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_6218374.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_6218374.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6218374.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 =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.30, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 357.0 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 - 0.91: 534 0.91 - 1.17: 1108 1.17 - 1.42: 643 1.42 - 1.68: 837 1.68 - 1.94: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.686 -0.227 1.25e-02 6.40e+03 3.31e+02 bond pdb=" C PRO A 73 " pdb=" O PRO A 73 " ideal model delta sigma weight residual 1.232 0.999 0.232 1.31e-02 5.83e+03 3.14e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.049 0.187 1.08e-02 8.57e+03 2.99e+02 bond pdb=" CA VAL A 8 " pdb=" CB VAL A 8 " ideal model delta sigma weight residual 1.537 1.745 -0.208 1.26e-02 6.30e+03 2.72e+02 bond pdb=" N ALA A 6 " pdb=" CA ALA A 6 " ideal model delta sigma weight residual 1.455 1.657 -0.202 1.25e-02 6.40e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 3130 4.60 - 9.21: 1832 9.21 - 13.81: 657 13.81 - 18.41: 147 18.41 - 23.02: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.15 15.62 1.00e+00 1.00e+00 2.44e+02 angle pdb=" O THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " ideal model delta sigma weight residual 122.92 106.88 16.04 1.17e+00 7.31e-01 1.88e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 128.25 -13.50 9.90e-01 1.02e+00 1.86e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.15 137.42 -15.27 1.14e+00 7.69e-01 1.79e+02 angle pdb=" CA GLY A 100 " pdb=" C GLY A 100 " pdb=" O GLY A 100 " ideal model delta sigma weight residual 121.23 135.40 -14.17 1.08e+00 8.57e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 930 16.69 - 33.37: 123 33.37 - 50.05: 40 50.05 - 66.73: 15 66.73 - 83.41: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+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 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.270: 112 0.270 - 0.538: 96 0.538 - 0.806: 26 0.806 - 1.074: 7 1.074 - 1.342: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.78 -1.34 2.00e-01 2.50e+01 4.50e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA GLU A 176 " pdb=" N GLU A 176 " pdb=" C GLU A 176 " pdb=" CB GLU A 176 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.037 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.066 2.00e-02 2.50e+03 5.74e-02 9.88e+01 pdb=" CG PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.120 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.065 2.00e-02 2.50e+03 4.96e-02 7.37e+01 pdb=" CG TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.089 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 952 2.31 - 2.88: 8002 2.88 - 3.45: 10574 3.45 - 4.03: 15252 4.03 - 4.60: 21810 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.733 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.828 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.834 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.834 2.450 nonbonded pdb=" HD3 ARG A 28 " pdb="HH11 ARG A 28 " model vdw 1.837 2.270 ... (remaining 56585 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_6218374_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1966 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788164 | | target function (ml) not normalized (work): 232270.773334 | | target function (ml) not normalized (free): 11796.557822 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3016 0.2145 6.9974 4.9515| | 2: 3.57 - 2.84 1.00 2876 122 0.2462 0.1819 4.3578 4.3437| | 3: 2.84 - 2.48 1.00 2833 165 0.2329 0.1822 4.1376 4.1862| | 4: 2.47 - 2.25 1.00 2825 136 0.2364 0.1435 3.8416 3.8287| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1482 3.8106 3.8152| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1723 3.4625 3.5781| | 7: 1.97 - 1.87 1.00 2787 165 0.2546 0.1747 3.146 3.2049| | 8: 1.87 - 1.79 1.00 2789 144 0.2452 0.1989 3.0554 3.1335| | 9: 1.79 - 1.72 1.00 2745 138 0.2376 0.2041 2.9098 2.9973| | 10: 1.72 - 1.66 1.00 2789 158 0.2385 0.1931 2.7937 2.8511| | 11: 1.66 - 1.61 1.00 2740 147 0.2516 0.1953 2.7536 2.7618| | 12: 1.61 - 1.56 1.00 2787 146 0.2502 0.1946 2.6255 2.6039| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1839 2.5856 2.5926| | 14: 1.52 - 1.48 1.00 2803 134 0.2553 0.1863 2.4918 2.5103| | 15: 1.48 - 1.45 1.00 2738 128 0.2604 0.2197 2.4076 2.4698| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2196 2.3787 2.4215| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.1947 2.3277 2.3273| | 18: 1.39 - 1.36 1.00 2741 179 0.2708 0.2128 2.2954 2.2801| | 19: 1.36 - 1.34 1.00 2807 134 0.2699 0.2323 2.2518 2.2739| | 20: 1.34 - 1.32 1.00 2696 147 0.2673 0.2445 2.1811 2.2617| | 21: 1.32 - 1.30 1.00 2785 112 0.2702 0.1982 2.1393 2.0954| | 22: 1.29 - 1.27 1.00 2704 152 0.2741 0.2700 2.1239 2.1927| | 23: 1.27 - 1.26 1.00 2802 156 0.2717 0.2352 2.0875 2.1451| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2505 2.0745 2.1127| | 25: 1.24 - 1.22 1.00 2734 148 0.2893 0.2609 2.0558 2.1359| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2271 2.011 2.0853| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2792 2.0064 2.0471| | 28: 1.19 - 1.18 1.00 2671 147 0.2991 0.2826 1.9809 1.9903| | 29: 1.18 - 1.16 1.00 2800 134 0.2977 0.2830 1.9549 2.0665| | 30: 1.16 - 1.15 1.00 2740 148 0.3104 0.2822 1.9466 1.9565| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.98 0.76 0.23 1517.78| | 2: 3.57 - 2.84 2876 122 0.80 26.51 1.28 0.23 1517.78| | 3: 2.84 - 2.48 2833 165 0.74 32.29 1.24 0.23 1258.41| | 4: 2.47 - 2.25 2825 136 0.81 25.97 1.26 0.25 585.32| | 5: 2.25 - 2.09 2756 127 0.77 29.67 1.28 0.25 585.32| | 6: 2.09 - 1.97 2846 113 0.83 23.05 1.29 0.25 319.65| | 7: 1.97 - 1.87 2787 165 0.90 16.60 1.28 0.26 93.08| | 8: 1.87 - 1.79 2789 144 0.85 21.37 1.25 0.26 93.08| | 9: 1.79 - 1.72 2745 138 0.88 18.44 1.23 0.26 55.44| | 10: 1.72 - 1.66 2789 158 0.87 19.97 1.22 0.26 47.90| | 11: 1.66 - 1.61 2740 147 0.86 21.16 1.24 0.26 46.18| | 12: 1.61 - 1.56 2787 146 0.89 18.15 1.23 0.25 28.70| | 13: 1.56 - 1.52 2745 130 0.87 19.82 1.23 0.25 28.70| | 14: 1.52 - 1.48 2803 134 0.87 20.00 1.23 0.25 25.56| | 15: 1.48 - 1.45 2738 128 0.88 19.57 1.23 0.25 19.82| | 16: 1.45 - 1.42 2756 161 0.86 20.95 1.24 0.25 19.82| | 17: 1.42 - 1.39 2785 139 0.87 20.11 1.23 0.25 16.75| | 18: 1.39 - 1.36 2741 179 0.87 20.42 1.22 0.25 14.97| | 19: 1.36 - 1.34 2807 134 0.86 21.14 1.22 0.25 14.97| | 20: 1.34 - 1.32 2696 147 0.87 20.94 1.21 0.25 12.67| | 21: 1.32 - 1.30 2785 112 0.86 21.93 1.21 0.25 12.51| | 22: 1.29 - 1.27 2704 152 0.86 22.12 1.21 0.24 12.27| | 23: 1.27 - 1.26 2802 156 0.86 21.76 1.22 0.24 11.03| | 24: 1.26 - 1.24 2744 132 0.85 22.77 1.21 0.24 11.03| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.21 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 24.35 1.20 0.23 10.10| | 27: 1.21 - 1.19 2814 148 0.83 24.93 1.20 0.23 10.10| | 28: 1.19 - 1.18 2671 147 0.82 25.59 1.19 0.23 9.57| | 29: 1.18 - 1.16 2800 134 0.82 25.76 1.17 0.23 9.37| | 30: 1.16 - 1.15 2740 148 0.80 27.43 1.16 0.23 9.37| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.37 max = 1517.78 mean = 219.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.52| |phase err.(test): min = 0.00 max = 89.85 mean = 22.56| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.239 1557 Z= 5.325 Angle : 5.304 16.901 2118 Z= 3.669 Chirality : 0.395 1.342 243 Planarity : 0.032 0.089 284 Dihedral : 13.779 83.411 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.11 % 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: -2.32 (0.48), residues: 224 helix: -2.65 (0.40), residues: 103 sheet: 0.21 (0.88), residues: 28 loop : -0.45 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.020 ARG A 48 TYR 0.089 0.035 TYR A 139 PHE 0.077 0.029 PHE A 162 HIS 0.060 0.028 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= 0.2606 r_free= 0.1966 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788164 | | target function (ml) not normalized (work): 232270.773334 | | target function (ml) not normalized (free): 11796.557822 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1967 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1967 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1967 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2009 0.1981 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1639 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1639 0.1785 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 0.3817 386.399 360.761 0.680 1.002 0.408 11.894-9.307 99.02 97 4 0.1799 613.776 593.996 0.926 1.003 0.390 9.237-7.194 100.00 213 7 0.2183 501.993 491.615 0.957 1.003 0.350 7.162-5.571 100.00 427 22 0.2213 376.718 364.077 0.940 1.003 0.320 5.546-4.326 100.00 867 58 0.1306 517.141 511.256 0.958 1.003 0.214 4.315-3.360 100.00 1859 96 0.1159 491.804 487.639 1.005 1.003 0.158 3.356-2.611 100.00 3867 181 0.1438 323.090 320.012 0.998 1.002 0.119 2.608-2.026 99.99 8198 413 0.1356 214.179 212.045 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.594 104.029 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.381 45.044 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2586 29.223 26.931 0.979 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.097358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2030.263708 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 0.1469 0.0256 0.008 1.0 1.0 0.5 0.0 0 13.049 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 14.69 2.56 3.013 19.055 2030.264 0.017 12.47 15.48 3.01 3.388 19.669 2030.264 0.016 Individual atomic B min max mean iso aniso Overall: 8.75 118.59 21.24 2.90 0 1785 Protein: 8.75 118.59 18.04 2.90 0 1519 Water: 11.30 114.50 39.83 N/A 0 258 Other: 23.53 38.12 30.06 N/A 0 8 Chain A: 8.75 118.59 21.24 N/A 0 1785 Histogram: Values Number of atoms 8.75 - 19.74 1208 19.74 - 30.72 227 30.72 - 41.70 157 41.70 - 52.69 103 52.69 - 63.67 55 63.67 - 74.66 19 74.66 - 85.64 9 85.64 - 96.62 2 96.62 - 107.61 2 107.61 - 118.59 3 =========================== Idealize ADP of riding H ========================== r_work=0.1247 r_free=0.1548 r_work=0.1251 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1553 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 = 0.1251 r_free = 0.1556 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1251 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015456 | | target function (ls_wunit_k1) not normalized (work): 1287.431297 | | target function (ls_wunit_k1) not normalized (free): 113.888454 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1266 0.1251 0.1556 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1708 0.1707 0.1778 n_refl.: 87593 remove outliers: r(all,work,free)=0.1708 0.1707 0.1778 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1729 0.1729 0.1792 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1264 0.1249 0.1548 n_refl.: 87593 remove outliers: r(all,work,free)=0.1263 0.1249 0.1548 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3584 298.421 279.038 0.629 1.002 0.372 11.894-9.307 99.02 97 4 0.1637 478.053 466.290 0.904 1.003 0.367 9.237-7.194 100.00 213 7 0.1824 390.989 385.807 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1698 293.415 288.472 0.929 1.003 0.280 5.546-4.326 100.00 867 58 0.0906 402.787 400.137 0.946 1.003 0.194 4.315-3.360 100.00 1859 96 0.0767 383.053 382.049 0.995 1.002 0.170 3.356-2.611 100.00 3867 181 0.1018 251.646 250.928 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0984 166.818 166.190 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1226 81.465 81.611 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1663 36.125 35.583 1.007 0.997 0.000 1.221-1.150 99.97 13689 708 0.2366 22.761 21.268 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0505 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1249 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1249 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1548 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1255 r_free=0.1543 | n_water=254 | time (s): 25.870 (total time: 28.240) Filter (q & B) r_work=0.1258 r_free=0.1542 | n_water=251 | time (s): 3.770 (total time: 32.010) Compute maps r_work=0.1258 r_free=0.1542 | n_water=251 | time (s): 1.820 (total time: 33.830) Filter (map) r_work=0.1277 r_free=0.1550 | n_water=238 | time (s): 3.790 (total time: 37.620) Find peaks r_work=0.1277 r_free=0.1550 | n_water=238 | time (s): 0.670 (total time: 38.290) Add new water r_work=0.1425 r_free=0.1693 | n_water=452 | time (s): 3.510 (total time: 41.800) Refine new water occ: r_work=0.1332 r_free=0.1560 adp: r_work=0.1255 r_free=0.1517 occ: r_work=0.1269 r_free=0.1505 adp: r_work=0.1234 r_free=0.1491 occ: r_work=0.1238 r_free=0.1481 adp: r_work=0.1228 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1477 r_work=0.1228 r_free=0.1477 | n_water=452 | time (s): 106.140 (total time: 147.940) Filter (q & B) r_work=0.1232 r_free=0.1479 | n_water=436 | time (s): 3.760 (total time: 151.700) Filter (dist only) r_work=0.1232 r_free=0.1479 | n_water=436 | time (s): 41.380 (total time: 193.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.210539 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1647.065530 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 0.1227 0.1497 0.0270 0.007 0.9 1.3 0.5 0.0 0 12.605 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.97 2.70 3.829 23.408 1647.066 0.015 11.94 14.60 2.66 4.269 23.205 1647.066 0.014 Individual atomic B min max mean iso aniso Overall: 8.79 113.72 23.40 2.64 198 1765 Protein: 8.79 113.72 17.79 2.64 0 1519 Water: 11.02 72.57 42.88 N/A 198 238 Other: 23.18 35.46 28.21 N/A 0 8 Chain A: 8.79 113.72 20.60 N/A 0 1765 Chain S: 13.59 72.48 48.39 N/A 198 0 Histogram: Values Number of atoms 8.79 - 19.28 1205 19.28 - 29.78 249 29.78 - 40.27 186 40.27 - 50.76 137 50.76 - 61.26 114 61.26 - 71.75 58 71.75 - 82.24 8 82.24 - 92.73 2 92.73 - 103.23 2 103.23 - 113.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1460 r_work=0.1194 r_free=0.1460 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1460 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1465 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1199 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013801 | | target function (ls_wunit_k1) not normalized (work): 1149.545716 | | target function (ls_wunit_k1) not normalized (free): 98.132852 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1199 0.1465 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1601 0.1711 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1601 0.1711 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1610 0.1606 0.1714 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1195 0.1465 n_refl.: 87592 remove outliers: r(all,work,free)=0.1206 0.1193 0.1465 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 0.3213 291.131 276.635 0.639 0.939 0.364 11.894-9.307 99.02 97 4 0.1463 478.053 474.613 0.979 0.940 0.360 9.237-7.194 100.00 213 7 0.1694 390.989 391.731 1.045 0.940 0.280 7.162-5.571 100.00 427 22 0.1488 293.415 290.018 1.000 0.941 0.229 5.546-4.326 100.00 867 58 0.0841 402.787 399.793 1.017 0.941 0.200 4.315-3.360 100.00 1859 96 0.0705 383.053 381.812 1.064 0.941 0.190 3.356-2.611 100.00 3867 181 0.0948 251.646 251.013 1.073 0.942 0.140 2.608-2.026 99.99 8198 413 0.0960 166.818 166.465 1.082 0.943 0.000 2.025-1.573 100.00 17313 902 0.1176 81.465 81.660 1.089 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1611 36.125 35.638 1.075 0.946 0.000 1.221-1.150 99.97 13689 708 0.2339 22.761 21.326 1.030 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0478 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1465 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1465 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1465 | n_water=436 | time (s): 2.140 (total time: 2.140) Filter (dist) r_work=0.1196 r_free=0.1464 | n_water=433 | time (s): 36.210 (total time: 38.350) Filter (q & B) r_work=0.1196 r_free=0.1464 | n_water=433 | time (s): 0.910 (total time: 39.260) Compute maps r_work=0.1196 r_free=0.1464 | n_water=433 | time (s): 1.590 (total time: 40.850) Filter (map) r_work=0.1237 r_free=0.1474 | n_water=292 | time (s): 3.650 (total time: 44.500) Find peaks r_work=0.1237 r_free=0.1474 | n_water=292 | time (s): 0.600 (total time: 45.100) Add new water r_work=0.1363 r_free=0.1572 | n_water=489 | time (s): 3.470 (total time: 48.570) Refine new water occ: r_work=0.1261 r_free=0.1491 adp: r_work=0.1262 r_free=0.1492 occ: r_work=0.1239 r_free=0.1476 adp: r_work=0.1236 r_free=0.1475 occ: r_work=0.1222 r_free=0.1465 adp: r_work=0.1215 r_free=0.1461 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1461 r_work=0.1215 r_free=0.1461 | n_water=489 | time (s): 177.130 (total time: 225.700) Filter (q & B) r_work=0.1219 r_free=0.1465 | n_water=453 | time (s): 2.620 (total time: 228.320) Filter (dist only) r_work=0.1219 r_free=0.1463 | n_water=452 | time (s): 38.580 (total time: 266.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.000304 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.744358 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1431 0.0205 0.006 0.9 1.6 0.5 0.0 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.31 2.05 3.659 22.317 49.744 3.721 12.14 13.86 1.73 4.160 22.131 49.744 3.651 Individual atomic B min max mean iso aniso Overall: 9.22 108.75 21.93 2.36 217 1762 Protein: 9.22 108.75 17.34 2.36 0 1519 Water: 11.50 71.52 37.26 N/A 217 235 Other: 20.04 31.90 26.21 N/A 0 8 Chain A: 9.22 108.75 20.11 N/A 0 1762 Chain S: 15.55 68.03 36.66 N/A 217 0 Histogram: Values Number of atoms 9.22 - 19.17 1229 19.17 - 29.12 263 29.12 - 39.08 225 39.08 - 49.03 131 49.03 - 58.98 92 58.98 - 68.94 26 68.94 - 78.89 7 78.89 - 88.84 3 88.84 - 98.80 1 98.80 - 108.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1386 r_work=0.1215 r_free=0.1387 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1387 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1388 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.649031 | | target function (ml) not normalized (work): 303935.063991 | | target function (ml) not normalized (free): 16048.557716 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1209 0.1388 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1546 0.1544 0.1610 n_refl.: 87588 remove outliers: r(all,work,free)=0.1546 0.1544 0.1610 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1543 0.1541 0.1608 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1200 0.1366 n_refl.: 87588 remove outliers: r(all,work,free)=0.1206 0.1197 0.1366 n_refl.: 87581 ======================== 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 0.3890 287.774 257.996 0.468 1.000 0.320 11.894-9.307 97.06 95 4 0.2354 478.275 456.662 0.855 1.001 0.320 9.237-7.194 98.64 210 7 0.2339 384.557 385.887 0.943 1.002 0.190 7.162-5.571 100.00 427 22 0.2053 293.415 284.514 0.917 1.002 0.170 5.546-4.326 100.00 867 58 0.1066 402.787 398.519 0.951 1.002 0.166 4.315-3.360 100.00 1859 96 0.0907 383.053 380.699 0.993 1.002 0.162 3.356-2.611 100.00 3867 181 0.1164 251.646 249.832 1.000 1.002 0.067 2.608-2.026 99.99 8198 413 0.1052 166.818 165.897 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1022 81.465 81.617 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1292 36.125 35.715 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2130 22.761 21.389 0.982 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0480 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1366 | n_water=452 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1198 r_free=0.1367 | n_water=451 | time (s): 41.110 (total time: 42.720) Filter (q & B) r_work=0.1198 r_free=0.1367 | n_water=451 | time (s): 0.850 (total time: 43.570) Compute maps r_work=0.1198 r_free=0.1367 | n_water=451 | time (s): 1.280 (total time: 44.850) Filter (map) r_work=0.1221 r_free=0.1393 | n_water=318 | time (s): 2.910 (total time: 47.760) Find peaks r_work=0.1221 r_free=0.1393 | n_water=318 | time (s): 0.570 (total time: 48.330) Add new water r_work=0.1287 r_free=0.1460 | n_water=477 | time (s): 2.930 (total time: 51.260) Refine new water occ: r_work=0.1216 r_free=0.1375 adp: r_work=0.1216 r_free=0.1379 occ: r_work=0.1201 r_free=0.1356 adp: r_work=0.1199 r_free=0.1358 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1186 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1343 r_work=0.1186 r_free=0.1343 | n_water=477 | time (s): 163.950 (total time: 215.210) Filter (q & B) r_work=0.1194 r_free=0.1351 | n_water=438 | time (s): 2.830 (total time: 218.040) Filter (dist only) r_work=0.1194 r_free=0.1351 | n_water=437 | time (s): 37.280 (total time: 255.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.954875 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.368278 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1362 0.0167 0.006 1.0 1.6 0.5 0.0 0 0.977 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.62 1.67 3.463 21.662 49.368 3.638 11.81 13.56 1.75 3.846 21.535 49.368 3.624 Individual atomic B min max mean iso aniso Overall: 9.27 104.24 21.40 2.20 204 1760 Protein: 9.27 104.24 17.05 2.20 0 1519 Water: 11.54 70.31 36.44 N/A 204 233 Other: 20.08 29.15 24.55 N/A 0 8 Chain A: 9.27 104.24 19.75 N/A 0 1760 Chain S: 15.90 61.48 35.64 N/A 204 0 Histogram: Values Number of atoms 9.27 - 18.77 1219 18.77 - 28.26 275 28.26 - 37.76 208 37.76 - 47.26 137 47.26 - 56.75 78 56.75 - 66.25 31 66.25 - 75.75 11 75.75 - 85.24 2 85.24 - 94.74 1 94.74 - 104.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1356 r_work=0.1181 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1356 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1176 r_free = 0.1350 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1176 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621572 | | target function (ml) not normalized (work): 301622.660201 | | target function (ml) not normalized (free): 15929.121556 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1184 0.1176 0.1350 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1505 0.1502 0.1580 n_refl.: 87581 remove outliers: r(all,work,free)=0.1505 0.1502 0.1580 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1501 0.1499 0.1578 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1176 0.1353 n_refl.: 87581 remove outliers: r(all,work,free)=0.1182 0.1173 0.1353 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3927 283.074 257.402 0.448 0.999 0.283 11.894-9.307 94.12 92 4 0.2243 477.347 456.635 0.856 1.001 0.263 9.237-7.194 98.18 209 7 0.2395 382.547 378.707 0.922 1.001 0.150 7.162-5.571 100.00 427 22 0.2111 293.415 284.011 0.910 1.002 0.140 5.546-4.326 100.00 867 58 0.1107 402.787 398.909 0.951 1.002 0.140 4.315-3.360 100.00 1859 96 0.0925 383.053 380.836 0.995 1.002 0.137 3.356-2.611 100.00 3867 181 0.1141 251.646 249.879 1.001 1.001 0.110 2.608-2.026 99.99 8198 413 0.1024 166.818 165.955 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0974 81.465 81.723 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.125 35.748 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2127 22.761 21.395 0.984 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0533 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1173 r_free=0.1353 After: r_work=0.1174 r_free=0.1353 ================================== NQH flips ================================== r_work=0.1174 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1175 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1355 | n_water=437 | time (s): 1.570 (total time: 1.570) Filter (dist) r_work=0.1175 r_free=0.1355 | n_water=437 | time (s): 34.740 (total time: 36.310) Filter (q & B) r_work=0.1175 r_free=0.1355 | n_water=436 | time (s): 2.640 (total time: 38.950) Compute maps r_work=0.1175 r_free=0.1355 | n_water=436 | time (s): 1.300 (total time: 40.250) Filter (map) r_work=0.1206 r_free=0.1376 | n_water=330 | time (s): 2.800 (total time: 43.050) Find peaks r_work=0.1206 r_free=0.1376 | n_water=330 | time (s): 0.560 (total time: 43.610) Add new water r_work=0.1259 r_free=0.1421 | n_water=485 | time (s): 3.240 (total time: 46.850) Refine new water occ: r_work=0.1188 r_free=0.1357 adp: r_work=0.1188 r_free=0.1359 occ: r_work=0.1177 r_free=0.1348 adp: r_work=0.1175 r_free=0.1349 occ: r_work=0.1168 r_free=0.1345 adp: r_work=0.1165 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1165 r_free=0.1343 r_work=0.1165 r_free=0.1343 | n_water=485 | time (s): 133.430 (total time: 180.280) Filter (q & B) r_work=0.1172 r_free=0.1344 | n_water=446 | time (s): 2.550 (total time: 182.830) Filter (dist only) r_work=0.1172 r_free=0.1342 | n_water=444 | time (s): 37.580 (total time: 220.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850925 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.942194 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1359 0.0164 0.007 1.0 2.2 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.59 1.64 3.330 21.324 48.942 3.628 11.97 13.65 1.67 3.641 21.228 48.942 3.621 Individual atomic B min max mean iso aniso Overall: 9.29 99.91 21.19 2.05 213 1758 Protein: 9.29 99.91 16.80 2.06 0 1519 Water: 11.54 69.20 36.14 N/A 213 231 Other: 20.28 27.98 24.05 N/A 0 8 Chain A: 9.29 99.91 19.46 N/A 0 1758 Chain S: 14.14 61.75 35.41 N/A 213 0 Histogram: Values Number of atoms 9.29 - 18.36 1209 18.36 - 27.42 273 27.42 - 36.48 201 36.48 - 45.54 164 45.54 - 54.60 71 54.60 - 63.67 33 63.67 - 72.73 15 72.73 - 81.79 2 81.79 - 90.85 1 90.85 - 99.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1365 r_work=0.1198 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1195 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619617 | | target function (ml) not normalized (work): 301441.672408 | | target function (ml) not normalized (free): 15927.243803 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1397 0.1370 5.6903 5.5907| | 2: 3.57 - 2.84 1.00 2888 124 0.1110 0.1474 5.1792 5.2497| | 3: 2.83 - 2.48 1.00 2820 163 0.1232 0.1236 4.9858 5.0004| | 4: 2.47 - 2.25 1.00 2825 136 0.1030 0.1177 4.6903 4.749| | 5: 2.25 - 2.09 1.00 2756 127 0.1006 0.1148 4.629 4.7096| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1209 4.3438 4.4795| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1177 4.0786 4.166| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1270 3.9938 4.0919| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1307 3.7163 3.9057| | 10: 1.72 - 1.66 1.00 2831 160 0.1004 0.1224 3.6364 3.7453| | 11: 1.66 - 1.61 1.00 2712 147 0.0962 0.1086 3.5686 3.6101| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1170 3.3444 3.49| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1082 3.3416 3.4585| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1109 3.2618 3.3343| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1333 3.1691 3.3313| | 16: 1.45 - 1.42 1.00 2756 161 0.1081 0.1253 3.1564 3.2445| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1272 3.1187 3.2146| | 18: 1.39 - 1.36 1.00 2741 179 0.1152 0.1363 3.0874 3.2722| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1612 3.0956 3.2719| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1479 3.0898 3.1389| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1658 3.089 3.1723| | 22: 1.29 - 1.27 1.00 2704 152 0.1475 0.1950 3.0843 3.2992| | 23: 1.27 - 1.26 1.00 2802 156 0.1568 0.1873 3.1022 3.2111| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1747 3.0937 3.1832| | 25: 1.24 - 1.22 1.00 2733 148 0.1801 0.2344 3.1099 3.2926| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1792 3.1217 3.2048| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2104 3.1395 3.151| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2336 3.1382 3.1614| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2365 3.1257 3.2224| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2497 3.1149 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 2918 171 0.95 8.53 1.00 0.97 5782.63| | 2: 3.57 - 2.84 2888 124 0.93 12.65 1.01 0.97 5782.63| | 3: 2.83 - 2.48 2820 163 0.89 16.82 0.99 0.97 4860.93| | 4: 2.47 - 2.25 2825 136 0.91 14.13 1.00 0.98 2484.14| | 5: 2.25 - 2.09 2756 127 0.90 16.36 1.01 0.98 2484.14| | 6: 2.09 - 1.97 2846 113 0.92 13.39 1.02 0.97 1483.59| | 7: 1.97 - 1.87 2787 165 0.94 10.86 1.02 0.97 630.26| | 8: 1.87 - 1.79 2789 144 0.91 14.47 1.00 0.97 630.26| | 9: 1.79 - 1.72 2745 138 0.93 11.47 0.98 0.97 340.84| | 10: 1.72 - 1.66 2831 160 0.93 12.31 0.98 0.97 282.88| | 11: 1.66 - 1.61 2712 147 0.93 12.97 0.98 0.97 270.11| | 12: 1.61 - 1.56 2773 144 0.95 9.62 0.99 0.97 149.63| | 13: 1.56 - 1.52 2745 130 0.94 11.20 1.02 0.97 149.63| | 14: 1.52 - 1.48 2803 134 0.94 11.36 1.02 0.97 133.54| | 15: 1.48 - 1.45 2738 128 0.95 10.51 1.01 0.98 104.08| | 16: 1.45 - 1.42 2756 161 0.94 11.69 1.02 0.98 104.08| | 17: 1.42 - 1.39 2785 139 0.94 11.52 1.01 0.98 93.98| | 18: 1.39 - 1.36 2741 179 0.94 11.85 1.01 0.98 88.13| | 19: 1.36 - 1.34 2807 134 0.94 12.42 1.00 0.98 88.13| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.96 83.05| | 21: 1.32 - 1.30 2785 112 0.93 13.47 0.99 0.96 82.69| | 22: 1.29 - 1.27 2704 152 0.93 13.97 0.98 0.96 82.84| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 83.57| | 24: 1.26 - 1.24 2744 132 0.92 15.06 0.97 0.95 83.57| | 25: 1.24 - 1.22 2733 148 0.91 16.47 0.96 0.94 85.00| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.58| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.58| | 28: 1.19 - 1.18 2671 147 0.88 20.30 1.01 0.93 89.55| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.92 90.67| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.92 90.67| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.69 max = 5782.63 mean = 918.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.99| |phase err.(test): min = 0.00 max = 87.40 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1195 0.1362 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1584 n_refl.: 87576 remove outliers: r(all,work,free)=0.1514 0.1512 0.1584 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1511 0.1509 0.1582 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1195 0.1367 n_refl.: 87576 remove outliers: r(all,work,free)=0.1203 0.1194 0.1367 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 0.3870 285.651 248.839 0.456 0.953 0.299 11.894-9.307 93.14 91 4 0.2392 471.116 455.524 0.892 0.955 0.211 9.237-7.194 97.73 208 7 0.2471 383.620 375.680 0.952 0.955 0.138 7.162-5.571 100.00 427 22 0.2245 293.415 281.945 0.942 0.955 0.134 5.546-4.326 100.00 867 58 0.1181 402.787 398.703 0.998 0.955 0.127 4.315-3.360 100.00 1859 96 0.0966 383.053 380.791 1.043 0.955 0.117 3.356-2.611 100.00 3867 181 0.1186 251.646 249.695 1.051 0.954 0.080 2.608-2.026 99.99 8198 413 0.1044 166.818 165.885 1.064 0.953 0.000 2.025-1.573 100.00 17313 902 0.0980 81.465 81.701 1.080 0.952 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.125 35.757 1.075 0.949 0.000 1.221-1.150 99.97 13689 708 0.2120 22.761 21.392 1.031 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0398 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1966 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1785 0.080 5.304 9.0 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1785 0.080 5.304 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1786 0.080 5.304 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1786 0.080 5.304 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1214 0.1469 0.008 0.964 9.0 119.5 20.1 258 0.125 1_adp: 0.1247 0.1548 0.008 0.964 8.8 118.6 21.2 258 0.125 1_regHadp: 0.1251 0.1553 0.008 0.964 8.8 118.6 21.2 258 0.125 1_occ: 0.1251 0.1556 0.008 0.964 8.8 118.6 21.2 258 0.125 2_bss: 0.1249 0.1548 0.008 0.964 8.9 118.7 21.4 258 0.125 2_settarget: 0.1249 0.1548 0.008 0.964 8.9 118.7 21.4 258 0.125 2_updatecdl: 0.1249 0.1548 0.008 0.975 8.9 118.7 21.4 258 0.125 2_nqh: 0.1249 0.1548 0.008 0.975 8.9 118.7 21.4 258 0.125 2_sol: 0.1232 0.1479 0.008 0.975 8.9 118.7 23.8 436 n/a 2_weight: 0.1232 0.1479 0.008 0.975 8.9 118.7 23.8 436 n/a 2_xyzrec: 0.1227 0.1497 0.007 0.875 8.9 118.7 23.8 436 n/a 2_adp: 0.1194 0.1460 0.007 0.875 8.8 113.7 23.4 436 n/a 2_regHadp: 0.1194 0.1460 0.007 0.875 8.8 113.7 23.4 436 n/a 2_occ: 0.1199 0.1465 0.007 0.875 8.8 113.7 23.4 436 n/a 3_bss: 0.1193 0.1465 0.007 0.875 8.8 113.8 23.4 436 n/a 3_settarget: 0.1193 0.1465 0.007 0.875 8.8 113.8 23.4 436 n/a 3_updatecdl: 0.1193 0.1465 0.007 0.876 8.8 113.8 23.4 436 n/a 3_nqh: 0.1193 0.1465 0.007 0.876 8.8 113.8 23.4 436 n/a 3_sol: 0.1219 0.1463 0.007 0.876 8.8 113.8 22.3 452 n/a 3_weight: 0.1219 0.1463 0.007 0.876 8.8 113.8 22.3 452 n/a 3_xyzrec: 0.1226 0.1431 0.006 0.920 8.8 113.8 22.3 452 n/a 3_adp: 0.1214 0.1386 0.006 0.920 9.2 108.8 21.9 452 n/a 3_regHadp: 0.1215 0.1387 0.006 0.920 9.2 108.8 21.9 452 n/a 3_occ: 0.1209 0.1388 0.006 0.920 9.2 108.8 21.9 452 n/a 4_bss: 0.1197 0.1366 0.006 0.920 9.2 108.7 21.9 452 n/a 4_settarget: 0.1197 0.1366 0.006 0.920 9.2 108.7 21.9 452 n/a 4_updatecdl: 0.1197 0.1366 0.006 0.917 9.2 108.7 21.9 452 n/a 4_nqh: 0.1197 0.1366 0.006 0.917 9.2 108.7 21.9 452 n/a 4_sol: 0.1194 0.1351 0.006 0.917 9.2 108.7 21.6 437 n/a 4_weight: 0.1194 0.1351 0.006 0.917 9.2 108.7 21.6 437 n/a 4_xyzrec: 0.1195 0.1362 0.006 0.954 9.2 108.7 21.6 437 n/a 4_adp: 0.1181 0.1356 0.006 0.954 9.3 104.2 21.4 437 n/a 4_regHadp: 0.1181 0.1356 0.006 0.954 9.3 104.2 21.4 437 n/a 4_occ: 0.1176 0.1350 0.006 0.954 9.3 104.2 21.4 437 n/a 5_bss: 0.1173 0.1353 0.006 0.954 9.3 104.2 21.4 437 n/a 5_settarget: 0.1173 0.1353 0.006 0.954 9.3 104.2 21.4 437 n/a 5_updatecdl: 0.1173 0.1353 0.006 0.957 9.3 104.2 21.4 437 n/a 5_setrh: 0.1174 0.1353 0.006 0.957 9.3 104.2 21.4 437 n/a 5_nqh: 0.1175 0.1355 0.006 0.957 9.3 104.2 21.4 437 n/a 5_sol: 0.1172 0.1342 0.006 0.957 9.3 104.2 21.4 444 n/a 5_weight: 0.1172 0.1342 0.006 0.957 9.3 104.2 21.4 444 n/a 5_xyzrec: 0.1195 0.1359 0.007 1.045 9.3 104.2 21.4 444 n/a 5_adp: 0.1197 0.1365 0.007 1.045 9.3 99.9 21.2 444 n/a 5_regHadp: 0.1198 0.1365 0.007 1.045 9.3 99.9 21.2 444 n/a 5_occ: 0.1195 0.1362 0.007 1.045 9.3 99.9 21.2 444 n/a end: 0.1194 0.1367 0.007 1.045 9.3 99.9 21.2 444 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6218374_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6218374_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8600 Refinement macro-cycles (run) : 3365.6200 Write final files (write_after_run_outputs) : 74.1200 Total : 3444.6000 Total CPU time: 58.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:44 PST -0800 (1735452584.42 s) Start R-work = 0.1639, R-free = 0.1785 Final R-work = 0.1194, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3595.60 seconds wall clock time: 65 minutes 12.19 seconds (3912.19 seconds total)