Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4035888.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 { 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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4035888.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4035888.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } 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 =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.26, per 1000 atoms: 0.34 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: 2.676 distance_ideal: 2.720 ideal - model: 0.044 slack: 0.000 delta_slack: 0.044 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: 2.775 distance_ideal: 2.710 ideal - model: -0.065 slack: 0.000 delta_slack: -0.065 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: 0.93 Conformation dependent library (CDL) restraints added in 118.8 milliseconds Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 798 1.02 - 1.26: 2582 1.26 - 1.50: 1573 1.50 - 1.74: 968 1.74 - 1.98: 13 Bond restraints: 5934 Sorted by residual: bond pdb=" C ASP A 117 " pdb=" N ILE A 118 " ideal model delta sigma weight residual 1.335 1.564 -0.228 1.09e-02 8.42e+03 4.39e+02 bond pdb=" C VAL B 145 " pdb=" O VAL B 145 " ideal model delta sigma weight residual 1.237 1.445 -0.207 1.08e-02 8.57e+03 3.69e+02 bond pdb=" N VAL B 173 " pdb=" H VAL B 173 " ideal model delta sigma weight residual 0.860 1.238 -0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.456 1.616 -0.161 8.70e-03 1.32e+04 3.41e+02 bond pdb=" CG HIS B 179 " pdb=" ND1 HIS B 179 " ideal model delta sigma weight residual 1.378 1.579 -0.201 1.10e-02 8.26e+03 3.33e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 6053 4.59 - 9.18: 3507 9.18 - 13.77: 1104 13.77 - 18.36: 138 18.36 - 22.95: 8 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY B 122 " pdb=" C GLY B 122 " pdb=" N ASN B 123 " ideal model delta sigma weight residual 115.34 101.67 13.67 8.40e-01 1.42e+00 2.65e+02 angle pdb=" C VAL A 173 " pdb=" CA VAL A 173 " pdb=" CB VAL A 173 " ideal model delta sigma weight residual 110.88 128.06 -17.18 1.09e+00 8.42e-01 2.48e+02 angle pdb=" CD2 HIS B 179 " pdb=" NE2 HIS B 179 " pdb=" CE1 HIS B 179 " ideal model delta sigma weight residual 109.00 123.78 -14.78 1.00e+00 1.00e+00 2.19e+02 angle pdb=" N SER A 48 " pdb=" CA SER A 48 " pdb=" C SER A 48 " ideal model delta sigma weight residual 112.54 129.19 -16.65 1.22e+00 6.72e-01 1.86e+02 angle pdb=" CA GLY A 126 " pdb=" C GLY A 126 " pdb=" O GLY A 126 " ideal model delta sigma weight residual 121.08 105.86 15.22 1.12e+00 7.97e-01 1.85e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 1843 17.92 - 35.83: 139 35.83 - 53.74: 47 53.74 - 71.66: 20 71.66 - 89.57: 1 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -146.28 -33.72 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 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: 213 0.215 - 0.431: 153 0.431 - 0.646: 93 0.646 - 0.861: 27 0.861 - 1.076: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 3.59 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CG LEU A 152 " pdb=" CB LEU A 152 " pdb=" CD1 LEU A 152 " pdb=" CD2 LEU A 152 " both_signs ideal model delta sigma weight residual False -2.59 -3.64 1.05 2.00e-01 2.50e+01 2.76e+01 chirality pdb=" CA LEU A 24 " pdb=" N LEU A 24 " pdb=" C LEU A 24 " pdb=" CB LEU A 24 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.76e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.105 2.00e-02 2.50e+03 7.71e-02 1.79e+02 pdb=" CG TYR A 194 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.126 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.137 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.086 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " 0.050 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.032 2.00e-02 2.50e+03 6.07e-02 1.48e+02 pdb=" CG TRP B 146 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.142 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.049 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " -0.020 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR B 195 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " -0.127 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " -0.072 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " 0.099 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TYR B 195 " 0.112 2.00e-02 2.50e+03 pdb=" HD2 TYR B 195 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR B 195 " -0.070 2.00e-02 2.50e+03 pdb=" HE2 TYR B 195 " 0.023 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.67: 40 1.67 - 2.40: 3007 2.40 - 3.13: 22609 3.13 - 3.87: 32742 3.87 - 4.60: 51810 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110208 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.933 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.989 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.002 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.140 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.188 2.620 ... (remaining 110203 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_4035888_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= 0.2034 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.301467 | | target function (ml) not normalized (work): 805720.643617 | | target function (ml) not normalized (free): 16583.861067 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2139 0.1844 6.695 6.2957| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1727 5.5337 5.6017| | 3: 2.33 - 2.04 0.96 6939 150 0.1625 0.1483 5.1483 5.1257| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1641 4.9842 5.0872| | 5: 1.85 - 1.72 0.99 7113 159 0.1920 0.1720 4.7932 4.8644| | 6: 1.72 - 1.62 0.99 7102 142 0.1977 0.2002 4.6674 4.7078| | 7: 1.62 - 1.54 0.99 7104 148 0.2034 0.1979 4.5797 4.5625| | 8: 1.54 - 1.47 0.96 6798 152 0.2056 0.2219 4.4909 4.5725| | 9: 1.47 - 1.41 0.98 6938 155 0.2094 0.2356 4.389 4.4924| | 10: 1.41 - 1.36 0.99 7022 150 0.2134 0.2062 4.3075 4.3266| | 11: 1.36 - 1.32 0.99 6997 151 0.2080 0.2230 4.2213 4.3388| | 12: 1.32 - 1.28 0.98 6976 149 0.2095 0.1722 4.1707 4.1357| | 13: 1.28 - 1.25 0.98 6907 166 0.2002 0.1970 4.1044 4.1049| | 14: 1.25 - 1.22 0.98 7015 113 0.2073 0.2371 4.0674 4.2701| | 15: 1.22 - 1.19 0.98 6957 137 0.2121 0.2134 4.0413 4.035| | 16: 1.19 - 1.17 0.93 6604 132 0.2111 0.2273 4.0004 4.0534| | 17: 1.17 - 1.14 0.98 6941 135 0.2174 0.2036 3.9634 4.0058| | 18: 1.14 - 1.12 0.98 6875 142 0.2233 0.2706 3.9401 4.036| | 19: 1.12 - 1.10 0.97 6949 106 0.2275 0.2202 3.8769 3.8866| | 20: 1.10 - 1.08 0.97 6884 147 0.2339 0.2311 3.831 3.8785| | 21: 1.08 - 1.07 0.97 6852 152 0.2455 0.2587 3.8041 3.7884| | 22: 1.07 - 1.05 0.97 6838 135 0.2555 0.2702 3.7576 3.7769| | 23: 1.05 - 1.03 0.97 6829 159 0.2747 0.2747 3.7344 3.8208| | 24: 1.03 - 1.02 0.96 6785 133 0.2880 0.2891 3.6958 3.8306| | 25: 1.02 - 1.01 0.93 6552 130 0.3095 0.2686 3.6794 3.6805| | 26: 1.01 - 0.99 0.96 6767 158 0.3173 0.3308 3.6221 3.62| | 27: 0.99 - 0.98 0.94 6648 131 0.3361 0.3414 3.6263 3.6652| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.13 0.91 0.97 34473.86| | 2: 2.94 - 2.33 7339 128 0.86 20.98 1.08 1.02 14831.55| | 3: 2.33 - 2.04 6939 150 0.93 12.81 1.11 1.05 4269.45| | 4: 2.04 - 1.85 7170 155 0.92 14.02 1.11 1.04 2899.09| | 5: 1.85 - 1.72 7113 159 0.90 16.10 1.12 1.06 2149.30| | 6: 1.72 - 1.62 7102 142 0.90 17.03 1.11 1.08 1700.43| | 7: 1.62 - 1.54 7104 148 0.89 17.90 1.11 1.09 1400.70| | 8: 1.54 - 1.47 6798 152 0.88 18.82 1.10 1.07 1220.73| | 9: 1.47 - 1.41 6938 155 0.88 19.57 1.10 1.06 1026.01| | 10: 1.41 - 1.36 7022 150 0.87 20.16 1.10 1.05 860.40| | 11: 1.36 - 1.32 6997 151 0.88 19.39 1.08 1.05 693.41| | 12: 1.32 - 1.28 6976 149 0.88 18.69 1.08 1.04 584.23| | 13: 1.28 - 1.25 6907 166 0.89 18.55 1.07 1.05 544.60| | 14: 1.25 - 1.22 7015 113 0.87 20.40 1.08 1.05 549.40| | 15: 1.22 - 1.19 6957 137 0.86 20.95 1.08 1.04 541.02| | 16: 1.19 - 1.17 6604 132 0.86 21.23 1.08 1.01 514.82| | 17: 1.17 - 1.14 6941 135 0.85 21.93 1.08 1.00 467.21| | 18: 1.14 - 1.12 6875 142 0.85 22.23 1.08 0.99 430.59| | 19: 1.12 - 1.10 6949 106 0.85 22.79 1.07 0.99 395.93| | 20: 1.10 - 1.08 6884 147 0.84 23.46 1.06 0.97 362.96| | 21: 1.08 - 1.07 6852 152 0.83 24.48 1.06 0.95 340.40| | 22: 1.07 - 1.05 6838 135 0.81 26.40 1.05 0.94 337.94| | 23: 1.05 - 1.03 6829 159 0.79 28.57 1.05 0.94 338.62| | 24: 1.03 - 1.02 6785 133 0.77 30.41 1.05 0.95 337.53| | 25: 1.02 - 1.01 6552 130 0.76 31.15 1.03 0.91 312.43| | 26: 1.01 - 0.99 6767 158 0.73 33.78 1.02 0.89 310.03| | 27: 0.99 - 0.98 6648 131 0.70 36.10 1.04 0.87 327.83| |alpha: min = 0.87 max = 1.09 mean = 1.01| |beta: min = 310.03 max = 34473.86 mean = 2798.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.89 mean = 22.05| |phase err.(test): min = 0.00 max = 89.51 mean = 21.85| |-----------------------------------------------------------------------------| ----------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 0.234 2950 Z= 5.422 Angle : 5.277 17.728 4018 Z= 3.732 Chirality : 0.369 1.076 492 Planarity : 0.033 0.179 512 Dihedral : 13.096 89.568 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 26.97 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.96 (0.39), residues: 386 helix: -2.54 (0.30), residues: 146 sheet: -0.65 (0.52), residues: 86 loop : -0.04 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.109 0.022 ARG A 49 TYR 0.138 0.045 TYR A 194 PHE 0.091 0.031 PHE A 164 TRP 0.134 0.039 TRP B 146 HIS 0.063 0.023 HIS A 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= 0.2034 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.301467 | | target function (ml) not normalized (work): 805720.643617 | | target function (ml) not normalized (free): 16583.861067 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2034 0.1988 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2034 0.1988 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2034 0.1988 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2034 0.1988 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1802 0.1928 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1799 0.1926 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4067 402.814 293.655 0.435 0.913 0.295 13.296-10.522 99.01 99 1 0.2484 528.187 518.185 0.781 0.914 0.240 10.503-8.327 98.90 177 3 0.2468 564.205 560.087 0.973 0.914 0.214 8.318-6.595 100.00 360 8 0.2425 414.736 404.355 0.970 0.914 0.160 6.588-5.215 100.00 711 7 0.2286 381.101 366.158 0.958 0.914 0.160 5.214-4.128 98.38 1367 28 0.1503 557.435 550.238 1.077 0.914 0.090 4.126-3.266 94.74 2603 46 0.1324 508.132 499.473 1.146 0.914 0.019 3.266-2.585 99.86 5447 97 0.1440 342.774 337.479 1.123 0.913 0.010 2.585-2.046 97.45 10613 204 0.1399 258.603 254.415 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.800 1.144 0.912 0.000 1.619-1.281 98.00 42464 925 0.1926 82.395 80.152 1.128 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2319 44.202 41.679 1.114 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0103 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1799 r_free=0.1926 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1799 r_free=0.1926 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.046132 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 583.937991 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 0.1272 0.1503 0.0232 0.038 1.1 11.0 0.0 0.3 0 11.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.03 2.32 1.118 13.107 583.938 0.018 12.94 15.66 2.72 1.224 13.315 583.938 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 14.97 1.40 435 3274 Protein: 5.17 40.52 10.97 1.40 0 2902 Water: 6.25 73.04 29.37 N/A 435 370 Other: 16.08 29.57 22.82 N/A 0 2 Chain A: 5.37 60.13 13.01 N/A 0 1626 Chain B: 5.17 73.04 12.73 N/A 0 1648 Chain S: 11.79 65.11 30.79 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2170 11.96 - 18.74 639 18.74 - 25.53 315 25.53 - 32.32 261 32.32 - 39.10 158 39.10 - 45.89 101 45.89 - 52.68 41 52.68 - 59.47 18 59.47 - 66.25 5 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1294 r_free=0.1566 r_work=0.1293 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1293 r_free = 0.1561 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 = 0.1279 r_free = 0.1552 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015500 | | target function (ls_wunit_k1) not normalized (work): 2903.087585 | | target function (ls_wunit_k1) not normalized (free): 115.402341 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1284 0.1279 0.1552 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1463 0.1460 0.1627 n_refl.: 191137 remove outliers: r(all,work,free)=0.1463 0.1460 0.1627 n_refl.: 191137 overall B=0.17 to atoms: r(all,work,free)=0.1488 0.1485 0.1637 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1276 0.1271 0.1543 n_refl.: 191137 remove outliers: r(all,work,free)=0.1276 0.1271 0.1543 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3609 402.814 381.565 0.487 0.964 0.275 13.296-10.522 99.01 99 1 0.2087 528.187 522.303 0.739 0.965 0.245 10.503-8.327 98.90 177 3 0.1723 564.205 562.239 0.886 0.965 0.193 8.318-6.595 100.00 360 8 0.1710 414.736 412.613 0.908 0.965 0.150 6.588-5.215 100.00 711 7 0.1537 381.101 373.541 0.888 0.965 0.150 5.214-4.128 98.38 1367 28 0.0905 557.435 554.339 0.976 0.965 0.080 4.126-3.266 94.74 2603 46 0.0832 508.132 504.369 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.421 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.381 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.389 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1272 82.395 81.413 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.164 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=0.0392 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1543 | n_water=805 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1276 r_free=0.1546 | n_water=794 | time (s): 99.130 (total time: 101.550) Filter (q & B) r_work=0.1276 r_free=0.1546 | n_water=791 | time (s): 4.290 (total time: 105.840) Compute maps r_work=0.1276 r_free=0.1546 | n_water=791 | time (s): 2.150 (total time: 107.990) Filter (map) r_work=0.1302 r_free=0.1528 | n_water=651 | time (s): 4.190 (total time: 112.180) Find peaks r_work=0.1302 r_free=0.1528 | n_water=651 | time (s): 0.660 (total time: 112.840) Add new water r_work=0.1325 r_free=0.1563 | n_water=956 | time (s): 5.240 (total time: 118.080) Refine new water occ: r_work=0.1281 r_free=0.1513 adp: r_work=0.1269 r_free=0.1511 occ: r_work=0.1271 r_free=0.1509 adp: r_work=0.1265 r_free=0.1509 occ: r_work=0.1266 r_free=0.1506 adp: r_work=0.1264 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1506 r_work=0.1264 r_free=0.1506 | n_water=956 | time (s): 88.800 (total time: 206.880) Filter (q & B) r_work=0.1267 r_free=0.1506 | n_water=890 | time (s): 4.410 (total time: 211.290) Filter (dist only) r_work=0.1267 r_free=0.1505 | n_water=889 | time (s): 111.720 (total time: 323.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.938208 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.894427 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 0.1251 0.1517 0.0266 0.040 1.1 21.2 0.0 0.0 0 11.469 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.51 15.17 2.66 2.039 15.199 594.894 0.014 12.31 15.06 2.75 2.394 15.235 594.894 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 68.77 16.35 1.21 521 3272 Protein: 5.45 40.48 10.97 1.21 0 2902 Water: 6.62 68.77 33.89 N/A 521 368 Other: 16.40 33.39 24.90 N/A 0 2 Chain A: 5.57 56.35 12.97 N/A 0 1624 Chain B: 5.45 68.39 12.81 N/A 0 1648 Chain S: 13.13 68.77 38.11 N/A 521 0 Histogram: Values Number of atoms 5.45 - 11.78 2087 11.78 - 18.11 695 18.11 - 24.45 258 24.45 - 30.78 227 30.78 - 37.11 152 37.11 - 43.44 176 43.44 - 49.78 97 49.78 - 56.11 47 56.11 - 62.44 41 62.44 - 68.77 13 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1506 r_work=0.1232 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1507 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 = 0.1506 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1506 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013398 | | target function (ls_wunit_k1) not normalized (work): 2509.392043 | | target function (ls_wunit_k1) not normalized (free): 101.270358 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1506 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1605 n_refl.: 191137 remove outliers: r(all,work,free)=0.1436 0.1433 0.1605 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1603 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1513 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1513 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3212 402.814 379.504 0.493 0.963 0.276 13.296-10.522 99.01 99 1 0.1869 528.187 520.588 0.753 0.964 0.222 10.503-8.327 98.90 177 3 0.1407 564.205 566.584 0.918 0.964 0.169 8.318-6.595 100.00 360 8 0.1598 414.736 414.363 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1326 381.101 376.903 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0830 557.435 556.115 0.994 0.963 0.090 4.126-3.266 94.74 2603 46 0.0758 508.132 505.614 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0857 342.774 341.366 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.743 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.599 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.337 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.212 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0467 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1513 | n_water=889 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1234 r_free=0.1516 | n_water=884 | time (s): 107.390 (total time: 110.340) Filter (q & B) r_work=0.1234 r_free=0.1516 | n_water=883 | time (s): 5.540 (total time: 115.880) Compute maps r_work=0.1234 r_free=0.1516 | n_water=883 | time (s): 1.670 (total time: 117.550) Filter (map) r_work=0.1274 r_free=0.1520 | n_water=694 | time (s): 4.940 (total time: 122.490) Find peaks r_work=0.1274 r_free=0.1520 | n_water=694 | time (s): 0.860 (total time: 123.350) Add new water r_work=0.1298 r_free=0.1548 | n_water=1028 | time (s): 4.130 (total time: 127.480) Refine new water occ: r_work=0.1251 r_free=0.1506 adp: r_work=0.1252 r_free=0.1507 occ: r_work=0.1247 r_free=0.1503 adp: r_work=0.1247 r_free=0.1504 occ: r_work=0.1244 r_free=0.1501 adp: r_work=0.1244 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1503 r_work=0.1244 r_free=0.1503 | n_water=1028 | time (s): 373.490 (total time: 500.970) Filter (q & B) r_work=0.1249 r_free=0.1505 | n_water=880 | time (s): 4.610 (total time: 505.580) Filter (dist only) r_work=0.1249 r_free=0.1505 | n_water=878 | time (s): 112.550 (total time: 618.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.708796 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.719885 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 0.1237 0.1436 0.0198 0.035 1.1 7.6 0.0 0.0 0 0.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.36 1.98 1.932 14.595 15.720 3.938 12.32 13.97 1.65 2.205 14.508 15.720 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 68.05 15.30 1.06 511 3271 Protein: 5.52 36.97 10.75 1.06 0 2902 Water: 6.69 68.05 30.32 N/A 511 367 Other: 14.08 28.93 21.50 N/A 0 2 Chain A: 5.52 55.63 12.76 N/A 0 1624 Chain B: 5.55 68.05 12.54 N/A 0 1647 Chain S: 14.34 64.48 32.28 N/A 511 0 Histogram: Values Number of atoms 5.52 - 11.77 2134 11.77 - 18.03 691 18.03 - 24.28 290 24.28 - 30.53 240 30.53 - 36.78 170 36.78 - 43.04 148 43.04 - 49.29 68 49.29 - 55.54 29 55.54 - 61.79 9 61.79 - 68.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1397 r_work=0.1233 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1398 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1392 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891453 | | target function (ml) not normalized (work): 728853.629782 | | target function (ml) not normalized (free): 15219.467027 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1392 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1495 n_refl.: 191137 remove outliers: r(all,work,free)=0.1443 0.1442 0.1495 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1492 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1387 n_refl.: 191137 remove outliers: r(all,work,free)=0.1227 0.1224 0.1387 n_refl.: 191134 ======================== 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 0.3725 398.008 365.425 0.427 0.946 0.251 13.296-10.522 99.01 99 1 0.2464 528.187 509.206 0.710 0.948 0.225 10.503-8.327 97.80 175 3 0.1899 554.286 559.220 0.881 0.948 0.189 8.318-6.595 100.00 360 8 0.2105 414.736 408.797 0.898 0.947 0.133 6.588-5.215 100.00 711 7 0.1842 381.101 370.569 0.885 0.947 0.107 5.214-4.128 98.38 1367 28 0.1160 557.435 552.164 0.970 0.947 0.060 4.126-3.266 94.74 2603 46 0.1094 508.132 500.971 1.033 0.948 0.015 3.266-2.585 99.86 5447 97 0.1090 342.774 339.151 1.020 0.947 0.005 2.585-2.046 97.45 10613 204 0.0959 258.603 255.804 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.390 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.480 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.316 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0952 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1387 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1387 | n_water=878 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1224 r_free=0.1385 | n_water=877 | time (s): 108.220 (total time: 111.310) Filter (q & B) r_work=0.1224 r_free=0.1382 | n_water=864 | time (s): 5.540 (total time: 116.850) Compute maps r_work=0.1224 r_free=0.1382 | n_water=864 | time (s): 1.980 (total time: 118.830) Filter (map) r_work=0.1249 r_free=0.1385 | n_water=719 | time (s): 5.930 (total time: 124.760) Find peaks r_work=0.1249 r_free=0.1385 | n_water=719 | time (s): 0.890 (total time: 125.650) Add new water r_work=0.1263 r_free=0.1394 | n_water=982 | time (s): 4.210 (total time: 129.860) Refine new water occ: r_work=0.1213 r_free=0.1362 adp: r_work=0.1205 r_free=0.1356 occ: r_work=0.1203 r_free=0.1357 adp: r_work=0.1203 r_free=0.1356 occ: r_work=0.1201 r_free=0.1358 adp: r_work=0.1200 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1357 | n_water=982 | time (s): 371.830 (total time: 501.690) Filter (q & B) r_work=0.1206 r_free=0.1366 | n_water=879 | time (s): 4.460 (total time: 506.150) Filter (dist only) r_work=0.1207 r_free=0.1365 | n_water=878 | time (s): 111.340 (total time: 617.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.588880 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.294621 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 0.1206 0.1369 0.0163 0.036 1.1 6.8 0.0 0.3 0 0.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.69 1.63 1.836 14.262 16.295 3.874 11.98 13.62 1.64 1.990 14.206 16.295 3.864 Individual atomic B min max mean iso aniso Overall: 5.46 67.47 15.03 1.00 511 3271 Protein: 5.46 33.34 10.64 1.00 0 2902 Water: 5.95 67.47 29.52 N/A 511 367 Other: 13.95 27.43 20.69 N/A 0 2 Chain A: 5.58 54.27 12.59 N/A 0 1624 Chain B: 5.46 67.47 12.42 N/A 0 1647 Chain S: 5.95 64.36 31.19 N/A 511 0 Histogram: Values Number of atoms 5.46 - 11.66 2115 11.66 - 17.86 735 17.86 - 24.06 290 24.06 - 30.27 237 30.27 - 36.47 173 36.47 - 42.67 139 42.67 - 48.87 65 48.87 - 55.07 19 55.07 - 61.27 6 61.27 - 67.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1362 r_work=0.1198 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1362 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1361 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861806 | | target function (ml) not normalized (work): 723289.195796 | | target function (ml) not normalized (free): 15134.000656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1420 0.1419 0.1467 n_refl.: 191134 remove outliers: r(all,work,free)=0.1420 0.1419 0.1467 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1413 0.1412 0.1463 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1361 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 94.06 92 3 0.3800 360.362 326.371 0.413 0.946 0.247 13.296-10.522 98.02 98 1 0.2442 478.874 454.653 0.694 0.947 0.191 10.503-8.327 97.80 175 3 0.2098 501.859 496.292 0.866 0.947 0.163 8.318-6.595 100.00 360 8 0.2161 375.508 371.424 0.889 0.947 0.100 6.588-5.215 100.00 711 7 0.1883 345.055 335.661 0.887 0.947 0.090 5.214-4.128 98.38 1367 28 0.1185 504.710 499.666 0.976 0.948 0.080 4.126-3.266 94.74 2603 46 0.1119 460.070 453.670 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1092 310.352 307.144 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0934 234.143 231.707 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0910 138.577 137.271 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0984 74.602 73.892 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.021 38.364 1.037 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1128 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1361 | n_water=878 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1194 r_free=0.1362 | n_water=877 | time (s): 115.040 (total time: 118.160) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=867 | time (s): 4.880 (total time: 123.040) Compute maps r_work=0.1195 r_free=0.1363 | n_water=867 | time (s): 2.140 (total time: 125.180) Filter (map) r_work=0.1218 r_free=0.1359 | n_water=749 | time (s): 5.110 (total time: 130.290) Find peaks r_work=0.1218 r_free=0.1359 | n_water=749 | time (s): 0.560 (total time: 130.850) Add new water r_work=0.1231 r_free=0.1374 | n_water=985 | time (s): 4.230 (total time: 135.080) Refine new water occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1346 occ: r_work=0.1189 r_free=0.1346 adp: r_work=0.1189 r_free=0.1345 occ: r_work=0.1186 r_free=0.1345 adp: r_work=0.1186 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1345 r_work=0.1186 r_free=0.1345 | n_water=985 | time (s): 245.350 (total time: 380.430) Filter (q & B) r_work=0.1191 r_free=0.1353 | n_water=903 | time (s): 5.030 (total time: 385.460) Filter (dist only) r_work=0.1192 r_free=0.1352 | n_water=902 | time (s): 116.330 (total time: 501.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.655080 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.396229 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1355 0.0161 0.036 1.1 7.2 0.0 0.3 0 0.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.55 1.61 1.788 14.162 15.396 3.762 11.97 13.58 1.61 1.817 14.150 15.396 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 67.28 15.04 0.97 536 3270 Protein: 5.57 32.43 10.60 0.97 0 2902 Water: 5.99 67.28 29.33 N/A 536 366 Other: 13.77 26.91 20.34 N/A 0 2 Chain A: 5.62 53.86 12.53 N/A 0 1624 Chain B: 5.57 67.28 12.34 N/A 0 1646 Chain S: 5.99 64.30 30.95 N/A 536 0 Histogram: Values Number of atoms 5.57 - 11.74 2146 11.74 - 17.91 719 17.91 - 24.08 290 24.08 - 30.25 245 30.25 - 36.42 173 36.42 - 42.59 136 42.59 - 48.76 71 48.76 - 54.93 18 54.93 - 61.11 5 61.11 - 67.28 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1359 r_work=0.1197 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758887 | | target function (ml) not normalized (work): 704009.409309 | | target function (ml) not normalized (free): 14746.531848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191133 remove outliers: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1409 0.1408 0.1479 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191133 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 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 94.06 92 3 0.3842 360.362 324.431 0.405 0.947 0.240 13.296-10.522 98.02 98 1 0.2476 478.874 459.583 0.692 0.949 0.174 10.503-8.327 97.80 175 3 0.2134 501.859 495.936 0.861 0.949 0.143 8.318-6.595 100.00 360 8 0.2151 375.508 371.619 0.884 0.948 0.080 6.588-5.215 100.00 711 7 0.1896 345.055 335.445 0.887 0.949 0.080 5.214-4.128 98.38 1367 28 0.1182 504.710 499.864 0.973 0.949 0.040 4.126-3.266 94.74 2603 46 0.1129 460.070 453.249 1.034 0.949 0.009 3.266-2.585 99.86 5447 97 0.1108 310.352 307.026 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0942 234.143 231.695 1.032 0.949 0.000 2.046-1.619 99.39 21536 464 0.0911 138.577 137.268 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0974 74.602 73.891 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.021 38.353 1.036 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1232 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1359 | n_water=902 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1194 r_free=0.1359 | n_water=900 | time (s): 113.380 (total time: 115.760) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=890 | time (s): 5.700 (total time: 121.460) Compute maps r_work=0.1195 r_free=0.1359 | n_water=890 | time (s): 2.320 (total time: 123.780) Filter (map) r_work=0.1218 r_free=0.1353 | n_water=768 | time (s): 4.360 (total time: 128.140) Find peaks r_work=0.1218 r_free=0.1353 | n_water=768 | time (s): 0.780 (total time: 128.920) Add new water r_work=0.1228 r_free=0.1370 | n_water=997 | time (s): 4.840 (total time: 133.760) Refine new water occ: r_work=0.1191 r_free=0.1349 adp: r_work=0.1191 r_free=0.1349 occ: r_work=0.1189 r_free=0.1349 adp: r_work=0.1189 r_free=0.1349 occ: r_work=0.1187 r_free=0.1350 adp: r_work=0.1187 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1349 r_work=0.1187 r_free=0.1349 | n_water=997 | time (s): 231.040 (total time: 364.800) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=909 | time (s): 4.660 (total time: 369.460) Filter (dist only) r_work=0.1193 r_free=0.1353 | n_water=907 | time (s): 118.060 (total time: 487.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524638 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.565173 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 0.1197 0.1357 0.0160 0.037 1.1 7.0 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.60 1.769 14.088 14.565 3.760 12.02 13.61 1.59 1.931 14.041 14.565 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 66.08 14.90 0.90 541 3270 Protein: 5.58 29.30 10.48 0.90 0 2902 Water: 6.02 66.08 29.06 N/A 541 366 Other: 13.84 23.88 18.86 N/A 0 2 Chain A: 5.63 52.80 12.38 N/A 0 1624 Chain B: 5.58 66.08 12.20 N/A 0 1646 Chain S: 6.02 64.07 30.72 N/A 541 0 Histogram: Values Number of atoms 5.58 - 11.63 2126 11.63 - 17.68 766 17.68 - 23.73 280 23.73 - 29.78 221 29.78 - 35.83 178 35.83 - 41.88 140 41.88 - 47.93 65 47.93 - 53.98 27 53.98 - 60.03 4 60.03 - 66.08 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1362 r_work=0.1202 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1362 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758457 | | target function (ml) not normalized (work): 703929.016415 | | target function (ml) not normalized (free): 14736.128443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1360 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1419 0.1419 0.1483 n_refl.: 191133 remove outliers: r(all,work,free)=0.1419 0.1419 0.1483 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1412 0.1411 0.1478 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191133 remove outliers: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3800 361.166 320.045 0.390 0.949 0.224 13.296-10.522 97.03 97 1 0.2432 481.147 458.946 0.683 0.950 0.156 10.503-8.327 97.80 175 3 0.2163 501.859 495.628 0.857 0.950 0.127 8.318-6.595 100.00 360 8 0.2174 375.508 371.362 0.883 0.950 0.094 6.588-5.215 100.00 711 7 0.1896 345.055 336.060 0.884 0.950 0.073 5.214-4.128 98.38 1367 28 0.1204 504.710 499.859 0.971 0.950 0.030 4.126-3.266 94.74 2603 46 0.1148 460.070 453.025 1.033 0.951 0.005 3.266-2.585 99.86 5447 97 0.1114 310.352 306.983 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0953 234.143 231.681 1.032 0.949 0.000 2.046-1.619 99.39 21536 464 0.0913 138.577 137.275 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0971 74.602 73.900 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.021 38.353 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1279 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1357 | n_water=907 | time (s): 2.970 (total time: 2.970) Filter (dist) r_work=0.1198 r_free=0.1357 | n_water=907 | time (s): 108.050 (total time: 111.020) Filter (q & B) r_work=0.1199 r_free=0.1358 | n_water=892 | time (s): 5.400 (total time: 116.420) Compute maps r_work=0.1199 r_free=0.1358 | n_water=892 | time (s): 2.050 (total time: 118.470) Filter (map) r_work=0.1221 r_free=0.1359 | n_water=783 | time (s): 4.400 (total time: 122.870) Find peaks r_work=0.1221 r_free=0.1359 | n_water=783 | time (s): 0.610 (total time: 123.480) Add new water r_work=0.1228 r_free=0.1369 | n_water=994 | time (s): 4.280 (total time: 127.760) Refine new water occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1343 occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1342 r_work=0.1191 r_free=0.1342 | n_water=994 | time (s): 250.970 (total time: 378.730) Filter (q & B) r_work=0.1196 r_free=0.1349 | n_water=916 | time (s): 4.190 (total time: 382.920) Filter (dist only) r_work=0.1196 r_free=0.1349 | n_water=915 | time (s): 115.860 (total time: 498.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.503022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.934972 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1360 0.0161 0.038 1.1 6.0 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.60 1.61 1.718 13.953 13.935 3.759 12.01 13.62 1.61 1.774 13.928 13.935 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 65.02 14.84 0.88 549 3270 Protein: 5.58 28.48 10.42 0.88 0 2902 Water: 6.12 65.02 28.88 N/A 549 366 Other: 13.88 22.44 18.16 N/A 0 2 Chain A: 5.66 52.47 12.27 N/A 0 1624 Chain B: 5.58 65.02 12.11 N/A 0 1646 Chain S: 6.12 64.01 30.63 N/A 549 0 Histogram: Values Number of atoms 5.58 - 11.53 2105 11.53 - 17.47 788 17.47 - 23.41 271 23.41 - 29.36 222 29.36 - 35.30 184 35.30 - 41.24 135 41.24 - 47.19 73 47.19 - 53.13 33 53.13 - 59.07 4 59.07 - 65.02 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1362 r_work=0.1202 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757280 | | target function (ml) not normalized (work): 703701.013545 | | target function (ml) not normalized (free): 14738.908304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1400 0.1399 0.1482 n_refl.: 191131 remove outliers: r(all,work,free)=0.1400 0.1399 0.1482 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1366 0.1365 0.1462 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1361 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3891 361.166 322.184 0.389 0.952 0.199 13.296-10.522 97.03 97 1 0.2398 481.147 463.419 0.703 0.953 0.148 10.503-8.327 97.80 175 3 0.2174 501.859 495.201 0.877 0.954 0.123 8.318-6.595 100.00 360 8 0.2154 375.508 371.153 0.903 0.953 0.091 6.588-5.215 100.00 711 7 0.1902 345.055 336.143 0.905 0.953 0.070 5.214-4.128 98.38 1367 28 0.1213 504.710 499.847 0.994 0.954 0.035 4.126-3.266 94.74 2603 46 0.1154 460.070 452.988 1.056 0.954 0.009 3.266-2.585 99.86 5447 97 0.1122 310.352 306.888 1.040 0.953 0.000 2.585-2.046 97.45 10613 204 0.0955 234.143 231.614 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0911 138.577 137.271 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0967 74.602 73.899 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.021 38.347 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1362 | n_water=915 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1200 r_free=0.1362 | n_water=913 | time (s): 117.350 (total time: 120.670) Filter (q & B) r_work=0.1200 r_free=0.1363 | n_water=903 | time (s): 4.790 (total time: 125.460) Compute maps r_work=0.1200 r_free=0.1363 | n_water=903 | time (s): 2.490 (total time: 127.950) Filter (map) r_work=0.1224 r_free=0.1359 | n_water=790 | time (s): 4.630 (total time: 132.580) Find peaks r_work=0.1224 r_free=0.1359 | n_water=790 | time (s): 0.660 (total time: 133.240) Add new water r_work=0.1231 r_free=0.1366 | n_water=1011 | time (s): 4.180 (total time: 137.420) Refine new water occ: r_work=0.1197 r_free=0.1347 adp: r_work=0.1197 r_free=0.1347 occ: r_work=0.1195 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1349 r_work=0.1193 r_free=0.1349 | n_water=1011 | time (s): 263.630 (total time: 401.050) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=929 | time (s): 5.480 (total time: 406.530) Filter (dist only) r_work=0.1198 r_free=0.1355 | n_water=927 | time (s): 116.040 (total time: 522.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538685 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.856042 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 0.1358 0.0157 0.038 1.1 8.3 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.58 1.57 1.696 13.704 13.856 3.759 12.02 13.60 1.59 1.702 13.698 13.856 3.757 Individual atomic B min max mean iso aniso Overall: 5.34 64.47 14.65 0.87 561 3270 Protein: 5.34 28.09 10.21 0.87 0 2902 Water: 5.82 64.47 28.53 N/A 561 366 Other: 13.65 22.14 17.89 N/A 0 2 Chain A: 5.44 52.12 12.03 N/A 0 1624 Chain B: 5.34 64.47 11.88 N/A 0 1646 Chain S: 5.82 63.85 30.31 N/A 561 0 Histogram: Values Number of atoms 5.34 - 11.25 2087 11.25 - 17.16 803 17.16 - 23.08 273 23.08 - 28.99 233 28.99 - 34.90 184 34.90 - 40.81 133 40.81 - 46.73 74 46.73 - 52.64 35 52.64 - 58.55 5 58.55 - 64.47 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757279 | | target function (ml) not normalized (work): 703700.776646 | | target function (ml) not normalized (free): 14742.920534 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1476 n_refl.: 191131 remove outliers: r(all,work,free)=0.1373 0.1371 0.1476 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1380 0.1378 0.1480 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1349 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3773 356.313 317.081 0.333 0.996 0.120 13.296-10.522 97.03 97 1 0.2405 481.147 463.069 0.670 0.997 0.118 10.503-8.327 97.80 175 3 0.2167 501.859 494.363 0.847 0.998 0.117 8.318-6.595 100.00 360 8 0.2171 375.508 369.705 0.871 0.997 0.093 6.588-5.215 100.00 711 7 0.1943 345.055 335.189 0.873 0.998 0.077 5.214-4.128 98.38 1367 28 0.1225 504.710 498.989 0.960 0.999 0.044 4.126-3.266 94.74 2603 46 0.1156 460.070 452.452 1.020 1.000 0.009 3.266-2.585 99.86 5447 97 0.1121 310.352 306.732 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.143 231.551 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0910 138.577 137.197 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0948 74.602 73.944 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.021 38.329 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0634 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1349 | n_water=927 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1191 r_free=0.1349 | n_water=924 | time (s): 115.860 (total time: 118.880) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=912 | time (s): 4.070 (total time: 122.950) Compute maps r_work=0.1192 r_free=0.1347 | n_water=912 | time (s): 2.510 (total time: 125.460) Filter (map) r_work=0.1217 r_free=0.1345 | n_water=797 | time (s): 4.760 (total time: 130.220) Find peaks r_work=0.1217 r_free=0.1345 | n_water=797 | time (s): 0.570 (total time: 130.790) Add new water r_work=0.1223 r_free=0.1357 | n_water=1001 | time (s): 4.120 (total time: 134.910) Refine new water occ: r_work=0.1189 r_free=0.1326 adp: r_work=0.1189 r_free=0.1326 occ: r_work=0.1187 r_free=0.1327 adp: r_work=0.1187 r_free=0.1327 occ: r_work=0.1185 r_free=0.1327 adp: r_work=0.1185 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1328 r_work=0.1185 r_free=0.1328 | n_water=1001 | time (s): 215.680 (total time: 350.590) Filter (q & B) r_work=0.1189 r_free=0.1336 | n_water=929 | time (s): 5.060 (total time: 355.650) Filter (dist only) r_work=0.1189 r_free=0.1335 | n_water=927 | time (s): 118.640 (total time: 474.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527110 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.285651 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 0.1342 0.0149 0.038 1.1 8.0 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.42 1.49 1.664 13.727 14.286 3.755 11.91 13.41 1.50 1.671 13.727 14.286 3.753 Individual atomic B min max mean iso aniso Overall: 5.48 64.06 14.68 0.87 561 3270 Protein: 5.48 28.03 10.28 0.87 0 2902 Water: 5.84 64.06 28.46 N/A 561 366 Other: 13.74 22.06 17.90 N/A 0 2 Chain A: 5.56 51.87 12.07 N/A 0 1624 Chain B: 5.48 63.73 11.93 N/A 0 1646 Chain S: 5.84 64.06 30.29 N/A 561 0 Histogram: Values Number of atoms 5.48 - 11.34 2082 11.34 - 17.20 817 17.20 - 23.06 271 23.06 - 28.92 222 28.92 - 34.77 185 34.77 - 40.63 130 40.63 - 46.49 80 46.49 - 52.35 36 52.35 - 58.21 4 58.21 - 64.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1341 r_work=0.1192 r_free=0.1341 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1341 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1341 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752360 | | target function (ml) not normalized (work): 702772.013057 | | target function (ml) not normalized (free): 14724.605754 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1341 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1375 0.1373 0.1476 n_refl.: 191129 remove outliers: r(all,work,free)=0.1375 0.1373 0.1476 n_refl.: 191129 overall B=0.02 to atoms: r(all,work,free)=0.1377 0.1375 0.1478 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1338 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1338 n_refl.: 191128 ======================== 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 0.3685 356.080 321.865 0.321 0.987 0.070 13.296-10.522 97.03 97 1 0.2430 481.147 462.407 0.671 0.988 0.105 10.503-8.327 97.80 175 3 0.2179 501.859 493.955 0.852 0.988 0.105 8.318-6.595 100.00 360 8 0.2176 375.508 370.225 0.876 0.988 0.086 6.588-5.215 100.00 711 7 0.1929 345.055 335.520 0.878 0.989 0.070 5.214-4.128 98.38 1367 28 0.1218 504.710 499.132 0.968 0.989 0.030 4.126-3.266 94.74 2603 46 0.1161 460.070 452.360 1.029 0.990 0.005 3.266-2.585 99.86 5447 97 0.1121 310.352 306.660 1.013 0.991 0.000 2.585-2.046 97.45 10613 204 0.0958 234.143 231.530 1.020 0.993 0.000 2.046-1.619 99.39 21536 464 0.0908 138.577 137.212 1.036 0.997 0.000 1.619-1.281 98.00 42464 925 0.0943 74.602 73.944 1.026 1.002 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.021 38.310 0.994 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0249 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1338 After: r_work=0.1190 r_free=0.1339 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1339 | n_water=927 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1190 r_free=0.1339 | n_water=927 | time (s): 117.990 (total time: 120.910) Filter (q & B) r_work=0.1190 r_free=0.1339 | n_water=916 | time (s): 4.660 (total time: 125.570) Compute maps r_work=0.1190 r_free=0.1339 | n_water=916 | time (s): 2.360 (total time: 127.930) Filter (map) r_work=0.1214 r_free=0.1343 | n_water=802 | time (s): 4.520 (total time: 132.450) Find peaks r_work=0.1214 r_free=0.1343 | n_water=802 | time (s): 0.780 (total time: 133.230) Add new water r_work=0.1220 r_free=0.1351 | n_water=1004 | time (s): 4.010 (total time: 137.240) Refine new water occ: r_work=0.1187 r_free=0.1322 adp: r_work=0.1187 r_free=0.1322 occ: r_work=0.1185 r_free=0.1323 adp: r_work=0.1185 r_free=0.1322 occ: r_work=0.1184 r_free=0.1324 adp: r_work=0.1184 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1324 r_work=0.1184 r_free=0.1324 | n_water=1004 | time (s): 209.500 (total time: 346.740) Filter (q & B) r_work=0.1188 r_free=0.1335 | n_water=928 | time (s): 5.400 (total time: 352.140) Filter (dist only) r_work=0.1189 r_free=0.1335 | n_water=925 | time (s): 116.890 (total time: 469.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531666 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.503006 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1341 0.0148 0.039 1.2 8.7 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.41 1.48 1.670 13.739 14.503 3.756 11.93 13.43 1.49 1.668 13.742 14.503 3.755 Individual atomic B min max mean iso aniso Overall: 5.52 64.15 14.68 0.86 559 3270 Protein: 5.52 28.02 10.31 0.86 0 2902 Water: 5.95 64.15 28.37 N/A 559 366 Other: 13.80 22.09 17.94 N/A 0 2 Chain A: 5.61 51.64 12.08 N/A 0 1624 Chain B: 5.52 62.97 11.95 N/A 0 1646 Chain S: 5.95 64.15 30.25 N/A 559 0 Histogram: Values Number of atoms 5.52 - 11.38 2085 11.38 - 17.25 826 17.25 - 23.11 265 23.11 - 28.97 224 28.97 - 34.84 178 34.84 - 40.70 133 40.70 - 46.56 74 46.56 - 52.42 38 52.42 - 58.29 2 58.29 - 64.15 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1343 r_work=0.1194 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1343 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1343 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754814 | | target function (ml) not normalized (work): 703227.870355 | | target function (ml) not normalized (free): 14732.836828 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1350 0.1413 5.6799 5.7542| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1290 5.0764 5.1591| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1184 4.6547 4.7538| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1056 4.3912 4.5623| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.1009 4.1534 4.2552| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1078 3.9462 4.0641| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0977 3.7997 3.9394| | 8: 1.54 - 1.47 0.96 6798 152 0.0896 0.1310 3.7044 3.9042| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1123 3.6245 3.7577| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1183 3.5584 3.6847| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1136 3.4894 3.5934| | 12: 1.32 - 1.28 0.98 6975 149 0.1037 0.1141 3.4622 3.592| | 13: 1.28 - 1.25 0.98 6907 166 0.1046 0.1251 3.4417 3.5737| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1598 3.4343 3.6899| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1246 3.4502 3.4957| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1521 3.4647 3.647| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1220 3.4323 3.4389| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1713 3.4383 3.5337| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1783 3.4207 3.6007| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1584 3.4108 3.4372| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2156 3.4188 3.5066| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1956 3.4135 3.4135| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2023 3.4335 3.4899| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2253 3.4359 3.5084| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2497 3.4493 3.5213| | 26: 1.01 - 0.99 0.96 6767 158 0.2762 0.2871 3.4158 3.4227| | 27: 0.99 - 0.98 0.94 6647 131 0.3048 0.2801 3.4698 3.3943| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 11.47 1.00 0.95 10918.87| | 2: 2.94 - 2.33 7339 128 0.93 12.58 0.99 0.95 5025.24| | 3: 2.33 - 2.04 6939 150 0.96 7.63 1.01 0.95 1694.23| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.95 1005.06| | 5: 1.85 - 1.72 7113 159 0.96 8.10 1.00 0.96 638.05| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.96 443.46| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.97 338.46| | 8: 1.54 - 1.47 6798 152 0.96 8.34 1.01 0.97 281.87| | 9: 1.47 - 1.41 6938 155 0.96 8.57 1.00 0.97 234.16| | 10: 1.41 - 1.36 7022 150 0.96 9.03 1.00 0.97 205.76| | 11: 1.36 - 1.32 6997 151 0.96 9.06 0.99 0.96 178.06| | 12: 1.32 - 1.28 6975 149 0.96 9.11 0.98 0.94 163.41| | 13: 1.28 - 1.25 6907 166 0.96 9.66 1.01 0.96 160.69| | 14: 1.25 - 1.22 7015 112 0.95 10.81 1.01 0.96 165.02| | 15: 1.22 - 1.19 6956 137 0.95 11.29 1.01 0.98 167.67| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.96 160.33| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 153.70| | 18: 1.14 - 1.12 6875 142 0.94 12.78 1.01 0.94 147.99| | 19: 1.12 - 1.10 6948 106 0.93 14.20 1.00 0.94 151.96| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.93 151.17| | 21: 1.08 - 1.07 6852 152 0.91 16.70 1.00 0.93 154.04| | 22: 1.07 - 1.05 6836 135 0.89 18.35 0.99 0.92 155.35| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.92 165.02| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.92 179.00| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.97 0.89 181.82| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.98 0.88 176.12| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.98 0.87 160.41| |alpha: min = 0.87 max = 0.98 mean = 0.94| |beta: min = 147.99 max = 10918.87 mean = 911.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.89 mean = 13.31| |phase err.(test): min = 0.00 max = 86.13 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1381 0.1379 0.1483 n_refl.: 191128 remove outliers: r(all,work,free)=0.1381 0.1379 0.1483 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1381 0.1379 0.1482 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1341 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1341 n_refl.: 191128 ======================== 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 0.3682 356.080 327.604 0.323 0.995 0.070 13.296-10.522 97.03 97 1 0.2450 481.147 461.665 0.658 0.996 0.093 10.503-8.327 97.80 175 3 0.2181 501.859 493.897 0.843 0.997 0.102 8.318-6.595 100.00 360 8 0.2161 375.508 370.768 0.868 0.996 0.088 6.588-5.215 100.00 711 7 0.1909 345.055 335.248 0.871 0.997 0.077 5.214-4.128 98.38 1367 28 0.1221 504.710 499.225 0.959 0.998 0.039 4.126-3.266 94.74 2603 46 0.1164 460.070 452.295 1.021 0.999 0.005 3.266-2.585 99.86 5447 97 0.1122 310.352 306.753 1.005 1.000 0.000 2.585-2.046 97.45 10613 204 0.0963 234.143 231.525 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0911 138.577 137.209 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0948 74.602 73.940 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.021 38.300 0.988 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0023 ================= 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 : 0.2034 0.1988 0.081 5.277 5.2 78.0 14.6 805 0.000 1_bss: 0.1799 0.1926 0.081 5.277 5.2 78.0 14.6 805 0.000 1_settarget: 0.1799 0.1926 0.081 5.277 5.2 78.0 14.6 805 0.000 1_nqh: 0.1799 0.1926 0.081 5.277 5.2 78.0 14.6 805 0.000 1_weight: 0.1799 0.1926 0.081 5.277 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1503 0.038 1.150 5.2 78.0 14.6 805 0.155 1_adp: 0.1294 0.1566 0.038 1.150 5.2 73.0 15.0 805 0.155 1_regHadp: 0.1293 0.1561 0.038 1.150 5.2 73.0 15.0 805 0.155 1_occ: 0.1279 0.1552 0.038 1.150 5.2 73.0 15.0 805 0.155 2_bss: 0.1271 0.1543 0.038 1.150 5.3 73.2 15.1 805 0.155 2_settarget: 0.1271 0.1543 0.038 1.150 5.3 73.2 15.1 805 0.155 2_updatecdl: 0.1271 0.1543 0.038 1.164 5.3 73.2 15.1 805 0.155 2_nqh: 0.1271 0.1543 0.038 1.164 5.3 73.2 15.1 805 0.155 2_sol: 0.1267 0.1505 0.038 1.164 5.3 73.2 16.3 889 n/a 2_weight: 0.1267 0.1505 0.038 1.164 5.3 73.2 16.3 889 n/a 2_xyzrec: 0.1251 0.1517 0.040 1.133 5.3 73.2 16.3 889 n/a 2_adp: 0.1231 0.1506 0.040 1.133 5.4 68.8 16.4 889 n/a 2_regHadp: 0.1232 0.1507 0.040 1.133 5.4 68.8 16.4 889 n/a 2_occ: 0.1226 0.1506 0.040 1.133 5.4 68.8 16.4 889 n/a 3_bss: 0.1233 0.1513 0.040 1.133 5.4 68.8 16.3 889 n/a 3_settarget: 0.1233 0.1513 0.040 1.133 5.4 68.8 16.3 889 n/a 3_updatecdl: 0.1233 0.1513 0.040 1.135 5.4 68.8 16.3 889 n/a 3_nqh: 0.1233 0.1513 0.040 1.135 5.4 68.8 16.3 889 n/a 3_sol: 0.1249 0.1505 0.040 1.135 5.4 68.4 15.5 878 n/a 3_weight: 0.1249 0.1505 0.040 1.135 5.4 68.4 15.5 878 n/a 3_xyzrec: 0.1237 0.1436 0.035 1.099 5.4 68.4 15.5 878 n/a 3_adp: 0.1232 0.1397 0.035 1.099 5.5 68.0 15.3 878 n/a 3_regHadp: 0.1233 0.1398 0.035 1.099 5.5 68.0 15.3 878 n/a 3_occ: 0.1228 0.1392 0.035 1.099 5.5 68.0 15.3 878 n/a 4_bss: 0.1224 0.1387 0.035 1.099 5.5 68.0 15.3 878 n/a 4_settarget: 0.1224 0.1387 0.035 1.099 5.5 68.0 15.3 878 n/a 4_updatecdl: 0.1224 0.1387 0.035 1.104 5.5 68.0 15.3 878 n/a 4_nqh: 0.1224 0.1387 0.035 1.104 5.5 68.0 15.3 878 n/a 4_sol: 0.1207 0.1365 0.035 1.104 5.5 68.0 15.1 878 n/a 4_weight: 0.1207 0.1365 0.035 1.104 5.5 68.0 15.1 878 n/a 4_xyzrec: 0.1206 0.1369 0.036 1.124 5.5 68.0 15.1 878 n/a 4_adp: 0.1198 0.1362 0.036 1.124 5.5 67.5 15.0 878 n/a 4_regHadp: 0.1198 0.1362 0.036 1.124 5.5 67.5 15.0 878 n/a 4_occ: 0.1195 0.1361 0.036 1.124 5.5 67.5 15.0 878 n/a 5_bss: 0.1194 0.1361 0.036 1.124 5.4 67.4 15.0 878 n/a 5_settarget: 0.1194 0.1361 0.036 1.124 5.4 67.4 15.0 878 n/a 5_updatecdl: 0.1194 0.1361 0.036 1.124 5.4 67.4 15.0 878 n/a 5_nqh: 0.1194 0.1361 0.036 1.124 5.4 67.4 15.0 878 n/a 5_sol: 0.1192 0.1352 0.036 1.124 5.4 67.4 15.1 902 n/a 5_weight: 0.1192 0.1352 0.036 1.124 5.4 67.4 15.1 902 n/a 5_xyzrec: 0.1194 0.1355 0.036 1.139 5.4 67.4 15.1 902 n/a 5_adp: 0.1197 0.1359 0.036 1.139 5.6 67.3 15.0 902 n/a 5_regHadp: 0.1197 0.1359 0.036 1.139 5.6 67.3 15.0 902 n/a 5_occ: 0.1195 0.1359 0.036 1.139 5.6 67.3 15.0 902 n/a 6_bss: 0.1194 0.1359 0.036 1.139 5.5 67.2 15.0 902 n/a 6_settarget: 0.1194 0.1359 0.036 1.139 5.5 67.2 15.0 902 n/a 6_updatecdl: 0.1194 0.1359 0.036 1.138 5.5 67.2 15.0 902 n/a 6_nqh: 0.1194 0.1359 0.036 1.138 5.5 67.2 15.0 902 n/a 6_sol: 0.1193 0.1353 0.036 1.138 5.5 67.2 15.0 907 n/a 6_weight: 0.1193 0.1353 0.036 1.138 5.5 67.2 15.0 907 n/a 6_xyzrec: 0.1197 0.1357 0.037 1.131 5.5 67.2 15.0 907 n/a 6_adp: 0.1202 0.1362 0.037 1.131 5.6 66.1 14.9 907 n/a 6_regHadp: 0.1202 0.1362 0.037 1.131 5.6 66.1 14.9 907 n/a 6_occ: 0.1200 0.1360 0.037 1.131 5.6 66.1 14.9 907 n/a 7_bss: 0.1198 0.1357 0.037 1.131 5.5 66.0 14.9 907 n/a 7_settarget: 0.1198 0.1357 0.037 1.131 5.5 66.0 14.9 907 n/a 7_updatecdl: 0.1198 0.1357 0.037 1.131 5.5 66.0 14.9 907 n/a 7_nqh: 0.1198 0.1357 0.037 1.131 5.5 66.0 14.9 907 n/a 7_sol: 0.1196 0.1349 0.037 1.131 5.5 66.0 14.9 915 n/a 7_weight: 0.1196 0.1349 0.037 1.131 5.5 66.0 14.9 915 n/a 7_xyzrec: 0.1199 0.1360 0.038 1.119 5.5 66.0 14.9 915 n/a 7_adp: 0.1201 0.1362 0.038 1.119 5.6 65.0 14.8 915 n/a 7_regHadp: 0.1202 0.1362 0.038 1.119 5.6 65.0 14.8 915 n/a 7_occ: 0.1200 0.1363 0.038 1.119 5.6 65.0 14.8 915 n/a 8_bss: 0.1200 0.1362 0.038 1.119 5.4 64.8 14.6 915 n/a 8_settarget: 0.1200 0.1362 0.038 1.119 5.4 64.8 14.6 915 n/a 8_updatecdl: 0.1200 0.1362 0.038 1.118 5.4 64.8 14.6 915 n/a 8_nqh: 0.1200 0.1362 0.038 1.118 5.4 64.8 14.6 915 n/a 8_sol: 0.1198 0.1355 0.038 1.118 5.4 64.8 14.7 927 n/a 8_weight: 0.1198 0.1355 0.038 1.118 5.4 64.8 14.7 927 n/a 8_xyzrec: 0.1201 0.1358 0.038 1.121 5.4 64.8 14.7 927 n/a 8_adp: 0.1202 0.1361 0.038 1.121 5.3 64.5 14.6 927 n/a 8_regHadp: 0.1202 0.1361 0.038 1.121 5.3 64.5 14.6 927 n/a 8_occ: 0.1201 0.1363 0.038 1.121 5.3 64.5 14.6 927 n/a 9_bss: 0.1191 0.1349 0.038 1.121 5.4 64.5 14.7 927 n/a 9_settarget: 0.1191 0.1349 0.038 1.121 5.4 64.5 14.7 927 n/a 9_updatecdl: 0.1191 0.1349 0.038 1.122 5.4 64.5 14.7 927 n/a 9_nqh: 0.1191 0.1349 0.038 1.122 5.4 64.5 14.7 927 n/a 9_sol: 0.1189 0.1335 0.038 1.122 5.4 64.5 14.7 927 n/a 9_weight: 0.1189 0.1335 0.038 1.122 5.4 64.5 14.7 927 n/a 9_xyzrec: 0.1192 0.1342 0.038 1.119 5.4 64.5 14.7 927 n/a 9_adp: 0.1191 0.1341 0.038 1.119 5.5 64.1 14.7 927 n/a 9_regHadp: 0.1192 0.1341 0.038 1.119 5.5 64.1 14.7 927 n/a 9_occ: 0.1190 0.1341 0.038 1.119 5.5 64.1 14.7 927 n/a 10_bss: 0.1189 0.1338 0.038 1.119 5.5 64.1 14.7 927 n/a 10_settarget: 0.1189 0.1338 0.038 1.119 5.5 64.1 14.7 927 n/a 10_updatecdl: 0.1189 0.1338 0.038 1.119 5.5 64.1 14.7 927 n/a 10_setrh: 0.1190 0.1339 0.038 1.119 5.5 64.1 14.7 927 n/a 10_nqh: 0.1190 0.1339 0.038 1.119 5.5 64.1 14.7 927 n/a 10_sol: 0.1189 0.1335 0.038 1.119 5.5 64.1 14.7 925 n/a 10_weight: 0.1189 0.1335 0.038 1.119 5.5 64.1 14.7 925 n/a 10_xyzrec: 0.1194 0.1341 0.039 1.179 5.5 64.1 14.7 925 n/a 10_adp: 0.1193 0.1343 0.039 1.179 5.5 64.1 14.7 925 n/a 10_regHadp: 0.1194 0.1343 0.039 1.179 5.5 64.1 14.7 925 n/a 10_occ: 0.1192 0.1343 0.039 1.179 5.5 64.1 14.7 925 n/a end: 0.1191 0.1341 0.039 1.179 5.5 64.1 14.7 925 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4035888_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4035888_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.4900 Refinement macro-cycles (run) : 12329.4500 Write final files (write_after_run_outputs) : 141.6800 Total : 12477.6200 Total CPU time: 3.48 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:12 PST -0800 (1736736312.26 s) Start R-work = 0.1799, R-free = 0.1926 Final R-work = 0.1191, R-free = 0.1341 =============================================================================== Job complete usr+sys time: 12741.64 seconds wall clock time: 213 minutes 23.10 seconds (12803.10 seconds total)