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_4279219.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" 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: 2.07, per 1000 atoms: 0.61 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 252.6 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 540 0.91 - 1.18: 1116 1.18 - 1.44: 680 1.44 - 1.70: 797 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.109 0.265 1.10e-02 8.26e+03 5.80e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.674 -0.140 6.80e-03 2.16e+04 4.22e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.031 0.206 1.13e-02 7.83e+03 3.32e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.02e+02 bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.351 0.167 1.00e-02 1.00e+04 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3244 4.79 - 9.58: 1845 9.58 - 14.36: 584 14.36 - 19.15: 98 19.15 - 23.94: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.71 -12.48 8.10e-01 1.52e+00 2.38e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.03 107.07 15.96 1.11e+00 8.12e-01 2.07e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.25 9.04 6.50e-01 2.37e+00 1.93e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 112.85 9.60 7.20e-01 1.93e+00 1.78e+02 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 112.04 125.10 -13.06 1.02e+00 9.61e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 918 16.41 - 32.82: 129 32.82 - 49.22: 42 49.22 - 65.63: 18 65.63 - 82.04: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+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 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 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 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 89 0.198 - 0.396: 95 0.396 - 0.593: 35 0.593 - 0.791: 15 0.791 - 0.989: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.60 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.070 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.036 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.054 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.045 9.50e-02 1.11e+02 6.26e-02 8.32e+01 pdb=" NE ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.093 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.108 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1297 2.36 - 2.92: 8286 2.92 - 3.48: 10469 3.48 - 4.04: 15144 4.04 - 4.60: 21483 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb="HH12 ARG A 5 " pdb=" O BGLU A 64 " model vdw 1.829 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.833 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.833 2.100 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.850 2.450 ... (remaining 56674 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_4279219_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= 0.2603 r_free= 0.1921 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788322 | | target function (ml) not normalized (work): 232283.981254 | | target function (ml) not normalized (free): 11788.859775 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3043 0.2084 7.0855 4.9399| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1731 4.345 4.3458| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1604 4.1238 4.1494| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1376 3.8264 3.8243| | 5: 2.25 - 2.09 1.00 2756 127 0.2454 0.1672 3.7944 3.8097| | 6: 2.09 - 1.97 1.00 2846 113 0.2522 0.1878 3.4514 3.5562| | 7: 1.97 - 1.87 1.00 2787 165 0.2546 0.1756 3.1293 3.18| | 8: 1.87 - 1.79 1.00 2789 144 0.2426 0.1785 3.0726 3.1082| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1828 2.9138 2.8897| | 10: 1.72 - 1.66 1.00 2789 158 0.2410 0.2112 2.7975 2.9304| | 11: 1.66 - 1.61 1.00 2740 147 0.2516 0.1631 2.7277 2.7015| | 12: 1.61 - 1.56 1.00 2787 146 0.2530 0.2150 2.6278 2.7164| | 13: 1.56 - 1.52 1.00 2745 130 0.2551 0.1786 2.5624 2.5672| | 14: 1.52 - 1.48 1.00 2803 134 0.2581 0.1767 2.5012 2.5316| | 15: 1.48 - 1.45 1.00 2738 128 0.2575 0.1945 2.4003 2.4255| | 16: 1.45 - 1.42 1.00 2756 161 0.2619 0.2123 2.375 2.4462| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.2116 2.333 2.3484| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2399 2.2619 2.4263| | 19: 1.36 - 1.34 1.00 2807 134 0.2684 0.2450 2.257 2.2736| | 20: 1.34 - 1.32 1.00 2696 147 0.2663 0.2338 2.1829 2.236| | 21: 1.32 - 1.30 1.00 2785 112 0.2780 0.2278 2.1664 2.1883| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2591 2.1264 2.2209| | 23: 1.27 - 1.26 1.00 2802 156 0.2775 0.2308 2.1092 2.1277| | 24: 1.26 - 1.24 1.00 2744 132 0.2783 0.2422 2.0776 2.1359| | 25: 1.24 - 1.22 1.00 2734 148 0.2831 0.2487 2.047 2.0583| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2337 2.0093 2.0521| | 27: 1.21 - 1.19 1.00 2814 148 0.2960 0.2778 2.0071 2.0615| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2667 1.9882 1.9678| | 29: 1.18 - 1.16 1.00 2800 134 0.2938 0.2611 1.9623 1.9711| | 30: 1.16 - 1.15 1.00 2740 148 0.3068 0.2723 1.9289 1.9438| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.72 0.76 0.23 1459.89| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1459.89| | 3: 2.84 - 2.48 2833 165 0.74 31.80 1.24 0.23 1211.35| | 4: 2.47 - 2.25 2825 136 0.81 25.49 1.26 0.25 566.37| | 5: 2.25 - 2.09 2756 127 0.77 29.14 1.28 0.25 566.37| | 6: 2.09 - 1.97 2846 113 0.83 22.71 1.29 0.25 311.07| | 7: 1.97 - 1.87 2787 165 0.90 16.83 1.28 0.26 93.34| | 8: 1.87 - 1.79 2789 144 0.86 21.10 1.24 0.26 93.34| | 9: 1.79 - 1.72 2745 138 0.88 18.23 1.23 0.26 54.93| | 10: 1.72 - 1.66 2789 158 0.87 19.92 1.22 0.26 47.23| | 11: 1.66 - 1.61 2740 147 0.86 21.21 1.25 0.26 45.55| | 12: 1.61 - 1.56 2787 146 0.89 17.99 1.23 0.25 28.46| | 13: 1.56 - 1.52 2745 130 0.87 20.08 1.24 0.25 28.46| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.24 0.25 25.48| | 15: 1.48 - 1.45 2738 128 0.87 19.87 1.23 0.25 20.01| | 16: 1.45 - 1.42 2756 161 0.86 21.03 1.24 0.25 20.01| | 17: 1.42 - 1.39 2785 139 0.87 20.68 1.23 0.25 17.44| | 18: 1.39 - 1.36 2741 179 0.86 21.46 1.23 0.25 15.95| | 19: 1.36 - 1.34 2807 134 0.85 22.10 1.22 0.25 15.95| | 20: 1.34 - 1.32 2696 147 0.87 21.17 1.21 0.24 13.36| | 21: 1.32 - 1.30 2785 112 0.85 22.70 1.22 0.24 13.18| | 22: 1.29 - 1.27 2704 152 0.85 22.60 1.22 0.24 12.85| | 23: 1.27 - 1.26 2802 156 0.86 22.19 1.21 0.24 11.19| | 24: 1.26 - 1.24 2744 132 0.85 23.14 1.20 0.24 11.19| | 25: 1.24 - 1.22 2734 148 0.84 23.72 1.20 0.23 10.44| | 26: 1.22 - 1.21 2727 135 0.85 23.45 1.19 0.23 9.62| | 27: 1.21 - 1.19 2814 148 0.84 24.39 1.20 0.23 9.62| | 28: 1.19 - 1.18 2671 147 0.84 24.39 1.18 0.23 8.78| | 29: 1.18 - 1.16 2800 134 0.84 24.31 1.16 0.23 8.47| | 30: 1.16 - 1.15 2740 148 0.82 26.25 1.16 0.23 8.47| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.47 max = 1459.89 mean = 212.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.44| |phase err.(test): min = 0.00 max = 89.78 mean = 22.39| |-----------------------------------------------------------------------------| ----------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 0.265 1557 Z= 5.480 Angle : 5.250 16.235 2118 Z= 3.755 Chirality : 0.363 0.989 243 Planarity : 0.033 0.112 284 Dihedral : 13.970 82.037 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % 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: -2.70 (0.47), residues: 224 helix: -2.63 (0.39), residues: 102 sheet: -0.96 (0.92), residues: 28 loop : -0.76 (0.53), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.013 ARG A 27 TYR 0.078 0.033 TYR A 141 PHE 0.088 0.037 PHE A 162 HIS 0.088 0.049 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1921 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788322 | | target function (ml) not normalized (work): 232283.981254 | | target function (ml) not normalized (free): 11788.859775 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1970 0.1975 0.1921 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1995 0.2000 0.1935 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1635 0.1630 0.1734 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1629 0.1734 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 0.3849 386.345 357.073 0.739 0.912 0.402 11.894-9.307 99.02 97 4 0.1820 613.690 593.376 1.020 0.912 0.385 9.237-7.194 100.00 213 7 0.2069 501.923 491.061 1.045 0.913 0.380 7.162-5.571 100.00 427 22 0.2241 376.665 364.213 1.022 0.914 0.288 5.546-4.326 100.00 867 58 0.1296 517.069 511.973 1.057 0.915 0.218 4.315-3.360 100.00 1859 96 0.1131 491.736 487.866 1.102 0.916 0.189 3.356-2.611 100.00 3867 181 0.1440 323.045 319.930 1.086 0.918 0.109 2.608-2.026 99.99 8198 413 0.1347 214.149 211.823 1.091 0.922 0.000 2.025-1.573 100.00 17313 902 0.1626 104.579 103.945 1.088 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.375 45.128 1.066 0.940 0.000 1.221-1.150 99.97 13689 708 0.2599 29.219 26.983 1.020 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1734 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1633 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.548505 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2008.762726 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 0.1211 0.1463 0.0252 0.007 1.0 1.3 0.5 0.0 0 12.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.63 2.52 3.013 19.064 2008.763 0.017 12.33 15.32 2.99 2.997 19.428 2008.763 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.05 20.78 2.88 0 1785 Protein: 8.47 118.05 17.69 2.89 0 1519 Water: 11.04 115.00 38.73 N/A 0 258 Other: 22.16 34.18 27.78 N/A 0 8 Chain A: 8.47 118.05 20.78 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.43 1212 19.43 - 30.38 236 30.38 - 41.34 159 41.34 - 52.30 97 52.30 - 63.26 52 63.26 - 74.22 18 74.22 - 85.17 4 85.17 - 96.13 4 96.13 - 107.09 0 107.09 - 118.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1532 r_work=0.1237 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1536 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 = 0.1236 r_free = 0.1540 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.30 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= 0.1236 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015315 | | target function (ls_wunit_k1) not normalized (work): 1275.728582 | | target function (ls_wunit_k1) not normalized (free): 113.635262 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1251 0.1236 0.1540 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1689 0.1688 0.1760 n_refl.: 87593 remove outliers: r(all,work,free)=0.1689 0.1688 0.1760 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1711 0.1710 0.1775 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1249 0.1235 0.1533 n_refl.: 87593 remove outliers: r(all,work,free)=0.1249 0.1234 0.1533 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 0.3578 299.421 278.829 0.631 1.002 0.373 11.894-9.307 99.02 97 4 0.1621 479.656 468.208 0.909 1.003 0.369 9.237-7.194 100.00 213 7 0.1807 392.299 387.786 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1731 294.399 289.066 0.922 1.003 0.253 5.546-4.326 100.00 867 58 0.0931 404.137 401.389 0.951 1.003 0.204 4.315-3.360 100.00 1859 96 0.0783 384.337 383.404 0.997 1.003 0.190 3.356-2.611 100.00 3867 181 0.1023 252.489 251.800 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0967 167.377 166.806 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1193 81.738 81.949 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1628 36.246 35.707 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2351 22.838 21.350 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0520 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1533 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=0.1234 r_free=0.1533 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1533 | n_water=258 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1244 r_free=0.1530 | n_water=252 | time (s): 25.770 (total time: 28.210) Filter (q & B) r_work=0.1247 r_free=0.1530 | n_water=249 | time (s): 3.690 (total time: 31.900) Compute maps r_work=0.1247 r_free=0.1530 | n_water=249 | time (s): 1.830 (total time: 33.730) Filter (map) r_work=0.1258 r_free=0.1539 | n_water=237 | time (s): 3.800 (total time: 37.530) Find peaks r_work=0.1258 r_free=0.1539 | n_water=237 | time (s): 0.710 (total time: 38.240) Add new water r_work=0.1417 r_free=0.1709 | n_water=457 | time (s): 3.740 (total time: 41.980) Refine new water occ: r_work=0.1322 r_free=0.1574 adp: r_work=0.1243 r_free=0.1527 occ: r_work=0.1257 r_free=0.1514 adp: r_work=0.1221 r_free=0.1503 occ: r_work=0.1226 r_free=0.1491 adp: r_work=0.1214 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1491 r_work=0.1214 r_free=0.1491 | n_water=457 | time (s): 81.240 (total time: 123.220) Filter (q & B) r_work=0.1220 r_free=0.1498 | n_water=435 | time (s): 4.090 (total time: 127.310) Filter (dist only) r_work=0.1220 r_free=0.1496 | n_water=434 | time (s): 45.170 (total time: 172.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.914300 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1587.153936 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 0.1216 0.1503 0.0287 0.007 0.9 1.9 0.5 0.0 0 12.957 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 15.03 2.87 3.755 22.953 1587.154 0.015 11.94 14.88 2.95 4.043 22.800 1587.154 0.015 Individual atomic B min max mean iso aniso Overall: 8.72 113.99 23.02 2.60 197 1764 Protein: 8.72 113.99 17.53 2.60 0 1519 Water: 11.02 73.79 42.10 N/A 197 237 Other: 24.75 36.29 29.55 N/A 0 8 Chain A: 8.72 113.99 20.21 N/A 0 1764 Chain S: 17.99 69.00 48.15 N/A 197 0 Histogram: Values Number of atoms 8.72 - 19.25 1209 19.25 - 29.77 249 29.77 - 40.30 190 40.30 - 50.83 150 50.83 - 61.36 104 61.36 - 71.88 48 71.88 - 82.41 5 82.41 - 92.94 3 92.94 - 103.46 1 103.46 - 113.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1489 r_work=0.1194 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1489 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1482 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= 0.1197 r_free= 0.1482 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014016 | | target function (ls_wunit_k1) not normalized (work): 1167.509396 | | target function (ls_wunit_k1) not normalized (free): 105.778286 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1197 0.1482 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1593 0.1588 0.1730 n_refl.: 87592 remove outliers: r(all,work,free)=0.1593 0.1588 0.1730 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1600 0.1595 0.1734 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1194 0.1480 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1193 0.1480 n_refl.: 87590 ======================== 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 93.75 85 5 0.3450 297.979 270.215 0.592 1.002 0.370 11.894-9.307 99.02 97 4 0.1558 479.656 476.435 0.912 1.003 0.350 9.237-7.194 100.00 213 7 0.1690 392.299 393.151 0.973 1.003 0.290 7.162-5.571 100.00 427 22 0.1516 294.399 290.504 0.940 1.003 0.231 5.546-4.326 100.00 867 58 0.0837 404.137 401.358 0.959 1.003 0.216 4.315-3.360 100.00 1859 96 0.0707 384.337 383.356 1.002 1.003 0.210 3.356-2.611 100.00 3867 181 0.0960 252.489 251.745 1.008 1.002 0.140 2.608-2.026 99.99 8198 413 0.0953 167.377 166.934 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1169 81.738 81.948 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1605 36.246 35.758 1.016 0.997 0.000 1.221-1.150 99.97 13689 708 0.2337 22.838 21.360 0.975 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0707 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1480 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=0.1193 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1480 | n_water=434 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1193 r_free=0.1480 | n_water=432 | time (s): 37.750 (total time: 39.960) Filter (q & B) r_work=0.1193 r_free=0.1481 | n_water=431 | time (s): 2.730 (total time: 42.690) Compute maps r_work=0.1193 r_free=0.1481 | n_water=431 | time (s): 1.270 (total time: 43.960) Filter (map) r_work=0.1234 r_free=0.1487 | n_water=291 | time (s): 3.080 (total time: 47.040) Find peaks r_work=0.1234 r_free=0.1487 | n_water=291 | time (s): 0.550 (total time: 47.590) Add new water r_work=0.1361 r_free=0.1627 | n_water=474 | time (s): 3.080 (total time: 50.670) Refine new water occ: r_work=0.1264 r_free=0.1535 adp: r_work=0.1265 r_free=0.1538 occ: r_work=0.1241 r_free=0.1510 adp: r_work=0.1239 r_free=0.1513 occ: r_work=0.1226 r_free=0.1496 adp: r_work=0.1218 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1495 r_work=0.1218 r_free=0.1495 | n_water=474 | time (s): 208.850 (total time: 259.520) Filter (q & B) r_work=0.1223 r_free=0.1494 | n_water=443 | time (s): 3.280 (total time: 262.800) Filter (dist only) r_work=0.1223 r_free=0.1492 | n_water=442 | time (s): 36.840 (total time: 299.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.045893 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.094930 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 0.1458 0.0232 0.006 0.9 1.9 0.5 0.0 0 1.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.58 2.32 3.599 21.974 46.095 3.725 12.10 14.13 2.02 4.037 21.803 46.095 3.654 Individual atomic B min max mean iso aniso Overall: 9.09 109.85 21.56 2.32 207 1762 Protein: 9.09 109.85 17.16 2.32 0 1519 Water: 11.42 73.05 36.55 N/A 207 235 Other: 21.58 32.59 27.27 N/A 0 8 Chain A: 9.09 109.85 19.82 N/A 0 1762 Chain S: 16.99 62.73 36.34 N/A 207 0 Histogram: Values Number of atoms 9.09 - 19.17 1236 19.17 - 29.24 276 29.24 - 39.32 211 39.32 - 49.40 138 49.40 - 59.47 75 59.47 - 69.55 21 69.55 - 79.62 6 79.62 - 89.70 3 89.70 - 99.77 1 99.77 - 109.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1413 r_work=0.1212 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1413 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1411 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1207 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.652366 | | target function (ml) not normalized (work): 304220.149209 | | target function (ml) not normalized (free): 16058.600534 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1207 0.1411 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1529 0.1528 0.1586 n_refl.: 87590 remove outliers: r(all,work,free)=0.1529 0.1528 0.1586 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1529 0.1527 0.1586 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1383 n_refl.: 87590 remove outliers: r(all,work,free)=0.1201 0.1192 0.1383 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 90.62 82 5 0.3955 292.503 265.123 0.504 1.001 0.350 11.894-9.307 98.04 96 4 0.2517 477.220 465.086 0.849 1.002 0.320 9.237-7.194 97.73 208 7 0.2342 384.906 384.817 0.949 1.003 0.170 7.162-5.571 100.00 427 22 0.2102 294.399 283.335 0.915 1.003 0.158 5.546-4.326 100.00 867 58 0.1097 404.137 399.385 0.961 1.003 0.153 4.315-3.360 100.00 1859 96 0.0916 384.337 381.775 1.003 1.003 0.150 3.356-2.611 100.00 3867 181 0.1150 252.489 250.606 1.009 1.002 0.067 2.608-2.026 99.99 8198 413 0.1036 167.377 166.430 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1002 81.738 81.899 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.246 35.814 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2133 22.838 21.437 0.985 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0020 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1383 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=0.1192 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1383 | n_water=442 | time (s): 1.570 (total time: 1.570) Filter (dist) r_work=0.1192 r_free=0.1383 | n_water=442 | time (s): 35.870 (total time: 37.440) Filter (q & B) r_work=0.1192 r_free=0.1383 | n_water=442 | time (s): 0.810 (total time: 38.250) Compute maps r_work=0.1192 r_free=0.1383 | n_water=442 | time (s): 1.590 (total time: 39.840) Filter (map) r_work=0.1213 r_free=0.1396 | n_water=312 | time (s): 2.520 (total time: 42.360) Find peaks r_work=0.1213 r_free=0.1396 | n_water=312 | time (s): 0.560 (total time: 42.920) Add new water r_work=0.1279 r_free=0.1474 | n_water=474 | time (s): 2.750 (total time: 45.670) Refine new water occ: r_work=0.1209 r_free=0.1394 adp: r_work=0.1209 r_free=0.1397 occ: r_work=0.1193 r_free=0.1377 adp: r_work=0.1192 r_free=0.1380 occ: r_work=0.1182 r_free=0.1365 adp: r_work=0.1179 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1366 r_work=0.1179 r_free=0.1366 | n_water=474 | time (s): 237.680 (total time: 283.350) Filter (q & B) r_work=0.1186 r_free=0.1369 | n_water=436 | time (s): 3.380 (total time: 286.730) Filter (dist only) r_work=0.1186 r_free=0.1369 | n_water=435 | time (s): 38.320 (total time: 325.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.427128 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.237780 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 0.1189 0.1378 0.0189 0.007 1.0 3.8 0.5 0.0 0 1.214 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.78 1.89 3.418 21.376 50.238 3.636 11.78 13.73 1.95 3.865 21.215 50.238 3.620 Individual atomic B min max mean iso aniso Overall: 9.24 104.85 20.98 2.18 201 1761 Protein: 9.24 104.85 16.83 2.18 0 1519 Water: 11.48 71.79 35.38 N/A 201 234 Other: 21.24 29.93 25.62 N/A 0 8 Chain A: 9.24 104.85 19.44 N/A 0 1761 Chain S: 16.24 63.05 34.47 N/A 201 0 Histogram: Values Number of atoms 9.24 - 18.80 1236 18.80 - 28.36 277 28.36 - 37.92 217 37.92 - 47.48 128 47.48 - 57.04 65 57.04 - 66.60 26 66.60 - 76.16 8 76.16 - 85.73 2 85.73 - 95.29 1 95.29 - 104.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1374 r_work=0.1179 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1374 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1174 r_free = 0.1369 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1174 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618358 | | target function (ml) not normalized (work): 301354.967618 | | target function (ml) not normalized (free): 15939.394166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1183 0.1174 0.1369 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1504 0.1503 0.1558 n_refl.: 87581 remove outliers: r(all,work,free)=0.1504 0.1503 0.1558 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1504 0.1503 0.1558 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1174 0.1369 n_refl.: 87581 remove outliers: r(all,work,free)=0.1180 0.1170 0.1369 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 88.54 80 5 0.3958 290.072 249.350 0.461 1.000 0.313 11.894-9.307 92.16 90 4 0.2258 466.154 453.239 0.838 1.002 0.217 9.237-7.194 97.73 208 7 0.2454 384.906 377.200 0.919 1.002 0.140 7.162-5.571 100.00 427 22 0.2216 294.399 283.513 0.909 1.003 0.140 5.546-4.326 100.00 867 58 0.1125 404.137 399.831 0.964 1.003 0.133 4.315-3.360 100.00 1859 96 0.0952 384.337 381.871 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1156 252.489 250.483 1.010 1.002 0.057 2.608-2.026 99.99 8198 413 0.1017 167.377 166.516 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0946 81.738 82.017 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.246 35.879 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2118 22.838 21.462 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0016 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1170 r_free=0.1369 After: r_work=0.1171 r_free=0.1369 ================================== NQH flips ================================== r_work=0.1171 r_free=0.1369 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=0.1171 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1171 r_free=0.1369 | n_water=435 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1171 r_free=0.1369 | n_water=435 | time (s): 34.420 (total time: 36.440) Filter (q & B) r_work=0.1171 r_free=0.1370 | n_water=434 | time (s): 3.330 (total time: 39.770) Compute maps r_work=0.1171 r_free=0.1370 | n_water=434 | time (s): 1.350 (total time: 41.120) Filter (map) r_work=0.1195 r_free=0.1379 | n_water=334 | time (s): 2.500 (total time: 43.620) Find peaks r_work=0.1195 r_free=0.1379 | n_water=334 | time (s): 0.550 (total time: 44.170) Add new water r_work=0.1243 r_free=0.1419 | n_water=493 | time (s): 3.330 (total time: 47.500) Refine new water occ: r_work=0.1183 r_free=0.1370 adp: r_work=0.1184 r_free=0.1371 occ: r_work=0.1170 r_free=0.1361 adp: r_work=0.1170 r_free=0.1362 occ: r_work=0.1161 r_free=0.1353 adp: r_work=0.1159 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1159 r_free=0.1353 r_work=0.1159 r_free=0.1353 | n_water=493 | time (s): 219.690 (total time: 267.190) Filter (q & B) r_work=0.1168 r_free=0.1357 | n_water=446 | time (s): 2.860 (total time: 270.050) Filter (dist only) r_work=0.1169 r_free=0.1357 | n_water=445 | time (s): 37.970 (total time: 308.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935512 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.919095 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1389 0.0187 0.007 1.1 3.5 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.89 1.87 3.282 21.013 37.919 3.632 12.02 13.87 1.85 3.299 20.999 37.919 3.629 Individual atomic B min max mean iso aniso Overall: 9.23 104.34 20.97 2.13 214 1758 Protein: 9.23 104.34 16.79 2.13 0 1519 Water: 11.26 71.73 35.16 N/A 214 231 Other: 21.95 30.04 25.78 N/A 0 8 Chain A: 9.23 104.34 19.34 N/A 0 1758 Chain S: 16.15 55.42 34.37 N/A 214 0 Histogram: Values Number of atoms 9.23 - 18.74 1230 18.74 - 28.25 291 28.25 - 37.76 212 37.76 - 47.27 137 47.27 - 56.78 67 56.78 - 66.29 21 66.29 - 75.80 10 75.80 - 85.32 1 85.32 - 94.83 1 94.83 - 104.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1387 r_work=0.1202 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1388 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1382 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1199 r_free= 0.1382 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.628236 | | target function (ml) not normalized (work): 302148.637997 | | target function (ml) not normalized (free): 15975.437829 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1426 0.1455 5.6849 5.6366| | 2: 3.57 - 2.84 1.00 2888 124 0.1118 0.1447 5.2015 5.2724| | 3: 2.83 - 2.48 1.00 2820 163 0.1212 0.1248 5.0035 5.0295| | 4: 2.47 - 2.25 1.00 2825 136 0.1021 0.1161 4.7078 4.7657| | 5: 2.25 - 2.09 1.00 2756 127 0.0982 0.1094 4.6494 4.7155| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1223 4.3617 4.4774| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1289 4.09 4.2278| | 8: 1.87 - 1.79 1.00 2789 144 0.1023 0.1258 4.0024 4.0918| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1296 3.7315 3.9177| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1279 3.6447 3.7748| | 11: 1.66 - 1.61 1.00 2712 147 0.0977 0.1130 3.5813 3.6326| | 12: 1.61 - 1.56 1.00 2773 144 0.0932 0.1183 3.3657 3.4863| | 13: 1.56 - 1.52 1.00 2745 130 0.0990 0.1059 3.3545 3.4409| | 14: 1.52 - 1.48 1.00 2803 134 0.0992 0.1132 3.2712 3.357| | 15: 1.48 - 1.45 1.00 2738 128 0.1018 0.1344 3.1776 3.3276| | 16: 1.45 - 1.42 1.00 2756 161 0.1073 0.1274 3.1582 3.2661| | 17: 1.42 - 1.39 1.00 2785 139 0.1124 0.1281 3.1245 3.2254| | 18: 1.39 - 1.36 1.00 2741 179 0.1149 0.1394 3.089 3.2758| | 19: 1.36 - 1.34 1.00 2807 134 0.1213 0.1628 3.0959 3.2932| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1473 3.0903 3.1347| | 21: 1.32 - 1.30 1.00 2785 112 0.1417 0.1654 3.0893 3.176| | 22: 1.29 - 1.27 1.00 2704 152 0.1482 0.1925 3.0902 3.2854| | 23: 1.27 - 1.26 1.00 2802 156 0.1586 0.1845 3.1106 3.2086| | 24: 1.26 - 1.24 1.00 2744 132 0.1640 0.1797 3.1001 3.2049| | 25: 1.24 - 1.22 1.00 2733 148 0.1810 0.2296 3.1158 3.2878| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1805 3.1272 3.2112| | 27: 1.21 - 1.19 1.00 2814 148 0.2015 0.2132 3.1439 3.1562| | 28: 1.19 - 1.18 1.00 2671 147 0.2151 0.2313 3.1433 3.1611| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2339 3.1306 3.2168| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2528 3.1197 3.1776| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.94 9.18 1.00 0.96 6284.70| | 2: 3.57 - 2.84 2888 124 0.92 13.46 1.01 0.96 6284.70| | 3: 2.83 - 2.48 2820 163 0.89 17.47 0.99 0.96 5272.39| | 4: 2.47 - 2.25 2825 136 0.91 14.64 1.00 0.97 2661.97| | 5: 2.25 - 2.09 2756 127 0.89 16.90 1.01 0.97 2661.97| | 6: 2.09 - 1.97 2846 113 0.92 13.74 1.02 0.96 1572.51| | 7: 1.97 - 1.87 2787 165 0.94 11.00 1.02 0.96 643.36| | 8: 1.87 - 1.79 2789 144 0.91 14.62 1.00 0.96 643.36| | 9: 1.79 - 1.72 2745 138 0.93 11.64 0.98 0.96 350.07| | 10: 1.72 - 1.66 2831 160 0.93 12.49 0.98 0.96 291.33| | 11: 1.66 - 1.61 2712 147 0.93 13.13 0.98 0.96 278.09| | 12: 1.61 - 1.56 2773 144 0.95 9.71 0.99 0.96 153.15| | 13: 1.56 - 1.52 2745 130 0.94 11.41 1.02 0.96 153.15| | 14: 1.52 - 1.48 2803 134 0.94 11.44 1.02 0.96 136.11| | 15: 1.48 - 1.45 2738 128 0.95 10.53 1.01 0.97 104.91| | 16: 1.45 - 1.42 2756 161 0.94 11.71 1.01 0.97 104.91| | 17: 1.42 - 1.39 2785 139 0.94 11.49 1.01 0.97 94.54| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.97 88.54| | 19: 1.36 - 1.34 2807 134 0.94 12.40 1.00 0.97 88.54| | 20: 1.34 - 1.32 2696 147 0.94 12.48 0.99 0.96 83.14| | 21: 1.32 - 1.30 2785 112 0.94 13.38 0.98 0.95 82.76| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.95 82.94| | 23: 1.27 - 1.26 2802 156 0.92 14.92 0.97 0.94 83.83| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.96 0.94 83.83| | 25: 1.24 - 1.22 2733 148 0.91 16.48 0.96 0.93 85.25| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.92 86.82| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.92 86.82| | 28: 1.19 - 1.18 2671 147 0.88 20.24 1.01 0.92 89.84| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.91 90.97| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.91 90.97| |alpha: min = 0.91 max = 0.97 mean = 0.95| |beta: min = 82.76 max = 6284.70 mean = 984.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.14| |phase err.(test): min = 0.00 max = 87.79 mean = 14.19| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1199 0.1382 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1503 0.1503 0.1545 n_refl.: 87573 remove outliers: r(all,work,free)=0.1503 0.1503 0.1545 n_refl.: 87573 overall B=0.00 to atoms: r(all,work,free)=0.1504 0.1503 0.1545 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1383 n_refl.: 87573 remove outliers: r(all,work,free)=0.1208 0.1199 0.1383 n_refl.: 87571 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4054 290.072 255.627 0.434 1.000 0.275 11.894-9.307 90.20 88 4 0.2310 462.116 443.395 0.826 1.001 0.182 9.237-7.194 97.73 208 7 0.2522 384.906 376.065 0.910 1.002 0.115 7.162-5.571 100.00 427 22 0.2304 294.399 282.259 0.899 1.002 0.110 5.546-4.326 100.00 867 58 0.1201 404.137 399.996 0.964 1.002 0.105 4.315-3.360 100.00 1859 96 0.0991 384.337 381.638 1.004 1.001 0.100 3.356-2.611 100.00 3867 181 0.1185 252.489 250.377 1.012 1.001 0.080 2.608-2.026 99.99 8198 413 0.1034 167.377 166.460 1.023 1.000 0.000 2.025-1.573 100.00 17313 902 0.0983 81.738 81.994 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.246 35.885 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2126 22.838 21.455 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0035 ================= 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 : 0.2603 0.1921 0.082 5.250 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1734 0.082 5.250 9.1 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1734 0.082 5.250 9.1 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1739 0.082 5.250 9.1 119.5 20.1 258 0.006 1_weight: 0.1633 0.1739 0.082 5.250 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1211 0.1463 0.007 0.950 9.1 119.5 20.1 258 0.129 1_adp: 0.1233 0.1532 0.007 0.950 8.5 118.0 20.8 258 0.129 1_regHadp: 0.1237 0.1536 0.007 0.950 8.5 118.0 20.8 258 0.129 1_occ: 0.1236 0.1540 0.007 0.950 8.5 118.0 20.8 258 0.129 2_bss: 0.1234 0.1533 0.007 0.950 8.6 118.2 20.9 258 0.129 2_settarget: 0.1234 0.1533 0.007 0.950 8.6 118.2 20.9 258 0.129 2_updatecdl: 0.1234 0.1533 0.007 0.957 8.6 118.2 20.9 258 0.129 2_nqh: 0.1234 0.1533 0.007 0.957 8.6 118.2 20.9 258 0.129 2_sol: 0.1220 0.1496 0.007 0.957 8.6 118.2 23.3 434 n/a 2_weight: 0.1220 0.1496 0.007 0.957 8.6 118.2 23.3 434 n/a 2_xyzrec: 0.1216 0.1503 0.007 0.884 8.6 118.2 23.3 434 n/a 2_adp: 0.1194 0.1489 0.007 0.884 8.7 114.0 23.0 434 n/a 2_regHadp: 0.1194 0.1489 0.007 0.884 8.7 114.0 23.0 434 n/a 2_occ: 0.1197 0.1482 0.007 0.884 8.7 114.0 23.0 434 n/a 3_bss: 0.1193 0.1480 0.007 0.884 8.8 114.0 23.1 434 n/a 3_settarget: 0.1193 0.1480 0.007 0.884 8.8 114.0 23.1 434 n/a 3_updatecdl: 0.1193 0.1480 0.007 0.882 8.8 114.0 23.1 434 n/a 3_nqh: 0.1193 0.1480 0.007 0.882 8.8 114.0 23.1 434 n/a 3_sol: 0.1223 0.1492 0.007 0.882 8.8 114.0 21.9 442 n/a 3_weight: 0.1223 0.1492 0.007 0.882 8.8 114.0 21.9 442 n/a 3_xyzrec: 0.1226 0.1458 0.006 0.919 8.8 114.0 21.9 442 n/a 3_adp: 0.1211 0.1413 0.006 0.919 9.1 109.8 21.6 442 n/a 3_regHadp: 0.1212 0.1413 0.006 0.919 9.1 109.8 21.6 442 n/a 3_occ: 0.1207 0.1411 0.006 0.919 9.1 109.8 21.6 442 n/a 4_bss: 0.1192 0.1383 0.006 0.919 9.1 109.8 21.6 442 n/a 4_settarget: 0.1192 0.1383 0.006 0.919 9.1 109.8 21.6 442 n/a 4_updatecdl: 0.1192 0.1383 0.006 0.918 9.1 109.8 21.6 442 n/a 4_nqh: 0.1192 0.1383 0.006 0.918 9.1 109.8 21.6 442 n/a 4_sol: 0.1186 0.1369 0.006 0.918 9.1 109.8 21.3 435 n/a 4_weight: 0.1186 0.1369 0.006 0.918 9.1 109.8 21.3 435 n/a 4_xyzrec: 0.1189 0.1378 0.007 0.993 9.1 109.8 21.3 435 n/a 4_adp: 0.1178 0.1374 0.007 0.993 9.2 104.8 21.0 435 n/a 4_regHadp: 0.1179 0.1374 0.007 0.993 9.2 104.8 21.0 435 n/a 4_occ: 0.1174 0.1369 0.007 0.993 9.2 104.8 21.0 435 n/a 5_bss: 0.1170 0.1369 0.007 0.993 9.2 104.8 21.0 435 n/a 5_settarget: 0.1170 0.1369 0.007 0.993 9.2 104.8 21.0 435 n/a 5_updatecdl: 0.1170 0.1369 0.007 0.995 9.2 104.8 21.0 435 n/a 5_setrh: 0.1171 0.1369 0.007 0.995 9.2 104.8 21.0 435 n/a 5_nqh: 0.1171 0.1369 0.007 0.995 9.2 104.8 21.0 435 n/a 5_sol: 0.1169 0.1357 0.007 0.995 9.2 104.8 21.0 445 n/a 5_weight: 0.1169 0.1357 0.007 0.995 9.2 104.8 21.0 445 n/a 5_xyzrec: 0.1202 0.1389 0.007 1.105 9.2 104.8 21.0 445 n/a 5_adp: 0.1202 0.1387 0.007 1.105 9.2 104.3 21.0 445 n/a 5_regHadp: 0.1202 0.1388 0.007 1.105 9.2 104.3 21.0 445 n/a 5_occ: 0.1199 0.1382 0.007 1.105 9.2 104.3 21.0 445 n/a end: 0.1199 0.1383 0.007 1.105 9.2 104.3 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4279219_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4279219_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9200 Refinement macro-cycles (run) : 3581.3500 Write final files (write_after_run_outputs) : 59.2800 Total : 3645.5500 Total CPU time: 61.37 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:16 PST -0800 (1735452736.87 s) Start R-work = 0.1629, R-free = 0.1734 Final R-work = 0.1199, R-free = 0.1383 =============================================================================== Job complete usr+sys time: 3778.43 seconds wall clock time: 67 minutes 25.98 seconds (4045.98 seconds total)