Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8810963.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8810963.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8810963.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.56, per 1000 atoms: 0.38 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.713 distance_ideal: 2.720 ideal - model: 0.007 slack: 0.000 delta_slack: 0.007 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.642 distance_ideal: 2.710 ideal - model: 0.068 slack: 0.000 delta_slack: 0.068 sigma: 10.0000 Total number of added/changed bonds: 4 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: 0.91 Conformation dependent library (CDL) restraints added in 194.6 milliseconds Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 1022 1.04 - 1.28: 2423 1.28 - 1.52: 1610 1.52 - 1.75: 862 1.75 - 1.99: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 71 " pdb=" CB VAL B 71 " ideal model delta sigma weight residual 1.539 1.294 0.245 1.19e-02 7.06e+03 4.24e+02 bond pdb=" CA ALA A 10 " pdb=" C ALA A 10 " ideal model delta sigma weight residual 1.517 1.722 -0.205 1.02e-02 9.61e+03 4.04e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.236 1.034 0.201 1.01e-02 9.80e+03 3.97e+02 bond pdb=" N ILE B 134 " pdb=" CA ILE B 134 " ideal model delta sigma weight residual 1.462 1.662 -0.200 1.01e-02 9.80e+03 3.92e+02 bond pdb=" C PHE A 82 " pdb=" N ARG A 83 " ideal model delta sigma weight residual 1.335 1.577 -0.243 1.25e-02 6.40e+03 3.77e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 5479 4.09 - 8.17: 3581 8.17 - 12.26: 1430 12.26 - 16.35: 284 16.35 - 20.43: 36 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " ideal model delta sigma weight residual 117.37 106.52 10.85 7.40e-01 1.83e+00 2.15e+02 angle pdb=" O VAL B 32 " pdb=" C VAL B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 123.14 138.02 -14.88 1.02e+00 9.61e-01 2.13e+02 angle pdb=" CA GLY A 78 " pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 120.80 135.08 -14.28 9.80e-01 1.04e+00 2.12e+02 angle pdb=" O LEU A 24 " pdb=" C LEU A 24 " pdb=" N LEU A 25 " ideal model delta sigma weight residual 122.12 137.48 -15.36 1.06e+00 8.90e-01 2.10e+02 angle pdb=" O PHE B 127 " pdb=" C PHE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 121.30 134.09 -12.79 8.90e-01 1.26e+00 2.07e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.99: 1853 17.99 - 35.98: 139 35.98 - 53.97: 36 53.97 - 71.96: 18 71.96 - 89.95: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA B 44 " pdb=" C ALA B 44 " pdb=" N ILE B 45 " pdb=" CA ILE B 45 " ideal model delta harmonic sigma weight residual 180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA CYS A 47 " pdb=" C CYS A 47 " pdb=" N SER A 48 " pdb=" CA SER A 48 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.212: 188 0.212 - 0.423: 166 0.423 - 0.634: 93 0.634 - 0.844: 36 0.844 - 1.055: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 144 " pdb=" N VAL A 144 " pdb=" C VAL A 144 " pdb=" CB VAL A 144 " both_signs ideal model delta sigma weight residual False 2.44 3.50 -1.06 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 3.41 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA ARG B 175 " pdb=" N ARG B 175 " pdb=" C ARG B 175 " pdb=" CB ARG B 175 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.31e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.146 2.00e-02 2.50e+03 8.07e-02 1.95e+02 pdb=" CG PHE B 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.132 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.158 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.024 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 95 " 0.046 2.00e-02 2.50e+03 6.65e-02 1.33e+02 pdb=" CG PHE A 95 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 95 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 95 " -0.121 2.00e-02 2.50e+03 pdb=" CE1 PHE A 95 " 0.110 2.00e-02 2.50e+03 pdb=" CE2 PHE A 95 " 0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 95 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 PHE A 95 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 95 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 95 " -0.050 2.00e-02 2.50e+03 pdb=" HE2 PHE A 95 " 0.063 2.00e-02 2.50e+03 pdb=" HZ PHE A 95 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.005 2.00e-02 2.50e+03 6.33e-02 1.20e+02 pdb=" CG PHE A 119 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.115 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.069 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.101 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.073 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.57: 21 1.57 - 2.33: 1976 2.33 - 3.08: 21995 3.08 - 3.84: 33054 3.84 - 4.60: 53393 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110439 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.811 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.013 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.026 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.073 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.115 2.620 ... (remaining 110434 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 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 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 = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 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 = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 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 } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } 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_8810963_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2023 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.294983 | | target function (ml) not normalized (work): 804506.121592 | | target function (ml) not normalized (free): 16482.866197 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2138 0.1950 6.6797 6.3105| | 2: 2.94 - 2.33 1.00 7339 128 0.1598 0.1602 5.5383 5.6205| | 3: 2.33 - 2.04 0.96 6939 150 0.1612 0.1600 5.1275 5.137| | 4: 2.04 - 1.85 1.00 7170 155 0.1732 0.1554 4.9488 4.9694| | 5: 1.85 - 1.72 0.99 7113 159 0.1895 0.1723 4.7849 4.779| | 6: 1.72 - 1.62 0.99 7102 142 0.1962 0.1873 4.6588 4.6616| | 7: 1.62 - 1.54 0.99 7104 148 0.2050 0.1637 4.5602 4.4729| | 8: 1.54 - 1.47 0.96 6798 152 0.2040 0.1886 4.471 4.3767| | 9: 1.47 - 1.41 0.98 6938 155 0.2066 0.2093 4.3802 4.4131| | 10: 1.41 - 1.36 0.99 7022 150 0.2090 0.2109 4.2981 4.3266| | 11: 1.36 - 1.32 0.99 6997 151 0.2093 0.2141 4.2254 4.2223| | 12: 1.32 - 1.28 0.98 6976 149 0.2063 0.2038 4.1648 4.2068| | 13: 1.28 - 1.25 0.98 6907 166 0.2026 0.2021 4.115 4.1467| | 14: 1.25 - 1.22 0.98 7015 113 0.2056 0.2286 4.0676 4.2499| | 15: 1.22 - 1.19 0.98 6957 137 0.2098 0.1936 4.0371 3.9952| | 16: 1.19 - 1.17 0.93 6604 132 0.2121 0.2372 4.0124 4.0886| | 17: 1.17 - 1.14 0.98 6941 135 0.2123 0.1859 3.9473 3.9819| | 18: 1.14 - 1.12 0.98 6875 142 0.2246 0.2390 3.9241 3.9365| | 19: 1.12 - 1.10 0.97 6949 106 0.2266 0.2334 3.8716 3.9489| | 20: 1.10 - 1.08 0.97 6884 147 0.2316 0.2237 3.8199 3.8332| | 21: 1.08 - 1.07 0.97 6852 152 0.2412 0.2590 3.785 3.7941| | 22: 1.07 - 1.05 0.97 6838 135 0.2535 0.2574 3.7523 3.7768| | 23: 1.05 - 1.03 0.97 6829 159 0.2735 0.2508 3.7367 3.7621| | 24: 1.03 - 1.02 0.96 6785 133 0.2862 0.3119 3.706 3.8467| | 25: 1.02 - 1.01 0.93 6552 130 0.3082 0.3077 3.6736 3.7661| | 26: 1.01 - 0.99 0.96 6767 158 0.3209 0.3483 3.6303 3.688| | 27: 0.99 - 0.98 0.94 6648 131 0.3405 0.3246 3.6366 3.602| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 38.28 - 2.94 7412 127 0.85 20.78 0.91 0.98 36880.51| | 2: 2.94 - 2.33 7339 128 0.85 21.21 1.09 1.03 15318.43| | 3: 2.33 - 2.04 6939 150 0.94 11.79 1.11 1.07 3834.95| | 4: 2.04 - 1.85 7170 155 0.93 12.52 1.11 1.06 2494.07| | 5: 1.85 - 1.72 7113 159 0.92 14.65 1.11 1.08 1870.12| | 6: 1.72 - 1.62 7102 142 0.91 15.27 1.11 1.07 1412.97| | 7: 1.62 - 1.54 7104 148 0.91 16.07 1.12 1.07 1124.45| | 8: 1.54 - 1.47 6798 152 0.90 16.44 1.10 1.07 951.60| | 9: 1.47 - 1.41 6938 155 0.89 17.78 1.10 1.05 861.77| | 10: 1.41 - 1.36 7022 150 0.88 19.25 1.09 1.04 791.53| | 11: 1.36 - 1.32 6997 151 0.88 19.36 1.08 1.04 691.55| | 12: 1.32 - 1.28 6976 149 0.88 19.23 1.08 1.05 620.23| | 13: 1.28 - 1.25 6907 166 0.88 19.00 1.07 1.05 557.33| | 14: 1.25 - 1.22 7015 113 0.87 20.18 1.07 1.03 548.45| | 15: 1.22 - 1.19 6957 137 0.87 20.62 1.08 1.02 526.53| | 16: 1.19 - 1.17 6604 132 0.87 20.85 1.07 1.02 499.90| | 17: 1.17 - 1.14 6941 135 0.86 21.41 1.08 1.02 456.55| | 18: 1.14 - 1.12 6875 142 0.86 21.55 1.09 1.00 405.43| | 19: 1.12 - 1.10 6949 106 0.86 21.98 1.07 1.00 376.38| | 20: 1.10 - 1.08 6884 147 0.85 22.47 1.07 0.98 338.84| | 21: 1.08 - 1.07 6852 152 0.84 23.52 1.06 0.98 329.51| | 22: 1.07 - 1.05 6838 135 0.82 25.39 1.05 0.97 326.70| | 23: 1.05 - 1.03 6829 159 0.79 28.26 1.05 0.96 342.18| | 24: 1.03 - 1.02 6785 133 0.76 31.25 1.05 0.95 360.74| | 25: 1.02 - 1.01 6552 130 0.74 33.20 1.02 0.92 352.16| | 26: 1.01 - 0.99 6767 158 0.72 34.83 1.04 0.90 333.23| | 27: 0.99 - 0.98 6648 131 0.73 33.90 1.04 0.90 298.94| |alpha: min = 0.90 max = 1.08 mean = 1.01| |beta: min = 298.94 max = 36880.51 mean = 2830.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.49| |phase err.(test): min = 0.00 max = 89.71 mean = 21.78| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.249 2950 Z= 5.463 Angle : 5.217 16.746 4018 Z= 3.686 Chirality : 0.382 1.055 492 Planarity : 0.033 0.149 512 Dihedral : 12.920 89.952 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.29 % Allowed : 4.19 % Favored : 94.52 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.36), residues: 386 helix: -2.76 (0.28), residues: 144 sheet: -0.96 (0.49), residues: 82 loop : -0.78 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.018 ARG B 100 TYR 0.116 0.038 TYR B 194 PHE 0.117 0.040 PHE A 82 TRP 0.094 0.031 TRP B 146 HIS 0.060 0.023 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2023 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.294983 | | target function (ml) not normalized (work): 804506.121592 | | target function (ml) not normalized (free): 16482.866197 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2021 0.2023 0.1953 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2021 0.2023 0.1953 n_refl.: 191155 remove outliers: r(all,work,free)=0.2021 0.2023 0.1953 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2021 0.2024 0.1953 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1792 0.1790 0.1897 n_refl.: 191145 remove outliers: r(all,work,free)=0.1790 0.1788 0.1897 n_refl.: 191140 ======================== 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 38.277-13.317 96.04 94 3 0.4236 400.535 295.412 0.432 0.915 0.299 13.296-10.522 99.01 99 1 0.2498 528.187 518.971 0.784 0.916 0.250 10.503-8.327 99.45 178 3 0.2510 565.118 555.521 0.968 0.916 0.227 8.318-6.595 100.00 360 8 0.2490 414.736 403.065 0.963 0.916 0.175 6.588-5.215 100.00 711 7 0.2244 381.101 365.925 0.961 0.916 0.170 5.214-4.128 98.38 1367 28 0.1483 557.435 550.193 1.072 0.916 0.070 4.126-3.266 94.74 2603 46 0.1339 508.132 499.424 1.141 0.916 0.018 3.266-2.585 99.86 5447 97 0.1423 342.774 337.773 1.117 0.915 0.000 2.585-2.046 97.45 10613 204 0.1381 258.603 254.436 1.121 0.915 0.000 2.046-1.619 99.39 21536 464 0.1600 153.054 149.993 1.140 0.913 0.000 1.619-1.281 98.00 42464 925 0.1915 82.395 80.217 1.127 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2313 44.203 41.659 1.109 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0040 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1788 r_free=0.1897 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 156 GLN Total number of N/Q/H flips: 2 r_work=0.1796 r_free=0.1898 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.117061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.529902 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 0.1274 0.1504 0.0230 0.038 1.2 10.7 0.0 0.3 0 11.059 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 15.04 2.30 1.117 13.113 573.530 0.019 13.01 15.73 2.72 1.263 13.361 573.530 0.017 Individual atomic B min max mean iso aniso Overall: 5.24 73.05 15.05 1.41 435 3274 Protein: 5.24 40.36 11.01 1.41 0 2902 Water: 6.31 73.05 29.60 N/A 435 370 Other: 16.02 29.87 22.95 N/A 0 2 Chain A: 5.37 59.88 13.06 N/A 0 1626 Chain B: 5.24 73.05 12.79 N/A 0 1648 Chain S: 11.93 65.68 31.04 N/A 435 0 Histogram: Values Number of atoms 5.24 - 12.02 2180 12.02 - 18.80 629 18.80 - 25.58 310 25.58 - 32.36 264 32.36 - 39.14 158 39.14 - 45.92 100 45.92 - 52.71 45 52.71 - 59.49 19 59.49 - 66.27 3 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1573 r_work=0.1300 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1568 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1285 r_free = 0.1558 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015652 | | target function (ls_wunit_k1) not normalized (work): 2931.632122 | | target function (ls_wunit_k1) not normalized (free): 116.851874 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1558 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1474 0.1471 0.1637 n_refl.: 191140 remove outliers: r(all,work,free)=0.1474 0.1471 0.1637 n_refl.: 191140 overall B=0.17 to atoms: r(all,work,free)=0.1499 0.1496 0.1648 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1277 0.1548 n_refl.: 191140 remove outliers: r(all,work,free)=0.1282 0.1277 0.1547 n_refl.: 191138 ======================== 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 38.277-13.317 95.05 93 3 0.3608 402.814 377.646 0.462 1.001 0.269 13.296-10.522 99.01 99 1 0.2118 528.187 519.642 0.708 1.002 0.240 10.503-8.327 99.45 178 3 0.1763 565.118 562.283 0.856 1.002 0.198 8.318-6.595 100.00 360 8 0.1717 414.736 411.803 0.874 1.002 0.160 6.588-5.215 100.00 711 7 0.1526 381.101 373.836 0.857 1.002 0.160 5.214-4.128 98.38 1367 28 0.0899 557.435 554.283 0.939 1.003 0.060 4.126-3.266 94.74 2603 46 0.0833 508.132 504.473 1.004 1.003 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.441 0.987 1.003 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.403 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.397 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.407 1.007 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.161 0.985 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0393 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1547 | n_water=805 | time (s): 2.880 (total time: 2.880) Filter (dist) r_work=0.1282 r_free=0.1551 | n_water=794 | time (s): 104.020 (total time: 106.900) Filter (q & B) r_work=0.1282 r_free=0.1552 | n_water=789 | time (s): 4.910 (total time: 111.810) Compute maps r_work=0.1282 r_free=0.1552 | n_water=789 | time (s): 1.660 (total time: 113.470) Filter (map) r_work=0.1309 r_free=0.1529 | n_water=648 | time (s): 5.330 (total time: 118.800) Find peaks r_work=0.1309 r_free=0.1529 | n_water=648 | time (s): 0.840 (total time: 119.640) Add new water r_work=0.1331 r_free=0.1553 | n_water=949 | time (s): 4.320 (total time: 123.960) Refine new water occ: r_work=0.1289 r_free=0.1515 adp: r_work=0.1277 r_free=0.1510 occ: r_work=0.1279 r_free=0.1507 adp: r_work=0.1272 r_free=0.1507 occ: r_work=0.1274 r_free=0.1504 adp: r_work=0.1271 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1505 r_work=0.1271 r_free=0.1505 | n_water=949 | time (s): 87.990 (total time: 211.950) Filter (q & B) r_work=0.1274 r_free=0.1508 | n_water=884 | time (s): 4.350 (total time: 216.300) Filter (dist only) r_work=0.1274 r_free=0.1508 | n_water=883 | time (s): 114.860 (total time: 331.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.952724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 583.209829 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 0.1256 0.1522 0.0267 0.041 1.1 16.5 0.0 0.3 0 11.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.22 2.67 2.048 15.207 583.210 0.014 12.34 15.11 2.76 2.420 15.238 583.210 0.014 Individual atomic B min max mean iso aniso Overall: 5.46 69.59 16.32 1.20 515 3272 Protein: 5.46 40.22 11.00 1.20 0 2902 Water: 6.64 69.59 33.79 N/A 515 368 Other: 16.31 32.83 24.57 N/A 0 2 Chain A: 5.61 56.46 13.02 N/A 0 1624 Chain B: 5.46 68.22 12.84 N/A 0 1648 Chain S: 13.35 69.59 37.87 N/A 515 0 Histogram: Values Number of atoms 5.46 - 11.88 2102 11.88 - 18.29 689 18.29 - 24.70 258 24.70 - 31.12 212 31.12 - 37.53 180 37.53 - 43.94 155 43.94 - 50.36 97 50.36 - 56.77 49 56.77 - 63.18 37 63.18 - 69.59 8 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1511 r_work=0.1235 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1507 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013456 | | target function (ls_wunit_k1) not normalized (work): 2520.270988 | | target function (ls_wunit_k1) not normalized (free): 99.768034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1507 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1441 0.1438 0.1608 n_refl.: 191138 remove outliers: r(all,work,free)=0.1441 0.1438 0.1608 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1606 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1235 0.1513 n_refl.: 191138 remove outliers: r(all,work,free)=0.1241 0.1235 0.1513 n_refl.: 191138 ======================== 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 38.277-13.317 95.05 93 3 0.3213 402.814 379.451 0.493 0.962 0.265 13.296-10.522 99.01 99 1 0.1879 528.187 520.327 0.756 0.963 0.219 10.503-8.327 99.45 178 3 0.1428 565.118 567.868 0.920 0.963 0.179 8.318-6.595 100.00 360 8 0.1555 414.736 414.849 0.939 0.963 0.160 6.588-5.215 100.00 711 7 0.1348 381.101 376.656 0.915 0.963 0.160 5.214-4.128 98.38 1367 28 0.0819 557.435 556.106 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0763 508.132 505.550 1.060 0.963 0.015 3.266-2.585 99.86 5447 97 0.0852 342.774 341.345 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0901 258.603 256.741 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.617 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.351 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.220 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0535 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1513 | n_water=883 | time (s): 3.330 (total time: 3.330) Filter (dist) r_work=0.1237 r_free=0.1514 | n_water=877 | time (s): 119.800 (total time: 123.130) Filter (q & B) r_work=0.1237 r_free=0.1514 | n_water=875 | time (s): 4.750 (total time: 127.880) Compute maps r_work=0.1237 r_free=0.1514 | n_water=875 | time (s): 2.100 (total time: 129.980) Filter (map) r_work=0.1279 r_free=0.1514 | n_water=686 | time (s): 5.060 (total time: 135.040) Find peaks r_work=0.1279 r_free=0.1514 | n_water=686 | time (s): 0.640 (total time: 135.680) Add new water r_work=0.1304 r_free=0.1548 | n_water=989 | time (s): 4.860 (total time: 140.540) Refine new water occ: r_work=0.1258 r_free=0.1503 adp: r_work=0.1258 r_free=0.1502 occ: r_work=0.1253 r_free=0.1502 adp: r_work=0.1253 r_free=0.1501 occ: r_work=0.1250 r_free=0.1502 adp: r_work=0.1249 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1249 r_free=0.1501 r_work=0.1249 r_free=0.1501 | n_water=989 | time (s): 223.620 (total time: 364.160) Filter (q & B) r_work=0.1253 r_free=0.1511 | n_water=875 | time (s): 4.840 (total time: 369.000) Filter (dist only) r_work=0.1253 r_free=0.1511 | n_water=874 | time (s): 130.280 (total time: 499.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.682238 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.276423 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 0.1244 0.1437 0.0193 0.035 1.1 7.0 0.0 0.0 0 0.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.44 14.37 1.93 1.936 14.594 16.276 3.943 12.37 13.96 1.58 2.250 14.493 16.276 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.79 15.25 1.06 507 3271 Protein: 5.53 36.57 10.74 1.06 0 2902 Water: 6.68 67.79 30.21 N/A 507 367 Other: 13.98 28.65 21.32 N/A 0 2 Chain A: 5.57 55.52 12.77 N/A 0 1624 Chain B: 5.53 67.79 12.55 N/A 0 1647 Chain S: 12.97 60.93 32.01 N/A 507 0 Histogram: Values Number of atoms 5.53 - 11.75 2134 11.75 - 17.98 677 17.98 - 24.20 300 24.20 - 30.43 235 30.43 - 36.66 177 36.66 - 42.88 147 42.88 - 49.11 75 49.11 - 55.33 24 55.33 - 61.56 8 61.56 - 67.79 1 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1396 r_work=0.1238 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1396 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1389 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892938 | | target function (ml) not normalized (work): 729135.604015 | | target function (ml) not normalized (free): 15230.325219 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1389 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1501 n_refl.: 191138 remove outliers: r(all,work,free)=0.1447 0.1446 0.1501 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1440 0.1497 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1384 n_refl.: 191138 remove outliers: r(all,work,free)=0.1230 0.1227 0.1384 n_refl.: 191135 ======================== 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 38.277-13.317 94.06 92 3 0.3932 398.008 359.170 0.422 0.946 0.249 13.296-10.522 99.01 99 1 0.2437 528.187 508.084 0.702 0.947 0.206 10.503-8.327 98.35 176 3 0.2044 555.265 557.437 0.883 0.947 0.183 8.318-6.595 100.00 360 8 0.2092 414.736 409.555 0.899 0.947 0.133 6.588-5.215 100.00 711 7 0.1841 381.101 369.880 0.887 0.947 0.107 5.214-4.128 98.38 1367 28 0.1167 557.435 551.831 0.972 0.947 0.060 4.126-3.266 94.74 2603 46 0.1086 508.132 501.391 1.034 0.947 0.015 3.266-2.585 99.86 5447 97 0.1088 342.774 339.223 1.021 0.946 0.010 2.585-2.046 97.45 10613 204 0.0975 258.603 255.633 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0981 153.054 151.387 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.484 1.054 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.316 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1040 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1384 | n_water=874 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1227 r_free=0.1384 | n_water=872 | time (s): 112.690 (total time: 115.650) Filter (q & B) r_work=0.1228 r_free=0.1384 | n_water=863 | time (s): 3.990 (total time: 119.640) Compute maps r_work=0.1228 r_free=0.1384 | n_water=863 | time (s): 2.200 (total time: 121.840) Filter (map) r_work=0.1251 r_free=0.1388 | n_water=718 | time (s): 4.950 (total time: 126.790) Find peaks r_work=0.1251 r_free=0.1388 | n_water=718 | time (s): 0.690 (total time: 127.480) Add new water r_work=0.1266 r_free=0.1403 | n_water=956 | time (s): 3.980 (total time: 131.460) Refine new water occ: r_work=0.1217 r_free=0.1358 adp: r_work=0.1209 r_free=0.1354 occ: r_work=0.1207 r_free=0.1354 adp: r_work=0.1207 r_free=0.1354 occ: r_work=0.1205 r_free=0.1354 adp: r_work=0.1204 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1354 r_work=0.1204 r_free=0.1354 | n_water=956 | time (s): 323.360 (total time: 454.820) Filter (q & B) r_work=0.1208 r_free=0.1363 | n_water=870 | time (s): 5.080 (total time: 459.900) Filter (dist only) r_work=0.1209 r_free=0.1362 | n_water=869 | time (s): 111.370 (total time: 571.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.593345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.535560 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 0.1207 0.1366 0.0159 0.036 1.1 7.0 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.66 1.59 1.833 14.220 15.536 3.875 11.99 13.62 1.63 1.919 14.186 15.536 3.866 Individual atomic B min max mean iso aniso Overall: 5.53 67.39 15.01 1.01 503 3270 Protein: 5.53 33.55 10.68 1.01 0 2902 Water: 5.92 67.39 29.45 N/A 503 366 Other: 13.97 27.80 20.89 N/A 0 2 Chain A: 5.54 54.59 12.65 N/A 0 1624 Chain B: 5.53 67.39 12.45 N/A 0 1646 Chain S: 5.92 60.96 30.99 N/A 503 0 Histogram: Values Number of atoms 5.53 - 11.71 2119 11.71 - 17.90 718 17.90 - 24.08 296 24.08 - 30.27 231 30.27 - 36.46 176 36.46 - 42.64 137 42.64 - 48.83 68 48.83 - 55.01 22 55.01 - 61.20 5 61.20 - 67.39 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1362 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864534 | | target function (ml) not normalized (work): 723804.014846 | | target function (ml) not normalized (free): 15144.514458 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1426 0.1425 0.1482 n_refl.: 191135 remove outliers: r(all,work,free)=0.1426 0.1425 0.1482 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1418 0.1477 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1360 n_refl.: 191135 remove outliers: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191132 ======================== 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 38.277-13.317 93.07 91 3 0.3806 361.184 320.003 0.413 0.947 0.247 13.296-10.522 98.02 98 1 0.2443 480.498 454.673 0.697 0.949 0.203 10.503-8.327 97.80 175 3 0.2045 501.885 497.860 0.866 0.949 0.180 8.318-6.595 100.00 360 8 0.2156 375.528 370.767 0.891 0.948 0.110 6.588-5.215 100.00 711 7 0.1875 345.073 335.173 0.884 0.949 0.084 5.214-4.128 98.38 1367 28 0.1173 504.736 499.919 0.971 0.949 0.044 4.126-3.266 94.74 2603 46 0.1111 460.094 453.626 1.033 0.949 0.009 3.266-2.585 99.86 5447 97 0.1087 310.369 307.301 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0934 234.155 231.632 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.585 137.293 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0990 74.606 73.885 1.055 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.023 38.365 1.044 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1360 | n_water=869 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1194 r_free=0.1360 | n_water=868 | time (s): 109.060 (total time: 111.570) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=860 | time (s): 4.500 (total time: 116.070) Compute maps r_work=0.1195 r_free=0.1361 | n_water=860 | time (s): 1.870 (total time: 117.940) Filter (map) r_work=0.1219 r_free=0.1370 | n_water=737 | time (s): 4.070 (total time: 122.010) Find peaks r_work=0.1219 r_free=0.1370 | n_water=737 | time (s): 0.670 (total time: 122.680) Add new water r_work=0.1231 r_free=0.1373 | n_water=966 | time (s): 4.430 (total time: 127.110) Refine new water occ: r_work=0.1193 r_free=0.1345 adp: r_work=0.1193 r_free=0.1345 occ: r_work=0.1190 r_free=0.1345 adp: r_work=0.1190 r_free=0.1344 occ: r_work=0.1188 r_free=0.1345 adp: r_work=0.1187 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1344 r_work=0.1187 r_free=0.1344 | n_water=966 | time (s): 198.590 (total time: 325.700) Filter (q & B) r_work=0.1190 r_free=0.1353 | n_water=905 | time (s): 4.330 (total time: 330.030) Filter (dist only) r_work=0.1190 r_free=0.1352 | n_water=904 | time (s): 117.950 (total time: 447.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541623 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.710732 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 0.1193 0.1362 0.0169 0.037 1.1 6.5 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.62 1.69 1.798 14.194 15.711 3.764 11.97 13.64 1.67 1.897 14.153 15.711 3.761 Individual atomic B min max mean iso aniso Overall: 5.55 66.89 15.01 0.96 539 3269 Protein: 5.55 31.96 10.59 0.96 0 2902 Water: 6.09 66.89 29.21 N/A 539 365 Other: 13.83 26.32 20.08 N/A 0 2 Chain A: 5.55 53.43 12.51 N/A 0 1623 Chain B: 5.58 66.89 12.33 N/A 0 1646 Chain S: 6.09 60.98 30.72 N/A 539 0 Histogram: Values Number of atoms 5.55 - 11.68 2131 11.68 - 17.82 729 17.82 - 23.95 297 23.95 - 30.08 243 30.08 - 36.22 173 36.22 - 42.35 136 42.35 - 48.49 64 48.49 - 54.62 30 54.62 - 60.75 3 60.75 - 66.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1364 r_work=0.1197 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1365 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1367 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760089 | | target function (ml) not normalized (work): 704230.827315 | | target function (ml) not normalized (free): 14757.181350 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1368 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1496 n_refl.: 191132 remove outliers: r(all,work,free)=0.1404 0.1402 0.1496 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1395 0.1491 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1367 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1194 0.1367 n_refl.: 191131 ======================== 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 38.277-13.317 93.07 91 3 0.3842 361.184 323.370 0.404 0.952 0.235 13.296-10.522 97.03 97 1 0.2436 481.172 455.563 0.691 0.953 0.189 10.503-8.327 97.80 175 3 0.2099 501.885 496.513 0.860 0.953 0.167 8.318-6.595 100.00 360 8 0.2134 375.528 371.211 0.886 0.953 0.100 6.588-5.215 100.00 711 7 0.1878 345.073 335.409 0.882 0.953 0.080 5.214-4.128 98.38 1367 28 0.1180 504.736 500.222 0.970 0.953 0.070 4.126-3.266 94.74 2603 46 0.1119 460.094 453.292 1.029 0.954 0.009 3.266-2.585 99.86 5447 97 0.1103 310.369 307.193 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0950 234.155 231.588 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.585 137.279 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0977 74.606 73.896 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.023 38.356 1.039 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1275 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1367 | n_water=904 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1195 r_free=0.1365 | n_water=901 | time (s): 112.770 (total time: 115.420) Filter (q & B) r_work=0.1196 r_free=0.1365 | n_water=890 | time (s): 4.860 (total time: 120.280) Compute maps r_work=0.1196 r_free=0.1365 | n_water=890 | time (s): 1.580 (total time: 121.860) Filter (map) r_work=0.1217 r_free=0.1365 | n_water=771 | time (s): 5.360 (total time: 127.220) Find peaks r_work=0.1217 r_free=0.1365 | n_water=771 | time (s): 0.870 (total time: 128.090) Add new water r_work=0.1228 r_free=0.1373 | n_water=977 | time (s): 5.230 (total time: 133.320) Refine new water occ: r_work=0.1195 r_free=0.1356 adp: r_work=0.1195 r_free=0.1355 occ: r_work=0.1193 r_free=0.1356 adp: r_work=0.1193 r_free=0.1355 occ: r_work=0.1191 r_free=0.1357 adp: r_work=0.1191 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1355 r_work=0.1191 r_free=0.1355 | n_water=977 | time (s): 293.670 (total time: 426.990) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=914 | time (s): 4.510 (total time: 431.500) Filter (dist only) r_work=0.1195 r_free=0.1358 | n_water=913 | time (s): 119.360 (total time: 550.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.493537 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.842198 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 0.1198 0.1362 0.0163 0.037 1.1 6.8 0.0 0.3 0 0.747 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.62 1.63 1.762 14.068 15.842 3.761 11.98 13.59 1.61 1.874 14.032 15.842 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 65.80 14.90 0.92 548 3269 Protein: 5.57 29.70 10.50 0.92 0 2902 Water: 6.00 65.80 28.91 N/A 548 365 Other: 13.87 23.68 18.77 N/A 0 2 Chain A: 5.60 51.82 12.38 N/A 0 1623 Chain B: 5.57 65.80 12.22 N/A 0 1646 Chain S: 6.00 60.92 30.45 N/A 548 0 Histogram: Values Number of atoms 5.57 - 11.59 2113 11.59 - 17.62 775 17.62 - 23.64 276 23.64 - 29.66 235 29.66 - 35.69 179 35.69 - 41.71 133 41.71 - 47.73 71 47.73 - 53.75 29 53.75 - 59.78 3 59.78 - 65.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1359 r_work=0.1198 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756502 | | target function (ml) not normalized (work): 703555.323050 | | target function (ml) not normalized (free): 14735.530412 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1487 n_refl.: 191131 remove outliers: r(all,work,free)=0.1401 0.1400 0.1487 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1394 0.1392 0.1482 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191131 ======================== 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 38.277-13.317 93.07 91 3 0.3939 361.184 319.642 0.382 0.951 0.209 13.296-10.522 97.03 97 1 0.2461 481.172 459.809 0.690 0.952 0.170 10.503-8.327 97.80 175 3 0.2153 501.885 494.857 0.855 0.953 0.150 8.318-6.595 100.00 360 8 0.2167 375.528 370.771 0.881 0.952 0.093 6.588-5.215 100.00 711 7 0.1946 345.073 334.499 0.880 0.953 0.069 5.214-4.128 98.38 1367 28 0.1201 504.736 500.056 0.970 0.953 0.053 4.126-3.266 94.74 2603 46 0.1131 460.094 453.353 1.031 0.953 0.000 3.266-2.585 99.86 5447 97 0.1113 310.369 307.137 1.018 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.155 231.589 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0909 138.585 137.276 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0968 74.606 73.905 1.049 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.023 38.357 1.037 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1333 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=913 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1196 r_free=0.1361 | n_water=913 | time (s): 109.000 (total time: 111.300) Filter (q & B) r_work=0.1196 r_free=0.1361 | n_water=907 | time (s): 4.410 (total time: 115.710) Compute maps r_work=0.1196 r_free=0.1361 | n_water=907 | time (s): 1.770 (total time: 117.480) Filter (map) r_work=0.1216 r_free=0.1367 | n_water=796 | time (s): 5.090 (total time: 122.570) Find peaks r_work=0.1216 r_free=0.1367 | n_water=796 | time (s): 0.760 (total time: 123.330) Add new water r_work=0.1224 r_free=0.1373 | n_water=994 | time (s): 3.890 (total time: 127.220) Refine new water occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1348 occ: r_work=0.1190 r_free=0.1345 adp: r_work=0.1190 r_free=0.1346 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1346 r_work=0.1189 r_free=0.1346 | n_water=994 | time (s): 302.290 (total time: 429.510) Filter (q & B) r_work=0.1193 r_free=0.1350 | n_water=921 | time (s): 4.700 (total time: 434.210) Filter (dist only) r_work=0.1193 r_free=0.1350 | n_water=920 | time (s): 118.350 (total time: 552.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568751 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.998178 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 0.1196 0.1355 0.0159 0.038 1.1 6.0 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 1.727 13.965 13.998 3.757 11.99 13.58 1.58 1.746 13.954 13.998 3.757 Individual atomic B min max mean iso aniso Overall: 5.55 65.42 14.87 0.89 555 3269 Protein: 5.55 29.20 10.46 0.89 0 2902 Water: 5.97 65.42 28.78 N/A 555 365 Other: 13.85 23.14 18.49 N/A 0 2 Chain A: 5.60 51.67 12.31 N/A 0 1623 Chain B: 5.55 65.42 12.16 N/A 0 1646 Chain S: 5.97 60.89 30.38 N/A 555 0 Histogram: Values Number of atoms 5.55 - 11.54 2106 11.54 - 17.52 783 17.52 - 23.51 278 23.51 - 29.50 236 29.50 - 35.49 181 35.49 - 41.47 133 41.47 - 47.46 70 47.46 - 53.45 30 53.45 - 59.44 2 59.44 - 65.42 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1358 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756808 | | target function (ml) not normalized (work): 703612.503315 | | target function (ml) not normalized (free): 14736.225217 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1492 n_refl.: 191131 remove outliers: r(all,work,free)=0.1401 0.1399 0.1492 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1368 0.1366 0.1469 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191131 ======================== 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 38.277-13.317 93.07 91 3 0.3932 361.184 319.673 0.387 0.951 0.198 13.296-10.522 97.03 97 1 0.2506 481.172 459.568 0.703 0.953 0.155 10.503-8.327 97.80 175 3 0.2138 501.885 494.992 0.877 0.953 0.138 8.318-6.595 100.00 360 8 0.2157 375.528 371.038 0.905 0.953 0.091 6.588-5.215 100.00 711 7 0.1933 345.073 335.266 0.904 0.953 0.073 5.214-4.128 98.38 1367 28 0.1206 504.736 499.843 0.997 0.953 0.070 4.126-3.266 94.74 2603 46 0.1139 460.094 453.194 1.057 0.953 0.005 3.266-2.585 99.86 5447 97 0.1123 310.369 307.139 1.040 0.953 0.000 2.585-2.046 97.45 10613 204 0.0955 234.155 231.562 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0910 138.585 137.280 1.065 0.953 0.000 1.619-1.281 98.00 42464 925 0.0965 74.606 73.904 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.023 38.348 1.023 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1360 | n_water=920 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1198 r_free=0.1359 | n_water=919 | time (s): 117.300 (total time: 119.720) Filter (q & B) r_work=0.1199 r_free=0.1359 | n_water=907 | time (s): 5.310 (total time: 125.030) Compute maps r_work=0.1199 r_free=0.1359 | n_water=907 | time (s): 1.980 (total time: 127.010) Filter (map) r_work=0.1220 r_free=0.1372 | n_water=793 | time (s): 4.070 (total time: 131.080) Find peaks r_work=0.1220 r_free=0.1372 | n_water=793 | time (s): 0.720 (total time: 131.800) Add new water r_work=0.1229 r_free=0.1378 | n_water=1006 | time (s): 4.710 (total time: 136.510) Refine new water occ: r_work=0.1196 r_free=0.1351 adp: r_work=0.1196 r_free=0.1351 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1350 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=1006 | time (s): 205.760 (total time: 342.270) Filter (q & B) r_work=0.1197 r_free=0.1358 | n_water=925 | time (s): 4.460 (total time: 346.730) Filter (dist only) r_work=0.1197 r_free=0.1358 | n_water=923 | time (s): 117.580 (total time: 464.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567451 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.517543 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 0.1201 0.1363 0.0162 0.039 1.1 6.3 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.63 1.62 1.709 13.716 13.518 3.759 12.04 13.66 1.61 1.763 13.696 13.518 3.759 Individual atomic B min max mean iso aniso Overall: 5.38 64.20 14.60 0.86 558 3269 Protein: 5.38 27.94 10.21 0.86 0 2902 Water: 5.80 64.20 28.40 N/A 558 365 Other: 13.65 21.97 17.81 N/A 0 2 Chain A: 5.43 51.10 12.03 N/A 0 1623 Chain B: 5.38 64.20 11.89 N/A 0 1646 Chain S: 5.80 60.66 30.06 N/A 558 0 Histogram: Values Number of atoms 5.38 - 11.26 2085 11.26 - 17.14 807 17.14 - 23.02 268 23.02 - 28.91 241 28.91 - 34.79 175 34.79 - 40.67 138 40.67 - 46.55 72 46.55 - 52.43 33 52.43 - 58.31 3 58.31 - 64.20 5 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1366 r_work=0.1204 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758287 | | target function (ml) not normalized (work): 703889.497935 | | target function (ml) not normalized (free): 14745.382060 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1368 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1379 0.1377 0.1481 n_refl.: 191131 remove outliers: r(all,work,free)=0.1379 0.1377 0.1481 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1379 0.1377 0.1481 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191131 ======================== 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 38.277-13.317 93.07 91 3 0.3973 361.184 317.512 0.365 0.976 0.187 13.296-10.522 97.03 97 1 0.2456 481.172 459.603 0.676 0.978 0.145 10.503-8.327 97.80 175 3 0.2201 501.885 493.418 0.845 0.978 0.123 8.318-6.595 100.00 360 8 0.2172 375.528 369.815 0.873 0.978 0.093 6.588-5.215 100.00 711 7 0.1975 345.073 334.484 0.871 0.979 0.073 5.214-4.128 98.38 1367 28 0.1231 504.736 499.196 0.964 0.979 0.070 4.126-3.266 94.74 2603 46 0.1147 460.094 452.598 1.021 0.981 0.005 3.266-2.585 99.86 5447 97 0.1127 310.369 306.781 1.004 0.981 0.000 2.585-2.046 97.45 10613 204 0.0962 234.155 231.467 1.009 0.983 0.000 2.046-1.619 99.39 21536 464 0.0911 138.585 137.195 1.023 0.986 0.000 1.619-1.281 98.00 42464 925 0.0950 74.606 73.939 1.008 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.023 38.323 0.969 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1358 | n_water=923 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1194 r_free=0.1358 | n_water=923 | time (s): 110.910 (total time: 113.360) Filter (q & B) r_work=0.1195 r_free=0.1358 | n_water=914 | time (s): 4.240 (total time: 117.600) Compute maps r_work=0.1195 r_free=0.1358 | n_water=914 | time (s): 1.810 (total time: 119.410) Filter (map) r_work=0.1217 r_free=0.1370 | n_water=798 | time (s): 4.250 (total time: 123.660) Find peaks r_work=0.1217 r_free=0.1370 | n_water=798 | time (s): 0.730 (total time: 124.390) Add new water r_work=0.1225 r_free=0.1378 | n_water=998 | time (s): 4.770 (total time: 129.160) Refine new water occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1343 adp: r_work=0.1188 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1343 r_work=0.1188 r_free=0.1343 | n_water=998 | time (s): 226.980 (total time: 356.140) Filter (q & B) r_work=0.1192 r_free=0.1350 | n_water=928 | time (s): 4.670 (total time: 360.810) Filter (dist only) r_work=0.1192 r_free=0.1351 | n_water=927 | time (s): 121.020 (total time: 481.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.545714 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.207076 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1356 0.0161 0.039 1.1 7.2 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.56 1.61 1.664 13.658 14.207 3.757 11.94 13.55 1.61 1.673 13.655 14.207 3.754 Individual atomic B min max mean iso aniso Overall: 5.42 63.26 14.60 0.87 562 3269 Protein: 5.42 27.92 10.22 0.87 0 2902 Water: 5.79 63.26 28.28 N/A 562 365 Other: 13.66 22.05 17.85 N/A 0 2 Chain A: 5.46 50.75 12.01 N/A 0 1623 Chain B: 5.42 63.26 11.88 N/A 0 1646 Chain S: 5.79 60.61 30.01 N/A 562 0 Histogram: Values Number of atoms 5.42 - 11.21 2064 11.21 - 16.99 822 16.99 - 22.77 269 22.77 - 28.56 241 28.56 - 34.34 180 34.34 - 40.12 128 40.12 - 45.91 82 45.91 - 51.69 35 51.69 - 57.47 5 57.47 - 63.26 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1355 r_work=0.1194 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1355 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753734 | | target function (ml) not normalized (work): 703036.908070 | | target function (ml) not normalized (free): 14732.208409 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1381 0.1380 0.1486 n_refl.: 191131 remove outliers: r(all,work,free)=0.1381 0.1380 0.1486 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1381 0.1380 0.1486 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191131 ======================== 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 38.277-13.317 93.07 91 3 0.3973 361.184 317.983 0.364 0.976 0.187 13.296-10.522 97.03 97 1 0.2450 481.172 460.622 0.674 0.978 0.145 10.503-8.327 97.80 175 3 0.2182 501.885 494.196 0.846 0.979 0.123 8.318-6.595 100.00 360 8 0.2169 375.528 369.974 0.873 0.978 0.091 6.588-5.215 100.00 711 7 0.1964 345.073 334.703 0.870 0.979 0.070 5.214-4.128 98.38 1367 28 0.1228 504.736 499.077 0.962 0.980 0.060 4.126-3.266 94.74 2603 46 0.1153 460.094 452.514 1.021 0.981 0.000 3.266-2.585 99.86 5447 97 0.1130 310.369 306.786 1.004 0.982 0.000 2.585-2.046 97.45 10613 204 0.0960 234.155 231.473 1.010 0.984 0.000 2.046-1.619 99.39 21536 464 0.0909 138.585 137.220 1.024 0.987 0.000 1.619-1.281 98.00 42464 925 0.0944 74.606 73.950 1.010 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.023 38.312 0.974 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0886 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1354 After: r_work=0.1192 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1355 | n_water=927 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1192 r_free=0.1355 | n_water=926 | time (s): 123.930 (total time: 127.060) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=913 | time (s): 4.560 (total time: 131.620) Compute maps r_work=0.1194 r_free=0.1357 | n_water=913 | time (s): 1.740 (total time: 133.360) Filter (map) r_work=0.1216 r_free=0.1369 | n_water=797 | time (s): 4.380 (total time: 137.740) Find peaks r_work=0.1216 r_free=0.1369 | n_water=797 | time (s): 0.870 (total time: 138.610) Add new water r_work=0.1224 r_free=0.1380 | n_water=1010 | time (s): 5.140 (total time: 143.750) Refine new water occ: r_work=0.1190 r_free=0.1352 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1188 r_free=0.1352 occ: r_work=0.1187 r_free=0.1352 adp: r_work=0.1187 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1352 r_work=0.1187 r_free=0.1352 | n_water=1010 | time (s): 264.370 (total time: 408.120) Filter (q & B) r_work=0.1191 r_free=0.1358 | n_water=927 | time (s): 4.890 (total time: 413.010) Filter (dist only) r_work=0.1192 r_free=0.1358 | n_water=925 | time (s): 122.260 (total time: 535.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.607754 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 0.1194 0.1359 0.0165 0.039 1.2 10.4 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.59 1.65 1.664 13.657 13.608 3.756 11.96 13.62 1.66 1.665 13.654 13.608 3.756 Individual atomic B min max mean iso aniso Overall: 5.43 62.99 14.59 0.85 560 3269 Protein: 5.43 27.79 10.23 0.85 0 2902 Water: 5.89 62.99 28.23 N/A 560 365 Other: 13.68 21.99 17.83 N/A 0 2 Chain A: 5.48 50.65 12.00 N/A 0 1623 Chain B: 5.43 62.99 11.88 N/A 0 1646 Chain S: 5.89 60.57 30.03 N/A 560 0 Histogram: Values Number of atoms 5.43 - 11.18 2054 11.18 - 16.94 835 16.94 - 22.70 272 22.70 - 28.45 233 28.45 - 34.21 181 34.21 - 39.96 122 39.96 - 45.72 85 45.72 - 51.48 37 51.48 - 57.23 5 57.23 - 62.99 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1362 r_work=0.1196 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1363 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756249 | | target function (ml) not normalized (work): 703507.850477 | | target function (ml) not normalized (free): 14738.900984 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1361 0.1484 5.6935 5.7854| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1374 5.089 5.2058| | 3: 2.33 - 2.04 0.96 6939 150 0.0911 0.1186 4.6639 4.7578| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1075 4.3961 4.5804| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.1000 4.1568 4.244| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1068 3.9493 4.0671| | 7: 1.62 - 1.54 0.99 7104 148 0.0898 0.0990 3.8073 3.9583| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1319 3.7059 3.9061| | 9: 1.47 - 1.41 0.98 6938 155 0.0926 0.1122 3.6236 3.7539| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1165 3.5579 3.6732| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1129 3.4847 3.5899| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1116 3.4593 3.5746| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1240 3.439 3.5551| | 14: 1.25 - 1.22 0.98 7015 112 0.1112 0.1606 3.4323 3.683| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1256 3.448 3.4945| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1552 3.4649 3.6545| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1240 3.4342 3.4475| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1704 3.4384 3.533| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1742 3.4196 3.5949| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1572 3.4098 3.4328| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2122 3.4187 3.5014| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1954 3.4127 3.4151| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2026 3.4331 3.4864| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2259 3.4355 3.5107| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2501 3.4487 3.5227| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2869 3.4156 3.4222| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2810 3.4679 3.3974| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 38.28 - 2.94 7399 127 0.93 12.06 1.00 0.97 11801.07| | 2: 2.94 - 2.33 7339 128 0.92 13.21 0.99 0.96 5368.92| | 3: 2.33 - 2.04 6939 150 0.96 7.80 1.01 0.97 1745.33| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.97 1024.87| | 5: 1.85 - 1.72 7113 159 0.96 8.12 1.00 0.97 642.42| | 6: 1.72 - 1.62 7102 142 0.96 8.09 1.00 0.98 448.45| | 7: 1.62 - 1.54 7104 148 0.96 8.30 1.01 0.98 344.65| | 8: 1.54 - 1.47 6798 152 0.96 8.40 1.01 0.99 284.43| | 9: 1.47 - 1.41 6938 155 0.96 8.54 1.00 0.99 233.35| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.98 202.70| | 11: 1.36 - 1.32 6997 151 0.96 8.92 0.99 0.97 174.69| | 12: 1.32 - 1.28 6975 149 0.96 8.95 0.98 0.96 160.20| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.97 157.24| | 14: 1.25 - 1.22 7015 112 0.95 10.66 1.02 0.98 161.95| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.99 166.14| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.98 160.35| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.98 154.51| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.96 147.89| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.96 151.06| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.95 149.86| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.94 152.89| | 22: 1.07 - 1.05 6836 135 0.89 18.26 0.99 0.94 154.56| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.93 164.50| | 24: 1.03 - 1.02 6784 133 0.85 23.13 0.99 0.94 178.79| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.97 0.91 181.79| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.89 176.56| | 27: 0.99 - 0.98 6647 131 0.82 26.35 0.98 0.88 161.65| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 147.89 max = 11801.07 mean = 962.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.34| |phase err.(test): min = 0.00 max = 89.69 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1497 n_refl.: 191131 remove outliers: r(all,work,free)=0.1391 0.1389 0.1497 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1391 0.1389 0.1497 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191129 ======================== 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 38.277-13.317 91.09 89 3 0.3828 356.332 314.097 0.319 0.984 0.100 13.296-10.522 97.03 97 1 0.2492 481.172 459.144 0.658 0.985 0.115 10.503-8.327 97.80 175 3 0.2187 501.885 494.012 0.841 0.986 0.115 8.318-6.595 100.00 360 8 0.2160 375.528 369.801 0.867 0.985 0.089 6.588-5.215 100.00 711 7 0.1958 345.073 334.629 0.864 0.986 0.070 5.214-4.128 98.38 1367 28 0.1229 504.736 499.473 0.954 0.987 0.029 4.126-3.266 94.74 2603 46 0.1154 460.094 452.498 1.015 0.988 0.000 3.266-2.585 99.86 5447 97 0.1131 310.369 306.886 0.998 0.989 0.000 2.585-2.046 97.45 10613 204 0.0967 234.155 231.490 1.004 0.992 0.000 2.046-1.619 99.39 21536 464 0.0913 138.585 137.226 1.018 0.996 0.000 1.619-1.281 98.00 42464 925 0.0949 74.606 73.957 1.005 1.002 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.023 38.315 0.970 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0548 ================= 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 : 0.2023 0.1953 0.081 5.217 5.2 78.0 14.6 805 0.000 1_bss: 0.1788 0.1897 0.081 5.217 5.2 78.0 14.6 805 0.000 1_settarget: 0.1788 0.1897 0.081 5.217 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1898 0.081 5.217 5.2 78.0 14.6 805 0.003 1_weight: 0.1796 0.1898 0.081 5.217 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1274 0.1504 0.038 1.150 5.2 78.0 14.6 805 0.158 1_adp: 0.1301 0.1573 0.038 1.150 5.2 73.0 15.1 805 0.158 1_regHadp: 0.1300 0.1568 0.038 1.150 5.2 73.0 15.1 805 0.158 1_occ: 0.1285 0.1558 0.038 1.150 5.2 73.0 15.1 805 0.158 2_bss: 0.1277 0.1547 0.038 1.150 5.4 73.2 15.2 805 0.158 2_settarget: 0.1277 0.1547 0.038 1.150 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1277 0.1547 0.038 1.167 5.4 73.2 15.2 805 0.158 2_nqh: 0.1277 0.1547 0.038 1.167 5.4 73.2 15.2 805 0.158 2_sol: 0.1274 0.1508 0.038 1.167 5.4 73.2 16.3 883 n/a 2_weight: 0.1274 0.1508 0.038 1.167 5.4 73.2 16.3 883 n/a 2_xyzrec: 0.1256 0.1522 0.041 1.145 5.4 73.2 16.3 883 n/a 2_adp: 0.1235 0.1511 0.041 1.145 5.5 69.6 16.3 883 n/a 2_regHadp: 0.1235 0.1512 0.041 1.145 5.5 69.6 16.3 883 n/a 2_occ: 0.1229 0.1507 0.041 1.145 5.5 69.6 16.3 883 n/a 3_bss: 0.1235 0.1513 0.041 1.145 5.4 69.6 16.3 883 n/a 3_settarget: 0.1235 0.1513 0.041 1.145 5.4 69.6 16.3 883 n/a 3_updatecdl: 0.1235 0.1513 0.041 1.143 5.4 69.6 16.3 883 n/a 3_nqh: 0.1235 0.1513 0.041 1.143 5.4 69.6 16.3 883 n/a 3_sol: 0.1253 0.1511 0.041 1.143 5.4 68.2 15.4 874 n/a 3_weight: 0.1253 0.1511 0.041 1.143 5.4 68.2 15.4 874 n/a 3_xyzrec: 0.1244 0.1437 0.035 1.093 5.4 68.2 15.4 874 n/a 3_adp: 0.1238 0.1396 0.035 1.093 5.5 67.8 15.3 874 n/a 3_regHadp: 0.1238 0.1396 0.035 1.093 5.5 67.8 15.3 874 n/a 3_occ: 0.1232 0.1389 0.035 1.093 5.5 67.8 15.3 874 n/a 4_bss: 0.1227 0.1384 0.035 1.093 5.5 67.8 15.2 874 n/a 4_settarget: 0.1227 0.1384 0.035 1.093 5.5 67.8 15.2 874 n/a 4_updatecdl: 0.1227 0.1384 0.035 1.099 5.5 67.8 15.2 874 n/a 4_nqh: 0.1227 0.1384 0.035 1.099 5.5 67.8 15.2 874 n/a 4_sol: 0.1209 0.1362 0.035 1.099 5.5 67.8 15.1 869 n/a 4_weight: 0.1209 0.1362 0.035 1.099 5.5 67.8 15.1 869 n/a 4_xyzrec: 0.1207 0.1366 0.036 1.119 5.5 67.8 15.1 869 n/a 4_adp: 0.1199 0.1362 0.036 1.119 5.5 67.4 15.0 869 n/a 4_regHadp: 0.1199 0.1362 0.036 1.119 5.5 67.4 15.0 869 n/a 4_occ: 0.1197 0.1361 0.036 1.119 5.5 67.4 15.0 869 n/a 5_bss: 0.1194 0.1360 0.036 1.119 5.5 67.4 15.0 869 n/a 5_settarget: 0.1194 0.1360 0.036 1.119 5.5 67.4 15.0 869 n/a 5_updatecdl: 0.1194 0.1360 0.036 1.119 5.5 67.4 15.0 869 n/a 5_nqh: 0.1194 0.1360 0.036 1.119 5.5 67.4 15.0 869 n/a 5_sol: 0.1190 0.1352 0.036 1.119 5.5 67.4 15.1 904 n/a 5_weight: 0.1190 0.1352 0.036 1.119 5.5 67.4 15.1 904 n/a 5_xyzrec: 0.1193 0.1362 0.037 1.123 5.5 67.4 15.1 904 n/a 5_adp: 0.1197 0.1364 0.037 1.123 5.5 66.9 15.0 904 n/a 5_regHadp: 0.1197 0.1365 0.037 1.123 5.5 66.9 15.0 904 n/a 5_occ: 0.1195 0.1367 0.037 1.123 5.5 66.9 15.0 904 n/a 6_bss: 0.1195 0.1367 0.037 1.123 5.5 66.9 15.0 904 n/a 6_settarget: 0.1195 0.1367 0.037 1.123 5.5 66.9 15.0 904 n/a 6_updatecdl: 0.1195 0.1367 0.037 1.123 5.5 66.9 15.0 904 n/a 6_nqh: 0.1195 0.1367 0.037 1.123 5.5 66.9 15.0 904 n/a 6_sol: 0.1195 0.1358 0.037 1.123 5.5 66.9 15.0 913 n/a 6_weight: 0.1195 0.1358 0.037 1.123 5.5 66.9 15.0 913 n/a 6_xyzrec: 0.1198 0.1362 0.037 1.123 5.5 66.9 15.0 913 n/a 6_adp: 0.1198 0.1359 0.037 1.123 5.6 65.8 14.9 913 n/a 6_regHadp: 0.1198 0.1360 0.037 1.123 5.6 65.8 14.9 913 n/a 6_occ: 0.1196 0.1362 0.037 1.123 5.6 65.8 14.9 913 n/a 7_bss: 0.1196 0.1361 0.037 1.123 5.5 65.8 14.9 913 n/a 7_settarget: 0.1196 0.1361 0.037 1.123 5.5 65.8 14.9 913 n/a 7_updatecdl: 0.1196 0.1361 0.037 1.122 5.5 65.8 14.9 913 n/a 7_nqh: 0.1196 0.1361 0.037 1.122 5.5 65.8 14.9 913 n/a 7_sol: 0.1193 0.1350 0.037 1.122 5.5 65.8 14.9 920 n/a 7_weight: 0.1193 0.1350 0.037 1.122 5.5 65.8 14.9 920 n/a 7_xyzrec: 0.1196 0.1355 0.038 1.127 5.5 65.8 14.9 920 n/a 7_adp: 0.1199 0.1358 0.038 1.127 5.5 65.4 14.9 920 n/a 7_regHadp: 0.1200 0.1358 0.038 1.127 5.5 65.4 14.9 920 n/a 7_occ: 0.1198 0.1360 0.038 1.127 5.5 65.4 14.9 920 n/a 8_bss: 0.1198 0.1360 0.038 1.127 5.3 65.2 14.6 920 n/a 8_settarget: 0.1198 0.1360 0.038 1.127 5.3 65.2 14.6 920 n/a 8_updatecdl: 0.1198 0.1360 0.038 1.127 5.3 65.2 14.6 920 n/a 8_nqh: 0.1198 0.1360 0.038 1.127 5.3 65.2 14.6 920 n/a 8_sol: 0.1197 0.1358 0.038 1.127 5.3 65.2 14.6 923 n/a 8_weight: 0.1197 0.1358 0.038 1.127 5.3 65.2 14.6 923 n/a 8_xyzrec: 0.1201 0.1363 0.039 1.131 5.3 65.2 14.6 923 n/a 8_adp: 0.1204 0.1366 0.039 1.131 5.4 64.2 14.6 923 n/a 8_regHadp: 0.1204 0.1366 0.039 1.131 5.4 64.2 14.6 923 n/a 8_occ: 0.1203 0.1368 0.039 1.131 5.4 64.2 14.6 923 n/a 9_bss: 0.1194 0.1358 0.039 1.131 5.4 64.2 14.6 923 n/a 9_settarget: 0.1194 0.1358 0.039 1.131 5.4 64.2 14.6 923 n/a 9_updatecdl: 0.1194 0.1358 0.039 1.131 5.4 64.2 14.6 923 n/a 9_nqh: 0.1194 0.1358 0.039 1.131 5.4 64.2 14.6 923 n/a 9_sol: 0.1192 0.1351 0.039 1.131 5.4 64.2 14.6 927 n/a 9_weight: 0.1192 0.1351 0.039 1.131 5.4 64.2 14.6 927 n/a 9_xyzrec: 0.1195 0.1356 0.039 1.127 5.4 64.2 14.6 927 n/a 9_adp: 0.1194 0.1355 0.039 1.127 5.4 63.3 14.6 927 n/a 9_regHadp: 0.1194 0.1355 0.039 1.127 5.4 63.3 14.6 927 n/a 9_occ: 0.1192 0.1355 0.039 1.127 5.4 63.3 14.6 927 n/a 10_bss: 0.1192 0.1354 0.039 1.127 5.4 63.3 14.6 927 n/a 10_settarget: 0.1192 0.1354 0.039 1.127 5.4 63.3 14.6 927 n/a 10_updatecdl: 0.1192 0.1354 0.039 1.127 5.4 63.3 14.6 927 n/a 10_setrh: 0.1192 0.1355 0.039 1.127 5.4 63.3 14.6 927 n/a 10_nqh: 0.1192 0.1355 0.039 1.127 5.4 63.3 14.6 927 n/a 10_sol: 0.1192 0.1358 0.039 1.127 5.4 63.3 14.6 925 n/a 10_weight: 0.1192 0.1358 0.039 1.127 5.4 63.3 14.6 925 n/a 10_xyzrec: 0.1194 0.1359 0.039 1.165 5.4 63.3 14.6 925 n/a 10_adp: 0.1196 0.1362 0.039 1.165 5.4 63.0 14.6 925 n/a 10_regHadp: 0.1196 0.1362 0.039 1.165 5.4 63.0 14.6 925 n/a 10_occ: 0.1195 0.1363 0.039 1.165 5.4 63.0 14.6 925 n/a end: 0.1194 0.1358 0.039 1.165 5.4 63.0 14.6 925 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8810963_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8810963_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2300 Refinement macro-cycles (run) : 11964.3500 Write final files (write_after_run_outputs) : 161.8500 Total : 12132.4300 Total CPU time: 3.38 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:22 PST -0800 (1736735962.20 s) Start R-work = 0.1788, R-free = 0.1897 Final R-work = 0.1194, R-free = 0.1358 =============================================================================== Job complete usr+sys time: 12436.56 seconds wall clock time: 208 minutes 14.25 seconds (12494.25 seconds total)