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_5431713.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_5431713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5431713.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 3 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: 2.01, per 1000 atoms: 0.59 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: 0.92 Conformation dependent library (CDL) restraints added in 314.2 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 481 0.90 - 1.16: 1143 1.16 - 1.41: 623 1.41 - 1.67: 871 1.67 - 1.92: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 8 " pdb=" O VAL A 8 " ideal model delta sigma weight residual 1.237 1.004 0.233 1.08e-02 8.57e+03 4.67e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.706 -0.247 1.20e-02 6.94e+03 4.23e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.526 -0.205 1.00e-02 1.00e+04 4.20e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.123 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.460 1.266 0.194 1.10e-02 8.26e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3189 4.76 - 9.52: 1851 9.52 - 14.29: 626 14.29 - 19.05: 104 19.05 - 23.81: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BASN A 97 " pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 122.12 137.77 -15.65 1.06e+00 8.90e-01 2.18e+02 angle pdb=" N MET A 26 " pdb=" CA MET A 26 " pdb=" C MET A 26 " ideal model delta sigma weight residual 111.28 125.26 -13.98 1.09e+00 8.42e-01 1.64e+02 angle pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" O LEU A 101 " ideal model delta sigma weight residual 121.05 135.61 -14.56 1.14e+00 7.69e-01 1.63e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 111.03 8.26 6.50e-01 2.37e+00 1.62e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.43 -10.20 8.10e-01 1.52e+00 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 935 17.00 - 34.00: 119 34.00 - 51.00: 40 51.00 - 68.00: 16 68.00 - 85.00: 1 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 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.35e+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 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.239: 107 0.239 - 0.476: 85 0.476 - 0.712: 34 0.712 - 0.949: 14 0.949 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA ASP A 55 " pdb=" N ASP A 55 " pdb=" C ASP A 55 " pdb=" CB ASP A 55 " both_signs ideal model delta sigma weight residual False 2.51 3.50 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA LEU A 113 " pdb=" N LEU A 113 " pdb=" C LEU A 113 " pdb=" CB LEU A 113 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.003 2.00e-02 2.50e+03 6.39e-02 1.23e+02 pdb=" CG ATYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.124 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.132 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.032 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.105 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.021 2.00e-02 2.50e+03 5.13e-02 7.88e+01 pdb=" CG PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1083 2.33 - 2.90: 8181 2.90 - 3.46: 10442 3.46 - 4.03: 15295 4.03 - 4.60: 21653 Nonbonded interactions: 56654 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.759 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.794 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.814 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.839 2.450 ... (remaining 56649 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_5431713_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= 0.1904 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789921 | | target function (ml) not normalized (work): 232417.117616 | | target function (ml) not normalized (free): 11754.765529 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3019 0.2068 7.0713 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1746 4.3468 4.3305| | 3: 2.84 - 2.48 1.00 2833 165 0.2354 0.1621 4.1284 4.1435| | 4: 2.47 - 2.25 1.00 2825 136 0.2318 0.1395 3.8294 3.8196| | 5: 2.25 - 2.09 1.00 2756 127 0.2461 0.1522 3.7975 3.8208| | 6: 2.09 - 1.97 1.00 2846 113 0.2576 0.1924 3.4525 3.556| | 7: 1.97 - 1.87 1.00 2787 165 0.2536 0.1834 3.1264 3.2336| | 8: 1.87 - 1.79 1.00 2789 144 0.2514 0.1890 3.0761 3.1099| | 9: 1.79 - 1.72 1.00 2745 138 0.2417 0.1839 2.9133 2.9507| | 10: 1.72 - 1.66 1.00 2789 158 0.2457 0.1957 2.8133 2.9293| | 11: 1.66 - 1.61 1.00 2740 147 0.2451 0.1655 2.7486 2.7321| | 12: 1.61 - 1.56 1.00 2787 146 0.2532 0.1802 2.629 2.571| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1851 2.546 2.5733| | 14: 1.52 - 1.48 1.00 2803 134 0.2558 0.2099 2.4861 2.5753| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.1891 2.415 2.4317| | 16: 1.45 - 1.42 1.00 2756 161 0.2635 0.1982 2.3799 2.3806| | 17: 1.42 - 1.39 1.00 2785 139 0.2701 0.2124 2.3411 2.3793| | 18: 1.39 - 1.36 1.00 2741 179 0.2715 0.2242 2.2745 2.3336| | 19: 1.36 - 1.34 1.00 2807 134 0.2629 0.2152 2.238 2.2853| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2129 2.2027 2.1826| | 21: 1.32 - 1.30 1.00 2785 112 0.2691 0.1981 2.1762 2.0672| | 22: 1.29 - 1.27 1.00 2704 152 0.2740 0.2486 2.1403 2.1873| | 23: 1.27 - 1.26 1.00 2802 156 0.2831 0.2375 2.098 2.1705| | 24: 1.26 - 1.24 1.00 2744 132 0.2844 0.2324 2.0776 2.0903| | 25: 1.24 - 1.22 1.00 2734 148 0.2889 0.2597 2.0503 2.0507| | 26: 1.22 - 1.21 1.00 2727 135 0.2882 0.2319 2.0183 2.087| | 27: 1.21 - 1.19 1.00 2814 148 0.2923 0.2864 1.9981 2.0828| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2737 1.9826 1.9603| | 29: 1.18 - 1.16 1.00 2800 134 0.2966 0.2698 1.9544 2.0017| | 30: 1.16 - 1.15 1.00 2740 148 0.3078 0.2717 1.9302 1.9176| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.79 0.76 0.23 1474.03| | 2: 3.57 - 2.84 2876 122 0.81 25.97 1.27 0.23 1474.03| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.24 1223.05| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.26 0.25 571.69| | 5: 2.25 - 2.09 2756 127 0.77 29.22 1.28 0.25 571.69| | 6: 2.09 - 1.97 2846 113 0.83 22.91 1.30 0.25 313.70| | 7: 1.97 - 1.87 2787 165 0.90 16.84 1.28 0.26 93.67| | 8: 1.87 - 1.79 2789 144 0.85 21.34 1.25 0.26 93.67| | 9: 1.79 - 1.72 2745 138 0.88 18.43 1.23 0.26 55.28| | 10: 1.72 - 1.66 2789 158 0.87 19.72 1.23 0.26 47.59| | 11: 1.66 - 1.61 2740 147 0.86 21.05 1.23 0.26 45.82| | 12: 1.61 - 1.56 2787 146 0.89 17.95 1.23 0.25 27.84| | 13: 1.56 - 1.52 2745 130 0.87 19.86 1.23 0.25 27.84| | 14: 1.52 - 1.48 2803 134 0.87 19.93 1.24 0.25 24.76| | 15: 1.48 - 1.45 2738 128 0.88 19.18 1.24 0.25 19.12| | 16: 1.45 - 1.42 2756 161 0.86 20.75 1.23 0.25 19.12| | 17: 1.42 - 1.39 2785 139 0.88 19.80 1.23 0.25 16.32| | 18: 1.39 - 1.36 2741 179 0.87 20.16 1.24 0.25 14.70| | 19: 1.36 - 1.34 2807 134 0.86 21.12 1.21 0.25 14.70| | 20: 1.34 - 1.32 2696 147 0.88 19.94 1.21 0.25 12.21| | 21: 1.32 - 1.30 2785 112 0.87 20.82 1.19 0.25 12.03| | 22: 1.29 - 1.27 2704 152 0.86 21.58 1.20 0.25 11.80| | 23: 1.27 - 1.26 2802 156 0.86 21.72 1.23 0.24 10.65| | 24: 1.26 - 1.24 2744 132 0.86 22.06 1.22 0.24 10.65| | 25: 1.24 - 1.22 2734 148 0.85 22.85 1.21 0.24 10.12| | 26: 1.22 - 1.21 2727 135 0.85 23.14 1.20 0.24 9.53| | 27: 1.21 - 1.19 2814 148 0.84 23.84 1.20 0.24 9.53| | 28: 1.19 - 1.18 2671 147 0.84 24.34 1.19 0.23 8.68| | 29: 1.18 - 1.16 2800 134 0.84 24.23 1.16 0.23 8.36| | 30: 1.16 - 1.15 2740 148 0.82 25.94 1.16 0.23 8.36| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 8.36 max = 1474.03 mean = 213.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.03| |phase err.(test): min = 0.00 max = 89.73 mean = 21.97| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.412 Angle : 5.242 17.749 2118 Z= 3.615 Chirality : 0.385 1.185 243 Planarity : 0.031 0.077 284 Dihedral : 13.529 84.996 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 29.19 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.46), residues: 224 helix: -3.13 (0.35), residues: 102 sheet: -0.48 (0.95), residues: 28 loop : -0.87 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.017 ARG A 27 TYR 0.110 0.034 TYR A 141 PHE 0.102 0.042 PHE A 162 HIS 0.067 0.029 HIS A 126 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= 0.1904 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789921 | | target function (ml) not normalized (work): 232417.117616 | | target function (ml) not normalized (free): 11754.765529 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2609 0.1905 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2609 0.1905 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1905 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2001 0.2007 0.1919 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1632 0.1735 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1630 0.1735 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 0.3820 386.475 356.575 0.666 1.002 0.401 11.894-9.307 98.04 96 4 0.1716 616.389 589.810 0.916 1.003 0.380 9.237-7.194 100.00 213 7 0.2134 502.092 491.291 0.956 1.004 0.340 7.162-5.571 100.00 427 22 0.2188 376.792 365.014 0.933 1.004 0.320 5.546-4.326 100.00 867 58 0.1289 517.243 511.756 0.960 1.004 0.225 4.315-3.360 100.00 1859 96 0.1115 491.902 488.121 1.001 1.003 0.209 3.356-2.611 100.00 3867 181 0.1448 323.154 320.338 0.997 1.003 0.119 2.608-2.026 99.99 8198 413 0.1324 214.222 212.164 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1656 104.615 104.048 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.390 45.018 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2589 29.229 26.958 0.976 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0475 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1735 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1635 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.084957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2047.957730 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1215 0.1461 0.0246 0.007 0.9 1.6 0.5 0.0 0 12.042 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 14.61 2.46 3.013 19.066 2047.958 0.017 12.43 15.34 2.91 3.234 19.588 2047.958 0.015 Individual atomic B min max mean iso aniso Overall: 8.50 118.55 21.08 2.88 0 1785 Protein: 8.50 118.55 17.95 2.88 0 1519 Water: 11.17 114.55 39.28 N/A 0 258 Other: 23.38 36.63 29.46 N/A 0 8 Chain A: 8.50 118.55 21.08 N/A 0 1785 Histogram: Values Number of atoms 8.50 - 19.50 1201 19.50 - 30.51 236 30.51 - 41.51 160 41.51 - 52.52 104 52.52 - 63.52 55 63.52 - 74.53 16 74.53 - 85.53 6 85.53 - 96.54 4 96.54 - 107.54 0 107.54 - 118.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1535 r_work=0.1248 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1540 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1542 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015281 | | target function (ls_wunit_k1) not normalized (work): 1272.856265 | | target function (ls_wunit_k1) not normalized (free): 112.831911 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1247 0.1542 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1706 0.1705 0.1773 n_refl.: 87592 remove outliers: r(all,work,free)=0.1706 0.1705 0.1773 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1727 0.1726 0.1788 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1536 n_refl.: 87592 remove outliers: r(all,work,free)=0.1259 0.1244 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 95.83 87 5 0.3606 297.933 278.284 0.632 1.003 0.380 11.894-9.307 98.04 96 4 0.1510 479.210 467.673 0.914 1.003 0.380 9.237-7.194 100.00 213 7 0.1810 390.350 385.162 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1731 292.936 287.762 0.924 1.003 0.290 5.546-4.326 100.00 867 58 0.0920 402.129 399.239 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0771 382.428 381.444 0.994 1.003 0.190 3.356-2.611 100.00 3867 181 0.1016 251.235 250.534 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.0976 166.546 165.953 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1216 81.332 81.507 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.066 35.526 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2369 22.724 21.234 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 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 80 GLN A A 144 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1248 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1248 r_free=0.1539 | n_water=258 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1257 r_free=0.1539 | n_water=252 | time (s): 27.690 (total time: 29.980) Filter (q & B) r_work=0.1260 r_free=0.1537 | n_water=249 | time (s): 3.830 (total time: 33.810) Compute maps r_work=0.1260 r_free=0.1537 | n_water=249 | time (s): 1.840 (total time: 35.650) Filter (map) r_work=0.1271 r_free=0.1546 | n_water=237 | time (s): 3.770 (total time: 39.420) Find peaks r_work=0.1271 r_free=0.1546 | n_water=237 | time (s): 0.660 (total time: 40.080) Add new water r_work=0.1421 r_free=0.1684 | n_water=446 | time (s): 3.680 (total time: 43.760) Refine new water occ: r_work=0.1332 r_free=0.1569 adp: r_work=0.1258 r_free=0.1515 occ: r_work=0.1272 r_free=0.1516 adp: r_work=0.1237 r_free=0.1496 occ: r_work=0.1241 r_free=0.1491 adp: r_work=0.1230 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1490 r_work=0.1230 r_free=0.1490 | n_water=446 | time (s): 110.130 (total time: 153.890) Filter (q & B) r_work=0.1237 r_free=0.1493 | n_water=424 | time (s): 3.700 (total time: 157.590) Filter (dist only) r_work=0.1237 r_free=0.1493 | n_water=424 | time (s): 38.460 (total time: 196.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.661697 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.999715 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 0.1514 0.0280 0.007 0.9 1.6 0.5 0.0 0 13.331 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 15.14 2.80 3.799 23.183 1486.000 0.016 12.05 14.91 2.86 4.177 22.990 1486.000 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.45 23.11 2.59 187 1764 Protein: 8.70 114.45 17.71 2.59 0 1519 Water: 11.03 73.06 42.34 N/A 187 237 Other: 24.07 35.60 28.83 N/A 0 8 Chain A: 8.70 114.45 20.41 N/A 0 1764 Chain S: 19.38 70.78 48.58 N/A 187 0 Histogram: Values Number of atoms 8.70 - 19.28 1199 19.28 - 29.85 255 29.85 - 40.42 188 40.42 - 51.00 145 51.00 - 61.57 108 61.57 - 72.15 45 72.15 - 82.72 5 82.72 - 93.30 3 93.30 - 103.87 1 103.87 - 114.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1491 r_work=0.1205 r_free=0.1490 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1490 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1492 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 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= 0.1207 r_free= 0.1492 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014177 | | target function (ls_wunit_k1) not normalized (work): 1180.893170 | | target function (ls_wunit_k1) not normalized (free): 106.018064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1207 0.1492 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1616 0.1612 0.1746 n_refl.: 87591 remove outliers: r(all,work,free)=0.1616 0.1612 0.1746 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1622 0.1617 0.1750 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1204 0.1487 n_refl.: 87591 remove outliers: r(all,work,free)=0.1216 0.1202 0.1487 n_refl.: 87587 ======================== 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 0.3317 290.655 270.175 0.558 1.002 0.332 11.894-9.307 98.04 96 4 0.1559 479.210 475.900 0.924 1.003 0.327 9.237-7.194 100.00 213 7 0.1714 390.350 391.309 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1524 292.936 289.534 0.936 1.003 0.250 5.546-4.326 100.00 867 58 0.0843 402.129 399.461 0.959 1.002 0.227 4.315-3.360 100.00 1859 96 0.0711 382.428 381.615 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0963 251.235 250.376 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0958 166.546 166.188 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.332 81.539 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1624 36.066 35.563 1.017 0.998 0.000 1.221-1.150 99.97 13689 708 0.2344 22.724 21.259 0.976 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0568 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1487 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=0.1202 r_free=0.1487 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1487 | n_water=424 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1202 r_free=0.1487 | n_water=422 | time (s): 39.080 (total time: 40.700) Filter (q & B) r_work=0.1202 r_free=0.1487 | n_water=422 | time (s): 1.200 (total time: 41.900) Compute maps r_work=0.1202 r_free=0.1487 | n_water=422 | time (s): 1.380 (total time: 43.280) Filter (map) r_work=0.1237 r_free=0.1499 | n_water=290 | time (s): 2.700 (total time: 45.980) Find peaks r_work=0.1237 r_free=0.1499 | n_water=290 | time (s): 0.500 (total time: 46.480) Add new water r_work=0.1374 r_free=0.1633 | n_water=502 | time (s): 2.940 (total time: 49.420) Refine new water occ: r_work=0.1272 r_free=0.1537 adp: r_work=0.1273 r_free=0.1539 occ: r_work=0.1248 r_free=0.1511 adp: r_work=0.1246 r_free=0.1512 occ: r_work=0.1230 r_free=0.1485 adp: r_work=0.1224 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1485 r_work=0.1224 r_free=0.1485 | n_water=502 | time (s): 152.880 (total time: 202.300) Filter (q & B) r_work=0.1230 r_free=0.1488 | n_water=458 | time (s): 3.490 (total time: 205.790) Filter (dist only) r_work=0.1230 r_free=0.1487 | n_water=457 | time (s): 41.320 (total time: 247.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.071419 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.456781 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 0.1236 0.1462 0.0226 0.006 0.9 1.9 0.5 0.0 0 1.036 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.62 2.26 3.626 22.189 49.457 3.729 12.17 14.07 1.90 4.145 21.997 49.457 3.652 Individual atomic B min max mean iso aniso Overall: 9.19 109.53 21.75 2.34 222 1762 Protein: 9.19 109.53 17.26 2.34 0 1519 Water: 11.47 72.10 36.60 N/A 222 235 Other: 19.65 31.32 25.74 N/A 0 8 Chain A: 9.19 109.53 19.94 N/A 0 1762 Chain S: 17.16 64.28 36.13 N/A 222 0 Histogram: Values Number of atoms 9.19 - 19.23 1228 19.23 - 29.26 276 29.26 - 39.29 235 39.29 - 49.33 135 49.33 - 59.36 77 59.36 - 69.40 19 69.40 - 79.43 8 79.43 - 89.46 3 89.46 - 99.50 1 99.50 - 109.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1407 r_work=0.1218 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1407 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1406 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649426 | | target function (ml) not normalized (work): 303964.312107 | | target function (ml) not normalized (free): 16055.016993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1211 0.1406 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1534 0.1534 0.1567 n_refl.: 87587 remove outliers: r(all,work,free)=0.1534 0.1534 0.1567 n_refl.: 87587 overall B=-0.00 to atoms: r(all,work,free)=0.1534 0.1534 0.1567 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1201 0.1379 n_refl.: 87587 remove outliers: r(all,work,free)=0.1205 0.1197 0.1379 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4026 287.304 256.714 0.453 1.000 0.320 11.894-9.307 95.10 93 4 0.2443 472.643 452.995 0.862 1.001 0.266 9.237-7.194 97.73 208 7 0.2346 382.994 385.132 0.954 1.001 0.199 7.162-5.571 100.00 427 22 0.2113 292.936 282.737 0.918 1.001 0.172 5.546-4.326 100.00 867 58 0.1095 402.129 397.423 0.961 1.002 0.162 4.315-3.360 100.00 1859 96 0.0914 382.428 379.959 1.002 1.002 0.160 3.356-2.611 100.00 3867 181 0.1148 251.235 249.231 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.1043 166.546 165.634 1.020 1.002 0.000 2.025-1.573 100.00 17313 902 0.1017 81.332 81.488 1.034 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.066 35.633 1.023 1.002 0.000 1.221-1.150 99.97 13689 708 0.2128 22.724 21.254 0.977 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0056 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1379 | n_water=457 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1197 r_free=0.1379 | n_water=456 | time (s): 40.790 (total time: 43.050) Filter (q & B) r_work=0.1197 r_free=0.1379 | n_water=452 | time (s): 2.980 (total time: 46.030) Compute maps r_work=0.1197 r_free=0.1379 | n_water=452 | time (s): 1.240 (total time: 47.270) Filter (map) r_work=0.1219 r_free=0.1387 | n_water=308 | time (s): 2.770 (total time: 50.040) Find peaks r_work=0.1219 r_free=0.1387 | n_water=308 | time (s): 0.570 (total time: 50.610) Add new water r_work=0.1287 r_free=0.1459 | n_water=472 | time (s): 2.750 (total time: 53.360) Refine new water occ: r_work=0.1211 r_free=0.1383 adp: r_work=0.1212 r_free=0.1386 occ: r_work=0.1197 r_free=0.1366 adp: r_work=0.1196 r_free=0.1368 occ: r_work=0.1186 r_free=0.1355 adp: r_work=0.1183 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1356 r_work=0.1183 r_free=0.1356 | n_water=472 | time (s): 115.020 (total time: 168.380) Filter (q & B) r_work=0.1190 r_free=0.1360 | n_water=431 | time (s): 3.090 (total time: 171.470) Filter (dist only) r_work=0.1190 r_free=0.1360 | n_water=430 | time (s): 38.890 (total time: 210.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.909501 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.367235 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 0.1196 0.1372 0.0176 0.006 0.9 1.9 0.5 0.0 0 0.955 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.72 1.76 3.440 21.446 33.367 3.636 11.94 13.70 1.76 3.489 21.420 33.367 3.632 Individual atomic B min max mean iso aniso Overall: 9.28 108.12 21.27 2.24 196 1761 Protein: 9.28 108.12 17.20 2.24 0 1519 Water: 11.60 71.96 35.53 N/A 196 234 Other: 19.30 30.12 25.40 N/A 0 8 Chain A: 9.28 108.12 19.85 N/A 0 1761 Chain S: 16.99 57.34 33.94 N/A 196 0 Histogram: Values Number of atoms 9.28 - 19.16 1235 19.16 - 29.04 280 29.04 - 38.93 213 38.93 - 48.81 128 48.81 - 58.70 68 58.70 - 68.58 19 68.58 - 78.46 9 78.46 - 88.35 2 88.35 - 98.23 1 98.23 - 108.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1370 r_work=0.1195 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1371 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1370 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1191 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.631283 | | target function (ml) not normalized (work): 302416.899229 | | target function (ml) not normalized (free): 15983.784718 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1191 0.1370 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1509 0.1510 0.1540 n_refl.: 87577 remove outliers: r(all,work,free)=0.1509 0.1510 0.1540 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1508 0.1539 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1189 0.1368 n_refl.: 87577 remove outliers: r(all,work,free)=0.1196 0.1187 0.1368 n_refl.: 87572 ======================== 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 0.3907 285.185 252.974 0.445 1.000 0.304 11.894-9.307 93.14 91 4 0.2320 470.146 443.132 0.843 1.001 0.300 9.237-7.194 97.27 207 7 0.2476 382.522 377.481 0.913 1.001 0.155 7.162-5.571 100.00 427 22 0.2170 292.936 282.080 0.904 1.002 0.130 5.546-4.326 100.00 867 58 0.1118 402.129 397.598 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0945 382.428 379.679 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1144 251.235 249.570 1.001 1.002 0.090 2.608-2.026 99.99 8198 413 0.1028 166.546 165.739 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.0998 81.332 81.648 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.066 35.688 1.017 1.001 0.000 1.221-1.150 99.97 13689 708 0.2124 22.724 21.307 0.973 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0248 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1368 After: r_work=0.1188 r_free=0.1368 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1368 | n_water=430 | time (s): 1.770 (total time: 1.770) Filter (dist) r_work=0.1188 r_free=0.1368 | n_water=430 | time (s): 34.100 (total time: 35.870) Filter (q & B) r_work=0.1189 r_free=0.1368 | n_water=425 | time (s): 3.170 (total time: 39.040) Compute maps r_work=0.1189 r_free=0.1368 | n_water=425 | time (s): 1.640 (total time: 40.680) Filter (map) r_work=0.1212 r_free=0.1389 | n_water=319 | time (s): 3.020 (total time: 43.700) Find peaks r_work=0.1212 r_free=0.1389 | n_water=319 | time (s): 0.560 (total time: 44.260) Add new water r_work=0.1268 r_free=0.1441 | n_water=489 | time (s): 2.450 (total time: 46.710) Refine new water occ: r_work=0.1199 r_free=0.1370 adp: r_work=0.1199 r_free=0.1372 occ: r_work=0.1186 r_free=0.1356 adp: r_work=0.1185 r_free=0.1358 occ: r_work=0.1177 r_free=0.1345 adp: r_work=0.1174 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1174 r_free=0.1346 r_work=0.1174 r_free=0.1346 | n_water=489 | time (s): 174.080 (total time: 220.790) Filter (q & B) r_work=0.1184 r_free=0.1349 | n_water=447 | time (s): 2.980 (total time: 223.770) Filter (dist only) r_work=0.1183 r_free=0.1348 | n_water=445 | time (s): 38.770 (total time: 262.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.981314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.822057 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 0.1205 0.1376 0.0172 0.006 1.0 2.9 0.5 0.0 0 0.991 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.76 1.72 3.393 21.421 35.822 3.637 11.99 13.81 1.82 3.630 21.336 35.822 3.632 Individual atomic B min max mean iso aniso Overall: 9.28 103.99 21.18 2.10 212 1760 Protein: 9.28 103.99 17.01 2.10 0 1519 Water: 11.52 71.41 35.34 N/A 212 233 Other: 19.43 28.73 24.77 N/A 0 8 Chain A: 9.28 103.99 19.64 N/A 0 1760 Chain S: 16.47 57.34 34.02 N/A 212 0 Histogram: Values Number of atoms 9.28 - 18.75 1224 18.75 - 28.22 286 28.22 - 37.69 214 37.69 - 47.16 131 47.16 - 56.63 80 56.63 - 66.11 21 66.11 - 75.58 11 75.58 - 85.05 2 85.05 - 94.52 1 94.52 - 103.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1381 r_work=0.1200 r_free=0.1381 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1381 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1370 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87572 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629629 | | target function (ml) not normalized (work): 302260.990545 | | target function (ml) not normalized (free): 15970.062702 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2914 171 0.1361 0.1383 5.6221 5.612| | 2: 3.57 - 2.84 1.00 2888 124 0.1111 0.1442 5.184 5.2535| | 3: 2.83 - 2.48 1.00 2820 163 0.1219 0.1288 4.9957 5.0101| | 4: 2.47 - 2.25 1.00 2825 136 0.1017 0.1135 4.6929 4.7573| | 5: 2.25 - 2.09 1.00 2756 127 0.0985 0.1074 4.6384 4.702| | 6: 2.09 - 1.97 1.00 2846 113 0.0984 0.1185 4.3532 4.4731| | 7: 1.97 - 1.87 1.00 2787 165 0.0991 0.1229 4.0733 4.1971| | 8: 1.87 - 1.79 1.00 2789 144 0.1043 0.1266 3.9969 4.0941| | 9: 1.79 - 1.72 1.00 2745 138 0.0977 0.1252 3.7296 3.8921| | 10: 1.72 - 1.66 1.00 2831 160 0.1029 0.1293 3.6559 3.8042| | 11: 1.66 - 1.61 1.00 2712 147 0.0987 0.1160 3.587 3.6428| | 12: 1.61 - 1.56 1.00 2773 144 0.0952 0.1194 3.3787 3.4875| | 13: 1.56 - 1.52 1.00 2745 130 0.1012 0.1092 3.365 3.4413| | 14: 1.52 - 1.48 1.00 2803 134 0.1026 0.1180 3.2871 3.3711| | 15: 1.48 - 1.45 1.00 2738 128 0.1065 0.1442 3.2048 3.3838| | 16: 1.45 - 1.42 1.00 2756 161 0.1108 0.1267 3.1807 3.2592| | 17: 1.42 - 1.39 1.00 2785 139 0.1153 0.1348 3.1413 3.2576| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1416 3.1118 3.2758| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1640 3.1141 3.2971| | 20: 1.34 - 1.32 1.00 2696 147 0.1341 0.1542 3.1003 3.169| | 21: 1.32 - 1.30 1.00 2785 112 0.1440 0.1614 3.0996 3.1613| | 22: 1.29 - 1.27 1.00 2704 152 0.1508 0.1970 3.098 3.286| | 23: 1.27 - 1.26 1.00 2802 156 0.1605 0.1875 3.1133 3.2109| | 24: 1.26 - 1.24 1.00 2744 132 0.1661 0.1758 3.1052 3.1854| | 25: 1.24 - 1.22 1.00 2733 148 0.1820 0.2361 3.1153 3.2913| | 26: 1.22 - 1.21 1.00 2727 135 0.1878 0.1791 3.1293 3.2068| | 27: 1.21 - 1.19 1.00 2814 148 0.2029 0.2088 3.1443 3.1435| | 28: 1.19 - 1.18 1.00 2671 147 0.2161 0.2292 3.142 3.1501| | 29: 1.18 - 1.16 1.00 2800 134 0.2229 0.2377 3.1285 3.2205| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2479 3.1157 3.1664| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2914 171 0.95 8.93 1.00 0.98 6048.72| | 2: 3.57 - 2.84 2888 124 0.92 13.05 1.01 0.98 6048.72| | 3: 2.83 - 2.48 2820 163 0.89 17.17 0.98 0.98 5076.91| | 4: 2.47 - 2.25 2825 136 0.91 14.36 1.00 0.98 2570.91| | 5: 2.25 - 2.09 2756 127 0.90 16.58 1.01 0.98 2570.91| | 6: 2.09 - 1.97 2846 113 0.92 13.58 1.02 0.98 1523.63| | 7: 1.97 - 1.87 2787 165 0.94 10.90 1.02 0.97 630.44| | 8: 1.87 - 1.79 2789 144 0.91 14.52 0.99 0.97 630.44| | 9: 1.79 - 1.72 2745 138 0.93 11.64 0.98 0.97 347.79| | 10: 1.72 - 1.66 2831 160 0.93 12.53 0.97 0.97 291.19| | 11: 1.66 - 1.61 2712 147 0.92 13.22 0.98 0.97 278.22| | 12: 1.61 - 1.56 2773 144 0.95 9.90 0.99 0.97 155.89| | 13: 1.56 - 1.52 2745 130 0.94 11.57 1.02 0.97 155.89| | 14: 1.52 - 1.48 2803 134 0.94 11.78 1.02 0.98 139.53| | 15: 1.48 - 1.45 2738 128 0.95 10.92 1.01 0.98 109.58| | 16: 1.45 - 1.42 2756 161 0.94 12.14 1.02 0.98 109.58| | 17: 1.42 - 1.39 2785 139 0.94 11.84 1.01 0.98 98.18| | 18: 1.39 - 1.36 2741 179 0.94 12.26 1.01 0.98 91.59| | 19: 1.36 - 1.34 2807 134 0.94 12.76 1.00 0.98 91.59| | 20: 1.34 - 1.32 2696 147 0.94 12.84 0.99 0.96 85.29| | 21: 1.32 - 1.30 2785 112 0.93 13.76 0.98 0.96 84.85| | 22: 1.29 - 1.27 2704 152 0.93 14.23 0.98 0.96 84.74| | 23: 1.27 - 1.26 2802 156 0.92 15.06 0.97 0.94 84.18| | 24: 1.26 - 1.24 2744 132 0.92 15.18 0.96 0.94 84.18| | 25: 1.24 - 1.22 2733 148 0.91 16.48 0.96 0.94 85.17| | 26: 1.22 - 1.21 2727 135 0.90 18.18 1.02 0.93 86.26| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.26| | 28: 1.19 - 1.18 2671 147 0.88 20.17 1.01 0.93 88.49| | 29: 1.18 - 1.16 2800 134 0.88 20.40 0.99 0.93 89.33| | 30: 1.16 - 1.15 2739 148 0.87 21.79 0.98 0.93 89.33| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 84.18 max = 6048.72 mean = 953.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.20| |phase err.(test): min = 0.00 max = 89.46 mean = 14.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1196 0.1370 n_refl.: 87572 re-set all scales: r(all,work,free)=0.1509 0.1507 0.1583 n_refl.: 87572 remove outliers: r(all,work,free)=0.1509 0.1507 0.1583 n_refl.: 87572 overall B=-0.00 to atoms: r(all,work,free)=0.1508 0.1506 0.1583 n_refl.: 87572 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1196 0.1372 n_refl.: 87572 remove outliers: r(all,work,free)=0.1204 0.1196 0.1372 n_refl.: 87572 ======================== 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 0.3911 285.185 251.124 0.440 0.999 0.294 11.894-9.307 93.14 91 4 0.2293 470.146 459.023 0.875 1.001 0.290 9.237-7.194 97.27 207 7 0.2458 382.522 375.848 0.914 1.001 0.130 7.162-5.571 100.00 427 22 0.2175 292.936 282.405 0.912 1.001 0.130 5.546-4.326 100.00 867 58 0.1129 402.129 397.787 0.961 1.002 0.130 4.315-3.360 100.00 1859 96 0.0975 382.428 379.736 1.006 1.002 0.130 3.356-2.611 100.00 3867 181 0.1171 251.235 249.264 1.010 1.001 0.062 2.608-2.026 99.99 8198 413 0.1034 166.546 165.610 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0995 81.332 81.581 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.066 35.691 1.027 0.999 0.000 1.221-1.150 99.97 13689 708 0.2130 22.724 21.317 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0149 ================= 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 0.1904 0.082 5.242 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1735 0.082 5.242 9.1 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1735 0.082 5.242 9.1 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1739 0.082 5.242 9.1 119.5 20.1 258 0.010 1_weight: 0.1635 0.1739 0.082 5.242 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1215 0.1461 0.007 0.935 9.1 119.5 20.1 258 0.133 1_adp: 0.1243 0.1535 0.007 0.935 8.5 118.5 21.1 258 0.133 1_regHadp: 0.1248 0.1540 0.007 0.935 8.5 118.5 21.1 258 0.133 1_occ: 0.1247 0.1542 0.007 0.935 8.5 118.5 21.1 258 0.133 2_bss: 0.1244 0.1536 0.007 0.935 8.6 118.7 21.2 258 0.133 2_settarget: 0.1244 0.1536 0.007 0.935 8.6 118.7 21.2 258 0.133 2_updatecdl: 0.1244 0.1536 0.007 0.950 8.6 118.7 21.2 258 0.133 2_nqh: 0.1248 0.1539 0.007 0.950 8.6 118.7 21.2 258 0.127 2_sol: 0.1237 0.1493 0.007 0.950 8.6 118.7 23.5 424 n/a 2_weight: 0.1237 0.1493 0.007 0.950 8.6 118.7 23.5 424 n/a 2_xyzrec: 0.1234 0.1514 0.007 0.886 8.6 118.7 23.5 424 n/a 2_adp: 0.1205 0.1491 0.007 0.886 8.7 114.4 23.1 424 n/a 2_regHadp: 0.1205 0.1490 0.007 0.886 8.7 114.4 23.1 424 n/a 2_occ: 0.1207 0.1492 0.007 0.886 8.7 114.4 23.1 424 n/a 3_bss: 0.1202 0.1487 0.007 0.886 8.7 114.5 23.1 424 n/a 3_settarget: 0.1202 0.1487 0.007 0.886 8.7 114.5 23.1 424 n/a 3_updatecdl: 0.1202 0.1487 0.007 0.888 8.7 114.5 23.1 424 n/a 3_nqh: 0.1202 0.1487 0.007 0.888 8.7 114.5 23.1 424 n/a 3_sol: 0.1230 0.1487 0.007 0.888 8.7 114.5 22.1 457 n/a 3_weight: 0.1230 0.1487 0.007 0.888 8.7 114.5 22.1 457 n/a 3_xyzrec: 0.1236 0.1462 0.006 0.921 8.7 114.5 22.1 457 n/a 3_adp: 0.1217 0.1407 0.006 0.921 9.2 109.5 21.7 457 n/a 3_regHadp: 0.1218 0.1407 0.006 0.921 9.2 109.5 21.7 457 n/a 3_occ: 0.1211 0.1406 0.006 0.921 9.2 109.5 21.7 457 n/a 4_bss: 0.1197 0.1379 0.006 0.921 9.2 109.5 21.7 457 n/a 4_settarget: 0.1197 0.1379 0.006 0.921 9.2 109.5 21.7 457 n/a 4_updatecdl: 0.1197 0.1379 0.006 0.920 9.2 109.5 21.7 457 n/a 4_nqh: 0.1197 0.1379 0.006 0.920 9.2 109.5 21.7 457 n/a 4_sol: 0.1190 0.1360 0.006 0.920 9.2 109.5 21.3 430 n/a 4_weight: 0.1190 0.1360 0.006 0.920 9.2 109.5 21.3 430 n/a 4_xyzrec: 0.1196 0.1372 0.006 0.944 9.2 109.5 21.3 430 n/a 4_adp: 0.1194 0.1370 0.006 0.944 9.3 108.1 21.3 430 n/a 4_regHadp: 0.1195 0.1371 0.006 0.944 9.3 108.1 21.3 430 n/a 4_occ: 0.1191 0.1370 0.006 0.944 9.3 108.1 21.3 430 n/a 5_bss: 0.1187 0.1368 0.006 0.944 9.3 108.1 21.3 430 n/a 5_settarget: 0.1187 0.1368 0.006 0.944 9.3 108.1 21.3 430 n/a 5_updatecdl: 0.1187 0.1368 0.006 0.946 9.3 108.1 21.3 430 n/a 5_setrh: 0.1188 0.1368 0.006 0.946 9.3 108.1 21.3 430 n/a 5_nqh: 0.1188 0.1368 0.006 0.946 9.3 108.1 21.3 430 n/a 5_sol: 0.1183 0.1348 0.006 0.946 9.3 108.1 21.3 445 n/a 5_weight: 0.1183 0.1348 0.006 0.946 9.3 108.1 21.3 445 n/a 5_xyzrec: 0.1205 0.1376 0.006 1.011 9.3 108.1 21.3 445 n/a 5_adp: 0.1199 0.1381 0.006 1.011 9.3 104.0 21.2 445 n/a 5_regHadp: 0.1200 0.1381 0.006 1.011 9.3 104.0 21.2 445 n/a 5_occ: 0.1196 0.1370 0.006 1.011 9.3 104.0 21.2 445 n/a end: 0.1196 0.1372 0.006 1.011 9.3 104.0 21.2 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5431713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5431713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9100 Refinement macro-cycles (run) : 3277.9100 Write final files (write_after_run_outputs) : 77.4200 Total : 3360.2400 Total CPU time: 56.61 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:07:35 PST -0800 (1735452455.82 s) Start R-work = 0.1630, R-free = 0.1735 Final R-work = 0.1196, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3522.73 seconds wall clock time: 63 minutes 14.16 seconds (3794.16 seconds total)