Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.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_8530786.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.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: 1.87, per 1000 atoms: 0.55 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: 0.37 Conformation dependent library (CDL) restraints added in 168.9 milliseconds Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.14: 1213 1.14 - 1.39: 566 1.39 - 1.64: 903 1.64 - 1.89: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 1.234 0.998 0.235 1.17e-02 7.31e+03 4.05e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.522 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.455 -0.218 1.17e-02 7.31e+03 3.49e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.144 0.182 1.10e-02 8.26e+03 2.75e+02 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.261 0.194 1.17e-02 7.31e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3259 4.94 - 9.87: 1874 9.87 - 14.81: 580 14.81 - 19.74: 60 19.74 - 24.67: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 124.34 -15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.27 139.65 -16.38 1.16e+00 7.43e-01 1.99e+02 angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 116.39 102.10 14.29 1.17e+00 7.31e-01 1.49e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 109.28 12.84 1.06e+00 8.90e-01 1.47e+02 angle pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 120.70 132.95 -12.25 1.03e+00 9.43e-01 1.41e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.23: 947 17.23 - 34.46: 108 34.46 - 51.68: 33 51.68 - 68.91: 20 68.91 - 86.13: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.214: 105 0.214 - 0.426: 61 0.426 - 0.638: 49 0.638 - 0.850: 21 0.850 - 1.062: 7 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 -1.53 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.67 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA AGLN A 80 " pdb=" N AGLN A 80 " pdb=" C AGLN A 80 " pdb=" CB AGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.31e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.028 2.00e-02 2.50e+03 5.93e-02 1.05e+02 pdb=" CG PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.095 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.052 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.030 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 1575 2.39 - 2.94: 8485 2.94 - 3.50: 10405 3.50 - 4.05: 15006 4.05 - 4.60: 21120 Nonbonded interactions: 56591 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.851 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.865 2.270 nonbonded pdb=" H BTYR A 67 " pdb=" O HOH A 324 " model vdw 1.870 1.850 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.874 1.816 ... (remaining 56586 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_8530786_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= 0.1964 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792489 | | target function (ml) not normalized (work): 232631.077968 | | target function (ml) not normalized (free): 11838.554933 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2112 6.9744 4.9452| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1883 4.3591 4.3519| | 3: 2.84 - 2.48 1.00 2833 165 0.2380 0.1704 4.1398 4.1678| | 4: 2.47 - 2.25 1.00 2825 136 0.2300 0.1412 3.8382 3.8352| | 5: 2.25 - 2.09 1.00 2756 127 0.2440 0.1691 3.809 3.849| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1700 3.4664 3.5676| | 7: 1.97 - 1.87 1.00 2787 165 0.2582 0.1841 3.1507 3.2216| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.2014 3.0639 3.145| | 9: 1.79 - 1.72 1.00 2745 138 0.2418 0.2061 2.931 2.9874| | 10: 1.72 - 1.66 1.00 2789 158 0.2468 0.1906 2.8198 2.8355| | 11: 1.66 - 1.61 1.00 2740 147 0.2480 0.1926 2.7517 2.7895| | 12: 1.61 - 1.56 1.00 2787 146 0.2541 0.1962 2.6267 2.6846| | 13: 1.56 - 1.52 1.00 2745 130 0.2480 0.1787 2.5632 2.5835| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1972 2.5267 2.5815| | 15: 1.48 - 1.45 1.00 2738 128 0.2605 0.2195 2.407 2.5604| | 16: 1.45 - 1.42 1.00 2756 161 0.2647 0.2106 2.3819 2.3876| | 17: 1.42 - 1.39 1.00 2785 139 0.2631 0.1996 2.3365 2.3702| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.1900 2.2724 2.2583| | 19: 1.36 - 1.34 1.00 2807 134 0.2653 0.2534 2.2469 2.3165| | 20: 1.34 - 1.32 1.00 2696 147 0.2656 0.2220 2.201 2.1857| | 21: 1.32 - 1.30 1.00 2785 112 0.2759 0.2313 2.1861 2.2195| | 22: 1.29 - 1.27 1.00 2704 152 0.2798 0.2738 2.1362 2.2564| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2385 2.0971 2.1433| | 24: 1.26 - 1.24 1.00 2744 132 0.2784 0.2572 2.0807 2.1602| | 25: 1.24 - 1.22 1.00 2734 148 0.2852 0.2460 2.0572 2.0924| | 26: 1.22 - 1.21 1.00 2727 135 0.2879 0.2331 2.0145 2.1041| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2727 2.0003 2.026| | 28: 1.19 - 1.18 1.00 2671 147 0.3008 0.2617 2.0001 1.9909| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2653 1.9671 2.023| | 30: 1.16 - 1.15 1.00 2740 148 0.3031 0.2806 1.9181 1.9345| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.09 0.76 0.23 1517.63| | 2: 3.57 - 2.84 2876 122 0.80 26.45 1.27 0.23 1517.63| | 3: 2.84 - 2.48 2833 165 0.73 32.46 1.25 0.23 1258.54| | 4: 2.47 - 2.25 2825 136 0.81 25.91 1.26 0.25 586.14| | 5: 2.25 - 2.09 2756 127 0.77 29.54 1.28 0.25 586.14| | 6: 2.09 - 1.97 2846 113 0.83 22.95 1.29 0.25 320.72| | 7: 1.97 - 1.87 2787 165 0.90 16.93 1.29 0.26 94.36| | 8: 1.87 - 1.79 2789 144 0.85 21.48 1.24 0.26 94.36| | 9: 1.79 - 1.72 2745 138 0.88 18.81 1.22 0.25 57.23| | 10: 1.72 - 1.66 2789 158 0.86 20.64 1.23 0.25 49.79| | 11: 1.66 - 1.61 2740 147 0.85 21.78 1.24 0.25 47.99| | 12: 1.61 - 1.56 2787 146 0.88 18.59 1.24 0.25 29.75| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.23 0.25 29.75| | 14: 1.52 - 1.48 2803 134 0.86 20.75 1.23 0.25 26.58| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.78| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.23 0.25 20.78| | 17: 1.42 - 1.39 2785 139 0.87 20.56 1.22 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.23 1.23 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.85 22.02 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.86 21.24 1.19 0.24 13.47| | 21: 1.32 - 1.30 2785 112 0.85 22.37 1.20 0.24 13.30| | 22: 1.29 - 1.27 2704 152 0.85 23.04 1.22 0.24 13.00| | 23: 1.27 - 1.26 2802 156 0.85 22.56 1.22 0.24 11.48| | 24: 1.26 - 1.24 2744 132 0.85 23.19 1.20 0.24 11.48| | 25: 1.24 - 1.22 2734 148 0.84 23.91 1.20 0.24 10.78| | 26: 1.22 - 1.21 2727 135 0.84 24.03 1.20 0.24 10.01| | 27: 1.21 - 1.19 2814 148 0.83 24.86 1.21 0.24 10.01| | 28: 1.19 - 1.18 2671 147 0.84 24.59 1.19 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.84 24.47 1.16 0.23 8.58| | 30: 1.16 - 1.15 2740 148 0.82 26.32 1.16 0.23 8.58| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.58 max = 1517.63 mean = 220.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.74| |phase err.(test): min = 0.00 max = 89.81 mean = 22.68| |-----------------------------------------------------------------------------| ----------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 0.254 1557 Z= 5.582 Angle : 5.191 16.376 2118 Z= 3.628 Chirality : 0.397 1.062 243 Planarity : 0.029 0.101 284 Dihedral : 13.965 86.132 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -2.07 (0.48), residues: 224 helix: -2.12 (0.37), residues: 109 sheet: -0.42 (0.91), residues: 28 loop : -0.32 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.014 ARG A 5 TYR 0.083 0.032 TYR A 139 PHE 0.088 0.041 PHE A 162 HIS 0.033 0.013 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= 0.1964 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792489 | | target function (ml) not normalized (work): 232631.077968 | | target function (ml) not normalized (free): 11838.554933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2606 0.1965 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2606 0.1965 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1982 0.1965 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2002 0.2005 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1643 0.1781 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1643 0.1781 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 0.3767 386.538 372.391 0.692 1.000 0.401 11.894-9.307 99.02 97 4 0.1791 613.997 594.724 0.930 1.000 0.375 9.237-7.194 100.00 213 7 0.2125 502.174 491.497 0.958 1.001 0.349 7.162-5.571 100.00 427 22 0.2232 376.854 364.539 0.927 1.001 0.283 5.546-4.326 100.00 867 58 0.1283 517.327 512.296 0.967 1.001 0.214 4.315-3.360 100.00 1859 96 0.1132 491.982 487.967 1.007 1.001 0.153 3.356-2.611 100.00 3867 181 0.1457 323.206 319.192 0.998 1.001 0.057 2.608-2.026 99.99 8198 413 0.1356 214.256 212.123 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1663 104.632 103.950 1.012 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2068 46.398 45.109 0.997 1.003 0.000 1.221-1.150 99.97 13689 708 0.2588 29.234 26.893 0.967 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0432 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1781 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1645 r_free=0.1782 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.629723 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.530473 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 0.1723 0.1836 0.0113 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1578 0.1713 0.0135 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1464 0.1635 0.0170 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1357 0.1542 0.0185 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1355 0.1552 0.0197 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1365 0.1561 0.0196 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1292 0.1508 0.0216 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1268 0.1492 0.0224 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1260 0.1490 0.0231 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1248 0.1482 0.0235 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1243 0.1478 0.0235 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1239 0.1477 0.0238 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1236 0.1475 0.0239 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1232 0.1473 0.0241 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1229 0.1469 0.0240 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1226 0.1476 0.0249 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1225 0.1478 0.0254 0.007 0.9 4.2 0.5 0.6 0 12.815 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 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 12.29 14.69 2.40 3.012 19.047 2026.530 0.017 12.29 14.68 2.39 2.988 19.047 60.796 0.017 12.36 14.67 2.31 2.668 19.046 253.316 0.017 12.72 15.36 2.64 2.797 19.261 1013.265 0.016 12.49 15.41 2.92 3.132 19.509 2026.530 0.016 12.42 15.43 3.00 3.211 19.569 3039.796 0.015 12.40 15.52 3.12 3.465 19.696 4053.061 0.015 12.26 15.44 3.19 3.354 19.644 5066.326 0.015 12.22 15.41 3.18 3.343 19.619 6079.591 0.015 12.16 15.41 3.25 3.265 19.557 7092.857 0.015 12.15 15.41 3.26 2.935 19.316 8106.122 0.015 12.29 15.70 3.40 3.549 19.680 9119.387 0.015 12.25 15.69 3.44 3.546 19.669 10132.652 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 253.316 Accepted refinement result: 12.36 14.67 2.31 2.668 19.046 253.316 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.07 3.31 0 1785 Protein: 9.06 114.99 16.98 3.32 0 1519 Water: 11.44 119.43 38.22 N/A 0 258 Other: 19.70 26.60 22.04 N/A 0 8 Chain A: 9.06 119.43 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1467 r_work=0.1237 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1470 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 = 0.1467 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= 0.1231 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016900 | | target function (ls_wunit_k1) not normalized (work): 1407.723394 | | target function (ls_wunit_k1) not normalized (free): 110.748733 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1231 0.1467 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1699 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1670 0.1699 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1676 0.1676 0.1704 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1462 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1462 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3500 304.364 283.722 0.669 1.002 0.393 11.894-9.307 99.02 97 4 0.1641 483.468 470.412 0.926 1.003 0.365 9.237-7.194 100.00 213 7 0.1865 395.417 390.160 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1834 296.739 290.627 0.933 1.003 0.259 5.546-4.326 100.00 867 58 0.1010 407.349 404.217 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 387.392 386.296 1.008 1.002 0.149 3.356-2.611 100.00 3867 181 0.1179 254.496 253.359 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1029 168.708 167.990 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.388 82.574 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.534 36.038 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 23.019 21.504 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0544 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1462 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1230 r_free=0.1463 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1463 | n_water=258 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1237 r_free=0.1460 | n_water=252 | time (s): 19.850 (total time: 21.590) Filter (q & B) r_work=0.1239 r_free=0.1459 | n_water=249 | time (s): 2.560 (total time: 24.150) Compute maps r_work=0.1239 r_free=0.1459 | n_water=249 | time (s): 1.710 (total time: 25.860) Filter (map) r_work=0.1253 r_free=0.1464 | n_water=227 | time (s): 3.040 (total time: 28.900) Find peaks r_work=0.1253 r_free=0.1464 | n_water=227 | time (s): 0.480 (total time: 29.380) Add new water r_work=0.1395 r_free=0.1614 | n_water=428 | time (s): 2.530 (total time: 31.910) Refine new water occ: r_work=0.1300 r_free=0.1501 adp: r_work=0.1222 r_free=0.1441 occ: r_work=0.1233 r_free=0.1441 adp: r_work=0.1202 r_free=0.1422 occ: r_work=0.1204 r_free=0.1420 adp: r_work=0.1196 r_free=0.1415 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1415 r_work=0.1196 r_free=0.1415 | n_water=428 | time (s): 54.880 (total time: 86.790) Filter (q & B) r_work=0.1198 r_free=0.1419 | n_water=416 | time (s): 2.950 (total time: 89.740) Filter (dist only) r_work=0.1198 r_free=0.1417 | n_water=415 | time (s): 34.810 (total time: 124.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.957387 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1476.213459 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 0.1742 0.1865 0.0123 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1549 0.1697 0.0148 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1399 0.1572 0.0173 0.002 0.4 6.1 0.0 0.0 0 0.500 0.1350 0.1538 0.0188 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1311 0.1507 0.0196 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1323 0.1520 0.0197 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1246 0.1462 0.0216 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1223 0.1442 0.0218 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1210 0.1431 0.0221 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1201 0.1428 0.0227 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1193 0.1422 0.0228 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1194 0.1423 0.0229 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1191 0.1421 0.0230 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1188 0.1426 0.0237 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1184 0.1419 0.0235 0.006 0.9 5.8 0.5 0.0 0 10.000 0.1183 0.1419 0.0236 0.007 0.9 5.1 0.5 0.6 0 11.000 0.1180 0.1419 0.0239 0.007 0.9 6.1 0.5 0.6 0 12.000 0.1179 0.1418 0.0239 0.007 0.9 5.1 0.5 0.6 0 13.000 0.1178 0.1417 0.0239 0.008 1.0 5.4 0.5 0.6 0 14.479 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1178 0.1417 0.0239 0.008 1.0 5.4 0.5 0.6 0 14.479 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 14.17 2.39 3.775 21.738 1476.213 0.015 11.78 14.17 2.39 3.775 21.738 44.286 0.015 11.78 14.17 2.39 3.775 21.738 184.527 0.015 11.95 14.57 2.62 3.627 21.743 738.107 0.015 11.98 14.91 2.93 3.542 21.810 1476.213 0.014 11.85 15.01 3.15 3.477 21.909 2214.320 0.014 11.67 14.79 3.13 3.452 21.968 2952.427 0.014 11.67 14.85 3.17 3.478 22.114 3690.534 0.014 11.62 14.80 3.18 3.485 22.063 4428.640 0.014 11.58 14.77 3.19 3.499 22.036 5166.747 0.014 11.55 14.77 3.21 3.522 22.057 5904.854 0.013 11.54 14.81 3.27 3.544 22.110 6642.961 0.013 11.57 14.92 3.35 3.572 22.171 7381.067 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.286 Accepted refinement result: 11.78 14.17 2.39 3.775 21.738 44.286 0.015 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 22.12 3.31 188 1754 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.48 76.68 40.82 N/A 188 227 Other: 19.74 26.63 22.08 N/A 0 8 Chain A: 9.10 115.02 19.47 N/A 0 1754 Chain S: 13.50 60.00 46.87 N/A 188 0 Histogram: Values Number of atoms 9.10 - 19.69 1261 19.69 - 30.28 245 30.28 - 40.88 163 40.88 - 51.47 127 51.47 - 62.06 123 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1417 r_work=0.1178 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1417 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1417 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1175 r_free= 0.1417 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014602 | | target function (ls_wunit_k1) not normalized (work): 1216.322580 | | target function (ls_wunit_k1) not normalized (free): 105.001772 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1175 0.1417 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1574 0.1571 0.1650 n_refl.: 87593 remove outliers: r(all,work,free)=0.1574 0.1571 0.1650 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1575 0.1573 0.1651 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1171 0.1412 n_refl.: 87593 remove outliers: r(all,work,free)=0.1181 0.1169 0.1412 n_refl.: 87589 ======================== 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 0.3183 297.142 277.752 0.598 1.003 0.350 11.894-9.307 99.02 97 4 0.1633 483.468 476.310 0.924 1.003 0.350 9.237-7.194 100.00 213 7 0.1672 395.417 395.612 0.984 1.003 0.269 7.162-5.571 100.00 427 22 0.1535 296.739 292.667 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0866 407.349 404.093 0.963 1.003 0.210 4.315-3.360 100.00 1859 96 0.0763 387.392 386.590 1.004 1.003 0.170 3.356-2.611 100.00 3867 181 0.1063 254.496 253.503 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.0994 168.708 168.171 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.388 82.619 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1438 36.534 36.072 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 23.019 21.537 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1169 r_free=0.1412 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=0.1169 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1169 r_free=0.1412 | n_water=415 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1170 r_free=0.1408 | n_water=413 | time (s): 36.230 (total time: 38.630) Filter (q & B) r_work=0.1170 r_free=0.1408 | n_water=413 | time (s): 0.910 (total time: 39.540) Compute maps r_work=0.1170 r_free=0.1408 | n_water=413 | time (s): 1.490 (total time: 41.030) Filter (map) r_work=0.1208 r_free=0.1391 | n_water=297 | time (s): 3.090 (total time: 44.120) Find peaks r_work=0.1208 r_free=0.1391 | n_water=297 | time (s): 0.680 (total time: 44.800) Add new water r_work=0.1327 r_free=0.1525 | n_water=483 | time (s): 3.070 (total time: 47.870) Refine new water occ: r_work=0.1236 r_free=0.1448 adp: r_work=0.1237 r_free=0.1450 occ: r_work=0.1214 r_free=0.1428 adp: r_work=0.1213 r_free=0.1429 occ: r_work=0.1196 r_free=0.1410 adp: r_work=0.1191 r_free=0.1408 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1408 r_work=0.1191 r_free=0.1408 | n_water=483 | time (s): 163.380 (total time: 211.250) Filter (q & B) r_work=0.1194 r_free=0.1412 | n_water=448 | time (s): 2.850 (total time: 214.100) Filter (dist only) r_work=0.1194 r_free=0.1411 | n_water=446 | time (s): 38.800 (total time: 252.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.725818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.425321 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 0.1237 0.1393 0.0155 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1185 0.1348 0.0163 0.003 0.7 4.2 0.5 0.0 0 0.259 0.1167 0.1334 0.0167 0.004 0.8 3.5 0.5 0.0 0 0.518 0.1160 0.1328 0.0167 0.005 0.9 3.2 0.5 0.6 0 0.777 0.1156 0.1325 0.0168 0.006 1.0 3.2 0.5 0.6 0 1.035 0.1153 0.1323 0.0171 0.007 1.0 3.2 0.5 0.6 0 1.294 0.1151 0.1320 0.0170 0.007 1.1 3.8 0.5 0.6 0 1.553 0.1149 0.1319 0.0170 0.008 1.1 3.8 0.5 0.6 0 1.812 0.1159 0.1325 0.0166 0.005 0.9 3.2 0.5 0.6 0 0.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1149 0.1319 0.0170 0.008 1.1 3.8 0.5 0.6 0 1.812 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.49 13.19 1.70 3.778 21.363 45.425 3.619 11.49 13.19 1.70 3.778 21.363 1.363 3.619 11.50 13.19 1.70 3.776 21.363 5.678 3.619 11.54 13.26 1.72 3.711 21.357 22.713 3.613 11.60 13.38 1.78 3.729 21.322 45.425 3.616 11.53 13.37 1.84 3.749 21.309 68.138 3.610 11.46 13.32 1.87 3.767 21.308 90.851 3.605 11.43 13.32 1.89 3.776 21.302 113.563 3.603 11.42 13.34 1.92 3.793 21.288 136.276 3.601 11.42 13.35 1.94 3.806 21.281 158.989 3.601 11.39 13.32 1.93 3.815 21.278 181.701 3.599 11.38 13.31 1.92 3.822 21.274 204.414 3.598 11.36 13.29 1.93 3.827 21.276 227.127 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: 1.363 Accepted refinement result: 11.49 13.19 1.70 3.778 21.363 1.363 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.43 3.31 221 1752 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.48 76.69 36.40 N/A 221 225 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.11 115.03 19.45 N/A 0 1752 Chain S: 13.51 60.01 37.06 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 282 30.29 - 40.89 216 40.89 - 51.48 121 51.48 - 62.07 68 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1319 r_work=0.1149 r_free=0.1319 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1319 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1316 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1141 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612358 | | target function (ml) not normalized (work): 300884.119838 | | target function (ml) not normalized (free): 15850.431208 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1141 0.1316 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1484 0.1484 0.1515 n_refl.: 87589 remove outliers: r(all,work,free)=0.1484 0.1484 0.1515 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1483 0.1483 0.1514 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1305 n_refl.: 87589 remove outliers: r(all,work,free)=0.1142 0.1134 0.1305 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3825 294.428 273.233 0.513 1.001 0.330 11.894-9.307 97.06 95 4 0.2268 483.692 464.759 0.886 1.002 0.290 9.237-7.194 98.64 210 7 0.2198 387.889 388.981 0.966 1.003 0.189 7.162-5.571 100.00 427 22 0.1977 296.739 287.460 0.926 1.003 0.165 5.546-4.326 100.00 867 58 0.1106 407.349 403.097 0.964 1.003 0.160 4.315-3.360 100.00 1859 96 0.0927 387.392 384.824 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1127 254.496 252.478 1.006 1.002 0.100 2.608-2.026 99.99 8198 413 0.0932 168.708 167.980 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.388 82.695 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.534 36.139 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2160 23.019 21.580 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0134 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1134 r_free=0.1305 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1134 r_free=0.1305 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1305 | n_water=446 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1134 r_free=0.1305 | n_water=446 | time (s): 43.530 (total time: 46.000) Filter (q & B) r_work=0.1135 r_free=0.1305 | n_water=445 | time (s): 4.060 (total time: 50.060) Compute maps r_work=0.1135 r_free=0.1305 | n_water=445 | time (s): 1.920 (total time: 51.980) Filter (map) r_work=0.1163 r_free=0.1301 | n_water=333 | time (s): 4.040 (total time: 56.020) Find peaks r_work=0.1163 r_free=0.1301 | n_water=333 | time (s): 0.710 (total time: 56.730) Add new water r_work=0.1234 r_free=0.1392 | n_water=499 | time (s): 3.740 (total time: 60.470) Refine new water occ: r_work=0.1162 r_free=0.1330 adp: r_work=0.1163 r_free=0.1332 occ: r_work=0.1146 r_free=0.1314 adp: r_work=0.1146 r_free=0.1315 occ: r_work=0.1133 r_free=0.1298 adp: r_work=0.1130 r_free=0.1297 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1297 r_work=0.1130 r_free=0.1297 | n_water=499 | time (s): 217.140 (total time: 277.610) Filter (q & B) r_work=0.1136 r_free=0.1302 | n_water=461 | time (s): 3.990 (total time: 281.600) Filter (dist only) r_work=0.1136 r_free=0.1300 | n_water=460 | time (s): 46.870 (total time: 328.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789564 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.082149 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 0.1343 0.0144 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1163 0.1317 0.0154 0.003 0.7 2.9 0.5 0.0 0 0.268 0.1147 0.1307 0.0160 0.005 0.9 3.5 0.5 0.0 0 0.537 0.1141 0.1300 0.0160 0.006 1.0 3.2 0.5 0.6 0 0.805 0.1137 0.1298 0.0162 0.007 1.0 3.2 0.5 0.6 0 1.074 0.1134 0.1298 0.0165 0.007 1.1 3.8 0.5 0.6 0 1.342 0.1132 0.1301 0.0169 0.008 1.1 3.5 0.5 0.6 0 1.611 0.1130 0.1297 0.0166 0.009 1.1 3.8 0.5 0.6 0 1.879 0.1139 0.1301 0.0162 0.006 1.0 3.2 0.5 0.6 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1297 0.0166 0.009 1.1 3.8 0.5 0.6 0 1.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.97 1.66 3.779 21.272 43.082 3.606 11.30 12.97 1.66 3.779 21.272 1.292 3.606 11.31 12.96 1.66 3.779 21.272 5.385 3.606 11.35 13.02 1.67 3.711 21.265 21.541 3.601 11.42 13.16 1.74 3.730 21.236 43.082 3.605 11.35 13.14 1.79 3.753 21.225 64.623 3.600 11.29 13.10 1.81 3.768 21.222 86.164 3.594 11.27 13.10 1.82 3.779 21.217 107.705 3.593 11.23 13.05 1.83 3.786 21.218 129.246 3.589 11.22 13.07 1.84 3.800 21.211 150.788 3.589 11.22 13.08 1.86 3.814 21.203 172.329 3.589 11.22 13.08 1.86 3.826 21.197 193.870 3.588 11.21 13.07 1.86 3.832 21.195 215.411 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.385 Accepted refinement result: 11.31 12.96 1.66 3.779 21.272 5.385 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.26 3.31 237 1750 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.48 76.68 35.26 N/A 237 223 Other: 19.74 26.64 22.08 N/A 0 8 Chain A: 9.10 115.02 19.42 N/A 0 1750 Chain S: 13.51 60.00 34.91 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.70 1266 19.70 - 30.29 296 30.29 - 40.88 227 40.88 - 51.47 121 51.47 - 62.06 55 62.06 - 72.66 11 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1296 r_work=0.1131 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1297 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1292 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1292 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602636 | | target function (ml) not normalized (work): 300052.781172 | | target function (ml) not normalized (free): 15814.976265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1125 0.1292 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1460 0.1460 0.1496 n_refl.: 87583 remove outliers: r(all,work,free)=0.1460 0.1460 0.1496 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1459 0.1459 0.1496 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1296 n_refl.: 87583 remove outliers: r(all,work,free)=0.1131 0.1122 0.1296 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 0.4029 284.148 255.675 0.456 1.000 0.314 11.894-9.307 96.08 94 4 0.2287 485.688 472.522 0.875 1.002 0.310 9.237-7.194 98.18 209 7 0.2293 386.880 382.257 0.937 1.002 0.160 7.162-5.571 100.00 427 22 0.2109 296.739 286.326 0.916 1.002 0.145 5.546-4.326 100.00 867 58 0.1097 407.349 403.386 0.965 1.002 0.141 4.315-3.360 100.00 1859 96 0.0909 387.392 385.083 1.004 1.002 0.132 3.356-2.611 100.00 3867 181 0.1099 254.496 252.603 1.008 1.002 0.060 2.608-2.026 99.99 8198 413 0.0909 168.708 168.050 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.388 82.707 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.534 36.140 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.019 21.568 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0102 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1122 r_free=0.1296 After: r_work=0.1124 r_free=0.1296 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1296 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1124 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1296 | n_water=460 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1124 r_free=0.1295 | n_water=459 | time (s): 50.640 (total time: 53.040) Filter (q & B) r_work=0.1124 r_free=0.1296 | n_water=458 | time (s): 3.980 (total time: 57.020) Compute maps r_work=0.1124 r_free=0.1296 | n_water=458 | time (s): 1.870 (total time: 58.890) Filter (map) r_work=0.1150 r_free=0.1299 | n_water=364 | time (s): 3.920 (total time: 62.810) Find peaks r_work=0.1150 r_free=0.1299 | n_water=364 | time (s): 0.700 (total time: 63.510) Add new water r_work=0.1195 r_free=0.1342 | n_water=507 | time (s): 3.810 (total time: 67.320) Refine new water occ: r_work=0.1142 r_free=0.1302 adp: r_work=0.1143 r_free=0.1304 occ: r_work=0.1131 r_free=0.1290 adp: r_work=0.1130 r_free=0.1292 occ: r_work=0.1123 r_free=0.1278 adp: r_work=0.1120 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1279 r_work=0.1120 r_free=0.1279 | n_water=507 | time (s): 251.810 (total time: 319.130) Filter (q & B) r_work=0.1128 r_free=0.1284 | n_water=466 | time (s): 4.010 (total time: 323.140) Filter (dist only) r_work=0.1128 r_free=0.1282 | n_water=465 | time (s): 48.610 (total time: 371.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.719191 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.535039 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 0.1209 0.1332 0.0123 0.004 0.7 5.1 0.0 0.6 0 0.086 0.1162 0.1301 0.0140 0.004 0.8 5.4 0.0 0.6 0 0.258 0.1144 0.1290 0.0146 0.005 0.9 4.8 0.5 0.6 0 0.516 0.1138 0.1287 0.0149 0.006 1.0 4.5 0.5 0.6 0 0.774 0.1134 0.1284 0.0150 0.007 1.1 4.5 0.5 0.6 0 1.032 0.1130 0.1282 0.0152 0.008 1.1 4.5 0.5 0.6 0 1.289 0.1129 0.1282 0.0153 0.008 1.1 4.5 0.5 0.6 0 1.547 0.1128 0.1282 0.0154 0.009 1.1 4.8 0.5 0.6 0 1.805 0.1137 0.1286 0.0150 0.006 1.0 4.5 0.5 0.6 0 0.860 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1282 0.0154 0.009 1.1 4.8 0.5 0.6 0 1.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.82 1.54 3.778 21.300 38.535 3.602 11.28 12.82 1.54 3.778 21.300 1.156 3.602 11.28 12.82 1.54 3.778 21.300 4.817 3.602 11.31 12.85 1.54 3.709 21.295 19.268 3.597 11.42 13.05 1.63 3.718 21.270 38.535 3.604 11.32 13.01 1.68 3.747 21.259 57.803 3.597 11.27 12.97 1.70 3.761 21.254 77.070 3.592 11.23 12.94 1.71 3.771 21.254 96.338 3.589 11.20 12.91 1.72 3.778 21.254 115.605 3.587 11.19 12.91 1.72 3.789 21.249 134.873 3.585 11.20 12.96 1.76 3.807 21.239 154.140 3.586 11.18 12.94 1.76 3.812 21.240 173.408 3.585 11.17 12.93 1.76 3.821 21.236 192.675 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.817 Accepted refinement result: 11.28 12.82 1.54 3.778 21.300 4.817 3.602 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.32 3.31 243 1749 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.48 76.68 35.35 N/A 243 222 Other: 19.74 26.63 22.08 N/A 0 8 Chain A: 9.10 115.02 19.40 N/A 0 1749 Chain S: 13.50 60.00 35.15 N/A 243 0 Histogram: Values Number of atoms 9.10 - 19.69 1267 19.69 - 30.28 300 30.28 - 40.88 220 40.88 - 51.47 129 51.47 - 62.06 54 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1128 r_free=0.1282 r_work=0.1128 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1282 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1280 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600619 | | target function (ml) not normalized (work): 299870.389030 | | target function (ml) not normalized (free): 15796.556493 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1322 0.1332 5.6496 5.5865| | 2: 3.57 - 2.84 1.00 2888 124 0.1064 0.1378 5.154 5.2308| | 3: 2.83 - 2.48 1.00 2820 163 0.1079 0.1216 4.9303 4.9784| | 4: 2.47 - 2.25 1.00 2825 136 0.0895 0.0965 4.6212 4.6394| | 5: 2.25 - 2.09 1.00 2756 127 0.0858 0.0956 4.5662 4.6207| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.1005 4.2576 4.3479| | 7: 1.97 - 1.87 1.00 2787 165 0.0879 0.1082 3.972 4.0667| | 8: 1.87 - 1.79 1.00 2789 144 0.0909 0.1081 3.882 3.9848| | 9: 1.79 - 1.72 1.00 2745 138 0.0868 0.1149 3.639 3.8167| | 10: 1.72 - 1.66 1.00 2831 160 0.0907 0.1178 3.56 3.7154| | 11: 1.66 - 1.61 1.00 2712 147 0.0859 0.1022 3.4914 3.5687| | 12: 1.61 - 1.56 1.00 2773 144 0.0896 0.1154 3.325 3.4653| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1020 3.3039 3.3849| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1058 3.236 3.3269| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1195 3.1533 3.2526| | 16: 1.45 - 1.42 1.00 2756 161 0.1046 0.1276 3.1336 3.2523| | 17: 1.42 - 1.39 1.00 2785 139 0.1133 0.1328 3.1168 3.2448| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1314 3.1037 3.232| | 19: 1.36 - 1.34 1.00 2807 134 0.1253 0.1552 3.1103 3.2634| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1460 3.1115 3.1451| | 21: 1.32 - 1.30 1.00 2785 112 0.1461 0.1542 3.1126 3.1185| | 22: 1.29 - 1.27 1.00 2704 152 0.1552 0.1997 3.1202 3.304| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1803 3.1334 3.2015| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1835 3.1271 3.2324| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2152 3.1426 3.2605| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1750 3.1492 3.1964| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2165 3.1719 3.1611| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2305 3.1661 3.1763| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2385 3.1479 3.2291| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2430 3.145 3.1648| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.19 1.00 0.97 5590.18| | 2: 3.57 - 2.84 2888 124 0.93 12.23 1.01 0.97 5590.18| | 3: 2.83 - 2.48 2820 163 0.90 16.28 0.99 0.97 4671.40| | 4: 2.47 - 2.25 2825 136 0.92 13.22 1.00 0.98 2302.15| | 5: 2.25 - 2.09 2756 127 0.91 15.39 1.01 0.98 2302.15| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.98 1332.49| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.98 505.49| | 8: 1.87 - 1.79 2789 144 0.93 12.51 1.00 0.98 505.49| | 9: 1.79 - 1.72 2745 138 0.94 10.04 0.98 0.97 288.01| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.97 244.45| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.97 234.24| | 12: 1.61 - 1.56 2773 144 0.95 8.89 0.99 0.97 137.94| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 137.94| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 123.75| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.98 97.78| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.78| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 89.22| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.27| | 19: 1.36 - 1.34 2807 134 0.94 11.87 1.00 0.98 84.27| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 80.25| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 79.97| | 22: 1.29 - 1.27 2704 152 0.93 13.66 0.98 0.96 80.38| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 82.47| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 82.47| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.35| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.03 0.93 86.43| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.43| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 89.97| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.92 91.30| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.92 91.30| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.97 max = 5590.18 mean = 866.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.91 mean = 13.37| |phase err.(test): min = 0.00 max = 88.93 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1125 0.1280 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1454 0.1454 0.1481 n_refl.: 87579 remove outliers: r(all,work,free)=0.1454 0.1454 0.1481 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1453 0.1454 0.1480 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1280 n_refl.: 87579 remove outliers: r(all,work,free)=0.1130 0.1122 0.1280 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3897 288.887 240.183 0.424 1.000 0.302 11.894-9.307 94.12 92 4 0.2395 479.960 466.460 0.876 1.002 0.238 9.237-7.194 98.18 209 7 0.2314 386.880 382.175 0.934 1.002 0.190 7.162-5.571 100.00 427 22 0.2118 296.739 285.991 0.913 1.003 0.135 5.546-4.326 100.00 867 58 0.1102 407.349 403.528 0.964 1.003 0.130 4.315-3.360 100.00 1859 96 0.0911 387.392 385.354 1.002 1.003 0.110 3.356-2.611 100.00 3867 181 0.1096 254.496 252.756 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0902 168.708 168.122 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.388 82.746 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.534 36.155 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.019 21.580 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0098 ================= 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 0.1964 0.083 5.191 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1781 0.083 5.191 9.0 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1781 0.083 5.191 9.0 119.5 20.1 258 0.000 1_nqh: 0.1645 0.1782 0.083 5.191 9.0 119.5 20.1 258 0.003 1_weight: 0.1645 0.1782 0.083 5.191 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1229 0.1469 0.006 0.879 9.0 119.5 20.1 258 0.139 1_adp: 0.1236 0.1467 0.006 0.879 9.1 119.4 20.1 258 0.139 1_regHadp: 0.1237 0.1470 0.006 0.879 9.1 119.4 20.1 258 0.139 1_occ: 0.1231 0.1467 0.006 0.879 9.1 119.4 20.1 258 0.139 2_bss: 0.1229 0.1462 0.006 0.879 9.1 119.5 20.1 258 0.139 2_settarget: 0.1229 0.1462 0.006 0.879 9.1 119.5 20.1 258 0.139 2_updatecdl: 0.1229 0.1462 0.006 0.886 9.1 119.5 20.1 258 0.139 2_nqh: 0.1230 0.1463 0.006 0.886 9.1 119.5 20.1 258 0.139 2_sol: 0.1198 0.1417 0.006 0.886 9.1 115.0 22.1 415 n/a 2_weight: 0.1198 0.1417 0.006 0.886 9.1 115.0 22.1 415 n/a 2_xyzrec: 0.1178 0.1417 0.008 0.963 9.1 115.0 22.1 415 n/a 2_adp: 0.1178 0.1417 0.008 0.963 9.1 115.0 22.1 415 n/a 2_regHadp: 0.1178 0.1417 0.008 0.963 9.1 115.0 22.1 415 n/a 2_occ: 0.1175 0.1417 0.008 0.963 9.1 115.0 22.1 415 n/a 3_bss: 0.1169 0.1412 0.008 0.963 9.1 115.0 22.1 415 n/a 3_settarget: 0.1169 0.1412 0.008 0.963 9.1 115.0 22.1 415 n/a 3_updatecdl: 0.1169 0.1412 0.008 0.964 9.1 115.0 22.1 415 n/a 3_nqh: 0.1169 0.1412 0.008 0.964 9.1 115.0 22.1 415 n/a 3_sol: 0.1194 0.1411 0.008 0.964 9.1 115.0 21.4 446 n/a 3_weight: 0.1194 0.1411 0.008 0.964 9.1 115.0 21.4 446 n/a 3_xyzrec: 0.1149 0.1319 0.008 1.090 9.1 115.0 21.4 446 n/a 3_adp: 0.1149 0.1319 0.008 1.090 9.1 115.0 21.4 446 n/a 3_regHadp: 0.1149 0.1319 0.008 1.090 9.1 115.0 21.4 446 n/a 3_occ: 0.1141 0.1316 0.008 1.090 9.1 115.0 21.4 446 n/a 4_bss: 0.1134 0.1305 0.008 1.090 9.1 115.0 21.4 446 n/a 4_settarget: 0.1134 0.1305 0.008 1.090 9.1 115.0 21.4 446 n/a 4_updatecdl: 0.1134 0.1305 0.008 1.091 9.1 115.0 21.4 446 n/a 4_nqh: 0.1134 0.1305 0.008 1.091 9.1 115.0 21.4 446 n/a 4_sol: 0.1136 0.1300 0.008 1.091 9.1 115.0 21.3 460 n/a 4_weight: 0.1136 0.1300 0.008 1.091 9.1 115.0 21.3 460 n/a 4_xyzrec: 0.1130 0.1297 0.009 1.135 9.1 115.0 21.3 460 n/a 4_adp: 0.1131 0.1296 0.009 1.135 9.1 115.0 21.3 460 n/a 4_regHadp: 0.1131 0.1297 0.009 1.135 9.1 115.0 21.3 460 n/a 4_occ: 0.1125 0.1292 0.009 1.135 9.1 115.0 21.3 460 n/a 5_bss: 0.1122 0.1296 0.009 1.135 9.1 115.0 21.3 460 n/a 5_settarget: 0.1122 0.1296 0.009 1.135 9.1 115.0 21.3 460 n/a 5_updatecdl: 0.1122 0.1296 0.009 1.136 9.1 115.0 21.3 460 n/a 5_setrh: 0.1124 0.1296 0.009 1.136 9.1 115.0 21.3 460 n/a 5_nqh: 0.1124 0.1296 0.009 1.136 9.1 115.0 21.3 460 n/a 5_sol: 0.1128 0.1282 0.009 1.136 9.1 115.0 21.3 465 n/a 5_weight: 0.1128 0.1282 0.009 1.136 9.1 115.0 21.3 465 n/a 5_xyzrec: 0.1128 0.1282 0.009 1.138 9.1 115.0 21.3 465 n/a 5_adp: 0.1128 0.1282 0.009 1.138 9.1 115.0 21.3 465 n/a 5_regHadp: 0.1128 0.1282 0.009 1.138 9.1 115.0 21.3 465 n/a 5_occ: 0.1125 0.1280 0.009 1.138 9.1 115.0 21.3 465 n/a end: 0.1122 0.1280 0.009 1.138 9.1 115.0 21.3 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8530786_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8530786_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 14023.1200 Write final files (write_after_run_outputs) : 86.2400 Total : 14112.5300 Total CPU time: 3.93 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:15:41 PST -0800 (1735366541.60 s) Start R-work = 0.1643, R-free = 0.1781 Final R-work = 0.1122, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 14271.60 seconds wall clock time: 259 minutes 28.46 seconds (15568.46 seconds total)