Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.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_8960824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8960824.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 =============================================================================== Symmetric amino acids flipped. Time to flip 4 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: 2.28, per 1000 atoms: 0.67 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: 0.88 Conformation dependent library (CDL) restraints added in 208.9 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 431 0.89 - 1.16: 1194 1.16 - 1.42: 654 1.42 - 1.68: 837 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 1.459 1.687 -0.229 1.16e-02 7.43e+03 3.89e+02 bond pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.335 1.593 -0.258 1.35e-02 5.49e+03 3.65e+02 bond pdb=" N LEU A 101 " pdb=" CA LEU A 101 " ideal model delta sigma weight residual 1.456 1.673 -0.217 1.22e-02 6.72e+03 3.17e+02 bond pdb=" N SER A 161 " pdb=" CA SER A 161 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.84e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.338 0.188 1.13e-02 7.83e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3126 4.69 - 9.38: 1925 9.38 - 14.07: 595 14.07 - 18.76: 114 18.76 - 23.44: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 131.10 -11.78 7.40e-01 1.83e+00 2.53e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 137.01 -16.46 1.06e+00 8.90e-01 2.41e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 135.28 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 108.76 12.74 1.00e+00 1.00e+00 1.62e+02 angle pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" O ALA A 107 " ideal model delta sigma weight residual 119.18 134.20 -15.02 1.19e+00 7.06e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 19.06: 950 19.06 - 38.11: 114 38.11 - 57.16: 39 57.16 - 76.20: 7 76.20 - 95.25: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.182: 80 0.182 - 0.362: 69 0.362 - 0.543: 54 0.543 - 0.724: 21 0.724 - 0.905: 19 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.53 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.055 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" CG TYR A 141 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.106 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.058 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.141 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1020 2.32 - 2.89: 8040 2.89 - 3.46: 10588 3.46 - 4.03: 15216 4.03 - 4.60: 21742 Nonbonded interactions: 56606 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.831 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.839 2.450 ... (remaining 56601 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_8960824_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= 0.2608 r_free= 0.1979 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791094 | | target function (ml) not normalized (work): 232514.855436 | | target function (ml) not normalized (free): 11859.384229 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2204 6.967 4.9604| | 2: 3.57 - 2.84 1.00 2876 122 0.2439 0.1772 4.3586 4.3555| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1720 4.143 4.1849| | 4: 2.47 - 2.25 1.00 2825 136 0.2303 0.1588 3.8393 3.859| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1505 3.81 3.8173| | 6: 2.09 - 1.97 1.00 2846 113 0.2569 0.1620 3.4804 3.5259| | 7: 1.97 - 1.87 1.00 2787 165 0.2552 0.1813 3.1301 3.1646| | 8: 1.87 - 1.79 1.00 2789 144 0.2542 0.2047 3.0619 3.1751| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1892 2.8952 2.9807| | 10: 1.72 - 1.66 1.00 2789 158 0.2408 0.1893 2.8157 2.888| | 11: 1.66 - 1.61 1.00 2740 147 0.2447 0.1985 2.7562 2.8262| | 12: 1.61 - 1.56 1.00 2787 146 0.2502 0.2055 2.6118 2.6586| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1634 2.5773 2.511| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.1895 2.5006 2.5211| | 15: 1.48 - 1.45 1.00 2738 128 0.2605 0.2093 2.4176 2.4592| | 16: 1.45 - 1.42 1.00 2756 161 0.2684 0.2222 2.3884 2.4846| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.1842 2.3205 2.2904| | 18: 1.39 - 1.36 1.00 2741 179 0.2737 0.2223 2.2818 2.3042| | 19: 1.36 - 1.34 1.00 2807 134 0.2630 0.2416 2.2417 2.3402| | 20: 1.34 - 1.32 1.00 2696 147 0.2724 0.2350 2.2177 2.2521| | 21: 1.32 - 1.30 1.00 2785 112 0.2709 0.2572 2.1543 2.2731| | 22: 1.29 - 1.27 1.00 2704 152 0.2757 0.2765 2.1417 2.2328| | 23: 1.27 - 1.26 1.00 2802 156 0.2771 0.2554 2.1181 2.1831| | 24: 1.26 - 1.24 1.00 2744 132 0.2835 0.2425 2.0934 2.1486| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2609 2.0383 2.1217| | 26: 1.22 - 1.21 1.00 2727 135 0.2896 0.2355 2.0265 2.0668| | 27: 1.21 - 1.19 1.00 2814 148 0.2950 0.2667 2.0144 2.0235| | 28: 1.19 - 1.18 1.00 2671 147 0.2998 0.3050 1.9977 2.0625| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2762 1.9594 2.0212| | 30: 1.16 - 1.15 1.00 2740 148 0.3044 0.2858 1.924 1.9691| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.16 0.76 0.23 1538.90| | 2: 3.57 - 2.84 2876 122 0.80 26.57 1.27 0.23 1538.90| | 3: 2.84 - 2.48 2833 165 0.74 32.38 1.24 0.24 1274.70| | 4: 2.47 - 2.25 2825 136 0.81 25.93 1.25 0.25 589.05| | 5: 2.25 - 2.09 2756 127 0.77 29.65 1.28 0.25 589.05| | 6: 2.09 - 1.97 2846 113 0.83 22.83 1.30 0.25 319.81| | 7: 1.97 - 1.87 2787 165 0.90 16.38 1.28 0.26 90.18| | 8: 1.87 - 1.79 2789 144 0.86 20.98 1.26 0.26 90.18| | 9: 1.79 - 1.72 2745 138 0.88 18.71 1.23 0.25 55.70| | 10: 1.72 - 1.66 2789 158 0.87 20.01 1.22 0.25 48.79| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.23 0.25 47.06| | 12: 1.61 - 1.56 2787 146 0.88 18.54 1.24 0.25 29.46| | 13: 1.56 - 1.52 2745 130 0.87 20.39 1.23 0.25 29.46| | 14: 1.52 - 1.48 2803 134 0.86 20.67 1.23 0.25 26.29| | 15: 1.48 - 1.45 2738 128 0.87 20.26 1.24 0.25 20.49| | 16: 1.45 - 1.42 2756 161 0.86 21.63 1.24 0.25 20.49| | 17: 1.42 - 1.39 2785 139 0.87 20.79 1.24 0.25 17.62| | 18: 1.39 - 1.36 2741 179 0.86 21.58 1.23 0.25 15.95| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.21 0.25 15.95| | 20: 1.34 - 1.32 2696 147 0.86 21.53 1.20 0.25 13.79| | 21: 1.32 - 1.30 2785 112 0.85 22.55 1.21 0.25 13.64| | 22: 1.29 - 1.27 2704 152 0.84 23.33 1.21 0.24 13.37| | 23: 1.27 - 1.26 2802 156 0.85 22.84 1.21 0.24 11.99| | 24: 1.26 - 1.24 2744 132 0.84 23.78 1.21 0.24 11.99| | 25: 1.24 - 1.22 2734 148 0.83 24.71 1.21 0.24 11.40| | 26: 1.22 - 1.21 2727 135 0.83 25.10 1.20 0.23 10.74| | 27: 1.21 - 1.19 2814 148 0.82 25.65 1.21 0.23 10.74| | 28: 1.19 - 1.18 2671 147 0.82 26.33 1.17 0.23 10.10| | 29: 1.18 - 1.16 2800 134 0.81 27.33 1.16 0.22 9.86| | 30: 1.16 - 1.15 2740 148 0.79 28.63 1.16 0.22 9.86| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.86 max = 1538.90 mean = 222.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.96 mean = 23.06| |phase err.(test): min = 0.00 max = 89.32 mean = 22.94| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.430 Angle : 5.342 16.459 2118 Z= 3.797 Chirality : 0.396 0.905 243 Planarity : 0.033 0.105 284 Dihedral : 14.246 95.252 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.45), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -1.10 (0.76), residues: 38 loop : -0.48 (0.58), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.012 ARG A 28 TYR 0.112 0.051 TYR A 141 PHE 0.123 0.054 PHE A 164 HIS 0.063 0.030 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= 0.2608 r_free= 0.1979 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791094 | | target function (ml) not normalized (work): 232514.855436 | | target function (ml) not normalized (free): 11859.384229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1979 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1979 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1980 0.1979 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2002 0.2005 0.1992 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1632 0.1800 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1631 0.1800 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 98.94 88 5 0.3774 386.567 359.431 0.675 1.002 0.407 11.894-9.307 98.04 96 4 0.1677 616.536 588.445 0.924 1.003 0.390 9.237-7.194 100.00 213 7 0.2144 502.212 491.733 0.959 1.003 0.380 7.162-5.571 100.00 427 22 0.2212 376.882 364.703 0.924 1.003 0.292 5.546-4.326 100.00 867 58 0.1267 517.366 511.396 0.960 1.003 0.214 4.315-3.360 100.00 1859 96 0.1134 492.019 488.711 1.002 1.003 0.189 3.356-2.611 100.00 3867 181 0.1445 323.231 319.717 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.1335 214.273 212.116 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.640 104.103 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.401 45.086 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2585 29.236 26.968 0.974 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1631 r_free=0.1800 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.689622 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2019.594547 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 0.1462 0.0250 0.007 0.9 1.0 0.5 0.0 0 11.845 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.62 2.50 3.013 19.057 2019.595 0.017 12.42 15.38 2.96 3.205 19.575 2019.595 0.016 Individual atomic B min max mean iso aniso Overall: 8.52 118.51 21.07 2.87 0 1785 Protein: 8.52 118.51 17.92 2.87 0 1519 Water: 11.11 114.63 39.31 N/A 0 258 Other: 23.05 36.13 29.18 N/A 0 8 Chain A: 8.52 118.51 21.07 N/A 0 1785 Histogram: Values Number of atoms 8.52 - 19.52 1199 19.52 - 30.52 236 30.52 - 41.52 163 41.52 - 52.52 102 52.52 - 63.52 56 63.52 - 74.51 15 74.51 - 85.51 7 85.51 - 96.51 4 96.51 - 107.51 0 107.51 - 118.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1538 r_work=0.1246 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1543 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 = 0.1246 r_free = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015378 | | target function (ls_wunit_k1) not normalized (work): 1280.938708 | | target function (ls_wunit_k1) not normalized (free): 116.018895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1246 0.1545 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1703 0.1702 0.1762 n_refl.: 87592 remove outliers: r(all,work,free)=0.1703 0.1702 0.1762 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1725 0.1724 0.1777 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1244 0.1539 n_refl.: 87592 remove outliers: r(all,work,free)=0.1258 0.1244 0.1539 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3627 298.095 277.748 0.629 1.003 0.380 11.894-9.307 98.04 96 4 0.1511 479.469 467.749 0.915 1.003 0.380 9.237-7.194 100.00 213 7 0.1837 390.562 384.790 0.946 1.003 0.350 7.162-5.571 100.00 427 22 0.1740 293.095 287.747 0.919 1.003 0.258 5.546-4.326 100.00 867 58 0.0924 402.347 399.648 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0771 382.635 381.706 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1022 251.371 250.712 0.999 1.002 0.100 2.608-2.026 99.99 8198 413 0.0977 166.636 166.056 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1212 81.376 81.545 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1651 36.086 35.543 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2364 22.736 21.244 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0506 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1540 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1254 r_free=0.1540 | n_water=252 | time (s): 25.850 (total time: 28.150) Filter (q & B) r_work=0.1258 r_free=0.1540 | n_water=249 | time (s): 3.650 (total time: 31.800) Compute maps r_work=0.1258 r_free=0.1540 | n_water=249 | time (s): 1.840 (total time: 33.640) Filter (map) r_work=0.1273 r_free=0.1544 | n_water=236 | time (s): 3.580 (total time: 37.220) Find peaks r_work=0.1273 r_free=0.1544 | n_water=236 | time (s): 0.680 (total time: 37.900) Add new water r_work=0.1432 r_free=0.1690 | n_water=455 | time (s): 3.590 (total time: 41.490) Refine new water occ: r_work=0.1346 r_free=0.1575 adp: r_work=0.1262 r_free=0.1512 occ: r_work=0.1276 r_free=0.1516 adp: r_work=0.1240 r_free=0.1491 occ: r_work=0.1244 r_free=0.1481 adp: r_work=0.1235 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1480 r_work=0.1235 r_free=0.1480 | n_water=455 | time (s): 83.950 (total time: 125.440) Filter (q & B) r_work=0.1241 r_free=0.1485 | n_water=436 | time (s): 3.830 (total time: 129.270) Filter (dist only) r_work=0.1241 r_free=0.1483 | n_water=435 | time (s): 44.190 (total time: 173.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.506836 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1367.675073 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 0.1234 0.1505 0.0270 0.007 0.9 3.2 0.5 0.0 0 12.253 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 15.05 2.70 3.794 23.300 1367.675 0.015 12.10 14.84 2.74 4.257 23.101 1367.675 0.015 Individual atomic B min max mean iso aniso Overall: 8.88 113.64 23.32 2.57 199 1763 Protein: 8.88 113.64 17.67 2.58 0 1519 Water: 11.10 72.14 43.03 N/A 199 236 Other: 21.81 32.53 26.36 N/A 0 8 Chain A: 8.88 113.64 20.37 N/A 0 1763 Chain S: 19.51 71.73 49.51 N/A 199 0 Histogram: Values Number of atoms 8.88 - 19.36 1205 19.36 - 29.83 251 29.83 - 40.31 182 40.31 - 50.78 148 50.78 - 61.26 104 61.26 - 71.74 60 71.74 - 82.21 6 82.21 - 92.69 3 92.69 - 103.16 1 103.16 - 113.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1484 r_work=0.1210 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1484 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1484 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1484 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014193 | | target function (ls_wunit_k1) not normalized (work): 1182.183469 | | target function (ls_wunit_k1) not normalized (free): 104.660573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1210 0.1484 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1616 0.1611 0.1735 n_refl.: 87591 remove outliers: r(all,work,free)=0.1616 0.1611 0.1735 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1620 0.1616 0.1738 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1207 0.1479 n_refl.: 87591 remove outliers: r(all,work,free)=0.1219 0.1205 0.1479 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 92.71 84 5 0.3311 293.493 271.653 0.627 0.937 0.360 11.894-9.307 98.04 96 4 0.1535 479.469 476.651 0.986 0.938 0.340 9.237-7.194 100.00 213 7 0.1670 390.562 390.126 1.047 0.938 0.290 7.162-5.571 100.00 427 22 0.1548 293.095 288.621 1.002 0.938 0.214 5.546-4.326 100.00 867 58 0.0841 402.347 399.656 1.021 0.939 0.200 4.315-3.360 100.00 1859 96 0.0722 382.635 381.402 1.069 0.939 0.200 3.356-2.611 100.00 3867 181 0.0974 251.371 250.559 1.076 0.940 0.150 2.608-2.026 99.99 8198 413 0.0969 166.636 166.221 1.084 0.941 0.000 2.025-1.573 100.00 17313 902 0.1184 81.376 81.565 1.091 0.942 0.000 1.573-1.221 100.00 36679 1900 0.1617 36.086 35.579 1.077 0.945 0.000 1.221-1.150 99.97 13689 708 0.2346 22.736 21.287 1.032 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0434 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1479 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1479 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1479 | n_water=435 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1205 r_free=0.1478 | n_water=433 | time (s): 39.400 (total time: 41.480) Filter (q & B) r_work=0.1205 r_free=0.1478 | n_water=433 | time (s): 1.240 (total time: 42.720) Compute maps r_work=0.1205 r_free=0.1478 | n_water=433 | time (s): 1.430 (total time: 44.150) Filter (map) r_work=0.1242 r_free=0.1473 | n_water=295 | time (s): 2.590 (total time: 46.740) Find peaks r_work=0.1242 r_free=0.1473 | n_water=295 | time (s): 0.680 (total time: 47.420) Add new water r_work=0.1373 r_free=0.1585 | n_water=495 | time (s): 2.860 (total time: 50.280) Refine new water occ: r_work=0.1274 r_free=0.1511 adp: r_work=0.1275 r_free=0.1511 occ: r_work=0.1250 r_free=0.1495 adp: r_work=0.1247 r_free=0.1491 occ: r_work=0.1233 r_free=0.1491 adp: r_work=0.1225 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1483 r_work=0.1225 r_free=0.1483 | n_water=495 | time (s): 168.660 (total time: 218.940) Filter (q & B) r_work=0.1231 r_free=0.1482 | n_water=454 | time (s): 2.770 (total time: 221.710) Filter (dist only) r_work=0.1230 r_free=0.1480 | n_water=453 | time (s): 41.340 (total time: 263.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.962757 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.359133 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1434 0.0201 0.005 0.9 1.9 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.34 2.01 3.603 22.200 39.359 3.721 12.22 13.86 1.64 4.066 22.024 39.359 3.651 Individual atomic B min max mean iso aniso Overall: 9.27 109.33 21.89 2.27 217 1763 Protein: 9.27 109.33 17.26 2.28 0 1519 Water: 11.63 71.26 37.40 N/A 217 236 Other: 18.19 28.94 23.93 N/A 0 8 Chain A: 9.27 109.33 19.98 N/A 0 1763 Chain S: 16.42 67.57 37.46 N/A 217 0 Histogram: Values Number of atoms 9.27 - 19.28 1232 19.28 - 29.28 277 29.28 - 39.29 215 39.29 - 49.30 135 49.30 - 59.30 84 59.30 - 69.31 24 69.31 - 79.32 7 79.32 - 89.32 3 89.32 - 99.33 1 99.33 - 109.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1222 r_free=0.1386 r_work=0.1223 r_free=0.1387 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1223 r_free = 0.1387 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1218 r_free = 0.1390 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1218 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649105 | | target function (ml) not normalized (work): 303941.272785 | | target function (ml) not normalized (free): 16035.404606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1218 0.1390 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1609 n_refl.: 87588 remove outliers: r(all,work,free)=0.1548 0.1547 0.1609 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1545 0.1543 0.1606 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1209 0.1373 n_refl.: 87588 remove outliers: r(all,work,free)=0.1213 0.1205 0.1373 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3756 290.059 260.838 0.473 1.000 0.314 11.894-9.307 94.12 92 4 0.2335 476.826 454.900 0.857 1.002 0.258 9.237-7.194 98.18 209 7 0.2301 382.130 382.898 0.947 1.002 0.210 7.162-5.571 100.00 427 22 0.1997 293.095 284.046 0.915 1.002 0.165 5.546-4.326 100.00 867 58 0.1102 402.347 398.015 0.951 1.002 0.160 4.315-3.360 100.00 1859 96 0.0940 382.635 379.767 0.994 1.002 0.160 3.356-2.611 100.00 3867 181 0.1160 251.371 249.322 1.000 1.002 0.072 2.608-2.026 99.99 8198 413 0.1065 166.636 165.661 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1026 81.376 81.531 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1300 36.086 35.658 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2133 22.736 21.354 0.983 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1373 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=0.1205 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1373 | n_water=453 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1205 r_free=0.1375 | n_water=452 | time (s): 41.150 (total time: 43.290) Filter (q & B) r_work=0.1205 r_free=0.1374 | n_water=451 | time (s): 3.250 (total time: 46.540) Compute maps r_work=0.1205 r_free=0.1374 | n_water=451 | time (s): 1.390 (total time: 47.930) Filter (map) r_work=0.1225 r_free=0.1366 | n_water=313 | time (s): 3.230 (total time: 51.160) Find peaks r_work=0.1225 r_free=0.1366 | n_water=313 | time (s): 0.600 (total time: 51.760) Add new water r_work=0.1295 r_free=0.1445 | n_water=482 | time (s): 2.820 (total time: 54.580) Refine new water occ: r_work=0.1221 r_free=0.1369 adp: r_work=0.1222 r_free=0.1372 occ: r_work=0.1206 r_free=0.1357 adp: r_work=0.1205 r_free=0.1358 occ: r_work=0.1196 r_free=0.1353 adp: r_work=0.1192 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1351 r_work=0.1192 r_free=0.1351 | n_water=482 | time (s): 110.930 (total time: 165.510) Filter (q & B) r_work=0.1198 r_free=0.1351 | n_water=446 | time (s): 3.150 (total time: 168.660) Filter (dist only) r_work=0.1198 r_free=0.1347 | n_water=444 | time (s): 37.760 (total time: 206.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934644 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.012900 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 0.1202 0.1361 0.0160 0.006 0.9 1.9 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.61 1.60 3.410 21.511 50.013 3.638 11.78 13.51 1.72 3.858 21.366 50.013 3.617 Individual atomic B min max mean iso aniso Overall: 9.24 105.48 21.22 2.16 210 1761 Protein: 9.24 105.48 16.92 2.17 0 1519 Water: 11.56 69.67 35.89 N/A 210 234 Other: 17.75 25.64 21.52 N/A 0 8 Chain A: 9.24 105.48 19.56 N/A 0 1761 Chain S: 15.93 66.01 35.14 N/A 210 0 Histogram: Values Number of atoms 9.24 - 18.86 1225 18.86 - 28.49 294 28.49 - 38.11 199 38.11 - 47.74 146 47.74 - 57.36 69 57.36 - 66.99 25 66.99 - 76.61 8 76.61 - 86.23 2 86.23 - 95.86 1 95.86 - 105.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1351 r_work=0.1179 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1351 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1173 r_free = 0.1347 target_work(ml) = 3.615 | | 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.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1173 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614849 | | target function (ml) not normalized (work): 301044.647358 | | target function (ml) not normalized (free): 15910.570086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1182 0.1173 0.1347 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1496 0.1494 0.1558 n_refl.: 87576 remove outliers: r(all,work,free)=0.1496 0.1494 0.1558 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1492 0.1557 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1181 0.1173 0.1352 n_refl.: 87576 remove outliers: r(all,work,free)=0.1180 0.1171 0.1352 n_refl.: 87571 ======================== 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 0.3889 285.340 255.518 0.440 1.000 0.290 11.894-9.307 91.18 89 4 0.2470 467.926 448.956 0.844 1.001 0.206 9.237-7.194 97.73 208 7 0.2419 383.202 375.593 0.912 1.002 0.150 7.162-5.571 100.00 427 22 0.2199 293.095 282.123 0.904 1.002 0.133 5.546-4.326 100.00 867 58 0.1127 402.347 398.273 0.951 1.002 0.130 4.315-3.360 100.00 1859 96 0.0931 382.635 380.097 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1143 251.371 249.499 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1016 166.636 165.778 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0953 81.376 81.651 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.086 35.702 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2123 22.736 21.356 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=-0.0374 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1171 r_free=0.1352 After: r_work=0.1172 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1351 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=0.1172 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1351 | n_water=444 | time (s): 1.550 (total time: 1.550) Filter (dist) r_work=0.1172 r_free=0.1351 | n_water=444 | time (s): 34.380 (total time: 35.930) Filter (q & B) r_work=0.1172 r_free=0.1351 | n_water=443 | time (s): 3.290 (total time: 39.220) Compute maps r_work=0.1172 r_free=0.1351 | n_water=443 | time (s): 1.350 (total time: 40.570) Filter (map) r_work=0.1200 r_free=0.1356 | n_water=329 | time (s): 2.450 (total time: 43.020) Find peaks r_work=0.1200 r_free=0.1356 | n_water=329 | time (s): 0.490 (total time: 43.510) Add new water r_work=0.1249 r_free=0.1400 | n_water=489 | time (s): 2.450 (total time: 45.960) Refine new water occ: r_work=0.1186 r_free=0.1341 adp: r_work=0.1186 r_free=0.1343 occ: r_work=0.1174 r_free=0.1332 adp: r_work=0.1173 r_free=0.1333 occ: r_work=0.1165 r_free=0.1328 adp: r_work=0.1162 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1327 r_work=0.1162 r_free=0.1327 | n_water=489 | time (s): 140.410 (total time: 186.370) Filter (q & B) r_work=0.1171 r_free=0.1328 | n_water=449 | time (s): 2.740 (total time: 189.110) Filter (dist only) r_work=0.1171 r_free=0.1324 | n_water=447 | time (s): 36.320 (total time: 225.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.021476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.631928 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 0.1192 0.1343 0.0151 0.007 1.0 4.2 0.5 0.0 0 1.011 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.43 1.51 3.285 21.107 44.632 3.620 11.93 13.39 1.47 3.384 21.068 44.632 3.613 Individual atomic B min max mean iso aniso Overall: 9.24 102.64 21.07 2.06 216 1758 Protein: 9.24 102.64 16.82 2.06 0 1519 Water: 11.59 69.27 35.51 N/A 216 231 Other: 17.68 25.06 21.40 N/A 0 8 Chain A: 9.24 102.64 19.39 N/A 0 1758 Chain S: 15.88 57.57 34.77 N/A 216 0 Histogram: Values Number of atoms 9.24 - 18.58 1218 18.58 - 27.92 292 27.92 - 37.26 203 37.26 - 46.60 147 46.60 - 55.94 74 55.94 - 65.28 25 65.28 - 74.62 10 74.62 - 83.96 2 83.96 - 93.30 1 93.30 - 102.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1340 r_work=0.1193 r_free=0.1340 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1340 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1336 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87571 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611951 | | target function (ml) not normalized (work): 300785.196116 | | target function (ml) not normalized (free): 15903.765332 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2913 171 0.1394 0.1360 5.6596 5.6169| | 2: 3.57 - 2.84 1.00 2888 124 0.1110 0.1391 5.1792 5.2295| | 3: 2.83 - 2.48 1.00 2820 163 0.1217 0.1223 4.9874 5.0065| | 4: 2.47 - 2.25 1.00 2825 136 0.1025 0.1132 4.6896 4.7434| | 5: 2.25 - 2.09 1.00 2756 127 0.0996 0.1102 4.6276 4.701| | 6: 2.09 - 1.97 1.00 2846 113 0.0963 0.1160 4.3321 4.4749| | 7: 1.97 - 1.87 1.00 2787 165 0.0985 0.1133 4.0604 4.1324| | 8: 1.87 - 1.79 1.00 2789 144 0.1011 0.1205 3.9751 4.0627| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1267 3.7063 3.8974| | 10: 1.72 - 1.66 1.00 2831 160 0.0995 0.1257 3.6219 3.7628| | 11: 1.66 - 1.61 1.00 2712 147 0.0959 0.1075 3.5604 3.5894| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1176 3.3386 3.4847| | 13: 1.56 - 1.52 1.00 2745 130 0.0967 0.1076 3.3277 3.4335| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1110 3.254 3.3434| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1321 3.1613 3.3215| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1272 3.1453 3.2516| | 17: 1.42 - 1.39 1.00 2785 139 0.1111 0.1310 3.1091 3.2392| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1366 3.0827 3.2564| | 19: 1.36 - 1.34 1.00 2807 134 0.1220 0.1573 3.0906 3.2682| | 20: 1.34 - 1.32 1.00 2696 147 0.1309 0.1485 3.0791 3.1328| | 21: 1.32 - 1.30 1.00 2785 112 0.1411 0.1632 3.0829 3.1575| | 22: 1.29 - 1.27 1.00 2704 152 0.1468 0.1912 3.0789 3.2759| | 23: 1.27 - 1.26 1.00 2802 156 0.1570 0.1845 3.0976 3.2007| | 24: 1.26 - 1.24 1.00 2744 132 0.1628 0.1776 3.0912 3.2005| | 25: 1.24 - 1.22 1.00 2733 148 0.1787 0.2324 3.1036 3.2963| | 26: 1.22 - 1.21 1.00 2727 135 0.1860 0.1761 3.1205 3.1928| | 27: 1.21 - 1.19 1.00 2814 148 0.2004 0.2075 3.1364 3.1407| | 28: 1.19 - 1.18 1.00 2671 147 0.2145 0.2326 3.1371 3.163| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2370 3.1217 3.22| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2437 3.113 3.1529| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2913 171 0.95 8.64 1.00 0.97 5887.26| | 2: 3.57 - 2.84 2888 124 0.92 12.82 1.01 0.97 5887.26| | 3: 2.83 - 2.48 2820 163 0.89 16.98 0.98 0.98 4939.22| | 4: 2.47 - 2.25 2825 136 0.91 14.17 1.00 0.98 2494.50| | 5: 2.25 - 2.09 2756 127 0.90 16.36 1.01 0.98 2494.50| | 6: 2.09 - 1.97 2846 113 0.92 13.26 1.02 0.98 1473.46| | 7: 1.97 - 1.87 2787 165 0.94 10.56 1.02 0.97 602.65| | 8: 1.87 - 1.79 2789 144 0.92 14.10 1.00 0.97 602.65| | 9: 1.79 - 1.72 2745 138 0.94 11.22 0.98 0.97 330.07| | 10: 1.72 - 1.66 2831 160 0.93 12.11 0.98 0.97 275.48| | 11: 1.66 - 1.61 2712 147 0.93 12.71 0.98 0.97 263.04| | 12: 1.61 - 1.56 2773 144 0.95 9.49 0.99 0.97 145.70| | 13: 1.56 - 1.52 2745 130 0.94 11.02 1.02 0.97 145.70| | 14: 1.52 - 1.48 2803 134 0.94 11.23 1.02 0.97 130.62| | 15: 1.48 - 1.45 2738 128 0.95 10.44 1.01 0.98 103.01| | 16: 1.45 - 1.42 2756 161 0.94 11.55 1.02 0.98 103.01| | 17: 1.42 - 1.39 2785 139 0.94 11.50 1.01 0.98 92.88| | 18: 1.39 - 1.36 2741 179 0.94 11.72 1.01 0.98 87.02| | 19: 1.36 - 1.34 2807 134 0.94 12.33 1.00 0.98 87.02| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.96 81.83| | 21: 1.32 - 1.30 2785 112 0.94 13.34 0.98 0.96 81.47| | 22: 1.29 - 1.27 2704 152 0.93 13.84 0.98 0.96 81.58| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.98 0.95 82.13| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.97 0.95 82.13| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 83.54| | 26: 1.22 - 1.21 2727 135 0.90 17.99 1.02 0.93 85.10| | 27: 1.21 - 1.19 2814 148 0.89 18.64 1.02 0.93 85.10| | 28: 1.19 - 1.18 2671 147 0.88 20.11 1.01 0.93 88.02| | 29: 1.18 - 1.16 2800 134 0.88 20.35 0.99 0.93 89.12| | 30: 1.16 - 1.15 2739 148 0.86 21.80 0.98 0.93 89.12| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.47 max = 5887.26 mean = 924.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.87| |phase err.(test): min = 0.00 max = 89.21 mean = 13.97| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1188 0.1336 n_refl.: 87571 re-set all scales: r(all,work,free)=0.1505 0.1505 0.1538 n_refl.: 87571 remove outliers: r(all,work,free)=0.1505 0.1505 0.1538 n_refl.: 87571 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1503 0.1536 n_refl.: 87571 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1339 n_refl.: 87571 remove outliers: r(all,work,free)=0.1196 0.1188 0.1339 n_refl.: 87571 ======================== 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 0.3966 285.340 254.425 0.431 0.999 0.285 11.894-9.307 91.18 89 4 0.2439 467.926 446.237 0.833 1.001 0.193 9.237-7.194 97.73 208 7 0.2497 383.202 375.549 0.910 1.001 0.133 7.162-5.571 100.00 427 22 0.2219 293.095 282.526 0.895 1.002 0.114 5.546-4.326 100.00 867 58 0.1178 402.347 398.140 0.951 1.002 0.110 4.315-3.360 100.00 1859 96 0.0971 382.635 379.898 0.995 1.002 0.110 3.356-2.611 100.00 3867 181 0.1179 251.371 249.379 1.002 1.001 0.048 2.608-2.026 99.99 8198 413 0.1038 166.636 165.685 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0969 81.376 81.659 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1223 36.086 35.720 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2115 22.736 21.368 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0316 ================= 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 : 0.2608 0.1979 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_weight: 0.1631 0.1800 0.082 5.342 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1462 0.007 0.928 9.0 119.5 20.1 258 0.126 1_adp: 0.1242 0.1538 0.007 0.928 8.5 118.5 21.1 258 0.126 1_regHadp: 0.1246 0.1543 0.007 0.928 8.5 118.5 21.1 258 0.126 1_occ: 0.1246 0.1545 0.007 0.928 8.5 118.5 21.1 258 0.126 2_bss: 0.1244 0.1539 0.007 0.928 8.7 118.6 21.2 258 0.126 2_settarget: 0.1244 0.1539 0.007 0.928 8.7 118.6 21.2 258 0.126 2_updatecdl: 0.1244 0.1539 0.007 0.939 8.7 118.6 21.2 258 0.126 2_nqh: 0.1245 0.1540 0.007 0.939 8.7 118.6 21.2 258 0.129 2_sol: 0.1241 0.1483 0.007 0.939 8.7 118.6 23.7 435 n/a 2_weight: 0.1241 0.1483 0.007 0.939 8.7 118.6 23.7 435 n/a 2_xyzrec: 0.1234 0.1505 0.007 0.872 8.7 118.6 23.7 435 n/a 2_adp: 0.1210 0.1484 0.007 0.872 8.9 113.6 23.3 435 n/a 2_regHadp: 0.1210 0.1484 0.007 0.872 8.9 113.6 23.3 435 n/a 2_occ: 0.1210 0.1484 0.007 0.872 8.9 113.6 23.3 435 n/a 3_bss: 0.1205 0.1479 0.007 0.872 8.9 113.7 23.4 435 n/a 3_settarget: 0.1205 0.1479 0.007 0.872 8.9 113.7 23.4 435 n/a 3_updatecdl: 0.1205 0.1479 0.007 0.872 8.9 113.7 23.4 435 n/a 3_nqh: 0.1205 0.1479 0.007 0.872 8.9 113.7 23.4 435 n/a 3_sol: 0.1230 0.1480 0.007 0.872 8.9 113.7 22.2 453 n/a 3_weight: 0.1230 0.1480 0.007 0.872 8.9 113.7 22.2 453 n/a 3_xyzrec: 0.1233 0.1434 0.005 0.910 8.9 113.7 22.2 453 n/a 3_adp: 0.1222 0.1386 0.005 0.910 9.3 109.3 21.9 453 n/a 3_regHadp: 0.1223 0.1387 0.005 0.910 9.3 109.3 21.9 453 n/a 3_occ: 0.1218 0.1390 0.005 0.910 9.3 109.3 21.9 453 n/a 4_bss: 0.1205 0.1373 0.005 0.910 9.3 109.3 21.9 453 n/a 4_settarget: 0.1205 0.1373 0.005 0.910 9.3 109.3 21.9 453 n/a 4_updatecdl: 0.1205 0.1373 0.006 0.910 9.3 109.3 21.9 453 n/a 4_nqh: 0.1205 0.1373 0.006 0.910 9.3 109.3 21.9 453 n/a 4_sol: 0.1198 0.1347 0.006 0.910 9.3 109.3 21.5 444 n/a 4_weight: 0.1198 0.1347 0.006 0.910 9.3 109.3 21.5 444 n/a 4_xyzrec: 0.1202 0.1361 0.006 0.948 9.3 109.3 21.5 444 n/a 4_adp: 0.1178 0.1351 0.006 0.948 9.2 105.5 21.2 444 n/a 4_regHadp: 0.1179 0.1351 0.006 0.948 9.2 105.5 21.2 444 n/a 4_occ: 0.1173 0.1347 0.006 0.948 9.2 105.5 21.2 444 n/a 5_bss: 0.1171 0.1352 0.006 0.948 9.2 105.5 21.2 444 n/a 5_settarget: 0.1171 0.1352 0.006 0.948 9.2 105.5 21.2 444 n/a 5_updatecdl: 0.1171 0.1352 0.006 0.948 9.2 105.5 21.2 444 n/a 5_setrh: 0.1172 0.1351 0.006 0.948 9.2 105.5 21.2 444 n/a 5_nqh: 0.1172 0.1351 0.006 0.948 9.2 105.5 21.2 444 n/a 5_sol: 0.1171 0.1324 0.006 0.948 9.2 105.5 21.1 447 n/a 5_weight: 0.1171 0.1324 0.006 0.948 9.2 105.5 21.1 447 n/a 5_xyzrec: 0.1192 0.1343 0.007 1.024 9.2 105.5 21.1 447 n/a 5_adp: 0.1193 0.1340 0.007 1.024 9.2 102.6 21.1 447 n/a 5_regHadp: 0.1193 0.1340 0.007 1.024 9.2 102.6 21.1 447 n/a 5_occ: 0.1188 0.1336 0.007 1.024 9.2 102.6 21.1 447 n/a end: 0.1188 0.1339 0.007 1.024 9.2 102.6 21.1 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8960824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8960824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3900 Refinement macro-cycles (run) : 3255.2800 Write final files (write_after_run_outputs) : 71.0400 Total : 3330.7100 Total CPU time: 56.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:57 PST -0800 (1735452477.79 s) Start R-work = 0.1631, R-free = 0.1800 Final R-work = 0.1188, R-free = 0.1339 =============================================================================== Job complete usr+sys time: 3479.51 seconds wall clock time: 63 minutes 22.25 seconds (3802.25 seconds total)