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_1664580.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_1664580.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.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 =============================================================================== 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: 2.05, per 1000 atoms: 0.61 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: 0.38 Conformation dependent library (CDL) restraints added in 164.9 milliseconds Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.88: 403 0.88 - 1.14: 1201 1.14 - 1.40: 589 1.40 - 1.66: 906 1.66 - 1.92: 54 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.673 -0.215 1.20e-02 6.94e+03 3.20e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.057 0.179 1.08e-02 8.57e+03 2.76e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.236 1.053 0.183 1.12e-02 7.97e+03 2.67e+02 bond pdb=" CA VAL A 44 " pdb=" CB VAL A 44 " ideal model delta sigma weight residual 1.540 1.739 -0.199 1.23e-02 6.61e+03 2.62e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 3071 4.64 - 9.27: 1907 9.27 - 13.91: 663 13.91 - 18.54: 124 18.54 - 23.18: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.07 107.39 14.68 1.03e+00 9.43e-01 2.03e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 107.84 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA VAL A 186 " pdb=" C VAL A 186 " pdb=" O VAL A 186 " ideal model delta sigma weight residual 120.78 137.07 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.37 -10.14 8.10e-01 1.52e+00 1.57e+02 angle pdb=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" O GLY A 136 " ideal model delta sigma weight residual 119.27 132.58 -13.31 1.07e+00 8.73e-01 1.55e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.66: 946 16.66 - 33.31: 107 33.31 - 49.96: 39 49.96 - 66.61: 16 66.61 - 83.26: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+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 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+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 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.267: 117 0.267 - 0.532: 88 0.532 - 0.798: 24 0.798 - 1.064: 11 1.064 - 1.330: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.33 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.45e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.095 9.50e-02 1.11e+02 7.29e-02 9.78e+01 pdb=" NE ARG A 145 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.101 2.00e-02 2.50e+03 5.43e-02 8.84e+01 pdb=" CG PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG BGLN A 80 " 0.059 2.00e-02 2.50e+03 7.62e-02 8.71e+01 pdb=" CD BGLN A 80 " -0.100 2.00e-02 2.50e+03 pdb=" OE1BGLN A 80 " -0.007 2.00e-02 2.50e+03 pdb=" NE2BGLN A 80 " 0.106 2.00e-02 2.50e+03 pdb="HE21BGLN A 80 " -0.094 2.00e-02 2.50e+03 pdb="HE22BGLN A 80 " 0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7812 2.86 - 3.44: 10667 3.44 - 4.02: 15259 4.02 - 4.60: 22099 Nonbonded interactions: 56621 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.697 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.836 2.100 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.840 1.850 ... (remaining 56616 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_1664580_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= 0.2600 r_free= 0.1923 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786099 | | target function (ml) not normalized (work): 232098.721947 | | target function (ml) not normalized (free): 11778.886318 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3047 0.2085 7.1149 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2423 0.1737 4.3411 4.324| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1680 4.1221 4.1724| | 4: 2.47 - 2.25 1.00 2825 136 0.2324 0.1482 3.8219 3.8151| | 5: 2.25 - 2.09 1.00 2756 127 0.2464 0.1644 3.7931 3.8308| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1623 3.4622 3.5318| | 7: 1.97 - 1.87 1.00 2787 165 0.2502 0.1803 3.1166 3.1775| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.1814 3.0518 3.146| | 9: 1.79 - 1.72 1.00 2745 138 0.2440 0.1807 2.8981 2.8589| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1855 2.7906 2.8662| | 11: 1.66 - 1.61 1.00 2740 147 0.2489 0.1794 2.7558 2.7483| | 12: 1.61 - 1.56 1.00 2787 146 0.2532 0.2032 2.6332 2.6722| | 13: 1.56 - 1.52 1.00 2745 130 0.2533 0.1940 2.5712 2.6345| | 14: 1.52 - 1.48 1.00 2803 134 0.2561 0.2027 2.4944 2.5731| | 15: 1.48 - 1.45 1.00 2738 128 0.2527 0.2099 2.4145 2.503| | 16: 1.45 - 1.42 1.00 2756 161 0.2638 0.2343 2.3983 2.5076| | 17: 1.42 - 1.39 1.00 2785 139 0.2621 0.1883 2.3319 2.3037| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2200 2.2659 2.3232| | 19: 1.36 - 1.34 1.00 2807 134 0.2650 0.2431 2.2356 2.3639| | 20: 1.34 - 1.32 1.00 2696 147 0.2685 0.1957 2.2116 2.1074| | 21: 1.32 - 1.30 1.00 2785 112 0.2677 0.2392 2.1593 2.222| | 22: 1.29 - 1.27 1.00 2704 152 0.2699 0.2398 2.1281 2.1228| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2522 2.0929 2.1974| | 24: 1.26 - 1.24 1.00 2744 132 0.2695 0.2350 2.054 2.1348| | 25: 1.24 - 1.22 1.00 2734 148 0.2809 0.2419 2.0331 2.0269| | 26: 1.22 - 1.21 1.00 2727 135 0.2849 0.2270 1.9901 2.0711| | 27: 1.21 - 1.19 1.00 2814 148 0.2945 0.2605 1.9966 2.0504| | 28: 1.19 - 1.18 1.00 2671 147 0.2994 0.2920 1.9745 2.0115| | 29: 1.18 - 1.16 1.00 2800 134 0.2982 0.2368 1.9531 1.9307| | 30: 1.16 - 1.15 1.00 2740 148 0.3049 0.2942 1.9174 1.9426| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.64 0.76 0.23 1455.17| | 2: 3.57 - 2.84 2876 122 0.81 25.80 1.27 0.23 1455.17| | 3: 2.84 - 2.48 2833 165 0.74 31.76 1.24 0.24 1207.20| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.26 0.25 563.67| | 5: 2.25 - 2.09 2756 127 0.78 28.99 1.28 0.25 563.67| | 6: 2.09 - 1.97 2846 113 0.83 22.66 1.29 0.25 309.41| | 7: 1.97 - 1.87 2787 165 0.90 16.67 1.28 0.26 92.56| | 8: 1.87 - 1.79 2789 144 0.86 21.27 1.25 0.26 92.56| | 9: 1.79 - 1.72 2745 138 0.88 18.69 1.24 0.25 55.59| | 10: 1.72 - 1.66 2789 158 0.86 20.31 1.22 0.25 48.19| | 11: 1.66 - 1.61 2740 147 0.86 21.40 1.24 0.25 46.54| | 12: 1.61 - 1.56 2787 146 0.88 18.69 1.23 0.25 29.85| | 13: 1.56 - 1.52 2745 130 0.87 20.51 1.24 0.25 29.85| | 14: 1.52 - 1.48 2803 134 0.86 21.09 1.24 0.25 26.68| | 15: 1.48 - 1.45 2738 128 0.87 20.07 1.22 0.25 20.87| | 16: 1.45 - 1.42 2756 161 0.86 21.46 1.22 0.25 20.87| | 17: 1.42 - 1.39 2785 139 0.87 20.70 1.22 0.25 17.64| | 18: 1.39 - 1.36 2741 179 0.87 20.98 1.23 0.25 15.77| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.22 0.25 15.77| | 20: 1.34 - 1.32 2696 147 0.87 20.58 1.22 0.25 12.78| | 21: 1.32 - 1.30 2785 112 0.86 21.66 1.20 0.25 12.57| | 22: 1.29 - 1.27 2704 152 0.86 21.84 1.21 0.25 12.27| | 23: 1.27 - 1.26 2802 156 0.86 21.86 1.21 0.24 10.78| | 24: 1.26 - 1.24 2744 132 0.86 22.04 1.19 0.24 10.78| | 25: 1.24 - 1.22 2734 148 0.85 23.18 1.21 0.24 10.20| | 26: 1.22 - 1.21 2727 135 0.85 23.38 1.21 0.23 9.56| | 27: 1.21 - 1.19 2814 148 0.84 24.12 1.20 0.23 9.56| | 28: 1.19 - 1.18 2671 147 0.83 24.81 1.19 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 24.81 1.17 0.23 8.67| | 30: 1.16 - 1.15 2740 148 0.82 26.26 1.17 0.23 8.67| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.67 max = 1455.17 mean = 211.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.40| |phase err.(test): min = 0.00 max = 89.94 mean = 22.38| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.259 1557 Z= 5.326 Angle : 5.330 17.017 2118 Z= 3.694 Chirality : 0.404 1.330 243 Planarity : 0.032 0.104 284 Dihedral : 13.685 83.258 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -2.85 (0.47), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -0.23 (0.89), residues: 28 loop : -0.69 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.025 ARG A 145 TYR 0.066 0.031 TYR A 141 PHE 0.082 0.042 PHE A 162 HIS 0.044 0.016 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= 0.2600 r_free= 0.1923 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786099 | | target function (ml) not normalized (work): 232098.721947 | | target function (ml) not normalized (free): 11778.886318 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2558 0.2601 0.1923 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2558 0.2601 0.1923 n_refl.: 87602 remove outliers: r(all,work,free)=0.1967 0.1971 0.1923 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1989 0.1994 0.1934 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1627 0.1621 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1627 0.1620 0.1756 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 0.3857 386.330 366.731 0.696 1.000 0.407 11.894-9.307 99.02 97 4 0.1853 613.666 592.202 0.927 1.001 0.390 9.237-7.194 100.00 213 7 0.2174 501.904 491.067 0.947 1.001 0.354 7.162-5.571 100.00 427 22 0.2172 376.651 365.741 0.931 1.001 0.293 5.546-4.326 100.00 867 58 0.1272 517.048 512.017 0.971 1.001 0.213 4.315-3.360 100.00 1859 96 0.1149 491.717 487.428 1.008 1.002 0.179 3.356-2.611 100.00 3867 181 0.1420 323.032 319.635 0.998 1.002 0.109 2.608-2.026 99.99 8198 413 0.1330 214.141 211.979 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1626 104.575 103.972 1.010 1.003 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.373 45.158 0.995 1.003 0.000 1.221-1.150 99.97 13689 708 0.2560 29.218 26.964 0.969 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0413 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1620 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1621 r_free=0.1757 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.082621 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2017.046845 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 0.1782 0.1888 0.0107 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1596 0.1730 0.0134 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1463 0.1626 0.0163 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1390 0.1573 0.0183 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1352 0.1553 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1362 0.1560 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1299 0.1517 0.0218 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1272 0.1497 0.0225 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1258 0.1489 0.0231 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1480 0.0232 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1477 0.0233 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1238 0.1473 0.0235 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1234 0.1468 0.0234 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1231 0.1467 0.0236 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1230 0.1469 0.0239 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1468 0.0239 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1470 0.0243 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1224 0.1470 0.0246 0.007 1.0 3.8 0.5 0.6 0 13.041 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1467 0.0236 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.67 2.36 3.013 19.039 2017.047 0.017 12.31 14.66 2.35 2.989 19.039 60.511 0.017 12.38 14.64 2.26 2.666 19.037 252.131 0.017 12.76 15.34 2.59 2.872 19.298 1008.523 0.017 12.58 15.40 2.82 3.333 19.629 2017.047 0.016 12.43 15.39 2.96 3.357 19.638 3025.570 0.015 12.31 15.32 3.02 3.347 19.628 4034.094 0.015 12.31 15.39 3.08 3.411 19.641 5042.617 0.015 12.30 15.41 3.11 3.447 19.651 6051.141 0.015 12.25 15.40 3.15 3.442 19.633 7059.664 0.015 12.29 15.55 3.25 3.544 19.684 8068.187 0.015 12.30 15.56 3.27 3.609 19.703 9076.711 0.015 12.17 15.41 3.24 3.585 19.685 10085.234 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.131 Accepted refinement result: 12.38 14.64 2.26 2.666 19.037 252.131 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.43 20.06 3.31 0 1785 Protein: 9.05 114.96 16.97 3.31 0 1519 Water: 11.43 119.43 38.21 N/A 0 258 Other: 19.70 26.59 22.04 N/A 0 8 Chain A: 9.05 119.43 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.24 42 64.24 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1464 r_work=0.1239 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1467 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 = 0.1233 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1233 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016894 | | target function (ls_wunit_k1) not normalized (work): 1407.230656 | | target function (ls_wunit_k1) not normalized (free): 109.462563 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1244 0.1233 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1690 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1677 0.1678 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1230 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1230 0.1454 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3492 302.291 282.168 0.653 1.003 0.380 11.894-9.307 99.02 97 4 0.1619 484.254 472.633 0.923 1.003 0.371 9.237-7.194 100.00 213 7 0.1891 396.060 391.241 0.962 1.003 0.322 7.162-5.571 100.00 427 22 0.1819 297.221 291.634 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1003 408.011 405.209 0.965 1.003 0.204 4.315-3.360 100.00 1859 96 0.0878 388.021 386.855 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1175 254.910 253.750 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1026 168.982 168.256 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.522 82.698 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.594 36.091 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 23.057 21.531 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0629 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1231 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1456 | n_water=258 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1241 r_free=0.1453 | n_water=251 | time (s): 19.880 (total time: 22.160) Filter (q & B) r_work=0.1243 r_free=0.1453 | n_water=248 | time (s): 2.730 (total time: 24.890) Compute maps r_work=0.1243 r_free=0.1453 | n_water=248 | time (s): 1.230 (total time: 26.120) Filter (map) r_work=0.1257 r_free=0.1454 | n_water=225 | time (s): 2.950 (total time: 29.070) Find peaks r_work=0.1257 r_free=0.1454 | n_water=225 | time (s): 0.520 (total time: 29.590) Add new water r_work=0.1401 r_free=0.1618 | n_water=435 | time (s): 2.720 (total time: 32.310) Refine new water occ: r_work=0.1307 r_free=0.1474 adp: r_work=0.1228 r_free=0.1425 occ: r_work=0.1242 r_free=0.1411 adp: r_work=0.1208 r_free=0.1400 occ: r_work=0.1212 r_free=0.1391 adp: r_work=0.1201 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1391 r_work=0.1201 r_free=0.1391 | n_water=435 | time (s): 54.790 (total time: 87.100) Filter (q & B) r_work=0.1205 r_free=0.1394 | n_water=419 | time (s): 2.740 (total time: 89.840) Filter (dist only) r_work=0.1205 r_free=0.1392 | n_water=418 | time (s): 34.780 (total time: 124.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.262967 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1469.058261 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 0.1714 0.1813 0.0099 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1531 0.1651 0.0121 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1410 0.1551 0.0141 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1343 0.1499 0.0156 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1318 0.1481 0.0164 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1323 0.1486 0.0164 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1245 0.1428 0.0182 0.003 0.6 4.8 0.5 0.0 0 2.000 0.1229 0.1427 0.0198 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1217 0.1423 0.0206 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1209 0.1419 0.0210 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1207 0.1420 0.0213 0.005 0.7 4.8 0.5 0.0 0 6.000 0.1202 0.1418 0.0216 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1196 0.1414 0.0218 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1193 0.1413 0.0220 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1190 0.1408 0.0218 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1188 0.1409 0.0221 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1187 0.1405 0.0218 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1186 0.1407 0.0222 0.008 0.9 4.8 0.5 0.6 0 13.000 0.1184 0.1404 0.0220 0.008 1.0 4.5 0.5 0.6 0 14.131 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1184 0.1404 0.0220 0.008 1.0 4.5 0.5 0.6 0 14.131 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 14.04 2.20 3.772 21.758 1469.058 0.016 11.84 14.04 2.20 3.772 21.758 44.072 0.016 11.84 14.04 2.20 3.772 21.758 183.632 0.016 11.99 14.39 2.39 3.631 21.761 734.529 0.015 12.04 14.77 2.74 3.541 21.834 1469.058 0.015 11.92 14.80 2.88 3.502 21.903 2203.587 0.014 11.77 14.60 2.83 3.456 22.086 2938.117 0.014 11.76 14.69 2.94 3.497 22.085 3672.646 0.014 11.71 14.73 3.02 3.493 22.052 4407.175 0.014 11.66 14.68 3.01 3.513 22.091 5141.704 0.014 11.65 14.69 3.04 3.541 22.140 5876.233 0.014 11.64 14.73 3.09 3.561 22.150 6610.762 0.013 11.62 14.72 3.10 3.578 22.160 7345.291 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 183.632 Accepted refinement result: 11.84 14.04 2.20 3.772 21.758 183.632 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.00 22.16 3.31 193 1752 Protein: 9.09 115.00 17.01 3.31 0 1519 Water: 11.47 76.67 40.89 N/A 193 225 Other: 19.74 26.63 22.08 N/A 0 8 Chain A: 9.09 115.00 19.43 N/A 0 1752 Chain S: 13.54 60.00 46.99 N/A 193 0 Histogram: Values Number of atoms 9.09 - 19.68 1260 19.68 - 30.27 245 30.27 - 40.86 165 40.86 - 51.45 129 51.45 - 62.04 123 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1404 r_work=0.1184 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1404 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 = 0.1184 r_free = 0.1405 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1184 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014866 | | target function (ls_wunit_k1) not normalized (work): 1238.252629 | | target function (ls_wunit_k1) not normalized (free): 103.602915 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1184 0.1405 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1580 0.1579 0.1632 n_refl.: 87592 remove outliers: r(all,work,free)=0.1580 0.1579 0.1632 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1583 0.1582 0.1633 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1181 0.1401 n_refl.: 87592 remove outliers: r(all,work,free)=0.1191 0.1180 0.1401 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 0.3295 300.835 276.584 0.591 1.003 0.350 11.894-9.307 99.02 97 4 0.1700 484.254 477.768 0.920 1.003 0.330 9.237-7.194 100.00 213 7 0.1617 396.060 397.187 0.984 1.003 0.280 7.162-5.571 100.00 427 22 0.1601 297.221 292.873 0.936 1.003 0.224 5.546-4.326 100.00 867 58 0.0879 408.011 405.097 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0771 388.021 387.241 1.006 1.003 0.200 3.356-2.611 100.00 3867 181 0.1074 254.910 254.087 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1014 168.982 168.458 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.522 82.752 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.594 36.129 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 23.057 21.562 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0222 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1180 r_free=0.1401 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1180 r_free=0.1403 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1403 | n_water=418 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1180 r_free=0.1402 | n_water=415 | time (s): 38.420 (total time: 40.000) Filter (q & B) r_work=0.1180 r_free=0.1402 | n_water=415 | time (s): 1.300 (total time: 41.300) Compute maps r_work=0.1180 r_free=0.1402 | n_water=415 | time (s): 1.610 (total time: 42.910) Filter (map) r_work=0.1223 r_free=0.1401 | n_water=281 | time (s): 2.670 (total time: 45.580) Find peaks r_work=0.1223 r_free=0.1401 | n_water=281 | time (s): 0.630 (total time: 46.210) Add new water r_work=0.1346 r_free=0.1549 | n_water=470 | time (s): 3.090 (total time: 49.300) Refine new water occ: r_work=0.1253 r_free=0.1453 adp: r_work=0.1255 r_free=0.1456 occ: r_work=0.1231 r_free=0.1427 adp: r_work=0.1231 r_free=0.1429 occ: r_work=0.1212 r_free=0.1403 adp: r_work=0.1209 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1402 r_work=0.1209 r_free=0.1402 | n_water=470 | time (s): 170.410 (total time: 219.710) Filter (q & B) r_work=0.1213 r_free=0.1413 | n_water=429 | time (s): 2.420 (total time: 222.130) Filter (dist only) r_work=0.1213 r_free=0.1412 | n_water=428 | time (s): 34.470 (total time: 256.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.783877 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.853157 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 0.1247 0.1381 0.0135 0.002 0.6 3.8 0.5 0.0 0 0.089 0.1202 0.1351 0.0149 0.003 0.7 3.2 0.5 0.0 0 0.268 0.1185 0.1341 0.0155 0.004 0.8 2.6 0.5 0.0 0 0.535 0.1176 0.1337 0.0162 0.005 0.9 2.9 0.5 0.0 0 0.803 0.1172 0.1336 0.0165 0.006 1.0 3.5 0.5 0.0 0 1.070 0.1169 0.1335 0.0166 0.007 1.0 2.6 0.5 0.6 0 1.338 0.1167 0.1335 0.0168 0.007 1.1 3.2 0.5 0.6 0 1.605 0.1165 0.1332 0.0167 0.008 1.1 3.2 0.5 0.6 0 1.873 0.1174 0.1336 0.0162 0.005 0.9 2.9 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1165 0.1332 0.0167 0.008 1.1 3.2 0.5 0.6 0 1.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 13.32 1.67 3.775 21.181 48.853 3.629 11.65 13.32 1.67 3.775 21.181 1.466 3.629 11.66 13.32 1.67 3.764 21.181 6.107 3.628 11.73 13.42 1.69 3.713 21.163 24.427 3.623 11.70 13.45 1.75 3.743 21.136 48.853 3.620 11.66 13.44 1.79 3.762 21.121 73.280 3.615 11.64 13.45 1.81 3.775 21.109 97.706 3.612 11.59 13.41 1.82 3.789 21.106 122.133 3.609 11.58 13.43 1.85 3.807 21.094 146.559 3.608 11.56 13.40 1.84 3.818 21.083 170.986 3.606 11.54 13.40 1.85 3.827 21.083 195.413 3.604 11.53 13.39 1.86 3.834 21.082 219.839 3.604 11.51 13.38 1.87 3.837 21.084 244.266 3.603 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.107 Accepted refinement result: 11.66 13.32 1.67 3.764 21.181 6.107 3.628 Individual atomic B min max mean iso aniso Overall: 9.11 114.88 21.10 3.27 207 1748 Protein: 9.11 114.88 17.03 3.28 0 1519 Water: 11.49 76.69 35.52 N/A 207 221 Other: 19.70 26.60 22.09 N/A 0 8 Chain A: 9.11 114.88 19.36 N/A 0 1748 Chain S: 13.56 60.01 35.72 N/A 207 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.26 288 30.26 - 40.84 205 40.84 - 51.42 128 51.42 - 61.99 49 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.30 0 104.30 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1166 r_free=0.1332 r_work=0.1166 r_free=0.1332 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1166 r_free = 0.1332 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1319 target_work(ml) = 3.620 | | 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= 0.1157 r_free= 0.1319 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619702 | | target function (ml) not normalized (work): 301499.476533 | | target function (ml) not normalized (free): 15872.617135 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1157 0.1319 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1502 0.1503 0.1511 n_refl.: 87590 remove outliers: r(all,work,free)=0.1502 0.1503 0.1511 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1502 0.1510 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1151 0.1307 n_refl.: 87590 remove outliers: r(all,work,free)=0.1156 0.1148 0.1307 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.4007 292.717 268.056 0.493 1.002 0.330 11.894-9.307 97.06 95 4 0.2263 483.936 470.759 0.874 1.003 0.330 9.237-7.194 98.18 209 7 0.2304 387.509 388.449 0.955 1.003 0.190 7.162-5.571 100.00 427 22 0.2150 297.221 287.067 0.921 1.003 0.173 5.546-4.326 100.00 867 58 0.1150 408.011 402.964 0.962 1.003 0.155 4.315-3.360 100.00 1859 96 0.0940 388.021 385.383 1.005 1.002 0.150 3.356-2.611 100.00 3867 181 0.1142 254.910 252.537 1.008 1.002 0.110 2.608-2.026 99.99 8198 413 0.0936 168.982 168.111 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.522 82.780 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.594 36.167 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 23.057 21.587 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=-0.0146 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1307 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=0.1148 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1307 | n_water=428 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1148 r_free=0.1308 | n_water=426 | time (s): 42.800 (total time: 45.280) Filter (q & B) r_work=0.1148 r_free=0.1309 | n_water=425 | time (s): 3.910 (total time: 49.190) Compute maps r_work=0.1148 r_free=0.1309 | n_water=425 | time (s): 1.950 (total time: 51.140) Filter (map) r_work=0.1167 r_free=0.1305 | n_water=321 | time (s): 3.920 (total time: 55.060) Find peaks r_work=0.1167 r_free=0.1305 | n_water=321 | time (s): 0.740 (total time: 55.800) Add new water r_work=0.1236 r_free=0.1377 | n_water=485 | time (s): 3.850 (total time: 59.650) Refine new water occ: r_work=0.1168 r_free=0.1313 adp: r_work=0.1169 r_free=0.1316 occ: r_work=0.1153 r_free=0.1294 adp: r_work=0.1153 r_free=0.1298 occ: r_work=0.1142 r_free=0.1281 adp: r_work=0.1139 r_free=0.1284 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1284 r_work=0.1139 r_free=0.1284 | n_water=485 | time (s): 201.310 (total time: 260.960) Filter (q & B) r_work=0.1145 r_free=0.1288 | n_water=449 | time (s): 4.010 (total time: 264.970) Filter (dist only) r_work=0.1146 r_free=0.1287 | n_water=447 | time (s): 45.120 (total time: 310.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.799373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.877510 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 0.1208 0.1325 0.0117 0.002 0.6 4.2 0.5 0.0 0 0.090 0.1169 0.1301 0.0131 0.003 0.8 3.5 0.5 0.0 0 0.270 0.1156 0.1297 0.0141 0.005 0.9 3.5 0.5 0.0 0 0.540 0.1150 0.1295 0.0146 0.006 0.9 3.2 0.5 0.0 0 0.810 0.1146 0.1294 0.0148 0.007 1.0 3.5 0.5 0.6 0 1.080 0.1143 0.1295 0.0152 0.007 1.1 2.9 0.5 0.6 0 1.350 0.1141 0.1291 0.0150 0.008 1.1 3.8 0.5 0.6 0 1.619 0.1139 0.1294 0.0155 0.008 1.1 2.9 0.5 0.6 0 1.889 0.1148 0.1293 0.0144 0.006 1.0 3.5 0.5 0.6 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1291 0.0150 0.008 1.1 3.8 0.5 0.6 0 1.619 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.91 1.50 3.761 21.186 35.878 3.611 11.41 12.91 1.50 3.761 21.186 1.076 3.611 11.41 12.91 1.50 3.761 21.186 4.485 3.611 11.43 12.94 1.50 3.700 21.177 17.939 3.606 11.45 13.01 1.56 3.716 21.163 35.878 3.606 11.49 13.11 1.62 3.735 21.137 53.816 3.607 11.42 13.06 1.65 3.753 21.132 71.755 3.601 11.39 13.05 1.67 3.765 21.128 89.694 3.598 11.36 13.03 1.67 3.769 21.130 107.633 3.595 11.34 13.03 1.69 3.780 21.125 125.571 3.594 11.35 13.07 1.72 3.800 21.110 143.510 3.594 11.33 13.05 1.72 3.808 21.106 161.449 3.593 11.32 13.02 1.70 3.812 21.105 179.388 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: 1.076 Accepted refinement result: 11.41 12.91 1.50 3.761 21.186 1.076 3.611 Individual atomic B min max mean iso aniso Overall: 9.10 114.87 21.11 3.27 228 1746 Protein: 9.10 114.87 17.02 3.28 0 1519 Water: 11.49 76.68 34.98 N/A 228 219 Other: 19.69 26.59 22.08 N/A 0 8 Chain A: 9.10 114.87 19.32 N/A 0 1746 Chain S: 13.55 60.01 34.83 N/A 228 0 Histogram: Values Number of atoms 9.10 - 19.68 1263 19.68 - 30.26 301 30.26 - 40.84 219 40.84 - 51.41 120 51.41 - 61.99 49 61.99 - 72.57 10 72.57 - 83.14 6 83.14 - 93.72 4 93.72 - 104.30 0 104.30 - 114.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1291 r_work=0.1141 r_free=0.1291 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1291 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1285 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.22 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= 0.1134 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608037 | | target function (ml) not normalized (work): 300498.969326 | | target function (ml) not normalized (free): 15825.964209 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1134 0.1285 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1483 0.1484 0.1493 n_refl.: 87582 remove outliers: r(all,work,free)=0.1483 0.1484 0.1493 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1482 0.1483 0.1492 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1286 n_refl.: 87582 remove outliers: r(all,work,free)=0.1140 0.1132 0.1286 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3898 297.542 248.829 0.452 1.001 0.320 11.894-9.307 96.08 94 4 0.2297 484.032 470.760 0.864 1.002 0.320 9.237-7.194 97.73 208 7 0.2308 388.596 380.981 0.926 1.002 0.170 7.162-5.571 100.00 427 22 0.2177 297.221 287.089 0.915 1.003 0.148 5.546-4.326 100.00 867 58 0.1146 408.011 403.344 0.963 1.003 0.119 4.315-3.360 100.00 1859 96 0.0917 388.021 386.190 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1116 254.910 253.165 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0908 168.982 168.425 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.522 82.920 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.594 36.209 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.057 21.604 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0127 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1132 r_free=0.1286 After: r_work=0.1134 r_free=0.1286 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1286 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1134 r_free=0.1286 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1286 | n_water=447 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1134 r_free=0.1286 | n_water=447 | time (s): 43.350 (total time: 45.910) Filter (q & B) r_work=0.1134 r_free=0.1286 | n_water=447 | time (s): 1.380 (total time: 47.290) Compute maps r_work=0.1134 r_free=0.1286 | n_water=447 | time (s): 1.920 (total time: 49.210) Filter (map) r_work=0.1157 r_free=0.1294 | n_water=357 | time (s): 3.950 (total time: 53.160) Find peaks r_work=0.1157 r_free=0.1294 | n_water=357 | time (s): 0.700 (total time: 53.860) Add new water r_work=0.1200 r_free=0.1336 | n_water=499 | time (s): 3.810 (total time: 57.670) Refine new water occ: r_work=0.1146 r_free=0.1284 adp: r_work=0.1147 r_free=0.1287 occ: r_work=0.1136 r_free=0.1273 adp: r_work=0.1135 r_free=0.1276 occ: r_work=0.1128 r_free=0.1266 adp: r_work=0.1125 r_free=0.1268 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1268 r_work=0.1125 r_free=0.1268 | n_water=499 | time (s): 240.550 (total time: 298.220) Filter (q & B) r_work=0.1132 r_free=0.1275 | n_water=462 | time (s): 3.930 (total time: 302.150) Filter (dist only) r_work=0.1132 r_free=0.1273 | n_water=461 | time (s): 49.010 (total time: 351.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.658543 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.187232 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 0.1231 0.1337 0.0106 0.004 0.7 8.0 0.0 0.0 0 0.083 0.1175 0.1299 0.0124 0.004 0.8 7.0 0.0 0.6 0 0.249 0.1152 0.1285 0.0133 0.005 0.9 7.4 0.5 0.6 0 0.498 0.1144 0.1280 0.0136 0.006 1.0 7.4 0.5 0.6 0 0.746 0.1138 0.1275 0.0137 0.006 1.1 6.7 0.5 0.6 0 0.995 0.1135 0.1273 0.0138 0.007 1.1 6.7 0.5 0.6 0 1.244 0.1133 0.1272 0.0140 0.008 1.1 6.7 0.5 0.6 0 1.493 0.1132 0.1272 0.0140 0.008 1.1 6.7 0.5 0.6 0 1.741 0.1142 0.1278 0.0136 0.006 1.0 7.4 0.5 0.6 0 0.829 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1272 0.0140 0.008 1.1 6.7 0.5 0.6 0 1.741 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.72 1.40 3.760 21.244 47.187 3.605 11.32 12.72 1.40 3.760 21.244 1.416 3.605 11.32 12.72 1.40 3.760 21.244 5.898 3.605 11.33 12.74 1.41 3.702 21.235 23.594 3.599 11.35 12.84 1.49 3.733 21.206 47.187 3.600 11.30 12.82 1.52 3.753 21.195 70.781 3.594 11.26 12.80 1.54 3.767 21.191 94.374 3.590 11.24 12.80 1.56 3.778 21.187 117.968 3.588 11.24 12.83 1.59 3.797 21.176 141.562 3.587 11.23 12.84 1.61 3.813 21.170 165.155 3.587 11.21 12.80 1.59 3.816 21.171 188.749 3.584 11.18 12.79 1.60 3.821 21.173 212.343 3.583 11.17 12.77 1.60 3.828 21.171 235.936 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.416 Accepted refinement result: 11.32 12.72 1.40 3.760 21.244 1.416 3.605 Individual atomic B min max mean iso aniso Overall: 9.10 114.87 21.22 3.27 242 1746 Protein: 9.10 114.87 17.02 3.28 0 1519 Water: 11.48 76.68 35.04 N/A 242 219 Other: 19.69 26.59 22.08 N/A 0 8 Chain A: 9.10 114.87 19.31 N/A 0 1746 Chain S: 13.55 60.00 34.98 N/A 242 0 Histogram: Values Number of atoms 9.10 - 19.68 1264 19.68 - 30.25 303 30.25 - 40.83 220 40.83 - 51.41 130 51.41 - 61.98 49 61.98 - 72.56 10 72.56 - 83.14 6 83.14 - 93.72 4 93.72 - 104.29 0 104.29 - 114.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1272 r_work=0.1132 r_free=0.1272 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1272 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1271 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1271 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603316 | | target function (ml) not normalized (work): 300091.378315 | | target function (ml) not normalized (free): 15796.347322 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1323 0.1312 5.6585 5.5922| | 2: 3.57 - 2.84 1.00 2888 124 0.1066 0.1358 5.1556 5.2043| | 3: 2.83 - 2.48 1.00 2820 163 0.1105 0.1174 4.9343 4.9577| | 4: 2.47 - 2.25 1.00 2825 136 0.0896 0.0966 4.6195 4.6451| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.0941 4.5646 4.61| | 6: 2.09 - 1.97 1.00 2846 113 0.0846 0.0989 4.2604 4.3571| | 7: 1.97 - 1.87 1.00 2787 165 0.0876 0.1110 3.9762 4.0837| | 8: 1.87 - 1.79 1.00 2789 144 0.0909 0.1091 3.8853 3.9886| | 9: 1.79 - 1.72 1.00 2745 138 0.0866 0.1206 3.6412 3.843| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1209 3.5633 3.7159| | 11: 1.66 - 1.61 1.00 2712 147 0.0870 0.1007 3.4957 3.5602| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1118 3.3311 3.4463| | 13: 1.56 - 1.52 1.00 2745 130 0.0939 0.1025 3.3066 3.3907| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1059 3.2393 3.327| | 15: 1.48 - 1.45 1.00 2738 128 0.0998 0.1211 3.153 3.2613| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1252 3.1351 3.2424| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1309 3.1206 3.2334| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1307 3.1062 3.234| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1560 3.1124 3.265| | 20: 1.34 - 1.32 1.00 2696 147 0.1361 0.1445 3.1122 3.1542| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1509 3.1156 3.1031| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1990 3.1237 3.3006| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1790 3.1364 3.2044| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1840 3.1305 3.2327| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2158 3.1455 3.2655| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1766 3.1523 3.2035| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2167 3.1735 3.1657| | 28: 1.19 - 1.18 1.00 2671 147 0.2197 0.2301 3.1689 3.176| | 29: 1.18 - 1.16 1.00 2800 134 0.2267 0.2368 3.151 3.2299| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2447 3.1462 3.1691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.15 1.00 0.97 5542.33| | 2: 3.57 - 2.84 2888 124 0.93 12.24 1.01 0.97 5542.33| | 3: 2.83 - 2.48 2820 163 0.90 16.18 0.99 0.97 4633.03| | 4: 2.47 - 2.25 2825 136 0.92 13.17 1.00 0.98 2288.24| | 5: 2.25 - 2.09 2756 127 0.91 15.29 1.01 0.98 2288.24| | 6: 2.09 - 1.97 2846 113 0.93 12.18 1.02 0.98 1327.02| | 7: 1.97 - 1.87 2787 165 0.95 9.20 1.02 0.98 507.23| | 8: 1.87 - 1.79 2789 144 0.93 12.54 0.99 0.98 507.23| | 9: 1.79 - 1.72 2745 138 0.94 9.98 0.98 0.97 288.52| | 10: 1.72 - 1.66 2831 160 0.94 11.10 0.98 0.97 244.72| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.97 234.40| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.98 137.10| | 13: 1.56 - 1.52 2745 130 0.95 10.34 1.02 0.98 137.10| | 14: 1.52 - 1.48 2803 134 0.94 10.72 1.02 0.98 122.98| | 15: 1.48 - 1.45 2738 128 0.95 9.82 1.02 0.99 97.12| | 16: 1.45 - 1.42 2756 161 0.94 10.99 1.02 0.99 97.12| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.99 88.68| | 18: 1.39 - 1.36 2741 179 0.94 11.49 1.01 0.99 83.80| | 19: 1.36 - 1.34 2807 134 0.94 11.77 0.99 0.99 83.80| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 80.12| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.97 79.86| | 22: 1.29 - 1.27 2704 152 0.93 13.61 0.98 0.96 80.31| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.61| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.61| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.59| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.78| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.78| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.34| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.98 0.93 91.68| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.93 91.68| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.86 max = 5542.33 mean = 860.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.35| |phase err.(test): min = 0.00 max = 89.52 mean = 13.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1129 0.1271 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1456 0.1457 0.1475 n_refl.: 87578 remove outliers: r(all,work,free)=0.1456 0.1457 0.1475 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1456 0.1456 0.1475 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1129 0.1270 n_refl.: 87578 remove outliers: r(all,work,free)=0.1134 0.1127 0.1270 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 0.3930 294.142 258.520 0.474 1.000 0.324 11.894-9.307 94.12 92 4 0.2194 479.049 468.478 0.872 1.002 0.320 9.237-7.194 97.73 208 7 0.2342 388.596 382.002 0.924 1.002 0.175 7.162-5.571 100.00 427 22 0.2155 297.221 287.464 0.914 1.003 0.150 5.546-4.326 100.00 867 58 0.1130 408.011 403.078 0.962 1.003 0.109 4.315-3.360 100.00 1859 96 0.0902 388.021 386.133 1.003 1.003 0.093 3.356-2.611 100.00 3867 181 0.1111 254.910 252.868 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0906 168.982 168.323 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.522 82.866 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.594 36.191 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.057 21.598 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0086 ================= 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 : 0.2600 0.1923 0.081 5.330 8.8 119.3 19.9 258 0.000 1_bss: 0.1620 0.1756 0.081 5.330 9.0 119.5 20.1 258 0.000 1_settarget: 0.1620 0.1756 0.081 5.330 9.0 119.5 20.1 258 0.000 1_nqh: 0.1621 0.1757 0.081 5.330 9.0 119.5 20.1 258 0.003 1_weight: 0.1621 0.1757 0.081 5.330 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1231 0.1467 0.006 0.859 9.0 119.5 20.1 258 0.138 1_adp: 0.1238 0.1464 0.006 0.859 9.0 119.4 20.1 258 0.138 1_regHadp: 0.1239 0.1467 0.006 0.859 9.0 119.4 20.1 258 0.138 1_occ: 0.1233 0.1462 0.006 0.859 9.0 119.4 20.1 258 0.138 2_bss: 0.1230 0.1454 0.006 0.859 9.1 119.5 20.1 258 0.138 2_settarget: 0.1230 0.1454 0.006 0.859 9.1 119.5 20.1 258 0.138 2_updatecdl: 0.1230 0.1454 0.006 0.869 9.1 119.5 20.1 258 0.138 2_nqh: 0.1231 0.1456 0.006 0.869 9.1 119.5 20.1 258 0.139 2_sol: 0.1205 0.1392 0.006 0.869 9.1 115.0 22.2 418 n/a 2_weight: 0.1205 0.1392 0.006 0.869 9.1 115.0 22.2 418 n/a 2_xyzrec: 0.1184 0.1404 0.008 0.955 9.1 115.0 22.2 418 n/a 2_adp: 0.1184 0.1404 0.008 0.955 9.1 115.0 22.2 418 n/a 2_regHadp: 0.1184 0.1404 0.008 0.955 9.1 115.0 22.2 418 n/a 2_occ: 0.1184 0.1405 0.008 0.955 9.1 115.0 22.2 418 n/a 3_bss: 0.1180 0.1401 0.008 0.955 9.1 115.0 22.2 418 n/a 3_settarget: 0.1180 0.1401 0.008 0.955 9.1 115.0 22.2 418 n/a 3_updatecdl: 0.1180 0.1401 0.008 0.955 9.1 115.0 22.2 418 n/a 3_nqh: 0.1180 0.1403 0.008 0.955 9.1 115.0 22.2 418 n/a 3_sol: 0.1213 0.1412 0.008 0.955 9.1 115.0 21.1 428 n/a 3_weight: 0.1213 0.1412 0.008 0.955 9.1 115.0 21.1 428 n/a 3_xyzrec: 0.1165 0.1332 0.008 1.089 9.1 115.0 21.1 428 n/a 3_adp: 0.1166 0.1332 0.008 1.089 9.1 114.9 21.1 428 n/a 3_regHadp: 0.1166 0.1332 0.008 1.089 9.1 114.9 21.1 428 n/a 3_occ: 0.1157 0.1319 0.008 1.089 9.1 114.9 21.1 428 n/a 4_bss: 0.1148 0.1307 0.008 1.089 9.1 114.9 21.1 428 n/a 4_settarget: 0.1148 0.1307 0.008 1.089 9.1 114.9 21.1 428 n/a 4_updatecdl: 0.1148 0.1307 0.008 1.091 9.1 114.9 21.1 428 n/a 4_nqh: 0.1148 0.1307 0.008 1.091 9.1 114.9 21.1 428 n/a 4_sol: 0.1146 0.1287 0.008 1.091 9.1 114.9 21.1 447 n/a 4_weight: 0.1146 0.1287 0.008 1.091 9.1 114.9 21.1 447 n/a 4_xyzrec: 0.1141 0.1291 0.008 1.099 9.1 114.9 21.1 447 n/a 4_adp: 0.1141 0.1291 0.008 1.099 9.1 114.9 21.1 447 n/a 4_regHadp: 0.1141 0.1291 0.008 1.099 9.1 114.9 21.1 447 n/a 4_occ: 0.1134 0.1285 0.008 1.099 9.1 114.9 21.1 447 n/a 5_bss: 0.1132 0.1286 0.008 1.099 9.1 114.9 21.1 447 n/a 5_settarget: 0.1132 0.1286 0.008 1.099 9.1 114.9 21.1 447 n/a 5_updatecdl: 0.1132 0.1286 0.008 1.101 9.1 114.9 21.1 447 n/a 5_setrh: 0.1134 0.1286 0.008 1.101 9.1 114.9 21.1 447 n/a 5_nqh: 0.1134 0.1286 0.008 1.101 9.1 114.9 21.1 447 n/a 5_sol: 0.1132 0.1273 0.008 1.101 9.1 114.9 21.2 461 n/a 5_weight: 0.1132 0.1273 0.008 1.101 9.1 114.9 21.2 461 n/a 5_xyzrec: 0.1132 0.1272 0.008 1.123 9.1 114.9 21.2 461 n/a 5_adp: 0.1132 0.1272 0.008 1.123 9.1 114.9 21.2 461 n/a 5_regHadp: 0.1132 0.1272 0.008 1.123 9.1 114.9 21.2 461 n/a 5_occ: 0.1129 0.1271 0.008 1.123 9.1 114.9 21.2 461 n/a end: 0.1127 0.1270 0.008 1.123 9.1 114.9 21.2 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1664580_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1664580_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9700 Refinement macro-cycles (run) : 14169.5200 Write final files (write_after_run_outputs) : 75.3500 Total : 14248.8400 Total CPU time: 3.97 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:17:49 PST -0800 (1735366669.59 s) Start R-work = 0.1620, R-free = 0.1756 Final R-work = 0.1127, R-free = 0.1270 =============================================================================== Job complete usr+sys time: 14409.20 seconds wall clock time: 261 minutes 37.49 seconds (15697.49 seconds total)