Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.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" 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_1664580.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1664580.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.31, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 222.3 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.88: 403 0.88 - 1.14: 1201 1.14 - 1.40: 589 1.40 - 1.66: 906 1.66 - 1.92: 54 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.673 -0.215 1.20e-02 6.94e+03 3.20e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.236 1.057 0.179 1.08e-02 8.57e+03 2.76e+02 bond pdb=" C VAL A 51 " pdb=" O VAL A 51 " ideal model delta sigma weight residual 1.236 1.053 0.183 1.12e-02 7.97e+03 2.67e+02 bond pdb=" CA VAL A 44 " pdb=" CB VAL A 44 " ideal model delta sigma weight residual 1.540 1.739 -0.199 1.23e-02 6.61e+03 2.62e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 3071 4.64 - 9.27: 1907 9.27 - 13.91: 663 13.91 - 18.54: 124 18.54 - 23.18: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.07 107.39 14.68 1.03e+00 9.43e-01 2.03e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 107.84 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA VAL A 186 " pdb=" C VAL A 186 " pdb=" O VAL A 186 " ideal model delta sigma weight residual 120.78 137.07 -16.29 1.25e+00 6.40e-01 1.70e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.37 -10.14 8.10e-01 1.52e+00 1.57e+02 angle pdb=" CA GLY A 136 " pdb=" C GLY A 136 " pdb=" O GLY A 136 " ideal model delta sigma weight residual 119.27 132.58 -13.31 1.07e+00 8.73e-01 1.55e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.66: 946 16.66 - 33.31: 107 33.31 - 49.96: 39 49.96 - 66.61: 16 66.61 - 83.26: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+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 180.00 156.62 23.38 0 5.00e+00 4.00e-02 2.19e+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 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.267: 117 0.267 - 0.532: 88 0.532 - 0.798: 24 0.798 - 1.064: 11 1.064 - 1.330: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+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 -1.33 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.45e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.095 9.50e-02 1.11e+02 7.29e-02 9.78e+01 pdb=" NE ARG A 145 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.091 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.065 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.101 2.00e-02 2.50e+03 5.43e-02 8.84e+01 pdb=" CG PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG BGLN A 80 " 0.059 2.00e-02 2.50e+03 7.62e-02 8.71e+01 pdb=" CD BGLN A 80 " -0.100 2.00e-02 2.50e+03 pdb=" OE1BGLN A 80 " -0.007 2.00e-02 2.50e+03 pdb=" NE2BGLN A 80 " 0.106 2.00e-02 2.50e+03 pdb="HE21BGLN A 80 " -0.094 2.00e-02 2.50e+03 pdb="HE22BGLN A 80 " 0.035 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7812 2.86 - 3.44: 10667 3.44 - 4.02: 15259 4.02 - 4.60: 22099 Nonbonded interactions: 56621 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.697 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.821 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.836 2.100 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.840 2.450 ... (remaining 56616 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_1664580_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= 0.2600 r_free= 0.1923 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786099 | | target function (ml) not normalized (work): 232098.721947 | | target function (ml) not normalized (free): 11778.886318 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3047 0.2085 7.1149 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2423 0.1737 4.3411 4.324| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1680 4.1221 4.1724| | 4: 2.47 - 2.25 1.00 2825 136 0.2324 0.1482 3.8219 3.8151| | 5: 2.25 - 2.09 1.00 2756 127 0.2464 0.1644 3.7931 3.8308| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1623 3.4622 3.5318| | 7: 1.97 - 1.87 1.00 2787 165 0.2502 0.1803 3.1166 3.1775| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.1814 3.0518 3.146| | 9: 1.79 - 1.72 1.00 2745 138 0.2440 0.1807 2.8981 2.8589| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1855 2.7906 2.8662| | 11: 1.66 - 1.61 1.00 2740 147 0.2489 0.1794 2.7558 2.7483| | 12: 1.61 - 1.56 1.00 2787 146 0.2532 0.2032 2.6332 2.6722| | 13: 1.56 - 1.52 1.00 2745 130 0.2533 0.1940 2.5712 2.6345| | 14: 1.52 - 1.48 1.00 2803 134 0.2561 0.2027 2.4944 2.5731| | 15: 1.48 - 1.45 1.00 2738 128 0.2527 0.2099 2.4145 2.503| | 16: 1.45 - 1.42 1.00 2756 161 0.2638 0.2343 2.3983 2.5076| | 17: 1.42 - 1.39 1.00 2785 139 0.2621 0.1883 2.3319 2.3037| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2200 2.2659 2.3232| | 19: 1.36 - 1.34 1.00 2807 134 0.2650 0.2431 2.2356 2.3639| | 20: 1.34 - 1.32 1.00 2696 147 0.2685 0.1957 2.2116 2.1074| | 21: 1.32 - 1.30 1.00 2785 112 0.2677 0.2392 2.1593 2.222| | 22: 1.29 - 1.27 1.00 2704 152 0.2699 0.2398 2.1281 2.1228| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2522 2.0929 2.1974| | 24: 1.26 - 1.24 1.00 2744 132 0.2695 0.2350 2.054 2.1348| | 25: 1.24 - 1.22 1.00 2734 148 0.2809 0.2419 2.0331 2.0269| | 26: 1.22 - 1.21 1.00 2727 135 0.2849 0.2270 1.9901 2.0711| | 27: 1.21 - 1.19 1.00 2814 148 0.2945 0.2605 1.9966 2.0504| | 28: 1.19 - 1.18 1.00 2671 147 0.2994 0.2920 1.9745 2.0115| | 29: 1.18 - 1.16 1.00 2800 134 0.2982 0.2368 1.9531 1.9307| | 30: 1.16 - 1.15 1.00 2740 148 0.3049 0.2942 1.9174 1.9426| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.64 0.76 0.23 1455.17| | 2: 3.57 - 2.84 2876 122 0.81 25.80 1.27 0.23 1455.17| | 3: 2.84 - 2.48 2833 165 0.74 31.76 1.24 0.24 1207.20| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.26 0.25 563.67| | 5: 2.25 - 2.09 2756 127 0.78 28.99 1.28 0.25 563.67| | 6: 2.09 - 1.97 2846 113 0.83 22.66 1.29 0.25 309.41| | 7: 1.97 - 1.87 2787 165 0.90 16.67 1.28 0.26 92.56| | 8: 1.87 - 1.79 2789 144 0.86 21.27 1.25 0.26 92.56| | 9: 1.79 - 1.72 2745 138 0.88 18.69 1.24 0.25 55.59| | 10: 1.72 - 1.66 2789 158 0.86 20.31 1.22 0.25 48.19| | 11: 1.66 - 1.61 2740 147 0.86 21.40 1.24 0.25 46.54| | 12: 1.61 - 1.56 2787 146 0.88 18.69 1.23 0.25 29.85| | 13: 1.56 - 1.52 2745 130 0.87 20.51 1.24 0.25 29.85| | 14: 1.52 - 1.48 2803 134 0.86 21.09 1.24 0.25 26.68| | 15: 1.48 - 1.45 2738 128 0.87 20.07 1.22 0.25 20.87| | 16: 1.45 - 1.42 2756 161 0.86 21.46 1.22 0.25 20.87| | 17: 1.42 - 1.39 2785 139 0.87 20.70 1.22 0.25 17.64| | 18: 1.39 - 1.36 2741 179 0.87 20.98 1.23 0.25 15.77| | 19: 1.36 - 1.34 2807 134 0.85 22.20 1.22 0.25 15.77| | 20: 1.34 - 1.32 2696 147 0.87 20.58 1.22 0.25 12.78| | 21: 1.32 - 1.30 2785 112 0.86 21.66 1.20 0.25 12.57| | 22: 1.29 - 1.27 2704 152 0.86 21.84 1.21 0.25 12.27| | 23: 1.27 - 1.26 2802 156 0.86 21.86 1.21 0.24 10.78| | 24: 1.26 - 1.24 2744 132 0.86 22.04 1.19 0.24 10.78| | 25: 1.24 - 1.22 2734 148 0.85 23.18 1.21 0.24 10.20| | 26: 1.22 - 1.21 2727 135 0.85 23.38 1.21 0.23 9.56| | 27: 1.21 - 1.19 2814 148 0.84 24.12 1.20 0.23 9.56| | 28: 1.19 - 1.18 2671 147 0.83 24.81 1.19 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 24.81 1.17 0.23 8.67| | 30: 1.16 - 1.15 2740 148 0.82 26.26 1.17 0.23 8.67| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.67 max = 1455.17 mean = 211.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.40| |phase err.(test): min = 0.00 max = 89.94 mean = 22.38| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.259 1557 Z= 5.326 Angle : 5.330 17.017 2118 Z= 3.694 Chirality : 0.404 1.330 243 Planarity : 0.032 0.104 284 Dihedral : 13.685 83.258 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -2.85 (0.47), residues: 224 helix: -3.06 (0.33), residues: 103 sheet: -0.23 (0.89), residues: 28 loop : -0.69 (0.59), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.025 ARG A 145 TYR 0.066 0.031 TYR A 141 PHE 0.082 0.042 PHE A 162 HIS 0.044 0.016 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= 0.2600 r_free= 0.1923 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786099 | | target function (ml) not normalized (work): 232098.721947 | | target function (ml) not normalized (free): 11778.886318 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2558 0.2601 0.1923 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2558 0.2601 0.1923 n_refl.: 87602 remove outliers: r(all,work,free)=0.1967 0.1971 0.1923 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1989 0.1994 0.1934 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1627 0.1621 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1627 0.1620 0.1756 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 0.3857 386.330 366.731 0.696 1.000 0.407 11.894-9.307 99.02 97 4 0.1853 613.666 592.202 0.927 1.001 0.390 9.237-7.194 100.00 213 7 0.2174 501.904 491.067 0.947 1.001 0.354 7.162-5.571 100.00 427 22 0.2172 376.651 365.741 0.931 1.001 0.293 5.546-4.326 100.00 867 58 0.1272 517.048 512.017 0.971 1.001 0.213 4.315-3.360 100.00 1859 96 0.1149 491.717 487.428 1.008 1.002 0.179 3.356-2.611 100.00 3867 181 0.1420 323.032 319.635 0.998 1.002 0.109 2.608-2.026 99.99 8198 413 0.1330 214.141 211.979 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1626 104.575 103.972 1.010 1.003 0.000 1.573-1.221 100.00 36679 1900 0.2044 46.373 45.158 0.995 1.003 0.000 1.221-1.150 99.97 13689 708 0.2560 29.218 26.964 0.969 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0413 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1620 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1621 r_free=0.1757 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.112551 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2017.046845 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 0.1213 0.1461 0.0248 0.007 0.9 1.3 0.5 0.0 0 12.056 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.61 2.48 3.013 19.039 2017.047 0.017 12.43 15.35 2.92 3.184 19.513 2017.047 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.59 20.96 2.87 0 1785 Protein: 8.47 118.59 17.83 2.87 0 1519 Water: 11.03 114.85 39.17 N/A 0 258 Other: 22.91 36.35 29.14 N/A 0 8 Chain A: 8.47 118.59 20.96 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.48 1211 19.48 - 30.50 227 30.50 - 41.51 162 41.51 - 52.52 103 52.52 - 63.53 53 63.53 - 74.55 17 74.55 - 85.56 5 85.56 - 96.57 4 96.57 - 107.58 0 107.58 - 118.59 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1535 r_work=0.1247 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 r_free = 0.1540 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1246 r_free = 0.1543 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015368 | | target function (ls_wunit_k1) not normalized (work): 1280.104694 | | target function (ls_wunit_k1) not normalized (free): 113.394146 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1246 0.1543 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1696 0.1766 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1696 0.1766 n_refl.: 87593 overall B=0.15 to atoms: r(all,work,free)=0.1721 0.1720 0.1782 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1243 0.1535 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1243 0.1535 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 0.3595 299.613 279.424 0.683 0.923 0.374 11.894-9.307 99.02 97 4 0.1637 479.964 468.285 0.983 0.924 0.370 9.237-7.194 100.00 213 7 0.1809 392.551 387.207 1.027 0.924 0.340 7.162-5.571 100.00 427 22 0.1712 294.588 289.347 0.999 0.925 0.258 5.546-4.326 100.00 867 58 0.0915 404.397 401.787 1.030 0.926 0.199 4.315-3.360 100.00 1859 96 0.0772 384.584 383.643 1.076 0.927 0.180 3.356-2.611 100.00 3867 181 0.1020 252.652 251.931 1.076 0.929 0.057 2.608-2.026 99.99 8198 413 0.0977 167.485 166.900 1.084 0.933 0.000 2.025-1.573 100.00 17313 902 0.1210 81.791 81.959 1.083 0.939 0.000 1.573-1.221 100.00 36679 1900 0.1654 36.269 35.734 1.056 0.950 0.000 1.221-1.150 99.97 13689 708 0.2362 22.852 21.380 1.010 0.958 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0580 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1535 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1245 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1536 | n_water=258 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1254 r_free=0.1536 | n_water=252 | time (s): 26.800 (total time: 29.080) Filter (q & B) r_work=0.1257 r_free=0.1535 | n_water=249 | time (s): 3.380 (total time: 32.460) Compute maps r_work=0.1257 r_free=0.1535 | n_water=249 | time (s): 1.760 (total time: 34.220) Filter (map) r_work=0.1276 r_free=0.1540 | n_water=235 | time (s): 3.570 (total time: 37.790) Find peaks r_work=0.1276 r_free=0.1540 | n_water=235 | time (s): 0.690 (total time: 38.480) Add new water r_work=0.1429 r_free=0.1688 | n_water=459 | time (s): 3.510 (total time: 41.990) Refine new water occ: r_work=0.1341 r_free=0.1563 adp: r_work=0.1259 r_free=0.1502 occ: r_work=0.1273 r_free=0.1504 adp: r_work=0.1237 r_free=0.1482 occ: r_work=0.1241 r_free=0.1478 adp: r_work=0.1231 r_free=0.1474 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1474 r_work=0.1231 r_free=0.1474 | n_water=459 | time (s): 116.130 (total time: 158.120) Filter (q & B) r_work=0.1236 r_free=0.1479 | n_water=439 | time (s): 3.940 (total time: 162.060) Filter (dist only) r_work=0.1236 r_free=0.1479 | n_water=439 | time (s): 41.740 (total time: 203.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.093606 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1554.360454 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1509 0.0277 0.007 0.9 1.9 0.5 0.0 0 12.047 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.09 2.77 3.784 23.251 1554.360 0.015 11.99 14.79 2.81 4.201 23.078 1554.360 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 114.29 23.35 2.61 204 1762 Protein: 8.80 114.29 17.62 2.61 0 1519 Water: 11.14 72.15 43.07 N/A 204 235 Other: 24.28 34.96 28.57 N/A 0 8 Chain A: 8.80 114.29 20.33 N/A 0 1762 Chain S: 14.42 72.15 49.46 N/A 204 0 Histogram: Values Number of atoms 8.80 - 19.35 1209 19.35 - 29.90 246 29.90 - 40.45 189 40.45 - 51.00 132 51.00 - 61.55 123 61.55 - 72.09 56 72.09 - 82.64 5 82.64 - 93.19 3 93.19 - 103.74 1 103.74 - 114.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1479 r_work=0.1199 r_free=0.1479 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1479 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1483 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 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= 0.1201 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014057 | | target function (ls_wunit_k1) not normalized (work): 1170.902677 | | target function (ls_wunit_k1) not normalized (free): 105.200513 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1597 0.1592 0.1728 n_refl.: 87592 remove outliers: r(all,work,free)=0.1597 0.1592 0.1728 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1604 0.1600 0.1733 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1197 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1210 0.1196 0.1481 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3465 295.542 271.188 0.628 0.937 0.364 11.894-9.307 99.02 97 4 0.1427 479.964 475.303 0.977 0.937 0.360 9.237-7.194 100.00 213 7 0.1629 392.551 392.517 1.048 0.938 0.280 7.162-5.571 100.00 427 22 0.1525 294.588 291.429 1.002 0.938 0.224 5.546-4.326 100.00 867 58 0.0843 404.397 401.444 1.024 0.938 0.205 4.315-3.360 100.00 1859 96 0.0710 384.584 383.336 1.068 0.939 0.200 3.356-2.611 100.00 3867 181 0.0960 252.652 251.952 1.075 0.940 0.170 2.608-2.026 99.99 8198 413 0.0965 167.485 166.979 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1177 81.791 81.967 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1606 36.269 35.775 1.066 0.950 0.000 1.221-1.150 99.97 13689 708 0.2331 22.852 21.402 1.019 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0710 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1481 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=0.1196 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1481 | n_water=439 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1197 r_free=0.1479 | n_water=436 | time (s): 37.760 (total time: 39.510) Filter (q & B) r_work=0.1197 r_free=0.1479 | n_water=436 | time (s): 0.980 (total time: 40.490) Compute maps r_work=0.1197 r_free=0.1479 | n_water=436 | time (s): 1.170 (total time: 41.660) Filter (map) r_work=0.1242 r_free=0.1474 | n_water=289 | time (s): 3.760 (total time: 45.420) Find peaks r_work=0.1242 r_free=0.1474 | n_water=289 | time (s): 0.690 (total time: 46.110) Add new water r_work=0.1364 r_free=0.1580 | n_water=468 | time (s): 3.250 (total time: 49.360) Refine new water occ: r_work=0.1266 r_free=0.1511 adp: r_work=0.1267 r_free=0.1509 occ: r_work=0.1244 r_free=0.1497 adp: r_work=0.1241 r_free=0.1492 occ: r_work=0.1228 r_free=0.1491 adp: r_work=0.1221 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1482 r_work=0.1221 r_free=0.1482 | n_water=468 | time (s): 221.100 (total time: 270.460) Filter (q & B) r_work=0.1224 r_free=0.1475 | n_water=437 | time (s): 3.630 (total time: 274.090) Filter (dist only) r_work=0.1224 r_free=0.1475 | n_water=436 | time (s): 38.150 (total time: 312.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.073409 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.714196 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 0.1225 0.1445 0.0220 0.006 0.9 1.6 0.5 0.0 0 1.037 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.45 2.20 3.618 22.072 45.714 3.723 12.17 14.09 1.91 4.092 21.886 45.714 3.656 Individual atomic B min max mean iso aniso Overall: 9.22 109.68 21.63 2.31 204 1759 Protein: 9.22 109.68 17.21 2.31 0 1519 Water: 11.56 69.33 36.94 N/A 204 232 Other: 20.42 31.33 26.24 N/A 0 8 Chain A: 9.22 109.68 19.87 N/A 0 1759 Chain S: 15.35 60.41 36.81 N/A 204 0 Histogram: Values Number of atoms 9.22 - 19.27 1235 19.27 - 29.32 271 29.32 - 39.36 214 39.36 - 49.41 131 49.41 - 59.45 78 59.45 - 69.50 22 69.50 - 79.55 6 79.55 - 89.59 3 89.59 - 99.64 1 99.64 - 109.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1409 r_work=0.1219 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1410 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1215 r_free = 0.1414 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1215 r_free= 0.1414 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655555 | | target function (ml) not normalized (work): 304482.145730 | | target function (ml) not normalized (free): 16089.184138 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1215 0.1414 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1597 n_refl.: 87589 remove outliers: r(all,work,free)=0.1548 0.1547 0.1597 n_refl.: 87589 overall B=0.00 to atoms: r(all,work,free)=0.1549 0.1548 0.1597 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1208 0.1392 n_refl.: 87589 remove outliers: r(all,work,free)=0.1215 0.1206 0.1392 n_refl.: 87583 ======================== 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 0.3977 292.691 261.332 0.486 1.000 0.330 11.894-9.307 98.04 96 4 0.2451 473.279 460.058 0.860 1.001 0.259 9.237-7.194 98.64 210 7 0.2335 385.077 384.319 0.950 1.002 0.190 7.162-5.571 100.00 427 22 0.2065 294.588 285.279 0.916 1.002 0.177 5.546-4.326 100.00 867 58 0.1105 404.397 399.498 0.960 1.002 0.172 4.315-3.360 100.00 1859 96 0.0945 384.584 381.919 1.001 1.002 0.170 3.356-2.611 100.00 3867 181 0.1163 252.652 250.888 1.008 1.002 0.170 2.608-2.026 99.99 8198 413 0.1058 167.485 166.426 1.019 1.002 0.000 2.025-1.573 100.00 17313 902 0.1021 81.791 81.929 1.032 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.269 35.792 1.022 1.003 0.000 1.221-1.150 99.97 13689 708 0.2125 22.852 21.325 0.974 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0048 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1392 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=0.1206 r_free=0.1392 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1392 | n_water=436 | time (s): 2.110 (total time: 2.110) Filter (dist) r_work=0.1206 r_free=0.1390 | n_water=434 | time (s): 39.120 (total time: 41.230) Filter (q & B) r_work=0.1206 r_free=0.1390 | n_water=433 | time (s): 3.630 (total time: 44.860) Compute maps r_work=0.1206 r_free=0.1390 | n_water=433 | time (s): 1.540 (total time: 46.400) Filter (map) r_work=0.1236 r_free=0.1389 | n_water=304 | time (s): 3.420 (total time: 49.820) Find peaks r_work=0.1236 r_free=0.1389 | n_water=304 | time (s): 0.520 (total time: 50.340) Add new water r_work=0.1305 r_free=0.1441 | n_water=461 | time (s): 3.250 (total time: 53.590) Refine new water occ: r_work=0.1229 r_free=0.1371 adp: r_work=0.1230 r_free=0.1373 occ: r_work=0.1214 r_free=0.1357 adp: r_work=0.1212 r_free=0.1357 occ: r_work=0.1202 r_free=0.1355 adp: r_work=0.1199 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1352 r_work=0.1199 r_free=0.1352 | n_water=461 | time (s): 188.760 (total time: 242.350) Filter (q & B) r_work=0.1205 r_free=0.1358 | n_water=431 | time (s): 3.330 (total time: 245.680) Filter (dist only) r_work=0.1211 r_free=0.1356 | n_water=429 | time (s): 36.060 (total time: 281.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.906105 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.540489 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1366 0.0154 0.006 0.9 1.6 0.5 0.0 0 0.953 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 13.66 1.54 3.424 21.435 46.540 3.645 11.96 13.55 1.60 3.743 21.328 46.540 3.629 Individual atomic B min max mean iso aniso Overall: 9.29 105.96 21.14 2.17 201 1755 Protein: 9.29 105.96 16.99 2.17 0 1519 Water: 11.49 66.55 35.75 N/A 201 228 Other: 21.24 29.79 25.51 N/A 0 8 Chain A: 9.29 105.96 19.54 N/A 0 1755 Chain S: 15.24 60.00 35.05 N/A 201 0 Histogram: Values Number of atoms 9.29 - 18.96 1230 18.96 - 28.63 279 28.63 - 38.30 210 38.30 - 47.96 134 47.96 - 57.63 68 57.63 - 67.30 24 67.30 - 76.96 6 76.96 - 86.63 2 86.63 - 96.30 1 96.30 - 105.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1355 r_work=0.1196 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1356 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1354 target_work(ml) = 3.628 | | 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.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1191 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627514 | | target function (ml) not normalized (work): 302124.779259 | | target function (ml) not normalized (free): 15952.890533 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1191 0.1354 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1530 0.1532 0.1535 n_refl.: 87583 remove outliers: r(all,work,free)=0.1530 0.1532 0.1535 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1528 0.1529 0.1534 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1190 0.1350 n_refl.: 87583 remove outliers: r(all,work,free)=0.1194 0.1186 0.1350 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4116 290.258 248.252 0.442 1.000 0.314 11.894-9.307 94.12 92 4 0.2216 481.756 451.368 0.832 1.002 0.310 9.237-7.194 97.73 208 7 0.2440 385.154 377.758 0.913 1.002 0.183 7.162-5.571 100.00 427 22 0.2177 294.588 285.051 0.899 1.002 0.156 5.546-4.326 100.00 867 58 0.1159 404.397 399.830 0.953 1.002 0.140 4.315-3.360 100.00 1859 96 0.0959 384.584 382.207 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1156 252.652 250.973 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1032 167.485 166.677 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.0973 81.791 82.088 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.269 35.907 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2126 22.852 21.479 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0344 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1350 After: r_work=0.1186 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1186 r_free=0.1350 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=0.1186 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1350 | n_water=429 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1186 r_free=0.1352 | n_water=428 | time (s): 34.730 (total time: 36.790) Filter (q & B) r_work=0.1186 r_free=0.1352 | n_water=428 | time (s): 1.020 (total time: 37.810) Compute maps r_work=0.1186 r_free=0.1352 | n_water=428 | time (s): 1.490 (total time: 39.300) Filter (map) r_work=0.1209 r_free=0.1357 | n_water=328 | time (s): 3.390 (total time: 42.690) Find peaks r_work=0.1209 r_free=0.1357 | n_water=328 | time (s): 0.460 (total time: 43.150) Add new water r_work=0.1265 r_free=0.1398 | n_water=477 | time (s): 2.650 (total time: 45.800) Refine new water occ: r_work=0.1202 r_free=0.1350 adp: r_work=0.1202 r_free=0.1352 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1181 r_free=0.1334 adp: r_work=0.1178 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1178 r_free=0.1335 r_work=0.1178 r_free=0.1335 | n_water=477 | time (s): 186.920 (total time: 232.720) Filter (q & B) r_work=0.1185 r_free=0.1345 | n_water=444 | time (s): 3.240 (total time: 235.960) Filter (dist only) r_work=0.1185 r_free=0.1346 | n_water=440 | time (s): 36.740 (total time: 272.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.949611 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.681659 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1356 0.0151 0.007 1.0 1.9 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.56 1.51 3.310 21.175 44.682 3.633 12.11 13.60 1.50 3.585 21.088 44.682 3.628 Individual atomic B min max mean iso aniso Overall: 9.27 101.59 20.98 2.03 215 1752 Protein: 9.27 101.59 16.77 2.03 0 1519 Water: 11.47 66.21 35.48 N/A 215 225 Other: 20.82 28.97 24.90 N/A 0 8 Chain A: 9.27 101.59 19.25 N/A 0 1752 Chain S: 14.40 60.06 35.09 N/A 215 0 Histogram: Values Number of atoms 9.27 - 18.50 1223 18.50 - 27.73 274 27.73 - 36.96 215 36.96 - 46.20 137 46.20 - 55.43 76 55.43 - 64.66 28 64.66 - 73.89 9 73.89 - 83.13 2 83.13 - 92.36 1 92.36 - 101.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1360 r_work=0.1211 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1360 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1357 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626363 | | target function (ml) not normalized (work): 301999.900948 | | target function (ml) not normalized (free): 15947.460509 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1419 0.1365 5.7138 5.5924| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1353 5.1903 5.2269| | 3: 2.83 - 2.48 1.00 2820 163 0.1243 0.1357 4.9918 5.0152| | 4: 2.47 - 2.25 1.00 2825 136 0.1040 0.1066 4.6941 4.7183| | 5: 2.25 - 2.09 1.00 2756 127 0.1006 0.1095 4.6329 4.7003| | 6: 2.09 - 1.97 1.00 2846 113 0.0987 0.1210 4.3514 4.4709| | 7: 1.97 - 1.87 1.00 2787 165 0.1006 0.1275 4.0856 4.2232| | 8: 1.87 - 1.79 1.00 2789 144 0.1039 0.1236 4.003 4.0766| | 9: 1.79 - 1.72 1.00 2745 138 0.0957 0.1288 3.7273 3.891| | 10: 1.72 - 1.66 1.00 2831 160 0.1010 0.1275 3.6439 3.7945| | 11: 1.66 - 1.61 1.00 2712 147 0.0973 0.1147 3.5816 3.6419| | 12: 1.61 - 1.56 1.00 2773 144 0.0923 0.1167 3.3568 3.4889| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1112 3.3532 3.4587| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1123 3.272 3.3558| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1370 3.1769 3.334| | 16: 1.45 - 1.42 1.00 2756 161 0.1076 0.1283 3.1625 3.2567| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1290 3.1265 3.2305| | 18: 1.39 - 1.36 1.00 2741 179 0.1158 0.1385 3.0934 3.2676| | 19: 1.36 - 1.34 1.00 2807 134 0.1208 0.1610 3.0962 3.2699| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1473 3.0938 3.1372| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1591 3.0872 3.1516| | 22: 1.29 - 1.27 1.00 2704 152 0.1477 0.1916 3.089 3.2972| | 23: 1.27 - 1.26 1.00 2802 156 0.1574 0.1869 3.105 3.2156| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1759 3.0966 3.1971| | 25: 1.24 - 1.22 1.00 2733 148 0.1796 0.2366 3.1124 3.3021| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1801 3.1276 3.2099| | 27: 1.21 - 1.19 1.00 2814 148 0.2015 0.2111 3.1438 3.1583| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2292 3.1427 3.1631| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2344 3.1285 3.224| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2475 3.1184 3.1629| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.51 1.00 0.97 5758.43| | 2: 3.57 - 2.84 2888 124 0.93 12.69 1.01 0.97 5758.43| | 3: 2.83 - 2.48 2820 163 0.89 16.75 0.98 0.98 4842.18| | 4: 2.47 - 2.25 2825 136 0.91 14.05 1.00 0.98 2479.49| | 5: 2.25 - 2.09 2756 127 0.90 16.16 1.01 0.98 2479.49| | 6: 2.09 - 1.97 2846 113 0.92 13.34 1.02 0.98 1484.15| | 7: 1.97 - 1.87 2787 165 0.94 10.90 1.02 0.98 635.26| | 8: 1.87 - 1.79 2789 144 0.91 14.47 1.00 0.98 635.26| | 9: 1.79 - 1.72 2745 138 0.93 11.58 0.98 0.97 347.27| | 10: 1.72 - 1.66 2831 160 0.93 12.45 0.98 0.97 289.60| | 11: 1.66 - 1.61 2712 147 0.93 13.08 0.98 0.97 276.48| | 12: 1.61 - 1.56 2773 144 0.95 9.76 0.99 0.97 152.73| | 13: 1.56 - 1.52 2745 130 0.94 11.33 1.02 0.97 152.73| | 14: 1.52 - 1.48 2803 134 0.94 11.49 1.02 0.98 136.10| | 15: 1.48 - 1.45 2738 128 0.95 10.58 1.01 0.98 105.65| | 16: 1.45 - 1.42 2756 161 0.94 11.75 1.01 0.98 105.65| | 17: 1.42 - 1.39 2785 139 0.94 11.55 1.01 0.99 94.86| | 18: 1.39 - 1.36 2741 179 0.94 11.85 1.01 0.99 88.62| | 19: 1.36 - 1.34 2807 134 0.94 12.32 1.00 0.99 88.62| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.97 83.06| | 21: 1.32 - 1.30 2785 112 0.94 13.37 0.98 0.97 82.67| | 22: 1.29 - 1.27 2704 152 0.93 13.87 0.98 0.97 82.82| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 83.58| | 24: 1.26 - 1.24 2744 132 0.92 14.96 0.97 0.95 83.58| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 85.03| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.94 86.64| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.94 86.64| | 28: 1.19 - 1.18 2671 147 0.88 20.18 1.01 0.93 89.55| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 90.65| | 30: 1.16 - 1.15 2739 148 0.86 21.85 0.98 0.93 90.65| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.67 max = 5758.43 mean = 916.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.98| |phase err.(test): min = 0.00 max = 89.57 mean = 14.06| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1206 0.1357 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1528 0.1529 0.1542 n_refl.: 87575 remove outliers: r(all,work,free)=0.1528 0.1529 0.1542 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1525 0.1527 0.1540 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1206 0.1359 n_refl.: 87575 remove outliers: r(all,work,free)=0.1212 0.1204 0.1359 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4227 290.258 250.061 0.439 1.002 0.310 11.894-9.307 92.16 90 4 0.2222 482.527 466.160 0.863 1.003 0.260 9.237-7.194 97.27 207 7 0.2486 384.679 377.334 0.905 1.002 0.180 7.162-5.571 100.00 427 22 0.2222 294.588 284.269 0.890 1.002 0.150 5.546-4.326 100.00 867 58 0.1205 404.397 399.471 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.0998 384.584 381.831 0.995 1.002 0.117 3.356-2.611 100.00 3867 181 0.1197 252.652 250.512 1.001 1.002 0.043 2.608-2.026 99.99 8198 413 0.1054 167.485 166.533 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0989 81.791 82.030 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1232 36.269 35.900 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2118 22.852 21.479 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0315 ================= 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 : 0.2600 0.1923 0.081 5.330 8.8 119.3 19.9 258 0.000 1_bss: 0.1620 0.1756 0.081 5.330 9.0 119.5 20.1 258 0.000 1_settarget: 0.1620 0.1756 0.081 5.330 9.0 119.5 20.1 258 0.000 1_nqh: 0.1621 0.1757 0.081 5.330 9.0 119.5 20.1 258 0.003 1_weight: 0.1621 0.1757 0.081 5.330 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1461 0.007 0.949 9.0 119.5 20.1 258 0.132 1_adp: 0.1243 0.1535 0.007 0.949 8.5 118.6 21.0 258 0.132 1_regHadp: 0.1247 0.1540 0.007 0.949 8.5 118.6 21.0 258 0.132 1_occ: 0.1246 0.1543 0.007 0.949 8.5 118.6 21.0 258 0.132 2_bss: 0.1243 0.1535 0.007 0.949 8.6 118.7 21.1 258 0.132 2_settarget: 0.1243 0.1535 0.007 0.949 8.6 118.7 21.1 258 0.132 2_updatecdl: 0.1243 0.1535 0.007 0.955 8.6 118.7 21.1 258 0.132 2_nqh: 0.1245 0.1536 0.007 0.955 8.6 118.7 21.1 258 0.132 2_sol: 0.1236 0.1479 0.007 0.955 8.6 118.7 23.7 439 n/a 2_weight: 0.1236 0.1479 0.007 0.955 8.6 118.7 23.7 439 n/a 2_xyzrec: 0.1232 0.1509 0.007 0.872 8.6 118.7 23.7 439 n/a 2_adp: 0.1199 0.1479 0.007 0.872 8.8 114.3 23.4 439 n/a 2_regHadp: 0.1199 0.1479 0.007 0.872 8.8 114.3 23.4 439 n/a 2_occ: 0.1201 0.1483 0.007 0.872 8.8 114.3 23.4 439 n/a 3_bss: 0.1196 0.1481 0.007 0.872 8.8 114.3 23.4 439 n/a 3_settarget: 0.1196 0.1481 0.007 0.872 8.8 114.3 23.4 439 n/a 3_updatecdl: 0.1196 0.1481 0.007 0.873 8.8 114.3 23.4 439 n/a 3_nqh: 0.1196 0.1481 0.007 0.873 8.8 114.3 23.4 439 n/a 3_sol: 0.1224 0.1475 0.007 0.873 8.8 114.3 22.0 436 n/a 3_weight: 0.1224 0.1475 0.007 0.873 8.8 114.3 22.0 436 n/a 3_xyzrec: 0.1225 0.1445 0.006 0.929 8.8 114.3 22.0 436 n/a 3_adp: 0.1218 0.1409 0.006 0.929 9.2 109.7 21.6 436 n/a 3_regHadp: 0.1219 0.1410 0.006 0.929 9.2 109.7 21.6 436 n/a 3_occ: 0.1215 0.1414 0.006 0.929 9.2 109.7 21.6 436 n/a 4_bss: 0.1206 0.1392 0.006 0.929 9.2 109.7 21.6 436 n/a 4_settarget: 0.1206 0.1392 0.006 0.929 9.2 109.7 21.6 436 n/a 4_updatecdl: 0.1206 0.1392 0.006 0.929 9.2 109.7 21.6 436 n/a 4_nqh: 0.1206 0.1392 0.006 0.929 9.2 109.7 21.6 436 n/a 4_sol: 0.1211 0.1356 0.006 0.929 9.2 109.7 21.3 429 n/a 4_weight: 0.1211 0.1356 0.006 0.929 9.2 109.7 21.3 429 n/a 4_xyzrec: 0.1212 0.1366 0.006 0.949 9.2 109.7 21.3 429 n/a 4_adp: 0.1196 0.1355 0.006 0.949 9.3 106.0 21.1 429 n/a 4_regHadp: 0.1196 0.1356 0.006 0.949 9.3 106.0 21.1 429 n/a 4_occ: 0.1191 0.1354 0.006 0.949 9.3 106.0 21.1 429 n/a 5_bss: 0.1186 0.1350 0.006 0.949 9.3 106.0 21.1 429 n/a 5_settarget: 0.1186 0.1350 0.006 0.949 9.3 106.0 21.1 429 n/a 5_updatecdl: 0.1186 0.1350 0.006 0.949 9.3 106.0 21.1 429 n/a 5_setrh: 0.1186 0.1350 0.006 0.949 9.3 106.0 21.1 429 n/a 5_nqh: 0.1186 0.1350 0.006 0.949 9.3 106.0 21.1 429 n/a 5_sol: 0.1185 0.1346 0.006 0.949 9.3 106.0 21.1 440 n/a 5_weight: 0.1185 0.1346 0.006 0.949 9.3 106.0 21.1 440 n/a 5_xyzrec: 0.1205 0.1356 0.007 1.004 9.3 106.0 21.1 440 n/a 5_adp: 0.1211 0.1360 0.007 1.004 9.3 101.6 21.0 440 n/a 5_regHadp: 0.1211 0.1360 0.007 1.004 9.3 101.6 21.0 440 n/a 5_occ: 0.1206 0.1357 0.007 1.004 9.3 101.6 21.0 440 n/a end: 0.1204 0.1359 0.007 1.004 9.3 101.6 21.0 440 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1664580_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1664580_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3600 Refinement macro-cycles (run) : 3470.1500 Write final files (write_after_run_outputs) : 64.8900 Total : 3539.4000 Total CPU time: 59.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:30 PST -0800 (1735452690.34 s) Start R-work = 0.1620, R-free = 0.1756 Final R-work = 0.1204, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 3671.23 seconds wall clock time: 66 minutes 40.09 seconds (4000.09 seconds total)