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_3120282.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.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" } 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: 1.30, per 1000 atoms: 0.38 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: 0.47 Conformation dependent library (CDL) restraints added in 135.0 milliseconds Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 397 0.89 - 1.14: 1208 1.14 - 1.39: 565 1.39 - 1.64: 914 1.64 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.506 -0.185 1.00e-02 1.00e+04 3.42e+02 bond pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " ideal model delta sigma weight residual 1.459 1.670 -0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " ideal model delta sigma weight residual 1.459 1.244 0.215 1.21e-02 6.83e+03 3.17e+02 bond pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta sigma weight residual 1.454 1.229 0.225 1.27e-02 6.20e+03 3.14e+02 bond pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.22e-02 6.72e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 3188 4.77 - 9.53: 1877 9.53 - 14.30: 618 14.30 - 19.07: 88 19.07 - 23.83: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 140.42 -17.75 1.02e+00 9.61e-01 3.03e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.53 -15.03 1.00e+00 1.00e+00 2.26e+02 angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 134.92 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 134.31 -13.76 1.06e+00 8.90e-01 1.69e+02 angle pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 120.55 134.06 -13.51 1.06e+00 8.90e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 929 17.29 - 34.58: 127 34.58 - 51.88: 43 51.88 - 69.17: 9 69.17 - 86.46: 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 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 98 0.222 - 0.441: 79 0.441 - 0.660: 48 0.660 - 0.879: 16 0.879 - 1.099: 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 -1.49 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.023 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.135 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.145 9.50e-02 1.11e+02 7.50e-02 7.62e+01 pdb=" NE ARG A 27 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.016 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.010 2.00e-02 2.50e+03 4.87e-02 7.12e+01 pdb=" CG PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.051 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1409 2.37 - 2.93: 8343 2.93 - 3.48: 10434 3.48 - 4.04: 15114 4.04 - 4.60: 21323 Nonbonded interactions: 56623 Sorted by model distance: nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.811 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.828 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.846 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.858 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.868 2.100 ... (remaining 56618 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_3120282_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= 0.2607 r_free= 0.1932 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789145 | | target function (ml) not normalized (work): 232352.472847 | | target function (ml) not normalized (free): 11822.019991 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3034 0.2137 7.054 4.9576| | 2: 3.57 - 2.84 1.00 2876 122 0.2443 0.1743 4.3523 4.3211| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1606 4.1316 4.1622| | 4: 2.47 - 2.25 1.00 2825 136 0.2338 0.1415 3.8342 3.8193| | 5: 2.25 - 2.09 1.00 2756 127 0.2482 0.1614 3.7975 3.8344| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1681 3.4736 3.5122| | 7: 1.97 - 1.87 1.00 2787 165 0.2488 0.1688 3.1201 3.1539| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1914 3.0574 3.1974| | 9: 1.79 - 1.72 1.00 2745 138 0.2399 0.1837 2.883 2.9101| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1938 2.7944 2.9247| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1823 2.7418 2.7453| | 12: 1.61 - 1.56 1.00 2787 146 0.2534 0.1940 2.6209 2.6264| | 13: 1.56 - 1.52 1.00 2745 130 0.2561 0.1841 2.5641 2.6238| | 14: 1.52 - 1.48 1.00 2803 134 0.2519 0.1901 2.494 2.5343| | 15: 1.48 - 1.45 1.00 2738 128 0.2611 0.2306 2.4279 2.5735| | 16: 1.45 - 1.42 1.00 2756 161 0.2645 0.2074 2.3775 2.4019| | 17: 1.42 - 1.39 1.00 2785 139 0.2690 0.2138 2.3339 2.3968| | 18: 1.39 - 1.36 1.00 2741 179 0.2711 0.2284 2.2965 2.3522| | 19: 1.36 - 1.34 1.00 2807 134 0.2684 0.2364 2.2627 2.32| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2200 2.2013 2.2105| | 21: 1.32 - 1.30 1.00 2785 112 0.2683 0.2359 2.1692 2.179| | 22: 1.29 - 1.27 1.00 2704 152 0.2700 0.2854 2.1261 2.2789| | 23: 1.27 - 1.26 1.00 2802 156 0.2761 0.2445 2.0977 2.1568| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2377 2.0624 2.1304| | 25: 1.24 - 1.22 1.00 2734 148 0.2870 0.2318 2.0553 2.02| | 26: 1.22 - 1.21 1.00 2727 135 0.2846 0.2435 2.0029 2.0955| | 27: 1.21 - 1.19 1.00 2814 148 0.2966 0.2573 2.0096 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.2971 0.2779 1.9844 1.9983| | 29: 1.18 - 1.16 1.00 2800 134 0.2988 0.2795 1.97 2.0311| | 30: 1.16 - 1.15 1.00 2740 148 0.3041 0.2983 1.9213 1.9742| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.83 0.76 0.23 1494.09| | 2: 3.57 - 2.84 2876 122 0.80 26.12 1.27 0.23 1494.09| | 3: 2.84 - 2.48 2833 165 0.74 32.07 1.24 0.24 1239.15| | 4: 2.47 - 2.25 2825 136 0.81 25.73 1.26 0.25 577.54| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.29 0.25 577.54| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 316.03| | 7: 1.97 - 1.87 2787 165 0.90 16.79 1.28 0.26 93.01| | 8: 1.87 - 1.79 2789 144 0.85 21.38 1.25 0.26 93.01| | 9: 1.79 - 1.72 2745 138 0.88 18.91 1.23 0.25 56.50| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.25 49.19| | 11: 1.66 - 1.61 2740 147 0.86 21.46 1.24 0.25 47.37| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.24 0.25 28.97| | 13: 1.56 - 1.52 2745 130 0.87 20.33 1.25 0.25 28.97| | 14: 1.52 - 1.48 2803 134 0.87 20.47 1.23 0.25 26.07| | 15: 1.48 - 1.45 2738 128 0.87 20.13 1.24 0.25 20.76| | 16: 1.45 - 1.42 2756 161 0.86 21.57 1.23 0.25 20.76| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 17.84| | 18: 1.39 - 1.36 2741 179 0.86 21.23 1.22 0.25 16.15| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.22 0.25 16.15| | 20: 1.34 - 1.32 2696 147 0.87 21.13 1.22 0.25 13.55| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.20 0.25 13.37| | 22: 1.29 - 1.27 2704 152 0.85 22.66 1.22 0.25 13.04| | 23: 1.27 - 1.26 2802 156 0.85 22.48 1.21 0.24 11.38| | 24: 1.26 - 1.24 2744 132 0.84 23.42 1.22 0.24 11.38| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.21 0.24 10.76| | 26: 1.22 - 1.21 2727 135 0.84 24.32 1.21 0.23 10.07| | 27: 1.21 - 1.19 2814 148 0.83 25.17 1.20 0.23 10.07| | 28: 1.19 - 1.18 2671 147 0.82 25.71 1.18 0.23 9.51| | 29: 1.18 - 1.16 2800 134 0.82 26.17 1.16 0.22 9.29| | 30: 1.16 - 1.15 2740 148 0.80 27.90 1.16 0.22 9.29| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.29 max = 1494.09 mean = 217.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 22.82| |phase err.(test): min = 0.00 max = 89.85 mean = 22.89| |-----------------------------------------------------------------------------| ----------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 0.291 1557 Z= 5.341 Angle : 5.232 17.755 2118 Z= 3.705 Chirality : 0.382 1.099 243 Planarity : 0.029 0.073 284 Dihedral : 13.950 86.460 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % 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: -2.51 (0.47), residues: 224 helix: -2.60 (0.37), residues: 108 sheet: -0.34 (0.88), residues: 28 loop : -0.50 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.034 ARG A 48 TYR 0.100 0.043 TYR A 139 PHE 0.073 0.033 PHE A 162 HIS 0.060 0.029 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2607 r_free= 0.1932 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789145 | | target function (ml) not normalized (work): 232352.472847 | | target function (ml) not normalized (free): 11822.019991 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1932 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1932 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1984 0.1932 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2009 0.1946 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1636 0.1743 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1635 0.1743 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 0.3814 386.557 358.037 0.668 1.003 0.407 11.894-9.307 99.02 97 4 0.1793 614.028 594.853 0.929 1.004 0.390 9.237-7.194 100.00 213 7 0.2175 502.199 490.361 0.959 1.004 0.380 7.162-5.571 100.00 427 22 0.2317 376.872 362.064 0.927 1.004 0.320 5.546-4.326 100.00 867 58 0.1326 517.353 511.126 0.960 1.004 0.222 4.315-3.360 100.00 1859 96 0.1171 492.006 487.746 1.002 1.003 0.199 3.356-2.611 100.00 3867 181 0.1440 323.223 320.128 0.996 1.003 0.080 2.608-2.026 99.99 8198 413 0.1332 214.267 211.946 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1614 104.637 103.968 1.011 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.400 45.088 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2595 29.235 26.907 0.974 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0456 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1743 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1643 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.748421 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1983.061624 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 0.1729 0.1846 0.0117 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1586 0.1721 0.0135 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1439 0.1609 0.0170 0.001 0.5 3.5 0.0 0.0 0 0.500 0.1397 0.1587 0.0189 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1368 0.1570 0.0202 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1371 0.1571 0.0199 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1304 0.1526 0.0222 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1278 0.1505 0.0227 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1257 0.1484 0.0227 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1250 0.1482 0.0231 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1478 0.0234 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1241 0.1479 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1236 0.1473 0.0237 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1233 0.1474 0.0241 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1230 0.1469 0.0240 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1231 0.1479 0.0248 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1484 0.0257 0.007 1.0 4.2 0.5 0.6 0 12.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1469 0.0240 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 12.30 14.69 2.40 3.013 19.057 1983.062 0.017 12.30 14.69 2.39 2.994 19.057 59.492 0.017 12.36 14.65 2.29 2.665 19.058 247.883 0.017 12.69 15.29 2.59 2.734 19.226 991.531 0.017 12.52 15.38 2.86 3.128 19.516 1983.062 0.016 12.44 15.42 2.98 3.285 19.619 2974.592 0.015 12.25 15.24 2.99 2.900 19.380 3966.123 0.015 12.27 15.36 3.09 3.314 19.618 4957.654 0.015 12.20 15.33 3.13 3.240 19.575 5949.185 0.015 12.15 15.28 3.13 3.333 19.623 6940.716 0.015 12.14 15.30 3.16 3.342 19.615 7932.246 0.015 12.19 15.41 3.21 3.245 19.545 8923.777 0.015 12.19 15.48 3.29 3.358 19.593 9915.308 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: 247.883 Accepted refinement result: 12.36 14.65 2.29 2.665 19.058 247.883 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.30 0 1785 Protein: 9.07 114.96 16.99 3.31 0 1519 Water: 11.48 119.44 38.23 N/A 0 258 Other: 19.73 26.59 22.06 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 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 = 0.1231 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1231 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016994 | | target function (ls_wunit_k1) not normalized (work): 1415.512724 | | target function (ls_wunit_k1) not normalized (free): 108.752021 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1677 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1677 0.1693 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1229 0.1450 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1450 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 0.3536 301.168 281.546 0.648 1.003 0.374 11.894-9.307 99.02 97 4 0.1658 482.454 471.286 0.925 1.003 0.370 9.237-7.194 100.00 213 7 0.1926 394.588 387.287 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1843 296.117 290.014 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.1003 406.495 403.631 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0878 386.579 385.414 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1178 253.963 252.857 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1021 168.354 167.651 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.215 82.396 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.458 35.965 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.971 21.454 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1450 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1227 r_free=0.1447 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1447 | n_water=258 | time (s): 1.520 (total time: 1.520) Filter (dist) r_work=0.1237 r_free=0.1447 | n_water=251 | time (s): 22.860 (total time: 24.380) Filter (q & B) r_work=0.1240 r_free=0.1447 | n_water=248 | time (s): 2.810 (total time: 27.190) Compute maps r_work=0.1240 r_free=0.1447 | n_water=248 | time (s): 1.150 (total time: 28.340) Filter (map) r_work=0.1253 r_free=0.1451 | n_water=226 | time (s): 2.600 (total time: 30.940) Find peaks r_work=0.1253 r_free=0.1451 | n_water=226 | time (s): 0.680 (total time: 31.620) Add new water r_work=0.1394 r_free=0.1642 | n_water=436 | time (s): 3.060 (total time: 34.680) Refine new water occ: r_work=0.1302 r_free=0.1493 adp: r_work=0.1222 r_free=0.1434 occ: r_work=0.1235 r_free=0.1421 adp: r_work=0.1202 r_free=0.1405 occ: r_work=0.1205 r_free=0.1394 adp: r_work=0.1195 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1394 r_work=0.1195 r_free=0.1394 | n_water=436 | time (s): 61.330 (total time: 96.010) Filter (q & B) r_work=0.1199 r_free=0.1395 | n_water=418 | time (s): 2.680 (total time: 98.690) Filter (dist only) r_work=0.1199 r_free=0.1395 | n_water=417 | time (s): 33.760 (total time: 132.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.280445 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1480.733244 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 0.1690 0.1809 0.0119 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1525 0.1659 0.0134 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1395 0.1550 0.0155 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1363 0.1526 0.0163 0.001 0.4 4.8 0.0 0.0 0 0.750 0.1323 0.1494 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1325 0.1495 0.0170 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1257 0.1451 0.0194 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1225 0.1431 0.0205 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1217 0.1432 0.0215 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1215 0.1439 0.0224 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1207 0.1431 0.0224 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1201 0.1428 0.0227 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1198 0.1421 0.0223 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1195 0.1424 0.0230 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1193 0.1426 0.0233 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1192 0.1426 0.0235 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1188 0.1423 0.0235 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1188 0.1426 0.0238 0.008 0.9 4.8 0.5 0.0 0 13.640 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1421 0.0223 0.005 0.8 3.5 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 14.21 2.23 3.772 21.791 1480.733 0.016 11.98 14.21 2.23 3.772 21.791 44.422 0.016 11.98 14.21 2.23 3.772 21.791 185.092 0.016 12.19 14.69 2.50 3.622 21.799 740.367 0.016 12.14 15.03 2.89 3.531 21.882 1480.733 0.015 12.00 14.99 2.99 3.445 22.041 2221.100 0.015 11.90 14.86 2.97 3.480 22.181 2961.466 0.014 11.85 14.86 3.00 3.495 22.159 3701.833 0.014 11.83 14.95 3.12 3.529 22.243 4442.200 0.014 11.81 14.95 3.15 3.541 22.213 5182.566 0.014 11.79 15.02 3.23 3.548 22.159 5922.933 0.014 11.75 14.96 3.21 3.565 22.220 6663.300 0.014 11.71 14.89 3.18 3.574 22.232 7403.666 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: 185.092 Accepted refinement result: 11.98 14.21 2.23 3.772 21.791 185.092 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 22.21 3.30 191 1753 Protein: 9.10 114.99 17.02 3.31 0 1519 Water: 11.51 76.69 41.11 N/A 191 226 Other: 19.76 26.62 22.09 N/A 0 8 Chain A: 9.10 114.99 19.45 N/A 0 1753 Chain S: 12.77 60.00 47.58 N/A 191 0 Histogram: Values Number of atoms 9.10 - 19.69 1257 19.69 - 30.28 244 30.28 - 40.87 168 40.87 - 51.45 127 51.45 - 62.04 126 62.04 - 72.63 11 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1421 r_work=0.1198 r_free=0.1421 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1421 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1196 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015210 | | target function (ls_wunit_k1) not normalized (work): 1266.971988 | | target function (ls_wunit_k1) not normalized (free): 100.490718 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1196 0.1416 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1588 0.1586 0.1656 n_refl.: 87592 remove outliers: r(all,work,free)=0.1588 0.1586 0.1656 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1587 0.1657 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1192 0.1407 n_refl.: 87592 remove outliers: r(all,work,free)=0.1202 0.1191 0.1407 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 0.3332 299.717 278.455 0.602 1.002 0.354 11.894-9.307 99.02 97 4 0.1646 482.454 476.161 0.929 1.003 0.314 9.237-7.194 100.00 213 7 0.1680 394.588 394.193 0.986 1.003 0.280 7.162-5.571 100.00 427 22 0.1554 296.117 291.031 0.933 1.003 0.224 5.546-4.326 100.00 867 58 0.0889 406.495 403.530 0.962 1.003 0.205 4.315-3.360 100.00 1859 96 0.0800 386.579 385.672 1.005 1.002 0.200 3.356-2.611 100.00 3867 181 0.1093 253.963 252.960 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.1014 168.354 167.727 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.215 82.398 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.458 35.989 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2259 22.971 21.477 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0143 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1407 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1407 | n_water=417 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1191 r_free=0.1405 | n_water=414 | time (s): 35.230 (total time: 37.020) Filter (q & B) r_work=0.1191 r_free=0.1405 | n_water=414 | time (s): 1.240 (total time: 38.260) Compute maps r_work=0.1191 r_free=0.1405 | n_water=414 | time (s): 1.740 (total time: 40.000) Filter (map) r_work=0.1228 r_free=0.1404 | n_water=284 | time (s): 3.490 (total time: 43.490) Find peaks r_work=0.1228 r_free=0.1404 | n_water=284 | time (s): 0.550 (total time: 44.040) Add new water r_work=0.1347 r_free=0.1534 | n_water=465 | time (s): 2.370 (total time: 46.410) Refine new water occ: r_work=0.1260 r_free=0.1452 adp: r_work=0.1261 r_free=0.1453 occ: r_work=0.1238 r_free=0.1429 adp: r_work=0.1238 r_free=0.1429 occ: r_work=0.1221 r_free=0.1409 adp: r_work=0.1216 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1406 r_work=0.1216 r_free=0.1406 | n_water=465 | time (s): 175.900 (total time: 222.310) Filter (q & B) r_work=0.1221 r_free=0.1407 | n_water=437 | time (s): 3.340 (total time: 225.650) Filter (dist only) r_work=0.1221 r_free=0.1406 | n_water=436 | time (s): 37.700 (total time: 263.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767871 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.234155 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1236 0.1374 0.0139 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1198 0.1345 0.0147 0.003 0.7 3.2 0.5 0.0 0 0.265 0.1180 0.1328 0.0148 0.004 0.8 3.2 0.5 0.0 0 0.530 0.1172 0.1324 0.0152 0.005 0.9 2.9 0.5 0.0 0 0.796 0.1167 0.1322 0.0155 0.006 1.0 3.2 0.5 0.0 0 1.061 0.1165 0.1321 0.0156 0.007 1.0 3.2 0.5 0.0 0 1.326 0.1162 0.1319 0.0157 0.007 1.0 3.8 0.5 0.0 0 1.591 0.1160 0.1320 0.0160 0.008 1.1 3.8 0.5 0.0 0 1.856 0.1170 0.1323 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1319 0.0157 0.007 1.0 3.8 0.5 0.0 0 1.591 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.19 1.57 3.775 21.248 48.234 3.624 11.62 13.19 1.57 3.775 21.248 1.447 3.624 11.63 13.19 1.56 3.757 21.248 6.029 3.624 11.67 13.32 1.65 3.709 21.233 24.117 3.619 11.64 13.38 1.74 3.737 21.205 48.234 3.616 11.56 13.34 1.78 3.759 21.198 72.351 3.610 11.54 13.35 1.81 3.773 21.184 96.468 3.606 11.49 13.30 1.81 3.783 21.185 120.585 3.603 11.52 13.38 1.86 3.807 21.158 144.702 3.603 11.50 13.35 1.86 3.817 21.158 168.820 3.602 11.46 13.31 1.85 3.826 21.157 192.937 3.599 11.45 13.31 1.86 3.833 21.156 217.054 3.598 11.44 13.30 1.86 3.837 21.158 241.171 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.447 Accepted refinement result: 11.62 13.19 1.57 3.775 21.248 1.447 3.624 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.21 3.30 213 1750 Protein: 9.11 115.00 17.03 3.31 0 1519 Water: 11.52 76.70 35.75 N/A 213 223 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.11 115.00 19.40 N/A 0 1750 Chain S: 12.78 60.01 36.08 N/A 213 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 286 30.29 - 40.87 216 40.87 - 51.46 126 51.46 - 62.05 54 62.05 - 72.64 11 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1319 r_work=0.1162 r_free=0.1319 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1319 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1323 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.21 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= 0.1151 r_free= 0.1323 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616095 | | target function (ml) not normalized (work): 301199.046551 | | target function (ml) not normalized (free): 15864.897375 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1323 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1504 0.1502 0.1557 n_refl.: 87590 remove outliers: r(all,work,free)=0.1504 0.1502 0.1557 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1503 0.1502 0.1557 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1318 n_refl.: 87590 remove outliers: r(all,work,free)=0.1153 0.1144 0.1318 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3911 297.075 271.398 0.495 0.999 0.320 11.894-9.307 98.04 96 4 0.2193 482.579 465.732 0.880 1.001 0.320 9.237-7.194 98.18 209 7 0.2317 386.069 387.248 0.950 1.001 0.204 7.162-5.571 100.00 427 22 0.2126 296.117 284.816 0.921 1.001 0.185 5.546-4.326 100.00 867 58 0.1111 406.495 401.265 0.964 1.001 0.180 4.315-3.360 100.00 1859 96 0.0929 386.579 384.144 1.004 1.002 0.180 3.356-2.611 100.00 3867 181 0.1141 253.963 251.831 1.007 1.002 0.100 2.608-2.026 99.99 8198 413 0.0931 168.354 167.675 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.215 82.517 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.458 36.026 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 22.971 21.416 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0044 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1318 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=0.1144 r_free=0.1318 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1318 | n_water=436 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1146 r_free=0.1317 | n_water=433 | time (s): 43.340 (total time: 45.730) Filter (q & B) r_work=0.1146 r_free=0.1317 | n_water=433 | time (s): 1.270 (total time: 47.000) Compute maps r_work=0.1146 r_free=0.1317 | n_water=433 | time (s): 1.780 (total time: 48.780) Filter (map) r_work=0.1170 r_free=0.1309 | n_water=318 | time (s): 3.660 (total time: 52.440) Find peaks r_work=0.1170 r_free=0.1309 | n_water=318 | time (s): 0.660 (total time: 53.100) Add new water r_work=0.1240 r_free=0.1406 | n_water=473 | time (s): 3.320 (total time: 56.420) Refine new water occ: r_work=0.1168 r_free=0.1342 adp: r_work=0.1169 r_free=0.1343 occ: r_work=0.1153 r_free=0.1323 adp: r_work=0.1152 r_free=0.1325 occ: r_work=0.1140 r_free=0.1306 adp: r_work=0.1137 r_free=0.1308 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1308 r_work=0.1137 r_free=0.1308 | n_water=473 | time (s): 167.970 (total time: 224.390) Filter (q & B) r_work=0.1143 r_free=0.1312 | n_water=439 | time (s): 4.220 (total time: 228.610) Filter (dist only) r_work=0.1149 r_free=0.1311 | n_water=437 | time (s): 45.310 (total time: 273.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.864067 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.134707 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 0.1353 0.0140 0.002 0.6 3.8 0.5 0.0 0 0.093 0.1174 0.1323 0.0149 0.003 0.8 2.9 0.5 0.0 0 0.280 0.1159 0.1312 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.559 0.1154 0.1312 0.0158 0.006 1.0 3.2 0.5 0.0 0 0.839 0.1150 0.1311 0.0161 0.007 1.0 3.2 0.5 0.0 0 1.118 0.1148 0.1308 0.0161 0.007 1.1 3.2 0.5 0.0 0 1.398 0.1145 0.1308 0.0162 0.008 1.1 3.5 0.5 0.0 0 1.678 0.1144 0.1308 0.0165 0.009 1.1 3.5 0.5 0.0 0 1.957 0.1152 0.1311 0.0159 0.006 1.0 3.2 0.5 0.0 0 0.932 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1308 0.0162 0.008 1.1 3.5 0.5 0.0 0 1.678 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 13.08 1.62 3.776 21.146 44.135 3.611 11.45 13.08 1.62 3.776 21.146 1.324 3.611 11.45 13.08 1.62 3.776 21.146 5.517 3.611 11.48 13.12 1.64 3.711 21.137 22.067 3.605 11.56 13.28 1.72 3.729 21.105 44.135 3.609 11.48 13.27 1.78 3.749 21.094 66.202 3.603 11.42 13.22 1.80 3.769 21.093 88.269 3.599 11.40 13.21 1.81 3.780 21.089 110.337 3.596 11.37 13.19 1.82 3.790 21.086 132.404 3.594 11.39 13.25 1.86 3.812 21.070 154.471 3.595 11.36 13.21 1.86 3.819 21.069 176.539 3.593 11.35 13.19 1.84 3.826 21.067 198.606 3.592 11.32 13.15 1.82 3.828 21.065 220.674 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: 1.324 Accepted refinement result: 11.45 13.08 1.62 3.776 21.146 1.324 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.03 3.30 217 1747 Protein: 9.11 115.00 17.03 3.31 0 1519 Water: 11.52 76.70 34.89 N/A 217 220 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.11 115.00 19.39 N/A 0 1747 Chain S: 12.78 60.01 34.21 N/A 217 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.28 298 30.28 - 40.87 208 40.87 - 51.46 125 51.46 - 62.05 47 62.05 - 72.64 11 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1308 r_work=0.1145 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1308 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1307 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1307 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.609049 | | target function (ml) not normalized (work): 300590.505639 | | target function (ml) not normalized (free): 15843.494223 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1140 0.1307 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1488 0.1487 0.1529 n_refl.: 87584 remove outliers: r(all,work,free)=0.1488 0.1487 0.1529 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1487 0.1486 0.1528 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1306 n_refl.: 87584 remove outliers: r(all,work,free)=0.1144 0.1136 0.1306 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3805 290.423 258.063 0.463 1.001 0.308 11.894-9.307 96.08 94 4 0.2324 475.824 463.816 0.863 1.002 0.233 9.237-7.194 98.18 209 7 0.2431 386.069 379.216 0.921 1.003 0.170 7.162-5.571 100.00 427 22 0.2162 296.117 284.783 0.915 1.003 0.150 5.546-4.326 100.00 867 58 0.1128 406.495 401.283 0.964 1.003 0.145 4.315-3.360 100.00 1859 96 0.0916 386.579 384.510 1.004 1.003 0.140 3.356-2.611 100.00 3867 181 0.1119 253.963 252.019 1.010 1.002 0.038 2.608-2.026 99.99 8198 413 0.0919 168.354 167.704 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.215 82.542 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.458 36.065 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.971 21.518 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0170 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1306 After: r_work=0.1137 r_free=0.1306 ================================== NQH flips ================================== r_work=0.1137 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** Total number of N/Q/H flips: 0 r_work=0.1137 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1306 | n_water=437 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1137 r_free=0.1306 | n_water=437 | time (s): 45.810 (total time: 48.330) Filter (q & B) r_work=0.1137 r_free=0.1307 | n_water=436 | time (s): 4.020 (total time: 52.350) Compute maps r_work=0.1137 r_free=0.1307 | n_water=436 | time (s): 1.700 (total time: 54.050) Filter (map) r_work=0.1164 r_free=0.1316 | n_water=347 | time (s): 3.890 (total time: 57.940) Find peaks r_work=0.1164 r_free=0.1316 | n_water=347 | time (s): 0.740 (total time: 58.680) Add new water r_work=0.1217 r_free=0.1367 | n_water=501 | time (s): 3.500 (total time: 62.180) Refine new water occ: r_work=0.1157 r_free=0.1308 adp: r_work=0.1158 r_free=0.1309 occ: r_work=0.1144 r_free=0.1294 adp: r_work=0.1143 r_free=0.1294 occ: r_work=0.1134 r_free=0.1284 adp: r_work=0.1131 r_free=0.1282 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1282 r_work=0.1131 r_free=0.1282 | n_water=501 | time (s): 257.750 (total time: 319.930) Filter (q & B) r_work=0.1138 r_free=0.1296 | n_water=457 | time (s): 4.140 (total time: 324.070) Filter (dist only) r_work=0.1138 r_free=0.1296 | n_water=455 | time (s): 48.840 (total time: 372.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.712801 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.200954 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 0.1242 0.1367 0.0125 0.003 0.7 6.7 0.0 0.0 0 0.086 0.1182 0.1325 0.0143 0.004 0.8 5.8 0.0 0.0 0 0.257 0.1164 0.1312 0.0148 0.005 0.9 5.8 0.5 0.0 0 0.514 0.1154 0.1304 0.0150 0.006 1.0 6.1 0.5 0.0 0 0.771 0.1148 0.1300 0.0152 0.006 1.0 5.8 0.5 0.0 0 1.028 0.1141 0.1296 0.0155 0.007 1.1 6.1 0.5 0.0 0 1.285 0.1139 0.1295 0.0157 0.008 1.1 5.8 0.5 0.0 0 1.542 0.1138 0.1295 0.0157 0.008 1.1 5.8 0.5 0.0 0 1.798 0.1152 0.1303 0.0151 0.006 1.0 5.8 0.5 0.0 0 0.856 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1295 0.0157 0.008 1.1 5.8 0.5 0.0 0 1.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 12.95 1.57 3.776 21.228 35.201 3.606 11.38 12.95 1.57 3.776 21.228 1.056 3.606 11.38 12.95 1.57 3.776 21.228 4.400 3.606 11.42 13.00 1.58 3.705 21.221 17.600 3.603 11.41 13.07 1.66 3.723 21.209 35.201 3.601 11.41 13.13 1.73 3.746 21.186 52.801 3.600 11.37 13.13 1.77 3.759 21.179 70.402 3.596 11.33 13.11 1.78 3.771 21.177 88.002 3.594 11.32 13.11 1.79 3.779 21.174 105.603 3.592 11.28 13.05 1.78 3.782 21.178 123.203 3.589 11.28 13.10 1.82 3.798 21.168 140.804 3.589 11.28 13.11 1.83 3.811 21.161 158.404 3.589 11.28 13.12 1.84 3.821 21.157 176.005 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: 1.056 Accepted refinement result: 11.38 12.95 1.57 3.776 21.228 1.056 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 21.18 3.30 236 1746 Protein: 9.10 114.99 17.03 3.31 0 1519 Water: 11.51 76.69 35.03 N/A 236 219 Other: 19.76 26.62 22.09 N/A 0 8 Chain A: 9.10 114.99 19.36 N/A 0 1746 Chain S: 12.77 60.00 34.62 N/A 236 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 305 30.28 - 40.87 213 40.87 - 51.46 132 51.46 - 62.04 46 62.04 - 72.63 11 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1138 r_free=0.1295 r_work=0.1138 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1295 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1293 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604460 | | target function (ml) not normalized (work): 300190.208168 | | target function (ml) not normalized (free): 15816.853933 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1327 0.1350 5.6364 5.6241| | 2: 3.57 - 2.84 1.00 2888 124 0.1084 0.1424 5.1757 5.2298| | 3: 2.83 - 2.48 1.00 2820 163 0.1097 0.1216 4.9532 4.9863| | 4: 2.47 - 2.25 1.00 2825 136 0.0903 0.0985 4.6375 4.6702| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0973 4.587 4.6402| | 6: 2.09 - 1.97 1.00 2846 113 0.0857 0.0980 4.2704 4.3635| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1085 3.9703 4.0829| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1126 3.8866 3.999| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1206 3.6458 3.8198| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1199 3.5644 3.7239| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1034 3.4973 3.5672| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1161 3.3347 3.4779| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1034 3.3092 3.3989| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1037 3.2407 3.3184| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1221 3.1524 3.2608| | 16: 1.45 - 1.42 1.00 2756 161 0.1049 0.1252 3.133 3.2487| | 17: 1.42 - 1.39 1.00 2785 139 0.1147 0.1302 3.1216 3.2307| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1311 3.1045 3.2319| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1571 3.1092 3.263| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1478 3.1113 3.1588| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1494 3.1135 3.0988| | 22: 1.29 - 1.27 1.00 2704 152 0.1559 0.1978 3.121 3.2911| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1787 3.1322 3.1979| | 24: 1.26 - 1.24 1.00 2744 132 0.1704 0.1844 3.1255 3.2328| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2149 3.1425 3.2603| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1756 3.1467 3.1972| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2172 3.1696 3.1636| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2285 3.1649 3.1692| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2384 3.1479 3.2265| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2452 3.1428 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 2921 171 0.95 8.84 1.00 0.97 5960.48| | 2: 3.57 - 2.84 2888 124 0.92 12.86 1.01 0.97 5960.48| | 3: 2.83 - 2.48 2820 163 0.89 16.81 0.99 0.97 4972.00| | 4: 2.47 - 2.25 2825 136 0.92 13.69 1.00 0.98 2423.04| | 5: 2.25 - 2.09 2756 127 0.90 15.86 1.01 0.98 2423.04| | 6: 2.09 - 1.97 2846 113 0.92 12.40 1.02 0.98 1386.96| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.97 503.33| | 8: 1.87 - 1.79 2789 144 0.93 12.49 1.00 0.97 503.33| | 9: 1.79 - 1.72 2745 138 0.94 10.09 0.98 0.97 289.06| | 10: 1.72 - 1.66 2831 160 0.94 11.21 0.98 0.97 246.15| | 11: 1.66 - 1.61 2712 147 0.93 11.81 0.98 0.97 235.84| | 12: 1.61 - 1.56 2773 144 0.95 8.97 0.99 0.97 138.61| | 13: 1.56 - 1.52 2745 130 0.95 10.46 1.03 0.97 138.61| | 14: 1.52 - 1.48 2803 134 0.94 10.85 1.02 0.98 124.26| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.98 97.98| | 16: 1.45 - 1.42 2756 161 0.94 11.10 1.02 0.98 97.98| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.00| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.98 83.80| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 83.80| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.84| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.56| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 79.96| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 81.99| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 81.99| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 83.99| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.20| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.20| | 28: 1.19 - 1.18 2671 147 0.88 20.40 1.01 0.93 89.89| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 91.28| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 91.28| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.56 max = 5960.48 mean = 912.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.81 mean = 13.50| |phase err.(test): min = 0.00 max = 89.31 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1134 0.1293 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1463 0.1461 0.1518 n_refl.: 87579 remove outliers: r(all,work,free)=0.1463 0.1461 0.1518 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1462 0.1460 0.1517 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1134 0.1294 n_refl.: 87579 remove outliers: r(all,work,free)=0.1142 0.1134 0.1294 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 88.54 80 5 0.3967 285.680 253.976 0.447 1.000 0.300 11.894-9.307 96.08 94 4 0.2375 475.824 461.797 0.859 1.002 0.223 9.237-7.194 98.18 209 7 0.2447 386.069 378.661 0.918 1.002 0.150 7.162-5.571 100.00 427 22 0.2133 296.117 285.261 0.910 1.002 0.130 5.546-4.326 100.00 867 58 0.1106 406.495 401.445 0.963 1.002 0.111 4.315-3.360 100.00 1859 96 0.0921 386.579 384.294 1.003 1.002 0.100 3.356-2.611 100.00 3867 181 0.1123 253.963 252.001 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0910 168.354 167.717 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.215 82.534 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.458 36.059 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.971 21.515 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0164 ================= 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 : 0.2607 0.1932 0.081 5.232 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1743 0.081 5.232 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1743 0.081 5.232 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1754 0.081 5.232 9.0 119.5 20.1 258 0.003 1_weight: 0.1643 0.1754 0.081 5.232 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1230 0.1469 0.006 0.882 9.0 119.5 20.1 258 0.137 1_adp: 0.1236 0.1465 0.006 0.882 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1237 0.1469 0.006 0.882 9.1 119.4 20.1 258 0.137 1_occ: 0.1231 0.1460 0.006 0.882 9.1 119.4 20.1 258 0.137 2_bss: 0.1228 0.1450 0.006 0.882 9.1 119.5 20.1 258 0.137 2_settarget: 0.1228 0.1450 0.006 0.882 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1228 0.1450 0.006 0.886 9.1 119.5 20.1 258 0.137 2_nqh: 0.1227 0.1447 0.006 0.886 9.1 119.5 20.1 258 0.137 2_sol: 0.1199 0.1395 0.006 0.886 9.1 115.0 22.2 417 n/a 2_weight: 0.1199 0.1395 0.006 0.886 9.1 115.0 22.2 417 n/a 2_xyzrec: 0.1198 0.1421 0.005 0.800 9.1 115.0 22.2 417 n/a 2_adp: 0.1198 0.1421 0.005 0.800 9.1 115.0 22.2 417 n/a 2_regHadp: 0.1198 0.1421 0.005 0.800 9.1 115.0 22.2 417 n/a 2_occ: 0.1196 0.1416 0.005 0.800 9.1 115.0 22.2 417 n/a 3_bss: 0.1191 0.1407 0.005 0.800 9.1 115.0 22.2 417 n/a 3_settarget: 0.1191 0.1407 0.005 0.800 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1191 0.1407 0.005 0.802 9.1 115.0 22.2 417 n/a 3_nqh: 0.1191 0.1407 0.005 0.802 9.1 115.0 22.2 417 n/a 3_sol: 0.1221 0.1406 0.005 0.802 9.1 115.0 21.2 436 n/a 3_weight: 0.1221 0.1406 0.005 0.802 9.1 115.0 21.2 436 n/a 3_xyzrec: 0.1162 0.1319 0.007 1.043 9.1 115.0 21.2 436 n/a 3_adp: 0.1162 0.1319 0.007 1.043 9.1 115.0 21.2 436 n/a 3_regHadp: 0.1162 0.1319 0.007 1.043 9.1 115.0 21.2 436 n/a 3_occ: 0.1151 0.1323 0.007 1.043 9.1 115.0 21.2 436 n/a 4_bss: 0.1144 0.1318 0.007 1.043 9.1 115.0 21.2 436 n/a 4_settarget: 0.1144 0.1318 0.007 1.043 9.1 115.0 21.2 436 n/a 4_updatecdl: 0.1144 0.1318 0.007 1.045 9.1 115.0 21.2 436 n/a 4_nqh: 0.1144 0.1318 0.007 1.045 9.1 115.0 21.2 436 n/a 4_sol: 0.1149 0.1311 0.007 1.045 9.1 115.0 21.0 437 n/a 4_weight: 0.1149 0.1311 0.007 1.045 9.1 115.0 21.0 437 n/a 4_xyzrec: 0.1145 0.1308 0.008 1.102 9.1 115.0 21.0 437 n/a 4_adp: 0.1145 0.1308 0.008 1.102 9.1 115.0 21.0 437 n/a 4_regHadp: 0.1145 0.1308 0.008 1.102 9.1 115.0 21.0 437 n/a 4_occ: 0.1140 0.1307 0.008 1.102 9.1 115.0 21.0 437 n/a 5_bss: 0.1136 0.1306 0.008 1.102 9.1 115.0 21.0 437 n/a 5_settarget: 0.1136 0.1306 0.008 1.102 9.1 115.0 21.0 437 n/a 5_updatecdl: 0.1136 0.1306 0.008 1.102 9.1 115.0 21.0 437 n/a 5_setrh: 0.1137 0.1306 0.008 1.102 9.1 115.0 21.0 437 n/a 5_nqh: 0.1137 0.1306 0.008 1.102 9.1 115.0 21.0 437 n/a 5_sol: 0.1138 0.1296 0.008 1.102 9.1 115.0 21.2 455 n/a 5_weight: 0.1138 0.1296 0.008 1.102 9.1 115.0 21.2 455 n/a 5_xyzrec: 0.1138 0.1295 0.008 1.128 9.1 115.0 21.2 455 n/a 5_adp: 0.1138 0.1295 0.008 1.128 9.1 115.0 21.2 455 n/a 5_regHadp: 0.1138 0.1295 0.008 1.128 9.1 115.0 21.2 455 n/a 5_occ: 0.1134 0.1293 0.008 1.128 9.1 115.0 21.2 455 n/a end: 0.1134 0.1294 0.008 1.128 9.1 115.0 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3120282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3120282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8800 Refinement macro-cycles (run) : 13076.9700 Write final files (write_after_run_outputs) : 92.0000 Total : 13171.8500 Total CPU time: 3.67 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:01:07 PST -0800 (1735365667.04 s) Start R-work = 0.1635, R-free = 0.1743 Final R-work = 0.1134, R-free = 0.1294 =============================================================================== Job complete usr+sys time: 13355.32 seconds wall clock time: 245 minutes 38.65 seconds (14738.65 seconds total)