Starting phenix.refine on Sat Dec 28 21:06:31 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 } } 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: 2.30, per 1000 atoms: 0.68 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: 0.83 Conformation dependent library (CDL) restraints added in 277.6 milliseconds Time building geometry restraints manager: 0.82 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 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.823 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.826 2.450 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 } 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 } } 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 = 26.637200 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 0.1208 0.1461 0.0253 0.008 1.0 1.0 0.5 0.0 0 13.319 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.61 2.53 3.013 19.054 2006.410 0.017 12.39 15.39 2.99 3.190 19.537 2006.410 0.016 Individual atomic B min max mean iso aniso Overall: 8.43 118.80 21.00 2.87 0 1785 Protein: 8.43 118.80 17.89 2.87 0 1519 Water: 11.09 114.49 39.02 N/A 0 258 Other: 22.49 36.08 28.96 N/A 0 8 Chain A: 8.43 118.80 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.43 - 19.46 1204 19.46 - 30.50 231 30.50 - 41.54 170 41.54 - 52.57 100 52.57 - 63.61 51 63.61 - 74.65 17 74.65 - 85.69 5 85.69 - 96.72 4 96.72 - 107.76 0 107.76 - 118.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1539 r_work=0.1244 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1544 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1244 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015423 | | target function (ls_wunit_k1) not normalized (work): 1284.666994 | | target function (ls_wunit_k1) not normalized (free): 114.284163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1244 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1777 n_refl.: 87593 remove outliers: r(all,work,free)=0.1704 0.1703 0.1777 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1723 0.1722 0.1791 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1242 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1241 0.1539 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3584 298.827 277.876 0.640 1.002 0.380 11.894-9.307 99.02 97 4 0.1634 478.704 467.009 0.910 1.002 0.380 9.237-7.194 100.00 213 7 0.1839 391.521 387.121 0.949 1.003 0.314 7.162-5.571 100.00 427 22 0.1717 293.815 288.532 0.924 1.003 0.258 5.546-4.326 100.00 867 58 0.0913 403.335 400.666 0.951 1.003 0.214 4.315-3.360 100.00 1859 96 0.0778 383.575 382.594 0.996 1.002 0.200 3.356-2.611 100.00 3867 181 0.1022 251.989 251.245 0.997 1.002 0.120 2.608-2.026 99.99 8198 413 0.0976 167.045 166.460 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1205 81.576 81.768 1.018 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1646 36.174 35.628 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2358 22.792 21.308 0.971 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0447 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1539 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=0.1242 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1540 | n_water=258 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1251 r_free=0.1537 | n_water=252 | time (s): 27.930 (total time: 30.400) Filter (q & B) r_work=0.1254 r_free=0.1537 | n_water=249 | time (s): 3.840 (total time: 34.240) Compute maps r_work=0.1254 r_free=0.1537 | n_water=249 | time (s): 1.960 (total time: 36.200) Filter (map) r_work=0.1279 r_free=0.1549 | n_water=233 | time (s): 3.920 (total time: 40.120) Find peaks r_work=0.1279 r_free=0.1549 | n_water=233 | time (s): 0.730 (total time: 40.850) Add new water r_work=0.1433 r_free=0.1705 | n_water=450 | time (s): 3.870 (total time: 44.720) Refine new water occ: r_work=0.1329 r_free=0.1559 adp: r_work=0.1250 r_free=0.1512 occ: r_work=0.1263 r_free=0.1505 adp: r_work=0.1228 r_free=0.1493 occ: r_work=0.1232 r_free=0.1484 adp: r_work=0.1221 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1482 r_work=0.1221 r_free=0.1482 | n_water=450 | time (s): 118.380 (total time: 163.100) Filter (q & B) r_work=0.1227 r_free=0.1485 | n_water=429 | time (s): 4.020 (total time: 167.120) Filter (dist only) r_work=0.1227 r_free=0.1485 | n_water=429 | time (s): 40.550 (total time: 207.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.920313 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1548.931149 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 0.1228 0.1519 0.0291 0.007 0.9 2.2 0.5 0.0 0 12.460 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.19 2.91 3.788 23.109 1548.931 0.015 11.97 14.92 2.94 4.181 22.920 1548.931 0.015 Individual atomic B min max mean iso aniso Overall: 8.74 114.88 23.04 2.61 196 1760 Protein: 8.74 114.88 17.66 2.62 0 1519 Water: 10.89 72.60 41.92 N/A 196 233 Other: 26.59 39.11 31.89 N/A 0 8 Chain A: 8.74 114.88 20.35 N/A 0 1760 Chain S: 15.10 71.93 47.19 N/A 196 0 Histogram: Values Number of atoms 8.74 - 19.36 1209 19.36 - 29.97 246 29.97 - 40.59 197 40.59 - 51.20 148 51.20 - 61.81 105 61.81 - 72.43 40 72.43 - 83.04 5 83.04 - 93.66 3 93.66 - 104.27 1 104.27 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1492 r_work=0.1197 r_free=0.1491 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1491 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013966 | | target function (ls_wunit_k1) not normalized (work): 1163.297671 | | target function (ls_wunit_k1) not normalized (free): 106.533016 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1609 0.1733 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1609 0.1733 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1621 0.1617 0.1738 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1199 0.1482 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1197 0.1482 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3444 294.766 270.991 0.593 1.001 0.364 11.894-9.307 99.02 97 4 0.1500 478.704 477.141 0.917 1.001 0.360 9.237-7.194 100.00 213 7 0.1690 391.521 393.247 0.976 1.001 0.270 7.162-5.571 100.00 427 22 0.1514 293.815 290.205 0.943 1.001 0.239 5.546-4.326 100.00 867 58 0.0830 403.335 400.820 0.958 1.002 0.225 4.315-3.360 100.00 1859 96 0.0726 383.575 382.542 1.001 1.002 0.220 3.356-2.611 100.00 3867 181 0.0952 251.989 251.485 1.007 1.002 0.160 2.608-2.026 99.99 8198 413 0.0964 167.045 166.646 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1176 81.576 81.809 1.025 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.174 35.656 1.012 1.002 0.000 1.221-1.150 99.97 13689 708 0.2338 22.792 21.210 0.966 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0722 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1482 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1482 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1482 | n_water=429 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1199 r_free=0.1481 | n_water=427 | time (s): 38.390 (total time: 40.710) Filter (q & B) r_work=0.1201 r_free=0.1483 | n_water=424 | time (s): 2.730 (total time: 43.440) Compute maps r_work=0.1201 r_free=0.1483 | n_water=424 | time (s): 1.620 (total time: 45.060) Filter (map) r_work=0.1244 r_free=0.1489 | n_water=289 | time (s): 3.480 (total time: 48.540) Find peaks r_work=0.1244 r_free=0.1489 | n_water=289 | time (s): 0.670 (total time: 49.210) Add new water r_work=0.1371 r_free=0.1624 | n_water=477 | time (s): 3.350 (total time: 52.560) Refine new water occ: r_work=0.1269 r_free=0.1536 adp: r_work=0.1271 r_free=0.1536 occ: r_work=0.1247 r_free=0.1512 adp: r_work=0.1246 r_free=0.1513 occ: r_work=0.1232 r_free=0.1495 adp: r_work=0.1226 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1494 r_work=0.1226 r_free=0.1494 | n_water=477 | time (s): 199.700 (total time: 252.260) Filter (q & B) r_work=0.1228 r_free=0.1497 | n_water=442 | time (s): 2.950 (total time: 255.210) Filter (dist only) r_work=0.1228 r_free=0.1497 | n_water=442 | time (s): 35.930 (total time: 291.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.100061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.312046 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1451 0.0215 0.006 0.9 3.5 0.5 0.0 0 1.050 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.51 2.15 3.626 22.089 42.312 3.724 12.28 14.18 1.90 4.158 21.889 42.312 3.659 Individual atomic B min max mean iso aniso Overall: 9.21 109.93 21.59 2.30 212 1757 Protein: 9.21 109.93 17.20 2.30 0 1519 Water: 11.49 71.43 36.55 N/A 212 230 Other: 22.62 35.15 29.01 N/A 0 8 Chain A: 9.21 109.93 19.84 N/A 0 1757 Chain S: 16.36 61.04 36.13 N/A 212 0 Histogram: Values Number of atoms 9.21 - 19.29 1235 19.29 - 29.36 272 29.36 - 39.43 220 39.43 - 49.50 140 49.50 - 59.57 69 59.57 - 69.64 20 69.64 - 79.72 7 79.72 - 89.79 3 89.79 - 99.86 1 99.86 - 109.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1418 r_work=0.1229 r_free=0.1418 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1418 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1416 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1224 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.657718 | | target function (ml) not normalized (work): 304662.271277 | | target function (ml) not normalized (free): 16074.470764 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1224 0.1416 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1553 0.1552 0.1596 n_refl.: 87589 remove outliers: r(all,work,free)=0.1553 0.1552 0.1596 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1550 0.1550 0.1595 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1212 0.1380 n_refl.: 87589 remove outliers: r(all,work,free)=0.1216 0.1208 0.1380 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 90.62 82 5 0.4043 291.518 256.483 0.465 1.000 0.295 11.894-9.307 94.12 92 4 0.2470 472.285 457.564 0.845 1.001 0.277 9.237-7.194 98.18 209 7 0.2408 383.068 383.608 0.939 1.002 0.198 7.162-5.571 100.00 427 22 0.2081 293.815 282.927 0.910 1.002 0.167 5.546-4.326 100.00 867 58 0.1133 403.335 398.965 0.951 1.002 0.158 4.315-3.360 100.00 1859 96 0.0944 383.575 380.602 0.993 1.002 0.150 3.356-2.611 100.00 3867 181 0.1157 251.989 250.017 1.000 1.002 0.067 2.608-2.026 99.99 8198 413 0.1055 167.045 165.990 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1019 81.576 81.717 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1298 36.174 35.752 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2140 22.792 21.405 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0397 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1208 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1208 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1208 r_free=0.1380 | n_water=442 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1208 r_free=0.1377 | n_water=441 | time (s): 37.270 (total time: 39.470) Filter (q & B) r_work=0.1208 r_free=0.1377 | n_water=440 | time (s): 2.610 (total time: 42.080) Compute maps r_work=0.1208 r_free=0.1377 | n_water=440 | time (s): 1.580 (total time: 43.660) Filter (map) r_work=0.1232 r_free=0.1384 | n_water=307 | time (s): 2.610 (total time: 46.270) Find peaks r_work=0.1232 r_free=0.1384 | n_water=307 | time (s): 0.610 (total time: 46.880) Add new water r_work=0.1296 r_free=0.1450 | n_water=473 | time (s): 2.680 (total time: 49.560) Refine new water occ: r_work=0.1223 r_free=0.1387 adp: r_work=0.1224 r_free=0.1387 occ: r_work=0.1208 r_free=0.1379 adp: r_work=0.1206 r_free=0.1378 occ: r_work=0.1197 r_free=0.1377 adp: r_work=0.1193 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1372 r_work=0.1193 r_free=0.1372 | n_water=473 | time (s): 259.850 (total time: 309.410) Filter (q & B) r_work=0.1198 r_free=0.1375 | n_water=441 | time (s): 3.010 (total time: 312.420) Filter (dist only) r_work=0.1198 r_free=0.1374 | n_water=439 | time (s): 37.430 (total time: 349.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.353655 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.489818 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 0.1198 0.1382 0.0184 0.007 1.0 6.4 0.5 0.0 0 1.177 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.82 1.84 3.417 21.439 48.490 3.640 11.80 13.74 1.94 3.838 21.310 48.490 3.622 Individual atomic B min max mean iso aniso Overall: 9.23 105.40 21.13 2.17 210 1756 Protein: 9.23 105.40 16.90 2.17 0 1519 Water: 11.45 69.96 35.65 N/A 210 229 Other: 22.50 32.47 27.42 N/A 0 8 Chain A: 9.23 105.40 19.48 N/A 0 1756 Chain S: 15.23 61.43 34.89 N/A 210 0 Histogram: Values Number of atoms 9.23 - 18.85 1230 18.85 - 28.46 284 28.46 - 38.08 218 38.08 - 47.70 121 47.70 - 57.31 73 57.31 - 66.93 26 66.93 - 76.55 9 76.55 - 86.16 2 86.16 - 95.78 1 95.78 - 105.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1374 r_work=0.1180 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1374 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1176 r_free = 0.1370 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1176 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620543 | | target function (ml) not normalized (work): 301526.045903 | | target function (ml) not normalized (free): 15933.950699 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1176 0.1370 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1507 0.1505 0.1568 n_refl.: 87578 remove outliers: r(all,work,free)=0.1507 0.1505 0.1568 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1504 0.1502 0.1566 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1175 0.1370 n_refl.: 87578 remove outliers: r(all,work,free)=0.1185 0.1175 0.1370 n_refl.: 87577 ======================== 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 90.62 82 5 0.4265 291.518 253.115 0.450 1.000 0.304 11.894-9.307 93.14 91 4 0.2433 465.986 452.403 0.839 1.002 0.222 9.237-7.194 98.18 209 7 0.2482 383.068 377.144 0.911 1.002 0.150 7.162-5.571 100.00 427 22 0.2207 293.815 282.383 0.903 1.002 0.138 5.546-4.326 100.00 867 58 0.1151 403.335 398.673 0.951 1.002 0.128 4.315-3.360 100.00 1859 96 0.0948 383.575 381.094 0.994 1.002 0.127 3.356-2.611 100.00 3867 181 0.1141 251.989 250.114 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1010 167.045 166.145 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0955 81.576 81.842 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.174 35.814 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2126 22.792 21.435 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0461 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1175 r_free=0.1370 After: r_work=0.1176 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1176 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1370 | n_water=439 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1176 r_free=0.1370 | n_water=439 | time (s): 39.410 (total time: 41.870) Filter (q & B) r_work=0.1176 r_free=0.1370 | n_water=436 | time (s): 3.240 (total time: 45.110) Compute maps r_work=0.1176 r_free=0.1370 | n_water=436 | time (s): 1.820 (total time: 46.930) Filter (map) r_work=0.1205 r_free=0.1378 | n_water=327 | time (s): 2.890 (total time: 49.820) Find peaks r_work=0.1205 r_free=0.1378 | n_water=327 | time (s): 0.490 (total time: 50.310) Add new water r_work=0.1256 r_free=0.1420 | n_water=489 | time (s): 2.550 (total time: 52.860) Refine new water occ: r_work=0.1189 r_free=0.1365 adp: r_work=0.1189 r_free=0.1367 occ: r_work=0.1176 r_free=0.1355 adp: r_work=0.1175 r_free=0.1356 occ: r_work=0.1167 r_free=0.1348 adp: r_work=0.1165 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1348 r_work=0.1165 r_free=0.1348 | n_water=489 | time (s): 205.210 (total time: 258.070) Filter (q & B) r_work=0.1171 r_free=0.1353 | n_water=452 | time (s): 3.070 (total time: 261.140) Filter (dist only) r_work=0.1171 r_free=0.1351 | n_water=451 | time (s): 39.380 (total time: 300.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.016613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.306390 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 0.1201 0.1383 0.0182 0.007 1.0 5.4 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.83 1.82 3.289 21.069 42.306 3.632 12.05 13.90 1.84 3.396 21.029 42.306 3.628 Individual atomic B min max mean iso aniso Overall: 9.24 102.32 20.98 2.05 223 1755 Protein: 9.24 102.32 16.78 2.05 0 1519 Water: 11.48 69.56 35.02 N/A 223 228 Other: 22.07 31.33 26.98 N/A 0 8 Chain A: 9.24 102.32 19.34 N/A 0 1755 Chain S: 14.65 61.47 33.89 N/A 223 0 Histogram: Values Number of atoms 9.24 - 18.55 1224 18.55 - 27.86 292 27.86 - 37.16 206 37.16 - 46.47 148 46.47 - 55.78 66 55.78 - 65.09 25 65.09 - 74.40 12 74.40 - 83.70 2 83.70 - 93.01 1 93.01 - 102.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1390 r_work=0.1206 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1390 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1387 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1202 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626772 | | target function (ml) not normalized (work): 302041.211966 | | target function (ml) not normalized (free): 15965.826577 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1451 0.1442 5.7144 5.6648| | 2: 3.57 - 2.84 1.00 2888 124 0.1117 0.1488 5.2093 5.2837| | 3: 2.83 - 2.48 1.00 2820 163 0.1210 0.1327 5.0166 5.0427| | 4: 2.47 - 2.25 1.00 2825 136 0.1022 0.1179 4.7188 4.7704| | 5: 2.25 - 2.09 1.00 2756 127 0.0990 0.1059 4.6595 4.7173| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1207 4.3627 4.4784| | 7: 1.97 - 1.87 1.00 2787 165 0.1000 0.1235 4.0829 4.1811| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1279 3.9975 4.0922| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1346 3.7248 3.9199| | 10: 1.72 - 1.66 1.00 2831 160 0.1011 0.1295 3.643 3.7732| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1081 3.5755 3.6164| | 12: 1.61 - 1.56 1.00 2773 144 0.0920 0.1132 3.3486 3.4592| | 13: 1.56 - 1.52 1.00 2745 130 0.0975 0.1045 3.3334 3.4103| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1120 3.262 3.3499| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1349 3.1699 3.3133| | 16: 1.45 - 1.42 1.00 2756 161 0.1067 0.1272 3.1499 3.2546| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1302 3.1157 3.2553| | 18: 1.39 - 1.36 1.00 2741 179 0.1160 0.1374 3.0905 3.2768| | 19: 1.36 - 1.34 1.00 2807 134 0.1211 0.1649 3.0944 3.3012| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1497 3.0912 3.1495| | 21: 1.32 - 1.30 1.00 2785 112 0.1417 0.1641 3.0904 3.1726| | 22: 1.29 - 1.27 1.00 2704 152 0.1471 0.1944 3.0869 3.2855| | 23: 1.27 - 1.26 1.00 2802 156 0.1578 0.1851 3.1058 3.2066| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1781 3.0957 3.2004| | 25: 1.24 - 1.22 1.00 2733 148 0.1802 0.2320 3.1119 3.2909| | 26: 1.22 - 1.21 1.00 2727 135 0.1863 0.1742 3.1255 3.1887| | 27: 1.21 - 1.19 1.00 2814 148 0.2013 0.2121 3.1413 3.1582| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2318 3.1412 3.1639| | 29: 1.18 - 1.16 1.00 2800 134 0.2227 0.2356 3.1295 3.2189| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2503 3.1178 3.1691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.94 9.28 1.00 0.97 6531.41| | 2: 3.57 - 2.84 2888 124 0.92 13.69 1.01 0.97 6531.41| | 3: 2.83 - 2.48 2820 163 0.88 17.87 0.99 0.97 5472.73| | 4: 2.47 - 2.25 2825 136 0.91 14.94 1.00 0.98 2742.72| | 5: 2.25 - 2.09 2756 127 0.89 17.20 1.01 0.98 2742.72| | 6: 2.09 - 1.97 2846 113 0.91 13.88 1.02 0.97 1606.88| | 7: 1.97 - 1.87 2787 165 0.94 10.91 1.02 0.97 638.17| | 8: 1.87 - 1.79 2789 144 0.91 14.55 1.00 0.97 638.17| | 9: 1.79 - 1.72 2745 138 0.93 11.56 0.98 0.97 345.43| | 10: 1.72 - 1.66 2831 160 0.93 12.34 0.98 0.97 286.80| | 11: 1.66 - 1.61 2712 147 0.93 13.01 0.98 0.97 273.45| | 12: 1.61 - 1.56 2773 144 0.95 9.51 0.99 0.97 147.55| | 13: 1.56 - 1.52 2745 130 0.94 11.14 1.02 0.97 147.55| | 14: 1.52 - 1.48 2803 134 0.94 11.23 1.02 0.97 131.98| | 15: 1.48 - 1.45 2738 128 0.95 10.43 1.01 0.98 103.47| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.02 0.98 103.47| | 17: 1.42 - 1.39 2785 139 0.94 11.48 1.01 0.98 94.13| | 18: 1.39 - 1.36 2741 179 0.94 11.89 1.01 0.98 88.73| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.98 88.73| | 20: 1.34 - 1.32 2696 147 0.94 12.60 0.99 0.96 84.06| | 21: 1.32 - 1.30 2785 112 0.93 13.55 0.98 0.96 83.73| | 22: 1.29 - 1.27 2704 152 0.93 14.01 0.98 0.96 83.79| | 23: 1.27 - 1.26 2802 156 0.92 14.96 0.98 0.95 84.10| | 24: 1.26 - 1.24 2744 132 0.92 15.09 0.97 0.95 84.10| | 25: 1.24 - 1.22 2733 148 0.91 16.50 0.96 0.94 85.39| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.02 0.93 86.81| | 27: 1.21 - 1.19 2814 148 0.89 18.86 1.02 0.93 86.81| | 28: 1.19 - 1.18 2671 147 0.88 20.30 1.01 0.92 89.91| | 29: 1.18 - 1.16 2800 134 0.88 20.61 0.99 0.92 91.08| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.92 91.08| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 83.73 max = 6531.41 mean = 1013.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 14.17| |phase err.(test): min = 0.00 max = 87.82 mean = 14.26| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1202 0.1387 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1519 0.1518 0.1567 n_refl.: 87577 remove outliers: r(all,work,free)=0.1519 0.1518 0.1567 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1516 0.1516 0.1565 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1202 0.1387 n_refl.: 87577 remove outliers: r(all,work,free)=0.1210 0.1201 0.1387 n_refl.: 87574 ======================== 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 0.4298 286.906 252.649 0.434 1.000 0.297 11.894-9.307 92.16 90 4 0.2472 467.917 441.561 0.819 1.001 0.202 9.237-7.194 97.73 208 7 0.2628 382.592 376.020 0.899 1.002 0.125 7.162-5.571 100.00 427 22 0.2334 293.815 281.834 0.894 1.002 0.120 5.546-4.326 100.00 867 58 0.1215 403.335 398.795 0.952 1.002 0.115 4.315-3.360 100.00 1859 96 0.0989 383.575 380.985 0.995 1.002 0.110 3.356-2.611 100.00 3867 181 0.1176 251.989 250.037 1.002 1.002 0.080 2.608-2.026 99.99 8198 413 0.1037 167.045 166.106 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0984 81.576 81.835 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1227 36.174 35.819 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2121 22.792 21.424 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0384 ================= 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: 0.1208 0.1461 0.008 0.963 9.0 119.5 20.1 258 0.127 1_adp: 0.1240 0.1539 0.008 0.963 8.4 118.8 21.0 258 0.127 1_regHadp: 0.1244 0.1544 0.008 0.963 8.4 118.8 21.0 258 0.127 1_occ: 0.1244 0.1547 0.008 0.963 8.4 118.8 21.0 258 0.127 2_bss: 0.1241 0.1539 0.008 0.963 8.5 118.9 21.1 258 0.127 2_settarget: 0.1241 0.1539 0.008 0.963 8.5 118.9 21.1 258 0.127 2_updatecdl: 0.1241 0.1539 0.008 0.978 8.5 118.9 21.1 258 0.127 2_nqh: 0.1242 0.1540 0.008 0.978 8.5 118.9 21.1 258 0.124 2_sol: 0.1227 0.1485 0.008 0.978 8.5 118.9 23.4 429 n/a 2_weight: 0.1227 0.1485 0.008 0.978 8.5 118.9 23.4 429 n/a 2_xyzrec: 0.1228 0.1519 0.007 0.883 8.5 118.9 23.4 429 n/a 2_adp: 0.1197 0.1492 0.007 0.883 8.7 114.9 23.0 429 n/a 2_regHadp: 0.1197 0.1491 0.007 0.883 8.7 114.9 23.0 429 n/a 2_occ: 0.1201 0.1483 0.007 0.883 8.7 114.9 23.0 429 n/a 3_bss: 0.1197 0.1482 0.007 0.883 8.8 114.9 23.1 429 n/a 3_settarget: 0.1197 0.1482 0.007 0.883 8.8 114.9 23.1 429 n/a 3_updatecdl: 0.1197 0.1482 0.007 0.883 8.8 114.9 23.1 429 n/a 3_nqh: 0.1197 0.1482 0.007 0.883 8.8 114.9 23.1 429 n/a 3_sol: 0.1228 0.1497 0.007 0.883 8.8 114.9 22.0 442 n/a 3_weight: 0.1228 0.1497 0.007 0.883 8.8 114.9 22.0 442 n/a 3_xyzrec: 0.1235 0.1451 0.006 0.924 8.8 114.9 22.0 442 n/a 3_adp: 0.1228 0.1418 0.006 0.924 9.2 109.9 21.6 442 n/a 3_regHadp: 0.1229 0.1418 0.006 0.924 9.2 109.9 21.6 442 n/a 3_occ: 0.1224 0.1416 0.006 0.924 9.2 109.9 21.6 442 n/a 4_bss: 0.1208 0.1380 0.006 0.924 9.2 109.9 21.6 442 n/a 4_settarget: 0.1208 0.1380 0.006 0.924 9.2 109.9 21.6 442 n/a 4_updatecdl: 0.1208 0.1380 0.006 0.923 9.2 109.9 21.6 442 n/a 4_nqh: 0.1208 0.1380 0.006 0.923 9.2 109.9 21.6 442 n/a 4_sol: 0.1198 0.1374 0.006 0.923 9.2 109.9 21.4 439 n/a 4_weight: 0.1198 0.1374 0.006 0.923 9.2 109.9 21.4 439 n/a 4_xyzrec: 0.1198 0.1382 0.007 0.984 9.2 109.9 21.4 439 n/a 4_adp: 0.1180 0.1374 0.007 0.984 9.2 105.4 21.1 439 n/a 4_regHadp: 0.1180 0.1374 0.007 0.984 9.2 105.4 21.1 439 n/a 4_occ: 0.1176 0.1370 0.007 0.984 9.2 105.4 21.1 439 n/a 5_bss: 0.1175 0.1370 0.007 0.984 9.2 105.4 21.1 439 n/a 5_settarget: 0.1175 0.1370 0.007 0.984 9.2 105.4 21.1 439 n/a 5_updatecdl: 0.1175 0.1370 0.007 0.985 9.2 105.4 21.1 439 n/a 5_setrh: 0.1176 0.1370 0.007 0.985 9.2 105.4 21.1 439 n/a 5_nqh: 0.1176 0.1370 0.007 0.985 9.2 105.4 21.1 439 n/a 5_sol: 0.1171 0.1351 0.007 0.985 9.2 105.4 21.1 451 n/a 5_weight: 0.1171 0.1351 0.007 0.985 9.2 105.4 21.1 451 n/a 5_xyzrec: 0.1201 0.1383 0.007 1.048 9.2 105.4 21.1 451 n/a 5_adp: 0.1205 0.1390 0.007 1.048 9.2 102.3 21.0 451 n/a 5_regHadp: 0.1206 0.1390 0.007 1.048 9.2 102.3 21.0 451 n/a 5_occ: 0.1202 0.1387 0.007 1.048 9.2 102.3 21.0 451 n/a end: 0.1201 0.1387 0.007 1.048 9.2 102.3 21.0 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7445011_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7445011_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8100 Refinement macro-cycles (run) : 3680.8400 Write final files (write_after_run_outputs) : 59.1000 Total : 3744.7500 Total CPU time: 63.03 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:14:08 PST -0800 (1735452848.82 s) Start R-work = 0.1625, R-free = 0.1781 Final R-work = 0.1201, R-free = 0.1387 =============================================================================== Job complete usr+sys time: 3880.03 seconds wall clock time: 69 minutes 20.65 seconds (4160.65 seconds total)