Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.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_8230669.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.pdb" 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" 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 } 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 =============================================================================== 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: 2.06, per 1000 atoms: 0.61 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: 0.72 Conformation dependent library (CDL) restraints added in 205.2 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 537 0.91 - 1.17: 1108 1.17 - 1.43: 657 1.43 - 1.68: 821 1.68 - 1.94: 30 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.763 -0.237 1.14e-02 7.69e+03 4.32e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.236 1.494 -0.258 1.26e-02 6.30e+03 4.19e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.231 0.230 1.19e-02 7.06e+03 3.73e+02 bond pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.374 1.162 0.212 1.10e-02 8.26e+03 3.73e+02 bond pdb=" CA GLU A 116 " pdb=" C GLU A 116 " ideal model delta sigma weight residual 1.528 1.738 -0.210 1.25e-02 6.40e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.10: 2787 4.10 - 8.19: 1926 8.19 - 12.29: 811 12.29 - 16.38: 221 16.38 - 20.47: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 134.46 -12.96 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.36 108.72 10.64 8.40e-01 1.42e+00 1.60e+02 angle pdb=" CA SER A 161 " pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 117.07 131.07 -14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.83 108.26 12.57 1.07e+00 8.73e-01 1.38e+02 angle pdb=" O VAL A 186 " pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 122.57 107.93 14.64 1.25e+00 6.40e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 903 15.63 - 31.26: 141 31.26 - 46.88: 46 46.88 - 62.51: 18 62.51 - 78.14: 3 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 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CD1 PHE A 119 " pdb=" CE1 PHE A 119 " pdb=" CZ PHE A 119 " pdb=" HZ PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.243: 116 0.243 - 0.486: 76 0.486 - 0.728: 34 0.728 - 0.970: 16 0.970 - 1.212: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 29 " pdb=" N ALA A 29 " pdb=" C ALA A 29 " pdb=" CB ALA A 29 " both_signs ideal model delta sigma weight residual False 2.48 1.27 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.004 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.039 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG TYR A 141 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.087 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.074 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 791 2.28 - 2.86: 7857 2.86 - 3.44: 10640 3.44 - 4.02: 15198 4.02 - 4.60: 22153 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.799 1.816 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.831 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.836 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.877 2.450 ... (remaining 56634 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_8230669_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= 0.2606 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788006 | | target function (ml) not normalized (work): 232257.622457 | | target function (ml) not normalized (free): 11788.552248 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2150 7.0006 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2425 0.1903 4.3568 4.368| | 3: 2.84 - 2.48 1.00 2833 165 0.2338 0.1705 4.1339 4.1704| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1475 3.8353 3.8318| | 5: 2.25 - 2.09 1.00 2756 127 0.2460 0.1683 3.801 3.831| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1678 3.4776 3.55| | 7: 1.97 - 1.87 1.00 2787 165 0.2576 0.1769 3.1307 3.1563| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1958 3.0551 3.1355| | 9: 1.79 - 1.72 1.00 2745 138 0.2456 0.1629 2.8959 2.8717| | 10: 1.72 - 1.66 1.00 2789 158 0.2382 0.2065 2.7952 2.8719| | 11: 1.66 - 1.61 1.00 2740 147 0.2541 0.1807 2.7606 2.7619| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.1885 2.6221 2.6638| | 13: 1.56 - 1.52 1.00 2745 130 0.2554 0.1746 2.5682 2.5737| | 14: 1.52 - 1.48 1.00 2803 134 0.2559 0.2036 2.5137 2.5721| | 15: 1.48 - 1.45 1.00 2738 128 0.2617 0.2048 2.4273 2.4557| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2165 2.3822 2.4394| | 17: 1.42 - 1.39 1.00 2785 139 0.2634 0.2114 2.3073 2.3301| | 18: 1.39 - 1.36 1.00 2741 179 0.2646 0.2170 2.2652 2.2956| | 19: 1.36 - 1.34 1.00 2807 134 0.2657 0.2483 2.2404 2.3304| | 20: 1.34 - 1.32 1.00 2696 147 0.2651 0.2191 2.1983 2.1779| | 21: 1.32 - 1.30 1.00 2785 112 0.2694 0.2281 2.1841 2.1939| | 22: 1.29 - 1.27 1.00 2704 152 0.2767 0.2435 2.1486 2.1602| | 23: 1.27 - 1.26 1.00 2802 156 0.2734 0.2456 2.0895 2.1965| | 24: 1.26 - 1.24 1.00 2744 132 0.2785 0.2620 2.0757 2.1977| | 25: 1.24 - 1.22 1.00 2734 148 0.2795 0.2680 2.0374 2.1094| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2132 2.0123 2.047| | 27: 1.21 - 1.19 1.00 2814 148 0.2934 0.2763 1.9936 2.037| | 28: 1.19 - 1.18 1.00 2671 147 0.3006 0.2563 1.9866 1.9643| | 29: 1.18 - 1.16 1.00 2800 134 0.2990 0.2564 1.9635 1.992| | 30: 1.16 - 1.15 1.00 2740 148 0.3065 0.2901 1.9286 1.9653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.06 0.76 0.23 1515.10| | 2: 3.57 - 2.84 2876 122 0.80 26.30 1.27 0.23 1515.10| | 3: 2.84 - 2.48 2833 165 0.74 32.21 1.24 0.23 1255.45| | 4: 2.47 - 2.25 2825 136 0.81 25.78 1.26 0.25 581.60| | 5: 2.25 - 2.09 2756 127 0.77 29.61 1.28 0.25 581.60| | 6: 2.09 - 1.97 2846 113 0.83 22.74 1.29 0.25 316.50| | 7: 1.97 - 1.87 2787 165 0.90 16.53 1.29 0.26 90.40| | 8: 1.87 - 1.79 2789 144 0.86 20.86 1.25 0.26 90.40| | 9: 1.79 - 1.72 2745 138 0.88 18.70 1.24 0.25 54.53| | 10: 1.72 - 1.66 2789 158 0.87 19.79 1.22 0.25 47.34| | 11: 1.66 - 1.61 2740 147 0.86 20.99 1.24 0.25 45.70| | 12: 1.61 - 1.56 2787 146 0.88 18.47 1.23 0.25 29.08| | 13: 1.56 - 1.52 2745 130 0.86 20.51 1.24 0.25 29.08| | 14: 1.52 - 1.48 2803 134 0.87 20.61 1.23 0.25 25.93| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.24 0.25 20.16| | 16: 1.45 - 1.42 2756 161 0.86 21.23 1.23 0.25 20.16| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.23 0.25 17.14| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.22 0.25 15.40| | 19: 1.36 - 1.34 2807 134 0.86 21.88 1.21 0.25 15.40| | 20: 1.34 - 1.32 2696 147 0.87 20.67 1.21 0.25 12.98| | 21: 1.32 - 1.30 2785 112 0.86 21.60 1.19 0.25 12.80| | 22: 1.29 - 1.27 2704 152 0.86 22.21 1.21 0.25 12.53| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.20 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 22.97 1.21 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.52 1.20 0.24 10.55| | 26: 1.22 - 1.21 2727 135 0.84 23.94 1.20 0.23 9.87| | 27: 1.21 - 1.19 2814 148 0.83 24.60 1.21 0.23 9.87| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.18 0.23 8.95| | 29: 1.18 - 1.16 2800 134 0.83 24.89 1.16 0.23 8.61| | 30: 1.16 - 1.15 2740 148 0.81 26.65 1.15 0.23 8.61| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.61 max = 1515.10 mean = 218.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.50| |phase err.(test): min = 0.00 max = 89.87 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 : 0.082 0.259 1557 Z= 5.417 Angle : 5.274 17.862 2118 Z= 3.651 Chirality : 0.388 1.212 243 Planarity : 0.030 0.083 284 Dihedral : 13.735 78.136 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.45), residues: 224 helix: -2.67 (0.35), residues: 108 sheet: -1.30 (0.77), residues: 40 loop : -1.07 (0.57), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 28 TYR 0.072 0.025 TYR A 139 PHE 0.097 0.036 PHE A 119 HIS 0.079 0.024 HIS A 115 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= 0.2606 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788006 | | target function (ml) not normalized (work): 232257.622457 | | target function (ml) not normalized (free): 11788.552248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2606 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2606 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1961 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2005 0.2008 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1772 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 0.3811 386.357 358.327 0.728 0.916 0.401 11.894-9.307 99.02 97 4 0.1812 613.709 593.358 1.010 0.917 0.380 9.237-7.194 100.00 213 7 0.2134 501.938 492.414 1.049 0.918 0.370 7.162-5.571 100.00 427 22 0.2267 376.677 363.512 1.018 0.918 0.282 5.546-4.326 100.00 867 58 0.1310 517.084 511.193 1.051 0.919 0.239 4.315-3.360 100.00 1859 96 0.1145 491.751 487.787 1.093 0.920 0.189 3.356-2.611 100.00 3867 181 0.1430 323.055 319.897 1.084 0.921 0.048 2.608-2.026 99.99 8198 413 0.1341 214.156 211.994 1.090 0.923 0.000 2.025-1.573 100.00 17313 902 0.1657 104.583 103.971 1.093 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.376 45.037 1.070 0.933 0.000 1.221-1.150 99.97 13689 708 0.2589 29.220 26.922 1.035 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0505 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1636 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.351289 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2050.256697 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 0.1212 0.1464 0.0252 0.007 0.9 0.6 0.5 0.0 0 12.176 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.64 2.52 3.013 19.079 2050.257 0.017 12.43 15.42 2.99 3.244 19.587 2050.257 0.016 Individual atomic B min max mean iso aniso Overall: 8.55 118.91 21.07 2.88 0 1785 Protein: 8.55 118.91 17.94 2.88 0 1519 Water: 11.10 114.95 39.23 N/A 0 258 Other: 22.80 36.60 29.42 N/A 0 8 Chain A: 8.55 118.91 21.07 N/A 0 1785 Histogram: Values Number of atoms 8.55 - 19.59 1209 19.59 - 30.63 230 30.63 - 41.66 165 41.66 - 52.70 99 52.70 - 63.73 52 63.73 - 74.77 17 74.77 - 85.80 6 85.80 - 96.84 4 96.84 - 107.88 0 107.88 - 118.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1542 r_work=0.1247 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1547 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 = 0.1247 r_free = 0.1551 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= 0.1247 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015378 | | target function (ls_wunit_k1) not normalized (work): 1280.946233 | | target function (ls_wunit_k1) not normalized (free): 113.624146 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1551 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1706 0.1705 0.1776 n_refl.: 87593 remove outliers: r(all,work,free)=0.1706 0.1705 0.1776 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1726 0.1725 0.1790 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1246 0.1545 n_refl.: 87593 remove outliers: r(all,work,free)=0.1260 0.1246 0.1545 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 0.3547 298.169 278.731 0.630 1.002 0.373 11.894-9.307 99.02 97 4 0.1619 477.651 466.590 0.905 1.003 0.369 9.237-7.194 100.00 213 7 0.1830 390.660 385.136 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1709 293.168 288.136 0.927 1.003 0.280 5.546-4.326 100.00 867 58 0.0910 402.448 399.987 0.949 1.003 0.204 4.315-3.360 100.00 1859 96 0.0774 382.731 381.652 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1019 251.434 250.721 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0980 166.678 166.121 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1217 81.397 81.568 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.095 35.551 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2366 22.742 21.246 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=0.0462 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1247 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1546 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1258 r_free=0.1544 | n_water=251 | time (s): 26.150 (total time: 28.640) Filter (q & B) r_work=0.1261 r_free=0.1543 | n_water=248 | time (s): 3.860 (total time: 32.500) Compute maps r_work=0.1261 r_free=0.1543 | n_water=248 | time (s): 1.870 (total time: 34.370) Filter (map) r_work=0.1278 r_free=0.1548 | n_water=235 | time (s): 4.100 (total time: 38.470) Find peaks r_work=0.1278 r_free=0.1548 | n_water=235 | time (s): 0.750 (total time: 39.220) Add new water r_work=0.1428 r_free=0.1706 | n_water=447 | time (s): 3.990 (total time: 43.210) Refine new water occ: r_work=0.1335 r_free=0.1564 adp: r_work=0.1256 r_free=0.1514 occ: r_work=0.1269 r_free=0.1506 adp: r_work=0.1235 r_free=0.1492 occ: r_work=0.1240 r_free=0.1488 adp: r_work=0.1229 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1485 r_work=0.1229 r_free=0.1485 | n_water=447 | time (s): 99.050 (total time: 142.260) Filter (q & B) r_work=0.1235 r_free=0.1493 | n_water=425 | time (s): 4.080 (total time: 146.340) Filter (dist only) r_work=0.1235 r_free=0.1493 | n_water=425 | time (s): 40.060 (total time: 186.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.066203 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1524.157968 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 0.1230 0.1519 0.0289 0.007 0.9 1.6 0.5 0.0 0 13.033 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.19 2.89 3.801 23.186 1524.158 0.015 11.99 14.86 2.86 4.215 23.006 1524.158 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 114.88 23.13 2.62 190 1762 Protein: 8.73 114.88 17.72 2.62 0 1519 Water: 10.88 72.79 42.36 N/A 190 235 Other: 24.06 35.69 29.09 N/A 0 8 Chain A: 8.73 114.88 20.42 N/A 0 1762 Chain S: 17.51 70.04 48.31 N/A 190 0 Histogram: Values Number of atoms 8.73 - 19.35 1204 19.35 - 29.96 248 29.96 - 40.58 197 40.58 - 51.19 141 51.19 - 61.80 100 61.80 - 72.42 50 72.42 - 83.03 6 83.03 - 93.65 3 93.65 - 104.26 1 104.26 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1485 r_work=0.1199 r_free=0.1485 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1485 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 = 0.1200 r_free = 0.1478 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1478 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013924 | | target function (ls_wunit_k1) not normalized (work): 1159.851642 | | target function (ls_wunit_k1) not normalized (free): 100.703064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1200 0.1478 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1611 0.1718 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1611 0.1718 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1619 0.1615 0.1721 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1474 n_refl.: 87592 remove outliers: r(all,work,free)=0.1208 0.1195 0.1474 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 0.3334 290.886 271.794 0.626 0.938 0.352 11.894-9.307 99.02 97 4 0.1579 477.651 476.849 0.979 0.939 0.340 9.237-7.194 100.00 213 7 0.1688 390.660 390.838 1.044 0.939 0.280 7.162-5.571 100.00 427 22 0.1495 293.168 288.983 1.002 0.940 0.239 5.546-4.326 100.00 867 58 0.0815 402.448 399.623 1.020 0.940 0.215 4.315-3.360 100.00 1859 96 0.0718 382.731 381.664 1.068 0.940 0.210 3.356-2.611 100.00 3867 181 0.0953 251.434 250.794 1.074 0.941 0.150 2.608-2.026 99.99 8198 413 0.0962 166.678 166.291 1.083 0.942 0.000 2.025-1.573 100.00 17313 902 0.1178 81.397 81.598 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1607 36.095 35.599 1.075 0.946 0.000 1.221-1.150 99.97 13689 708 0.2339 22.742 21.296 1.032 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0429 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1474 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1474 | n_water=425 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1197 r_free=0.1474 | n_water=424 | time (s): 37.200 (total time: 39.080) Filter (q & B) r_work=0.1197 r_free=0.1474 | n_water=424 | time (s): 1.160 (total time: 40.240) Compute maps r_work=0.1197 r_free=0.1474 | n_water=424 | time (s): 1.310 (total time: 41.550) Filter (map) r_work=0.1237 r_free=0.1472 | n_water=288 | time (s): 2.910 (total time: 44.460) Find peaks r_work=0.1237 r_free=0.1472 | n_water=288 | time (s): 0.530 (total time: 44.990) Add new water r_work=0.1376 r_free=0.1596 | n_water=486 | time (s): 2.630 (total time: 47.620) Refine new water occ: r_work=0.1268 r_free=0.1511 adp: r_work=0.1269 r_free=0.1511 occ: r_work=0.1243 r_free=0.1492 adp: r_work=0.1241 r_free=0.1488 occ: r_work=0.1226 r_free=0.1482 adp: r_work=0.1219 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1475 r_work=0.1219 r_free=0.1475 | n_water=486 | time (s): 176.990 (total time: 224.610) Filter (q & B) r_work=0.1223 r_free=0.1471 | n_water=452 | time (s): 3.590 (total time: 228.200) Filter (dist only) r_work=0.1223 r_free=0.1471 | n_water=452 | time (s): 36.370 (total time: 264.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.115765 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.192484 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 0.1226 0.1430 0.0204 0.006 0.9 2.6 0.5 0.0 0 1.058 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.30 2.04 3.634 22.216 45.192 3.717 12.14 13.89 1.75 4.119 22.034 45.192 3.649 Individual atomic B min max mean iso aniso Overall: 9.25 110.16 21.83 2.32 221 1758 Protein: 9.25 110.16 17.29 2.32 0 1519 Water: 11.54 71.76 36.99 N/A 221 231 Other: 19.89 31.61 25.95 N/A 0 8 Chain A: 9.25 110.16 19.92 N/A 0 1758 Chain S: 16.04 67.50 36.95 N/A 221 0 Histogram: Values Number of atoms 9.25 - 19.34 1231 19.34 - 29.43 277 29.43 - 39.52 215 39.52 - 49.61 146 49.61 - 59.70 75 59.70 - 69.79 22 69.79 - 79.88 7 79.88 - 89.97 3 89.97 - 100.06 1 100.06 - 110.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1389 r_work=0.1216 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1390 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1386 target_work(ml) = 3.647 | | 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= 0.1209 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.646856 | | target function (ml) not normalized (work): 303753.928019 | | target function (ml) not normalized (free): 16030.362461 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1386 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1543 0.1542 0.1589 n_refl.: 87588 remove outliers: r(all,work,free)=0.1543 0.1542 0.1589 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1540 0.1539 0.1587 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1200 0.1359 n_refl.: 87588 remove outliers: r(all,work,free)=0.1204 0.1196 0.1359 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 87.50 79 5 0.3749 285.411 256.240 0.461 0.999 0.297 11.894-9.307 96.08 94 4 0.2289 471.087 457.305 0.857 1.001 0.281 9.237-7.194 98.18 209 7 0.2294 382.225 384.310 0.942 1.002 0.190 7.162-5.571 100.00 427 22 0.2043 293.168 282.930 0.912 1.002 0.176 5.546-4.326 100.00 867 58 0.1089 402.448 398.219 0.949 1.002 0.153 4.315-3.360 100.00 1859 96 0.0938 382.731 380.091 0.993 1.002 0.143 3.356-2.611 100.00 3867 181 0.1151 251.434 249.508 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1044 166.678 165.691 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.397 81.551 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1299 36.095 35.666 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2135 22.742 21.350 0.981 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0459 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=452 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1196 r_free=0.1359 | n_water=452 | time (s): 37.290 (total time: 39.580) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=452 | time (s): 1.250 (total time: 40.830) Compute maps r_work=0.1196 r_free=0.1359 | n_water=452 | time (s): 1.720 (total time: 42.550) Filter (map) r_work=0.1220 r_free=0.1374 | n_water=316 | time (s): 3.410 (total time: 45.960) Find peaks r_work=0.1220 r_free=0.1374 | n_water=316 | time (s): 0.650 (total time: 46.610) Add new water r_work=0.1285 r_free=0.1442 | n_water=487 | time (s): 2.810 (total time: 49.420) Refine new water occ: r_work=0.1213 r_free=0.1363 adp: r_work=0.1213 r_free=0.1366 occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1196 r_free=0.1349 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1183 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1337 r_work=0.1183 r_free=0.1337 | n_water=487 | time (s): 153.990 (total time: 203.410) Filter (q & B) r_work=0.1189 r_free=0.1340 | n_water=451 | time (s): 2.910 (total time: 206.320) Filter (dist only) r_work=0.1189 r_free=0.1340 | n_water=451 | time (s): 37.290 (total time: 243.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.919504 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.377624 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 0.1195 0.1350 0.0154 0.006 0.9 2.2 0.5 0.0 0 0.960 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.50 1.54 3.436 21.611 46.378 3.635 11.81 13.44 1.63 3.889 21.470 46.378 3.618 Individual atomic B min max mean iso aniso Overall: 9.20 105.68 21.34 2.16 223 1755 Protein: 9.20 105.68 16.95 2.16 0 1519 Water: 11.50 70.25 36.11 N/A 223 228 Other: 19.30 28.33 23.73 N/A 0 8 Chain A: 9.20 105.68 19.48 N/A 0 1755 Chain S: 15.49 60.17 36.03 N/A 223 0 Histogram: Values Number of atoms 9.20 - 18.85 1223 18.85 - 28.50 293 28.50 - 38.15 206 38.15 - 47.79 140 47.79 - 57.44 79 57.44 - 67.09 24 67.09 - 76.74 8 76.74 - 86.38 2 86.38 - 96.03 1 96.03 - 105.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1344 r_work=0.1181 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1344 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1340 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1340 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617056 | | target function (ml) not normalized (work): 301232.071686 | | target function (ml) not normalized (free): 15896.185694 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1178 0.1340 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1505 0.1503 0.1569 n_refl.: 87577 remove outliers: r(all,work,free)=0.1505 0.1503 0.1569 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1502 0.1499 0.1566 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1177 0.1344 n_refl.: 87577 remove outliers: r(all,work,free)=0.1184 0.1176 0.1344 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3874 285.411 252.993 0.456 0.952 0.297 11.894-9.307 95.10 93 4 0.2464 473.017 450.905 0.886 0.954 0.229 9.237-7.194 97.73 208 7 0.2457 383.297 375.451 0.953 0.954 0.152 7.162-5.571 100.00 427 22 0.2188 293.168 281.157 0.950 0.955 0.125 5.546-4.326 100.00 867 58 0.1136 402.448 398.245 0.996 0.955 0.119 4.315-3.360 100.00 1859 96 0.0956 382.731 380.414 1.044 0.955 0.113 3.356-2.611 100.00 3867 181 0.1132 251.434 249.787 1.051 0.954 0.048 2.608-2.026 99.99 8198 413 0.1015 166.678 165.925 1.064 0.954 0.000 2.025-1.573 100.00 17313 902 0.0961 81.397 81.674 1.080 0.952 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.095 35.727 1.075 0.950 0.000 1.221-1.150 99.97 13689 708 0.2128 22.742 21.377 1.032 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0504 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1176 r_free=0.1344 After: r_work=0.1177 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1177 r_free=0.1344 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=0.1177 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1177 r_free=0.1344 | n_water=451 | time (s): 2.150 (total time: 2.150) Filter (dist) r_work=0.1177 r_free=0.1344 | n_water=451 | time (s): 36.860 (total time: 39.010) Filter (q & B) r_work=0.1177 r_free=0.1345 | n_water=449 | time (s): 2.780 (total time: 41.790) Compute maps r_work=0.1177 r_free=0.1345 | n_water=449 | time (s): 1.360 (total time: 43.150) Filter (map) r_work=0.1205 r_free=0.1373 | n_water=335 | time (s): 3.330 (total time: 46.480) Find peaks r_work=0.1205 r_free=0.1373 | n_water=335 | time (s): 0.570 (total time: 47.050) Add new water r_work=0.1249 r_free=0.1399 | n_water=491 | time (s): 2.680 (total time: 49.730) Refine new water occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1343 occ: r_work=0.1176 r_free=0.1331 adp: r_work=0.1175 r_free=0.1334 occ: r_work=0.1168 r_free=0.1325 adp: r_work=0.1165 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1327 r_work=0.1165 r_free=0.1327 | n_water=491 | time (s): 193.510 (total time: 243.240) Filter (q & B) r_work=0.1172 r_free=0.1338 | n_water=451 | time (s): 2.980 (total time: 246.220) Filter (dist only) r_work=0.1172 r_free=0.1336 | n_water=450 | time (s): 40.170 (total time: 286.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.893676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.087534 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 0.1203 0.1370 0.0167 0.007 1.0 4.8 0.5 0.0 0 0.947 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.70 1.67 3.289 21.148 52.088 3.630 12.05 13.70 1.65 3.541 21.079 52.088 3.619 Individual atomic B min max mean iso aniso Overall: 9.27 101.42 21.04 2.04 223 1754 Protein: 9.27 101.42 16.73 2.04 0 1519 Water: 11.55 69.06 35.56 N/A 223 227 Other: 19.47 27.07 23.39 N/A 0 8 Chain A: 9.27 101.42 19.24 N/A 0 1754 Chain S: 14.42 59.95 35.26 N/A 223 0 Histogram: Values Number of atoms 9.27 - 18.49 1218 18.49 - 27.70 287 27.70 - 36.92 206 36.92 - 46.13 157 46.13 - 55.35 72 55.35 - 64.56 21 64.56 - 73.78 11 73.78 - 82.99 2 82.99 - 92.21 1 92.21 - 101.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1370 r_work=0.1206 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1370 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1368 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1202 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618457 | | target function (ml) not normalized (work): 301341.518293 | | target function (ml) not normalized (free): 15935.167001 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1435 0.1399 5.6896 5.6435| | 2: 3.57 - 2.84 1.00 2888 124 0.1141 0.1467 5.2075 5.2626| | 3: 2.83 - 2.48 1.00 2820 163 0.1239 0.1258 5.0102 5.0134| | 4: 2.47 - 2.25 1.00 2825 136 0.1032 0.1182 4.7101 4.7667| | 5: 2.25 - 2.09 1.00 2756 127 0.1005 0.1117 4.655 4.7261| | 6: 2.09 - 1.97 1.00 2846 113 0.0964 0.1148 4.3497 4.4736| | 7: 1.97 - 1.87 1.00 2787 165 0.0987 0.1235 4.0699 4.1766| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1229 3.989 4.0706| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1318 3.7085 3.9003| | 10: 1.72 - 1.66 1.00 2831 160 0.1001 0.1263 3.6327 3.7669| | 11: 1.66 - 1.61 1.00 2712 147 0.0962 0.1120 3.5656 3.6191| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1185 3.3417 3.4909| | 13: 1.56 - 1.52 1.00 2745 130 0.0974 0.1043 3.3351 3.4228| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1107 3.2559 3.3291| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1349 3.1598 3.3413| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1264 3.1481 3.2434| | 17: 1.42 - 1.39 1.00 2785 139 0.1108 0.1326 3.1067 3.2455| | 18: 1.39 - 1.36 1.00 2741 179 0.1141 0.1384 3.078 3.256| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1598 3.0885 3.2755| | 20: 1.34 - 1.32 1.00 2696 147 0.1309 0.1464 3.0806 3.1289| | 21: 1.32 - 1.30 1.00 2785 112 0.1411 0.1608 3.0845 3.1452| | 22: 1.29 - 1.27 1.00 2704 152 0.1475 0.1921 3.0812 3.2797| | 23: 1.27 - 1.26 1.00 2802 156 0.1561 0.1862 3.0954 3.2134| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1779 3.0912 3.1952| | 25: 1.24 - 1.22 1.00 2733 148 0.1781 0.2274 3.1018 3.2828| | 26: 1.22 - 1.21 1.00 2727 135 0.1857 0.1795 3.1169 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2005 0.2098 3.1371 3.1495| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2333 3.1363 3.1686| | 29: 1.18 - 1.16 1.00 2800 134 0.2210 0.2366 3.1211 3.2172| | 30: 1.16 - 1.15 1.00 2739 148 0.2374 0.2443 3.1117 3.155| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.94 9.28 1.00 0.97 6343.85| | 2: 3.57 - 2.84 2888 124 0.92 13.45 1.01 0.97 6343.85| | 3: 2.83 - 2.48 2820 163 0.88 17.66 0.99 0.97 5315.35| | 4: 2.47 - 2.25 2825 136 0.91 14.72 1.00 0.98 2663.18| | 5: 2.25 - 2.09 2756 127 0.89 16.95 1.01 0.98 2663.18| | 6: 2.09 - 1.97 2846 113 0.92 13.65 1.02 0.97 1561.34| | 7: 1.97 - 1.87 2787 165 0.94 10.81 1.02 0.97 621.62| | 8: 1.87 - 1.79 2789 144 0.91 14.37 1.00 0.97 621.62| | 9: 1.79 - 1.72 2745 138 0.93 11.47 0.98 0.97 338.63| | 10: 1.72 - 1.66 2831 160 0.93 12.28 0.98 0.97 281.96| | 11: 1.66 - 1.61 2712 147 0.93 12.94 0.98 0.97 269.16| | 12: 1.61 - 1.56 2773 144 0.95 9.65 0.99 0.97 148.44| | 13: 1.56 - 1.52 2745 130 0.94 11.19 1.02 0.97 148.44| | 14: 1.52 - 1.48 2803 134 0.94 11.34 1.02 0.97 132.41| | 15: 1.48 - 1.45 2738 128 0.95 10.45 1.01 0.98 103.07| | 16: 1.45 - 1.42 2756 161 0.94 11.59 1.02 0.98 103.07| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 92.92| | 18: 1.39 - 1.36 2741 179 0.94 11.74 1.01 0.98 87.05| | 19: 1.36 - 1.34 2807 134 0.94 12.31 1.00 0.98 87.05| | 20: 1.34 - 1.32 2696 147 0.94 12.43 0.99 0.96 81.74| | 21: 1.32 - 1.30 2785 112 0.94 13.30 0.98 0.96 81.37| | 22: 1.29 - 1.27 2704 152 0.93 13.96 0.98 0.96 81.52| | 23: 1.27 - 1.26 2802 156 0.92 14.78 0.98 0.95 82.33| | 24: 1.26 - 1.24 2744 132 0.93 14.91 0.97 0.95 82.33| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 83.83| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.02 0.93 85.48| | 27: 1.21 - 1.19 2814 148 0.89 18.68 1.02 0.93 85.48| | 28: 1.19 - 1.18 2671 147 0.88 20.19 1.01 0.93 88.74| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 89.96| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.93 89.96| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.37 max = 6343.85 mean = 985.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.06| |phase err.(test): min = 0.00 max = 89.80 mean = 14.15| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1202 0.1368 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1520 0.1518 0.1580 n_refl.: 87575 remove outliers: r(all,work,free)=0.1520 0.1518 0.1580 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1515 0.1578 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1203 0.1372 n_refl.: 87575 remove outliers: r(all,work,free)=0.1211 0.1202 0.1372 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 87.50 79 5 0.3932 285.411 251.167 0.437 1.000 0.310 11.894-9.307 94.12 92 4 0.2445 476.945 455.619 0.847 1.002 0.237 9.237-7.194 97.73 208 7 0.2568 383.297 375.161 0.902 1.002 0.133 7.162-5.571 100.00 427 22 0.2279 293.168 281.158 0.899 1.002 0.100 5.546-4.326 100.00 867 58 0.1195 402.448 397.931 0.949 1.002 0.100 4.315-3.360 100.00 1859 96 0.1017 382.731 380.112 0.994 1.002 0.098 3.356-2.611 100.00 3867 181 0.1205 251.434 249.421 1.000 1.001 0.090 2.608-2.026 99.99 8198 413 0.1046 166.678 165.748 1.015 1.000 0.000 2.025-1.573 100.00 17313 902 0.0974 81.397 81.646 1.029 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1221 36.095 35.719 1.025 0.995 0.000 1.221-1.150 99.97 13689 708 0.2114 22.742 21.368 0.984 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0418 ================= 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 : 0.2606 0.1961 0.082 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_weight: 0.1636 0.1772 0.082 5.274 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1464 0.007 0.937 9.1 119.5 20.1 258 0.128 1_adp: 0.1243 0.1542 0.007 0.937 8.6 118.9 21.1 258 0.128 1_regHadp: 0.1247 0.1547 0.007 0.937 8.6 118.9 21.1 258 0.128 1_occ: 0.1247 0.1551 0.007 0.937 8.6 118.9 21.1 258 0.128 2_bss: 0.1246 0.1545 0.007 0.937 8.7 119.0 21.2 258 0.128 2_settarget: 0.1246 0.1545 0.007 0.937 8.7 119.0 21.2 258 0.128 2_updatecdl: 0.1246 0.1545 0.007 0.944 8.7 119.0 21.2 258 0.128 2_nqh: 0.1247 0.1546 0.007 0.944 8.7 119.0 21.2 258 0.131 2_sol: 0.1235 0.1493 0.007 0.944 8.7 119.0 23.5 425 n/a 2_weight: 0.1235 0.1493 0.007 0.944 8.7 119.0 23.5 425 n/a 2_xyzrec: 0.1230 0.1519 0.007 0.879 8.7 119.0 23.5 425 n/a 2_adp: 0.1199 0.1485 0.007 0.879 8.7 114.9 23.1 425 n/a 2_regHadp: 0.1199 0.1485 0.007 0.879 8.7 114.9 23.1 425 n/a 2_occ: 0.1200 0.1478 0.007 0.879 8.7 114.9 23.1 425 n/a 3_bss: 0.1195 0.1474 0.007 0.879 8.8 114.9 23.2 425 n/a 3_settarget: 0.1195 0.1474 0.007 0.879 8.8 114.9 23.2 425 n/a 3_updatecdl: 0.1195 0.1474 0.007 0.880 8.8 114.9 23.2 425 n/a 3_nqh: 0.1195 0.1474 0.007 0.880 8.8 114.9 23.2 425 n/a 3_sol: 0.1223 0.1471 0.007 0.880 8.8 114.9 22.2 452 n/a 3_weight: 0.1223 0.1471 0.007 0.880 8.8 114.9 22.2 452 n/a 3_xyzrec: 0.1226 0.1430 0.006 0.924 8.8 114.9 22.2 452 n/a 3_adp: 0.1214 0.1389 0.006 0.924 9.2 110.2 21.8 452 n/a 3_regHadp: 0.1216 0.1390 0.006 0.924 9.2 110.2 21.8 452 n/a 3_occ: 0.1209 0.1386 0.006 0.924 9.2 110.2 21.8 452 n/a 4_bss: 0.1196 0.1359 0.006 0.924 9.2 110.1 21.8 452 n/a 4_settarget: 0.1196 0.1359 0.006 0.924 9.2 110.1 21.8 452 n/a 4_updatecdl: 0.1196 0.1359 0.006 0.922 9.2 110.1 21.8 452 n/a 4_nqh: 0.1196 0.1359 0.006 0.922 9.2 110.1 21.8 452 n/a 4_sol: 0.1189 0.1340 0.006 0.922 9.2 110.1 21.6 451 n/a 4_weight: 0.1189 0.1340 0.006 0.922 9.2 110.1 21.6 451 n/a 4_xyzrec: 0.1195 0.1350 0.006 0.947 9.2 110.1 21.6 451 n/a 4_adp: 0.1181 0.1344 0.006 0.947 9.2 105.7 21.3 451 n/a 4_regHadp: 0.1181 0.1344 0.006 0.947 9.2 105.7 21.3 451 n/a 4_occ: 0.1178 0.1340 0.006 0.947 9.2 105.7 21.3 451 n/a 5_bss: 0.1176 0.1344 0.006 0.947 9.2 105.7 21.3 451 n/a 5_settarget: 0.1176 0.1344 0.006 0.947 9.2 105.7 21.3 451 n/a 5_updatecdl: 0.1176 0.1344 0.006 0.948 9.2 105.7 21.3 451 n/a 5_setrh: 0.1177 0.1344 0.006 0.948 9.2 105.7 21.3 451 n/a 5_nqh: 0.1177 0.1344 0.006 0.948 9.2 105.7 21.3 451 n/a 5_sol: 0.1172 0.1336 0.006 0.948 9.2 105.7 21.2 450 n/a 5_weight: 0.1172 0.1336 0.006 0.948 9.2 105.7 21.2 450 n/a 5_xyzrec: 0.1203 0.1370 0.007 1.024 9.2 105.7 21.2 450 n/a 5_adp: 0.1205 0.1370 0.007 1.024 9.3 101.4 21.0 450 n/a 5_regHadp: 0.1206 0.1370 0.007 1.024 9.3 101.4 21.0 450 n/a 5_occ: 0.1202 0.1368 0.007 1.024 9.3 101.4 21.0 450 n/a end: 0.1202 0.1372 0.007 1.024 9.3 101.4 21.0 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8230669_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8230669_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7700 Refinement macro-cycles (run) : 3509.5100 Write final files (write_after_run_outputs) : 69.2200 Total : 3583.5000 Total CPU time: 60.34 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:14 PST -0800 (1735452674.95 s) Start R-work = 0.1636, R-free = 0.1772 Final R-work = 0.1202, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3718.09 seconds wall clock time: 66 minutes 25.76 seconds (3985.76 seconds total)