Starting phenix.refine on Sat Dec 28 21:06:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7783516.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_7783516.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7783516.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: 2.31, 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: 0.90 Conformation dependent library (CDL) restraints added in 301.9 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 457 0.90 - 1.16: 1171 1.16 - 1.42: 639 1.42 - 1.68: 854 1.68 - 1.94: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.409 0.130 5.40e-03 3.43e+04 5.79e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.032 0.205 1.15e-02 7.56e+03 3.17e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.729 -0.209 1.23e-02 6.61e+03 2.88e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.545 -0.214 1.30e-02 5.92e+03 2.71e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.244 1.083 0.161 1.00e-02 1.00e+04 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3022 4.36 - 8.71: 1846 8.71 - 13.07: 726 13.07 - 17.42: 159 17.42 - 21.78: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 120.70 138.95 -18.25 1.09e+00 8.42e-01 2.80e+02 angle pdb=" O GLY A 30 " pdb=" C GLY A 30 " pdb=" N ILE A 31 " ideal model delta sigma weight residual 122.30 140.94 -18.64 1.19e+00 7.06e-01 2.45e+02 angle pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" O ALYS A 41 " ideal model delta sigma weight residual 119.49 138.25 -18.76 1.21e+00 6.83e-01 2.40e+02 angle pdb=" O ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " ideal model delta sigma weight residual 122.39 102.59 19.80 1.30e+00 5.92e-01 2.32e+02 angle pdb=" O MET A 133 " pdb=" C MET A 133 " pdb=" N MET A 134 " ideal model delta sigma weight residual 122.15 105.06 17.09 1.14e+00 7.69e-01 2.25e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 958 18.00 - 35.99: 104 35.99 - 53.98: 38 53.98 - 71.97: 8 71.97 - 89.96: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -151.62 -28.38 0 5.00e+00 4.00e-02 3.22e+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 -153.71 -26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 101 0.208 - 0.416: 70 0.416 - 0.623: 48 0.623 - 0.831: 14 0.831 - 1.039: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.64 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.093 9.50e-02 1.11e+02 7.14e-02 9.42e+01 pdb=" NE ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.159 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.024 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.079 2.00e-02 2.50e+03 5.47e-02 8.99e+01 pdb=" CG PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.125 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.085 2.00e-02 2.50e+03 6.08e-02 8.32e+01 pdb=" CG HIS A 126 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.083 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.055 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.043 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 1582 2.39 - 2.94: 8410 2.94 - 3.49: 10392 3.49 - 4.05: 15052 4.05 - 4.60: 21167 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.862 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.862 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" O ALA A 79 " pdb=" H SER A 83 " model vdw 1.878 2.450 ... (remaining 56598 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_7783516_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= 0.2607 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789287 | | target function (ml) not normalized (work): 232364.306624 | | target function (ml) not normalized (free): 11797.564200 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2022 7.0773 4.9377| | 2: 3.57 - 2.84 1.00 2876 122 0.2436 0.1791 4.3445 4.3377| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1740 4.1245 4.1504| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1579 3.8278 3.8493| | 5: 2.25 - 2.09 1.00 2756 127 0.2478 0.1543 3.7969 3.8144| | 6: 2.09 - 1.97 1.00 2846 113 0.2560 0.1776 3.4689 3.5212| | 7: 1.97 - 1.87 1.00 2787 165 0.2548 0.1839 3.1458 3.2014| | 8: 1.87 - 1.79 1.00 2789 144 0.2458 0.1959 3.0683 3.1735| | 9: 1.79 - 1.72 1.00 2745 138 0.2423 0.1867 2.9031 2.9232| | 10: 1.72 - 1.66 1.00 2789 158 0.2416 0.2229 2.799 2.9642| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.1880 2.7645 2.7841| | 12: 1.61 - 1.56 1.00 2787 146 0.2488 0.1945 2.6318 2.6177| | 13: 1.56 - 1.52 1.00 2745 130 0.2542 0.1808 2.5604 2.5714| | 14: 1.52 - 1.48 1.00 2803 134 0.2562 0.1854 2.5119 2.529| | 15: 1.48 - 1.45 1.00 2738 128 0.2624 0.2000 2.4234 2.4943| | 16: 1.45 - 1.42 1.00 2756 161 0.2593 0.2076 2.3669 2.4162| | 17: 1.42 - 1.39 1.00 2785 139 0.2650 0.1986 2.3239 2.3036| | 18: 1.39 - 1.36 1.00 2741 179 0.2713 0.2231 2.2678 2.3731| | 19: 1.36 - 1.34 1.00 2807 134 0.2656 0.2232 2.2238 2.2567| | 20: 1.34 - 1.32 1.00 2696 147 0.2738 0.2023 2.208 2.1348| | 21: 1.32 - 1.30 1.00 2785 112 0.2707 0.1981 2.1517 2.0635| | 22: 1.29 - 1.27 1.00 2704 152 0.2795 0.2350 2.1342 2.139| | 23: 1.27 - 1.26 1.00 2802 156 0.2800 0.2484 2.0967 2.1913| | 24: 1.26 - 1.24 1.00 2744 132 0.2796 0.2539 2.064 2.1724| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2492 2.0523 2.079| | 26: 1.22 - 1.21 1.00 2727 135 0.2883 0.2415 2.0112 2.1221| | 27: 1.21 - 1.19 1.00 2814 148 0.2986 0.2690 2.0045 2.0072| | 28: 1.19 - 1.18 1.00 2671 147 0.2985 0.2779 1.9834 1.9898| | 29: 1.18 - 1.16 1.00 2800 134 0.2889 0.2812 1.9515 2.0675| | 30: 1.16 - 1.15 1.00 2740 148 0.3020 0.3049 1.9343 2.0048| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.74 0.76 0.23 1461.89| | 2: 3.57 - 2.84 2876 122 0.80 26.03 1.27 0.23 1461.89| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.23 1213.12| | 4: 2.47 - 2.25 2825 136 0.81 25.52 1.26 0.25 567.53| | 5: 2.25 - 2.09 2756 127 0.77 29.22 1.28 0.25 567.53| | 6: 2.09 - 1.97 2846 113 0.83 22.79 1.29 0.25 312.14| | 7: 1.97 - 1.87 2787 165 0.90 16.71 1.28 0.26 94.34| | 8: 1.87 - 1.79 2789 144 0.85 21.48 1.25 0.26 94.34| | 9: 1.79 - 1.72 2745 138 0.87 19.09 1.24 0.25 57.15| | 10: 1.72 - 1.66 2789 158 0.87 20.23 1.23 0.25 49.71| | 11: 1.66 - 1.61 2740 147 0.85 21.51 1.24 0.25 47.86| | 12: 1.61 - 1.56 2787 146 0.89 18.31 1.23 0.25 29.13| | 13: 1.56 - 1.52 2745 130 0.87 20.30 1.24 0.25 29.13| | 14: 1.52 - 1.48 2803 134 0.87 20.16 1.23 0.25 25.66| | 15: 1.48 - 1.45 2738 128 0.88 19.36 1.24 0.25 19.30| | 16: 1.45 - 1.42 2756 161 0.87 20.65 1.23 0.25 19.30| | 17: 1.42 - 1.39 2785 139 0.88 19.69 1.22 0.25 16.20| | 18: 1.39 - 1.36 2741 179 0.87 20.00 1.23 0.25 14.41| | 19: 1.36 - 1.34 2807 134 0.87 20.88 1.22 0.25 14.41| | 20: 1.34 - 1.32 2696 147 0.88 19.69 1.21 0.25 11.61| | 21: 1.32 - 1.30 2785 112 0.87 20.46 1.20 0.25 11.41| | 22: 1.29 - 1.27 2704 152 0.86 21.28 1.22 0.25 11.26| | 23: 1.27 - 1.26 2802 156 0.87 21.33 1.22 0.24 10.49| | 24: 1.26 - 1.24 2744 132 0.86 21.98 1.21 0.24 10.49| | 25: 1.24 - 1.22 2734 148 0.85 22.94 1.20 0.24 10.28| | 26: 1.22 - 1.21 2727 135 0.84 24.05 1.20 0.24 10.04| | 27: 1.21 - 1.19 2814 148 0.83 24.63 1.21 0.24 10.04| | 28: 1.19 - 1.18 2671 147 0.82 25.98 1.19 0.23 9.91| | 29: 1.18 - 1.16 2800 134 0.82 26.52 1.16 0.23 9.86| | 30: 1.16 - 1.15 2740 148 0.79 28.37 1.15 0.23 9.86| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.86 max = 1461.89 mean = 212.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.33| |phase err.(test): min = 0.00 max = 89.95 mean = 22.04| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.217 1557 Z= 5.585 Angle : 5.378 19.804 2118 Z= 3.831 Chirality : 0.387 1.039 243 Planarity : 0.031 0.081 284 Dihedral : 14.039 89.962 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 1.62 % Allowed : 2.16 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.48), residues: 224 helix: -3.07 (0.36), residues: 109 sheet: 0.22 (0.97), residues: 28 loop : -1.10 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.021 ARG A 27 TYR 0.104 0.032 TYR A 139 PHE 0.055 0.027 PHE A 119 HIS 0.037 0.021 HIS A 115 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= 0.2607 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789287 | | target function (ml) not normalized (work): 232364.306624 | | target function (ml) not normalized (free): 11797.564200 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1983 0.1940 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2008 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1634 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1634 0.1772 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 0.3866 386.745 357.941 0.671 1.003 0.407 11.894-9.307 99.02 97 4 0.1816 614.325 595.815 0.930 1.003 0.390 9.237-7.194 100.00 213 7 0.2176 502.443 491.881 0.954 1.004 0.370 7.162-5.571 100.00 427 22 0.2207 377.055 365.186 0.930 1.003 0.288 5.546-4.326 100.00 867 58 0.1270 517.604 511.603 0.956 1.003 0.218 4.315-3.360 100.00 1859 96 0.1134 492.245 489.017 1.003 1.003 0.189 3.356-2.611 100.00 3867 181 0.1447 323.379 319.515 0.998 1.002 0.043 2.608-2.026 99.99 8198 413 0.1346 214.371 212.241 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1650 104.688 104.169 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2053 46.423 45.076 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2576 29.250 27.025 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0461 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1634 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.936140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1995.007165 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 0.1210 0.1461 0.0251 0.008 1.0 1.3 0.5 0.0 0 12.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.61 2.51 3.013 19.060 1995.007 0.017 12.40 15.39 2.99 3.159 19.541 1995.007 0.016 Individual atomic B min max mean iso aniso Overall: 8.47 118.32 21.00 2.87 0 1785 Protein: 8.47 118.32 17.86 2.87 0 1519 Water: 11.05 114.60 39.21 N/A 0 258 Other: 23.12 36.20 29.15 N/A 0 8 Chain A: 8.47 118.32 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.45 1201 19.45 - 30.44 237 30.44 - 41.42 162 41.42 - 52.41 99 52.41 - 63.39 57 63.39 - 74.38 17 74.38 - 85.36 5 85.36 - 96.35 4 96.35 - 107.33 0 107.33 - 118.32 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1539 r_work=0.1245 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1545 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 = 0.1244 r_free = 0.1547 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= 0.1244 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015363 | | target function (ls_wunit_k1) not normalized (work): 1279.712128 | | target function (ls_wunit_k1) not normalized (free): 114.170183 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1244 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1768 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1699 0.1768 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1723 0.1722 0.1785 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1256 0.1241 0.1540 n_refl.: 87593 remove outliers: r(all,work,free)=0.1255 0.1241 0.1540 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 0.3559 298.617 278.642 0.692 0.923 0.380 11.894-9.307 99.02 97 4 0.1594 478.368 466.031 0.985 0.923 0.380 9.237-7.194 100.00 213 7 0.1817 391.246 386.001 1.031 0.924 0.340 7.162-5.571 100.00 427 22 0.1734 293.608 287.896 0.999 0.924 0.258 5.546-4.326 100.00 867 58 0.0923 403.052 400.183 1.028 0.925 0.209 4.315-3.360 100.00 1859 96 0.0773 383.305 382.342 1.076 0.926 0.190 3.356-2.611 100.00 3867 181 0.1018 251.811 251.110 1.078 0.928 0.052 2.608-2.026 99.99 8198 413 0.0974 166.928 166.321 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1207 81.519 81.697 1.085 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.149 35.619 1.060 0.947 0.000 1.221-1.150 99.97 13689 708 0.2359 22.776 21.314 1.014 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0548 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1241 r_free=0.1540 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** Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1541 | n_water=258 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1252 r_free=0.1540 | n_water=252 | time (s): 26.310 (total time: 28.780) Filter (q & B) r_work=0.1255 r_free=0.1539 | n_water=249 | time (s): 3.780 (total time: 32.560) Compute maps r_work=0.1255 r_free=0.1539 | n_water=249 | time (s): 1.860 (total time: 34.420) Filter (map) r_work=0.1266 r_free=0.1545 | n_water=237 | time (s): 3.760 (total time: 38.180) Find peaks r_work=0.1266 r_free=0.1545 | n_water=237 | time (s): 0.710 (total time: 38.890) Add new water r_work=0.1420 r_free=0.1702 | n_water=457 | time (s): 3.730 (total time: 42.620) Refine new water occ: r_work=0.1329 r_free=0.1572 adp: r_work=0.1250 r_free=0.1520 occ: r_work=0.1263 r_free=0.1516 adp: r_work=0.1229 r_free=0.1500 occ: r_work=0.1233 r_free=0.1493 adp: r_work=0.1223 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1491 r_work=0.1223 r_free=0.1491 | n_water=457 | time (s): 140.590 (total time: 183.210) Filter (q & B) r_work=0.1230 r_free=0.1495 | n_water=435 | time (s): 3.680 (total time: 186.890) Filter (dist only) r_work=0.1231 r_free=0.1494 | n_water=433 | time (s): 45.020 (total time: 231.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.852966 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1464.567518 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 0.1516 0.0284 0.007 0.9 2.9 0.5 0.0 0 12.426 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.16 2.84 3.783 23.206 1464.568 0.016 12.05 14.98 2.92 4.160 23.018 1464.568 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 113.83 23.23 2.58 196 1764 Protein: 8.71 113.83 17.64 2.58 0 1519 Water: 10.98 73.05 42.73 N/A 196 237 Other: 25.19 35.99 29.76 N/A 0 8 Chain A: 8.71 113.83 20.36 N/A 0 1764 Chain S: 14.19 71.80 49.12 N/A 196 0 Histogram: Values Number of atoms 8.71 - 19.22 1200 19.22 - 29.74 254 29.74 - 40.25 189 40.25 - 50.76 140 50.76 - 61.27 105 61.27 - 71.78 59 71.78 - 82.30 7 82.30 - 92.81 3 92.81 - 103.32 1 103.32 - 113.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1498 r_work=0.1205 r_free=0.1497 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1497 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 = 0.1209 r_free = 0.1496 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 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= 0.1209 r_free= 0.1496 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014181 | | target function (ls_wunit_k1) not normalized (work): 1181.182032 | | target function (ls_wunit_k1) not normalized (free): 106.747234 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1209 0.1496 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1610 0.1606 0.1722 n_refl.: 87592 remove outliers: r(all,work,free)=0.1610 0.1606 0.1722 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1616 0.1612 0.1726 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1207 0.1494 n_refl.: 87592 remove outliers: r(all,work,free)=0.1220 0.1206 0.1494 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 0.3378 297.178 271.751 0.600 1.002 0.364 11.894-9.307 99.02 97 4 0.1457 478.368 475.602 0.920 1.003 0.360 9.237-7.194 100.00 213 7 0.1717 391.246 391.025 0.980 1.003 0.280 7.162-5.571 100.00 427 22 0.1514 293.608 290.124 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0857 403.052 400.114 0.956 1.003 0.210 4.315-3.360 100.00 1859 96 0.0727 383.305 382.226 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0975 251.811 251.072 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.0963 166.928 166.504 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.519 81.722 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1617 36.149 35.632 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2342 22.776 21.306 0.977 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0633 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1494 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1494 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1494 | n_water=433 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1206 r_free=0.1495 | n_water=432 | time (s): 39.050 (total time: 41.410) Filter (q & B) r_work=0.1207 r_free=0.1496 | n_water=431 | time (s): 3.230 (total time: 44.640) Compute maps r_work=0.1207 r_free=0.1496 | n_water=431 | time (s): 1.540 (total time: 46.180) Filter (map) r_work=0.1239 r_free=0.1482 | n_water=289 | time (s): 2.930 (total time: 49.110) Find peaks r_work=0.1239 r_free=0.1482 | n_water=289 | time (s): 0.540 (total time: 49.650) Add new water r_work=0.1371 r_free=0.1624 | n_water=493 | time (s): 3.150 (total time: 52.800) Refine new water occ: r_work=0.1267 r_free=0.1531 adp: r_work=0.1269 r_free=0.1533 occ: r_work=0.1244 r_free=0.1507 adp: r_work=0.1243 r_free=0.1509 occ: r_work=0.1229 r_free=0.1489 adp: r_work=0.1222 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1487 r_work=0.1222 r_free=0.1487 | n_water=493 | time (s): 219.320 (total time: 272.120) Filter (q & B) r_work=0.1226 r_free=0.1493 | n_water=453 | time (s): 3.070 (total time: 275.190) Filter (dist only) r_work=0.1226 r_free=0.1491 | n_water=452 | time (s): 40.400 (total time: 315.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.154185 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.644227 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 0.1230 0.1460 0.0230 0.006 0.9 2.2 0.5 0.0 0 1.077 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.60 2.30 3.608 22.098 50.644 3.728 12.09 14.05 1.96 4.107 21.905 50.644 3.652 Individual atomic B min max mean iso aniso Overall: 9.19 109.34 21.65 2.33 216 1763 Protein: 9.19 109.34 17.21 2.33 0 1519 Water: 11.39 72.07 36.47 N/A 216 236 Other: 21.07 32.01 26.76 N/A 0 8 Chain A: 9.19 109.34 19.92 N/A 0 1763 Chain S: 16.68 65.31 35.75 N/A 216 0 Histogram: Values Number of atoms 9.19 - 19.21 1232 19.21 - 29.22 286 29.22 - 39.24 224 39.24 - 49.25 117 49.25 - 59.27 85 59.27 - 69.28 22 69.28 - 79.30 7 79.30 - 89.31 3 89.31 - 99.33 1 99.33 - 109.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1405 r_work=0.1210 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1405 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1403 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.13 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= 0.1203 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648967 | | target function (ml) not normalized (work): 303937.052357 | | target function (ml) not normalized (free): 16053.181325 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1203 0.1403 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1533 0.1531 0.1585 n_refl.: 87590 remove outliers: r(all,work,free)=0.1533 0.1531 0.1585 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1531 0.1530 0.1583 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1194 0.1368 n_refl.: 87590 remove outliers: r(all,work,free)=0.1198 0.1189 0.1368 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3805 293.926 262.356 0.475 1.000 0.297 11.894-9.307 96.08 94 4 0.2309 471.793 456.298 0.855 1.002 0.280 9.237-7.194 98.18 209 7 0.2338 382.799 384.573 0.945 1.002 0.174 7.162-5.571 100.00 427 22 0.2019 293.608 283.622 0.908 1.002 0.162 5.546-4.326 100.00 867 58 0.1089 403.052 398.608 0.951 1.002 0.153 4.315-3.360 100.00 1859 96 0.0929 383.305 380.531 0.994 1.002 0.149 3.356-2.611 100.00 3867 181 0.1145 251.811 249.865 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1041 166.928 165.957 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1002 81.519 81.670 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.149 35.726 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2127 22.776 21.394 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0254 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1368 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=0.1189 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1368 | n_water=452 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1189 r_free=0.1368 | n_water=452 | time (s): 39.450 (total time: 41.890) Filter (q & B) r_work=0.1190 r_free=0.1368 | n_water=450 | time (s): 3.060 (total time: 44.950) Compute maps r_work=0.1190 r_free=0.1368 | n_water=450 | time (s): 1.310 (total time: 46.260) Filter (map) r_work=0.1226 r_free=0.1389 | n_water=315 | time (s): 2.860 (total time: 49.120) Find peaks r_work=0.1226 r_free=0.1389 | n_water=315 | time (s): 0.480 (total time: 49.600) Add new water r_work=0.1293 r_free=0.1456 | n_water=485 | time (s): 3.280 (total time: 52.880) Refine new water occ: r_work=0.1211 r_free=0.1364 adp: r_work=0.1211 r_free=0.1367 occ: r_work=0.1195 r_free=0.1353 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1184 r_free=0.1353 adp: r_work=0.1180 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1350 r_work=0.1180 r_free=0.1350 | n_water=485 | time (s): 232.370 (total time: 285.250) Filter (q & B) r_work=0.1187 r_free=0.1352 | n_water=448 | time (s): 3.160 (total time: 288.410) Filter (dist only) r_work=0.1187 r_free=0.1351 | n_water=447 | time (s): 36.490 (total time: 324.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.335230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.970774 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 0.1188 0.1377 0.0188 0.006 1.0 3.8 0.5 0.0 0 1.168 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.77 1.88 3.427 21.507 51.971 3.633 11.81 13.72 1.92 3.976 21.327 51.971 3.619 Individual atomic B min max mean iso aniso Overall: 9.23 104.37 21.15 2.15 213 1761 Protein: 9.23 104.37 16.80 2.15 0 1519 Water: 11.42 70.07 35.87 N/A 213 234 Other: 20.57 29.08 24.67 N/A 0 8 Chain A: 9.23 104.37 19.46 N/A 0 1761 Chain S: 14.51 56.84 35.13 N/A 213 0 Histogram: Values Number of atoms 9.23 - 18.74 1228 18.74 - 28.26 282 28.26 - 37.77 207 37.77 - 47.28 146 47.28 - 56.80 72 56.80 - 66.31 27 66.31 - 75.82 7 75.82 - 85.34 2 85.34 - 94.85 1 94.85 - 104.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1373 r_work=0.1181 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1373 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1371 target_work(ml) = 3.617 | | 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.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617400 | | target function (ml) not normalized (work): 301267.956439 | | target function (ml) not normalized (free): 15923.585458 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1371 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1488 0.1486 0.1564 n_refl.: 87579 remove outliers: r(all,work,free)=0.1488 0.1486 0.1564 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1486 0.1484 0.1563 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1176 0.1377 n_refl.: 87579 remove outliers: r(all,work,free)=0.1184 0.1174 0.1377 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 0.4063 289.293 256.547 0.438 0.999 0.281 11.894-9.307 92.16 90 4 0.2401 461.767 449.747 0.838 1.001 0.187 9.237-7.194 97.73 208 7 0.2425 383.873 377.562 0.914 1.001 0.118 7.162-5.571 100.00 427 22 0.2216 293.608 282.134 0.899 1.002 0.115 5.546-4.326 100.00 867 58 0.1133 403.052 398.601 0.952 1.002 0.114 4.315-3.360 100.00 1859 96 0.0950 383.305 380.592 0.993 1.002 0.113 3.356-2.611 100.00 3867 181 0.1152 251.811 249.915 1.000 1.002 0.090 2.608-2.026 99.99 8198 413 0.1021 166.928 166.026 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0950 81.519 81.792 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.149 35.766 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2124 22.776 21.390 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0271 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1377 After: r_work=0.1175 r_free=0.1377 ================================== NQH flips ================================== r_work=0.1175 r_free=0.1377 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=0.1175 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1377 | n_water=447 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1175 r_free=0.1377 | n_water=447 | time (s): 39.410 (total time: 41.610) Filter (q & B) r_work=0.1175 r_free=0.1377 | n_water=446 | time (s): 3.180 (total time: 44.790) Compute maps r_work=0.1175 r_free=0.1377 | n_water=446 | time (s): 1.230 (total time: 46.020) Filter (map) r_work=0.1210 r_free=0.1379 | n_water=336 | time (s): 3.310 (total time: 49.330) Find peaks r_work=0.1210 r_free=0.1379 | n_water=336 | time (s): 0.660 (total time: 49.990) Add new water r_work=0.1255 r_free=0.1412 | n_water=505 | time (s): 3.280 (total time: 53.270) Refine new water occ: r_work=0.1185 r_free=0.1363 adp: r_work=0.1186 r_free=0.1365 occ: r_work=0.1173 r_free=0.1353 adp: r_work=0.1172 r_free=0.1356 occ: r_work=0.1164 r_free=0.1349 adp: r_work=0.1161 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1349 r_work=0.1161 r_free=0.1349 | n_water=505 | time (s): 232.880 (total time: 286.150) Filter (q & B) r_work=0.1172 r_free=0.1351 | n_water=457 | time (s): 3.660 (total time: 289.810) Filter (dist only) r_work=0.1172 r_free=0.1349 | n_water=455 | time (s): 39.040 (total time: 328.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.871652 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.045842 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 0.1199 0.1377 0.0178 0.007 1.0 3.8 0.5 0.0 0 0.936 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.77 1.78 3.260 21.061 45.046 3.626 11.99 13.78 1.79 3.369 21.016 45.046 3.620 Individual atomic B min max mean iso aniso Overall: 9.25 101.17 21.08 2.04 222 1760 Protein: 9.25 101.17 16.69 2.04 0 1519 Water: 11.48 69.58 35.67 N/A 222 233 Other: 20.72 28.71 24.74 N/A 0 8 Chain A: 9.25 101.17 19.34 N/A 0 1760 Chain S: 14.14 56.85 34.82 N/A 222 0 Histogram: Values Number of atoms 9.25 - 18.44 1220 18.44 - 27.63 275 27.63 - 36.82 214 36.82 - 46.02 157 46.02 - 55.21 71 55.21 - 64.40 28 64.40 - 73.59 12 73.59 - 82.78 2 82.78 - 91.98 1 91.98 - 101.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1378 r_work=0.1199 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1378 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1374 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.618760 | | target function (ml) not normalized (work): 301359.457227 | | target function (ml) not normalized (free): 15939.991383 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1430 0.1493 5.6742 5.6753| | 2: 3.57 - 2.84 1.00 2888 124 0.1119 0.1407 5.2098 5.2606| | 3: 2.83 - 2.48 1.00 2820 163 0.1232 0.1247 5.0207 5.038| | 4: 2.47 - 2.25 1.00 2825 136 0.1029 0.1153 4.7165 4.7577| | 5: 2.25 - 2.09 1.00 2756 127 0.0988 0.1147 4.6559 4.7356| | 6: 2.09 - 1.97 1.00 2846 113 0.0980 0.1170 4.3607 4.4641| | 7: 1.97 - 1.87 1.00 2787 165 0.0985 0.1179 4.0721 4.1631| | 8: 1.87 - 1.79 1.00 2789 144 0.1007 0.1242 3.9839 4.0794| | 9: 1.79 - 1.72 1.00 2745 138 0.0950 0.1266 3.7051 3.8999| | 10: 1.72 - 1.66 1.00 2831 160 0.0994 0.1260 3.6239 3.7603| | 11: 1.66 - 1.61 1.00 2712 147 0.0957 0.1089 3.5599 3.6014| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1166 3.3347 3.4728| | 13: 1.56 - 1.52 1.00 2745 130 0.0967 0.1042 3.3306 3.4169| | 14: 1.52 - 1.48 1.00 2803 134 0.0974 0.1088 3.2526 3.3222| | 15: 1.48 - 1.45 1.00 2738 128 0.0994 0.1334 3.1582 3.3322| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1243 3.1424 3.2403| | 17: 1.42 - 1.39 1.00 2785 139 0.1097 0.1316 3.1065 3.2442| | 18: 1.39 - 1.36 1.00 2741 179 0.1143 0.1382 3.0823 3.2691| | 19: 1.36 - 1.34 1.00 2807 134 0.1207 0.1625 3.0882 3.2816| | 20: 1.34 - 1.32 1.00 2696 147 0.1316 0.1464 3.0829 3.1363| | 21: 1.32 - 1.30 1.00 2785 112 0.1409 0.1601 3.0821 3.166| | 22: 1.29 - 1.27 1.00 2704 152 0.1467 0.1858 3.0795 3.2655| | 23: 1.27 - 1.26 1.00 2802 156 0.1566 0.1874 3.0991 3.2131| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1763 3.0942 3.1878| | 25: 1.24 - 1.22 1.00 2733 148 0.1797 0.2315 3.1077 3.2923| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1767 3.1231 3.196| | 27: 1.21 - 1.19 1.00 2814 148 0.2011 0.2122 3.1405 3.1584| | 28: 1.19 - 1.18 1.00 2671 147 0.2146 0.2318 3.141 3.164| | 29: 1.18 - 1.16 1.00 2800 134 0.2219 0.2383 3.1271 3.2276| | 30: 1.16 - 1.15 1.00 2739 148 0.2377 0.2490 3.1151 3.1636| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.37 1.00 0.97 6517.90| | 2: 3.57 - 2.84 2888 124 0.92 13.66 1.01 0.97 6517.90| | 3: 2.83 - 2.48 2820 163 0.88 17.84 0.99 0.97 5457.24| | 4: 2.47 - 2.25 2825 136 0.91 14.92 1.00 0.97 2722.14| | 5: 2.25 - 2.09 2756 127 0.89 17.15 1.01 0.97 2722.14| | 6: 2.09 - 1.97 2846 113 0.92 13.76 1.02 0.97 1588.11| | 7: 1.97 - 1.87 2787 165 0.94 10.75 1.02 0.97 620.94| | 8: 1.87 - 1.79 2789 144 0.91 14.36 0.99 0.97 620.94| | 9: 1.79 - 1.72 2745 138 0.93 11.36 0.98 0.97 335.20| | 10: 1.72 - 1.66 2831 160 0.93 12.16 0.98 0.97 277.97| | 11: 1.66 - 1.61 2712 147 0.93 12.84 0.98 0.97 265.31| | 12: 1.61 - 1.56 2773 144 0.95 9.49 0.99 0.97 145.87| | 13: 1.56 - 1.52 2745 130 0.94 11.04 1.02 0.97 145.87| | 14: 1.52 - 1.48 2803 134 0.94 11.17 1.02 0.97 130.48| | 15: 1.48 - 1.45 2738 128 0.95 10.31 1.01 0.98 102.30| | 16: 1.45 - 1.42 2756 161 0.94 11.52 1.01 0.98 102.30| | 17: 1.42 - 1.39 2785 139 0.94 11.35 1.01 0.98 92.74| | 18: 1.39 - 1.36 2741 179 0.94 11.68 1.01 0.98 87.21| | 19: 1.36 - 1.34 2807 134 0.94 12.30 1.00 0.98 87.21| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.96 82.16| | 21: 1.32 - 1.30 2785 112 0.94 13.31 0.98 0.96 81.80| | 22: 1.29 - 1.27 2704 152 0.93 13.88 0.98 0.96 81.94| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.98 0.94 82.65| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.96 0.94 82.65| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 84.24| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.93 86.00| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.00| | 28: 1.19 - 1.18 2671 147 0.88 20.30 1.01 0.92 89.63| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 90.99| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.92 90.99| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.80 max = 6517.90 mean = 1007.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.07| |phase err.(test): min = 0.00 max = 89.39 mean = 14.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1196 0.1374 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1494 0.1491 0.1563 n_refl.: 87573 remove outliers: r(all,work,free)=0.1494 0.1491 0.1563 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1493 0.1490 0.1563 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1377 n_refl.: 87573 remove outliers: r(all,work,free)=0.1205 0.1196 0.1377 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 0.4036 289.293 257.291 0.405 0.998 0.239 11.894-9.307 92.16 90 4 0.2565 461.767 440.001 0.784 1.000 0.144 9.237-7.194 97.73 208 7 0.2503 383.873 377.545 0.883 1.000 0.108 7.162-5.571 100.00 427 22 0.2303 293.608 282.712 0.866 1.001 0.103 5.546-4.326 100.00 867 58 0.1206 403.052 398.448 0.926 1.001 0.101 4.315-3.360 100.00 1859 96 0.0997 383.305 380.720 0.965 1.001 0.100 3.356-2.611 100.00 3867 181 0.1189 251.811 249.942 0.972 1.000 0.043 2.608-2.026 99.99 8198 413 0.1040 166.928 165.917 0.984 1.000 0.000 2.025-1.573 100.00 17313 902 0.0970 81.519 81.778 0.997 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1218 36.149 35.780 0.989 0.996 0.000 1.221-1.150 99.97 13689 708 0.2117 22.776 21.403 0.948 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9743 b_overall=-0.0203 ================= 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 : 0.2607 0.1940 0.083 5.378 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1772 0.083 5.378 9.0 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1772 0.083 5.378 9.0 119.5 20.1 258 0.000 1_nqh: 0.1634 0.1772 0.083 5.378 9.0 119.5 20.1 258 0.003 1_weight: 0.1634 0.1772 0.083 5.378 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1210 0.1461 0.008 0.951 9.0 119.5 20.1 258 0.124 1_adp: 0.1241 0.1539 0.008 0.951 8.5 118.3 21.0 258 0.124 1_regHadp: 0.1245 0.1545 0.008 0.951 8.5 118.3 21.0 258 0.124 1_occ: 0.1244 0.1547 0.008 0.951 8.5 118.3 21.0 258 0.124 2_bss: 0.1241 0.1540 0.008 0.951 8.6 118.5 21.1 258 0.124 2_settarget: 0.1241 0.1540 0.008 0.951 8.6 118.5 21.1 258 0.124 2_updatecdl: 0.1241 0.1540 0.008 0.956 8.6 118.5 21.1 258 0.124 2_nqh: 0.1242 0.1541 0.008 0.956 8.6 118.5 21.1 258 0.127 2_sol: 0.1231 0.1494 0.008 0.956 8.6 118.5 23.6 433 n/a 2_weight: 0.1231 0.1494 0.008 0.956 8.6 118.5 23.6 433 n/a 2_xyzrec: 0.1232 0.1516 0.007 0.866 8.6 118.5 23.6 433 n/a 2_adp: 0.1206 0.1498 0.007 0.866 8.7 113.8 23.2 433 n/a 2_regHadp: 0.1205 0.1497 0.007 0.866 8.7 113.8 23.2 433 n/a 2_occ: 0.1209 0.1496 0.007 0.866 8.7 113.8 23.2 433 n/a 3_bss: 0.1206 0.1494 0.007 0.866 8.8 113.9 23.3 433 n/a 3_settarget: 0.1206 0.1494 0.007 0.866 8.8 113.9 23.3 433 n/a 3_updatecdl: 0.1206 0.1494 0.007 0.867 8.8 113.9 23.3 433 n/a 3_nqh: 0.1206 0.1494 0.007 0.867 8.8 113.9 23.3 433 n/a 3_sol: 0.1226 0.1491 0.007 0.867 8.8 113.9 22.0 452 n/a 3_weight: 0.1226 0.1491 0.007 0.867 8.8 113.9 22.0 452 n/a 3_xyzrec: 0.1230 0.1460 0.006 0.922 8.8 113.9 22.0 452 n/a 3_adp: 0.1209 0.1405 0.006 0.922 9.2 109.3 21.6 452 n/a 3_regHadp: 0.1210 0.1405 0.006 0.922 9.2 109.3 21.6 452 n/a 3_occ: 0.1203 0.1403 0.006 0.922 9.2 109.3 21.6 452 n/a 4_bss: 0.1189 0.1368 0.006 0.922 9.2 109.3 21.6 452 n/a 4_settarget: 0.1189 0.1368 0.006 0.922 9.2 109.3 21.6 452 n/a 4_updatecdl: 0.1189 0.1368 0.006 0.920 9.2 109.3 21.6 452 n/a 4_nqh: 0.1189 0.1368 0.006 0.920 9.2 109.3 21.6 452 n/a 4_sol: 0.1187 0.1351 0.006 0.920 9.2 109.3 21.5 447 n/a 4_weight: 0.1187 0.1351 0.006 0.920 9.2 109.3 21.5 447 n/a 4_xyzrec: 0.1188 0.1377 0.006 0.983 9.2 109.3 21.5 447 n/a 4_adp: 0.1181 0.1373 0.006 0.983 9.2 104.4 21.2 447 n/a 4_regHadp: 0.1181 0.1373 0.006 0.983 9.2 104.4 21.2 447 n/a 4_occ: 0.1178 0.1371 0.006 0.983 9.2 104.4 21.2 447 n/a 5_bss: 0.1174 0.1377 0.006 0.983 9.2 104.4 21.1 447 n/a 5_settarget: 0.1174 0.1377 0.006 0.983 9.2 104.4 21.1 447 n/a 5_updatecdl: 0.1174 0.1377 0.006 0.984 9.2 104.4 21.1 447 n/a 5_setrh: 0.1175 0.1377 0.006 0.984 9.2 104.4 21.1 447 n/a 5_nqh: 0.1175 0.1377 0.006 0.984 9.2 104.4 21.1 447 n/a 5_sol: 0.1172 0.1349 0.006 0.984 9.2 104.4 21.2 455 n/a 5_weight: 0.1172 0.1349 0.006 0.984 9.2 104.4 21.2 455 n/a 5_xyzrec: 0.1199 0.1377 0.007 1.016 9.2 104.4 21.2 455 n/a 5_adp: 0.1199 0.1378 0.007 1.016 9.2 101.2 21.1 455 n/a 5_regHadp: 0.1199 0.1378 0.007 1.016 9.2 101.2 21.1 455 n/a 5_occ: 0.1196 0.1374 0.007 1.016 9.2 101.2 21.1 455 n/a end: 0.1196 0.1377 0.007 1.016 9.2 101.2 21.1 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7783516_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7783516_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8300 Refinement macro-cycles (run) : 3694.6500 Write final files (write_after_run_outputs) : 56.5200 Total : 3756.0000 Total CPU time: 63.21 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:14:14 PST -0800 (1735452854.27 s) Start R-work = 0.1634, R-free = 0.1772 Final R-work = 0.1196, R-free = 0.1377 =============================================================================== Job complete usr+sys time: 3883.29 seconds wall clock time: 69 minutes 15.17 seconds (4155.17 seconds total)