 60.00 34.67 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.30 308 30.30 - 40.90 219 40.90 - 51.50 118 51.50 - 62.10 49 62.10 - 72.71 12 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=0.1139 r_free=0.1300 r_work=0.1139 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1299 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1298 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1298 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604007 | | target function (ml) not normalized (work): 300163.321073 | | target function (ml) not normalized (free): 15823.466944 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1133 0.1298 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1471 0.1471 0.1501 n_refl.: 87582 remove outliers: r(all,work,free)=0.1471 0.1471 0.1501 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1470 0.1470 0.1500 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1132 0.1302 n_refl.: 87582 remove outliers: r(all,work,free)=0.1138 0.1129 0.1302 n_refl.: 87576 ======================== 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 0.4019 286.285 254.336 0.463 0.999 0.314 11.894-9.307 94.12 92 4 0.2179 473.797 458.630 0.856 1.001 0.253 9.237-7.194 98.18 209 7 0.2399 386.323 380.139 0.931 1.002 0.167 7.162-5.571 100.00 427 22 0.2102 296.311 286.434 0.912 1.002 0.137 5.546-4.326 100.00 867 58 0.1114 406.762 401.928 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0915 386.833 384.414 1.004 1.002 0.107 3.356-2.611 100.00 3867 181 0.1121 254.129 252.300 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0915 168.465 167.834 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.269 82.611 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.482 36.083 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.986 21.526 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1129 r_free=0.1302 After: r_work=0.1131 r_free=0.1302 ================================== NQH flips ================================== r_work=0.1131 r_free=0.1302 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=0.1131 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1131 r_free=0.1302 | n_water=454 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1131 r_free=0.1302 | n_water=454 | time (s): 44.710 (total time: 47.160) Filter (q & B) r_work=0.1131 r_free=0.1302 | n_water=454 | time (s): 1.470 (total time: 48.630) Compute maps r_work=0.1131 r_free=0.1302 | n_water=454 | time (s): 1.880 (total time: 50.510) Filter (map) r_work=0.1174 r_free=0.1323 | n_water=347 | time (s): 4.010 (total time: 54.520) Find peaks r_work=0.1174 r_free=0.1323 | n_water=347 | time (s): 0.710 (total time: 55.230) Add new water r_work=0.1227 r_free=0.1367 | n_water=515 | time (s): 3.740 (total time: 58.970) Refine new water occ: r_work=0.1152 r_free=0.1300 adp: r_work=0.1152 r_free=0.1301 occ: r_work=0.1140 r_free=0.1289 adp: r_work=0.1139 r_free=0.1291 occ: r_work=0.1130 r_free=0.1282 adp: r_work=0.1128 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1281 r_work=0.1128 r_free=0.1281 | n_water=515 | time (s): 303.830 (total time: 362.800) Filter (q & B) r_work=0.1136 r_free=0.1296 | n_water=464 | time (s): 3.950 (total time: 366.750) Filter (dist only) r_work=0.1137 r_free=0.1295 | n_water=463 | time (s): 48.370 (total time: 415.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.786801 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.879832 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1352 0.0123 0.004 0.7 7.0 0.0 0.0 0 0.089 0.1177 0.1319 0.0142 0.004 0.8 6.7 0.0 0.0 0 0.268 0.1157 0.1305 0.0148 0.005 0.9 6.1 0.5 0.0 0 0.536 0.1149 0.1300 0.0151 0.006 1.0 5.8 0.5 0.0 0 0.804 0.1144 0.1297 0.0153 0.006 1.1 5.8 0.5 0.0 0 1.072 0.1140 0.1295 0.0155 0.007 1.1 5.8 0.5 0.0 0 1.340 0.1138 0.1294 0.0156 0.008 1.1 5.8 0.5 0.0 0 1.608 0.1137 0.1294 0.0158 0.009 1.2 5.8 0.5 0.0 0 1.876 0.1146 0.1298 0.0152 0.006 1.0 5.8 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1294 0.0158 0.009 1.2 5.8 0.5 0.0 0 1.876 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.94 1.58 3.786 21.232 45.880 3.606 11.37 12.94 1.58 3.786 21.232 1.376 3.606 11.37 12.95 1.57 3.775 21.232 5.735 3.605 11.42 13.01 1.59 3.716 21.221 22.940 3.602 11.42 13.08 1.67 3.743 21.203 45.880 3.601 11.38 13.10 1.72 3.764 21.186 68.820 3.598 11.33 13.07 1.74 3.777 21.183 91.760 3.593 11.29 13.01 1.72 3.781 21.185 114.700 3.590 11.30 13.07 1.77 3.801 21.172 137.639 3.590 11.28 13.08 1.80 3.812 21.169 160.579 3.589 11.28 13.07 1.80 3.824 21.164 183.519 3.588 11.27 13.07 1.80 3.832 21.163 206.459 3.587 11.26 13.07 1.80 3.842 21.159 229.399 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.376 Accepted refinement result: 11.37 12.94 1.58 3.786 21.232 1.376 3.606 Individual atomic B min max mean iso aniso Overall: 9.09 115.10 21.18 3.32 248 1742 Protein: 9.09 115.10 17.03 3.33 0 1519 Water: 11.51 76.70 34.80 N/A 248 215 Other: 19.72 26.63 22.09 N/A 0 8 Chain A: 9.09 115.10 19.31 N/A 0 1742 Chain S: 14.13 60.00 34.34 N/A 248 0 Histogram: Values Number of atoms 9.09 - 19.70 1265 19.70 - 30.30 309 30.30 - 40.90 221 40.90 - 51.50 130 51.50 - 62.10 42 62.10 - 72.70 12 72.70 - 83.30 5 83.30 - 93.90 4 93.90 - 104.50 0 104.50 - 115.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1294 r_work=0.1137 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1294 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1294 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603826 | | target function (ml) not normalized (work): 300126.669922 | | target function (ml) not normalized (free): 15816.576729 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1320 0.1394 5.611 5.6447| | 2: 3.57 - 2.84 1.00 2888 124 0.1066 0.1379 5.1728 5.2209| | 3: 2.83 - 2.48 1.00 2820 163 0.1109 0.1206 4.9617 4.9985| | 4: 2.47 - 2.25 1.00 2825 136 0.0901 0.0992 4.6426 4.666| | 5: 2.25 - 2.09 1.00 2756 127 0.0872 0.0943 4.5895 4.6381| | 6: 2.09 - 1.97 1.00 2846 113 0.0862 0.1013 4.2779 4.3837| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1091 3.9783 4.0825| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1073 3.8888 3.9856| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1186 3.6478 3.8326| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1189 3.5639 3.7074| | 11: 1.66 - 1.61 1.00 2712 147 0.0867 0.1042 3.4948 3.5761| | 12: 1.61 - 1.56 1.00 2773 144 0.0898 0.1171 3.3274 3.4594| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1051 3.3065 3.4003| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1018 3.2379 3.301| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1214 3.1483 3.2594| | 16: 1.45 - 1.42 1.00 2756 161 0.1049 0.1223 3.1301 3.234| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1318 3.1149 3.2377| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1310 3.1012 3.2307| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1561 3.1123 3.2685| | 20: 1.34 - 1.32 1.00 2696 147 0.1362 0.1484 3.1097 3.1627| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1512 3.1131 3.1134| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1976 3.1224 3.2877| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1790 3.1322 3.197| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1836 3.1266 3.2232| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2177 3.1421 3.2633| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1761 3.1481 3.1999| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2163 3.1721 3.1603| | 28: 1.19 - 1.18 1.00 2671 147 0.2207 0.2300 3.1668 3.1734| | 29: 1.18 - 1.16 1.00 2800 134 0.2267 0.2393 3.1482 3.2295| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2450 3.1427 3.1669| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.73 1.00 0.97 5993.60| | 2: 3.57 - 2.84 2888 124 0.92 12.81 1.01 0.97 5993.60| | 3: 2.83 - 2.48 2820 163 0.89 16.84 0.99 0.97 5001.46| | 4: 2.47 - 2.25 2825 136 0.92 13.77 1.00 0.98 2443.02| | 5: 2.25 - 2.09 2756 127 0.90 15.95 1.01 0.98 2443.02| | 6: 2.09 - 1.97 2846 113 0.92 12.47 1.02 0.98 1400.91| | 7: 1.97 - 1.87 2787 165 0.95 9.25 1.02 0.98 512.13| | 8: 1.87 - 1.79 2789 144 0.93 12.61 1.00 0.98 512.13| | 9: 1.79 - 1.72 2745 138 0.94 10.07 0.98 0.97 289.80| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.97 245.28| | 11: 1.66 - 1.61 2712 147 0.93 11.78 0.98 0.97 234.94| | 12: 1.61 - 1.56 2773 144 0.96 8.86 0.99 0.97 137.41| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 137.41| | 14: 1.52 - 1.48 2803 134 0.94 10.72 1.02 0.98 123.08| | 15: 1.48 - 1.45 2738 128 0.95 9.83 1.02 0.98 96.84| | 16: 1.45 - 1.42 2756 161 0.94 11.01 1.02 0.98 96.84| | 17: 1.42 - 1.39 2785 139 0.95 10.85 1.01 0.98 88.42| | 18: 1.39 - 1.36 2741 179 0.94 11.48 1.01 0.98 83.55| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.98 83.55| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.97 79.93| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.96 79.68| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 80.10| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.94 82.22| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.22| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.18| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.03 0.93 86.36| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.36| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.00| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.92 91.37| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.92 91.37| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.68 max = 5993.60 mean = 917.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.49| |phase err.(test): min = 0.00 max = 89.53 mean = 13.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1294 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1458 0.1458 0.1491 n_refl.: 87576 remove outliers: r(all,work,free)=0.1458 0.1458 0.1491 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1457 0.1457 0.1491 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1131 0.1294 n_refl.: 87576 remove outliers: r(all,work,free)=0.1139 0.1131 0.1294 n_refl.: 87576 ======================== 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 0.4080 286.285 245.864 0.430 0.999 0.303 11.894-9.307 94.12 92 4 0.2290 473.797 457.335 0.848 1.002 0.218 9.237-7.194 98.18 209 7 0.2336 386.323 381.050 0.922 1.002 0.150 7.162-5.571 100.00 427 22 0.2105 296.311 287.175 0.908 1.002 0.110 5.546-4.326 100.00 867 58 0.1122 406.762 401.765 0.962 1.002 0.096 4.315-3.360 100.00 1859 96 0.0921 386.833 384.629 1.004 1.002 0.087 3.356-2.611 100.00 3867 181 0.1119 254.129 252.307 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0912 168.465 167.781 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.269 82.628 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.482 36.091 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.986 21.535 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0166 ================= 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 : 0.2603 0.1921 0.082 5.250 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1734 0.082 5.250 9.1 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1734 0.082 5.250 9.1 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1739 0.082 5.250 9.1 119.5 20.1 258 0.006 1_weight: 0.1633 0.1739 0.082 5.250 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1226 0.1468 0.007 0.904 9.1 119.5 20.1 258 0.136 1_adp: 0.1232 0.1465 0.007 0.904 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1234 0.1468 0.007 0.904 9.1 119.5 20.1 258 0.136 1_occ: 0.1226 0.1463 0.007 0.904 9.1 119.5 20.1 258 0.136 2_bss: 0.1224 0.1455 0.007 0.904 9.1 119.5 20.1 258 0.136 2_settarget: 0.1224 0.1455 0.007 0.904 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1224 0.1455 0.007 0.914 9.1 119.5 20.1 258 0.136 2_nqh: 0.1224 0.1455 0.007 0.914 9.1 119.5 20.1 258 0.136 2_sol: 0.1200 0.1387 0.007 0.914 9.1 115.1 22.1 409 n/a 2_weight: 0.1200 0.1387 0.007 0.914 9.1 115.1 22.1 409 n/a 2_xyzrec: 0.1192 0.1408 0.006 0.835 9.1 115.1 22.1 409 n/a 2_adp: 0.1192 0.1408 0.006 0.835 9.1 115.1 22.1 409 n/a 2_regHadp: 0.1192 0.1408 0.006 0.835 9.1 115.1 22.1 409 n/a 2_occ: 0.1194 0.1399 0.006 0.835 9.1 115.1 22.1 409 n/a 3_bss: 0.1189 0.1397 0.006 0.835 9.1 115.1 22.1 409 n/a 3_settarget: 0.1189 0.1397 0.006 0.835 9.1 115.1 22.1 409 n/a 3_updatecdl: 0.1189 0.1397 0.006 0.836 9.1 115.1 22.1 409 n/a 3_nqh: 0.1191 0.1398 0.006 0.836 9.1 115.1 22.1 409 n/a 3_sol: 0.1214 0.1398 0.006 0.836 9.1 115.1 21.2 436 n/a 3_weight: 0.1214 0.1398 0.006 0.836 9.1 115.1 21.2 436 n/a 3_xyzrec: 0.1156 0.1320 0.008 1.100 9.1 115.1 21.2 436 n/a 3_adp: 0.1156 0.1320 0.008 1.100 9.1 115.1 21.2 436 n/a 3_regHadp: 0.1156 0.1320 0.008 1.100 9.1 115.1 21.2 436 n/a 3_occ: 0.1146 0.1318 0.008 1.100 9.1 115.1 21.2 436 n/a 4_bss: 0.1137 0.1316 0.008 1.100 9.1 115.1 21.2 436 n/a 4_settarget: 0.1137 0.1316 0.008 1.100 9.1 115.1 21.2 436 n/a 4_updatecdl: 0.1137 0.1316 0.008 1.101 9.1 115.1 21.2 436 n/a 4_nqh: 0.1137 0.1316 0.008 1.101 9.1 115.1 21.2 436 n/a 4_sol: 0.1142 0.1295 0.008 1.101 9.1 115.1 21.2 454 n/a 4_weight: 0.1142 0.1295 0.008 1.101 9.1 115.1 21.2 454 n/a 4_xyzrec: 0.1139 0.1300 0.009 1.138 9.1 115.1 21.2 454 n/a 4_adp: 0.1139 0.1300 0.009 1.138 9.1 115.1 21.2 454 n/a 4_regHadp: 0.1139 0.1299 0.009 1.138 9.1 115.1 21.2 454 n/a 4_occ: 0.1133 0.1298 0.009 1.138 9.1 115.1 21.2 454 n/a 5_bss: 0.1129 0.1302 0.009 1.138 9.1 115.1 21.2 454 n/a 5_settarget: 0.1129 0.1302 0.009 1.138 9.1 115.1 21.2 454 n/a 5_updatecdl: 0.1129 0.1302 0.009 1.139 9.1 115.1 21.2 454 n/a 5_setrh: 0.1131 0.1302 0.009 1.139 9.1 115.1 21.2 454 n/a 5_nqh: 0.1131 0.1302 0.009 1.139 9.1 115.1 21.2 454 n/a 5_sol: 0.1137 0.1295 0.009 1.139 9.1 115.1 21.2 463 n/a 5_weight: 0.1137 0.1295 0.009 1.139 9.1 115.1 21.2 463 n/a 5_xyzrec: 0.1137 0.1294 0.009 1.152 9.1 115.1 21.2 463 n/a 5_adp: 0.1137 0.1294 0.009 1.152 9.1 115.1 21.2 463 n/a 5_regHadp: 0.1137 0.1294 0.009 1.152 9.1 115.1 21.2 463 n/a 5_occ: 0.1131 0.1294 0.009 1.152 9.1 115.1 21.2 463 n/a end: 0.1131 0.1294 0.009 1.152 9.1 115.1 21.2 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4279219_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4279219_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1400 Refinement macro-cycles (run) : 13551.4600 Write final files (write_after_run_outputs) : 93.2000 Total : 13648.8000 Total CPU time: 3.80 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:10:15 PST -0800 (1735366215.97 s) Start R-work = 0.1629, R-free = 0.1734 Final R-work = 0.1131, R-free = 0.1294 =============================================================================== Job complete usr+sys time: 13831.47 seconds wall clock time: 254 minutes 26.94 seconds (15266.94 seconds total)