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_7445011.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_7445011.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7445011.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 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: 1.55, 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: 0.52 Conformation dependent library (CDL) restraints added in 185.8 milliseconds Time building geometry restraints manager: 0.71 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: 565 0.92 - 1.17: 1086 1.17 - 1.43: 689 1.43 - 1.69: 779 1.69 - 1.95: 34 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.633 -0.185 9.00e-03 1.23e+04 4.22e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.234 1.453 -0.218 1.20e-02 6.94e+03 3.31e+02 bond pdb=" N VAL A 8 " pdb=" CA VAL A 8 " ideal model delta sigma weight residual 1.459 1.673 -0.214 1.24e-02 6.50e+03 2.97e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.315 0.206 1.21e-02 6.83e+03 2.91e+02 bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3178 4.72 - 9.43: 1878 9.43 - 14.15: 614 14.15 - 18.86: 95 18.86 - 23.58: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 107.20 121.65 -14.45 1.00e+00 1.00e+00 2.09e+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 92.21 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 121.18 -10.73 7.80e-01 1.64e+00 1.89e+02 angle pdb=" O BLYS A 175 " pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 122.09 136.56 -14.47 1.08e+00 8.57e-01 1.79e+02 angle pdb=" CA AGLY A 65 " pdb=" C AGLY A 65 " pdb=" O AGLY A 65 " ideal model delta sigma weight residual 121.62 108.23 13.39 1.05e+00 9.07e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 927 16.90 - 33.81: 126 33.81 - 50.71: 36 50.71 - 67.62: 21 67.62 - 84.52: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA BGLU A 64 " pdb=" C BGLU A 64 " pdb=" N BGLY A 65 " pdb=" CA BGLY A 65 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 130 0.246 - 0.491: 67 0.491 - 0.737: 31 0.737 - 0.982: 11 0.982 - 1.228: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 42 " pdb=" N ASP A 42 " pdb=" C ASP A 42 " pdb=" CB ASP A 42 " both_signs ideal model delta sigma weight residual False 2.51 3.74 -1.23 2.00e-01 2.50e+01 3.77e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.45 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.052 2.00e-02 2.50e+03 6.31e-02 1.19e+02 pdb=" CG PHE A 164 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.002 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.011 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG PHE A 119 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 801 2.28 - 2.86: 7823 2.86 - 3.44: 10644 3.44 - 4.02: 15320 4.02 - 4.60: 22098 Nonbonded interactions: 56686 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.791 1.850 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.823 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.826 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.826 1.850 x-y,-y,-z-4/3 ... (remaining 56681 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_7445011_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= 0.2604 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784351 | | target function (ml) not normalized (work): 231953.159301 | | target function (ml) not normalized (free): 11829.985628 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3026 0.2096 6.9848 4.9384| | 2: 3.57 - 2.84 1.00 2876 122 0.2428 0.1941 4.3581 4.3662| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1655 4.1334 4.1676| | 4: 2.47 - 2.25 1.00 2825 136 0.2342 0.1513 3.8422 3.8502| | 5: 2.25 - 2.09 1.00 2756 127 0.2498 0.1786 3.806 3.8492| | 6: 2.09 - 1.97 1.00 2846 113 0.2560 0.1679 3.4685 3.5824| | 7: 1.97 - 1.87 1.00 2787 165 0.2592 0.1791 3.1593 3.1941| | 8: 1.87 - 1.79 1.00 2789 144 0.2458 0.1754 3.0587 3.116| | 9: 1.79 - 1.72 1.00 2745 138 0.2383 0.1837 2.8942 2.9012| | 10: 1.72 - 1.66 1.00 2789 158 0.2389 0.1908 2.8022 2.8854| | 11: 1.66 - 1.61 1.00 2740 147 0.2544 0.1982 2.7363 2.8042| | 12: 1.61 - 1.56 1.00 2787 146 0.2550 0.2134 2.6301 2.6971| | 13: 1.56 - 1.52 1.00 2745 130 0.2517 0.1728 2.5579 2.552| | 14: 1.52 - 1.48 1.00 2803 134 0.2571 0.1979 2.5057 2.5507| | 15: 1.48 - 1.45 1.00 2738 128 0.2545 0.2031 2.3956 2.4864| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.2310 2.3774 2.5325| | 17: 1.42 - 1.39 1.00 2785 139 0.2618 0.2073 2.317 2.3449| | 18: 1.39 - 1.36 1.00 2741 179 0.2644 0.2253 2.2758 2.3408| | 19: 1.36 - 1.34 1.00 2807 134 0.2626 0.2432 2.2331 2.3158| | 20: 1.34 - 1.32 1.00 2696 147 0.2650 0.2085 2.1827 2.1716| | 21: 1.32 - 1.30 1.00 2785 112 0.2669 0.2075 2.1453 2.1305| | 22: 1.29 - 1.27 1.00 2704 152 0.2713 0.2576 2.113 2.1731| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2590 2.0894 2.213| | 24: 1.26 - 1.24 1.00 2744 132 0.2802 0.2414 2.0735 2.104| | 25: 1.24 - 1.22 1.00 2734 148 0.2836 0.2486 2.0346 2.0642| | 26: 1.22 - 1.21 1.00 2727 135 0.2877 0.2299 2.0095 2.0933| | 27: 1.21 - 1.19 1.00 2814 148 0.2985 0.2661 2.0035 2.0147| | 28: 1.19 - 1.18 1.00 2671 147 0.3023 0.2705 1.9931 1.9832| | 29: 1.18 - 1.16 1.00 2800 134 0.2951 0.2812 1.961 2.0746| | 30: 1.16 - 1.15 1.00 2740 148 0.3076 0.2709 1.9351 1.9474| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.11 0.76 0.23 1514.78| | 2: 3.57 - 2.84 2876 122 0.80 26.43 1.27 0.23 1514.78| | 3: 2.84 - 2.48 2833 165 0.73 32.48 1.24 0.23 1256.08| | 4: 2.47 - 2.25 2825 136 0.81 26.03 1.25 0.25 584.72| | 5: 2.25 - 2.09 2756 127 0.77 29.77 1.29 0.25 584.72| | 6: 2.09 - 1.97 2846 113 0.83 23.10 1.29 0.25 319.66| | 7: 1.97 - 1.87 2787 165 0.90 16.91 1.29 0.25 93.61| | 8: 1.87 - 1.79 2789 144 0.85 21.43 1.25 0.25 93.61| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.23 0.25 55.58| | 10: 1.72 - 1.66 2789 158 0.87 20.01 1.22 0.25 47.97| | 11: 1.66 - 1.61 2740 147 0.85 21.46 1.25 0.25 46.32| | 12: 1.61 - 1.56 2787 146 0.89 18.26 1.24 0.25 29.58| | 13: 1.56 - 1.52 2745 130 0.86 20.58 1.24 0.25 29.58| | 14: 1.52 - 1.48 2803 134 0.86 20.85 1.23 0.25 26.50| | 15: 1.48 - 1.45 2738 128 0.87 20.34 1.23 0.25 20.86| | 16: 1.45 - 1.42 2756 161 0.85 21.80 1.23 0.25 20.86| | 17: 1.42 - 1.39 2785 139 0.86 20.90 1.23 0.25 17.82| | 18: 1.39 - 1.36 2741 179 0.86 21.33 1.21 0.25 16.06| | 19: 1.36 - 1.34 2807 134 0.85 22.30 1.22 0.25 16.06| | 20: 1.34 - 1.32 2696 147 0.87 20.96 1.21 0.24 13.15| | 21: 1.32 - 1.30 2785 112 0.86 22.00 1.21 0.24 12.95| | 22: 1.29 - 1.27 2704 152 0.85 22.38 1.21 0.24 12.65| | 23: 1.27 - 1.26 2802 156 0.85 22.48 1.22 0.24 11.12| | 24: 1.26 - 1.24 2744 132 0.85 22.88 1.21 0.24 11.12| | 25: 1.24 - 1.22 2734 148 0.84 23.82 1.20 0.24 10.55| | 26: 1.22 - 1.21 2727 135 0.84 24.25 1.20 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.21 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.83 25.35 1.20 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.82 25.76 1.16 0.22 9.06| | 30: 1.16 - 1.15 2740 148 0.80 27.41 1.15 0.22 9.06| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.06 max = 1514.78 mean = 219.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.80| |phase err.(test): min = 0.00 max = 89.75 mean = 22.52| |-----------------------------------------------------------------------------| ----------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 0.280 1557 Z= 5.469 Angle : 5.315 16.752 2118 Z= 3.778 Chirality : 0.375 1.228 243 Planarity : 0.032 0.101 284 Dihedral : 13.984 84.523 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 23.24 % 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: -1.66 (0.48), residues: 224 helix: -1.85 (0.42), residues: 103 sheet: 0.01 (0.93), residues: 28 loop : -0.27 (0.54), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.024 ARG A 48 TYR 0.104 0.035 TYR A 139 PHE 0.107 0.042 PHE A 164 HIS 0.084 0.038 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= 0.2604 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784351 | | target function (ml) not normalized (work): 231953.159301 | | target function (ml) not normalized (free): 11829.985628 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2605 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2605 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1973 0.1976 0.1963 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1997 0.2001 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1626 0.1781 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1625 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 0.3851 386.474 357.624 0.664 1.001 0.407 11.894-9.307 99.02 97 4 0.1823 613.895 593.575 0.923 1.003 0.390 9.237-7.194 100.00 213 7 0.2083 502.091 491.765 0.960 1.003 0.370 7.162-5.571 100.00 427 22 0.2173 376.791 363.156 0.935 1.003 0.320 5.546-4.326 100.00 867 58 0.1281 517.241 509.969 0.963 1.003 0.224 4.315-3.360 100.00 1859 96 0.1154 491.900 488.756 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1416 323.153 319.745 0.994 1.002 0.109 2.608-2.026 99.99 8198 413 0.1350 214.221 211.802 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1641 104.614 104.034 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2033 46.390 45.073 1.004 0.995 0.000 1.221-1.150 99.97 13689 708 0.2592 29.229 26.939 0.979 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1781 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 3 r_work=0.1628 r_free=0.1788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.439821 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2006.409777 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 0.1627 0.1753 0.0126 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1553 0.1693 0.0140 0.002 0.5 4.5 0.0 0.0 0 0.250 0.1425 0.1588 0.0162 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1382 0.1558 0.0176 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1356 0.1550 0.0194 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1344 0.1535 0.0191 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1283 0.1498 0.0215 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1272 0.1497 0.0225 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1260 0.1495 0.0234 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1486 0.0238 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1240 0.1474 0.0235 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1239 0.1479 0.0241 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1239 0.1480 0.0241 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1234 0.1478 0.0244 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1231 0.1474 0.0242 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1229 0.1469 0.0239 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1470 0.0242 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1226 0.1469 0.0243 0.007 0.9 4.2 0.5 0.0 0 13.000 0.1225 0.1473 0.0248 0.008 1.0 4.5 0.5 0.6 0 14.220 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1469 0.0239 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.69 2.39 3.013 19.054 2006.410 0.017 12.29 14.69 2.39 3.013 19.054 60.192 0.017 12.36 14.65 2.28 2.669 19.054 250.801 0.017 12.70 15.33 2.63 2.737 19.218 1003.205 0.017 12.56 15.50 2.94 3.272 19.604 2006.410 0.016 12.45 15.49 3.04 3.326 19.640 3009.615 0.015 12.39 15.54 3.14 3.385 19.656 4012.820 0.015 12.30 15.48 3.18 3.386 19.650 5016.024 0.015 12.26 15.50 3.24 3.456 19.690 6019.229 0.015 12.31 15.61 3.29 3.377 19.627 7022.434 0.015 12.17 15.43 3.26 3.354 19.611 8025.639 0.015 12.15 15.41 3.27 3.416 19.641 9028.844 0.015 12.16 15.47 3.31 3.532 19.693 10032.049 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 250.801 Accepted refinement result: 12.36 14.65 2.28 2.669 19.054 250.801 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.43 20.08 3.31 0 1785 Protein: 9.07 114.99 16.99 3.32 0 1519 Water: 11.47 119.43 38.22 N/A 0 258 Other: 19.70 26.60 22.05 N/A 0 8 Chain A: 9.07 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 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=0.1465 r_work=0.1238 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1468 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 = 0.1232 r_free = 0.1466 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1232 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017010 | | target function (ls_wunit_k1) not normalized (work): 1416.882169 | | target function (ls_wunit_k1) not normalized (free): 110.849265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1244 0.1232 0.1466 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1677 0.1678 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1677 0.1678 0.1695 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1685 0.1700 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1230 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1455 n_refl.: 87591 ======================== 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 94.79 86 5 0.3546 297.917 282.067 0.641 1.002 0.377 11.894-9.307 99.02 97 4 0.1689 482.756 469.249 0.919 1.003 0.374 9.237-7.194 100.00 213 7 0.1881 394.835 388.876 0.961 1.003 0.360 7.162-5.571 100.00 427 22 0.1853 296.302 289.904 0.937 1.003 0.269 5.546-4.326 100.00 867 58 0.1009 406.749 403.436 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0869 386.822 385.721 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1174 254.122 252.950 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1027 168.459 167.724 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.267 82.468 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.480 35.983 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.985 21.468 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0534 ============================ 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 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 1 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): 1.950 (total time: 1.950) Filter (dist) r_work=0.1235 r_free=0.1452 | n_water=252 | time (s): 22.350 (total time: 24.300) Filter (q & B) r_work=0.1237 r_free=0.1451 | n_water=249 | time (s): 2.520 (total time: 26.820) Compute maps r_work=0.1237 r_free=0.1451 | n_water=249 | time (s): 1.280 (total time: 28.100) Filter (map) r_work=0.1255 r_free=0.1455 | n_water=227 | time (s): 2.750 (total time: 30.850) Find peaks r_work=0.1255 r_free=0.1455 | n_water=227 | time (s): 0.520 (total time: 31.370) Add new water r_work=0.1397 r_free=0.1630 | n_water=428 | time (s): 3.040 (total time: 34.410) Refine new water occ: r_work=0.1300 r_free=0.1489 adp: r_work=0.1227 r_free=0.1436 occ: r_work=0.1239 r_free=0.1428 adp: r_work=0.1208 r_free=0.1415 occ: r_work=0.1211 r_free=0.1407 adp: r_work=0.1200 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1406 r_work=0.1200 r_free=0.1406 | n_water=428 | time (s): 53.320 (total time: 87.730) Filter (q & B) r_work=0.1204 r_free=0.1415 | n_water=408 | time (s): 3.540 (total time: 91.270) Filter (dist only) r_work=0.1205 r_free=0.1412 | n_water=407 | time (s): 32.450 (total time: 123.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.955878 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.082958 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 0.1682 0.1802 0.0120 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1536 0.1676 0.0139 0.001 0.4 5.8 0.0 0.0 0 0.250 0.1416 0.1578 0.0162 0.001 0.4 5.1 0.0 0.0 0 0.500 0.1342 0.1518 0.0176 0.001 0.5 4.5 0.0 0.0 0 0.750 0.1311 0.1499 0.0188 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1319 0.1508 0.0189 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1256 0.1464 0.0208 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1231 0.1449 0.0218 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1221 0.1441 0.0220 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1215 0.1438 0.0223 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1208 0.1432 0.0224 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1207 0.1429 0.0222 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1200 0.1421 0.0221 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1200 0.1428 0.0228 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1197 0.1427 0.0230 0.006 0.8 3.8 0.5 0.0 0 10.000 0.1196 0.1433 0.0237 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1197 0.1435 0.0238 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1193 0.1436 0.0242 0.008 0.9 3.8 0.5 0.0 0 13.978 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1421 0.0221 0.005 0.8 4.2 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 14.21 2.21 3.775 21.679 1485.083 0.016 12.00 14.21 2.21 3.775 21.679 44.552 0.016 12.00 14.21 2.21 3.775 21.679 185.635 0.016 12.29 14.82 2.53 3.577 21.718 742.541 0.016 12.19 15.02 2.83 3.561 21.739 1485.083 0.015 12.00 14.85 2.85 3.451 21.998 2227.624 0.015 11.99 14.95 2.97 3.508 22.052 2970.166 0.015 11.82 14.85 3.03 3.539 21.806 3712.707 0.015 11.82 14.83 3.01 3.514 21.955 4455.249 0.014 11.83 14.95 3.12 3.531 21.950 5197.790 0.014 11.78 14.97 3.19 3.540 21.943 5940.332 0.014 11.79 15.01 3.22 3.560 22.021 6682.873 0.014 11.76 14.98 3.22 3.568 21.978 7425.415 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.552 Accepted refinement result: 12.00 14.21 2.21 3.775 21.679 44.552 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 22.01 3.31 180 1754 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 40.63 N/A 180 227 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.11 115.03 19.47 N/A 0 1754 Chain S: 16.60 60.00 46.76 N/A 180 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 244 30.29 - 40.88 165 40.88 - 51.47 133 51.47 - 62.07 110 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1421 r_work=0.1200 r_free=0.1421 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1421 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1414 target_work(ls_wunit_k1) = 0.016 | | 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1414 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015560 | | target function (ls_wunit_k1) not normalized (work): 1296.061387 | | target function (ls_wunit_k1) not normalized (free): 101.399950 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1197 0.1414 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1599 0.1599 0.1637 n_refl.: 87591 remove outliers: r(all,work,free)=0.1599 0.1599 0.1637 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1600 0.1600 0.1638 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1194 0.1409 n_refl.: 87591 remove outliers: r(all,work,free)=0.1203 0.1192 0.1409 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 0.3240 293.995 272.189 0.581 1.002 0.350 11.894-9.307 99.02 97 4 0.1643 482.756 473.959 0.916 1.003 0.325 9.237-7.194 100.00 213 7 0.1797 394.835 393.437 0.980 1.003 0.300 7.162-5.571 100.00 427 22 0.1652 296.302 290.965 0.936 1.003 0.230 5.546-4.326 100.00 867 58 0.0910 406.749 403.199 0.961 1.003 0.204 4.315-3.360 100.00 1859 96 0.0811 386.822 385.740 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1090 254.122 253.051 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1011 168.459 167.913 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.267 82.481 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.480 36.015 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.985 21.499 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=0.0126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1409 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1409 | n_water=407 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1194 r_free=0.1412 | n_water=404 | time (s): 35.480 (total time: 37.520) Filter (q & B) r_work=0.1194 r_free=0.1412 | n_water=404 | time (s): 0.990 (total time: 38.510) Compute maps r_work=0.1194 r_free=0.1412 | n_water=404 | time (s): 1.590 (total time: 40.100) Filter (map) r_work=0.1227 r_free=0.1403 | n_water=285 | time (s): 2.710 (total time: 42.810) Find peaks r_work=0.1227 r_free=0.1403 | n_water=285 | time (s): 0.660 (total time: 43.470) Add new water r_work=0.1343 r_free=0.1518 | n_water=459 | time (s): 2.860 (total time: 46.330) Refine new water occ: r_work=0.1251 r_free=0.1436 adp: r_work=0.1252 r_free=0.1437 occ: r_work=0.1231 r_free=0.1414 adp: r_work=0.1230 r_free=0.1415 occ: r_work=0.1216 r_free=0.1394 adp: r_work=0.1211 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1211 r_free=0.1393 r_work=0.1211 r_free=0.1393 | n_water=459 | time (s): 235.320 (total time: 281.650) Filter (q & B) r_work=0.1215 r_free=0.1395 | n_water=433 | time (s): 2.420 (total time: 284.070) Filter (dist only) r_work=0.1215 r_free=0.1394 | n_water=432 | time (s): 36.310 (total time: 320.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.759091 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.770681 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 0.1241 0.1357 0.0115 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1193 0.1324 0.0131 0.003 0.7 3.8 0.5 0.0 0 0.264 0.1177 0.1317 0.0141 0.004 0.8 2.9 0.5 0.0 0 0.528 0.1169 0.1318 0.0149 0.005 0.9 3.2 0.5 0.0 0 0.792 0.1165 0.1316 0.0151 0.006 1.0 2.9 0.5 0.0 0 1.055 0.1162 0.1318 0.0156 0.007 1.0 3.2 0.5 0.0 0 1.319 0.1160 0.1320 0.0160 0.007 1.1 3.8 0.5 0.0 0 1.583 0.1159 0.1315 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.847 0.1169 0.1317 0.0148 0.005 0.9 2.9 0.5 0.0 0 0.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1315 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.847 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.15 1.56 3.779 21.184 48.771 3.617 11.59 13.15 1.56 3.779 21.184 1.463 3.617 11.59 13.15 1.56 3.764 21.184 6.096 3.617 11.66 13.26 1.60 3.712 21.169 24.385 3.613 11.65 13.35 1.69 3.735 21.140 48.771 3.613 11.59 13.32 1.74 3.754 21.129 73.156 3.606 11.54 13.27 1.73 3.765 21.125 97.541 3.602 11.50 13.26 1.76 3.782 21.118 121.927 3.599 11.50 13.30 1.79 3.798 21.103 146.312 3.599 11.46 13.26 1.79 3.808 21.105 170.697 3.596 11.45 13.24 1.79 3.816 21.103 195.083 3.595 11.46 13.26 1.80 3.828 21.093 219.468 3.595 11.44 13.24 1.80 3.833 21.094 243.853 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.463 Accepted refinement result: 11.59 13.15 1.56 3.779 21.184 1.463 3.617 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.10 3.31 208 1751 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.51 76.69 35.37 N/A 208 224 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.11 115.04 19.43 N/A 0 1751 Chain S: 15.93 60.01 35.16 N/A 208 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.30 281 30.30 - 40.89 220 40.89 - 51.48 124 51.48 - 62.07 47 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1315 r_work=0.1159 r_free=0.1315 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1315 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1310 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1152 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610861 | | target function (ml) not normalized (work): 300755.838657 | | target function (ml) not normalized (free): 15824.406501 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1310 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1505 0.1504 0.1554 n_refl.: 87588 remove outliers: r(all,work,free)=0.1505 0.1504 0.1554 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1504 0.1503 0.1554 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1149 0.1307 n_refl.: 87588 remove outliers: r(all,work,free)=0.1153 0.1145 0.1307 n_refl.: 87580 ======================== 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 0.3715 290.605 261.675 0.483 1.000 0.298 11.894-9.307 97.06 95 4 0.2332 476.091 461.639 0.867 1.001 0.283 9.237-7.194 98.18 209 7 0.2246 386.311 386.646 0.955 1.002 0.200 7.162-5.571 100.00 427 22 0.2094 296.302 285.893 0.921 1.002 0.190 5.546-4.326 100.00 867 58 0.1128 406.749 401.831 0.967 1.002 0.180 4.315-3.360 100.00 1859 96 0.0929 386.822 384.366 1.006 1.002 0.170 3.356-2.611 100.00 3867 181 0.1159 254.122 251.654 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0935 168.459 167.645 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.267 82.543 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.480 36.053 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.985 21.515 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0127 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1307 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=0.1145 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1307 | n_water=432 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1148 r_free=0.1305 | n_water=428 | time (s): 46.680 (total time: 49.210) Filter (q & B) r_work=0.1148 r_free=0.1305 | n_water=428 | time (s): 1.320 (total time: 50.530) Compute maps r_work=0.1148 r_free=0.1305 | n_water=428 | time (s): 1.920 (total time: 52.450) Filter (map) r_work=0.1169 r_free=0.1310 | n_water=317 | time (s): 3.940 (total time: 56.390) Find peaks r_work=0.1169 r_free=0.1310 | n_water=317 | time (s): 0.700 (total time: 57.090) Add new water r_work=0.1240 r_free=0.1391 | n_water=463 | time (s): 3.790 (total time: 60.880) Refine new water occ: r_work=0.1174 r_free=0.1330 adp: r_work=0.1175 r_free=0.1333 occ: r_work=0.1159 r_free=0.1312 adp: r_work=0.1159 r_free=0.1315 occ: r_work=0.1148 r_free=0.1295 adp: r_work=0.1145 r_free=0.1297 ADP+occupancy (water only), MIN, final r_work=0.1145 r_free=0.1297 r_work=0.1145 r_free=0.1297 | n_water=463 | time (s): 321.270 (total time: 382.150) Filter (q & B) r_work=0.1149 r_free=0.1296 | n_water=427 | time (s): 4.000 (total time: 386.150) Filter (dist only) r_work=0.1156 r_free=0.1294 | n_water=425 | time (s): 45.480 (total time: 431.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.816166 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.819297 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 0.1215 0.1323 0.0108 0.002 0.6 3.5 0.5 0.0 0 0.091 0.1182 0.1302 0.0120 0.003 0.7 2.6 0.5 0.0 0 0.272 0.1167 0.1294 0.0127 0.005 0.9 2.9 0.5 0.0 0 0.545 0.1160 0.1293 0.0133 0.006 0.9 2.9 0.5 0.0 0 0.817 0.1157 0.1292 0.0135 0.006 1.0 2.6 0.5 0.0 0 1.090 0.1154 0.1291 0.0137 0.007 1.1 2.9 0.5 0.0 0 1.362 0.1152 0.1290 0.0138 0.008 1.1 3.2 0.5 0.0 0 1.635 0.1150 0.1289 0.0139 0.009 1.1 3.2 0.5 0.0 0 1.907 0.1159 0.1292 0.0133 0.006 1.0 3.2 0.5 0.0 0 0.908 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1150 0.1289 0.0139 0.009 1.1 3.2 0.5 0.0 0 1.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 12.89 1.39 3.779 21.133 45.819 3.609 11.50 12.89 1.39 3.779 21.133 1.375 3.609 11.50 12.89 1.39 3.773 21.133 5.727 3.609 11.53 12.94 1.41 3.713 21.124 22.910 3.603 11.58 13.10 1.52 3.736 21.094 45.819 3.606 11.51 13.08 1.57 3.758 21.084 68.729 3.600 11.45 13.03 1.58 3.773 21.082 91.639 3.595 11.44 13.02 1.59 3.782 21.077 114.548 3.593 11.41 13.00 1.59 3.793 21.075 137.458 3.591 11.42 13.05 1.62 3.811 21.058 160.368 3.592 11.39 13.01 1.61 3.817 21.056 183.277 3.589 11.38 13.00 1.62 3.826 21.058 206.187 3.588 11.37 12.99 1.62 3.834 21.055 229.096 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: 1.375 Accepted refinement result: 11.50 12.89 1.39 3.779 21.133 1.375 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.01 3.31 204 1748 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.51 76.69 35.21 N/A 204 221 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.11 115.03 19.41 N/A 0 1748 Chain S: 15.93 60.00 34.67 N/A 204 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 286 30.29 - 40.89 205 40.89 - 51.48 129 51.48 - 62.07 43 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1289 r_work=0.1150 r_free=0.1289 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1150 r_free = 0.1289 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1283 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1145 r_free= 0.1283 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605876 | | target function (ml) not normalized (work): 300311.797947 | | target function (ml) not normalized (free): 15802.620061 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1145 0.1283 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1486 0.1483 0.1542 n_refl.: 87580 remove outliers: r(all,work,free)=0.1486 0.1483 0.1542 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1485 0.1483 0.1542 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1284 n_refl.: 87580 remove outliers: r(all,work,free)=0.1151 0.1144 0.1284 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3768 288.462 256.830 0.468 0.998 0.297 11.894-9.307 97.06 95 4 0.2516 476.091 462.600 0.854 1.001 0.280 9.237-7.194 98.18 209 7 0.2372 386.311 380.095 0.927 1.001 0.190 7.162-5.571 100.00 427 22 0.2142 296.302 284.645 0.913 1.001 0.178 5.546-4.326 100.00 867 58 0.1130 406.749 401.668 0.965 1.002 0.144 4.315-3.360 100.00 1859 96 0.0948 386.822 384.582 1.005 1.001 0.123 3.356-2.611 100.00 3867 181 0.1139 254.122 252.198 1.010 1.001 0.060 2.608-2.026 99.99 8198 413 0.0927 168.459 167.811 1.026 1.000 0.000 2.025-1.573 100.00 17313 902 0.0893 82.267 82.601 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.480 36.079 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.985 21.529 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=-0.0103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1144 r_free=0.1284 After: r_work=0.1146 r_free=0.1284 ================================== NQH flips ================================== r_work=0.1146 r_free=0.1284 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=0.1146 r_free=0.1284 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1284 | n_water=425 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1146 r_free=0.1283 | n_water=423 | time (s): 47.190 (total time: 49.640) Filter (q & B) r_work=0.1146 r_free=0.1283 | n_water=422 | time (s): 3.850 (total time: 53.490) Compute maps r_work=0.1146 r_free=0.1283 | n_water=422 | time (s): 1.880 (total time: 55.370) Filter (map) r_work=0.1181 r_free=0.1321 | n_water=335 | time (s): 3.760 (total time: 59.130) Find peaks r_work=0.1181 r_free=0.1321 | n_water=335 | time (s): 0.650 (total time: 59.780) Add new water r_work=0.1243 r_free=0.1383 | n_water=489 | time (s): 3.760 (total time: 63.540) Refine new water occ: r_work=0.1171 r_free=0.1319 adp: r_work=0.1171 r_free=0.1320 occ: r_work=0.1158 r_free=0.1303 adp: r_work=0.1156 r_free=0.1305 occ: r_work=0.1147 r_free=0.1293 adp: r_work=0.1143 r_free=0.1293 ADP+occupancy (water only), MIN, final r_work=0.1143 r_free=0.1293 r_work=0.1143 r_free=0.1293 | n_water=489 | time (s): 262.930 (total time: 326.470) Filter (q & B) r_work=0.1150 r_free=0.1300 | n_water=447 | time (s): 3.900 (total time: 330.370) Filter (dist only) r_work=0.1150 r_free=0.1298 | n_water=446 | time (s): 47.590 (total time: 377.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.744652 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.296180 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 0.1233 0.1351 0.0118 0.004 0.7 4.8 0.0 0.0 0 0.087 0.1182 0.1316 0.0134 0.004 0.8 3.8 0.0 0.0 0 0.262 0.1168 0.1306 0.0138 0.005 0.9 3.5 0.5 0.0 0 0.523 0.1160 0.1301 0.0141 0.006 1.0 2.9 0.5 0.0 0 0.785 0.1156 0.1299 0.0143 0.007 1.1 2.9 0.5 0.0 0 1.047 0.1153 0.1298 0.0145 0.007 1.1 2.9 0.5 0.0 0 1.308 0.1152 0.1298 0.0146 0.008 1.1 2.9 0.5 0.0 0 1.570 0.1151 0.1298 0.0147 0.008 1.1 2.9 0.5 0.0 0 1.832 0.1158 0.1300 0.0142 0.006 1.0 2.9 0.5 0.0 0 0.872 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1152 0.1298 0.0146 0.008 1.1 2.9 0.5 0.0 0 1.570 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.52 12.98 1.46 3.779 21.225 51.296 3.612 11.52 12.98 1.46 3.779 21.225 1.539 3.612 11.52 12.98 1.45 3.764 21.225 6.412 3.611 11.56 13.03 1.47 3.715 21.212 25.648 3.606 11.59 13.19 1.61 3.735 21.181 51.296 3.606 11.51 13.16 1.65 3.765 21.173 76.944 3.602 11.47 13.12 1.65 3.779 21.172 102.592 3.597 11.43 13.08 1.65 3.788 21.172 128.240 3.594 11.45 13.15 1.70 3.812 21.153 153.889 3.595 11.42 13.12 1.70 3.822 21.152 179.537 3.594 11.41 13.11 1.70 3.831 21.149 205.185 3.592 11.39 13.08 1.70 3.836 21.151 230.833 3.591 11.39 13.10 1.71 3.847 21.147 256.481 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.539 Accepted refinement result: 11.52 12.98 1.46 3.779 21.225 1.539 3.612 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.18 3.31 227 1746 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.31 N/A 227 219 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.11 115.03 19.39 N/A 0 1746 Chain S: 14.97 60.00 34.92 N/A 227 0 Histogram: Values Number of atoms 9.11 - 19.70 1267 19.70 - 30.29 286 30.29 - 40.88 220 40.88 - 51.47 134 51.47 - 62.07 43 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1298 r_work=0.1152 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1298 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1295 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1148 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.610154 | | target function (ml) not normalized (work): 300660.825719 | | target function (ml) not normalized (free): 15815.517912 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1374 0.1381 5.6789 5.6218| | 2: 3.57 - 2.84 1.00 2888 124 0.1097 0.1435 5.189 5.2564| | 3: 2.83 - 2.48 1.00 2820 163 0.1112 0.1238 4.9664 4.9988| | 4: 2.47 - 2.25 1.00 2825 136 0.0907 0.0939 4.6456 4.669| | 5: 2.25 - 2.09 1.00 2756 127 0.0867 0.0932 4.5922 4.6357| | 6: 2.09 - 1.97 1.00 2846 113 0.0873 0.1018 4.2833 4.3679| | 7: 1.97 - 1.87 1.00 2787 165 0.0901 0.1085 3.9899 4.0894| | 8: 1.87 - 1.79 1.00 2789 144 0.0929 0.1116 3.8969 4.0031| | 9: 1.79 - 1.72 1.00 2745 138 0.0885 0.1168 3.6542 3.8086| | 10: 1.72 - 1.66 1.00 2831 160 0.0924 0.1142 3.5658 3.6953| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1042 3.4979 3.574| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1154 3.3342 3.4697| | 13: 1.56 - 1.52 1.00 2745 130 0.0957 0.1039 3.3118 3.396| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1040 3.2411 3.3155| | 15: 1.48 - 1.45 1.00 2738 128 0.1010 0.1228 3.1559 3.2619| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1241 3.1349 3.2408| | 17: 1.42 - 1.39 1.00 2785 139 0.1148 0.1292 3.1228 3.2292| | 18: 1.39 - 1.36 1.00 2741 179 0.1205 0.1337 3.1076 3.2387| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1563 3.113 3.2634| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1457 3.1138 3.1494| | 21: 1.32 - 1.30 1.00 2785 112 0.1476 0.1501 3.1158 3.1069| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1974 3.1225 3.2972| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1823 3.1328 3.2088| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1826 3.1272 3.2217| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2139 3.1439 3.2574| | 26: 1.22 - 1.21 1.00 2727 135 0.1913 0.1773 3.1485 3.1989| | 27: 1.21 - 1.19 1.00 2814 148 0.2079 0.2150 3.1721 3.1626| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2268 3.1666 3.1657| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2390 3.1479 3.2296| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2445 3.1435 3.1636| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.88 1.00 0.97 6062.19| | 2: 3.57 - 2.84 2888 124 0.92 13.05 1.01 0.97 6062.19| | 3: 2.83 - 2.48 2820 163 0.89 16.98 0.99 0.97 5057.59| | 4: 2.47 - 2.25 2825 136 0.92 13.79 1.00 0.98 2467.07| | 5: 2.25 - 2.09 2756 127 0.90 16.01 1.01 0.98 2467.07| | 6: 2.09 - 1.97 2846 113 0.92 12.53 1.02 0.98 1412.57| | 7: 1.97 - 1.87 2787 165 0.95 9.33 1.02 0.97 513.22| | 8: 1.87 - 1.79 2789 144 0.93 12.61 1.00 0.97 513.22| | 9: 1.79 - 1.72 2745 138 0.94 10.13 0.98 0.97 289.61| | 10: 1.72 - 1.66 2831 160 0.94 11.10 0.98 0.97 244.82| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.97 234.58| | 12: 1.61 - 1.56 2773 144 0.96 8.88 0.99 0.97 137.93| | 13: 1.56 - 1.52 2745 130 0.95 10.43 1.03 0.97 137.93| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.66| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.98 97.51| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.51| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 88.94| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.97| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.98 83.97| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.97 79.95| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.67| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.96 80.08| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.13| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.13| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 83.95| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.93 85.97| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 85.97| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.93 89.40| | 29: 1.18 - 1.16 2800 134 0.88 20.42 0.99 0.93 90.68| | 30: 1.16 - 1.15 2739 148 0.86 21.91 0.98 0.93 90.68| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.67 max = 6062.19 mean = 926.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.51| |phase err.(test): min = 0.00 max = 89.62 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1148 0.1295 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1476 0.1475 0.1521 n_refl.: 87578 remove outliers: r(all,work,free)=0.1476 0.1475 0.1521 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1476 0.1474 0.1521 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1148 0.1298 n_refl.: 87578 remove outliers: r(all,work,free)=0.1154 0.1147 0.1298 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 87.50 79 5 0.3808 288.462 252.045 0.451 0.999 0.302 11.894-9.307 96.08 94 4 0.2545 476.122 454.829 0.837 1.001 0.245 9.237-7.194 97.73 208 7 0.2394 388.033 378.599 0.914 1.002 0.168 7.162-5.571 100.00 427 22 0.2244 296.302 284.331 0.905 1.002 0.137 5.546-4.326 100.00 867 58 0.1140 406.749 401.575 0.963 1.002 0.111 4.315-3.360 100.00 1859 96 0.0945 386.822 384.951 1.004 1.002 0.093 3.356-2.611 100.00 3867 181 0.1137 254.122 252.179 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0916 168.459 167.898 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.267 82.627 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.480 36.093 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.985 21.533 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=-0.0118 ================= 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 : 0.2604 0.1963 0.083 5.315 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1781 0.083 5.315 9.0 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1781 0.083 5.315 9.0 119.5 20.1 258 0.000 1_nqh: 0.1628 0.1788 0.083 5.315 9.0 119.5 20.1 258 0.010 1_weight: 0.1628 0.1788 0.083 5.315 9.0 119.5 20.1 258 0.010 1_xyzrec: 0.1229 0.1469 0.007 0.900 9.0 119.5 20.1 258 0.137 1_adp: 0.1236 0.1465 0.007 0.900 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1238 0.1468 0.007 0.900 9.1 119.4 20.1 258 0.137 1_occ: 0.1232 0.1466 0.007 0.900 9.1 119.4 20.1 258 0.137 2_bss: 0.1229 0.1455 0.007 0.900 9.1 119.5 20.1 258 0.137 2_settarget: 0.1229 0.1455 0.007 0.900 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1229 0.1455 0.007 0.920 9.1 119.5 20.1 258 0.137 2_nqh: 0.1228 0.1454 0.007 0.920 9.1 119.5 20.1 258 0.134 2_sol: 0.1205 0.1412 0.007 0.920 9.1 115.0 22.0 407 n/a 2_weight: 0.1205 0.1412 0.007 0.920 9.1 115.0 22.0 407 n/a 2_xyzrec: 0.1200 0.1421 0.005 0.801 9.1 115.0 22.0 407 n/a 2_adp: 0.1200 0.1421 0.005 0.801 9.1 115.0 22.0 407 n/a 2_regHadp: 0.1200 0.1421 0.005 0.801 9.1 115.0 22.0 407 n/a 2_occ: 0.1197 0.1414 0.005 0.801 9.1 115.0 22.0 407 n/a 3_bss: 0.1192 0.1409 0.005 0.801 9.1 115.0 22.0 407 n/a 3_settarget: 0.1192 0.1409 0.005 0.801 9.1 115.0 22.0 407 n/a 3_updatecdl: 0.1192 0.1409 0.005 0.801 9.1 115.0 22.0 407 n/a 3_nqh: 0.1192 0.1409 0.005 0.801 9.1 115.0 22.0 407 n/a 3_sol: 0.1215 0.1394 0.005 0.801 9.1 115.0 21.1 432 n/a 3_weight: 0.1215 0.1394 0.005 0.801 9.1 115.0 21.1 432 n/a 3_xyzrec: 0.1159 0.1315 0.008 1.092 9.1 115.0 21.1 432 n/a 3_adp: 0.1159 0.1315 0.008 1.092 9.1 115.0 21.1 432 n/a 3_regHadp: 0.1159 0.1315 0.008 1.092 9.1 115.0 21.1 432 n/a 3_occ: 0.1152 0.1310 0.008 1.092 9.1 115.0 21.1 432 n/a 4_bss: 0.1145 0.1307 0.008 1.092 9.1 115.0 21.1 432 n/a 4_settarget: 0.1145 0.1307 0.008 1.092 9.1 115.0 21.1 432 n/a 4_updatecdl: 0.1145 0.1307 0.008 1.093 9.1 115.0 21.1 432 n/a 4_nqh: 0.1145 0.1307 0.008 1.093 9.1 115.0 21.1 432 n/a 4_sol: 0.1156 0.1294 0.008 1.093 9.1 115.0 21.0 425 n/a 4_weight: 0.1156 0.1294 0.008 1.093 9.1 115.0 21.0 425 n/a 4_xyzrec: 0.1150 0.1289 0.009 1.131 9.1 115.0 21.0 425 n/a 4_adp: 0.1150 0.1289 0.009 1.131 9.1 115.0 21.0 425 n/a 4_regHadp: 0.1150 0.1289 0.009 1.131 9.1 115.0 21.0 425 n/a 4_occ: 0.1145 0.1283 0.009 1.131 9.1 115.0 21.0 425 n/a 5_bss: 0.1144 0.1284 0.009 1.131 9.1 115.0 21.0 425 n/a 5_settarget: 0.1144 0.1284 0.009 1.131 9.1 115.0 21.0 425 n/a 5_updatecdl: 0.1144 0.1284 0.009 1.134 9.1 115.0 21.0 425 n/a 5_setrh: 0.1146 0.1284 0.009 1.134 9.1 115.0 21.0 425 n/a 5_nqh: 0.1146 0.1284 0.009 1.134 9.1 115.0 21.0 425 n/a 5_sol: 0.1150 0.1298 0.009 1.134 9.1 115.0 21.2 446 n/a 5_weight: 0.1150 0.1298 0.009 1.134 9.1 115.0 21.2 446 n/a 5_xyzrec: 0.1152 0.1298 0.008 1.131 9.1 115.0 21.2 446 n/a 5_adp: 0.1152 0.1298 0.008 1.131 9.1 115.0 21.2 446 n/a 5_regHadp: 0.1152 0.1298 0.008 1.131 9.1 115.0 21.2 446 n/a 5_occ: 0.1148 0.1295 0.008 1.131 9.1 115.0 21.2 446 n/a end: 0.1147 0.1298 0.008 1.131 9.1 115.0 21.2 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7445011_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7445011_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5500 Refinement macro-cycles (run) : 14025.1800 Write final files (write_after_run_outputs) : 91.8400 Total : 14120.5700 Total CPU time: 3.93 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:15:13 PST -0800 (1735366513.98 s) Start R-work = 0.1625, R-free = 0.1781 Final R-work = 0.1147, R-free = 0.1298 =============================================================================== Job complete usr+sys time: 14283.82 seconds wall clock time: 259 minutes 6.52 seconds (15546.52 seconds total)