Starting phenix.refine on Fri Dec 27 17:58:26 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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" } 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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 1.23, per 1000 atoms: 0.36 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: 0.42 Conformation dependent library (CDL) restraints added in 203.5 milliseconds Time building geometry restraints manager: 0.59 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 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.862 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.862 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 1.850 nonbonded pdb=" O ALA A 79 " pdb=" H SER A 83 " model vdw 1.878 1.850 ... (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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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 = 27.261679 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 0.1621 0.1734 0.0112 0.002 0.5 3.8 0.0 0.0 0 0.125 0.1490 0.1622 0.0131 0.001 0.5 3.5 0.0 0.0 0 0.250 0.1423 0.1573 0.0149 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1376 0.1546 0.0170 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1351 0.1533 0.0182 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1339 0.1525 0.0186 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1277 0.1484 0.0207 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1271 0.1490 0.0220 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1258 0.1487 0.0228 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1482 0.0233 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1242 0.1474 0.0233 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1237 0.1473 0.0237 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1231 0.1470 0.0239 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1473 0.0242 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1230 0.1472 0.0242 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1226 0.1470 0.0243 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1473 0.0246 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1223 0.1470 0.0247 0.008 1.0 3.8 0.5 0.0 0 13.631 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1470 0.0243 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.70 2.43 3.013 19.060 1995.007 0.017 12.26 14.69 2.43 2.989 19.060 59.850 0.017 12.33 14.67 2.34 2.669 19.060 249.376 0.017 12.67 15.34 2.67 2.741 19.238 997.504 0.016 12.52 15.46 2.94 3.249 19.610 1995.007 0.016 12.43 15.52 3.09 3.293 19.638 2992.511 0.015 12.31 15.48 3.17 3.349 19.661 3990.014 0.015 12.27 15.44 3.17 3.321 19.629 4987.518 0.015 12.23 15.49 3.26 3.361 19.651 5985.021 0.015 12.11 15.36 3.25 3.303 19.610 6982.525 0.015 12.08 15.33 3.26 3.241 19.564 7980.029 0.015 12.11 15.45 3.34 3.409 19.641 8977.532 0.015 12.15 15.51 3.36 3.443 19.654 9975.036 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 249.376 Accepted refinement result: 12.33 14.67 2.34 2.669 19.060 249.376 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.44 20.09 3.31 0 1785 Protein: 9.05 115.00 16.99 3.32 0 1519 Water: 11.47 119.44 38.23 N/A 0 258 Other: 19.70 26.60 22.06 N/A 0 8 Chain A: 9.05 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1467 r_work=0.1235 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1470 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1227 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016813 | | target function (ls_wunit_k1) not normalized (work): 1400.503256 | | target function (ls_wunit_k1) not normalized (free): 109.183140 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1227 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1673 0.1674 0.1693 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1679 0.1680 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1236 0.1225 0.1454 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 0.3543 301.183 281.528 0.649 1.003 0.380 11.894-9.307 99.02 97 4 0.1642 482.479 470.644 0.922 1.003 0.371 9.237-7.194 100.00 213 7 0.1919 394.608 387.638 0.960 1.004 0.350 7.162-5.571 100.00 427 22 0.1834 296.132 290.252 0.935 1.004 0.259 5.546-4.326 100.00 867 58 0.0995 406.516 403.730 0.964 1.003 0.230 4.315-3.360 100.00 1859 96 0.0864 386.599 385.556 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1172 253.976 252.826 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1020 168.363 167.627 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.220 82.423 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.460 35.967 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2249 22.972 21.461 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0491 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1454 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=0.1226 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1455 | n_water=258 | time (s): 2.190 (total time: 2.190) Filter (dist) r_work=0.1235 r_free=0.1449 | n_water=250 | time (s): 20.370 (total time: 22.560) Filter (q & B) r_work=0.1238 r_free=0.1449 | n_water=247 | time (s): 2.450 (total time: 25.010) Compute maps r_work=0.1238 r_free=0.1449 | n_water=247 | time (s): 1.140 (total time: 26.150) Filter (map) r_work=0.1258 r_free=0.1452 | n_water=224 | time (s): 2.540 (total time: 28.690) Find peaks r_work=0.1258 r_free=0.1452 | n_water=224 | time (s): 0.440 (total time: 29.130) Add new water r_work=0.1401 r_free=0.1635 | n_water=429 | time (s): 2.410 (total time: 31.540) Refine new water occ: r_work=0.1306 r_free=0.1490 adp: r_work=0.1224 r_free=0.1438 occ: r_work=0.1238 r_free=0.1419 adp: r_work=0.1203 r_free=0.1405 occ: r_work=0.1207 r_free=0.1390 adp: r_work=0.1197 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1389 r_work=0.1197 r_free=0.1389 | n_water=429 | time (s): 58.040 (total time: 89.580) Filter (q & B) r_work=0.1201 r_free=0.1390 | n_water=416 | time (s): 2.970 (total time: 92.550) Filter (dist only) r_work=0.1201 r_free=0.1389 | n_water=415 | time (s): 35.040 (total time: 127.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.935893 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1494.607577 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 0.1688 0.1790 0.0103 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1545 0.1663 0.0118 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1412 0.1556 0.0144 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1344 0.1505 0.0161 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1316 0.1485 0.0169 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1312 0.1480 0.0168 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1252 0.1442 0.0191 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1224 0.1422 0.0198 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1214 0.1413 0.0199 0.003 0.7 5.4 0.5 0.0 0 4.000 0.1204 0.1410 0.0206 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1202 0.1410 0.0208 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1196 0.1403 0.0207 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1192 0.1401 0.0209 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1189 0.1404 0.0214 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1186 0.1396 0.0210 0.006 0.8 5.1 0.5 0.0 0 10.000 0.1184 0.1401 0.0217 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1184 0.1402 0.0218 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1183 0.1408 0.0224 0.008 0.9 5.1 0.5 0.0 0 13.968 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1186 0.1396 0.0210 0.006 0.8 5.1 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.86 13.96 2.10 3.776 21.744 1494.608 0.016 11.86 13.96 2.10 3.776 21.744 44.838 0.016 11.86 13.96 2.10 3.775 21.744 186.826 0.016 12.11 14.49 2.38 3.570 21.790 747.304 0.015 12.00 14.68 2.67 3.449 22.002 1494.608 0.015 11.87 14.63 2.76 3.452 22.101 2241.911 0.014 11.79 14.58 2.79 3.465 22.066 2989.215 0.014 11.79 14.70 2.91 3.487 22.090 3736.519 0.014 11.65 14.49 2.84 3.483 22.013 4483.823 0.014 11.72 14.69 2.97 3.533 22.099 5231.127 0.014 11.64 14.59 2.95 3.520 22.021 5978.430 0.014 11.65 14.66 3.02 3.544 22.087 6725.734 0.014 11.62 14.61 3.00 3.561 22.123 7473.038 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.838 Accepted refinement result: 11.86 13.96 2.10 3.776 21.744 44.838 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 22.13 3.31 191 1751 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.51 76.69 40.79 N/A 191 224 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.43 N/A 0 1751 Chain S: 15.17 60.00 46.80 N/A 191 0 Histogram: Values Number of atoms 9.09 - 19.68 1258 19.68 - 30.27 243 30.27 - 40.87 169 40.87 - 51.46 133 51.46 - 62.06 117 62.06 - 72.65 11 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1396 r_work=0.1186 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1396 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1402 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1402 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014880 | | target function (ls_wunit_k1) not normalized (work): 1239.445750 | | target function (ls_wunit_k1) not normalized (free): 99.584447 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1183 0.1402 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1577 0.1577 0.1623 n_refl.: 87592 remove outliers: r(all,work,free)=0.1577 0.1577 0.1623 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1579 0.1579 0.1624 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1181 0.1395 n_refl.: 87592 remove outliers: r(all,work,free)=0.1190 0.1179 0.1395 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 0.3372 297.091 276.764 0.611 1.003 0.368 11.894-9.307 99.02 97 4 0.1520 482.479 476.345 0.928 1.003 0.324 9.237-7.194 100.00 213 7 0.1648 394.608 395.224 0.982 1.003 0.290 7.162-5.571 100.00 427 22 0.1559 296.132 292.017 0.932 1.003 0.234 5.546-4.326 100.00 867 58 0.0908 406.516 402.967 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0772 386.599 385.924 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1074 253.976 253.052 1.010 1.002 0.090 2.608-2.026 99.99 8198 413 0.1009 168.363 167.777 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1096 82.220 82.437 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.460 35.992 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.972 21.483 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0163 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1179 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1179 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1395 | n_water=415 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1179 r_free=0.1396 | n_water=414 | time (s): 33.690 (total time: 35.320) Filter (q & B) r_work=0.1179 r_free=0.1397 | n_water=413 | time (s): 2.570 (total time: 37.890) Compute maps r_work=0.1179 r_free=0.1397 | n_water=413 | time (s): 1.660 (total time: 39.550) Filter (map) r_work=0.1224 r_free=0.1401 | n_water=285 | time (s): 3.030 (total time: 42.580) Find peaks r_work=0.1224 r_free=0.1401 | n_water=285 | time (s): 0.680 (total time: 43.260) Add new water r_work=0.1342 r_free=0.1527 | n_water=472 | time (s): 2.800 (total time: 46.060) Refine new water occ: r_work=0.1245 r_free=0.1427 adp: r_work=0.1246 r_free=0.1430 occ: r_work=0.1222 r_free=0.1402 adp: r_work=0.1222 r_free=0.1405 occ: r_work=0.1205 r_free=0.1379 adp: r_work=0.1201 r_free=0.1380 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1380 r_work=0.1201 r_free=0.1380 | n_water=472 | time (s): 169.180 (total time: 215.240) Filter (q & B) r_work=0.1207 r_free=0.1381 | n_water=435 | time (s): 2.970 (total time: 218.210) Filter (dist only) r_work=0.1207 r_free=0.1380 | n_water=433 | time (s): 38.640 (total time: 256.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.745378 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.610823 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 0.1233 0.1359 0.0125 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1189 0.1328 0.0139 0.003 0.7 3.5 0.5 0.0 0 0.262 0.1174 0.1321 0.0147 0.004 0.8 3.2 0.5 0.0 0 0.524 0.1167 0.1321 0.0154 0.005 0.9 3.5 0.5 0.0 0 0.785 0.1162 0.1319 0.0157 0.006 1.0 3.2 0.5 0.0 0 1.047 0.1159 0.1319 0.0160 0.007 1.0 3.5 0.5 0.0 0 1.309 0.1158 0.1319 0.0161 0.007 1.1 3.5 0.5 0.0 0 1.571 0.1157 0.1320 0.0163 0.008 1.1 3.8 0.5 0.0 0 1.833 0.1163 0.1317 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.873 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1317 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 13.17 1.53 3.779 21.233 48.611 3.624 11.63 13.17 1.53 3.779 21.233 1.458 3.624 11.64 13.17 1.53 3.763 21.233 6.076 3.624 11.71 13.32 1.61 3.710 21.220 24.305 3.620 11.70 13.39 1.69 3.736 21.189 48.611 3.620 11.64 13.38 1.74 3.758 21.176 72.916 3.614 11.59 13.37 1.78 3.772 21.170 97.222 3.610 11.56 13.35 1.79 3.785 21.162 121.527 3.607 11.55 13.37 1.82 3.804 21.147 145.832 3.606 11.53 13.34 1.81 3.814 21.143 170.138 3.604 11.53 13.35 1.83 3.827 21.137 194.443 3.603 11.50 13.33 1.82 3.833 21.138 218.749 3.602 11.50 13.33 1.83 3.844 21.133 243.054 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.458 Accepted refinement result: 11.63 13.17 1.53 3.779 21.233 1.458 3.624 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.18 3.31 213 1747 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.52 76.70 35.70 N/A 213 220 Other: 19.74 26.64 22.10 N/A 0 8 Chain A: 9.10 115.04 19.39 N/A 0 1747 Chain S: 15.18 60.01 35.88 N/A 213 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 286 30.28 - 40.88 210 40.88 - 51.47 132 51.47 - 62.07 51 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1317 r_work=0.1163 r_free=0.1317 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1317 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1314 target_work(ml) = 3.618 | | 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= 0.1156 r_free= 0.1314 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.617737 | | target function (ml) not normalized (work): 301332.200316 | | target function (ml) not normalized (free): 15848.977157 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1156 0.1314 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1493 0.1493 0.1523 n_refl.: 87589 remove outliers: r(all,work,free)=0.1493 0.1493 0.1523 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1493 0.1493 0.1522 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1150 0.1300 n_refl.: 87589 remove outliers: r(all,work,free)=0.1154 0.1147 0.1300 n_refl.: 87580 ======================== 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 0.3737 293.817 266.673 0.501 1.002 0.320 11.894-9.307 96.08 94 4 0.2356 475.848 457.761 0.870 1.002 0.283 9.237-7.194 98.18 209 7 0.2282 386.089 387.716 0.952 1.003 0.200 7.162-5.571 100.00 427 22 0.2139 296.132 284.217 0.912 1.003 0.170 5.546-4.326 100.00 867 58 0.1113 406.516 401.471 0.964 1.003 0.160 4.315-3.360 100.00 1859 96 0.0926 386.599 384.396 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1133 253.976 251.898 1.009 1.002 0.038 2.608-2.026 99.99 8198 413 0.0934 168.363 167.591 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0906 82.220 82.503 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1269 36.460 36.032 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2174 22.972 21.498 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0113 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1300 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1150 r_free=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1300 | n_water=433 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1153 r_free=0.1301 | n_water=432 | time (s): 45.420 (total time: 47.740) Filter (q & B) r_work=0.1153 r_free=0.1302 | n_water=430 | time (s): 3.710 (total time: 51.450) Compute maps r_work=0.1153 r_free=0.1302 | n_water=430 | time (s): 1.800 (total time: 53.250) Filter (map) r_work=0.1171 r_free=0.1297 | n_water=327 | time (s): 4.090 (total time: 57.340) Find peaks r_work=0.1171 r_free=0.1297 | n_water=327 | time (s): 0.700 (total time: 58.040) Add new water r_work=0.1237 r_free=0.1366 | n_water=490 | time (s): 3.630 (total time: 61.670) Refine new water occ: r_work=0.1172 r_free=0.1309 adp: r_work=0.1172 r_free=0.1310 occ: r_work=0.1158 r_free=0.1295 adp: r_work=0.1157 r_free=0.1294 occ: r_work=0.1147 r_free=0.1286 adp: r_work=0.1144 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1283 r_work=0.1144 r_free=0.1283 | n_water=490 | time (s): 349.150 (total time: 410.820) Filter (q & B) r_work=0.1150 r_free=0.1289 | n_water=448 | time (s): 3.540 (total time: 414.360) Filter (dist only) r_work=0.1150 r_free=0.1288 | n_water=447 | time (s): 45.100 (total time: 459.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.786319 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.881038 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 0.1327 0.0123 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1164 0.1297 0.0133 0.003 0.8 3.8 0.5 0.0 0 0.268 0.1150 0.1288 0.0138 0.005 0.9 4.5 0.5 0.0 0 0.536 0.1143 0.1290 0.0148 0.006 0.9 3.5 0.5 0.0 0 0.804 0.1139 0.1288 0.0148 0.007 1.0 3.5 0.5 0.0 0 1.072 0.1136 0.1284 0.0148 0.007 1.1 3.8 0.5 0.0 0 1.340 0.1135 0.1283 0.0148 0.008 1.1 4.5 0.5 0.0 0 1.608 0.1133 0.1288 0.0155 0.009 1.1 3.5 0.5 0.0 0 1.876 0.1141 0.1286 0.0144 0.006 1.0 3.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1283 0.0148 0.008 1.1 4.5 0.5 0.0 0 1.608 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.83 1.48 3.780 21.243 45.881 3.604 11.35 12.83 1.48 3.780 21.243 1.376 3.604 11.35 12.83 1.48 3.768 21.243 5.735 3.604 11.37 12.90 1.53 3.714 21.237 22.941 3.599 11.42 13.02 1.59 3.736 21.204 45.881 3.601 11.36 12.99 1.62 3.756 21.193 68.822 3.596 11.30 12.95 1.65 3.773 21.189 91.762 3.592 11.28 12.95 1.67 3.784 21.186 114.703 3.589 11.26 12.95 1.70 3.797 21.182 137.643 3.588 11.25 12.97 1.71 3.812 21.174 160.584 3.587 11.24 12.96 1.72 3.826 21.165 183.524 3.586 11.22 12.94 1.72 3.831 21.168 206.465 3.585 11.21 12.92 1.71 3.835 21.167 229.405 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.376 Accepted refinement result: 11.35 12.83 1.48 3.780 21.243 1.376 3.604 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.20 3.31 228 1746 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 35.35 N/A 228 219 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.38 N/A 0 1746 Chain S: 15.18 60.01 35.13 N/A 228 0 Histogram: Values Number of atoms 9.09 - 19.69 1260 19.69 - 30.28 296 30.28 - 40.87 219 40.87 - 51.47 123 51.47 - 62.06 54 62.06 - 72.66 11 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1283 r_work=0.1135 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1283 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1280 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602636 | | target function (ml) not normalized (work): 300041.977837 | | target function (ml) not normalized (free): 15801.486594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1131 0.1280 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1460 0.1458 0.1518 n_refl.: 87580 remove outliers: r(all,work,free)=0.1460 0.1458 0.1518 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1459 0.1457 0.1518 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1130 0.1282 n_refl.: 87580 remove outliers: r(all,work,free)=0.1136 0.1128 0.1282 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3741 293.064 264.302 0.464 1.000 0.300 11.894-9.307 95.10 93 4 0.2455 472.108 459.994 0.862 1.002 0.246 9.237-7.194 97.73 208 7 0.2308 387.172 379.801 0.926 1.002 0.210 7.162-5.571 100.00 427 22 0.2149 296.132 285.604 0.911 1.002 0.160 5.546-4.326 100.00 867 58 0.1103 406.516 401.816 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0907 386.599 384.891 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1107 253.976 252.130 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0910 168.363 167.741 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.220 82.545 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.460 36.057 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.972 21.516 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1128 r_free=0.1282 After: r_work=0.1129 r_free=0.1282 ================================== NQH flips ================================== r_work=0.1129 r_free=0.1282 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1129 r_free=0.1283 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1129 r_free=0.1283 | n_water=447 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1129 r_free=0.1282 | n_water=446 | time (s): 47.140 (total time: 49.400) Filter (q & B) r_work=0.1129 r_free=0.1282 | n_water=444 | time (s): 3.670 (total time: 53.070) Compute maps r_work=0.1129 r_free=0.1282 | n_water=444 | time (s): 1.670 (total time: 54.740) Filter (map) r_work=0.1150 r_free=0.1295 | n_water=355 | time (s): 3.770 (total time: 58.510) Find peaks r_work=0.1150 r_free=0.1295 | n_water=355 | time (s): 0.710 (total time: 59.220) Add new water r_work=0.1200 r_free=0.1362 | n_water=511 | time (s): 3.680 (total time: 62.900) Refine new water occ: r_work=0.1146 r_free=0.1313 adp: r_work=0.1147 r_free=0.1314 occ: r_work=0.1136 r_free=0.1300 adp: r_work=0.1135 r_free=0.1300 occ: r_work=0.1127 r_free=0.1289 adp: r_work=0.1125 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1288 r_work=0.1125 r_free=0.1288 | n_water=511 | time (s): 218.300 (total time: 281.200) Filter (q & B) r_work=0.1131 r_free=0.1295 | n_water=463 | time (s): 3.720 (total time: 284.920) Filter (dist only) r_work=0.1132 r_free=0.1295 | n_water=461 | time (s): 48.150 (total time: 333.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.807607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.706706 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 0.1336 0.0131 0.003 0.7 5.8 0.5 0.0 0 0.090 0.1170 0.1313 0.0143 0.004 0.8 6.1 0.0 0.0 0 0.271 0.1156 0.1303 0.0148 0.005 0.9 5.4 0.5 0.0 0 0.542 0.1146 0.1298 0.0152 0.006 1.0 5.8 0.5 0.0 0 0.813 0.1139 0.1295 0.0156 0.006 1.0 5.8 0.5 0.0 0 1.085 0.1135 0.1293 0.0158 0.007 1.1 5.8 0.5 0.0 0 1.356 0.1132 0.1293 0.0161 0.008 1.1 5.8 0.5 0.0 0 1.627 0.1131 0.1293 0.0162 0.009 1.1 5.8 0.5 0.0 0 1.898 0.1143 0.1297 0.0154 0.006 1.0 5.8 0.5 0.0 0 0.904 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1293 0.0161 0.008 1.1 5.8 0.5 0.0 0 1.627 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.93 1.61 3.780 21.274 42.707 3.605 11.32 12.93 1.61 3.780 21.274 1.281 3.605 11.32 12.93 1.61 3.777 21.274 5.338 3.605 11.35 12.99 1.64 3.712 21.268 21.353 3.600 11.44 13.16 1.72 3.731 21.237 42.707 3.605 11.35 13.12 1.77 3.757 21.226 64.060 3.599 11.29 13.08 1.78 3.772 21.222 85.413 3.594 11.28 13.09 1.81 3.782 21.219 106.767 3.592 11.24 13.06 1.82 3.793 21.217 128.120 3.589 11.25 13.09 1.84 3.810 21.203 149.473 3.589 11.24 13.09 1.85 3.822 21.203 170.827 3.588 11.21 13.06 1.85 3.829 21.200 192.180 3.586 11.20 13.05 1.85 3.835 21.199 213.534 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.281 Accepted refinement result: 11.32 12.93 1.61 3.780 21.274 1.281 3.605 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.26 3.31 242 1746 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.51 76.69 35.20 N/A 242 219 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.38 N/A 0 1746 Chain S: 15.17 60.00 34.87 N/A 242 0 Histogram: Values Number of atoms 9.09 - 19.68 1258 19.68 - 30.27 307 30.27 - 40.87 219 40.87 - 51.46 130 51.46 - 62.06 52 62.06 - 72.65 11 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1293 r_work=0.1132 r_free=0.1293 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1293 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1290 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1290 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603013 | | target function (ml) not normalized (work): 300058.887700 | | target function (ml) not normalized (free): 15810.318433 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1323 0.1319 5.6279 5.5872| | 2: 3.57 - 2.84 1.00 2888 124 0.1063 0.1389 5.1557 5.2265| | 3: 2.83 - 2.48 1.00 2820 163 0.1099 0.1287 4.9409 4.9825| | 4: 2.47 - 2.25 1.00 2825 136 0.0886 0.0974 4.6208 4.6422| | 5: 2.25 - 2.09 1.00 2756 127 0.0863 0.0956 4.5716 4.6291| | 6: 2.09 - 1.97 1.00 2846 113 0.0846 0.0990 4.2601 4.3534| | 7: 1.97 - 1.87 1.00 2787 165 0.0891 0.1105 3.9831 4.0874| | 8: 1.87 - 1.79 1.00 2789 144 0.0904 0.1118 3.8856 3.9954| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1186 3.6494 3.8328| | 10: 1.72 - 1.66 1.00 2831 160 0.0911 0.1171 3.5632 3.7019| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1035 3.4982 3.5768| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1158 3.3344 3.4762| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1070 3.311 3.4225| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1074 3.2412 3.3291| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1245 3.155 3.2689| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1245 3.1383 3.2432| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1294 3.1198 3.2195| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1323 3.1044 3.2331| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1569 3.1142 3.2729| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1467 3.114 3.1595| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1510 3.1153 3.1041| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1967 3.125 3.289| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1803 3.1336 3.206| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1841 3.1267 3.2299| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2143 3.1431 3.2576| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1772 3.1476 3.2038| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2162 3.171 3.1629| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2299 3.1659 3.1766| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2401 3.1479 3.2295| | 30: 1.16 - 1.15 1.00 2739 148 0.2451 0.2453 3.1439 3.1675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 8.44 1.00 0.97 5669.49| | 2: 3.57 - 2.84 2888 124 0.93 12.44 1.01 0.97 5669.49| | 3: 2.83 - 2.48 2820 163 0.90 16.42 0.99 0.97 4737.72| | 4: 2.47 - 2.25 2825 136 0.92 13.41 1.00 0.98 2334.99| | 5: 2.25 - 2.09 2756 127 0.90 15.56 1.01 0.98 2334.99| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.98 1351.64| | 7: 1.97 - 1.87 2787 165 0.95 9.34 1.02 0.97 512.98| | 8: 1.87 - 1.79 2789 144 0.93 12.66 0.99 0.97 512.98| | 9: 1.79 - 1.72 2745 138 0.94 10.15 0.98 0.97 292.13| | 10: 1.72 - 1.66 2831 160 0.94 11.21 0.98 0.97 247.90| | 11: 1.66 - 1.61 2712 147 0.93 11.85 0.98 0.97 237.56| | 12: 1.61 - 1.56 2773 144 0.95 8.97 0.99 0.97 140.10| | 13: 1.56 - 1.52 2745 130 0.94 10.60 1.03 0.97 140.10| | 14: 1.52 - 1.48 2803 134 0.94 10.89 1.02 0.98 125.55| | 15: 1.48 - 1.45 2738 128 0.95 10.00 1.02 0.98 98.89| | 16: 1.45 - 1.42 2756 161 0.94 11.19 1.02 0.98 98.89| | 17: 1.42 - 1.39 2785 139 0.95 10.97 1.01 0.98 89.63| | 18: 1.39 - 1.36 2741 179 0.94 11.57 1.01 0.98 84.27| | 19: 1.36 - 1.34 2807 134 0.94 11.91 0.99 0.98 84.27| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.97 80.08| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.78| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.20| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.30| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.30| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.37| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.65| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 86.65| | 28: 1.19 - 1.18 2671 147 0.88 20.47 1.01 0.93 90.36| | 29: 1.18 - 1.16 2800 134 0.88 20.54 0.99 0.92 91.75| | 30: 1.16 - 1.15 2739 148 0.86 22.08 0.98 0.92 91.75| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.78 max = 5669.49 mean = 878.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.91 mean = 13.48| |phase err.(test): min = 0.00 max = 89.50 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1129 0.1290 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1452 0.1452 0.1492 n_refl.: 87576 remove outliers: r(all,work,free)=0.1452 0.1452 0.1492 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1451 0.1451 0.1492 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1128 0.1292 n_refl.: 87576 remove outliers: r(all,work,free)=0.1136 0.1128 0.1292 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 0.3887 293.064 261.552 0.457 1.001 0.298 11.894-9.307 94.12 92 4 0.2428 465.785 451.705 0.849 1.002 0.223 9.237-7.194 97.73 208 7 0.2359 387.172 379.570 0.928 1.003 0.160 7.162-5.571 100.00 427 22 0.2104 296.132 286.401 0.910 1.003 0.120 5.546-4.326 100.00 867 58 0.1106 406.516 401.393 0.962 1.003 0.106 4.315-3.360 100.00 1859 96 0.0918 386.599 384.703 1.002 1.003 0.093 3.356-2.611 100.00 3867 181 0.1108 253.976 252.027 1.009 1.002 0.019 2.608-2.026 99.99 8198 413 0.0904 168.363 167.694 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.220 82.540 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.460 36.051 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2168 22.972 21.514 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0137 ================= 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: 0.1226 0.1470 0.007 0.906 9.0 119.5 20.1 258 0.130 1_adp: 0.1233 0.1467 0.007 0.906 9.1 119.4 20.1 258 0.130 1_regHadp: 0.1235 0.1470 0.007 0.906 9.1 119.4 20.1 258 0.130 1_occ: 0.1227 0.1461 0.007 0.906 9.1 119.4 20.1 258 0.130 2_bss: 0.1225 0.1454 0.007 0.906 9.1 119.5 20.1 258 0.130 2_settarget: 0.1225 0.1454 0.007 0.906 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1225 0.1454 0.007 0.912 9.1 119.5 20.1 258 0.130 2_nqh: 0.1226 0.1455 0.007 0.912 9.1 119.5 20.1 258 0.133 2_sol: 0.1201 0.1389 0.007 0.912 9.1 115.0 22.1 415 n/a 2_weight: 0.1201 0.1389 0.007 0.912 9.1 115.0 22.1 415 n/a 2_xyzrec: 0.1186 0.1396 0.006 0.848 9.1 115.0 22.1 415 n/a 2_adp: 0.1186 0.1396 0.006 0.848 9.1 115.0 22.1 415 n/a 2_regHadp: 0.1186 0.1396 0.006 0.848 9.1 115.0 22.1 415 n/a 2_occ: 0.1183 0.1402 0.006 0.848 9.1 115.0 22.1 415 n/a 3_bss: 0.1179 0.1395 0.006 0.848 9.1 115.0 22.1 415 n/a 3_settarget: 0.1179 0.1395 0.006 0.848 9.1 115.0 22.1 415 n/a 3_updatecdl: 0.1179 0.1395 0.006 0.850 9.1 115.0 22.1 415 n/a 3_nqh: 0.1179 0.1395 0.006 0.850 9.1 115.0 22.1 415 n/a 3_sol: 0.1207 0.1380 0.006 0.850 9.1 115.0 21.2 433 n/a 3_weight: 0.1207 0.1380 0.006 0.850 9.1 115.0 21.2 433 n/a 3_xyzrec: 0.1163 0.1317 0.005 0.933 9.1 115.0 21.2 433 n/a 3_adp: 0.1163 0.1317 0.005 0.933 9.1 115.0 21.2 433 n/a 3_regHadp: 0.1163 0.1317 0.005 0.933 9.1 115.0 21.2 433 n/a 3_occ: 0.1156 0.1314 0.005 0.933 9.1 115.0 21.2 433 n/a 4_bss: 0.1147 0.1300 0.005 0.933 9.1 115.0 21.2 433 n/a 4_settarget: 0.1147 0.1300 0.005 0.933 9.1 115.0 21.2 433 n/a 4_updatecdl: 0.1147 0.1300 0.005 0.936 9.1 115.0 21.2 433 n/a 4_nqh: 0.1150 0.1300 0.005 0.936 9.1 115.0 21.2 433 n/a 4_sol: 0.1150 0.1288 0.005 0.936 9.1 115.0 21.2 447 n/a 4_weight: 0.1150 0.1288 0.005 0.936 9.1 115.0 21.2 447 n/a 4_xyzrec: 0.1135 0.1283 0.008 1.093 9.1 115.0 21.2 447 n/a 4_adp: 0.1135 0.1283 0.008 1.093 9.1 115.0 21.2 447 n/a 4_regHadp: 0.1135 0.1283 0.008 1.093 9.1 115.0 21.2 447 n/a 4_occ: 0.1131 0.1280 0.008 1.093 9.1 115.0 21.2 447 n/a 5_bss: 0.1128 0.1282 0.008 1.093 9.1 115.0 21.2 447 n/a 5_settarget: 0.1128 0.1282 0.008 1.093 9.1 115.0 21.2 447 n/a 5_updatecdl: 0.1128 0.1282 0.008 1.093 9.1 115.0 21.2 447 n/a 5_setrh: 0.1129 0.1282 0.008 1.093 9.1 115.0 21.2 447 n/a 5_nqh: 0.1129 0.1283 0.008 1.093 9.1 115.0 21.2 447 n/a 5_sol: 0.1132 0.1295 0.008 1.093 9.1 115.0 21.3 461 n/a 5_weight: 0.1132 0.1295 0.008 1.093 9.1 115.0 21.3 461 n/a 5_xyzrec: 0.1132 0.1293 0.008 1.126 9.1 115.0 21.3 461 n/a 5_adp: 0.1132 0.1293 0.008 1.126 9.1 115.0 21.3 461 n/a 5_regHadp: 0.1132 0.1293 0.008 1.126 9.1 115.0 21.3 461 n/a 5_occ: 0.1129 0.1290 0.008 1.126 9.1 115.0 21.3 461 n/a end: 0.1128 0.1292 0.008 1.126 9.1 115.0 21.3 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7783516_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7783516_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8100 Refinement macro-cycles (run) : 13266.1000 Write final files (write_after_run_outputs) : 96.7100 Total : 13366.6200 Total CPU time: 3.72 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:00:48 PST -0800 (1735365648.54 s) Start R-work = 0.1634, R-free = 0.1772 Final R-work = 0.1128, R-free = 0.1292 =============================================================================== Job complete usr+sys time: 13549.09 seconds wall clock time: 245 minutes 16.73 seconds (14716.73 seconds total)