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_3867824.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" } 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 4 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: 1.62, per 1000 atoms: 0.48 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: 0.29 Conformation dependent library (CDL) restraints added in 107.8 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: 0.62 - 0.88: 354 0.88 - 1.13: 1246 1.13 - 1.39: 558 1.39 - 1.64: 924 1.64 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.418 -0.174 9.50e-03 1.11e+04 3.37e+02 bond pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 1.513 1.700 -0.187 1.06e-02 8.90e+03 3.11e+02 bond pdb=" N ALA A 167 " pdb=" CA ALA A 167 " ideal model delta sigma weight residual 1.459 1.246 0.214 1.23e-02 6.61e+03 3.02e+02 bond pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 1.471 1.694 -0.223 1.32e-02 5.74e+03 2.86e+02 bond pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.20: 3866 6.20 - 12.39: 1644 12.39 - 18.58: 249 18.58 - 24.77: 15 24.77 - 30.96: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 134.60 -15.40 9.00e-01 1.23e+00 2.93e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.87 136.74 -14.87 9.70e-01 1.06e+00 2.35e+02 angle pdb=" O PRO A 43 " pdb=" C PRO A 43 " pdb=" N VAL A 44 " ideal model delta sigma weight residual 122.91 138.98 -16.07 1.21e+00 6.83e-01 1.76e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N AGLU A 96 " ideal model delta sigma weight residual 122.07 135.69 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 108.30 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.31: 934 16.31 - 32.61: 120 32.61 - 48.91: 35 48.91 - 65.21: 18 65.21 - 81.51: 4 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 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+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 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CD2 PHE A 119 " pdb=" CG PHE A 119 " pdb=" CD1 PHE A 119 " pdb=" HD1 PHE A 119 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.261: 113 0.261 - 0.520: 82 0.520 - 0.779: 35 0.779 - 1.038: 10 1.038 - 1.297: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.29 -1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.81e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.75e-02 1.37e+02 pdb=" CG PHE A 119 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.077 2.00e-02 2.50e+03 7.04e-02 1.11e+02 pdb=" CG HIS A 138 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.091 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.127 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.040 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1044 2.32 - 2.89: 8077 2.89 - 3.46: 10562 3.46 - 4.03: 15165 4.03 - 4.60: 21813 Nonbonded interactions: 56661 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.779 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.792 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.796 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.808 1.816 ... (remaining 56656 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_3867824_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= 0.2605 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790375 | | target function (ml) not normalized (work): 232454.944306 | | target function (ml) not normalized (free): 11857.683327 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2142 7.0721 4.9572| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1718 4.3482 4.3272| | 3: 2.84 - 2.48 1.00 2833 165 0.2378 0.1598 4.1236 4.1353| | 4: 2.47 - 2.25 1.00 2825 136 0.2333 0.1376 3.8248 3.8061| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1434 3.7928 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2514 0.1759 3.4599 3.5041| | 7: 1.97 - 1.87 1.00 2787 165 0.2553 0.1848 3.1279 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2529 0.1975 3.054 3.1213| | 9: 1.79 - 1.72 1.00 2745 138 0.2411 0.1913 2.8911 2.9682| | 10: 1.72 - 1.66 1.00 2789 158 0.2370 0.1950 2.7943 2.8839| | 11: 1.66 - 1.61 1.00 2740 147 0.2494 0.1663 2.7486 2.7015| | 12: 1.61 - 1.56 1.00 2787 146 0.2492 0.2044 2.6233 2.6629| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.2030 2.588 2.6711| | 14: 1.52 - 1.48 1.00 2803 134 0.2573 0.2118 2.5093 2.6275| | 15: 1.48 - 1.45 1.00 2738 128 0.2636 0.2259 2.4321 2.5638| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.2236 2.3895 2.451| | 17: 1.42 - 1.39 1.00 2785 139 0.2610 0.2106 2.3449 2.4042| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2122 2.2798 2.3341| | 19: 1.36 - 1.34 1.00 2807 134 0.2654 0.2497 2.2471 2.3881| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2282 2.195 2.2265| | 21: 1.32 - 1.30 1.00 2785 112 0.2733 0.2352 2.1707 2.1783| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2435 2.1196 2.1869| | 23: 1.27 - 1.26 1.00 2802 156 0.2752 0.2589 2.093 2.1823| | 24: 1.26 - 1.24 1.00 2744 132 0.2759 0.2288 2.0737 2.1278| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2682 2.0552 2.1597| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2285 2.0061 2.1084| | 27: 1.21 - 1.19 1.00 2814 148 0.2939 0.2673 2.0095 2.0091| | 28: 1.19 - 1.18 1.00 2671 147 0.2985 0.2724 1.992 1.9988| | 29: 1.18 - 1.16 1.00 2800 134 0.2971 0.2678 1.9607 2.0278| | 30: 1.16 - 1.15 1.00 2740 148 0.3030 0.2811 1.9279 1.9674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1465.85| | 2: 3.57 - 2.84 2876 122 0.81 25.95 1.27 0.23 1465.85| | 3: 2.84 - 2.48 2833 165 0.74 32.00 1.25 0.23 1214.53| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.26 0.25 562.28| | 5: 2.25 - 2.09 2756 127 0.77 29.15 1.28 0.25 562.28| | 6: 2.09 - 1.97 2846 113 0.84 22.23 1.29 0.25 306.09| | 7: 1.97 - 1.87 2787 165 0.90 16.25 1.28 0.26 87.59| | 8: 1.87 - 1.79 2789 144 0.86 20.72 1.26 0.26 87.59| | 9: 1.79 - 1.72 2745 138 0.88 18.74 1.23 0.25 55.37| | 10: 1.72 - 1.66 2789 158 0.86 20.31 1.22 0.25 48.92| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 47.26| | 12: 1.61 - 1.56 2787 146 0.88 18.80 1.24 0.25 30.37| | 13: 1.56 - 1.52 2745 130 0.86 20.65 1.23 0.25 30.37| | 14: 1.52 - 1.48 2803 134 0.86 21.05 1.24 0.25 27.38| | 15: 1.48 - 1.45 2738 128 0.86 20.89 1.24 0.25 21.90| | 16: 1.45 - 1.42 2756 161 0.85 22.47 1.23 0.25 21.90| | 17: 1.42 - 1.39 2785 139 0.86 21.19 1.22 0.25 18.68| | 18: 1.39 - 1.36 2741 179 0.85 21.97 1.23 0.25 16.82| | 19: 1.36 - 1.34 2807 134 0.84 23.06 1.22 0.25 16.82| | 20: 1.34 - 1.32 2696 147 0.86 21.52 1.22 0.24 13.78| | 21: 1.32 - 1.30 2785 112 0.85 22.67 1.21 0.24 13.57| | 22: 1.29 - 1.27 2704 152 0.85 22.99 1.22 0.24 13.23| | 23: 1.27 - 1.26 2802 156 0.85 22.79 1.22 0.24 11.50| | 24: 1.26 - 1.24 2744 132 0.85 23.16 1.21 0.24 11.50| | 25: 1.24 - 1.22 2734 148 0.84 24.18 1.21 0.24 10.92| | 26: 1.22 - 1.21 2727 135 0.84 24.33 1.20 0.23 10.26| | 27: 1.21 - 1.19 2814 148 0.83 25.22 1.20 0.23 10.26| | 28: 1.19 - 1.18 2671 147 0.82 25.91 1.18 0.23 9.67| | 29: 1.18 - 1.16 2800 134 0.82 26.20 1.17 0.22 9.44| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.16 0.22 9.44| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.44 max = 1465.85 mean = 212.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.92| |phase err.(test): min = 0.00 max = 89.66 mean = 22.81| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.239 1557 Z= 5.525 Angle : 5.460 18.696 2118 Z= 3.789 Chirality : 0.400 1.297 243 Planarity : 0.032 0.108 284 Dihedral : 13.864 81.513 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 40.00 % 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: -2.96 (0.48), residues: 224 helix: -2.91 (0.33), residues: 109 sheet: -0.97 (0.80), residues: 38 loop : -0.52 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.014 ARG A 156 TYR 0.080 0.038 TYR A 139 PHE 0.124 0.039 PHE A 119 HIS 0.068 0.035 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= 0.2605 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790375 | | target function (ml) not normalized (work): 232454.944306 | | target function (ml) not normalized (free): 11857.683327 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1936 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1936 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1980 0.1936 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2001 0.2006 0.1949 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1634 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1634 0.1770 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 0.3766 386.471 360.380 0.680 1.003 0.414 11.894-9.307 99.02 97 4 0.1823 613.891 596.211 0.927 1.004 0.402 9.237-7.194 100.00 213 7 0.2164 502.087 492.086 0.952 1.004 0.349 7.162-5.571 100.00 427 22 0.2219 376.788 365.149 0.930 1.004 0.340 5.546-4.326 100.00 867 58 0.1269 517.237 512.693 0.962 1.003 0.228 4.315-3.360 100.00 1859 96 0.1156 491.896 488.659 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1428 323.150 320.242 0.996 1.002 0.038 2.608-2.026 99.99 8198 413 0.1358 214.219 212.020 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1639 104.613 103.970 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2056 46.390 45.121 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2581 29.229 26.997 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0467 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1770 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 144 ASN Total number of N/Q/H flips: 2 r_work=0.1637 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.453108 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.209750 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 0.1744 0.1870 0.0126 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1558 0.1707 0.0149 0.002 0.4 3.8 0.0 0.0 0 0.250 0.1432 0.1604 0.0172 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1369 0.1558 0.0189 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1351 0.1555 0.0204 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1356 0.1557 0.0201 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1299 0.1519 0.0220 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1273 0.1502 0.0229 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1262 0.1491 0.0229 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1251 0.1479 0.0227 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1244 0.1475 0.0231 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1240 0.1475 0.0234 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1237 0.1469 0.0232 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1235 0.1469 0.0234 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1232 0.1470 0.0238 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1231 0.1472 0.0241 0.007 0.9 3.5 0.5 0.6 0 11.000 0.1226 0.1469 0.0243 0.007 0.9 3.8 0.5 0.6 0 12.727 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1469 0.0234 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.69 2.34 3.013 19.063 2007.210 0.018 12.35 14.68 2.33 2.975 19.063 60.216 0.018 12.42 14.67 2.25 2.657 19.062 250.901 0.018 12.74 15.31 2.57 2.741 19.228 1003.605 0.017 12.61 15.50 2.89 3.247 19.598 2007.210 0.016 12.47 15.50 3.03 3.304 19.632 3010.815 0.016 12.34 15.41 3.07 3.336 19.645 4014.420 0.015 12.34 15.45 3.11 3.372 19.642 5018.024 0.015 12.30 15.44 3.14 3.397 19.650 6021.629 0.015 12.31 15.52 3.21 3.482 19.682 7025.234 0.015 12.29 15.58 3.29 3.562 19.722 8028.839 0.015 12.29 15.58 3.29 3.581 19.713 9032.444 0.015 12.19 15.45 3.26 3.440 19.635 10036.049 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: 250.901 Accepted refinement result: 12.42 14.67 2.25 2.657 19.062 250.901 0.018 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.09 3.29 0 1785 Protein: 9.08 114.88 17.00 3.29 0 1519 Water: 11.45 119.45 38.23 N/A 0 258 Other: 19.74 26.63 22.07 N/A 0 8 Chain A: 9.08 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.26 42 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1467 r_work=0.1243 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1470 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1237 r_free = 0.1465 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1237 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017044 | | target function (ls_wunit_k1) not normalized (work): 1419.754624 | | target function (ls_wunit_k1) not normalized (free): 109.523156 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1248 0.1237 0.1465 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1680 0.1682 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1680 0.1682 0.1692 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1686 0.1687 0.1696 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1234 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1244 0.1233 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 0.3507 301.355 281.590 0.652 1.003 0.380 11.894-9.307 99.02 97 4 0.1656 482.754 470.637 0.924 1.003 0.370 9.237-7.194 100.00 213 7 0.1892 394.833 389.731 0.964 1.003 0.324 7.162-5.571 100.00 427 22 0.1828 296.300 290.594 0.938 1.003 0.268 5.546-4.326 100.00 867 58 0.1013 406.747 403.737 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 386.819 385.790 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1181 254.120 252.930 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1032 168.459 167.720 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.266 82.447 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1457 36.480 35.982 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 22.985 21.464 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1453 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 144 ASN Total number of N/Q/H flips: 1 r_work=0.1233 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1452 | n_water=258 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1241 r_free=0.1450 | n_water=251 | time (s): 21.550 (total time: 23.620) Filter (q & B) r_work=0.1243 r_free=0.1449 | n_water=248 | time (s): 3.260 (total time: 26.880) Compute maps r_work=0.1243 r_free=0.1449 | n_water=248 | time (s): 1.190 (total time: 28.070) Filter (map) r_work=0.1259 r_free=0.1455 | n_water=226 | time (s): 2.220 (total time: 30.290) Find peaks r_work=0.1259 r_free=0.1455 | n_water=226 | time (s): 0.500 (total time: 30.790) Add new water r_work=0.1408 r_free=0.1624 | n_water=439 | time (s): 3.130 (total time: 33.920) Refine new water occ: r_work=0.1310 r_free=0.1501 adp: r_work=0.1228 r_free=0.1440 occ: r_work=0.1242 r_free=0.1432 adp: r_work=0.1206 r_free=0.1412 occ: r_work=0.1209 r_free=0.1410 adp: r_work=0.1199 r_free=0.1403 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1403 r_work=0.1199 r_free=0.1403 | n_water=439 | time (s): 50.290 (total time: 84.210) Filter (q & B) r_work=0.1203 r_free=0.1407 | n_water=424 | time (s): 3.200 (total time: 87.410) Filter (dist only) r_work=0.1203 r_free=0.1406 | n_water=423 | time (s): 34.160 (total time: 121.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.275963 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.744291 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 0.1683 0.1802 0.0119 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1553 0.1691 0.0138 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1390 0.1558 0.0168 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1346 0.1526 0.0179 0.001 0.5 5.1 0.0 0.0 0 0.750 0.1308 0.1500 0.0192 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1327 0.1517 0.0190 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1245 0.1455 0.0210 0.002 0.6 4.8 0.5 0.0 0 2.000 0.1230 0.1448 0.0218 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1218 0.1444 0.0226 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1209 0.1437 0.0228 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1204 0.1431 0.0228 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1201 0.1431 0.0230 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1197 0.1429 0.0231 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1194 0.1421 0.0226 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1192 0.1421 0.0229 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1189 0.1422 0.0233 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1190 0.1425 0.0235 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1187 0.1420 0.0233 0.008 0.9 6.1 0.5 0.6 0 13.000 0.1186 0.1422 0.0236 0.008 0.9 5.1 0.5 0.6 0 14.138 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1420 0.0233 0.008 0.9 6.1 0.5 0.6 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.20 2.33 3.765 21.789 1483.744 0.016 11.87 14.20 2.33 3.765 21.789 44.512 0.016 11.87 14.20 2.33 3.765 21.789 185.468 0.016 12.07 14.58 2.50 3.623 21.796 741.872 0.015 12.04 14.86 2.82 3.538 21.876 1483.744 0.015 11.86 14.70 2.84 3.446 22.149 2225.616 0.014 11.77 14.72 2.95 3.440 22.089 2967.489 0.014 11.72 14.78 3.05 3.489 21.985 3709.361 0.014 11.66 14.73 3.07 3.508 21.975 4451.233 0.014 11.75 14.89 3.14 3.514 22.220 5193.105 0.014 11.64 14.69 3.05 3.502 22.141 5934.977 0.014 11.65 14.78 3.13 3.526 22.201 6676.849 0.014 11.59 14.72 3.14 3.529 22.070 7418.721 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: 185.468 Accepted refinement result: 11.87 14.20 2.33 3.765 21.789 185.468 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 22.20 3.29 197 1753 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.48 76.68 40.80 N/A 197 226 Other: 19.77 26.66 22.10 N/A 0 8 Chain A: 9.11 114.91 19.49 N/A 0 1753 Chain S: 12.96 60.00 46.38 N/A 197 0 Histogram: Values Number of atoms 9.11 - 19.69 1259 19.69 - 30.27 248 30.27 - 40.85 162 40.85 - 51.43 140 51.43 - 62.01 118 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1420 r_work=0.1187 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1420 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 = 0.1187 r_free = 0.1414 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1187 r_free= 0.1414 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014956 | | target function (ls_wunit_k1) not normalized (work): 1245.748686 | | target function (ls_wunit_k1) not normalized (free): 100.944960 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1187 0.1414 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1578 0.1576 0.1658 n_refl.: 87592 remove outliers: r(all,work,free)=0.1578 0.1576 0.1658 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1580 0.1577 0.1659 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1184 0.1410 n_refl.: 87592 remove outliers: r(all,work,free)=0.1194 0.1183 0.1410 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 0.3300 299.903 276.547 0.599 1.002 0.360 11.894-9.307 99.02 97 4 0.1762 482.754 474.248 0.920 1.003 0.346 9.237-7.194 100.00 213 7 0.1627 394.833 395.772 0.986 1.003 0.290 7.162-5.571 100.00 427 22 0.1568 296.300 291.572 0.937 1.003 0.220 5.546-4.326 100.00 867 58 0.0878 406.747 403.942 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0781 386.819 385.979 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1074 254.120 253.223 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1011 168.459 167.886 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.266 82.488 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.480 36.018 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.985 21.497 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=0.0106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1410 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=0.1183 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1410 | n_water=423 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1182 r_free=0.1408 | n_water=417 | time (s): 36.040 (total time: 37.700) Filter (q & B) r_work=0.1182 r_free=0.1408 | n_water=417 | time (s): 1.170 (total time: 38.870) Compute maps r_work=0.1182 r_free=0.1408 | n_water=417 | time (s): 1.320 (total time: 40.190) Filter (map) r_work=0.1216 r_free=0.1391 | n_water=292 | time (s): 3.080 (total time: 43.270) Find peaks r_work=0.1216 r_free=0.1391 | n_water=292 | time (s): 0.620 (total time: 43.890) Add new water r_work=0.1333 r_free=0.1533 | n_water=478 | time (s): 2.320 (total time: 46.210) Refine new water occ: r_work=0.1239 r_free=0.1444 adp: r_work=0.1241 r_free=0.1446 occ: r_work=0.1216 r_free=0.1421 adp: r_work=0.1216 r_free=0.1420 occ: r_work=0.1198 r_free=0.1395 adp: r_work=0.1194 r_free=0.1392 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1392 r_work=0.1194 r_free=0.1392 | n_water=478 | time (s): 219.040 (total time: 265.250) Filter (q & B) r_work=0.1198 r_free=0.1400 | n_water=446 | time (s): 2.590 (total time: 267.840) Filter (dist only) r_work=0.1200 r_free=0.1402 | n_water=444 | time (s): 35.720 (total time: 303.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.747635 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.843903 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 0.1387 0.0152 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1185 0.1345 0.0160 0.003 0.7 3.5 0.5 0.0 0 0.262 0.1171 0.1331 0.0161 0.004 0.8 3.2 0.5 0.0 0 0.524 0.1162 0.1325 0.0163 0.005 0.9 3.5 0.5 0.0 0 0.786 0.1157 0.1324 0.0167 0.006 1.0 3.2 0.5 0.0 0 1.049 0.1155 0.1323 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.311 0.1154 0.1324 0.0170 0.007 1.0 3.5 0.5 0.0 0 1.573 0.1153 0.1323 0.0170 0.008 1.1 3.5 0.5 0.6 0 1.835 0.1160 0.1326 0.0166 0.005 0.9 3.2 0.5 0.0 0 0.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1155 0.1323 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.311 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 13.23 1.68 3.768 21.284 41.844 3.623 11.55 13.23 1.68 3.768 21.284 1.255 3.623 11.56 13.23 1.67 3.757 21.284 5.230 3.622 11.57 13.28 1.71 3.701 21.276 20.922 3.615 11.63 13.42 1.79 3.718 21.240 41.844 3.616 11.52 13.36 1.84 3.751 21.230 62.766 3.609 11.47 13.33 1.86 3.766 21.223 83.688 3.604 11.43 13.28 1.85 3.772 21.224 104.610 3.601 11.42 13.30 1.88 3.788 21.214 125.532 3.599 11.42 13.31 1.89 3.805 21.200 146.454 3.599 11.43 13.32 1.89 3.819 21.190 167.376 3.599 11.39 13.28 1.89 3.823 21.193 188.298 3.596 11.39 13.28 1.88 3.834 21.187 209.220 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: 1.255 Accepted refinement result: 11.55 13.23 1.68 3.768 21.284 1.255 3.623 Individual atomic B min max mean iso aniso Overall: 9.11 114.92 21.28 3.29 221 1750 Protein: 9.11 114.92 17.03 3.29 0 1519 Water: 11.48 76.68 35.77 N/A 221 223 Other: 19.77 26.66 22.11 N/A 0 8 Chain A: 9.11 114.92 19.43 N/A 0 1750 Chain S: 12.96 60.01 35.86 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.27 288 30.27 - 40.86 206 40.86 - 51.44 137 51.44 - 62.02 53 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1323 r_work=0.1155 r_free=0.1323 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1323 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1318 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.19 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= 0.1145 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614194 | | target function (ml) not normalized (work): 301040.703912 | | target function (ml) not normalized (free): 15852.640058 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1145 0.1318 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1485 0.1485 0.1503 n_refl.: 87590 remove outliers: r(all,work,free)=0.1485 0.1485 0.1503 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1484 0.1484 0.1502 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1302 n_refl.: 87590 remove outliers: r(all,work,free)=0.1146 0.1138 0.1302 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 92.71 84 5 0.3905 297.260 269.207 0.511 1.000 0.330 11.894-9.307 96.08 94 4 0.2367 469.929 460.470 0.879 1.001 0.264 9.237-7.194 98.18 209 7 0.2253 386.309 387.818 0.955 1.002 0.211 7.162-5.571 100.00 427 22 0.2038 296.300 287.405 0.920 1.002 0.182 5.546-4.326 100.00 867 58 0.1104 406.747 401.654 0.965 1.002 0.155 4.315-3.360 100.00 1859 96 0.0921 386.819 384.386 1.005 1.002 0.135 3.356-2.611 100.00 3867 181 0.1123 254.120 251.919 1.008 1.002 0.070 2.608-2.026 99.99 8198 413 0.0928 168.459 167.600 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.266 82.537 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.480 36.055 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 22.985 21.518 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0177 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1302 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1138 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1302 | n_water=444 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1138 r_free=0.1302 | n_water=441 | time (s): 44.750 (total time: 47.220) Filter (q & B) r_work=0.1139 r_free=0.1303 | n_water=439 | time (s): 3.970 (total time: 51.190) Compute maps r_work=0.1139 r_free=0.1303 | n_water=439 | time (s): 1.840 (total time: 53.030) Filter (map) r_work=0.1176 r_free=0.1324 | n_water=340 | time (s): 3.740 (total time: 56.770) Find peaks r_work=0.1176 r_free=0.1324 | n_water=340 | time (s): 0.700 (total time: 57.470) Add new water r_work=0.1242 r_free=0.1392 | n_water=504 | time (s): 3.700 (total time: 61.170) Refine new water occ: r_work=0.1167 r_free=0.1324 adp: r_work=0.1167 r_free=0.1325 occ: r_work=0.1153 r_free=0.1306 adp: r_work=0.1151 r_free=0.1308 occ: r_work=0.1141 r_free=0.1294 adp: r_work=0.1138 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1295 r_work=0.1138 r_free=0.1295 | n_water=504 | time (s): 247.950 (total time: 309.120) Filter (q & B) r_work=0.1145 r_free=0.1297 | n_water=466 | time (s): 3.920 (total time: 313.040) Filter (dist only) r_work=0.1146 r_free=0.1296 | n_water=465 | time (s): 46.910 (total time: 359.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.822373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.289479 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 0.1199 0.1337 0.0138 0.002 0.6 3.5 0.5 0.0 0 0.091 0.1167 0.1312 0.0145 0.003 0.7 2.6 0.5 0.0 0 0.273 0.1151 0.1304 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.547 0.1146 0.1297 0.0151 0.006 1.0 2.9 0.5 0.0 0 0.820 0.1141 0.1300 0.0159 0.007 1.0 2.9 0.5 0.0 0 1.093 0.1139 0.1298 0.0158 0.007 1.1 3.2 0.5 0.0 0 1.367 0.1137 0.1300 0.0163 0.008 1.1 3.2 0.5 0.0 0 1.640 0.1135 0.1298 0.0163 0.009 1.1 3.2 0.5 0.0 0 1.913 0.1143 0.1302 0.0159 0.006 1.0 2.9 0.5 0.0 0 0.911 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1297 0.0151 0.006 1.0 2.9 0.5 0.0 0 0.820 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 12.97 1.51 3.769 21.306 40.289 3.611 11.46 12.97 1.51 3.769 21.306 1.209 3.611 11.46 12.97 1.51 3.769 21.306 5.036 3.611 11.48 13.00 1.52 3.704 21.300 20.145 3.605 11.55 13.14 1.59 3.725 21.271 40.289 3.609 11.47 13.13 1.65 3.744 21.260 60.434 3.603 11.41 13.09 1.68 3.759 21.256 80.579 3.598 11.39 13.08 1.69 3.768 21.255 100.724 3.596 11.35 13.04 1.69 3.777 21.255 120.868 3.592 11.35 13.06 1.71 3.791 21.246 141.013 3.592 11.35 13.07 1.72 3.807 21.237 161.158 3.592 11.33 13.04 1.71 3.813 21.235 181.303 3.590 11.32 13.05 1.73 3.820 21.236 201.447 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.036 Accepted refinement result: 11.46 12.97 1.51 3.769 21.306 5.036 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.32 3.29 245 1747 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.48 76.68 35.32 N/A 245 220 Other: 19.77 26.66 22.10 N/A 0 8 Chain A: 9.11 114.91 19.37 N/A 0 1747 Chain S: 12.96 60.00 35.19 N/A 245 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.27 301 30.27 - 40.85 219 40.85 - 51.43 139 51.43 - 62.01 50 62.01 - 72.59 10 72.59 - 83.17 5 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1297 r_work=0.1146 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1297 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1295 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.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1141 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.609489 | | target function (ml) not normalized (work): 300619.928872 | | target function (ml) not normalized (free): 15825.424825 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1141 0.1295 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1472 0.1472 0.1494 n_refl.: 87582 remove outliers: r(all,work,free)=0.1472 0.1472 0.1494 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1470 0.1471 0.1493 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1139 0.1297 n_refl.: 87582 remove outliers: r(all,work,free)=0.1145 0.1137 0.1297 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4170 291.016 256.179 0.456 1.001 0.314 11.894-9.307 95.10 93 4 0.2184 469.896 452.241 0.860 1.002 0.244 9.237-7.194 98.18 209 7 0.2278 386.309 381.592 0.927 1.003 0.164 7.162-5.571 100.00 427 22 0.2120 296.300 285.819 0.911 1.003 0.150 5.546-4.326 100.00 867 58 0.1133 406.747 402.067 0.964 1.003 0.120 4.315-3.360 100.00 1859 96 0.0924 386.819 384.604 1.005 1.003 0.120 3.356-2.611 100.00 3867 181 0.1114 254.120 252.380 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0918 168.459 167.834 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.266 82.616 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1264 36.480 36.090 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2173 22.985 21.536 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=-0.0164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1297 After: r_work=0.1138 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1138 r_free=0.1297 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=0.1138 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1297 | n_water=465 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1138 r_free=0.1298 | n_water=464 | time (s): 51.500 (total time: 53.980) Filter (q & B) r_work=0.1138 r_free=0.1298 | n_water=464 | time (s): 1.360 (total time: 55.340) Compute maps r_work=0.1138 r_free=0.1298 | n_water=464 | time (s): 1.900 (total time: 57.240) Filter (map) r_work=0.1166 r_free=0.1319 | n_water=361 | time (s): 3.740 (total time: 60.980) Find peaks r_work=0.1166 r_free=0.1319 | n_water=361 | time (s): 0.680 (total time: 61.660) Add new water r_work=0.1211 r_free=0.1360 | n_water=505 | time (s): 3.730 (total time: 65.390) Refine new water occ: r_work=0.1152 r_free=0.1311 adp: r_work=0.1153 r_free=0.1313 occ: r_work=0.1142 r_free=0.1299 adp: r_work=0.1141 r_free=0.1300 occ: r_work=0.1134 r_free=0.1289 adp: r_work=0.1131 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1290 r_work=0.1131 r_free=0.1290 | n_water=505 | time (s): 235.000 (total time: 300.390) Filter (q & B) r_work=0.1137 r_free=0.1297 | n_water=472 | time (s): 3.930 (total time: 304.320) Filter (dist only) r_work=0.1138 r_free=0.1295 | n_water=471 | time (s): 48.700 (total time: 353.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.685432 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.753856 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 0.1225 0.1352 0.0127 0.004 0.7 6.7 0.0 0.0 0 0.084 0.1174 0.1319 0.0144 0.004 0.8 7.4 0.0 0.0 0 0.253 0.1153 0.1305 0.0152 0.005 0.9 7.7 0.5 0.0 0 0.506 0.1139 0.1296 0.0157 0.006 1.0 7.4 0.5 0.0 0 0.758 0.1136 0.1295 0.0159 0.007 1.0 7.0 0.5 0.0 0 1.011 0.1134 0.1294 0.0160 0.007 1.1 7.4 0.5 0.0 0 1.264 0.1133 0.1294 0.0161 0.008 1.1 7.4 0.5 0.0 0 1.517 0.1131 0.1294 0.0162 0.009 1.1 7.0 0.5 0.0 0 1.770 0.1138 0.1295 0.0158 0.006 1.0 7.0 0.5 0.0 0 0.843 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1294 0.0162 0.009 1.1 7.0 0.5 0.0 0 1.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.94 1.62 3.768 21.283 43.754 3.603 11.31 12.94 1.62 3.768 21.283 1.313 3.603 11.31 12.94 1.62 3.766 21.283 5.469 3.603 11.34 12.97 1.64 3.704 21.275 21.877 3.598 11.39 13.09 1.70 3.728 21.245 43.754 3.600 11.31 13.06 1.76 3.750 21.237 65.631 3.594 11.27 13.05 1.77 3.763 21.231 87.508 3.590 11.25 13.05 1.80 3.777 21.229 109.385 3.588 11.22 13.03 1.81 3.788 21.225 131.262 3.586 11.19 13.00 1.81 3.794 21.226 153.138 3.584 11.22 13.05 1.84 3.816 21.214 175.015 3.584 11.19 13.02 1.83 3.819 21.217 196.892 3.583 11.17 13.01 1.84 3.823 21.218 218.769 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.313 Accepted refinement result: 11.31 12.94 1.62 3.768 21.283 1.313 3.603 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 21.28 3.29 252 1746 Protein: 9.10 114.90 17.02 3.29 0 1519 Water: 11.47 76.67 35.01 N/A 252 219 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.10 114.90 19.35 N/A 0 1746 Chain S: 12.95 59.99 34.68 N/A 252 0 Histogram: Values Number of atoms 9.10 - 19.68 1263 19.68 - 30.26 311 30.26 - 40.84 213 40.84 - 51.42 140 51.42 - 62.00 50 62.00 - 72.58 10 72.58 - 83.16 5 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1294 r_work=0.1131 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1294 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1289 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601680 | | target function (ml) not normalized (work): 299955.154358 | | target function (ml) not normalized (free): 15804.056653 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1330 0.1330 5.6449 5.5914| | 2: 3.57 - 2.84 1.00 2888 124 0.1054 0.1341 5.1435 5.2096| | 3: 2.83 - 2.48 1.00 2820 163 0.1089 0.1269 4.9319 4.989| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.1039 4.6155 4.6622| | 5: 2.25 - 2.09 1.00 2756 127 0.0856 0.0925 4.5629 4.6088| | 6: 2.09 - 1.97 1.00 2846 113 0.0857 0.1021 4.2618 4.3538| | 7: 1.97 - 1.87 1.00 2787 165 0.0882 0.1087 3.9767 4.0696| | 8: 1.87 - 1.79 1.00 2789 144 0.0907 0.1139 3.8821 4.006| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1155 3.6416 3.8123| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1215 3.5649 3.7173| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1024 3.4982 3.5694| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1139 3.3299 3.4499| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1049 3.3075 3.4052| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1082 3.2425 3.3313| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1199 3.1563 3.2575| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1261 3.1358 3.2572| | 17: 1.42 - 1.39 1.00 2785 139 0.1144 0.1304 3.1217 3.2291| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1345 3.1042 3.2462| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1565 3.1139 3.2635| | 20: 1.34 - 1.32 1.00 2696 147 0.1362 0.1474 3.1103 3.1588| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1509 3.1141 3.0975| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1975 3.123 3.2871| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1808 3.1333 3.2037| | 24: 1.26 - 1.24 1.00 2744 132 0.1703 0.1827 3.1269 3.2276| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2134 3.1453 3.2584| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1776 3.1482 3.2026| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2172 3.1715 3.1652| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2298 3.167 3.1764| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2391 3.1487 3.2318| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2462 3.1428 3.1708| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.22 1.00 0.97 5536.16| | 2: 3.57 - 2.84 2888 124 0.93 12.27 1.01 0.97 5536.16| | 3: 2.83 - 2.48 2820 163 0.90 16.17 0.99 0.97 4627.05| | 4: 2.47 - 2.25 2825 136 0.92 13.19 1.00 0.98 2282.73| | 5: 2.25 - 2.09 2756 127 0.91 15.34 1.01 0.98 2282.73| | 6: 2.09 - 1.97 2846 113 0.93 12.19 1.02 0.97 1322.51| | 7: 1.97 - 1.87 2787 165 0.95 9.22 1.02 0.97 503.58| | 8: 1.87 - 1.79 2789 144 0.93 12.53 1.00 0.97 503.58| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.97 288.20| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.97 245.07| | 11: 1.66 - 1.61 2712 147 0.94 11.72 0.98 0.97 234.81| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.97 138.04| | 13: 1.56 - 1.52 2745 130 0.95 10.42 1.03 0.97 138.04| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.98 124.06| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 98.46| | 16: 1.45 - 1.42 2756 161 0.94 11.17 1.02 0.98 98.46| | 17: 1.42 - 1.39 2785 139 0.95 10.97 1.01 0.98 89.56| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.98 84.41| | 19: 1.36 - 1.34 2807 134 0.94 11.92 1.00 0.98 84.41| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.96 80.20| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.90| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.31| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.94 82.38| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.38| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.46| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.03 0.93 86.76| | 27: 1.21 - 1.19 2814 148 0.89 18.82 1.02 0.93 86.76| | 28: 1.19 - 1.18 2671 147 0.88 20.50 1.01 0.93 90.81| | 29: 1.18 - 1.16 2800 134 0.88 20.62 0.99 0.92 92.33| | 30: 1.16 - 1.15 2739 148 0.86 22.16 0.98 0.92 92.33| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.90 max = 5536.16 mean = 859.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.41| |phase err.(test): min = 0.00 max = 88.88 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1289 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1456 0.1457 0.1472 n_refl.: 87578 remove outliers: r(all,work,free)=0.1456 0.1457 0.1472 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1455 0.1457 0.1472 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1128 0.1290 n_refl.: 87578 remove outliers: r(all,work,free)=0.1134 0.1126 0.1290 n_refl.: 87572 ======================== 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 86.46 78 5 0.4075 285.891 247.453 0.427 1.000 0.300 11.894-9.307 93.14 91 4 0.2270 472.938 448.985 0.854 1.002 0.233 9.237-7.194 97.73 208 7 0.2282 387.392 379.715 0.925 1.003 0.170 7.162-5.571 100.00 427 22 0.2152 296.300 287.160 0.906 1.003 0.130 5.546-4.326 100.00 867 58 0.1130 406.747 401.847 0.963 1.003 0.115 4.315-3.360 100.00 1859 96 0.0899 386.819 384.786 1.004 1.003 0.110 3.356-2.611 100.00 3867 181 0.1098 254.120 252.302 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0903 168.459 167.944 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.266 82.645 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.480 36.091 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.985 21.532 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0112 ================= 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 : 0.2605 0.1935 0.083 5.460 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1770 0.083 5.460 9.1 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1770 0.083 5.460 9.1 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1773 0.083 5.460 9.1 119.5 20.1 258 0.006 1_weight: 0.1637 0.1773 0.083 5.460 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1235 0.1469 0.006 0.853 9.1 119.5 20.1 258 0.140 1_adp: 0.1242 0.1467 0.006 0.853 9.1 119.4 20.1 258 0.140 1_regHadp: 0.1243 0.1470 0.006 0.853 9.1 119.4 20.1 258 0.140 1_occ: 0.1237 0.1465 0.006 0.853 9.1 119.4 20.1 258 0.140 2_bss: 0.1233 0.1453 0.006 0.853 9.1 119.5 20.1 258 0.140 2_settarget: 0.1233 0.1453 0.006 0.853 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1233 0.1453 0.006 0.860 9.1 119.5 20.1 258 0.140 2_nqh: 0.1233 0.1452 0.006 0.860 9.1 119.5 20.1 258 0.137 2_sol: 0.1203 0.1406 0.006 0.860 9.1 114.9 22.2 423 n/a 2_weight: 0.1203 0.1406 0.006 0.860 9.1 114.9 22.2 423 n/a 2_xyzrec: 0.1187 0.1420 0.008 0.917 9.1 114.9 22.2 423 n/a 2_adp: 0.1187 0.1420 0.008 0.917 9.1 114.9 22.2 423 n/a 2_regHadp: 0.1187 0.1420 0.008 0.917 9.1 114.9 22.2 423 n/a 2_occ: 0.1187 0.1414 0.008 0.917 9.1 114.9 22.2 423 n/a 3_bss: 0.1183 0.1410 0.008 0.917 9.1 114.9 22.2 423 n/a 3_settarget: 0.1183 0.1410 0.008 0.917 9.1 114.9 22.2 423 n/a 3_updatecdl: 0.1183 0.1410 0.008 0.919 9.1 114.9 22.2 423 n/a 3_nqh: 0.1183 0.1410 0.008 0.919 9.1 114.9 22.2 423 n/a 3_sol: 0.1200 0.1402 0.008 0.919 9.1 114.9 21.3 444 n/a 3_weight: 0.1200 0.1402 0.008 0.919 9.1 114.9 21.3 444 n/a 3_xyzrec: 0.1155 0.1323 0.007 1.003 9.1 114.9 21.3 444 n/a 3_adp: 0.1155 0.1323 0.007 1.003 9.1 114.9 21.3 444 n/a 3_regHadp: 0.1155 0.1323 0.007 1.003 9.1 114.9 21.3 444 n/a 3_occ: 0.1145 0.1318 0.007 1.003 9.1 114.9 21.3 444 n/a 4_bss: 0.1138 0.1302 0.007 1.003 9.1 114.9 21.3 444 n/a 4_settarget: 0.1138 0.1302 0.007 1.003 9.1 114.9 21.3 444 n/a 4_updatecdl: 0.1138 0.1302 0.007 1.005 9.1 114.9 21.3 444 n/a 4_nqh: 0.1138 0.1302 0.007 1.005 9.1 114.9 21.3 444 n/a 4_sol: 0.1146 0.1296 0.007 1.005 9.1 114.9 21.3 465 n/a 4_weight: 0.1146 0.1296 0.007 1.005 9.1 114.9 21.3 465 n/a 4_xyzrec: 0.1146 0.1297 0.006 0.952 9.1 114.9 21.3 465 n/a 4_adp: 0.1146 0.1297 0.006 0.952 9.1 114.9 21.3 465 n/a 4_regHadp: 0.1146 0.1297 0.006 0.952 9.1 114.9 21.3 465 n/a 4_occ: 0.1141 0.1295 0.006 0.952 9.1 114.9 21.3 465 n/a 5_bss: 0.1137 0.1297 0.006 0.952 9.1 114.9 21.3 465 n/a 5_settarget: 0.1137 0.1297 0.006 0.952 9.1 114.9 21.3 465 n/a 5_updatecdl: 0.1137 0.1297 0.006 0.954 9.1 114.9 21.3 465 n/a 5_setrh: 0.1138 0.1297 0.006 0.954 9.1 114.9 21.3 465 n/a 5_nqh: 0.1138 0.1297 0.006 0.954 9.1 114.9 21.3 465 n/a 5_sol: 0.1138 0.1295 0.006 0.954 9.1 114.9 21.3 471 n/a 5_weight: 0.1138 0.1295 0.006 0.954 9.1 114.9 21.3 471 n/a 5_xyzrec: 0.1131 0.1294 0.009 1.147 9.1 114.9 21.3 471 n/a 5_adp: 0.1131 0.1294 0.009 1.147 9.1 114.9 21.3 471 n/a 5_regHadp: 0.1131 0.1294 0.009 1.147 9.1 114.9 21.3 471 n/a 5_occ: 0.1128 0.1289 0.009 1.147 9.1 114.9 21.3 471 n/a end: 0.1126 0.1290 0.009 1.147 9.1 114.9 21.3 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3867824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3867824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3700 Refinement macro-cycles (run) : 13455.7900 Write final files (write_after_run_outputs) : 94.1900 Total : 13553.3500 Total CPU time: 3.77 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:54 PST -0800 (1735366074.05 s) Start R-work = 0.1634, R-free = 0.1770 Final R-work = 0.1126, R-free = 0.1290 =============================================================================== Job complete usr+sys time: 13728.20 seconds wall clock time: 251 minutes 57.23 seconds (15117.23 seconds total)