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_6824987.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.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" } 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: 2.31, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 312.1 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 585 0.92 - 1.18: 1063 1.18 - 1.44: 702 1.44 - 1.70: 781 1.70 - 1.96: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 9 " pdb=" C ILE A 9 " ideal model delta sigma weight residual 1.526 1.308 0.217 1.13e-02 7.83e+03 3.70e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.527 -0.198 1.13e-02 7.83e+03 3.06e+02 bond pdb=" CA PHE A 164 " pdb=" C PHE A 164 " ideal model delta sigma weight residual 1.524 1.748 -0.224 1.29e-02 6.01e+03 3.02e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.671 -0.213 1.28e-02 6.10e+03 2.76e+02 bond pdb=" C ALA A 29 " pdb=" N GLY A 30 " ideal model delta sigma weight residual 1.330 1.131 0.199 1.23e-02 6.61e+03 2.63e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 2984 4.29 - 8.57: 1820 8.57 - 12.86: 780 12.86 - 17.14: 180 17.14 - 21.42: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 187 " pdb=" C LEU A 187 " pdb=" O LEU A 187 " ideal model delta sigma weight residual 121.47 106.45 15.02 1.15e+00 7.56e-01 1.71e+02 angle pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 120.42 106.68 13.74 1.06e+00 8.90e-01 1.68e+02 angle pdb=" O GLY A 100 " pdb=" C GLY A 100 " pdb=" N LEU A 101 " ideal model delta sigma weight residual 123.21 107.82 15.39 1.20e+00 6.94e-01 1.65e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.90 134.44 -13.54 1.07e+00 8.73e-01 1.60e+02 angle pdb=" C ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.23 124.79 -13.56 1.08e+00 8.57e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.85: 944 17.85 - 35.69: 120 35.69 - 53.53: 35 53.53 - 71.37: 10 71.37 - 89.21: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CD2 TYR A 139 " pdb=" CG TYR A 139 " pdb=" CD1 TYR A 139 " pdb=" HD1 TYR A 139 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.286: 132 0.286 - 0.571: 69 0.571 - 0.856: 36 0.856 - 1.141: 5 1.141 - 1.426: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.29 1.43 2.00e-01 2.50e+01 5.08e+01 chirality pdb=" CA SER A 3 " pdb=" N SER A 3 " pdb=" C SER A 3 " pdb=" CB SER A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.012 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.120 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.130 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 164 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.036 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.132 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.085 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 903 2.30 - 2.88: 8054 2.88 - 3.45: 10531 3.45 - 4.03: 15257 4.03 - 4.60: 21875 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.728 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.750 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.776 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.819 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.821 2.100 ... (remaining 56615 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_6824987_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= 0.2599 r_free= 0.1925 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781996 | | target function (ml) not normalized (work): 231756.974713 | | target function (ml) not normalized (free): 11769.389710 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2085 7.0086 4.9316| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1888 4.3568 4.3708| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1606 4.1312 4.1524| | 4: 2.47 - 2.25 1.00 2825 136 0.2345 0.1458 3.8347 3.8329| | 5: 2.25 - 2.09 1.00 2756 127 0.2457 0.1576 3.7972 3.8188| | 6: 2.09 - 1.97 1.00 2846 113 0.2519 0.1581 3.4616 3.4973| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1805 3.1231 3.1853| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1962 3.0507 3.1307| | 9: 1.79 - 1.72 1.00 2745 138 0.2416 0.1862 2.8834 2.9787| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2070 2.7919 2.885| | 11: 1.66 - 1.61 1.00 2740 147 0.2506 0.1729 2.7233 2.7134| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1763 2.6159 2.5907| | 13: 1.56 - 1.52 1.00 2745 130 0.2517 0.1723 2.547 2.5274| | 14: 1.52 - 1.48 1.00 2803 134 0.2582 0.2029 2.5147 2.5825| | 15: 1.48 - 1.45 1.00 2738 128 0.2554 0.1854 2.4198 2.3986| | 16: 1.45 - 1.42 1.00 2756 161 0.2606 0.2180 2.3795 2.4597| | 17: 1.42 - 1.39 1.00 2785 139 0.2648 0.2270 2.3247 2.4418| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2002 2.2632 2.2718| | 19: 1.36 - 1.34 1.00 2807 134 0.2639 0.2351 2.2361 2.2893| | 20: 1.34 - 1.32 1.00 2696 147 0.2634 0.2243 2.1838 2.1951| | 21: 1.32 - 1.30 1.00 2785 112 0.2728 0.2164 2.1618 2.1331| | 22: 1.29 - 1.27 1.00 2704 152 0.2688 0.2612 2.1103 2.2213| | 23: 1.27 - 1.26 1.00 2802 156 0.2827 0.2544 2.1162 2.1747| | 24: 1.26 - 1.24 1.00 2744 132 0.2794 0.2549 2.0652 2.1514| | 25: 1.24 - 1.22 1.00 2734 148 0.2793 0.2388 2.0375 2.0224| | 26: 1.22 - 1.21 1.00 2727 135 0.2830 0.2367 2.0036 2.1124| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2545 2.0008 1.9944| | 28: 1.19 - 1.18 1.00 2671 147 0.2970 0.2934 1.9841 2.0234| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2537 1.9447 2.0112| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2789 1.9333 1.9346| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.01 0.76 0.23 1505.99| | 2: 3.57 - 2.84 2876 122 0.80 26.33 1.27 0.23 1505.99| | 3: 2.84 - 2.48 2833 165 0.74 32.23 1.24 0.24 1247.12| | 4: 2.47 - 2.25 2825 136 0.81 25.57 1.26 0.25 575.30| | 5: 2.25 - 2.09 2756 127 0.77 29.32 1.28 0.25 575.30| | 6: 2.09 - 1.97 2846 113 0.84 22.18 1.29 0.25 311.00| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.28 0.26 85.59| | 8: 1.87 - 1.79 2789 144 0.86 20.38 1.24 0.26 85.59| | 9: 1.79 - 1.72 2745 138 0.89 17.85 1.23 0.26 51.84| | 10: 1.72 - 1.66 2789 158 0.87 19.37 1.22 0.26 45.08| | 11: 1.66 - 1.61 2740 147 0.86 20.56 1.25 0.25 43.46| | 12: 1.61 - 1.56 2787 146 0.89 17.83 1.24 0.25 27.04| | 13: 1.56 - 1.52 2745 130 0.87 19.44 1.24 0.25 27.04| | 14: 1.52 - 1.48 2803 134 0.87 19.83 1.23 0.25 24.48| | 15: 1.48 - 1.45 2738 128 0.87 19.81 1.23 0.25 19.80| | 16: 1.45 - 1.42 2756 161 0.86 20.94 1.23 0.25 19.80| | 17: 1.42 - 1.39 2785 139 0.87 20.59 1.22 0.25 17.18| | 18: 1.39 - 1.36 2741 179 0.86 21.17 1.22 0.25 15.66| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.21 0.25 15.66| | 20: 1.34 - 1.32 2696 147 0.87 20.87 1.21 0.24 13.18| | 21: 1.32 - 1.30 2785 112 0.85 22.27 1.21 0.24 13.00| | 22: 1.29 - 1.27 2704 152 0.85 22.40 1.22 0.24 12.71| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.22 0.24 11.23| | 24: 1.26 - 1.24 2744 132 0.85 22.85 1.22 0.24 11.23| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.20 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 23.72 1.20 0.23 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.21 0.23 9.93| | 28: 1.19 - 1.18 2671 147 0.83 25.08 1.18 0.23 9.26| | 29: 1.18 - 1.16 2800 134 0.83 25.57 1.16 0.23 9.01| | 30: 1.16 - 1.15 2740 148 0.81 26.79 1.14 0.23 9.01| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.01 max = 1505.99 mean = 216.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.36| |phase err.(test): min = 0.00 max = 89.60 mean = 22.26| |-----------------------------------------------------------------------------| ----------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 0.241 1557 Z= 5.406 Angle : 5.285 16.769 2118 Z= 3.659 Chirality : 0.394 1.426 243 Planarity : 0.033 0.126 284 Dihedral : 14.106 89.210 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % 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: -2.33 (0.45), residues: 224 helix: -2.54 (0.38), residues: 101 sheet: -0.64 (0.92), residues: 28 loop : -0.37 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.015 ARG A 98 TYR 0.072 0.026 TYR A 139 PHE 0.125 0.045 PHE A 164 HIS 0.042 0.025 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= 0.2599 r_free= 0.1925 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781996 | | target function (ml) not normalized (work): 231756.974713 | | target function (ml) not normalized (free): 11769.389710 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2558 0.2600 0.1924 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2558 0.2600 0.1924 n_refl.: 87602 remove outliers: r(all,work,free)=0.1969 0.1973 0.1924 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1994 0.1999 0.1940 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1628 0.1740 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1628 0.1740 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 0.3864 386.208 357.795 0.683 1.003 0.412 11.894-9.307 99.02 97 4 0.1821 613.473 595.061 0.929 1.004 0.400 9.237-7.194 100.00 213 7 0.2182 501.745 490.757 0.955 1.004 0.380 7.162-5.571 100.00 427 22 0.2221 376.532 363.088 0.929 1.004 0.310 5.546-4.326 100.00 867 58 0.1283 516.885 512.086 0.961 1.003 0.224 4.315-3.360 100.00 1859 96 0.1129 491.561 488.104 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1447 322.930 319.776 0.997 1.002 0.129 2.608-2.026 99.99 8198 413 0.1335 214.073 211.885 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1634 104.542 103.915 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2051 46.358 45.067 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2565 29.209 27.005 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0470 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1740 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1629 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.665455 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2003.687976 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 0.1214 0.1468 0.0254 0.007 0.9 1.3 0.5 0.0 0 11.833 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.68 2.54 3.013 19.064 2003.688 0.017 12.38 15.38 3.00 2.979 19.409 2003.688 0.016 Individual atomic B min max mean iso aniso Overall: 8.39 118.12 20.75 2.87 0 1785 Protein: 8.39 118.12 17.67 2.87 0 1519 Water: 11.11 115.10 38.61 N/A 0 258 Other: 22.31 34.91 27.87 N/A 0 8 Chain A: 8.39 118.12 20.75 N/A 0 1785 Histogram: Values Number of atoms 8.39 - 19.37 1209 19.37 - 30.34 243 30.34 - 41.31 156 41.31 - 52.28 99 52.28 - 63.26 49 63.26 - 74.23 18 74.23 - 85.20 4 85.20 - 96.18 3 96.18 - 107.15 1 107.15 - 118.12 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1539 r_work=0.1243 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 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 = 0.1242 r_free = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1242 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015464 | | target function (ls_wunit_k1) not normalized (work): 1288.118944 | | target function (ls_wunit_k1) not normalized (free): 115.430118 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1695 0.1694 0.1768 n_refl.: 87593 remove outliers: r(all,work,free)=0.1695 0.1694 0.1768 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1718 0.1717 0.1784 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1253 0.1239 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1252 0.1238 0.1536 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3487 301.594 276.424 0.676 0.925 0.370 11.894-9.307 99.02 97 4 0.1643 479.946 468.694 0.983 0.925 0.363 9.237-7.194 100.00 213 7 0.1839 392.537 387.670 1.029 0.926 0.340 7.162-5.571 100.00 427 22 0.1738 294.577 289.396 1.000 0.926 0.258 5.546-4.326 100.00 867 58 0.0929 404.381 401.730 1.029 0.927 0.214 4.315-3.360 100.00 1859 96 0.0780 384.569 383.662 1.076 0.928 0.200 3.356-2.611 100.00 3867 181 0.1019 252.642 251.955 1.075 0.930 0.120 2.608-2.026 99.99 8198 413 0.0967 167.479 166.957 1.083 0.933 0.000 2.025-1.573 100.00 17313 902 0.1194 81.788 81.997 1.084 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1642 36.268 35.737 1.060 0.947 0.000 1.221-1.150 99.97 13689 708 0.2366 22.851 21.375 1.014 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0528 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1238 r_free=0.1536 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** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1239 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1239 r_free=0.1539 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1248 r_free=0.1534 | n_water=252 | time (s): 25.980 (total time: 28.280) Filter (q & B) r_work=0.1251 r_free=0.1534 | n_water=249 | time (s): 3.740 (total time: 32.020) Compute maps r_work=0.1251 r_free=0.1534 | n_water=249 | time (s): 1.860 (total time: 33.880) Filter (map) r_work=0.1272 r_free=0.1547 | n_water=236 | time (s): 3.920 (total time: 37.800) Find peaks r_work=0.1272 r_free=0.1547 | n_water=236 | time (s): 0.750 (total time: 38.550) Add new water r_work=0.1430 r_free=0.1715 | n_water=458 | time (s): 3.790 (total time: 42.340) Refine new water occ: r_work=0.1339 r_free=0.1578 adp: r_work=0.1255 r_free=0.1532 occ: r_work=0.1270 r_free=0.1522 adp: r_work=0.1233 r_free=0.1511 occ: r_work=0.1238 r_free=0.1493 adp: r_work=0.1228 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1494 r_work=0.1228 r_free=0.1494 | n_water=458 | time (s): 95.710 (total time: 138.050) Filter (q & B) r_work=0.1233 r_free=0.1501 | n_water=436 | time (s): 3.600 (total time: 141.650) Filter (dist only) r_work=0.1233 r_free=0.1501 | n_water=435 | time (s): 44.270 (total time: 185.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.114700 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1376.320053 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1522 0.0294 0.007 0.9 1.9 0.5 0.0 0 12.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.22 2.94 3.745 22.931 1376.320 0.015 12.04 14.88 2.84 4.019 22.814 1376.320 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 113.26 23.07 2.54 199 1763 Protein: 8.73 113.26 17.58 2.54 0 1519 Water: 11.08 73.09 42.10 N/A 199 236 Other: 25.46 37.35 31.09 N/A 0 8 Chain A: 8.73 113.26 20.29 N/A 0 1763 Chain S: 19.62 68.39 47.68 N/A 199 0 Histogram: Values Number of atoms 8.73 - 19.19 1199 19.19 - 29.64 258 29.64 - 40.09 194 40.09 - 50.54 140 50.54 - 60.99 107 60.99 - 71.45 53 71.45 - 81.90 5 81.90 - 92.35 3 92.35 - 102.80 1 102.80 - 113.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1488 r_work=0.1204 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1488 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 = 0.1205 r_free = 0.1485 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1205 r_free= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014038 | | target function (ls_wunit_k1) not normalized (work): 1169.322351 | | target function (ls_wunit_k1) not normalized (free): 103.480949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1205 0.1485 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1570 0.1563 0.1724 n_refl.: 87591 remove outliers: r(all,work,free)=0.1570 0.1563 0.1724 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1572 0.1565 0.1726 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1202 0.1481 n_refl.: 87591 remove outliers: r(all,work,free)=0.1215 0.1201 0.1481 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 0.3223 292.283 282.692 0.625 0.945 0.338 11.894-9.307 99.02 97 4 0.1607 479.946 475.074 0.967 0.945 0.330 9.237-7.194 100.00 213 7 0.1623 392.537 394.543 1.044 0.946 0.280 7.162-5.571 100.00 427 22 0.1511 294.577 290.467 0.999 0.946 0.223 5.546-4.326 100.00 867 58 0.0830 404.381 401.610 1.016 0.947 0.213 4.315-3.360 100.00 1859 96 0.0716 384.569 383.033 1.061 0.947 0.210 3.356-2.611 100.00 3867 181 0.0973 252.642 251.926 1.066 0.948 0.160 2.608-2.026 99.99 8198 413 0.0975 167.479 167.034 1.074 0.950 0.000 2.025-1.573 100.00 17313 902 0.1183 81.788 82.081 1.080 0.953 0.000 1.573-1.221 100.00 36679 1900 0.1606 36.268 35.886 1.065 0.958 0.000 1.221-1.150 99.97 13689 708 0.2335 22.851 21.488 1.019 0.962 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1481 | n_water=435 | time (s): 1.870 (total time: 1.870) Filter (dist) r_work=0.1201 r_free=0.1480 | n_water=433 | time (s): 40.560 (total time: 42.430) Filter (q & B) r_work=0.1201 r_free=0.1480 | n_water=433 | time (s): 1.280 (total time: 43.710) Compute maps r_work=0.1201 r_free=0.1480 | n_water=433 | time (s): 1.590 (total time: 45.300) Filter (map) r_work=0.1235 r_free=0.1486 | n_water=300 | time (s): 3.380 (total time: 48.680) Find peaks r_work=0.1235 r_free=0.1486 | n_water=300 | time (s): 0.700 (total time: 49.380) Add new water r_work=0.1359 r_free=0.1610 | n_water=484 | time (s): 3.430 (total time: 52.810) Refine new water occ: r_work=0.1267 r_free=0.1539 adp: r_work=0.1268 r_free=0.1538 occ: r_work=0.1246 r_free=0.1517 adp: r_work=0.1244 r_free=0.1516 occ: r_work=0.1231 r_free=0.1499 adp: r_work=0.1224 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1496 r_work=0.1224 r_free=0.1496 | n_water=484 | time (s): 212.370 (total time: 265.180) Filter (q & B) r_work=0.1229 r_free=0.1497 | n_water=447 | time (s): 2.600 (total time: 267.780) Filter (dist only) r_work=0.1229 r_free=0.1497 | n_water=447 | time (s): 34.790 (total time: 302.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.054093 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.452279 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1460 0.0228 0.006 0.9 3.5 0.5 0.0 0 1.027 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.60 2.28 3.580 22.035 42.452 3.723 12.25 14.24 1.98 4.129 21.838 42.452 3.658 Individual atomic B min max mean iso aniso Overall: 9.19 108.95 21.62 2.28 212 1762 Protein: 9.19 108.95 17.11 2.28 0 1519 Water: 11.59 71.94 36.83 N/A 212 235 Other: 21.25 33.08 27.53 N/A 0 8 Chain A: 9.19 108.95 19.81 N/A 0 1762 Chain S: 16.80 64.74 36.64 N/A 212 0 Histogram: Values Number of atoms 9.19 - 19.17 1231 19.17 - 29.14 281 29.14 - 39.12 212 39.12 - 49.09 141 49.09 - 59.07 76 59.07 - 69.04 22 69.04 - 79.02 5 79.02 - 89.00 3 89.00 - 98.97 1 98.97 - 108.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1225 r_free=0.1424 r_work=0.1226 r_free=0.1425 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1226 r_free = 0.1425 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1427 target_work(ml) = 3.657 | | 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= 0.1223 r_free= 0.1427 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.657332 | | target function (ml) not normalized (work): 304626.466586 | | target function (ml) not normalized (free): 16080.705791 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1223 0.1427 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1553 0.1550 0.1632 n_refl.: 87588 remove outliers: r(all,work,free)=0.1553 0.1550 0.1632 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1550 0.1547 0.1629 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1215 0.1403 n_refl.: 87588 remove outliers: r(all,work,free)=0.1220 0.1211 0.1403 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4022 282.078 261.479 0.460 1.000 0.295 11.894-9.307 96.08 94 4 0.2480 469.630 457.899 0.849 1.001 0.251 9.237-7.194 98.18 209 7 0.2366 384.062 386.730 0.944 1.001 0.205 7.162-5.571 100.00 427 22 0.2118 294.577 284.544 0.910 1.002 0.174 5.546-4.326 100.00 867 58 0.1114 404.381 399.674 0.952 1.002 0.160 4.315-3.360 100.00 1859 96 0.0946 384.569 381.937 0.993 1.002 0.157 3.356-2.611 100.00 3867 181 0.1178 252.642 250.609 1.001 1.001 0.062 2.608-2.026 99.99 8198 413 0.1067 167.479 166.362 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1020 81.788 81.861 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1291 36.268 35.822 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2131 22.851 21.448 0.980 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1211 r_free=0.1403 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=0.1211 r_free=0.1403 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1211 r_free=0.1403 | n_water=447 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1211 r_free=0.1404 | n_water=446 | time (s): 39.570 (total time: 41.770) Filter (q & B) r_work=0.1211 r_free=0.1402 | n_water=445 | time (s): 3.060 (total time: 44.830) Compute maps r_work=0.1211 r_free=0.1402 | n_water=445 | time (s): 1.580 (total time: 46.410) Filter (map) r_work=0.1227 r_free=0.1388 | n_water=323 | time (s): 3.390 (total time: 49.800) Find peaks r_work=0.1227 r_free=0.1388 | n_water=323 | time (s): 0.450 (total time: 50.250) Add new water r_work=0.1295 r_free=0.1445 | n_water=483 | time (s): 2.400 (total time: 52.650) Refine new water occ: r_work=0.1225 r_free=0.1392 adp: r_work=0.1226 r_free=0.1392 occ: r_work=0.1210 r_free=0.1379 adp: r_work=0.1209 r_free=0.1378 occ: r_work=0.1199 r_free=0.1371 adp: r_work=0.1195 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1368 r_work=0.1195 r_free=0.1368 | n_water=483 | time (s): 158.000 (total time: 210.650) Filter (q & B) r_work=0.1201 r_free=0.1374 | n_water=451 | time (s): 2.520 (total time: 213.170) Filter (dist only) r_work=0.1201 r_free=0.1373 | n_water=450 | time (s): 37.320 (total time: 250.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952134 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.805285 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 0.1204 0.1388 0.0184 0.006 1.0 3.2 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.88 1.84 3.383 21.428 46.805 3.643 11.83 13.77 1.95 3.691 21.340 46.805 3.625 Individual atomic B min max mean iso aniso Overall: 9.28 104.36 21.30 2.14 216 1761 Protein: 9.28 104.36 16.90 2.14 0 1519 Water: 11.45 70.90 36.08 N/A 216 234 Other: 21.75 30.87 26.56 N/A 0 8 Chain A: 9.28 104.36 19.54 N/A 0 1761 Chain S: 16.71 58.43 35.67 N/A 216 0 Histogram: Values Number of atoms 9.28 - 18.78 1223 18.78 - 28.29 282 28.29 - 37.80 218 37.80 - 47.31 136 47.31 - 56.82 77 56.82 - 66.33 27 66.33 - 75.83 9 75.83 - 85.34 2 85.34 - 94.85 1 94.85 - 104.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1378 r_work=0.1183 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1378 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1373 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1180 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623727 | | target function (ml) not normalized (work): 301794.889314 | | target function (ml) not normalized (free): 15947.917092 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1180 0.1373 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1519 0.1518 0.1582 n_refl.: 87579 remove outliers: r(all,work,free)=0.1519 0.1518 0.1582 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1516 0.1514 0.1580 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1179 0.1375 n_refl.: 87579 remove outliers: r(all,work,free)=0.1187 0.1177 0.1375 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 0.4131 281.640 238.890 0.411 1.000 0.298 11.894-9.307 95.10 93 4 0.2398 469.623 451.731 0.833 1.002 0.214 9.237-7.194 97.73 208 7 0.2461 385.139 377.748 0.915 1.002 0.143 7.162-5.571 100.00 427 22 0.2197 294.577 284.561 0.906 1.002 0.129 5.546-4.326 100.00 867 58 0.1156 404.381 399.999 0.950 1.002 0.121 4.315-3.360 100.00 1859 96 0.0940 384.569 381.923 0.993 1.002 0.120 3.356-2.611 100.00 3867 181 0.1152 252.642 250.914 1.003 1.002 0.053 2.608-2.026 99.99 8198 413 0.1013 167.479 166.649 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0963 81.788 82.091 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.268 35.906 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.851 21.481 0.981 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0472 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1177 r_free=0.1375 After: r_work=0.1178 r_free=0.1375 ================================== NQH flips ================================== r_work=0.1178 r_free=0.1375 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=0.1178 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1375 | n_water=450 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1178 r_free=0.1375 | n_water=450 | time (s): 36.470 (total time: 38.670) Filter (q & B) r_work=0.1178 r_free=0.1377 | n_water=448 | time (s): 3.300 (total time: 41.970) Compute maps r_work=0.1178 r_free=0.1377 | n_water=448 | time (s): 1.350 (total time: 43.320) Filter (map) r_work=0.1204 r_free=0.1390 | n_water=333 | time (s): 2.710 (total time: 46.030) Find peaks r_work=0.1204 r_free=0.1390 | n_water=333 | time (s): 0.480 (total time: 46.510) Add new water r_work=0.1250 r_free=0.1417 | n_water=485 | time (s): 2.440 (total time: 48.950) Refine new water occ: r_work=0.1189 r_free=0.1369 adp: r_work=0.1189 r_free=0.1371 occ: r_work=0.1178 r_free=0.1358 adp: r_work=0.1177 r_free=0.1361 occ: r_work=0.1170 r_free=0.1351 adp: r_work=0.1167 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1167 r_free=0.1353 r_work=0.1167 r_free=0.1353 | n_water=485 | time (s): 251.460 (total time: 300.410) Filter (q & B) r_work=0.1175 r_free=0.1357 | n_water=447 | time (s): 2.430 (total time: 302.840) Filter (dist only) r_work=0.1175 r_free=0.1354 | n_water=445 | time (s): 38.990 (total time: 341.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.942400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.517252 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1378 0.0181 0.007 1.1 4.5 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.78 1.81 3.273 21.116 45.517 3.632 12.01 13.82 1.80 3.474 21.045 45.517 3.626 Individual atomic B min max mean iso aniso Overall: 9.24 100.74 21.02 2.02 211 1761 Protein: 9.24 100.74 16.72 2.02 0 1519 Water: 11.54 70.20 35.63 N/A 211 234 Other: 21.05 29.64 25.49 N/A 0 8 Chain A: 9.24 100.74 19.36 N/A 0 1761 Chain S: 16.03 59.71 34.90 N/A 211 0 Histogram: Values Number of atoms 9.24 - 18.39 1209 18.39 - 27.54 288 27.54 - 36.69 211 36.69 - 45.84 140 45.84 - 54.99 78 54.99 - 64.14 31 64.14 - 73.29 11 73.29 - 82.44 1 82.44 - 91.59 1 91.59 - 100.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1382 r_work=0.1202 r_free=0.1382 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1382 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1380 target_work(ml) = 3.625 | | 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= 0.1199 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624853 | | target function (ml) not normalized (work): 301874.129155 | | target function (ml) not normalized (free): 15957.318230 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1430 0.1489 5.6977 5.6629| | 2: 3.57 - 2.84 1.00 2888 124 0.1124 0.1453 5.2078 5.2577| | 3: 2.83 - 2.48 1.00 2820 163 0.1228 0.1256 5.0115 5.0291| | 4: 2.47 - 2.25 1.00 2825 136 0.1022 0.1129 4.7117 4.7621| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1108 4.654 4.7139| | 6: 2.09 - 1.97 1.00 2846 113 0.0967 0.1178 4.3508 4.4799| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1205 4.0756 4.1661| | 8: 1.87 - 1.79 1.00 2789 144 0.1021 0.1240 3.9923 4.0777| | 9: 1.79 - 1.72 1.00 2745 138 0.0950 0.1336 3.7171 3.9134| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1256 3.6325 3.7701| | 11: 1.66 - 1.61 1.00 2712 147 0.0957 0.1074 3.5673 3.609| | 12: 1.61 - 1.56 1.00 2773 144 0.0920 0.1184 3.3472 3.4812| | 13: 1.56 - 1.52 1.00 2745 130 0.0977 0.1063 3.3363 3.4338| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1093 3.2605 3.3398| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1326 3.1719 3.3165| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1261 3.1523 3.2502| | 17: 1.42 - 1.39 1.00 2785 139 0.1123 0.1297 3.1201 3.247| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1390 3.0912 3.2739| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1625 3.0974 3.2831| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1519 3.0953 3.1565| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1624 3.091 3.1632| | 22: 1.29 - 1.27 1.00 2704 152 0.1476 0.1927 3.0914 3.29| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1888 3.1072 3.2186| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1775 3.0976 3.2018| | 25: 1.24 - 1.22 1.00 2733 148 0.1796 0.2335 3.1132 3.3| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1757 3.1283 3.1955| | 27: 1.21 - 1.19 1.00 2814 148 0.2007 0.2098 3.1411 3.1553| | 28: 1.19 - 1.18 1.00 2671 147 0.2147 0.2307 3.1422 3.1661| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2367 3.1298 3.2292| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2476 3.1198 3.1624| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 9.16 1.00 0.97 6378.72| | 2: 3.57 - 2.84 2888 124 0.92 13.43 1.01 0.97 6378.72| | 3: 2.83 - 2.48 2820 163 0.88 17.65 0.98 0.98 5345.78| | 4: 2.47 - 2.25 2825 136 0.91 14.71 1.00 0.98 2682.16| | 5: 2.25 - 2.09 2756 127 0.89 16.93 1.01 0.98 2682.16| | 6: 2.09 - 1.97 2846 113 0.92 13.66 1.02 0.98 1573.78| | 7: 1.97 - 1.87 2787 165 0.94 10.79 1.02 0.98 628.48| | 8: 1.87 - 1.79 2789 144 0.91 14.40 1.00 0.98 628.48| | 9: 1.79 - 1.72 2745 138 0.93 11.34 0.98 0.97 339.81| | 10: 1.72 - 1.66 2831 160 0.93 12.17 0.98 0.97 282.00| | 11: 1.66 - 1.61 2712 147 0.93 12.86 0.98 0.97 269.15| | 12: 1.61 - 1.56 2773 144 0.95 9.57 0.99 0.97 147.91| | 13: 1.56 - 1.52 2745 130 0.94 11.10 1.02 0.97 147.91| | 14: 1.52 - 1.48 2803 134 0.94 11.25 1.02 0.98 132.32| | 15: 1.48 - 1.45 2738 128 0.95 10.41 1.01 0.98 103.77| | 16: 1.45 - 1.42 2756 161 0.94 11.60 1.02 0.98 103.77| | 17: 1.42 - 1.39 2785 139 0.94 11.44 1.01 0.98 94.14| | 18: 1.39 - 1.36 2741 179 0.94 11.84 1.01 0.98 88.57| | 19: 1.36 - 1.34 2807 134 0.94 12.38 1.00 0.98 88.57| | 20: 1.34 - 1.32 2696 147 0.94 12.55 0.99 0.97 83.96| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.99 0.97 83.64| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.96 83.75| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.98 0.95 84.30| | 24: 1.26 - 1.24 2744 132 0.92 15.07 0.97 0.95 84.30| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 85.60| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.94 87.05| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.94 87.05| | 28: 1.19 - 1.18 2671 147 0.88 20.19 1.01 0.93 89.82| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 90.87| | 30: 1.16 - 1.15 2739 148 0.86 21.87 0.98 0.93 90.87| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 83.64 max = 6378.72 mean = 992.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 14.07| |phase err.(test): min = 0.00 max = 89.36 mean = 14.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1199 0.1380 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1519 0.1517 0.1584 n_refl.: 87575 remove outliers: r(all,work,free)=0.1519 0.1517 0.1584 n_refl.: 87575 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1515 0.1582 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1199 0.1382 n_refl.: 87575 remove outliers: r(all,work,free)=0.1207 0.1198 0.1382 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4068 281.640 247.920 0.421 1.000 0.288 11.894-9.307 93.14 91 4 0.2513 469.713 452.542 0.834 1.002 0.216 9.237-7.194 97.73 208 7 0.2605 385.139 377.640 0.909 1.002 0.144 7.162-5.571 100.00 427 22 0.2292 294.577 283.745 0.899 1.002 0.120 5.546-4.326 100.00 867 58 0.1214 404.381 399.821 0.951 1.002 0.113 4.315-3.360 100.00 1859 96 0.0981 384.569 381.944 0.993 1.002 0.107 3.356-2.611 100.00 3867 181 0.1193 252.642 250.632 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1036 167.479 166.556 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.788 82.026 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.268 35.898 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2117 22.851 21.474 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0416 ================= 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 : 0.2599 0.1925 0.082 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1740 0.082 5.285 9.1 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1740 0.082 5.285 9.1 119.5 20.1 258 0.000 1_nqh: 0.1629 0.1739 0.082 5.285 9.1 119.5 20.1 258 0.003 1_weight: 0.1629 0.1739 0.082 5.285 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1468 0.007 0.937 9.1 119.5 20.1 258 0.126 1_adp: 0.1239 0.1539 0.007 0.937 8.4 118.1 20.7 258 0.126 1_regHadp: 0.1243 0.1543 0.007 0.937 8.4 118.1 20.7 258 0.126 1_occ: 0.1242 0.1546 0.007 0.937 8.4 118.1 20.7 258 0.126 2_bss: 0.1238 0.1536 0.007 0.937 8.5 118.3 20.9 258 0.126 2_settarget: 0.1238 0.1536 0.007 0.937 8.5 118.3 20.9 258 0.126 2_updatecdl: 0.1238 0.1536 0.007 0.946 8.5 118.3 20.9 258 0.126 2_nqh: 0.1239 0.1539 0.007 0.946 8.5 118.3 20.9 258 0.126 2_sol: 0.1233 0.1501 0.007 0.946 8.5 118.3 23.3 435 n/a 2_weight: 0.1233 0.1501 0.007 0.946 8.5 118.3 23.3 435 n/a 2_xyzrec: 0.1228 0.1522 0.007 0.877 8.5 118.3 23.3 435 n/a 2_adp: 0.1204 0.1488 0.007 0.877 8.7 113.3 23.1 435 n/a 2_regHadp: 0.1204 0.1488 0.007 0.877 8.7 113.3 23.1 435 n/a 2_occ: 0.1205 0.1485 0.007 0.877 8.7 113.3 23.1 435 n/a 3_bss: 0.1201 0.1481 0.007 0.877 8.7 113.3 23.1 435 n/a 3_settarget: 0.1201 0.1481 0.007 0.877 8.7 113.3 23.1 435 n/a 3_updatecdl: 0.1201 0.1481 0.007 0.877 8.7 113.3 23.1 435 n/a 3_nqh: 0.1201 0.1481 0.007 0.877 8.7 113.3 23.1 435 n/a 3_sol: 0.1229 0.1497 0.007 0.877 8.7 113.3 22.0 447 n/a 3_weight: 0.1229 0.1497 0.007 0.877 8.7 113.3 22.0 447 n/a 3_xyzrec: 0.1232 0.1460 0.006 0.920 8.7 113.3 22.0 447 n/a 3_adp: 0.1225 0.1424 0.006 0.920 9.2 108.9 21.6 447 n/a 3_regHadp: 0.1226 0.1425 0.006 0.920 9.2 108.9 21.6 447 n/a 3_occ: 0.1223 0.1427 0.006 0.920 9.2 108.9 21.6 447 n/a 4_bss: 0.1211 0.1403 0.006 0.920 9.2 108.9 21.6 447 n/a 4_settarget: 0.1211 0.1403 0.006 0.920 9.2 108.9 21.6 447 n/a 4_updatecdl: 0.1211 0.1403 0.006 0.919 9.2 108.9 21.6 447 n/a 4_nqh: 0.1211 0.1403 0.006 0.919 9.2 108.9 21.6 447 n/a 4_sol: 0.1201 0.1373 0.006 0.919 9.2 108.9 21.5 450 n/a 4_weight: 0.1201 0.1373 0.006 0.919 9.2 108.9 21.5 450 n/a 4_xyzrec: 0.1204 0.1388 0.006 0.953 9.2 108.9 21.5 450 n/a 4_adp: 0.1183 0.1378 0.006 0.953 9.3 104.4 21.3 450 n/a 4_regHadp: 0.1183 0.1378 0.006 0.953 9.3 104.4 21.3 450 n/a 4_occ: 0.1180 0.1373 0.006 0.953 9.3 104.4 21.3 450 n/a 5_bss: 0.1177 0.1375 0.006 0.953 9.3 104.3 21.3 450 n/a 5_settarget: 0.1177 0.1375 0.006 0.953 9.3 104.3 21.3 450 n/a 5_updatecdl: 0.1177 0.1375 0.006 0.954 9.3 104.3 21.3 450 n/a 5_setrh: 0.1178 0.1375 0.006 0.954 9.3 104.3 21.3 450 n/a 5_nqh: 0.1178 0.1375 0.006 0.954 9.3 104.3 21.3 450 n/a 5_sol: 0.1175 0.1354 0.006 0.954 9.3 104.3 21.2 445 n/a 5_weight: 0.1175 0.1354 0.006 0.954 9.3 104.3 21.2 445 n/a 5_xyzrec: 0.1197 0.1378 0.007 1.070 9.3 104.3 21.2 445 n/a 5_adp: 0.1201 0.1382 0.007 1.070 9.2 100.7 21.0 445 n/a 5_regHadp: 0.1202 0.1382 0.007 1.070 9.2 100.7 21.0 445 n/a 5_occ: 0.1199 0.1380 0.007 1.070 9.2 100.7 21.0 445 n/a end: 0.1198 0.1382 0.007 1.070 9.2 100.7 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6824987_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6824987_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7100 Refinement macro-cycles (run) : 3482.2500 Write final files (write_after_run_outputs) : 69.9200 Total : 3556.8800 Total CPU time: 59.88 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.84 s) Start R-work = 0.1628, R-free = 0.1740 Final R-work = 0.1198, R-free = 0.1382 =============================================================================== Job complete usr+sys time: 3692.12 seconds wall clock time: 66 minutes 55.67 seconds (4015.67 seconds total)