Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1990108.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_1990108.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1990108.pdb" 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" 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: 1.84, per 1000 atoms: 0.27 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: 2.766 distance_ideal: 2.720 ideal - model: -0.046 slack: 0.000 delta_slack: -0.046 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: 2.666 distance_ideal: 2.710 ideal - model: 0.044 slack: 0.000 delta_slack: 0.044 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: 0.66 Conformation dependent library (CDL) restraints added in 166.1 milliseconds Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 524 1.00 - 1.22: 2517 1.22 - 1.44: 1329 1.44 - 1.66: 1461 1.66 - 1.88: 103 Bond restraints: 5934 Sorted by residual: bond pdb=" N ASN B 42 " pdb=" CA ASN B 42 " ideal model delta sigma weight residual 1.456 1.209 0.247 1.23e-02 6.61e+03 4.03e+02 bond pdb=" N LEU A 185 " pdb=" H LEU A 185 " ideal model delta sigma weight residual 0.860 1.259 -0.399 2.00e-02 2.50e+03 3.98e+02 bond pdb=" CG1 VAL A 69 " pdb="HG13 VAL A 69 " ideal model delta sigma weight residual 0.970 1.367 -0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" CE1 HIS B 179 " pdb=" NE2 HIS B 179 " ideal model delta sigma weight residual 1.321 1.514 -0.193 1.00e-02 1.00e+04 3.73e+02 bond pdb=" C SER B 13 " pdb=" O SER B 13 " ideal model delta sigma weight residual 1.234 1.467 -0.233 1.24e-02 6.50e+03 3.52e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 5379 3.99 - 7.99: 3600 7.99 - 11.98: 1462 11.98 - 15.97: 341 15.97 - 19.97: 28 Bond angle restraints: 10810 Sorted by residual: angle pdb=" ND1 HIS B 179 " pdb=" CE1 HIS B 179 " pdb=" NE2 HIS B 179 " ideal model delta sigma weight residual 108.40 92.32 16.08 1.00e+00 1.00e+00 2.59e+02 angle pdb=" O GLU A 176 " pdb=" C GLU A 176 " pdb=" N LYS A 177 " ideal model delta sigma weight residual 122.12 137.26 -15.14 1.06e+00 8.90e-01 2.04e+02 angle pdb=" NE ARG A 175 " pdb=" CZ ARG A 175 " pdb=" NH2 ARG A 175 " ideal model delta sigma weight residual 119.20 132.02 -12.82 9.00e-01 1.23e+00 2.03e+02 angle pdb=" O VAL A 92 " pdb=" C VAL A 92 " pdb=" N LYS A 93 " ideal model delta sigma weight residual 121.87 135.63 -13.76 9.70e-01 1.06e+00 2.01e+02 angle pdb=" CA ALA A 189 " pdb=" C ALA A 189 " pdb=" O ALA A 189 " ideal model delta sigma weight residual 121.56 137.00 -15.44 1.09e+00 8.42e-01 2.01e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1840 17.19 - 34.37: 137 34.37 - 51.56: 49 51.56 - 68.74: 20 68.74 - 85.93: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS B 47 " pdb=" C CYS B 47 " pdb=" N SER B 48 " pdb=" CA SER B 48 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 222 0.215 - 0.430: 137 0.430 - 0.644: 89 0.644 - 0.859: 36 0.859 - 1.074: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.52 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.54 -1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA HIS B 116 " pdb=" N HIS B 116 " pdb=" C HIS B 116 " pdb=" CB HIS B 116 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.72e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.112 2.00e-02 2.50e+03 7.55e-02 1.71e+02 pdb=" CG PHE A 164 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.075 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.115 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " -0.109 2.00e-02 2.50e+03 7.53e-02 1.70e+02 pdb=" CG PHE B 127 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " 0.100 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " 0.078 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " -0.136 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " 0.120 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.117 2.00e-02 2.50e+03 7.05e-02 1.49e+02 pdb=" CG TYR A 194 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.097 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.041 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.053 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.112 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.044 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.68: 35 1.68 - 2.41: 3203 2.41 - 3.14: 22738 3.14 - 3.87: 32739 3.87 - 4.60: 51490 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110205 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.955 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.963 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.059 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.130 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.167 2.620 ... (remaining 110200 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_1990108_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= 0.2044 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.308884 | | target function (ml) not normalized (work): 807109.899490 | | target function (ml) not normalized (free): 16548.493288 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2137 0.1844 6.7021 6.2842| | 2: 2.94 - 2.33 1.00 7339 128 0.1617 0.1512 5.5275 5.553| | 3: 2.33 - 2.04 0.96 6939 150 0.1640 0.1573 5.1443 5.1757| | 4: 2.04 - 1.85 1.00 7170 155 0.1747 0.1574 4.9571 4.9958| | 5: 1.85 - 1.72 0.99 7113 159 0.1931 0.1767 4.8124 4.8185| | 6: 1.72 - 1.62 0.99 7102 142 0.2002 0.2150 4.6816 4.7631| | 7: 1.62 - 1.54 0.99 7104 148 0.2036 0.1780 4.5762 4.5786| | 8: 1.54 - 1.47 0.96 6798 152 0.2066 0.2214 4.4939 4.5034| | 9: 1.47 - 1.41 0.98 6938 155 0.2089 0.2414 4.3997 4.5477| | 10: 1.41 - 1.36 0.99 7022 150 0.2122 0.2026 4.3153 4.2886| | 11: 1.36 - 1.32 0.99 6997 151 0.2127 0.2107 4.2414 4.2319| | 12: 1.32 - 1.28 0.98 6976 149 0.2111 0.2003 4.1897 4.2125| | 13: 1.28 - 1.25 0.98 6907 166 0.2040 0.2014 4.1414 4.1574| | 14: 1.25 - 1.22 0.98 7015 113 0.2108 0.2249 4.0948 4.22| | 15: 1.22 - 1.19 0.98 6957 137 0.2148 0.1916 4.054 3.9779| | 16: 1.19 - 1.17 0.93 6604 132 0.2154 0.2307 4.0215 4.1212| | 17: 1.17 - 1.14 0.98 6941 135 0.2206 0.1867 3.9712 3.9301| | 18: 1.14 - 1.12 0.98 6875 142 0.2226 0.2516 3.9221 3.9575| | 19: 1.12 - 1.10 0.97 6949 106 0.2265 0.2546 3.8728 4.0158| | 20: 1.10 - 1.08 0.97 6884 147 0.2349 0.2309 3.8305 3.8457| | 21: 1.08 - 1.07 0.97 6852 152 0.2476 0.2544 3.8039 3.8219| | 22: 1.07 - 1.05 0.97 6838 135 0.2573 0.2662 3.7631 3.777| | 23: 1.05 - 1.03 0.97 6829 159 0.2720 0.2604 3.7355 3.8008| | 24: 1.03 - 1.02 0.96 6785 133 0.2904 0.2963 3.7118 3.8182| | 25: 1.02 - 1.01 0.93 6552 130 0.3101 0.2743 3.6829 3.6716| | 26: 1.01 - 0.99 0.96 6767 158 0.3211 0.3244 3.634 3.6621| | 27: 0.99 - 0.98 0.94 6648 131 0.3473 0.3185 3.647 3.5956| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.86 20.05 0.91 0.97 33794.82| | 2: 2.94 - 2.33 7339 128 0.86 20.81 1.09 1.01 14469.74| | 3: 2.33 - 2.04 6939 150 0.93 12.40 1.11 1.05 4045.81| | 4: 2.04 - 1.85 7170 155 0.93 12.92 1.11 1.07 2588.68| | 5: 1.85 - 1.72 7113 159 0.91 15.34 1.11 1.09 2033.41| | 6: 1.72 - 1.62 7102 142 0.90 16.59 1.11 1.08 1637.37| | 7: 1.62 - 1.54 7104 148 0.89 17.56 1.11 1.08 1353.14| | 8: 1.54 - 1.47 6798 152 0.89 18.15 1.10 1.07 1147.92| | 9: 1.47 - 1.41 6938 155 0.88 19.21 1.10 1.06 996.19| | 10: 1.41 - 1.36 7022 150 0.87 20.15 1.09 1.06 866.96| | 11: 1.36 - 1.32 6997 151 0.87 20.12 1.09 1.06 744.09| | 12: 1.32 - 1.28 6976 149 0.88 19.50 1.07 1.05 633.63| | 13: 1.28 - 1.25 6907 166 0.88 18.89 1.06 1.05 565.57| | 14: 1.25 - 1.22 7015 113 0.87 19.81 1.07 1.04 536.64| | 15: 1.22 - 1.19 6957 137 0.87 19.97 1.09 1.05 510.91| | 16: 1.19 - 1.17 6604 132 0.87 20.13 1.07 1.04 482.68| | 17: 1.17 - 1.14 6941 135 0.87 20.63 1.08 1.04 438.53| | 18: 1.14 - 1.12 6875 142 0.86 21.17 1.08 1.02 409.67| | 19: 1.12 - 1.10 6949 106 0.85 22.13 1.07 1.03 389.33| | 20: 1.10 - 1.08 6884 147 0.85 22.92 1.06 1.02 363.11| | 21: 1.08 - 1.07 6852 152 0.84 24.06 1.07 1.00 347.01| | 22: 1.07 - 1.05 6838 135 0.81 26.14 1.06 0.97 339.00| | 23: 1.05 - 1.03 6829 159 0.79 28.13 1.06 0.95 336.89| | 24: 1.03 - 1.02 6785 133 0.77 29.94 1.05 0.95 335.35| | 25: 1.02 - 1.01 6552 130 0.77 30.83 1.03 0.93 309.97| | 26: 1.01 - 0.99 6767 158 0.76 31.70 1.02 0.93 290.58| | 27: 0.99 - 0.98 6648 131 0.76 31.21 1.04 0.95 265.24| |alpha: min = 0.93 max = 1.09 mean = 1.02| |beta: min = 265.24 max = 33794.82 mean = 2722.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.41| |phase err.(test): min = 0.00 max = 88.51 mean = 21.59| |-----------------------------------------------------------------------------| ----------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 0.263 2950 Z= 5.477 Angle : 5.220 18.973 4018 Z= 3.718 Chirality : 0.375 1.074 492 Planarity : 0.033 0.143 512 Dihedral : 13.234 85.929 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.59 % Favored : 97.15 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 25.56 % 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: -2.15 (0.39), residues: 386 helix: -2.89 (0.30), residues: 146 sheet: -0.68 (0.53), residues: 86 loop : 0.03 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.022 ARG B 27 TYR 0.105 0.044 TYR B 67 PHE 0.143 0.040 PHE B 127 TRP 0.090 0.031 TRP B 139 HIS 0.089 0.032 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= 0.2044 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.308884 | | target function (ml) not normalized (work): 807109.899490 | | target function (ml) not normalized (free): 16548.493288 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2042 0.2044 0.1963 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2042 0.2044 0.1963 n_refl.: 191155 remove outliers: r(all,work,free)=0.2042 0.2044 0.1963 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2042 0.2044 0.1963 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1817 0.1815 0.1903 n_refl.: 191145 remove outliers: r(all,work,free)=0.1814 0.1813 0.1902 n_refl.: 191136 ======================== 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 0.4065 398.008 290.643 0.436 0.912 0.303 13.296-10.522 99.01 99 1 0.2518 528.187 519.751 0.791 0.913 0.256 10.503-8.327 99.45 178 3 0.2488 565.118 556.739 0.976 0.913 0.233 8.318-6.595 100.00 360 8 0.2536 414.736 403.638 0.973 0.913 0.175 6.588-5.215 100.00 711 7 0.2276 381.101 365.710 0.965 0.913 0.170 5.214-4.128 98.38 1367 28 0.1483 557.435 550.084 1.078 0.913 0.090 4.126-3.266 94.74 2603 46 0.1350 508.132 498.998 1.144 0.914 0.015 3.266-2.585 99.86 5447 97 0.1433 342.774 337.554 1.121 0.913 0.005 2.585-2.046 97.45 10613 204 0.1408 258.603 254.073 1.125 0.913 0.000 2.046-1.619 99.39 21536 464 0.1629 153.054 149.845 1.144 0.911 0.000 1.619-1.281 98.00 42463 925 0.1941 82.394 80.151 1.127 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2346 44.202 41.669 1.112 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0001 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1813 r_free=0.1902 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1813 r_free=0.1902 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.178542 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.645837 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 0.1273 0.1511 0.0238 0.040 1.1 11.2 0.0 0.0 0 11.089 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.11 2.38 1.117 13.110 570.646 0.018 13.03 15.84 2.81 1.263 13.327 570.646 0.017 Individual atomic B min max mean iso aniso Overall: 5.12 73.04 14.99 1.40 435 3274 Protein: 5.12 40.33 11.00 1.40 0 2902 Water: 6.26 73.04 29.37 N/A 435 370 Other: 16.02 30.84 23.43 N/A 0 2 Chain A: 5.32 59.61 13.03 N/A 0 1626 Chain B: 5.12 73.04 12.76 N/A 0 1648 Chain S: 11.58 67.02 30.79 N/A 435 0 Histogram: Values Number of atoms 5.12 - 11.91 2156 11.91 - 18.70 647 18.70 - 25.50 317 25.50 - 32.29 267 32.29 - 39.08 156 39.08 - 45.87 99 45.87 - 52.67 44 52.67 - 59.46 18 59.46 - 66.25 3 66.25 - 73.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1303 r_free=0.1585 r_work=0.1303 r_free=0.1579 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1303 r_free = 0.1579 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 = 0.1288 r_free = 0.1567 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1288 r_free= 0.1567 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015591 | | target function (ls_wunit_k1) not normalized (work): 2920.106553 | | target function (ls_wunit_k1) not normalized (free): 120.045727 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1288 0.1567 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1643 n_refl.: 191136 remove outliers: r(all,work,free)=0.1470 0.1467 0.1643 n_refl.: 191136 overall B=0.17 to atoms: r(all,work,free)=0.1495 0.1492 0.1653 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1285 0.1280 0.1558 n_refl.: 191136 remove outliers: r(all,work,free)=0.1285 0.1280 0.1558 n_refl.: 191136 ======================== 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 0.3583 398.008 374.666 0.485 0.963 0.281 13.296-10.522 99.01 99 1 0.2104 528.187 522.324 0.744 0.965 0.255 10.503-8.327 99.45 178 3 0.1745 565.118 561.541 0.889 0.965 0.203 8.318-6.595 100.00 360 8 0.1699 414.736 411.837 0.911 0.964 0.160 6.588-5.215 100.00 711 7 0.1525 381.101 373.730 0.890 0.965 0.160 5.214-4.128 98.38 1367 28 0.0901 557.435 554.378 0.977 0.965 0.080 4.126-3.266 94.74 2603 46 0.0827 508.132 504.452 1.043 0.965 0.019 3.266-2.585 99.86 5447 97 0.0921 342.774 340.435 1.026 0.965 0.005 2.585-2.046 97.45 10613 204 0.0953 258.603 256.379 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1097 153.054 151.373 1.055 0.965 0.000 1.619-1.281 98.00 42463 925 0.1290 82.394 81.379 1.046 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1884 44.202 42.150 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0396 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1280 r_free=0.1558 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1280 r_free=0.1558 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1558 | n_water=805 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1284 r_free=0.1565 | n_water=794 | time (s): 107.770 (total time: 110.500) Filter (q & B) r_work=0.1285 r_free=0.1565 | n_water=790 | time (s): 4.840 (total time: 115.340) Compute maps r_work=0.1285 r_free=0.1565 | n_water=790 | time (s): 2.060 (total time: 117.400) Filter (map) r_work=0.1308 r_free=0.1540 | n_water=655 | time (s): 4.510 (total time: 121.910) Find peaks r_work=0.1308 r_free=0.1540 | n_water=655 | time (s): 0.700 (total time: 122.610) Add new water r_work=0.1333 r_free=0.1577 | n_water=972 | time (s): 5.140 (total time: 127.750) Refine new water occ: r_work=0.1289 r_free=0.1532 adp: r_work=0.1276 r_free=0.1527 occ: r_work=0.1279 r_free=0.1525 adp: r_work=0.1273 r_free=0.1522 occ: r_work=0.1274 r_free=0.1521 adp: r_work=0.1272 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1272 r_free=0.1520 r_work=0.1272 r_free=0.1520 | n_water=972 | time (s): 68.850 (total time: 196.600) Filter (q & B) r_work=0.1275 r_free=0.1526 | n_water=894 | time (s): 4.330 (total time: 200.930) Filter (dist only) r_work=0.1275 r_free=0.1525 | n_water=893 | time (s): 114.260 (total time: 315.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.051493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 582.582399 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 0.1258 0.1543 0.0285 0.042 1.1 18.2 0.0 0.0 0 12.026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.58 15.43 2.85 2.042 15.063 582.582 0.015 12.32 15.17 2.84 2.437 15.153 582.582 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 68.42 16.18 1.20 525 3272 Protein: 5.43 40.43 10.97 1.20 0 2902 Water: 6.65 68.42 33.09 N/A 525 368 Other: 16.54 32.18 24.36 N/A 0 2 Chain A: 5.48 56.06 12.97 N/A 0 1624 Chain B: 5.43 68.42 12.82 N/A 0 1648 Chain S: 9.42 66.71 36.65 N/A 525 0 Histogram: Values Number of atoms 5.43 - 11.73 2080 11.73 - 18.03 692 18.03 - 24.33 271 24.33 - 30.63 221 30.63 - 36.92 181 36.92 - 43.22 176 43.22 - 49.52 101 49.52 - 55.82 49 55.82 - 62.12 21 62.12 - 68.42 5 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1517 r_work=0.1233 r_free=0.1518 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1518 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 = 0.1226 r_free = 0.1516 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1516 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013422 | | target function (ls_wunit_k1) not normalized (work): 2513.924173 | | target function (ls_wunit_k1) not normalized (free): 102.260123 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1516 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1607 n_refl.: 191136 remove outliers: r(all,work,free)=0.1435 0.1432 0.1607 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1605 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1523 n_refl.: 191136 remove outliers: r(all,work,free)=0.1238 0.1233 0.1523 n_refl.: 191136 ======================== 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 0.3279 398.008 372.244 0.482 0.962 0.266 13.296-10.522 99.01 99 1 0.1874 528.187 519.528 0.762 0.963 0.240 10.503-8.327 99.45 178 3 0.1442 565.118 567.080 0.922 0.963 0.183 8.318-6.595 100.00 360 8 0.1526 414.736 414.247 0.939 0.963 0.153 6.588-5.215 100.00 711 7 0.1347 381.101 376.320 0.914 0.963 0.136 5.214-4.128 98.38 1367 28 0.0828 557.435 556.075 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0758 508.132 505.592 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0854 342.774 341.331 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.738 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.608 1.080 0.959 0.000 1.619-1.281 98.00 42463 925 0.1255 82.394 81.343 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.221 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=-0.0505 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1523 | n_water=893 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1235 r_free=0.1522 | n_water=887 | time (s): 119.260 (total time: 121.910) Filter (q & B) r_work=0.1235 r_free=0.1522 | n_water=886 | time (s): 4.270 (total time: 126.180) Compute maps r_work=0.1235 r_free=0.1522 | n_water=886 | time (s): 1.640 (total time: 127.820) Filter (map) r_work=0.1277 r_free=0.1518 | n_water=697 | time (s): 4.290 (total time: 132.110) Find peaks r_work=0.1277 r_free=0.1518 | n_water=697 | time (s): 0.690 (total time: 132.800) Add new water r_work=0.1302 r_free=0.1544 | n_water=1022 | time (s): 4.090 (total time: 136.890) Refine new water occ: r_work=0.1243 r_free=0.1490 adp: r_work=0.1238 r_free=0.1486 occ: r_work=0.1234 r_free=0.1481 adp: r_work=0.1233 r_free=0.1483 occ: r_work=0.1230 r_free=0.1480 adp: r_work=0.1230 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1480 r_work=0.1230 r_free=0.1480 | n_water=1022 | time (s): 363.650 (total time: 500.540) Filter (q & B) r_work=0.1235 r_free=0.1482 | n_water=886 | time (s): 4.710 (total time: 505.250) Filter (dist only) r_work=0.1235 r_free=0.1483 | n_water=885 | time (s): 108.980 (total time: 614.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.687837 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.933990 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 0.1221 0.1404 0.0183 0.033 1.1 8.0 0.0 0.0 0 0.844 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.04 1.83 1.926 14.497 15.934 3.926 12.10 13.69 1.58 2.155 14.427 15.934 3.883 Individual atomic B min max mean iso aniso Overall: 5.49 68.06 15.17 1.08 518 3271 Protein: 5.49 37.08 10.78 1.08 0 2902 Water: 5.83 68.06 29.55 N/A 518 367 Other: 14.24 28.17 21.20 N/A 0 2 Chain A: 5.49 55.37 12.79 N/A 0 1624 Chain B: 5.52 68.06 12.57 N/A 0 1647 Chain S: 5.83 62.64 30.86 N/A 518 0 Histogram: Values Number of atoms 5.49 - 11.75 2125 11.75 - 18.01 688 18.01 - 24.26 317 24.26 - 30.52 266 30.52 - 36.78 171 36.78 - 43.03 129 43.03 - 49.29 61 49.29 - 55.55 25 55.55 - 61.80 5 61.80 - 68.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1369 r_work=0.1211 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1370 target_work(ml) = 3.883 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1367 target_work(ml) = 3.878 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.877831 | | target function (ml) not normalized (work): 726298.433081 | | target function (ml) not normalized (free): 15176.994658 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1367 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1481 n_refl.: 191136 remove outliers: r(all,work,free)=0.1424 0.1423 0.1481 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1417 0.1477 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1202 0.1363 n_refl.: 191136 remove outliers: r(all,work,free)=0.1205 0.1202 0.1363 n_refl.: 191133 ======================== 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 0.3772 393.525 357.860 0.424 0.947 0.265 13.296-10.522 99.01 99 1 0.2493 528.187 508.581 0.698 0.948 0.208 10.503-8.327 98.35 176 3 0.2018 555.265 557.169 0.885 0.948 0.180 8.318-6.595 100.00 360 8 0.2105 414.736 410.387 0.893 0.948 0.115 6.588-5.215 100.00 711 7 0.1801 381.101 371.274 0.885 0.948 0.094 5.214-4.128 98.38 1367 28 0.1164 557.435 551.542 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1072 508.132 501.282 1.031 0.948 0.000 3.266-2.585 99.86 5447 97 0.1059 342.774 339.056 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0934 258.603 255.782 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0939 153.054 151.495 1.056 0.946 0.000 1.619-1.281 98.00 42463 925 0.1024 82.394 81.507 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1679 44.202 42.329 1.037 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0947 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1363 | n_water=885 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1202 r_free=0.1363 | n_water=883 | time (s): 122.010 (total time: 124.190) Filter (q & B) r_work=0.1203 r_free=0.1361 | n_water=869 | time (s): 5.270 (total time: 129.460) Compute maps r_work=0.1203 r_free=0.1361 | n_water=869 | time (s): 1.780 (total time: 131.240) Filter (map) r_work=0.1226 r_free=0.1372 | n_water=723 | time (s): 4.210 (total time: 135.450) Find peaks r_work=0.1226 r_free=0.1372 | n_water=723 | time (s): 0.750 (total time: 136.200) Add new water r_work=0.1240 r_free=0.1394 | n_water=969 | time (s): 4.090 (total time: 140.290) Refine new water occ: r_work=0.1202 r_free=0.1356 adp: r_work=0.1202 r_free=0.1356 occ: r_work=0.1199 r_free=0.1354 adp: r_work=0.1199 r_free=0.1354 occ: r_work=0.1197 r_free=0.1353 adp: r_work=0.1196 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1353 r_work=0.1196 r_free=0.1353 | n_water=969 | time (s): 198.010 (total time: 338.300) Filter (q & B) r_work=0.1201 r_free=0.1362 | n_water=883 | time (s): 5.300 (total time: 343.600) Filter (dist only) r_work=0.1201 r_free=0.1361 | n_water=882 | time (s): 113.910 (total time: 457.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566781 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.921457 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 0.1360 0.0159 0.035 1.1 6.5 0.0 0.0 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.60 1.59 1.845 14.280 15.921 3.873 11.97 13.57 1.60 1.958 14.236 15.921 3.864 Individual atomic B min max mean iso aniso Overall: 5.52 67.67 15.05 1.02 515 3271 Protein: 5.52 34.13 10.68 1.02 0 2902 Water: 5.91 67.67 29.41 N/A 515 367 Other: 14.02 27.57 20.80 N/A 0 2 Chain A: 5.55 54.46 12.65 N/A 0 1624 Chain B: 5.52 67.67 12.47 N/A 0 1647 Chain S: 5.91 62.71 30.88 N/A 515 0 Histogram: Values Number of atoms 5.52 - 11.73 2129 11.73 - 17.95 709 17.95 - 24.16 311 24.16 - 30.38 239 30.38 - 36.59 177 36.59 - 42.81 128 42.81 - 49.02 63 49.02 - 55.24 23 55.24 - 61.45 5 61.45 - 67.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862292 | | target function (ml) not normalized (work): 723376.479908 | | target function (ml) not normalized (free): 15126.544483 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1419 0.1419 0.1465 n_refl.: 191133 remove outliers: r(all,work,free)=0.1419 0.1419 0.1465 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1412 0.1411 0.1460 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191133 remove outliers: r(all,work,free)=0.1195 0.1191 0.1353 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 92.08 90 3 0.3732 347.669 318.226 0.405 0.949 0.244 13.296-10.522 99.01 99 1 0.2533 478.027 459.329 0.689 0.950 0.185 10.503-8.327 98.35 176 3 0.2066 502.533 496.652 0.868 0.950 0.157 8.318-6.595 100.00 360 8 0.2130 375.350 369.934 0.884 0.950 0.090 6.588-5.215 100.00 711 7 0.1882 344.909 335.087 0.884 0.950 0.080 5.214-4.128 98.38 1367 28 0.1190 504.497 499.053 0.971 0.950 0.080 4.126-3.266 94.74 2603 46 0.1110 459.876 453.399 1.031 0.950 0.000 3.266-2.585 99.86 5447 97 0.1081 310.221 306.941 1.018 0.949 0.000 2.585-2.046 97.45 10613 204 0.0929 234.044 231.598 1.031 0.948 0.000 2.046-1.619 99.39 21536 464 0.0909 138.519 137.202 1.056 0.946 0.000 1.619-1.281 98.00 42463 925 0.0986 74.569 73.841 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.004 38.336 1.043 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1132 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=882 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1191 r_free=0.1353 | n_water=882 | time (s): 104.940 (total time: 108.080) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=868 | time (s): 4.940 (total time: 113.020) Compute maps r_work=0.1192 r_free=0.1356 | n_water=868 | time (s): 2.190 (total time: 115.210) Filter (map) r_work=0.1220 r_free=0.1362 | n_water=733 | time (s): 4.810 (total time: 120.020) Find peaks r_work=0.1220 r_free=0.1362 | n_water=733 | time (s): 0.550 (total time: 120.570) Add new water r_work=0.1230 r_free=0.1376 | n_water=963 | time (s): 4.850 (total time: 125.420) Refine new water occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1343 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=963 | time (s): 211.650 (total time: 337.070) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=877 | time (s): 5.070 (total time: 342.140) Filter (dist only) r_work=0.1192 r_free=0.1354 | n_water=875 | time (s): 111.090 (total time: 453.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535458 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.632888 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 0.1353 0.0157 0.036 1.1 5.8 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.53 1.57 1.803 14.122 15.633 3.763 12.00 13.57 1.57 1.887 14.091 15.633 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 67.25 14.90 0.97 510 3269 Protein: 5.57 32.47 10.61 0.97 0 2902 Water: 5.93 67.25 29.10 N/A 510 365 Other: 13.79 25.92 19.85 N/A 0 2 Chain A: 5.59 53.52 12.53 N/A 0 1623 Chain B: 5.57 67.25 12.36 N/A 0 1646 Chain S: 5.93 60.59 30.62 N/A 510 0 Histogram: Values Number of atoms 5.57 - 11.74 2142 11.74 - 17.91 718 17.91 - 24.08 303 24.08 - 30.24 230 30.24 - 36.41 170 36.41 - 42.58 123 42.58 - 48.74 63 48.74 - 54.91 24 54.91 - 61.08 5 61.08 - 67.25 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759590 | | target function (ml) not normalized (work): 704137.458565 | | target function (ml) not normalized (free): 14739.062295 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1479 n_refl.: 191132 remove outliers: r(all,work,free)=0.1425 0.1424 0.1479 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1417 0.1417 0.1473 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191130 ======================== 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 0.3462 347.217 301.192 0.391 0.948 0.239 13.296-10.522 98.02 98 1 0.2447 478.671 455.759 0.685 0.949 0.176 10.503-8.327 98.35 176 3 0.2138 502.533 496.342 0.863 0.949 0.147 8.318-6.595 100.00 360 8 0.2196 375.350 368.852 0.886 0.949 0.108 6.588-5.215 100.00 711 7 0.1908 344.909 335.332 0.884 0.949 0.087 5.214-4.128 98.38 1367 28 0.1210 504.497 499.053 0.972 0.949 0.070 4.126-3.266 94.74 2603 46 0.1136 459.876 453.222 1.034 0.950 0.005 3.266-2.585 99.86 5447 97 0.1101 310.221 307.031 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0947 234.044 231.648 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.519 137.235 1.057 0.947 0.000 1.619-1.281 98.00 42463 925 0.0976 74.569 73.874 1.055 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.004 38.341 1.043 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1274 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1357 | n_water=875 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1197 r_free=0.1357 | n_water=875 | time (s): 109.240 (total time: 112.310) Filter (q & B) r_work=0.1197 r_free=0.1358 | n_water=864 | time (s): 4.730 (total time: 117.040) Compute maps r_work=0.1197 r_free=0.1358 | n_water=864 | time (s): 2.450 (total time: 119.490) Filter (map) r_work=0.1221 r_free=0.1357 | n_water=743 | time (s): 4.570 (total time: 124.060) Find peaks r_work=0.1221 r_free=0.1357 | n_water=743 | time (s): 0.670 (total time: 124.730) Add new water r_work=0.1232 r_free=0.1366 | n_water=958 | time (s): 4.420 (total time: 129.150) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1340 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1341 r_work=0.1191 r_free=0.1341 | n_water=958 | time (s): 214.650 (total time: 343.800) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=891 | time (s): 4.600 (total time: 348.400) Filter (dist only) r_work=0.1195 r_free=0.1348 | n_water=890 | time (s): 119.330 (total time: 467.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510901 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.681781 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 0.1354 0.0156 0.037 1.1 8.0 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.56 1.769 14.059 14.682 3.760 12.02 13.58 1.56 1.927 14.006 14.682 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 66.06 14.84 0.90 525 3269 Protein: 5.58 29.30 10.49 0.90 0 2902 Water: 6.02 66.06 29.02 N/A 525 365 Other: 13.85 23.25 18.55 N/A 0 2 Chain A: 5.61 51.21 12.37 N/A 0 1623 Chain B: 5.58 66.06 12.21 N/A 0 1646 Chain S: 6.02 60.75 30.70 N/A 525 0 Histogram: Values Number of atoms 5.58 - 11.63 2119 11.63 - 17.67 767 17.67 - 23.72 283 23.72 - 29.77 218 29.77 - 35.82 173 35.82 - 41.87 128 41.87 - 47.91 66 47.91 - 53.96 34 53.96 - 60.01 3 60.01 - 66.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1358 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.758 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758436 | | target function (ml) not normalized (work): 703913.787746 | | target function (ml) not normalized (free): 14738.682711 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1487 n_refl.: 191130 remove outliers: r(all,work,free)=0.1416 0.1415 0.1487 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1378 0.1376 0.1462 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1198 0.1359 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 90.10 88 3 0.3397 347.904 314.532 0.414 0.950 0.225 13.296-10.522 98.02 98 1 0.2442 478.671 460.829 0.702 0.951 0.159 10.503-8.327 98.35 176 3 0.2173 502.533 495.968 0.884 0.951 0.130 8.318-6.595 100.00 360 8 0.2186 375.350 369.285 0.907 0.951 0.101 6.588-5.215 100.00 711 7 0.1933 344.909 335.298 0.905 0.951 0.082 5.214-4.128 98.38 1367 28 0.1208 504.497 499.231 0.994 0.951 0.044 4.126-3.266 94.74 2603 46 0.1145 459.876 453.047 1.058 0.952 0.005 3.266-2.585 99.86 5447 97 0.1111 310.221 307.032 1.041 0.951 0.000 2.585-2.046 97.45 10613 204 0.0955 234.044 231.603 1.049 0.951 0.000 2.046-1.619 99.39 21536 464 0.0916 138.519 137.208 1.067 0.950 0.000 1.619-1.281 98.00 42463 925 0.0971 74.569 73.865 1.055 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.004 38.341 1.027 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1360 | n_water=890 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1199 r_free=0.1360 | n_water=890 | time (s): 106.760 (total time: 109.740) Filter (q & B) r_work=0.1199 r_free=0.1361 | n_water=880 | time (s): 5.290 (total time: 115.030) Compute maps r_work=0.1199 r_free=0.1361 | n_water=880 | time (s): 1.750 (total time: 116.780) Filter (map) r_work=0.1220 r_free=0.1353 | n_water=768 | time (s): 4.680 (total time: 121.460) Find peaks r_work=0.1220 r_free=0.1353 | n_water=768 | time (s): 0.700 (total time: 122.160) Add new water r_work=0.1228 r_free=0.1362 | n_water=976 | time (s): 4.810 (total time: 126.970) Refine new water occ: r_work=0.1196 r_free=0.1343 adp: r_work=0.1196 r_free=0.1343 occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1345 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1348 r_work=0.1192 r_free=0.1348 | n_water=976 | time (s): 230.440 (total time: 357.410) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=902 | time (s): 3.810 (total time: 361.220) Filter (dist only) r_work=0.1197 r_free=0.1356 | n_water=900 | time (s): 117.320 (total time: 478.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529915 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.445098 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 0.1200 0.1359 0.0159 0.038 1.1 6.0 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.59 1.59 1.718 13.720 14.445 3.759 12.01 13.60 1.59 1.772 13.704 14.445 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.62 14.59 0.88 535 3269 Protein: 5.39 28.48 10.24 0.88 0 2902 Water: 5.84 64.62 28.61 N/A 535 365 Other: 13.71 21.98 17.84 N/A 0 2 Chain A: 5.44 50.63 12.08 N/A 0 1623 Chain B: 5.39 64.62 11.94 N/A 0 1646 Chain S: 5.84 60.62 30.36 N/A 535 0 Histogram: Values Number of atoms 5.39 - 11.31 2093 11.31 - 17.24 796 17.24 - 23.16 272 23.16 - 29.08 223 29.08 - 35.01 173 35.01 - 40.93 126 40.93 - 46.85 76 46.85 - 52.78 35 52.78 - 58.70 7 58.70 - 64.62 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.756 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756004 | | target function (ml) not normalized (work): 703454.427669 | | target function (ml) not normalized (free): 14728.203456 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1369 0.1367 0.1460 n_refl.: 191129 remove outliers: r(all,work,free)=0.1369 0.1367 0.1460 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1377 0.1375 0.1464 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1351 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 90.10 88 3 0.3384 347.904 319.746 0.438 0.909 0.221 13.296-10.522 98.02 98 1 0.2487 478.671 459.348 0.734 0.910 0.152 10.503-8.327 98.35 176 3 0.2189 502.533 495.386 0.930 0.911 0.123 8.318-6.595 100.00 360 8 0.2214 375.350 368.511 0.954 0.910 0.103 6.588-5.215 100.00 711 7 0.1931 344.909 334.862 0.954 0.911 0.083 5.214-4.128 98.38 1367 28 0.1221 504.497 498.452 1.049 0.912 0.039 4.126-3.266 94.74 2603 46 0.1155 459.876 452.465 1.117 0.913 0.005 3.266-2.585 99.86 5447 97 0.1114 310.221 306.712 1.099 0.913 0.000 2.585-2.046 97.45 10613 204 0.0958 234.044 231.476 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0909 138.519 137.137 1.124 0.917 0.000 1.619-1.281 98.00 42463 925 0.0950 74.569 73.906 1.112 0.921 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.004 38.315 1.076 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0578 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1351 | n_water=900 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1190 r_free=0.1351 | n_water=900 | time (s): 109.850 (total time: 112.440) Filter (q & B) r_work=0.1191 r_free=0.1352 | n_water=891 | time (s): 5.000 (total time: 117.440) Compute maps r_work=0.1191 r_free=0.1352 | n_water=891 | time (s): 2.470 (total time: 119.910) Filter (map) r_work=0.1213 r_free=0.1348 | n_water=770 | time (s): 3.930 (total time: 123.840) Find peaks r_work=0.1213 r_free=0.1348 | n_water=770 | time (s): 0.620 (total time: 124.460) Add new water r_work=0.1221 r_free=0.1358 | n_water=979 | time (s): 4.080 (total time: 128.540) Refine new water occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1333 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1184 r_free=0.1337 adp: r_work=0.1184 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1336 r_work=0.1184 r_free=0.1336 | n_water=979 | time (s): 252.680 (total time: 381.220) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=906 | time (s): 4.280 (total time: 385.500) Filter (dist only) r_work=0.1188 r_free=0.1345 | n_water=905 | time (s): 116.630 (total time: 502.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535962 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.216885 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 0.1191 0.1349 0.0158 0.038 1.1 6.8 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.49 1.58 1.676 13.723 13.217 3.754 11.93 13.51 1.58 1.676 13.721 13.217 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 64.51 14.64 0.86 540 3269 Protein: 5.50 28.35 10.32 0.86 0 2902 Water: 5.85 64.51 28.48 N/A 540 365 Other: 13.77 22.07 17.92 N/A 0 2 Chain A: 5.54 50.64 12.13 N/A 0 1623 Chain B: 5.50 64.51 12.00 N/A 0 1646 Chain S: 5.85 60.69 30.20 N/A 540 0 Histogram: Values Number of atoms 5.50 - 11.40 2096 11.40 - 17.30 797 17.30 - 23.20 278 23.20 - 29.10 227 29.10 - 35.01 169 35.01 - 40.91 120 40.91 - 46.81 76 46.81 - 52.71 35 52.71 - 58.61 8 58.61 - 64.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1351 r_work=0.1193 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1356 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754224 | | target function (ml) not normalized (work): 703121.099841 | | target function (ml) not normalized (free): 14723.306577 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1356 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1383 0.1382 0.1481 n_refl.: 191129 remove outliers: r(all,work,free)=0.1383 0.1382 0.1481 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1385 0.1384 0.1482 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1356 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1190 0.1356 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 90.10 88 3 0.3503 347.904 316.992 0.421 0.912 0.205 13.296-10.522 98.02 98 1 0.2476 478.671 460.034 0.728 0.914 0.149 10.503-8.327 98.35 176 3 0.2212 502.533 494.902 0.925 0.914 0.123 8.318-6.595 100.00 360 8 0.2182 375.350 369.081 0.948 0.914 0.091 6.588-5.215 100.00 711 7 0.1942 344.909 334.703 0.948 0.915 0.070 5.214-4.128 98.38 1367 28 0.1222 504.497 498.747 1.044 0.915 0.029 4.126-3.266 94.74 2603 46 0.1162 459.876 452.310 1.112 0.917 0.000 3.266-2.585 99.86 5447 97 0.1118 310.221 306.616 1.094 0.917 0.000 2.585-2.046 97.45 10613 204 0.0958 234.044 231.463 1.102 0.919 0.000 2.046-1.619 99.39 21536 464 0.0911 138.519 137.154 1.120 0.922 0.000 1.619-1.281 98.00 42463 925 0.0946 74.569 73.915 1.110 0.927 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.004 38.298 1.077 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1356 | n_water=905 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1190 r_free=0.1356 | n_water=905 | time (s): 105.870 (total time: 108.140) Filter (q & B) r_work=0.1191 r_free=0.1355 | n_water=892 | time (s): 5.280 (total time: 113.420) Compute maps r_work=0.1191 r_free=0.1355 | n_water=892 | time (s): 2.150 (total time: 115.570) Filter (map) r_work=0.1215 r_free=0.1340 | n_water=775 | time (s): 5.130 (total time: 120.700) Find peaks r_work=0.1215 r_free=0.1340 | n_water=775 | time (s): 0.790 (total time: 121.490) Add new water r_work=0.1222 r_free=0.1352 | n_water=991 | time (s): 4.540 (total time: 126.030) Refine new water occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1334 occ: r_work=0.1186 r_free=0.1333 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=991 | time (s): 330.750 (total time: 456.780) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=918 | time (s): 5.250 (total time: 462.030) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=917 | time (s): 121.750 (total time: 583.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544199 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.221062 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 0.1191 0.1348 0.0157 0.038 1.1 6.3 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.48 1.57 1.677 13.768 14.221 3.755 11.90 13.48 1.58 1.678 13.766 14.221 3.751 Individual atomic B min max mean iso aniso Overall: 5.52 64.13 14.69 0.87 552 3269 Protein: 5.52 28.26 10.35 0.87 0 2902 Water: 5.94 64.13 28.42 N/A 552 365 Other: 13.79 22.14 17.97 N/A 0 2 Chain A: 5.62 50.52 12.14 N/A 0 1623 Chain B: 5.52 64.13 12.01 N/A 0 1646 Chain S: 5.94 60.69 30.18 N/A 552 0 Histogram: Values Number of atoms 5.52 - 11.38 2081 11.38 - 17.25 815 17.25 - 23.11 275 23.11 - 28.97 236 28.97 - 34.83 172 34.83 - 40.69 115 40.69 - 46.55 82 46.55 - 52.41 32 52.41 - 58.27 9 58.27 - 64.13 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1348 r_work=0.1190 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1348 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1350 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750876 | | target function (ml) not normalized (work): 702494.068893 | | target function (ml) not normalized (free): 14715.396118 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1484 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1389 0.1484 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1390 0.1388 0.1484 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1190 0.1187 0.1350 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 90.10 88 3 0.3541 347.904 316.743 0.422 0.914 0.211 13.296-10.522 98.02 98 1 0.2476 478.671 459.209 0.729 0.915 0.158 10.503-8.327 98.35 176 3 0.2192 502.533 494.904 0.922 0.916 0.121 8.318-6.595 100.00 360 8 0.2163 375.350 369.222 0.947 0.916 0.091 6.588-5.215 100.00 711 7 0.1952 344.909 334.784 0.945 0.916 0.070 5.214-4.128 98.38 1367 28 0.1220 504.497 498.596 1.042 0.917 0.030 4.126-3.266 94.74 2603 46 0.1164 459.876 452.375 1.110 0.918 0.005 3.266-2.585 99.86 5447 97 0.1119 310.221 306.600 1.092 0.919 0.000 2.585-2.046 97.45 10613 204 0.0955 234.044 231.424 1.100 0.921 0.000 2.046-1.619 99.39 21536 464 0.0907 138.519 137.153 1.119 0.925 0.000 1.619-1.281 98.00 42463 925 0.0941 74.569 73.920 1.109 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.004 38.295 1.077 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0086 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1350 After: r_work=0.1188 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1351 | n_water=917 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1188 r_free=0.1351 | n_water=917 | time (s): 118.200 (total time: 120.880) Filter (q & B) r_work=0.1189 r_free=0.1351 | n_water=904 | time (s): 4.510 (total time: 125.390) Compute maps r_work=0.1189 r_free=0.1351 | n_water=904 | time (s): 1.930 (total time: 127.320) Filter (map) r_work=0.1210 r_free=0.1337 | n_water=790 | time (s): 4.390 (total time: 131.710) Find peaks r_work=0.1210 r_free=0.1337 | n_water=790 | time (s): 0.870 (total time: 132.580) Add new water r_work=0.1217 r_free=0.1351 | n_water=991 | time (s): 5.530 (total time: 138.110) Refine new water occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1335 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1334 occ: r_work=0.1183 r_free=0.1335 adp: r_work=0.1183 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1335 r_work=0.1183 r_free=0.1335 | n_water=991 | time (s): 210.250 (total time: 348.360) Filter (q & B) r_work=0.1187 r_free=0.1343 | n_water=919 | time (s): 4.760 (total time: 353.120) Filter (dist only) r_work=0.1187 r_free=0.1342 | n_water=918 | time (s): 122.170 (total time: 475.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.900992 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 0.1192 0.1350 0.0157 0.038 1.2 9.5 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.50 1.57 1.680 13.771 13.901 3.755 11.94 13.53 1.60 1.687 13.769 13.901 3.755 Individual atomic B min max mean iso aniso Overall: 5.56 63.41 14.68 0.86 553 3269 Protein: 5.56 28.08 10.35 0.86 0 2902 Water: 6.03 63.41 28.34 N/A 553 365 Other: 13.84 22.11 17.97 N/A 0 2 Chain A: 5.66 50.26 12.12 N/A 0 1623 Chain B: 5.56 63.41 12.00 N/A 0 1646 Chain S: 6.03 60.76 30.16 N/A 553 0 Histogram: Values Number of atoms 5.56 - 11.35 2070 11.35 - 17.13 826 17.13 - 22.91 272 22.91 - 28.70 231 28.70 - 34.48 175 34.48 - 40.27 115 40.27 - 46.05 85 46.05 - 51.84 35 51.84 - 57.62 8 57.62 - 63.41 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1353 r_work=0.1194 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1353 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1356 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755008 | | target function (ml) not normalized (work): 703267.932519 | | target function (ml) not normalized (free): 14728.159862 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1355 0.1443 5.6825 5.7387| | 2: 2.94 - 2.33 1.00 7339 128 0.1064 0.1347 5.0673 5.1608| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1201 4.6593 4.7443| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1046 4.3961 4.5566| | 5: 1.85 - 1.72 0.99 7113 159 0.0939 0.1040 4.1596 4.2858| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1077 3.9504 4.0708| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0959 3.8022 3.9246| | 8: 1.54 - 1.47 0.96 6798 152 0.0894 0.1306 3.702 3.8989| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1134 3.6239 3.7581| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1196 3.5598 3.6729| | 11: 1.36 - 1.32 0.99 6996 151 0.0998 0.1144 3.4904 3.5993| | 12: 1.32 - 1.28 0.98 6975 149 0.1037 0.1130 3.4636 3.5842| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1269 3.4423 3.5827| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1582 3.4344 3.6735| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1242 3.4475 3.4886| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1534 3.4637 3.6469| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1222 3.4321 3.4413| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1709 3.4373 3.5325| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1773 3.42 3.5999| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1585 3.4099 3.4372| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2148 3.4172 3.5056| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1946 3.4124 3.4135| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2007 3.4323 3.4848| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2269 3.4354 3.5148| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2501 3.4488 3.5208| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2850 3.4149 3.4218| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2789 3.4688 3.3951| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7398 127 0.93 11.24 1.00 0.95 10591.08| | 2: 2.94 - 2.33 7339 128 0.93 12.43 0.99 0.95 4910.87| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.95 1698.66| | 4: 2.04 - 1.85 7170 155 0.96 7.74 1.00 0.95 1016.24| | 5: 1.85 - 1.72 7113 159 0.96 8.30 1.00 0.96 654.44| | 6: 1.72 - 1.62 7102 142 0.96 8.11 1.00 0.96 448.93| | 7: 1.62 - 1.54 7104 148 0.96 8.14 1.01 0.97 337.80| | 8: 1.54 - 1.47 6798 152 0.96 8.26 1.01 0.97 278.76| | 9: 1.47 - 1.41 6938 155 0.96 8.53 1.00 0.98 232.30| | 10: 1.41 - 1.36 7022 150 0.96 9.01 1.00 0.97 204.86| | 11: 1.36 - 1.32 6996 151 0.96 9.07 0.99 0.96 178.18| | 12: 1.32 - 1.28 6975 149 0.96 9.12 0.98 0.95 163.91| | 13: 1.28 - 1.25 6907 166 0.95 9.67 1.01 0.96 160.96| | 14: 1.25 - 1.22 7015 112 0.95 10.77 1.01 0.96 164.58| | 15: 1.22 - 1.19 6956 137 0.95 11.25 1.01 0.98 166.53| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.96 159.29| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.14| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.95 147.90| | 19: 1.12 - 1.10 6948 106 0.93 14.20 1.00 0.94 151.86| | 20: 1.10 - 1.08 6884 147 0.92 15.28 1.00 0.94 150.92| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.46| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 154.70| | 23: 1.05 - 1.03 6827 159 0.87 20.48 0.99 0.92 164.43| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.93 178.89| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 181.72| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.98 0.88 176.00| | 27: 0.99 - 0.98 6647 131 0.82 26.21 0.99 0.87 160.05| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.90 max = 10591.08 mean = 894.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.30| |phase err.(test): min = 0.00 max = 89.19 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1356 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1400 0.1499 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1400 0.1499 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1393 0.1391 0.1493 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1355 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 90.10 88 3 0.3465 347.904 318.821 0.415 0.915 0.217 13.296-10.522 98.02 98 1 0.2508 478.671 458.566 0.706 0.916 0.152 10.503-8.327 98.35 176 3 0.2196 502.533 494.924 0.897 0.917 0.123 8.318-6.595 100.00 360 8 0.2162 375.350 369.388 0.921 0.917 0.089 6.588-5.215 100.00 711 7 0.1941 344.909 334.965 0.920 0.917 0.070 5.214-4.128 98.38 1367 28 0.1229 504.497 498.708 1.016 0.918 0.034 4.126-3.266 94.74 2603 46 0.1166 459.876 452.268 1.083 0.920 0.005 3.266-2.585 99.86 5447 97 0.1118 310.221 306.703 1.064 0.921 0.000 2.585-2.046 97.45 10613 204 0.0961 234.044 231.429 1.071 0.923 0.000 2.046-1.619 99.39 21536 464 0.0915 138.519 137.144 1.088 0.927 0.000 1.619-1.281 98.00 42463 925 0.0949 74.569 73.912 1.077 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.004 38.288 1.043 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0119 ================= 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 : 0.2044 0.1963 0.081 5.220 5.2 78.0 14.6 805 0.000 1_bss: 0.1813 0.1902 0.081 5.220 5.2 78.0 14.6 805 0.000 1_settarget: 0.1813 0.1902 0.081 5.220 5.2 78.0 14.6 805 0.000 1_nqh: 0.1813 0.1902 0.081 5.220 5.2 78.0 14.6 805 0.000 1_weight: 0.1813 0.1902 0.081 5.220 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1273 0.1511 0.040 1.146 5.2 78.0 14.6 805 0.157 1_adp: 0.1303 0.1585 0.040 1.146 5.1 73.0 15.0 805 0.157 1_regHadp: 0.1303 0.1579 0.040 1.146 5.1 73.0 15.0 805 0.157 1_occ: 0.1288 0.1567 0.040 1.146 5.1 73.0 15.0 805 0.157 2_bss: 0.1280 0.1558 0.040 1.146 5.3 73.2 15.2 805 0.157 2_settarget: 0.1280 0.1558 0.040 1.146 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1280 0.1558 0.040 1.163 5.3 73.2 15.2 805 0.157 2_nqh: 0.1280 0.1558 0.040 1.163 5.3 73.2 15.2 805 0.157 2_sol: 0.1275 0.1525 0.040 1.163 5.3 73.2 16.0 893 n/a 2_weight: 0.1275 0.1525 0.040 1.163 5.3 73.2 16.0 893 n/a 2_xyzrec: 0.1258 0.1543 0.042 1.141 5.3 73.2 16.0 893 n/a 2_adp: 0.1233 0.1517 0.042 1.141 5.4 68.4 16.2 893 n/a 2_regHadp: 0.1233 0.1518 0.042 1.141 5.4 68.4 16.2 893 n/a 2_occ: 0.1226 0.1516 0.042 1.141 5.4 68.4 16.2 893 n/a 3_bss: 0.1233 0.1523 0.042 1.141 5.4 68.4 16.2 893 n/a 3_settarget: 0.1233 0.1523 0.042 1.141 5.4 68.4 16.2 893 n/a 3_updatecdl: 0.1233 0.1523 0.042 1.144 5.4 68.4 16.2 893 n/a 3_nqh: 0.1233 0.1523 0.042 1.144 5.4 68.4 16.2 893 n/a 3_sol: 0.1235 0.1483 0.042 1.144 5.4 68.4 15.3 885 n/a 3_weight: 0.1235 0.1483 0.042 1.144 5.4 68.4 15.3 885 n/a 3_xyzrec: 0.1221 0.1404 0.033 1.104 5.4 68.4 15.3 885 n/a 3_adp: 0.1210 0.1369 0.033 1.104 5.5 68.1 15.2 885 n/a 3_regHadp: 0.1211 0.1370 0.033 1.104 5.5 68.1 15.2 885 n/a 3_occ: 0.1206 0.1367 0.033 1.104 5.5 68.1 15.2 885 n/a 4_bss: 0.1202 0.1363 0.033 1.104 5.5 68.0 15.1 885 n/a 4_settarget: 0.1202 0.1363 0.033 1.104 5.5 68.0 15.1 885 n/a 4_updatecdl: 0.1202 0.1363 0.033 1.108 5.5 68.0 15.1 885 n/a 4_nqh: 0.1202 0.1363 0.033 1.108 5.5 68.0 15.1 885 n/a 4_sol: 0.1201 0.1361 0.033 1.108 5.5 68.0 15.1 882 n/a 4_weight: 0.1201 0.1361 0.033 1.108 5.5 68.0 15.1 882 n/a 4_xyzrec: 0.1201 0.1360 0.035 1.122 5.5 68.0 15.1 882 n/a 4_adp: 0.1197 0.1357 0.035 1.122 5.5 67.7 15.1 882 n/a 4_regHadp: 0.1197 0.1358 0.035 1.122 5.5 67.7 15.1 882 n/a 4_occ: 0.1194 0.1355 0.035 1.122 5.5 67.7 15.1 882 n/a 5_bss: 0.1191 0.1353 0.035 1.122 5.5 67.6 15.0 882 n/a 5_settarget: 0.1191 0.1353 0.035 1.122 5.5 67.6 15.0 882 n/a 5_updatecdl: 0.1191 0.1353 0.035 1.122 5.5 67.6 15.0 882 n/a 5_nqh: 0.1191 0.1353 0.035 1.122 5.5 67.6 15.0 882 n/a 5_sol: 0.1192 0.1354 0.035 1.122 5.5 67.6 15.0 875 n/a 5_weight: 0.1192 0.1354 0.035 1.122 5.5 67.6 15.0 875 n/a 5_xyzrec: 0.1196 0.1353 0.036 1.126 5.5 67.6 15.0 875 n/a 5_adp: 0.1200 0.1357 0.036 1.126 5.6 67.2 14.9 875 n/a 5_regHadp: 0.1200 0.1357 0.036 1.126 5.6 67.2 14.9 875 n/a 5_occ: 0.1198 0.1359 0.036 1.126 5.6 67.2 14.9 875 n/a 6_bss: 0.1197 0.1357 0.036 1.126 5.5 67.2 14.9 875 n/a 6_settarget: 0.1197 0.1357 0.036 1.126 5.5 67.2 14.9 875 n/a 6_updatecdl: 0.1197 0.1357 0.036 1.125 5.5 67.2 14.9 875 n/a 6_nqh: 0.1197 0.1357 0.036 1.125 5.5 67.2 14.9 875 n/a 6_sol: 0.1195 0.1348 0.036 1.125 5.5 67.2 14.9 890 n/a 6_weight: 0.1195 0.1348 0.036 1.125 5.5 67.2 14.9 890 n/a 6_xyzrec: 0.1198 0.1354 0.037 1.118 5.5 67.2 14.9 890 n/a 6_adp: 0.1202 0.1358 0.037 1.118 5.6 66.1 14.8 890 n/a 6_regHadp: 0.1202 0.1359 0.037 1.118 5.6 66.1 14.8 890 n/a 6_occ: 0.1200 0.1361 0.037 1.118 5.6 66.1 14.8 890 n/a 7_bss: 0.1199 0.1360 0.037 1.118 5.4 65.8 14.6 890 n/a 7_settarget: 0.1199 0.1360 0.037 1.118 5.4 65.8 14.6 890 n/a 7_updatecdl: 0.1199 0.1360 0.037 1.118 5.4 65.8 14.6 890 n/a 7_nqh: 0.1199 0.1360 0.037 1.118 5.4 65.8 14.6 890 n/a 7_sol: 0.1197 0.1356 0.037 1.118 5.4 65.8 14.6 900 n/a 7_weight: 0.1197 0.1356 0.037 1.118 5.4 65.8 14.6 900 n/a 7_xyzrec: 0.1200 0.1359 0.038 1.126 5.4 65.8 14.6 900 n/a 7_adp: 0.1201 0.1360 0.038 1.126 5.4 64.6 14.6 900 n/a 7_regHadp: 0.1201 0.1360 0.038 1.126 5.4 64.6 14.6 900 n/a 7_occ: 0.1199 0.1362 0.038 1.126 5.4 64.6 14.6 900 n/a 8_bss: 0.1190 0.1351 0.038 1.126 5.5 64.7 14.7 900 n/a 8_settarget: 0.1190 0.1351 0.038 1.126 5.5 64.7 14.7 900 n/a 8_updatecdl: 0.1190 0.1351 0.038 1.126 5.5 64.7 14.7 900 n/a 8_nqh: 0.1190 0.1351 0.038 1.126 5.5 64.7 14.7 900 n/a 8_sol: 0.1188 0.1345 0.038 1.126 5.5 64.7 14.6 905 n/a 8_weight: 0.1188 0.1345 0.038 1.126 5.5 64.7 14.6 905 n/a 8_xyzrec: 0.1191 0.1349 0.038 1.117 5.5 64.7 14.6 905 n/a 8_adp: 0.1193 0.1351 0.038 1.117 5.5 64.5 14.6 905 n/a 8_regHadp: 0.1193 0.1352 0.038 1.117 5.5 64.5 14.6 905 n/a 8_occ: 0.1192 0.1356 0.038 1.117 5.5 64.5 14.6 905 n/a 9_bss: 0.1190 0.1356 0.038 1.117 5.5 64.5 14.6 905 n/a 9_settarget: 0.1190 0.1356 0.038 1.117 5.5 64.5 14.6 905 n/a 9_updatecdl: 0.1190 0.1356 0.038 1.116 5.5 64.5 14.6 905 n/a 9_nqh: 0.1190 0.1356 0.038 1.116 5.5 64.5 14.6 905 n/a 9_sol: 0.1189 0.1341 0.038 1.116 5.5 64.5 14.7 917 n/a 9_weight: 0.1189 0.1341 0.038 1.116 5.5 64.5 14.7 917 n/a 9_xyzrec: 0.1191 0.1348 0.038 1.115 5.5 64.5 14.7 917 n/a 9_adp: 0.1190 0.1348 0.038 1.115 5.5 64.1 14.7 917 n/a 9_regHadp: 0.1190 0.1348 0.038 1.115 5.5 64.1 14.7 917 n/a 9_occ: 0.1188 0.1350 0.038 1.115 5.5 64.1 14.7 917 n/a 10_bss: 0.1187 0.1350 0.038 1.115 5.5 64.1 14.7 917 n/a 10_settarget: 0.1187 0.1350 0.038 1.115 5.5 64.1 14.7 917 n/a 10_updatecdl: 0.1187 0.1350 0.038 1.116 5.5 64.1 14.7 917 n/a 10_setrh: 0.1188 0.1351 0.038 1.116 5.5 64.1 14.7 917 n/a 10_nqh: 0.1188 0.1351 0.038 1.116 5.5 64.1 14.7 917 n/a 10_sol: 0.1187 0.1342 0.038 1.116 5.5 64.1 14.7 918 n/a 10_weight: 0.1187 0.1342 0.038 1.116 5.5 64.1 14.7 918 n/a 10_xyzrec: 0.1192 0.1350 0.038 1.183 5.5 64.1 14.7 918 n/a 10_adp: 0.1194 0.1353 0.038 1.183 5.6 63.4 14.7 918 n/a 10_regHadp: 0.1194 0.1353 0.038 1.183 5.6 63.4 14.7 918 n/a 10_occ: 0.1193 0.1356 0.038 1.183 5.6 63.4 14.7 918 n/a end: 0.1192 0.1355 0.038 1.183 5.5 63.4 14.6 918 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1990108_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1990108_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3900 Refinement macro-cycles (run) : 12053.6800 Write final files (write_after_run_outputs) : 160.2700 Total : 12220.3400 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:55 PST -0800 (1736736055.56 s) Start R-work = 0.1813, R-free = 0.1902 Final R-work = 0.1192, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 12513.56 seconds wall clock time: 209 minutes 34.30 seconds (12574.30 seconds total)