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_3657390.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 { 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_3657390.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3657390.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 3 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: 1.55, per 1000 atoms: 0.46 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: 0.40 Conformation dependent library (CDL) restraints added in 113.3 milliseconds Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 550 0.92 - 1.17: 1109 1.17 - 1.43: 658 1.43 - 1.68: 799 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 1.334 1.581 -0.247 1.27e-02 6.20e+03 3.77e+02 bond pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.30e-02 5.92e+03 3.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.295 0.229 1.23e-02 6.61e+03 3.47e+02 bond pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 1.237 1.024 0.213 1.17e-02 7.31e+03 3.31e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.049 0.187 1.07e-02 8.73e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 3194 4.61 - 9.21: 1808 9.21 - 13.82: 668 13.82 - 18.43: 100 18.43 - 23.04: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.83 139.60 -17.77 1.03e+00 9.43e-01 2.98e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 120.74 -14.64 1.00e+00 1.00e+00 2.14e+02 angle pdb=" CA ASP A 131 " pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 120.85 134.81 -13.96 1.06e+00 8.90e-01 1.73e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 120.38 -9.93 7.80e-01 1.64e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 920 15.79 - 31.58: 128 31.58 - 47.37: 39 47.37 - 63.16: 22 63.16 - 78.95: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CD2 TYR A 139 " pdb=" CG TYR A 139 " pdb=" CD1 TYR A 139 " pdb=" HD1 TYR A 139 " ideal model delta harmonic sigma weight residual 180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.228: 103 0.228 - 0.451: 84 0.451 - 0.674: 37 0.674 - 0.897: 14 0.897 - 1.120: 5 Chirality restraints: 243 Sorted by residual: 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 1.52 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA ASN A 144 " pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CB ASN A 144 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.58 0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.003 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG PHE A 162 " -0.128 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.024 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.007 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.136 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 26 " -0.047 2.00e-02 2.50e+03 9.91e-02 9.82e+01 pdb=" N ARG A 27 " 0.170 2.00e-02 2.50e+03 pdb=" CA ARG A 27 " -0.044 2.00e-02 2.50e+03 pdb=" H ARG A 27 " -0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1028 2.32 - 2.89: 8144 2.89 - 3.46: 10513 3.46 - 4.03: 15152 4.03 - 4.60: 21723 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.754 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.791 1.850 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.806 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.830 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.831 1.850 ... (remaining 56555 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_3657390_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= 0.2602 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789427 | | target function (ml) not normalized (work): 232375.964958 | | target function (ml) not normalized (free): 11799.532204 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2045 7.055 4.9454| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1741 4.3459 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1679 4.1273 4.1632| | 4: 2.47 - 2.25 1.00 2825 136 0.2310 0.1538 3.8379 3.8355| | 5: 2.25 - 2.09 1.00 2756 127 0.2492 0.1650 3.8009 3.8376| | 6: 2.09 - 1.97 1.00 2846 113 0.2541 0.1643 3.4775 3.4862| | 7: 1.97 - 1.87 1.00 2787 165 0.2516 0.1957 3.1476 3.2513| | 8: 1.87 - 1.79 1.00 2789 144 0.2432 0.1931 3.0596 3.1598| | 9: 1.79 - 1.72 1.00 2745 138 0.2448 0.1770 2.9175 2.9247| | 10: 1.72 - 1.66 1.00 2789 158 0.2455 0.1902 2.8225 2.8217| | 11: 1.66 - 1.61 1.00 2740 147 0.2520 0.1876 2.7436 2.7696| | 12: 1.61 - 1.56 1.00 2787 146 0.2490 0.2100 2.6183 2.679| | 13: 1.56 - 1.52 1.00 2745 130 0.2509 0.1970 2.5529 2.6512| | 14: 1.52 - 1.48 1.00 2803 134 0.2520 0.2069 2.5096 2.6189| | 15: 1.48 - 1.45 1.00 2738 128 0.2585 0.2068 2.4261 2.5128| | 16: 1.45 - 1.42 1.00 2756 161 0.2630 0.2347 2.3597 2.4934| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.2042 2.3376 2.3136| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2227 2.2688 2.3443| | 19: 1.36 - 1.34 1.00 2807 134 0.2644 0.2284 2.234 2.2781| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2049 2.1906 2.1216| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2198 2.141 2.1474| | 22: 1.29 - 1.27 1.00 2704 152 0.2727 0.2467 2.145 2.1581| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2469 2.1132 2.1704| | 24: 1.26 - 1.24 1.00 2744 132 0.2802 0.2422 2.07 2.1507| | 25: 1.24 - 1.22 1.00 2734 148 0.2841 0.2230 2.0443 1.9795| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2312 2.0094 2.073| | 27: 1.21 - 1.19 1.00 2814 148 0.2944 0.2686 1.9975 2.0196| | 28: 1.19 - 1.18 1.00 2671 147 0.3029 0.2821 1.9845 1.994| | 29: 1.18 - 1.16 1.00 2800 134 0.2994 0.2643 1.9631 2.0057| | 30: 1.16 - 1.15 1.00 2740 148 0.3092 0.2873 1.9252 1.9772| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.82 0.76 0.23 1487.11| | 2: 3.57 - 2.84 2876 122 0.80 26.11 1.27 0.23 1487.11| | 3: 2.84 - 2.48 2833 165 0.74 32.15 1.24 0.24 1233.96| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.25 0.25 576.98| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.28 0.25 576.98| | 6: 2.09 - 1.97 2846 113 0.83 22.88 1.28 0.25 316.85| | 7: 1.97 - 1.87 2787 165 0.90 16.82 1.27 0.25 94.99| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 94.99| | 9: 1.79 - 1.72 2745 138 0.88 18.85 1.23 0.25 56.11| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.23 0.25 48.33| | 11: 1.66 - 1.61 2740 147 0.85 21.46 1.25 0.25 46.68| | 12: 1.61 - 1.56 2787 146 0.88 18.87 1.23 0.25 30.00| | 13: 1.56 - 1.52 2745 130 0.86 20.86 1.24 0.25 30.00| | 14: 1.52 - 1.48 2803 134 0.86 21.04 1.23 0.25 26.93| | 15: 1.48 - 1.45 2738 128 0.87 20.45 1.24 0.25 21.32| | 16: 1.45 - 1.42 2756 161 0.85 22.13 1.24 0.25 21.32| | 17: 1.42 - 1.39 2785 139 0.86 21.16 1.23 0.25 17.87| | 18: 1.39 - 1.36 2741 179 0.86 21.19 1.22 0.25 15.87| | 19: 1.36 - 1.34 2807 134 0.85 22.06 1.22 0.25 15.87| | 20: 1.34 - 1.32 2696 147 0.87 20.66 1.22 0.25 12.78| | 21: 1.32 - 1.30 2785 112 0.86 21.42 1.21 0.25 12.56| | 22: 1.29 - 1.27 2704 152 0.86 21.91 1.20 0.25 12.25| | 23: 1.27 - 1.26 2802 156 0.86 21.73 1.21 0.24 10.68| | 24: 1.26 - 1.24 2744 132 0.86 22.23 1.21 0.24 10.68| | 25: 1.24 - 1.22 2734 148 0.85 23.14 1.21 0.24 10.16| | 26: 1.22 - 1.21 2727 135 0.85 23.49 1.19 0.23 9.57| | 27: 1.21 - 1.19 2814 148 0.84 24.22 1.21 0.23 9.57| | 28: 1.19 - 1.18 2671 147 0.83 25.44 1.20 0.22 9.11| | 29: 1.18 - 1.16 2800 134 0.82 25.78 1.18 0.22 8.94| | 30: 1.16 - 1.15 2740 148 0.80 27.66 1.16 0.22 8.94| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 8.94 max = 1487.11 mean = 216.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.65| |phase err.(test): min = 0.00 max = 89.97 mean = 22.57| |-----------------------------------------------------------------------------| ----------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 : 0.086 0.247 1557 Z= 5.709 Angle : 5.210 17.773 2118 Z= 3.742 Chirality : 0.378 1.120 243 Planarity : 0.031 0.091 284 Dihedral : 13.578 78.948 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 29.73 % 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: -2.50 (0.48), residues: 224 helix: -2.32 (0.41), residues: 109 sheet: -0.85 (0.73), residues: 38 loop : -0.63 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.019 ARG A 27 TYR 0.091 0.041 TYR A 141 PHE 0.106 0.048 PHE A 162 HIS 0.043 0.022 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2602 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789427 | | target function (ml) not normalized (work): 232375.964958 | | target function (ml) not normalized (free): 11799.532204 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1938 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1938 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1974 0.1938 n_refl.: 87594 overall B=0.17 to atoms: r(all,work,free)=0.1991 0.1995 0.1950 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1629 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1628 0.1773 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 0.3774 386.270 359.358 0.726 0.929 0.407 11.894-9.307 99.02 97 4 0.1800 613.572 594.214 1.005 0.930 0.390 9.237-7.194 100.00 213 7 0.2140 501.826 490.685 1.035 0.930 0.339 7.162-5.571 100.00 427 22 0.2179 376.593 364.563 1.002 0.931 0.288 5.546-4.326 100.00 867 58 0.1278 516.969 510.966 1.041 0.931 0.228 4.315-3.360 100.00 1859 96 0.1130 491.641 488.192 1.086 0.931 0.199 3.356-2.611 100.00 3867 181 0.1409 322.983 319.598 1.077 0.931 0.109 2.608-2.026 99.99 8198 413 0.1361 214.108 211.800 1.083 0.930 0.000 2.025-1.573 100.00 17313 902 0.1656 104.559 103.772 1.086 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.366 45.109 1.078 0.928 0.000 1.221-1.150 99.97 13689 708 0.2576 29.214 27.022 1.052 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0396 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1631 r_free=0.1775 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.678413 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.646566 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 0.1637 0.1765 0.0128 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1547 0.1686 0.0138 0.002 0.5 4.5 0.0 0.0 0 0.250 0.1426 0.1587 0.0160 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1382 0.1555 0.0174 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1338 0.1522 0.0184 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1339 0.1528 0.0189 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1292 0.1501 0.0208 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1276 0.1497 0.0221 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1262 0.1494 0.0232 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1489 0.0240 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1240 0.1477 0.0238 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1239 0.1484 0.0245 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1234 0.1474 0.0240 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1227 0.1465 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1229 0.1474 0.0244 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1469 0.0243 0.007 0.9 2.9 0.5 0.0 0 11.000 0.1226 0.1472 0.0246 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1221 0.1469 0.0247 0.008 1.0 3.5 0.5 0.6 0 13.839 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1465 0.0238 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 12.27 14.65 2.38 3.012 19.031 2021.647 0.017 12.27 14.65 2.38 3.003 19.031 60.649 0.017 12.34 14.61 2.28 2.668 19.030 252.706 0.017 12.68 15.28 2.60 2.741 19.189 1010.823 0.017 12.55 15.45 2.90 3.345 19.612 2021.647 0.016 12.46 15.52 3.07 3.406 19.653 3032.470 0.015 12.26 15.29 3.03 2.910 19.345 4043.293 0.015 12.32 15.47 3.15 3.398 19.613 5054.116 0.015 12.24 15.46 3.22 3.455 19.648 6064.940 0.015 12.21 15.43 3.22 3.380 19.594 7075.763 0.015 12.23 15.51 3.29 3.488 19.646 8086.586 0.015 12.18 15.49 3.31 3.581 19.687 9097.410 0.015 12.14 15.47 3.32 3.499 19.629 10108.233 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.706 Accepted refinement result: 12.34 14.61 2.28 2.668 19.030 252.706 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.41 20.06 3.31 0 1785 Protein: 9.04 114.96 16.96 3.32 0 1519 Water: 11.47 119.41 38.20 N/A 0 258 Other: 19.68 26.58 22.03 N/A 0 8 Chain A: 9.04 119.41 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.11 227 31.11 - 42.15 125 42.15 - 53.19 94 53.19 - 64.22 42 64.22 - 75.26 11 75.26 - 86.30 7 86.30 - 97.34 4 97.34 - 108.37 1 108.37 - 119.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1461 r_work=0.1235 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1464 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 = 0.1229 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1229 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016953 | | target function (ls_wunit_k1) not normalized (work): 1412.163014 | | target function (ls_wunit_k1) not normalized (free): 109.690058 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1240 0.1229 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1671 0.1671 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1671 0.1671 0.1695 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1678 0.1679 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1455 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 0.3518 304.977 284.634 0.667 1.002 0.396 11.894-9.307 99.02 97 4 0.1628 484.441 471.363 0.927 1.002 0.385 9.237-7.194 100.00 213 7 0.1908 396.213 390.368 0.964 1.003 0.322 7.162-5.571 100.00 427 22 0.1844 297.336 291.473 0.935 1.003 0.263 5.546-4.326 100.00 867 58 0.1007 408.169 405.089 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0879 388.171 387.090 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1177 255.008 253.818 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1021 169.047 168.332 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.554 82.746 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.608 36.108 1.017 0.996 0.000 1.221-1.150 99.97 13689 708 0.2253 23.065 21.543 0.978 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0672 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1455 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1228 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1454 | n_water=258 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1238 r_free=0.1449 | n_water=250 | time (s): 21.050 (total time: 23.210) Filter (q & B) r_work=0.1241 r_free=0.1449 | n_water=247 | time (s): 2.760 (total time: 25.970) Compute maps r_work=0.1241 r_free=0.1449 | n_water=247 | time (s): 1.380 (total time: 27.350) Filter (map) r_work=0.1260 r_free=0.1454 | n_water=225 | time (s): 2.580 (total time: 29.930) Find peaks r_work=0.1260 r_free=0.1454 | n_water=225 | time (s): 0.440 (total time: 30.370) Add new water r_work=0.1414 r_free=0.1617 | n_water=440 | time (s): 3.150 (total time: 33.520) Refine new water occ: r_work=0.1318 r_free=0.1487 adp: r_work=0.1228 r_free=0.1423 occ: r_work=0.1242 r_free=0.1413 adp: r_work=0.1205 r_free=0.1400 occ: r_work=0.1208 r_free=0.1391 adp: r_work=0.1200 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1390 r_work=0.1200 r_free=0.1390 | n_water=440 | time (s): 55.820 (total time: 89.340) Filter (q & B) r_work=0.1204 r_free=0.1388 | n_water=428 | time (s): 2.880 (total time: 92.220) Filter (dist only) r_work=0.1204 r_free=0.1388 | n_water=427 | time (s): 35.150 (total time: 127.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.554141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1492.332537 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 0.1654 0.1757 0.0103 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1522 0.1642 0.0120 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1428 0.1568 0.0140 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1358 0.1514 0.0156 0.001 0.4 5.8 0.0 0.0 0 0.750 0.1323 0.1490 0.0168 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1317 0.1488 0.0170 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1247 0.1443 0.0196 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1224 0.1430 0.0206 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1211 0.1423 0.0212 0.004 0.7 4.2 0.5 0.0 0 4.000 0.1200 0.1412 0.0212 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1198 0.1409 0.0211 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1195 0.1407 0.0212 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1186 0.1403 0.0216 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1183 0.1397 0.0214 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1181 0.1397 0.0216 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1182 0.1403 0.0221 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1179 0.1404 0.0224 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1176 0.1402 0.0226 0.008 0.9 4.5 0.5 0.0 0 13.777 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1183 0.1397 0.0214 0.006 0.8 4.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 13.97 2.14 3.772 21.875 1492.333 0.016 11.83 13.97 2.14 3.772 21.875 44.770 0.016 11.83 13.97 2.14 3.772 21.875 186.542 0.016 12.03 14.42 2.39 3.610 21.886 746.166 0.015 12.03 14.72 2.69 3.453 22.190 1492.333 0.015 11.92 14.69 2.78 3.512 22.307 2238.499 0.014 11.81 14.65 2.84 3.502 22.289 2984.665 0.014 11.74 14.58 2.84 3.522 22.275 3730.831 0.014 11.70 14.62 2.92 3.528 22.258 4476.998 0.014 11.67 14.58 2.91 3.546 22.250 5223.164 0.014 11.66 14.62 2.95 3.562 22.259 5969.330 0.013 11.60 14.54 2.95 3.559 22.227 6715.496 0.013 11.60 14.58 2.98 3.606 22.322 7461.663 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: 186.542 Accepted refinement result: 11.83 13.97 2.14 3.772 21.875 186.542 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 115.01 22.38 3.31 202 1752 Protein: 9.08 115.01 17.01 3.32 0 1519 Water: 11.51 76.67 41.49 N/A 202 225 Other: 19.72 26.62 22.07 N/A 0 8 Chain A: 9.08 115.01 19.41 N/A 0 1752 Chain S: 11.75 60.00 48.10 N/A 202 0 Histogram: Values Number of atoms 9.08 - 19.68 1258 19.68 - 30.27 248 30.27 - 40.86 159 40.86 - 51.45 136 51.45 - 62.04 130 62.04 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1397 r_work=0.1183 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1397 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 = 0.1183 r_free = 0.1399 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 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= 0.1183 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014740 | | target function (ls_wunit_k1) not normalized (work): 1227.836680 | | target function (ls_wunit_k1) not normalized (free): 97.123430 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1183 0.1399 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1585 0.1585 0.1631 n_refl.: 87593 remove outliers: r(all,work,free)=0.1585 0.1585 0.1631 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1588 0.1587 0.1633 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1180 0.1394 n_refl.: 87593 remove outliers: r(all,work,free)=0.1188 0.1178 0.1394 n_refl.: 87588 ======================== 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 0.3117 295.021 280.121 0.619 1.002 0.360 11.894-9.307 99.02 97 4 0.1619 484.441 477.591 0.925 1.003 0.333 9.237-7.194 100.00 213 7 0.1696 396.213 395.653 0.981 1.003 0.249 7.162-5.571 100.00 427 22 0.1554 297.336 293.780 0.935 1.003 0.220 5.546-4.326 100.00 867 58 0.0874 408.169 404.816 0.958 1.003 0.194 4.315-3.360 100.00 1859 96 0.0790 388.171 387.443 1.003 1.003 0.180 3.356-2.611 100.00 3867 181 0.1078 255.008 254.055 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1003 169.047 168.450 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.554 82.767 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1438 36.608 36.142 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 23.065 21.566 0.985 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0254 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1394 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1394 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1394 | n_water=427 | time (s): 1.510 (total time: 1.510) Filter (dist) r_work=0.1178 r_free=0.1393 | n_water=426 | time (s): 38.290 (total time: 39.800) Filter (q & B) r_work=0.1179 r_free=0.1396 | n_water=425 | time (s): 2.610 (total time: 42.410) Compute maps r_work=0.1179 r_free=0.1396 | n_water=425 | time (s): 1.510 (total time: 43.920) Filter (map) r_work=0.1220 r_free=0.1392 | n_water=296 | time (s): 3.370 (total time: 47.290) Find peaks r_work=0.1220 r_free=0.1392 | n_water=296 | time (s): 0.460 (total time: 47.750) Add new water r_work=0.1330 r_free=0.1494 | n_water=490 | time (s): 2.330 (total time: 50.080) Refine new water occ: r_work=0.1240 r_free=0.1409 adp: r_work=0.1240 r_free=0.1410 occ: r_work=0.1219 r_free=0.1389 adp: r_work=0.1217 r_free=0.1389 occ: r_work=0.1202 r_free=0.1376 adp: r_work=0.1197 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1372 r_work=0.1197 r_free=0.1372 | n_water=490 | time (s): 141.830 (total time: 191.910) Filter (q & B) r_work=0.1201 r_free=0.1381 | n_water=455 | time (s): 2.490 (total time: 194.400) Filter (dist only) r_work=0.1201 r_free=0.1380 | n_water=454 | time (s): 37.210 (total time: 231.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705755 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.484942 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 0.1232 0.1352 0.0121 0.002 0.6 4.2 0.5 0.0 0 0.085 0.1187 0.1319 0.0132 0.003 0.7 3.5 0.5 0.0 0 0.256 0.1168 0.1311 0.0143 0.004 0.8 3.2 0.5 0.0 0 0.512 0.1161 0.1310 0.0149 0.005 0.9 2.9 0.5 0.0 0 0.768 0.1156 0.1308 0.0152 0.006 1.0 3.2 0.5 0.0 0 1.023 0.1154 0.1308 0.0155 0.007 1.0 3.5 0.5 0.0 0 1.279 0.1151 0.1309 0.0158 0.007 1.1 3.8 0.5 0.0 0 1.535 0.1149 0.1309 0.0160 0.008 1.1 3.8 0.5 0.0 0 1.791 0.1158 0.1308 0.0150 0.005 0.9 2.9 0.5 0.0 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1308 0.0152 0.006 1.0 3.2 0.5 0.0 0 1.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.08 1.52 3.777 21.362 47.485 3.624 11.56 13.08 1.52 3.777 21.362 1.425 3.624 11.56 13.08 1.52 3.766 21.362 5.936 3.624 11.63 13.17 1.54 3.707 21.347 23.742 3.620 11.60 13.20 1.60 3.731 21.323 47.485 3.618 11.55 13.21 1.66 3.749 21.311 71.227 3.612 11.50 13.18 1.68 3.759 21.307 94.970 3.608 11.49 13.21 1.72 3.775 21.287 118.712 3.607 11.45 13.17 1.73 3.785 21.295 142.455 3.604 11.43 13.17 1.74 3.799 21.284 166.197 3.602 11.43 13.17 1.75 3.811 21.276 189.940 3.602 11.43 13.18 1.75 3.821 21.273 213.682 3.602 11.41 13.17 1.75 3.826 21.270 237.425 3.600 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.425 Accepted refinement result: 11.56 13.08 1.52 3.777 21.362 1.425 3.624 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.43 3.31 230 1751 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.53 76.68 36.15 N/A 230 224 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.02 19.41 N/A 0 1751 Chain S: 11.77 60.02 36.78 N/A 230 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 292 30.28 - 40.88 217 40.88 - 51.47 133 51.47 - 62.06 57 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=0.1156 r_free=0.1308 r_work=0.1156 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1308 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1303 target_work(ml) = 3.619 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1147 r_free= 0.1303 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618503 | | target function (ml) not normalized (work): 301392.355495 | | target function (ml) not normalized (free): 15866.161954 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1147 0.1303 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1482 0.1481 0.1510 n_refl.: 87588 remove outliers: r(all,work,free)=0.1482 0.1481 0.1510 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1481 0.1481 0.1510 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1143 0.1297 n_refl.: 87588 remove outliers: r(all,work,free)=0.1149 0.1142 0.1297 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3822 295.021 269.682 0.502 1.001 0.330 11.894-9.307 98.04 96 4 0.2389 484.538 462.200 0.883 1.002 0.264 9.237-7.194 98.64 210 7 0.2157 390.228 391.202 0.956 1.003 0.210 7.162-5.571 100.00 427 22 0.2036 297.336 286.865 0.924 1.003 0.176 5.546-4.326 100.00 867 58 0.1095 408.169 403.091 0.965 1.003 0.172 4.315-3.360 100.00 1859 96 0.0914 388.171 386.269 1.004 1.002 0.146 3.356-2.611 100.00 3867 181 0.1141 255.008 252.835 1.007 1.002 0.100 2.608-2.026 99.99 8198 413 0.0939 169.047 168.274 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0902 82.554 82.818 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.608 36.189 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2167 23.065 21.594 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0060 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 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=0.1142 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1297 | n_water=454 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1144 r_free=0.1301 | n_water=451 | time (s): 50.440 (total time: 52.960) Filter (q & B) r_work=0.1144 r_free=0.1301 | n_water=449 | time (s): 3.820 (total time: 56.780) Compute maps r_work=0.1144 r_free=0.1301 | n_water=449 | time (s): 1.860 (total time: 58.640) Filter (map) r_work=0.1165 r_free=0.1286 | n_water=346 | time (s): 3.640 (total time: 62.280) Find peaks r_work=0.1165 r_free=0.1286 | n_water=346 | time (s): 0.710 (total time: 62.990) Add new water r_work=0.1233 r_free=0.1369 | n_water=500 | time (s): 3.820 (total time: 66.810) Refine new water occ: r_work=0.1167 r_free=0.1311 adp: r_work=0.1168 r_free=0.1313 occ: r_work=0.1153 r_free=0.1295 adp: r_work=0.1151 r_free=0.1297 occ: r_work=0.1141 r_free=0.1287 adp: r_work=0.1137 r_free=0.1285 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1285 r_work=0.1137 r_free=0.1285 | n_water=500 | time (s): 189.510 (total time: 256.320) Filter (q & B) r_work=0.1144 r_free=0.1290 | n_water=460 | time (s): 3.730 (total time: 260.050) Filter (dist only) r_work=0.1144 r_free=0.1290 | n_water=458 | time (s): 45.770 (total time: 305.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780849 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.471061 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 0.1197 0.1326 0.0128 0.002 0.6 3.5 0.5 0.0 0 0.089 0.1163 0.1302 0.0139 0.003 0.7 2.6 0.5 0.0 0 0.267 0.1149 0.1295 0.0147 0.005 0.9 2.9 0.5 0.0 0 0.534 0.1143 0.1292 0.0150 0.006 0.9 2.6 0.5 0.0 0 0.801 0.1139 0.1294 0.0155 0.006 1.0 2.6 0.5 0.0 0 1.069 0.1137 0.1293 0.0156 0.007 1.1 2.9 0.5 0.0 0 1.336 0.1135 0.1293 0.0158 0.008 1.1 2.9 0.5 0.0 0 1.603 0.1133 0.1292 0.0158 0.008 1.1 2.9 0.5 0.0 0 1.870 0.1142 0.1294 0.0152 0.006 1.0 2.6 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1292 0.0158 0.008 1.1 2.9 0.5 0.0 0 1.870 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.92 1.58 3.778 21.336 43.471 3.607 11.33 12.92 1.58 3.778 21.336 1.304 3.607 11.33 12.92 1.58 3.778 21.336 5.434 3.607 11.37 12.97 1.60 3.712 21.327 21.736 3.602 11.41 13.08 1.67 3.737 21.304 43.471 3.604 11.37 13.12 1.74 3.754 21.286 65.207 3.601 11.31 13.08 1.77 3.771 21.282 86.942 3.596 11.29 13.07 1.78 3.781 21.279 108.678 3.594 11.26 13.05 1.78 3.791 21.275 130.413 3.592 11.24 13.04 1.79 3.802 21.270 152.149 3.590 11.24 13.05 1.81 3.819 21.260 173.884 3.590 11.23 13.03 1.80 3.825 21.259 195.620 3.589 11.22 13.03 1.81 3.831 21.260 217.355 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.434 Accepted refinement result: 11.33 12.92 1.58 3.778 21.336 5.434 3.607 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.38 3.31 237 1748 Protein: 9.10 115.02 17.02 3.32 0 1519 Water: 11.52 76.68 35.82 N/A 237 221 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.10 115.02 19.38 N/A 0 1748 Chain S: 11.76 60.01 36.12 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.69 1261 19.69 - 30.28 295 30.28 - 40.87 220 40.87 - 51.47 132 51.47 - 62.06 54 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1292 r_work=0.1133 r_free=0.1292 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1292 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1289 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604048 | | target function (ml) not normalized (work): 300173.943086 | | target function (ml) not normalized (free): 15817.704259 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1127 0.1289 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1466 0.1465 0.1521 n_refl.: 87584 remove outliers: r(all,work,free)=0.1466 0.1465 0.1521 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1466 0.1464 0.1520 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1126 0.1293 n_refl.: 87584 remove outliers: r(all,work,free)=0.1131 0.1122 0.1293 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3767 294.256 260.380 0.475 1.000 0.310 11.894-9.307 95.10 93 4 0.2398 478.944 458.772 0.870 1.001 0.242 9.237-7.194 97.73 208 7 0.2242 387.177 386.494 0.939 1.002 0.180 7.162-5.571 100.00 427 22 0.2033 297.336 287.849 0.919 1.002 0.140 5.546-4.326 100.00 867 58 0.1096 408.169 403.572 0.964 1.002 0.140 4.315-3.360 100.00 1859 96 0.0907 388.171 386.558 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1106 255.008 253.176 1.009 1.001 0.029 2.608-2.026 99.99 8198 413 0.0917 169.047 168.426 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0877 82.554 82.866 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.608 36.212 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 23.065 21.610 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=-0.0078 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1122 r_free=0.1293 After: r_work=0.1124 r_free=0.1293 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1293 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=0.1293 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1293 | n_water=458 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1124 r_free=0.1294 | n_water=456 | time (s): 48.370 (total time: 50.930) Filter (q & B) r_work=0.1124 r_free=0.1294 | n_water=456 | time (s): 1.490 (total time: 52.420) Compute maps r_work=0.1124 r_free=0.1294 | n_water=456 | time (s): 1.860 (total time: 54.280) Filter (map) r_work=0.1150 r_free=0.1290 | n_water=361 | time (s): 4.220 (total time: 58.500) Find peaks r_work=0.1150 r_free=0.1290 | n_water=361 | time (s): 0.720 (total time: 59.220) Add new water r_work=0.1199 r_free=0.1350 | n_water=504 | time (s): 3.910 (total time: 63.130) Refine new water occ: r_work=0.1144 r_free=0.1288 adp: r_work=0.1144 r_free=0.1291 occ: r_work=0.1132 r_free=0.1275 adp: r_work=0.1131 r_free=0.1276 occ: r_work=0.1123 r_free=0.1267 adp: r_work=0.1120 r_free=0.1265 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1265 r_work=0.1120 r_free=0.1265 | n_water=504 | time (s): 231.380 (total time: 294.510) Filter (q & B) r_work=0.1126 r_free=0.1278 | n_water=470 | time (s): 4.090 (total time: 298.600) Filter (dist only) r_work=0.1126 r_free=0.1277 | n_water=468 | time (s): 51.420 (total time: 350.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.772138 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.655517 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 0.1218 0.1336 0.0118 0.004 0.7 5.8 0.0 0.0 0 0.089 0.1171 0.1308 0.0138 0.004 0.8 5.4 0.0 0.0 0 0.266 0.1151 0.1295 0.0144 0.005 0.9 5.1 0.5 0.0 0 0.532 0.1143 0.1290 0.0147 0.006 1.0 5.4 0.5 0.0 0 0.797 0.1137 0.1285 0.0148 0.006 1.0 5.4 0.5 0.0 0 1.063 0.1131 0.1280 0.0149 0.007 1.1 5.4 0.5 0.0 0 1.329 0.1127 0.1277 0.0150 0.008 1.1 5.4 0.5 0.0 0 1.595 0.1126 0.1277 0.0151 0.008 1.1 5.4 0.5 0.0 0 1.861 0.1140 0.1288 0.0148 0.006 1.0 5.4 0.5 0.0 0 0.886 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1277 0.0151 0.008 1.1 5.4 0.5 0.0 0 1.861 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.77 1.51 3.778 21.324 35.656 3.603 11.26 12.77 1.51 3.778 21.324 1.070 3.603 11.26 12.77 1.51 3.778 21.324 4.457 3.603 11.30 12.82 1.52 3.708 21.316 17.828 3.599 11.33 12.93 1.60 3.729 21.297 35.656 3.600 11.30 12.95 1.65 3.749 21.280 53.483 3.597 11.27 12.97 1.69 3.761 21.272 71.311 3.595 11.25 12.96 1.71 3.770 21.269 89.139 3.592 11.20 12.92 1.72 3.781 21.271 106.967 3.589 11.19 12.92 1.73 3.790 21.265 124.794 3.588 11.17 12.89 1.72 3.796 21.266 142.622 3.586 11.16 12.88 1.73 3.806 21.259 160.450 3.585 11.18 12.94 1.76 3.824 21.249 178.278 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.070 Accepted refinement result: 11.26 12.77 1.51 3.778 21.324 1.070 3.603 Individual atomic B min max mean iso aniso Overall: 9.09 115.02 21.36 3.31 248 1747 Protein: 9.09 115.02 17.02 3.32 0 1519 Water: 11.52 76.68 35.43 N/A 248 220 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.09 115.02 19.36 N/A 0 1747 Chain S: 11.76 60.01 35.44 N/A 248 0 Histogram: Values Number of atoms 9.09 - 19.69 1262 19.69 - 30.28 308 30.28 - 40.87 214 40.87 - 51.46 136 51.46 - 62.06 52 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1126 r_free=0.1277 r_work=0.1126 r_free=0.1277 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1277 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1122 r_free = 0.1272 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1122 r_free= 0.1272 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600682 | | target function (ml) not normalized (work): 299864.785323 | | target function (ml) not normalized (free): 15801.344713 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1316 0.1311 5.6314 5.5825| | 2: 3.57 - 2.84 1.00 2888 124 0.1056 0.1388 5.1545 5.2332| | 3: 2.83 - 2.48 1.00 2820 163 0.1082 0.1195 4.9325 4.967| | 4: 2.47 - 2.25 1.00 2825 136 0.0886 0.0958 4.6164 4.6392| | 5: 2.25 - 2.09 1.00 2756 127 0.0865 0.0936 4.568 4.6118| | 6: 2.09 - 1.97 1.00 2846 113 0.0845 0.0972 4.2537 4.3497| | 7: 1.97 - 1.87 1.00 2787 165 0.0879 0.1087 3.969 4.0645| | 8: 1.87 - 1.79 1.00 2789 144 0.0901 0.1096 3.874 3.9828| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1161 3.6414 3.8177| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1189 3.5602 3.719| | 11: 1.66 - 1.61 1.00 2712 147 0.0861 0.1022 3.491 3.5635| | 12: 1.61 - 1.56 1.00 2773 144 0.0894 0.1143 3.3257 3.4675| | 13: 1.56 - 1.52 1.00 2745 130 0.0931 0.1019 3.3048 3.3887| | 14: 1.52 - 1.48 1.00 2803 134 0.0974 0.1053 3.2374 3.3296| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1219 3.1525 3.2713| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1238 3.1374 3.244| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1333 3.1207 3.246| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1346 3.1048 3.2468| | 19: 1.36 - 1.34 1.00 2807 134 0.1252 0.1545 3.1124 3.2621| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1454 3.1148 3.1521| | 21: 1.32 - 1.30 1.00 2785 112 0.1463 0.1486 3.1149 3.1035| | 22: 1.29 - 1.27 1.00 2704 152 0.1550 0.2004 3.1227 3.3129| | 23: 1.27 - 1.26 1.00 2802 156 0.1642 0.1797 3.1345 3.2059| | 24: 1.26 - 1.24 1.00 2744 132 0.1705 0.1843 3.1299 3.2374| | 25: 1.24 - 1.22 1.00 2733 148 0.1877 0.2158 3.1448 3.2648| | 26: 1.22 - 1.21 1.00 2727 135 0.1903 0.1743 3.1511 3.1985| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2166 3.1747 3.1639| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2288 3.169 3.1778| | 29: 1.18 - 1.16 1.00 2800 134 0.2259 0.2369 3.1487 3.2287| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2431 3.1463 3.1664| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 8.31 1.00 0.97 5594.48| | 2: 3.57 - 2.84 2888 124 0.93 12.30 1.01 0.97 5594.48| | 3: 2.83 - 2.48 2820 163 0.90 16.17 0.99 0.97 4672.19| | 4: 2.47 - 2.25 2825 136 0.92 13.21 1.00 0.98 2293.92| | 5: 2.25 - 2.09 2756 127 0.91 15.30 1.01 0.98 2293.92| | 6: 2.09 - 1.97 2846 113 0.93 12.11 1.02 0.98 1323.40| | 7: 1.97 - 1.87 2787 165 0.95 9.06 1.02 0.98 495.69| | 8: 1.87 - 1.79 2789 144 0.93 12.35 1.00 0.98 495.69| | 9: 1.79 - 1.72 2745 138 0.94 9.94 0.98 0.98 285.48| | 10: 1.72 - 1.66 2831 160 0.94 11.05 0.98 0.98 243.39| | 11: 1.66 - 1.61 2712 147 0.94 11.60 0.98 0.98 233.32| | 12: 1.61 - 1.56 2773 144 0.95 8.93 0.99 0.98 138.38| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.03 0.98 138.38| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 124.30| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.99 98.53| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.99 98.53| | 17: 1.42 - 1.39 2785 139 0.95 10.96 1.01 0.99 89.89| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.99 84.88| | 19: 1.36 - 1.34 2807 134 0.94 11.93 1.00 0.99 84.88| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.74| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 80.45| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.87| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 83.00| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.95 83.00| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.83| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.03 0.93 86.85| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.85| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 90.25| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.93 91.53| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.93 91.53| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.45 max = 5594.48 mean = 865.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.36| |phase err.(test): min = 0.00 max = 89.81 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1122 0.1272 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1482 n_refl.: 87576 remove outliers: r(all,work,free)=0.1438 0.1437 0.1482 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1437 0.1436 0.1482 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1122 0.1270 n_refl.: 87576 remove outliers: r(all,work,free)=0.1128 0.1121 0.1270 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3982 289.468 260.524 0.450 1.000 0.281 11.894-9.307 94.12 92 4 0.2493 475.162 461.790 0.864 1.002 0.260 9.237-7.194 97.27 207 7 0.2202 388.911 383.395 0.932 1.002 0.160 7.162-5.571 100.00 427 22 0.2038 297.336 287.551 0.914 1.002 0.140 5.546-4.326 100.00 867 58 0.1133 408.169 403.158 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0913 388.171 386.346 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1095 255.008 253.126 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0900 169.047 168.473 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.554 82.870 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.608 36.211 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 23.065 21.611 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0083 ================= 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 : 0.2602 0.1939 0.086 5.210 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1773 0.086 5.210 9.0 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1773 0.086 5.210 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1775 0.086 5.210 9.0 119.5 20.1 258 0.003 1_weight: 0.1631 0.1775 0.086 5.210 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1227 0.1465 0.006 0.854 9.0 119.5 20.1 258 0.128 1_adp: 0.1234 0.1461 0.006 0.854 9.0 119.4 20.1 258 0.128 1_regHadp: 0.1235 0.1464 0.006 0.854 9.0 119.4 20.1 258 0.128 1_occ: 0.1229 0.1460 0.006 0.854 9.0 119.4 20.1 258 0.128 2_bss: 0.1229 0.1455 0.006 0.854 9.1 119.5 20.1 258 0.128 2_settarget: 0.1229 0.1455 0.006 0.854 9.1 119.5 20.1 258 0.128 2_updatecdl: 0.1229 0.1455 0.006 0.857 9.1 119.5 20.1 258 0.128 2_nqh: 0.1228 0.1454 0.006 0.857 9.1 119.5 20.1 258 0.128 2_sol: 0.1204 0.1388 0.006 0.857 9.1 115.0 22.4 427 n/a 2_weight: 0.1204 0.1388 0.006 0.857 9.1 115.0 22.4 427 n/a 2_xyzrec: 0.1183 0.1397 0.006 0.827 9.1 115.0 22.4 427 n/a 2_adp: 0.1183 0.1397 0.006 0.827 9.1 115.0 22.4 427 n/a 2_regHadp: 0.1183 0.1397 0.006 0.827 9.1 115.0 22.4 427 n/a 2_occ: 0.1183 0.1399 0.006 0.827 9.1 115.0 22.4 427 n/a 3_bss: 0.1178 0.1394 0.006 0.827 9.1 115.0 22.4 427 n/a 3_settarget: 0.1178 0.1394 0.006 0.827 9.1 115.0 22.4 427 n/a 3_updatecdl: 0.1178 0.1394 0.006 0.830 9.1 115.0 22.4 427 n/a 3_nqh: 0.1178 0.1394 0.006 0.830 9.1 115.0 22.4 427 n/a 3_sol: 0.1201 0.1380 0.006 0.830 9.1 115.0 21.4 454 n/a 3_weight: 0.1201 0.1380 0.006 0.830 9.1 115.0 21.4 454 n/a 3_xyzrec: 0.1156 0.1308 0.006 0.968 9.1 115.0 21.4 454 n/a 3_adp: 0.1156 0.1308 0.006 0.968 9.1 115.0 21.4 454 n/a 3_regHadp: 0.1156 0.1308 0.006 0.968 9.1 115.0 21.4 454 n/a 3_occ: 0.1147 0.1303 0.006 0.968 9.1 115.0 21.4 454 n/a 4_bss: 0.1142 0.1297 0.006 0.968 9.1 115.0 21.4 454 n/a 4_settarget: 0.1142 0.1297 0.006 0.968 9.1 115.0 21.4 454 n/a 4_updatecdl: 0.1142 0.1297 0.006 0.969 9.1 115.0 21.4 454 n/a 4_nqh: 0.1142 0.1297 0.006 0.969 9.1 115.0 21.4 454 n/a 4_sol: 0.1144 0.1290 0.006 0.969 9.1 115.0 21.4 458 n/a 4_weight: 0.1144 0.1290 0.006 0.969 9.1 115.0 21.4 458 n/a 4_xyzrec: 0.1133 0.1292 0.008 1.130 9.1 115.0 21.4 458 n/a 4_adp: 0.1133 0.1292 0.008 1.130 9.1 115.0 21.4 458 n/a 4_regHadp: 0.1133 0.1292 0.008 1.130 9.1 115.0 21.4 458 n/a 4_occ: 0.1127 0.1289 0.008 1.130 9.1 115.0 21.4 458 n/a 5_bss: 0.1122 0.1293 0.008 1.130 9.1 115.0 21.4 458 n/a 5_settarget: 0.1122 0.1293 0.008 1.130 9.1 115.0 21.4 458 n/a 5_updatecdl: 0.1122 0.1293 0.008 1.130 9.1 115.0 21.4 458 n/a 5_setrh: 0.1124 0.1293 0.008 1.130 9.1 115.0 21.4 458 n/a 5_nqh: 0.1124 0.1293 0.008 1.130 9.1 115.0 21.4 458 n/a 5_sol: 0.1126 0.1277 0.008 1.130 9.1 115.0 21.4 468 n/a 5_weight: 0.1126 0.1277 0.008 1.130 9.1 115.0 21.4 468 n/a 5_xyzrec: 0.1126 0.1277 0.008 1.147 9.1 115.0 21.4 468 n/a 5_adp: 0.1126 0.1277 0.008 1.147 9.1 115.0 21.4 468 n/a 5_regHadp: 0.1126 0.1277 0.008 1.147 9.1 115.0 21.4 468 n/a 5_occ: 0.1122 0.1272 0.008 1.147 9.1 115.0 21.4 468 n/a end: 0.1121 0.1270 0.008 1.147 9.1 115.0 21.4 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3657390_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3657390_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9800 Refinement macro-cycles (run) : 13355.9600 Write final files (write_after_run_outputs) : 92.7300 Total : 13451.6700 Total CPU time: 3.74 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:14 PST -0800 (1735366034.31 s) Start R-work = 0.1628, R-free = 0.1773 Final R-work = 0.1121, R-free = 0.1270 =============================================================================== Job complete usr+sys time: 13630.47 seconds wall clock time: 251 minutes 25.47 seconds (15085.47 seconds total)