Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.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_1522381.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.74, 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: 0.31 Conformation dependent library (CDL) restraints added in 108.7 milliseconds Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 391 0.89 - 1.14: 1224 1.14 - 1.40: 582 1.40 - 1.66: 894 1.66 - 1.91: 62 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.07e-02 8.73e+03 3.47e+02 bond pdb=" C CYS A 106 " pdb=" O CYS A 106 " ideal model delta sigma weight residual 1.235 1.470 -0.234 1.26e-02 6.30e+03 3.46e+02 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.459 1.240 0.220 1.19e-02 7.06e+03 3.41e+02 bond pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 1.233 1.001 0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.064 0.180 1.00e-02 1.00e+04 3.23e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 3295 4.91 - 9.83: 1855 9.83 - 14.74: 547 14.74 - 19.65: 71 19.65 - 24.57: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.15 134.91 -17.76 1.14e+00 7.69e-01 2.43e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 104.85 15.51 1.07e+00 8.73e-01 2.10e+02 angle pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" O ASN A 173 " ideal model delta sigma weight residual 119.05 133.57 -14.52 1.10e+00 8.26e-01 1.74e+02 angle pdb=" C VAL A 25 " pdb=" N MET A 26 " pdb=" CA MET A 26 " ideal model delta sigma weight residual 120.54 137.66 -17.12 1.35e+00 5.49e-01 1.61e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 120.03 107.87 12.16 9.90e-01 1.02e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.32: 943 17.32 - 34.63: 116 34.63 - 51.95: 37 51.95 - 69.26: 12 69.26 - 86.57: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 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 -153.83 -26.17 0 5.00e+00 4.00e-02 2.74e+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 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.276: 120 0.276 - 0.544: 80 0.544 - 0.813: 34 0.813 - 1.081: 7 1.081 - 1.349: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA THR A 124 " pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CB THR A 124 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.42 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.149 2.00e-02 2.50e+03 7.18e-02 1.55e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.079 2.00e-02 2.50e+03 6.58e-02 1.30e+02 pdb=" CG PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.048 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 BASN A 76 " -0.012 2.00e-02 2.50e+03 9.14e-02 1.25e+02 pdb=" CG BASN A 76 " 0.111 2.00e-02 2.50e+03 pdb=" OD1BASN A 76 " -0.086 2.00e-02 2.50e+03 pdb=" ND2BASN A 76 " 0.124 2.00e-02 2.50e+03 pdb="HD21BASN A 76 " -0.013 2.00e-02 2.50e+03 pdb="HD22BASN A 76 " -0.122 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1180 2.33 - 2.90: 8113 2.90 - 3.47: 10476 3.47 - 4.03: 15204 4.03 - 4.60: 21599 Nonbonded interactions: 56572 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.764 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.769 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.795 1.850 nonbonded pdb=" H THR A 124 " pdb=" OG1 THR A 154 " model vdw 1.821 1.850 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.831 2.100 ... (remaining 56567 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_1522381_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= 0.2609 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792011 | | target function (ml) not normalized (work): 232591.308943 | | target function (ml) not normalized (free): 11792.018701 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2094 7.0553 4.954| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1736 4.3522 4.3304| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1622 4.1283 4.1448| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1438 3.8347 3.8359| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1698 3.798 3.8329| | 6: 2.09 - 1.97 1.00 2846 113 0.2578 0.1869 3.4754 3.548| | 7: 1.97 - 1.87 1.00 2787 165 0.2552 0.1928 3.1425 3.2265| | 8: 1.87 - 1.79 1.00 2789 144 0.2402 0.1834 3.0656 3.1234| | 9: 1.79 - 1.72 1.00 2745 138 0.2439 0.1967 2.915 2.9377| | 10: 1.72 - 1.66 1.00 2789 158 0.2458 0.2029 2.7957 2.8935| | 11: 1.66 - 1.61 1.00 2740 147 0.2482 0.1718 2.7475 2.7401| | 12: 1.61 - 1.56 1.00 2787 146 0.2514 0.1908 2.6269 2.6354| | 13: 1.56 - 1.52 1.00 2745 130 0.2571 0.1906 2.5834 2.61| | 14: 1.52 - 1.48 1.00 2803 134 0.2570 0.1811 2.4963 2.4957| | 15: 1.48 - 1.45 1.00 2738 128 0.2637 0.2007 2.4351 2.4519| | 16: 1.45 - 1.42 1.00 2756 161 0.2672 0.2246 2.3881 2.5086| | 17: 1.42 - 1.39 1.00 2785 139 0.2632 0.2018 2.3352 2.3584| | 18: 1.39 - 1.36 1.00 2741 179 0.2656 0.2300 2.2923 2.3904| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2308 2.2447 2.2848| | 20: 1.34 - 1.32 1.00 2696 147 0.2659 0.2068 2.1907 2.1657| | 21: 1.32 - 1.30 1.00 2785 112 0.2698 0.2206 2.1542 2.1466| | 22: 1.29 - 1.27 1.00 2704 152 0.2774 0.2811 2.1253 2.2495| | 23: 1.27 - 1.26 1.00 2802 156 0.2792 0.2343 2.1167 2.1385| | 24: 1.26 - 1.24 1.00 2744 132 0.2746 0.2318 2.0695 2.126| | 25: 1.24 - 1.22 1.00 2734 148 0.2882 0.2321 2.0487 2.0213| | 26: 1.22 - 1.21 1.00 2727 135 0.2861 0.2164 2.0079 2.0493| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2644 1.9979 1.9889| | 28: 1.19 - 1.18 1.00 2671 147 0.2996 0.2465 1.9795 1.951| | 29: 1.18 - 1.16 1.00 2800 134 0.2995 0.2823 1.9683 2.0615| | 30: 1.16 - 1.15 1.00 2740 148 0.3040 0.2795 1.9333 1.9565| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.82 0.76 0.23 1475.89| | 2: 3.57 - 2.84 2876 122 0.80 26.03 1.27 0.23 1475.89| | 3: 2.84 - 2.48 2833 165 0.74 31.94 1.24 0.23 1224.00| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.25 0.25 570.30| | 5: 2.25 - 2.09 2756 127 0.77 29.33 1.28 0.25 570.30| | 6: 2.09 - 1.97 2846 113 0.84 22.61 1.29 0.25 312.12| | 7: 1.97 - 1.87 2787 165 0.90 16.50 1.28 0.26 91.93| | 8: 1.87 - 1.79 2789 144 0.86 20.99 1.24 0.26 91.93| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.25 55.12| | 10: 1.72 - 1.66 2789 158 0.86 20.28 1.23 0.25 47.75| | 11: 1.66 - 1.61 2740 147 0.86 21.21 1.23 0.25 46.05| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.23 0.25 28.87| | 13: 1.56 - 1.52 2745 130 0.87 19.90 1.24 0.25 28.87| | 14: 1.52 - 1.48 2803 134 0.86 20.81 1.24 0.25 25.83| | 15: 1.48 - 1.45 2738 128 0.87 20.04 1.24 0.25 20.27| | 16: 1.45 - 1.42 2756 161 0.86 21.37 1.23 0.25 20.27| | 17: 1.42 - 1.39 2785 139 0.87 20.46 1.23 0.25 17.42| | 18: 1.39 - 1.36 2741 179 0.87 20.72 1.22 0.25 15.78| | 19: 1.36 - 1.34 2807 134 0.85 22.03 1.22 0.25 15.78| | 20: 1.34 - 1.32 2696 147 0.87 20.53 1.21 0.24 12.89| | 21: 1.32 - 1.30 2785 112 0.86 21.57 1.20 0.24 12.69| | 22: 1.29 - 1.27 2704 152 0.85 22.29 1.22 0.24 12.38| | 23: 1.27 - 1.26 2802 156 0.86 21.87 1.21 0.24 10.81| | 24: 1.26 - 1.24 2744 132 0.86 22.32 1.20 0.24 10.81| | 25: 1.24 - 1.22 2734 148 0.85 23.35 1.21 0.24 10.19| | 26: 1.22 - 1.21 2727 135 0.84 23.57 1.20 0.23 9.49| | 27: 1.21 - 1.19 2814 148 0.84 24.19 1.20 0.23 9.49| | 28: 1.19 - 1.18 2671 147 0.83 24.74 1.19 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 25.24 1.17 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.81 26.53 1.15 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1475.89 mean = 214.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.38| |phase err.(test): min = 0.00 max = 89.71 mean = 22.25| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.253 1557 Z= 5.583 Angle : 5.316 19.200 2118 Z= 3.665 Chirality : 0.401 1.349 243 Planarity : 0.031 0.086 284 Dihedral : 13.837 86.569 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 5.59 % Favored : 93.17 % Cbeta Deviations : 35.68 % 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: -2.36 (0.49), residues: 224 helix: -2.65 (0.39), residues: 103 sheet: -0.39 (0.73), residues: 38 loop : -0.27 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.016 ARG A 156 TYR 0.143 0.050 TYR A 141 PHE 0.116 0.044 PHE A 119 HIS 0.047 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792011 | | target function (ml) not normalized (work): 232591.308943 | | target function (ml) not normalized (free): 11792.018701 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1934 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1934 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1990 0.1934 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2008 0.2013 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1647 0.1642 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 0.3835 386.628 358.003 0.735 0.915 0.401 11.894-9.307 99.02 97 4 0.1808 614.139 593.788 1.020 0.915 0.370 9.237-7.194 100.00 213 7 0.2162 502.290 491.393 1.053 0.916 0.360 7.162-5.571 100.00 427 22 0.2125 376.941 365.920 1.018 0.917 0.330 5.546-4.326 100.00 867 58 0.1307 517.447 510.547 1.054 0.917 0.219 4.315-3.360 100.00 1859 96 0.1142 492.095 488.493 1.099 0.919 0.163 3.356-2.611 100.00 3867 181 0.1443 323.281 320.004 1.085 0.920 0.129 2.608-2.026 99.99 8198 413 0.1366 214.306 212.016 1.091 0.923 0.000 2.025-1.573 100.00 17313 902 0.1654 104.656 103.931 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2065 46.409 45.173 1.069 0.936 0.000 1.221-1.150 99.97 13689 708 0.2586 29.241 27.019 1.031 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0438 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.231641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.434230 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 0.1704 0.1819 0.0114 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1605 0.1741 0.0136 0.002 0.4 5.1 0.0 0.0 0 0.250 0.1448 0.1624 0.0176 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1393 0.1587 0.0194 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1357 0.1569 0.0212 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1345 0.1548 0.0204 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1294 0.1518 0.0224 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1272 0.1503 0.0231 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1255 0.1491 0.0236 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1244 0.1478 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1241 0.1477 0.0236 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1239 0.1481 0.0242 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1231 0.1467 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1474 0.0243 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1228 0.1466 0.0238 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1470 0.0243 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1472 0.0246 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1223 0.1473 0.0249 0.008 1.0 4.2 0.5 0.6 0 13.616 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1466 0.0238 0.006 0.9 4.2 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.66 2.38 3.013 19.050 2029.434 0.017 12.28 14.65 2.37 2.989 19.050 60.883 0.017 12.35 14.65 2.30 2.668 19.048 253.679 0.017 12.67 15.31 2.64 2.737 19.207 1014.717 0.017 12.51 15.44 2.93 3.261 19.585 2029.434 0.016 12.39 15.36 2.97 3.080 19.476 3044.151 0.015 12.39 15.50 3.11 3.408 19.647 4058.868 0.015 12.30 15.44 3.14 3.338 19.608 5073.586 0.015 12.22 15.39 3.17 3.389 19.632 6088.303 0.015 12.19 15.40 3.21 3.342 19.603 7103.020 0.015 12.20 15.46 3.26 3.370 19.606 8117.737 0.015 12.20 15.50 3.30 3.374 19.586 9132.454 0.015 12.18 15.50 3.32 3.559 19.679 10147.171 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: 253.679 Accepted refinement result: 12.35 14.65 2.30 2.668 19.048 253.679 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.07 3.31 0 1785 Protein: 9.06 114.98 16.98 3.32 0 1519 Water: 11.46 119.44 38.22 N/A 0 258 Other: 19.70 26.60 22.05 N/A 0 8 Chain A: 9.06 119.44 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1465 r_work=0.1237 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1469 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 = 0.1230 r_free = 0.1460 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= 0.1230 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016993 | | target function (ls_wunit_k1) not normalized (work): 1415.465004 | | target function (ls_wunit_k1) not normalized (free): 108.235127 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1230 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1670 0.1695 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1676 0.1677 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1230 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1453 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 0.3571 301.840 281.337 0.642 1.003 0.373 11.894-9.307 99.02 97 4 0.1667 483.531 471.243 0.924 1.003 0.369 9.237-7.194 100.00 213 7 0.1918 395.469 389.130 0.964 1.003 0.346 7.162-5.571 100.00 427 22 0.1836 296.777 290.765 0.938 1.003 0.290 5.546-4.326 100.00 867 58 0.1000 407.402 404.714 0.962 1.003 0.199 4.315-3.360 100.00 1859 96 0.0873 387.442 386.285 1.008 1.003 0.170 3.356-2.611 100.00 3867 181 0.1177 254.529 253.407 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1024 168.730 168.031 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.399 82.591 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.539 36.041 1.018 0.996 0.000 1.221-1.150 99.97 13689 708 0.2255 23.022 21.494 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=0.0579 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1231 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1453 | n_water=258 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1240 r_free=0.1454 | n_water=250 | time (s): 21.640 (total time: 23.320) Filter (q & B) r_work=0.1242 r_free=0.1454 | n_water=247 | time (s): 2.380 (total time: 25.700) Compute maps r_work=0.1242 r_free=0.1454 | n_water=247 | time (s): 1.210 (total time: 26.910) Filter (map) r_work=0.1254 r_free=0.1452 | n_water=228 | time (s): 2.600 (total time: 29.510) Find peaks r_work=0.1254 r_free=0.1452 | n_water=228 | time (s): 0.680 (total time: 30.190) Add new water r_work=0.1392 r_free=0.1616 | n_water=430 | time (s): 3.380 (total time: 33.570) Refine new water occ: r_work=0.1302 r_free=0.1476 adp: r_work=0.1224 r_free=0.1429 occ: r_work=0.1237 r_free=0.1414 adp: r_work=0.1204 r_free=0.1401 occ: r_work=0.1207 r_free=0.1389 adp: r_work=0.1198 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1390 r_work=0.1198 r_free=0.1390 | n_water=430 | time (s): 66.970 (total time: 100.540) Filter (q & B) r_work=0.1201 r_free=0.1388 | n_water=415 | time (s): 2.620 (total time: 103.160) Filter (dist only) r_work=0.1202 r_free=0.1387 | n_water=414 | time (s): 33.010 (total time: 136.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.580719 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1481.960182 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 0.1653 0.1766 0.0113 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1535 0.1660 0.0125 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1407 0.1553 0.0146 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1350 0.1506 0.0156 0.001 0.5 5.1 0.0 0.0 0 0.750 0.1311 0.1474 0.0163 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1324 0.1485 0.0162 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1259 0.1441 0.0182 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1226 0.1421 0.0194 0.003 0.6 5.4 0.5 0.0 0 3.000 0.1215 0.1412 0.0197 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1210 0.1417 0.0208 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1208 0.1420 0.0212 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1200 0.1416 0.0216 0.005 0.8 6.1 0.5 0.0 0 7.000 0.1196 0.1409 0.0213 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1191 0.1407 0.0216 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1188 0.1406 0.0218 0.006 0.9 5.8 0.5 0.0 0 10.000 0.1185 0.1401 0.0216 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1184 0.1400 0.0217 0.007 0.9 6.1 0.5 0.0 0 12.000 0.1183 0.1403 0.0219 0.008 0.9 5.4 0.5 0.0 0 13.790 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1184 0.1400 0.0217 0.007 0.9 6.1 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 14.00 2.17 3.774 21.746 1481.960 0.016 11.84 14.00 2.17 3.774 21.746 44.459 0.016 11.84 14.00 2.17 3.774 21.746 185.245 0.016 12.01 14.41 2.40 3.632 21.747 740.980 0.015 12.03 14.73 2.69 3.558 21.805 1481.960 0.015 11.90 14.71 2.81 3.499 21.894 2222.940 0.014 11.80 14.66 2.86 3.513 21.884 2963.920 0.014 11.76 14.64 2.87 3.510 22.066 3704.900 0.014 11.69 14.60 2.90 3.507 21.991 4445.881 0.014 11.69 14.67 2.98 3.527 22.004 5186.861 0.014 11.67 14.65 2.97 3.552 22.040 5927.841 0.014 11.63 14.64 3.01 3.578 22.125 6668.821 0.014 11.62 14.65 3.03 3.586 22.082 7409.801 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: 44.459 Accepted refinement result: 11.84 14.00 2.17 3.774 21.746 44.459 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.02 22.14 3.31 186 1755 Protein: 9.09 115.02 17.02 3.32 0 1519 Water: 11.50 76.69 40.91 N/A 186 228 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.09 115.02 19.49 N/A 0 1755 Chain S: 13.52 60.00 47.09 N/A 186 0 Histogram: Values Number of atoms 9.09 - 19.69 1261 19.69 - 30.28 245 30.28 - 40.87 160 40.87 - 51.46 128 51.46 - 62.06 124 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1400 r_work=0.1184 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1400 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 = 0.1186 r_free = 0.1400 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1186 r_free= 0.1400 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015126 | | target function (ls_wunit_k1) not normalized (work): 1259.898658 | | target function (ls_wunit_k1) not normalized (free): 100.182032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1186 0.1400 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1583 0.1582 0.1637 n_refl.: 87592 remove outliers: r(all,work,free)=0.1583 0.1582 0.1637 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1585 0.1584 0.1639 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1183 0.1395 n_refl.: 87592 remove outliers: r(all,work,free)=0.1193 0.1182 0.1395 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 0.3441 300.386 277.215 0.591 1.002 0.360 11.894-9.307 99.02 97 4 0.1707 483.531 476.723 0.913 1.003 0.330 9.237-7.194 100.00 213 7 0.1689 395.469 393.756 0.981 1.003 0.270 7.162-5.571 100.00 427 22 0.1571 296.777 292.576 0.938 1.003 0.260 5.546-4.326 100.00 867 58 0.0894 407.402 404.390 0.958 1.003 0.200 4.315-3.360 100.00 1859 96 0.0779 387.442 386.612 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1089 254.529 253.733 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1004 168.730 168.247 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.399 82.617 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.539 36.076 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 23.022 21.525 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=0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1395 | n_water=414 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1182 r_free=0.1388 | n_water=411 | time (s): 31.200 (total time: 32.890) Filter (q & B) r_work=0.1182 r_free=0.1388 | n_water=411 | time (s): 0.760 (total time: 33.650) Compute maps r_work=0.1182 r_free=0.1388 | n_water=411 | time (s): 1.400 (total time: 35.050) Filter (map) r_work=0.1213 r_free=0.1389 | n_water=292 | time (s): 2.450 (total time: 37.500) Find peaks r_work=0.1213 r_free=0.1389 | n_water=292 | time (s): 0.570 (total time: 38.070) Add new water r_work=0.1323 r_free=0.1505 | n_water=465 | time (s): 3.050 (total time: 41.120) Refine new water occ: r_work=0.1242 r_free=0.1424 adp: r_work=0.1243 r_free=0.1427 occ: r_work=0.1221 r_free=0.1403 adp: r_work=0.1220 r_free=0.1403 occ: r_work=0.1205 r_free=0.1386 adp: r_work=0.1201 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1385 r_work=0.1201 r_free=0.1385 | n_water=465 | time (s): 114.540 (total time: 155.660) Filter (q & B) r_work=0.1205 r_free=0.1393 | n_water=437 | time (s): 2.650 (total time: 158.310) Filter (dist only) r_work=0.1205 r_free=0.1391 | n_water=436 | time (s): 35.620 (total time: 193.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.978056 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 0.1364 0.0129 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1189 0.1331 0.0142 0.003 0.7 3.2 0.5 0.0 0 0.267 0.1175 0.1319 0.0145 0.004 0.8 3.2 0.5 0.0 0 0.534 0.1167 0.1320 0.0153 0.005 0.9 2.9 0.5 0.0 0 0.801 0.1162 0.1318 0.0155 0.006 1.0 3.2 0.5 0.0 0 1.068 0.1160 0.1315 0.0155 0.007 1.0 3.8 0.5 0.0 0 1.335 0.1157 0.1316 0.0159 0.007 1.0 3.8 0.5 0.0 0 1.603 0.1156 0.1316 0.0160 0.008 1.1 3.8 0.5 0.0 0 1.870 0.1165 0.1319 0.0154 0.005 0.9 2.9 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1315 0.0155 0.007 1.0 3.8 0.5 0.0 0 1.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.15 1.55 3.778 21.294 48.978 3.626 11.60 13.15 1.55 3.778 21.294 1.469 3.626 11.61 13.15 1.55 3.768 21.294 6.122 3.626 11.64 13.23 1.59 3.713 21.278 24.489 3.619 11.65 13.30 1.65 3.735 21.242 48.978 3.617 11.56 13.25 1.70 3.763 21.233 73.467 3.610 11.50 13.21 1.71 3.775 21.233 97.956 3.605 11.50 13.25 1.75 3.794 21.212 122.445 3.605 11.50 13.25 1.76 3.812 21.197 146.934 3.603 11.46 13.23 1.76 3.822 21.198 171.423 3.601 11.44 13.19 1.74 3.828 21.192 195.912 3.599 11.43 13.19 1.76 3.835 21.194 220.401 3.598 11.41 13.16 1.75 3.843 21.189 244.890 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.469 Accepted refinement result: 11.60 13.15 1.55 3.778 21.294 1.469 3.626 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.29 3.31 208 1755 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 36.12 N/A 208 228 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.03 19.50 N/A 0 1755 Chain S: 13.53 60.01 36.40 N/A 208 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 284 30.29 - 40.88 202 40.88 - 51.48 135 51.48 - 62.07 56 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1315 r_work=0.1160 r_free=0.1315 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1315 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1312 target_work(ml) = 3.616 | | 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= 0.1149 r_free= 0.1312 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616284 | | target function (ml) not normalized (work): 301214.755712 | | target function (ml) not normalized (free): 15851.502953 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1149 0.1312 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1489 0.1489 0.1528 n_refl.: 87590 remove outliers: r(all,work,free)=0.1489 0.1489 0.1528 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1488 0.1488 0.1527 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1143 0.1306 n_refl.: 87590 remove outliers: r(all,work,free)=0.1148 0.1140 0.1306 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 0.3857 288.908 271.131 0.499 1.001 0.320 11.894-9.307 97.06 95 4 0.2385 483.755 461.059 0.870 1.002 0.280 9.237-7.194 98.64 210 7 0.2332 388.963 388.533 0.952 1.002 0.180 7.162-5.571 100.00 427 22 0.2074 296.777 285.509 0.918 1.002 0.164 5.546-4.326 100.00 867 58 0.1124 407.402 403.081 0.963 1.002 0.150 4.315-3.360 100.00 1859 96 0.0921 387.442 384.954 1.005 1.002 0.150 3.356-2.611 100.00 3867 181 0.1116 254.529 252.592 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.0932 168.730 168.025 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.399 82.668 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.539 36.126 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.022 21.561 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=-0.0128 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1306 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1140 r_free=0.1305 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1305 | n_water=436 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1140 r_free=0.1307 | n_water=433 | time (s): 47.690 (total time: 50.160) Filter (q & B) r_work=0.1140 r_free=0.1307 | n_water=433 | time (s): 1.320 (total time: 51.480) Compute maps r_work=0.1140 r_free=0.1307 | n_water=433 | time (s): 1.910 (total time: 53.390) Filter (map) r_work=0.1176 r_free=0.1318 | n_water=332 | time (s): 3.740 (total time: 57.130) Find peaks r_work=0.1176 r_free=0.1318 | n_water=332 | time (s): 0.660 (total time: 57.790) Add new water r_work=0.1241 r_free=0.1380 | n_water=498 | time (s): 3.660 (total time: 61.450) Refine new water occ: r_work=0.1165 r_free=0.1318 adp: r_work=0.1166 r_free=0.1317 occ: r_work=0.1148 r_free=0.1300 adp: r_work=0.1147 r_free=0.1299 occ: r_work=0.1136 r_free=0.1286 adp: r_work=0.1132 r_free=0.1284 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1284 r_work=0.1132 r_free=0.1284 | n_water=498 | time (s): 236.250 (total time: 297.700) Filter (q & B) r_work=0.1139 r_free=0.1285 | n_water=457 | time (s): 3.850 (total time: 301.550) Filter (dist only) r_work=0.1139 r_free=0.1284 | n_water=456 | time (s): 48.470 (total time: 350.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.726405 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 32.187941 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 0.1198 0.1317 0.0119 0.002 0.6 3.8 0.5 0.0 0 0.086 0.1157 0.1290 0.0133 0.003 0.8 4.2 0.5 0.0 0 0.259 0.1148 0.1288 0.0140 0.004 0.9 3.2 0.5 0.0 0 0.518 0.1142 0.1287 0.0145 0.006 0.9 2.9 0.5 0.0 0 0.777 0.1137 0.1284 0.0147 0.006 1.0 3.2 0.5 0.0 0 1.036 0.1134 0.1282 0.0148 0.007 1.1 3.5 0.5 0.0 0 1.295 0.1132 0.1282 0.0150 0.008 1.1 3.5 0.5 0.0 0 1.554 0.1131 0.1283 0.0152 0.008 1.1 3.5 0.5 0.0 0 1.813 0.1140 0.1284 0.0145 0.006 1.0 3.2 0.5 0.0 0 0.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1282 0.0150 0.008 1.1 3.5 0.5 0.0 0 1.554 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.82 1.50 3.779 21.329 32.188 3.606 11.32 12.82 1.50 3.779 21.329 0.966 3.606 11.32 12.82 1.50 3.779 21.329 4.023 3.606 11.36 12.85 1.49 3.708 21.322 16.094 3.603 11.39 12.93 1.55 3.722 21.309 32.188 3.603 11.39 12.99 1.59 3.738 21.288 48.282 3.602 11.34 12.96 1.62 3.754 21.282 64.376 3.599 11.30 12.93 1.63 3.764 21.278 80.470 3.595 11.29 12.92 1.63 3.771 21.275 96.564 3.593 11.25 12.89 1.64 3.778 21.275 112.658 3.591 11.25 12.92 1.66 3.788 21.266 128.752 3.591 11.24 12.91 1.68 3.797 21.263 144.846 3.589 11.23 12.92 1.69 3.805 21.260 160.940 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 0.966 Accepted refinement result: 11.32 12.82 1.50 3.779 21.329 0.966 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.36 3.31 230 1753 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 35.77 N/A 230 226 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.10 115.03 19.47 N/A 0 1753 Chain S: 13.53 60.01 35.75 N/A 230 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 291 30.29 - 40.88 211 40.88 - 51.47 143 51.47 - 62.06 52 62.06 - 72.66 11 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1282 r_work=0.1132 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1282 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1277 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603928 | | target function (ml) not normalized (work): 300156.753832 | | target function (ml) not normalized (free): 15812.804010 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1277 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1460 0.1458 0.1514 n_refl.: 87582 remove outliers: r(all,work,free)=0.1460 0.1458 0.1514 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1459 0.1458 0.1514 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1126 0.1282 n_refl.: 87582 remove outliers: r(all,work,free)=0.1131 0.1123 0.1282 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 0.3898 286.317 249.400 0.446 0.999 0.297 11.894-9.307 94.12 92 4 0.2515 466.800 461.656 0.865 1.001 0.223 9.237-7.194 98.18 209 7 0.2334 386.930 382.831 0.932 1.002 0.170 7.162-5.571 100.00 427 22 0.2104 296.777 285.456 0.912 1.002 0.130 5.546-4.326 100.00 867 58 0.1082 407.402 403.084 0.963 1.002 0.115 4.315-3.360 100.00 1859 96 0.0906 387.442 385.283 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1090 254.529 252.798 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0909 168.730 168.059 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.399 82.703 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.539 36.123 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2169 23.022 21.549 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0105 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1282 After: r_work=0.1124 r_free=0.1282 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1282 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=0.1124 r_free=0.1282 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1282 | n_water=456 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1124 r_free=0.1283 | n_water=454 | time (s): 49.600 (total time: 52.080) Filter (q & B) r_work=0.1126 r_free=0.1286 | n_water=451 | time (s): 3.970 (total time: 56.050) Compute maps r_work=0.1126 r_free=0.1286 | n_water=451 | time (s): 1.680 (total time: 57.730) Filter (map) r_work=0.1156 r_free=0.1299 | n_water=358 | time (s): 3.720 (total time: 61.450) Find peaks r_work=0.1156 r_free=0.1299 | n_water=358 | time (s): 0.680 (total time: 62.130) Add new water r_work=0.1196 r_free=0.1348 | n_water=500 | time (s): 3.720 (total time: 65.850) Refine new water occ: r_work=0.1143 r_free=0.1297 adp: r_work=0.1144 r_free=0.1300 occ: r_work=0.1133 r_free=0.1285 adp: r_work=0.1132 r_free=0.1286 occ: r_work=0.1126 r_free=0.1273 adp: r_work=0.1123 r_free=0.1274 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1274 r_work=0.1123 r_free=0.1274 | n_water=500 | time (s): 200.240 (total time: 266.090) Filter (q & B) r_work=0.1131 r_free=0.1277 | n_water=458 | time (s): 3.930 (total time: 270.020) Filter (dist only) r_work=0.1131 r_free=0.1275 | n_water=457 | time (s): 46.200 (total time: 316.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.804466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.985215 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 0.1213 0.1326 0.0113 0.004 0.7 6.7 0.0 0.0 0 0.090 0.1167 0.1298 0.0130 0.004 0.8 6.1 0.0 0.0 0 0.271 0.1152 0.1288 0.0136 0.005 0.9 6.4 0.5 0.0 0 0.541 0.1142 0.1281 0.0139 0.006 1.0 6.7 0.5 0.0 0 0.812 0.1135 0.1277 0.0141 0.007 1.1 6.1 0.5 0.0 0 1.083 0.1132 0.1275 0.0144 0.008 1.1 6.1 0.5 0.0 0 1.353 0.1131 0.1275 0.0144 0.008 1.1 6.1 0.5 0.0 0 1.624 0.1131 0.1275 0.0145 0.008 1.1 6.1 0.5 0.0 0 1.895 0.1139 0.1279 0.0140 0.006 1.0 6.1 0.5 0.0 0 0.902 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1275 0.0145 0.008 1.1 6.1 0.5 0.0 0 1.895 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.75 1.45 3.779 21.289 37.985 3.604 11.31 12.75 1.45 3.779 21.289 1.140 3.604 11.31 12.75 1.45 3.779 21.289 4.748 3.604 11.34 12.78 1.44 3.711 21.282 18.993 3.599 11.45 12.97 1.52 3.722 21.255 37.985 3.606 11.36 12.93 1.58 3.746 21.243 56.978 3.599 11.30 12.90 1.60 3.762 21.240 75.970 3.594 11.27 12.89 1.62 3.773 21.237 94.963 3.592 11.25 12.89 1.63 3.783 21.233 113.956 3.590 11.23 12.87 1.64 3.790 21.232 132.948 3.588 11.24 12.91 1.67 3.805 21.221 151.941 3.589 11.22 12.90 1.67 3.813 21.219 170.933 3.587 11.20 12.87 1.67 3.820 21.218 189.926 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: 1.140 Accepted refinement result: 11.31 12.75 1.45 3.779 21.289 1.140 3.604 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.29 3.31 233 1751 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.51 76.69 35.46 N/A 233 224 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.02 19.43 N/A 0 1751 Chain S: 13.52 60.00 35.27 N/A 233 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.28 291 30.28 - 40.88 217 40.88 - 51.47 138 51.47 - 62.06 50 62.06 - 72.65 11 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1275 r_work=0.1131 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1275 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1271 target_work(ml) = 3.602 | | 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= 0.1128 r_free= 0.1271 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601996 | | target function (ml) not normalized (work): 299974.227935 | | target function (ml) not normalized (free): 15796.659476 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1330 0.1309 5.6526 5.5835| | 2: 3.57 - 2.84 1.00 2888 124 0.1055 0.1360 5.1441 5.2131| | 3: 2.83 - 2.48 1.00 2820 163 0.1078 0.1182 4.9273 4.9636| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.0984 4.6143 4.643| | 5: 2.25 - 2.09 1.00 2756 127 0.0865 0.0921 4.5612 4.6041| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.1001 4.255 4.3507| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1092 3.9798 4.0833| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1123 3.8864 4.0059| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1153 3.6418 3.8157| | 10: 1.72 - 1.66 1.00 2831 160 0.0916 0.1191 3.5637 3.7166| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1025 3.4963 3.5739| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1141 3.3306 3.4598| | 13: 1.56 - 1.52 1.00 2745 130 0.0943 0.1030 3.3069 3.4063| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1064 3.2415 3.3277| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1188 3.1549 3.2509| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1227 3.1338 3.2398| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1322 3.1195 3.2391| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1337 3.1047 3.2403| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1539 3.1139 3.259| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1458 3.1119 3.1535| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1520 3.1156 3.1109| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.1996 3.1256 3.2959| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1802 3.1342 3.2015| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1823 3.129 3.2241| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2152 3.1443 3.2594| | 26: 1.22 - 1.21 1.00 2727 135 0.1912 0.1761 3.1514 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2155 3.1739 3.163| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2303 3.1684 3.1746| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2400 3.1505 3.2345| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2449 3.1448 3.1702| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.22 1.00 0.97 5449.68| | 2: 3.57 - 2.84 2888 124 0.93 12.07 1.01 0.97 5449.68| | 3: 2.83 - 2.48 2820 163 0.90 15.98 0.99 0.98 4558.27| | 4: 2.47 - 2.25 2825 136 0.92 13.03 1.00 0.98 2259.61| | 5: 2.25 - 2.09 2756 127 0.91 15.20 1.01 0.98 2259.61| | 6: 2.09 - 1.97 2846 113 0.93 12.13 1.02 0.98 1315.37| | 7: 1.97 - 1.87 2787 165 0.95 9.26 1.02 0.98 510.05| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.98 510.05| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.97 289.96| | 10: 1.72 - 1.66 2831 160 0.94 11.15 0.98 0.97 245.88| | 11: 1.66 - 1.61 2712 147 0.93 11.78 0.98 0.97 235.55| | 12: 1.61 - 1.56 2773 144 0.96 8.88 0.99 0.97 138.13| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.97 138.13| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.80| | 15: 1.48 - 1.45 2738 128 0.95 9.88 1.02 0.98 97.57| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.98 97.57| | 17: 1.42 - 1.39 2785 139 0.95 10.85 1.01 0.98 88.91| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.90| | 19: 1.36 - 1.34 2807 134 0.94 11.83 1.00 0.98 83.90| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 79.93| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.97 79.65| | 22: 1.29 - 1.27 2704 152 0.93 13.61 0.98 0.96 80.09| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.34| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.34| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.40| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.03 0.93 86.68| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.68| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.93 90.63| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.93 92.11| | 30: 1.16 - 1.15 2739 148 0.86 22.08 0.98 0.93 92.11| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 79.65 max = 5449.68 mean = 849.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.36| |phase err.(test): min = 0.00 max = 89.28 mean = 13.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1128 0.1271 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1448 0.1449 0.1470 n_refl.: 87576 remove outliers: r(all,work,free)=0.1448 0.1449 0.1470 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1448 0.1448 0.1469 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1127 0.1272 n_refl.: 87576 remove outliers: r(all,work,free)=0.1133 0.1126 0.1272 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4042 286.317 252.895 0.442 1.000 0.292 11.894-9.307 93.14 91 4 0.2461 470.691 449.956 0.835 1.001 0.207 9.237-7.194 97.27 207 7 0.2322 387.538 380.674 0.921 1.002 0.140 7.162-5.571 100.00 427 22 0.2128 296.777 285.269 0.907 1.002 0.120 5.546-4.326 100.00 867 58 0.1118 407.402 402.783 0.963 1.002 0.111 4.315-3.360 100.00 1859 96 0.0911 387.442 385.306 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1097 254.529 252.968 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0902 168.730 168.212 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.399 82.749 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.539 36.147 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 23.022 21.563 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0109 ================= 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 : 0.2609 0.1934 0.084 5.316 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_weight: 0.1642 0.1756 0.084 5.316 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1228 0.1466 0.006 0.887 9.0 119.5 20.1 258 0.135 1_adp: 0.1235 0.1465 0.006 0.887 9.1 119.4 20.1 258 0.135 1_regHadp: 0.1237 0.1469 0.006 0.887 9.1 119.4 20.1 258 0.135 1_occ: 0.1230 0.1460 0.006 0.887 9.1 119.4 20.1 258 0.135 2_bss: 0.1229 0.1453 0.006 0.887 9.1 119.5 20.1 258 0.135 2_settarget: 0.1229 0.1453 0.006 0.887 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1229 0.1453 0.006 0.890 9.1 119.5 20.1 258 0.135 2_nqh: 0.1231 0.1453 0.006 0.890 9.1 119.5 20.1 258 0.138 2_sol: 0.1202 0.1387 0.006 0.890 9.1 115.0 22.1 414 n/a 2_weight: 0.1202 0.1387 0.006 0.890 9.1 115.0 22.1 414 n/a 2_xyzrec: 0.1184 0.1400 0.007 0.907 9.1 115.0 22.1 414 n/a 2_adp: 0.1184 0.1400 0.007 0.907 9.1 115.0 22.1 414 n/a 2_regHadp: 0.1184 0.1400 0.007 0.907 9.1 115.0 22.1 414 n/a 2_occ: 0.1186 0.1400 0.007 0.907 9.1 115.0 22.1 414 n/a 3_bss: 0.1182 0.1395 0.007 0.907 9.1 115.0 22.1 414 n/a 3_settarget: 0.1182 0.1395 0.007 0.907 9.1 115.0 22.1 414 n/a 3_updatecdl: 0.1182 0.1395 0.007 0.909 9.1 115.0 22.1 414 n/a 3_nqh: 0.1182 0.1395 0.007 0.909 9.1 115.0 22.1 414 n/a 3_sol: 0.1205 0.1391 0.007 0.909 9.1 115.0 21.3 436 n/a 3_weight: 0.1205 0.1391 0.007 0.909 9.1 115.0 21.3 436 n/a 3_xyzrec: 0.1160 0.1315 0.007 1.013 9.1 115.0 21.3 436 n/a 3_adp: 0.1160 0.1315 0.007 1.013 9.1 115.0 21.3 436 n/a 3_regHadp: 0.1160 0.1315 0.007 1.013 9.1 115.0 21.3 436 n/a 3_occ: 0.1149 0.1312 0.007 1.013 9.1 115.0 21.3 436 n/a 4_bss: 0.1140 0.1306 0.007 1.013 9.1 115.0 21.3 436 n/a 4_settarget: 0.1140 0.1306 0.007 1.013 9.1 115.0 21.3 436 n/a 4_updatecdl: 0.1140 0.1306 0.007 1.016 9.1 115.0 21.3 436 n/a 4_nqh: 0.1140 0.1305 0.007 1.016 9.1 115.0 21.3 436 n/a 4_sol: 0.1139 0.1284 0.007 1.016 9.1 115.0 21.4 456 n/a 4_weight: 0.1139 0.1284 0.007 1.016 9.1 115.0 21.4 456 n/a 4_xyzrec: 0.1132 0.1282 0.008 1.091 9.1 115.0 21.4 456 n/a 4_adp: 0.1132 0.1282 0.008 1.091 9.1 115.0 21.4 456 n/a 4_regHadp: 0.1132 0.1282 0.008 1.091 9.1 115.0 21.4 456 n/a 4_occ: 0.1126 0.1277 0.008 1.091 9.1 115.0 21.4 456 n/a 5_bss: 0.1123 0.1282 0.008 1.091 9.1 115.0 21.4 456 n/a 5_settarget: 0.1123 0.1282 0.008 1.091 9.1 115.0 21.4 456 n/a 5_updatecdl: 0.1123 0.1282 0.008 1.092 9.1 115.0 21.4 456 n/a 5_setrh: 0.1124 0.1282 0.008 1.092 9.1 115.0 21.4 456 n/a 5_nqh: 0.1124 0.1282 0.008 1.092 9.1 115.0 21.4 456 n/a 5_sol: 0.1131 0.1275 0.008 1.092 9.1 115.0 21.3 457 n/a 5_weight: 0.1131 0.1275 0.008 1.092 9.1 115.0 21.3 457 n/a 5_xyzrec: 0.1131 0.1275 0.008 1.108 9.1 115.0 21.3 457 n/a 5_adp: 0.1131 0.1275 0.008 1.108 9.1 115.0 21.3 457 n/a 5_regHadp: 0.1131 0.1275 0.008 1.108 9.1 115.0 21.3 457 n/a 5_occ: 0.1128 0.1271 0.008 1.108 9.1 115.0 21.3 457 n/a end: 0.1126 0.1272 0.008 1.108 9.1 115.0 21.3 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1522381_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1522381_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1100 Refinement macro-cycles (run) : 13274.1500 Write final files (write_after_run_outputs) : 90.6700 Total : 13367.9300 Total CPU time: 3.72 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:05:35 PST -0800 (1735365935.36 s) Start R-work = 0.1642, R-free = 0.1756 Final R-work = 0.1126, R-free = 0.1272 =============================================================================== Job complete usr+sys time: 13551.45 seconds wall clock time: 249 minutes 53.33 seconds (14993.33 seconds total)