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_4328694.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 { 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_4328694.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4328694.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 2.51, per 1000 atoms: 0.38 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.782 distance_ideal: 2.720 ideal - model: -0.062 slack: 0.000 delta_slack: -0.062 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: 2.727 distance_ideal: 2.710 ideal - model: -0.017 slack: 0.000 delta_slack: -0.017 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: 1.12 Conformation dependent library (CDL) restraints added in 175.4 milliseconds Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1019 1.05 - 1.27: 2365 1.27 - 1.50: 1512 1.50 - 1.73: 1017 1.73 - 1.95: 21 Bond restraints: 5934 Sorted by residual: bond pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 1.230 1.036 0.194 9.00e-03 1.23e+04 4.65e+02 bond pdb=" CA VAL A 71 " pdb=" C VAL A 71 " ideal model delta sigma weight residual 1.522 1.759 -0.237 1.19e-02 7.06e+03 3.95e+02 bond pdb=" N GLN B 94 " pdb=" H GLN B 94 " ideal model delta sigma weight residual 0.860 1.240 -0.380 2.00e-02 2.50e+03 3.61e+02 bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.455 1.586 -0.131 7.00e-03 2.04e+04 3.51e+02 bond pdb=" C VAL A 37 " pdb=" O VAL A 37 " ideal model delta sigma weight residual 1.236 1.427 -0.191 1.02e-02 9.61e+03 3.50e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 5584 4.13 - 8.27: 3622 8.27 - 12.40: 1306 12.40 - 16.53: 265 16.53 - 20.66: 33 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL A 102 " pdb=" C VAL A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.18 107.17 16.01 1.05e+00 9.07e-01 2.33e+02 angle pdb=" O GLY A 126 " pdb=" C GLY A 126 " pdb=" N PHE A 127 " ideal model delta sigma weight residual 123.92 109.91 14.01 9.60e-01 1.09e+00 2.13e+02 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 120.42 135.73 -15.31 1.06e+00 8.90e-01 2.09e+02 angle pdb=" O VAL A 150 " pdb=" C VAL A 150 " pdb=" N LYS A 151 " ideal model delta sigma weight residual 122.05 107.50 14.55 1.05e+00 9.07e-01 1.92e+02 angle pdb=" CA LEU A 24 " pdb=" C LEU A 24 " pdb=" O LEU A 24 " ideal model delta sigma weight residual 120.92 136.29 -15.37 1.12e+00 7.97e-01 1.88e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.61: 1856 17.61 - 35.21: 133 35.21 - 52.80: 48 52.80 - 70.40: 8 70.40 - 88.00: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA CYS B 47 " pdb=" C CYS B 47 " pdb=" N SER B 48 " pdb=" CA SER B 48 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 -22.87 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 260 0.287 - 0.573: 151 0.573 - 0.859: 71 0.859 - 1.145: 8 1.145 - 1.432: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 4.08 -1.43 2.00e-01 2.50e+01 5.12e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.24 -1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CA ASN B 123 " pdb=" N ASN B 123 " pdb=" C ASN B 123 " pdb=" CB ASN B 123 " both_signs ideal model delta sigma weight residual False 2.51 3.57 -1.06 2.00e-01 2.50e+01 2.81e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.078 2.00e-02 2.50e+03 7.43e-02 2.21e+02 pdb=" CG TRP B 139 " -0.128 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.096 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.071 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.027 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.078 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.086 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.100 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.107 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.034 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.087 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.194 2.00e-02 2.50e+03 8.17e-02 2.00e+02 pdb=" CG PHE B 164 " -0.150 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.114 2.00e-02 2.50e+03 6.21e-02 1.54e+02 pdb=" CG TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.053 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.060 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.065 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.104 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 26 1.60 - 2.35: 2317 2.35 - 3.10: 22169 3.10 - 3.85: 32979 3.85 - 4.60: 52699 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110190 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.854 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.989 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.999 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.056 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.226 2.620 ... (remaining 110185 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_4328694_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= 0.2035 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301161 | | target function (ml) not normalized (work): 805663.324584 | | target function (ml) not normalized (free): 16596.222283 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2145 0.1927 6.6851 6.3159| | 2: 2.94 - 2.33 1.00 7339 128 0.1612 0.1501 5.5334 5.568| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1499 5.1295 5.0849| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1551 4.9616 4.9761| | 5: 1.85 - 1.72 0.99 7113 159 0.1908 0.1727 4.8061 4.8502| | 6: 1.72 - 1.62 0.99 7102 142 0.1971 0.2034 4.6592 4.7786| | 7: 1.62 - 1.54 0.99 7104 148 0.2025 0.1823 4.5733 4.6081| | 8: 1.54 - 1.47 0.96 6798 152 0.2057 0.1940 4.4666 4.4182| | 9: 1.47 - 1.41 0.98 6938 155 0.2053 0.2205 4.3789 4.4568| | 10: 1.41 - 1.36 0.99 7022 150 0.2136 0.2103 4.304 4.3475| | 11: 1.36 - 1.32 0.99 6997 151 0.2096 0.2295 4.2406 4.3525| | 12: 1.32 - 1.28 0.98 6976 149 0.2075 0.2078 4.1743 4.2842| | 13: 1.28 - 1.25 0.98 6907 166 0.2048 0.2183 4.1353 4.2154| | 14: 1.25 - 1.22 0.98 7015 113 0.2072 0.2321 4.0771 4.2498| | 15: 1.22 - 1.19 0.98 6957 137 0.2100 0.1893 4.0419 3.9948| | 16: 1.19 - 1.17 0.93 6604 132 0.2141 0.2118 4.0151 4.0997| | 17: 1.17 - 1.14 0.98 6941 135 0.2191 0.2126 3.965 4.0272| | 18: 1.14 - 1.12 0.98 6875 142 0.2202 0.2255 3.9201 3.902| | 19: 1.12 - 1.10 0.97 6949 106 0.2314 0.2297 3.8827 3.9574| | 20: 1.10 - 1.08 0.97 6884 147 0.2345 0.2432 3.8324 3.9006| | 21: 1.08 - 1.07 0.97 6852 152 0.2427 0.2714 3.792 3.8572| | 22: 1.07 - 1.05 0.97 6838 135 0.2554 0.2526 3.7533 3.7357| | 23: 1.05 - 1.03 0.97 6829 159 0.2691 0.2758 3.7333 3.8433| | 24: 1.03 - 1.02 0.96 6785 133 0.2894 0.2740 3.7099 3.7344| | 25: 1.02 - 1.01 0.93 6552 130 0.3098 0.3003 3.6809 3.7589| | 26: 1.01 - 0.99 0.96 6767 158 0.3217 0.3677 3.6297 3.7004| | 27: 0.99 - 0.98 0.94 6648 131 0.3427 0.3214 3.6384 3.6246| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.54 0.91 0.97 35639.41| | 2: 2.94 - 2.33 7339 128 0.86 20.80 1.08 1.02 14774.70| | 3: 2.33 - 2.04 6939 150 0.94 11.68 1.11 1.06 3730.75| | 4: 2.04 - 1.85 7170 155 0.93 12.94 1.11 1.07 2591.29| | 5: 1.85 - 1.72 7113 159 0.91 15.72 1.11 1.06 2083.44| | 6: 1.72 - 1.62 7102 142 0.90 17.08 1.11 1.06 1675.16| | 7: 1.62 - 1.54 7104 148 0.89 17.59 1.10 1.06 1332.47| | 8: 1.54 - 1.47 6798 152 0.89 17.85 1.11 1.06 1087.64| | 9: 1.47 - 1.41 6938 155 0.88 18.74 1.10 1.06 963.80| | 10: 1.41 - 1.36 7022 150 0.87 20.50 1.10 1.05 882.00| | 11: 1.36 - 1.32 6997 151 0.86 21.00 1.08 1.05 810.08| | 12: 1.32 - 1.28 6976 149 0.86 20.98 1.08 1.03 713.24| | 13: 1.28 - 1.25 6907 166 0.86 20.85 1.07 1.03 648.81| | 14: 1.25 - 1.22 7015 113 0.86 21.27 1.07 1.03 599.74| | 15: 1.22 - 1.19 6957 137 0.86 21.22 1.08 1.04 556.46| | 16: 1.19 - 1.17 6604 132 0.87 20.63 1.07 1.03 493.99| | 17: 1.17 - 1.14 6941 135 0.87 20.79 1.08 1.02 434.35| | 18: 1.14 - 1.12 6875 142 0.86 21.14 1.08 1.00 397.38| | 19: 1.12 - 1.10 6949 106 0.85 22.46 1.07 1.00 388.15| | 20: 1.10 - 1.08 6884 147 0.84 23.61 1.06 0.98 372.86| | 21: 1.08 - 1.07 6852 152 0.83 24.79 1.06 0.98 361.16| | 22: 1.07 - 1.05 6838 135 0.81 26.18 1.05 0.97 343.03| | 23: 1.05 - 1.03 6829 159 0.80 27.89 1.04 0.97 343.46| | 24: 1.03 - 1.02 6785 133 0.77 30.46 1.04 0.97 349.40| | 25: 1.02 - 1.01 6552 130 0.75 32.26 1.03 0.93 340.46| | 26: 1.01 - 0.99 6767 158 0.73 33.92 1.03 0.90 317.41| | 27: 0.99 - 0.98 6648 131 0.74 33.04 1.04 0.89 281.10| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 281.10 max = 35639.41 mean = 2812.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.98| |phase err.(test): min = 0.00 max = 89.01 mean = 21.91| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.256 2950 Z= 5.452 Angle : 5.195 18.159 4018 Z= 3.662 Chirality : 0.394 1.432 492 Planarity : 0.032 0.103 512 Dihedral : 12.851 88.003 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.15 % Favored : 95.34 % Rotamer: Outliers : 0.97 % Allowed : 5.48 % Favored : 93.55 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.39), residues: 386 helix: -2.66 (0.31), residues: 144 sheet: -0.78 (0.52), residues: 86 loop : -0.54 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.018 ARG A 49 TYR 0.113 0.038 TYR A 67 PHE 0.176 0.036 PHE B 164 TRP 0.127 0.036 TRP B 139 HIS 0.064 0.025 HIS A 96 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= 0.2035 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301161 | | target function (ml) not normalized (work): 805663.324584 | | target function (ml) not normalized (free): 16596.222283 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2035 0.1964 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2035 0.1964 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2035 0.1964 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2035 0.2037 0.1965 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1900 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1801 0.1900 n_refl.: 191139 ======================== 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 0.4104 402.814 291.913 0.425 0.933 0.303 13.296-10.522 100.00 100 1 0.2545 534.497 520.886 0.769 0.934 0.256 10.503-8.327 98.90 177 3 0.2484 564.205 558.384 0.944 0.935 0.233 8.318-6.595 100.00 360 8 0.2493 414.736 403.773 0.950 0.934 0.180 6.588-5.215 100.00 711 7 0.2262 381.101 365.937 0.935 0.934 0.150 5.214-4.128 98.38 1367 28 0.1517 557.435 549.713 1.046 0.933 0.080 4.126-3.266 94.74 2603 46 0.1364 508.132 499.573 1.122 0.933 0.040 3.266-2.585 99.86 5447 97 0.1439 342.774 337.937 1.093 0.930 0.000 2.585-2.046 97.45 10613 204 0.1392 258.603 254.541 1.105 0.927 0.000 2.046-1.619 99.39 21536 464 0.1623 153.054 149.825 1.126 0.921 0.000 1.619-1.281 98.00 42464 925 0.1912 82.395 80.204 1.123 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.676 1.120 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0198 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1900 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 42 ASN Total number of N/Q/H flips: 2 r_work=0.1810 r_free=0.1905 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.130916 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.297713 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1274 0.1502 0.0228 0.039 1.2 11.0 0.0 0.3 0 11.065 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 15.02 2.28 1.118 13.123 567.298 0.018 12.90 15.53 2.64 1.174 13.271 567.298 0.017 Individual atomic B min max mean iso aniso Overall: 5.21 73.06 14.88 1.38 435 3274 Protein: 5.21 40.36 10.96 1.38 0 2902 Water: 6.35 73.06 28.99 N/A 435 370 Other: 16.07 29.67 22.87 N/A 0 2 Chain A: 5.28 60.32 12.96 N/A 0 1626 Chain B: 5.21 73.06 12.70 N/A 0 1648 Chain S: 12.14 60.57 30.33 N/A 435 0 Histogram: Values Number of atoms 5.21 - 11.99 2162 11.99 - 18.78 651 18.78 - 25.56 327 25.56 - 32.35 261 32.35 - 39.13 155 39.13 - 45.92 98 45.92 - 52.70 33 52.70 - 59.49 17 59.49 - 66.27 4 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1290 r_free=0.1553 r_work=0.1289 r_free=0.1550 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1289 r_free = 0.1550 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 = 0.1275 r_free = 0.1541 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1275 r_free= 0.1541 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015544 | | target function (ls_wunit_k1) not normalized (work): 2911.273030 | | target function (ls_wunit_k1) not normalized (free): 116.297928 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1280 0.1275 0.1541 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1463 0.1460 0.1622 n_refl.: 191139 remove outliers: r(all,work,free)=0.1463 0.1460 0.1622 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1485 0.1482 0.1631 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1274 0.1269 0.1537 n_refl.: 191139 remove outliers: r(all,work,free)=0.1274 0.1269 0.1536 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3635 402.814 368.254 0.475 0.963 0.281 13.296-10.522 100.00 100 1 0.2123 534.497 525.956 0.742 0.965 0.241 10.503-8.327 98.90 177 3 0.1725 564.205 565.621 0.891 0.965 0.196 8.318-6.595 100.00 360 8 0.1733 414.736 411.715 0.908 0.964 0.154 6.588-5.215 100.00 711 7 0.1549 381.101 374.050 0.889 0.965 0.140 5.214-4.128 98.38 1367 28 0.0910 557.435 554.494 0.974 0.965 0.049 4.126-3.266 94.74 2603 46 0.0834 508.132 504.156 1.044 0.966 0.030 3.266-2.585 99.86 5447 97 0.0926 342.774 340.561 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.348 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1079 153.054 151.436 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1264 82.395 81.395 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1865 44.202 42.232 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0354 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1269 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 r_work=0.1272 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1543 | n_water=805 | time (s): 2.970 (total time: 2.970) Filter (dist) r_work=0.1277 r_free=0.1550 | n_water=795 | time (s): 101.420 (total time: 104.390) Filter (q & B) r_work=0.1277 r_free=0.1550 | n_water=791 | time (s): 5.220 (total time: 109.610) Compute maps r_work=0.1277 r_free=0.1550 | n_water=791 | time (s): 1.740 (total time: 111.350) Filter (map) r_work=0.1302 r_free=0.1525 | n_water=655 | time (s): 4.430 (total time: 115.780) Find peaks r_work=0.1302 r_free=0.1525 | n_water=655 | time (s): 0.760 (total time: 116.540) Add new water r_work=0.1323 r_free=0.1554 | n_water=961 | time (s): 4.030 (total time: 120.570) Refine new water occ: r_work=0.1280 r_free=0.1512 adp: r_work=0.1268 r_free=0.1509 occ: r_work=0.1270 r_free=0.1505 adp: r_work=0.1264 r_free=0.1506 occ: r_work=0.1266 r_free=0.1503 adp: r_work=0.1263 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1505 r_work=0.1263 r_free=0.1505 | n_water=961 | time (s): 86.930 (total time: 207.500) Filter (q & B) r_work=0.1266 r_free=0.1508 | n_water=884 | time (s): 5.070 (total time: 212.570) Filter (dist only) r_work=0.1267 r_free=0.1507 | n_water=882 | time (s): 111.750 (total time: 324.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.402340 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.165203 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 0.1252 0.1526 0.0274 0.042 1.1 17.8 0.0 0.3 0 11.701 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.26 2.74 2.022 15.054 576.165 0.015 12.33 15.11 2.78 2.345 15.112 576.165 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.21 16.17 1.19 514 3272 Protein: 5.38 39.97 10.96 1.19 0 2902 Water: 6.57 68.21 33.28 N/A 514 368 Other: 16.42 32.04 24.23 N/A 0 2 Chain A: 5.52 56.48 12.94 N/A 0 1624 Chain B: 5.38 68.21 12.77 N/A 0 1648 Chain S: 13.53 62.78 37.29 N/A 514 0 Histogram: Values Number of atoms 5.38 - 11.67 2059 11.67 - 17.95 713 17.95 - 24.23 273 24.23 - 30.51 204 30.51 - 36.80 190 36.80 - 43.08 160 43.08 - 49.36 95 49.36 - 55.65 48 55.65 - 61.93 38 61.93 - 68.21 6 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1511 r_work=0.1234 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1511 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013569 | | target function (ls_wunit_k1) not normalized (work): 2541.468225 | | target function (ls_wunit_k1) not normalized (free): 100.754983 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1228 0.1511 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1596 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1596 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1433 0.1594 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1235 0.1519 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1235 0.1519 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3372 402.814 375.756 0.485 0.961 0.267 13.296-10.522 100.00 100 1 0.1903 534.497 528.915 0.771 0.962 0.250 10.503-8.327 98.90 177 3 0.1385 564.205 567.253 0.919 0.962 0.181 8.318-6.595 100.00 360 8 0.1567 414.736 413.643 0.935 0.962 0.143 6.588-5.215 100.00 711 7 0.1379 381.101 377.056 0.913 0.962 0.123 5.214-4.128 98.38 1367 28 0.0839 557.435 555.880 0.995 0.962 0.080 4.126-3.266 94.74 2603 46 0.0762 508.132 505.137 1.062 0.962 0.014 3.266-2.585 99.86 5447 97 0.0864 342.774 341.336 1.048 0.961 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.742 1.060 0.960 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.628 1.081 0.958 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.349 1.074 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.223 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1519 | n_water=882 | time (s): 3.050 (total time: 3.050) Filter (dist) r_work=0.1237 r_free=0.1520 | n_water=875 | time (s): 111.930 (total time: 114.980) Filter (q & B) r_work=0.1237 r_free=0.1521 | n_water=872 | time (s): 4.860 (total time: 119.840) Compute maps r_work=0.1237 r_free=0.1521 | n_water=872 | time (s): 1.970 (total time: 121.810) Filter (map) r_work=0.1271 r_free=0.1520 | n_water=708 | time (s): 4.930 (total time: 126.740) Find peaks r_work=0.1271 r_free=0.1520 | n_water=708 | time (s): 0.910 (total time: 127.650) Add new water r_work=0.1292 r_free=0.1557 | n_water=1031 | time (s): 4.630 (total time: 132.280) Refine new water occ: r_work=0.1241 r_free=0.1505 adp: r_work=0.1236 r_free=0.1501 occ: r_work=0.1232 r_free=0.1497 adp: r_work=0.1232 r_free=0.1497 occ: r_work=0.1232 r_free=0.1497 adp: r_work=0.1232 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1498 r_work=0.1232 r_free=0.1498 | n_water=1031 | time (s): 287.990 (total time: 420.270) Filter (q & B) r_work=0.1238 r_free=0.1507 | n_water=853 | time (s): 5.190 (total time: 425.460) Filter (dist only) r_work=0.1238 r_free=0.1506 | n_water=851 | time (s): 107.570 (total time: 533.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.652132 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.840012 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 0.1225 0.1434 0.0209 0.034 1.1 7.0 0.0 0.0 0 0.826 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.34 2.09 1.922 14.434 15.840 3.929 12.21 13.96 1.75 2.284 14.328 15.840 3.885 Individual atomic B min max mean iso aniso Overall: 5.56 67.54 15.00 1.03 484 3271 Protein: 5.56 35.51 10.68 1.03 0 2902 Water: 5.65 67.54 29.70 N/A 484 367 Other: 13.74 27.75 20.75 N/A 0 2 Chain A: 5.60 55.19 12.67 N/A 0 1624 Chain B: 5.56 67.54 12.44 N/A 0 1647 Chain S: 5.65 62.89 31.53 N/A 484 0 Histogram: Values Number of atoms 5.56 - 11.76 2132 11.76 - 17.95 701 17.95 - 24.15 299 24.15 - 30.35 238 30.35 - 36.55 159 36.55 - 42.75 125 42.75 - 48.94 64 48.94 - 55.14 21 55.14 - 61.34 13 61.34 - 67.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1397 r_work=0.1222 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1222 r_free = 0.1397 target_work(ml) = 3.886 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1389 target_work(ml) = 3.879 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1214 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.879218 | | target function (ml) not normalized (work): 726565.917091 | | target function (ml) not normalized (free): 15183.956135 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1214 0.1389 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1434 0.1478 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1434 0.1478 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1428 0.1427 0.1474 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1211 0.1383 n_refl.: 191138 remove outliers: r(all,work,free)=0.1214 0.1210 0.1383 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3908 398.008 361.095 0.428 0.946 0.255 13.296-10.522 99.01 99 1 0.2462 528.187 510.942 0.710 0.947 0.208 10.503-8.327 98.35 176 3 0.2031 556.299 558.305 0.885 0.947 0.183 8.318-6.595 100.00 360 8 0.2125 414.736 409.256 0.896 0.947 0.129 6.588-5.215 100.00 711 7 0.1876 381.101 370.445 0.886 0.947 0.107 5.214-4.128 98.38 1367 28 0.1160 557.435 552.078 0.973 0.947 0.080 4.126-3.266 94.74 2603 46 0.1098 508.132 500.820 1.033 0.947 0.005 3.266-2.585 99.86 5447 97 0.1080 342.774 339.101 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 255.716 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0944 153.054 151.477 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1025 82.395 81.509 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1675 44.202 42.322 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1046 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1210 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1210 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1210 r_free=0.1383 | n_water=851 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1210 r_free=0.1383 | n_water=851 | time (s): 100.690 (total time: 103.890) Filter (q & B) r_work=0.1211 r_free=0.1380 | n_water=840 | time (s): 5.720 (total time: 109.610) Compute maps r_work=0.1211 r_free=0.1380 | n_water=840 | time (s): 2.080 (total time: 111.690) Filter (map) r_work=0.1232 r_free=0.1366 | n_water=719 | time (s): 5.530 (total time: 117.220) Find peaks r_work=0.1232 r_free=0.1366 | n_water=719 | time (s): 0.900 (total time: 118.120) Add new water r_work=0.1247 r_free=0.1389 | n_water=972 | time (s): 4.360 (total time: 122.480) Refine new water occ: r_work=0.1207 r_free=0.1356 adp: r_work=0.1207 r_free=0.1356 occ: r_work=0.1204 r_free=0.1356 adp: r_work=0.1204 r_free=0.1355 occ: r_work=0.1201 r_free=0.1357 adp: r_work=0.1201 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1357 r_work=0.1201 r_free=0.1357 | n_water=972 | time (s): 256.490 (total time: 378.970) Filter (q & B) r_work=0.1205 r_free=0.1363 | n_water=886 | time (s): 4.680 (total time: 383.650) Filter (dist only) r_work=0.1205 r_free=0.1361 | n_water=885 | time (s): 119.640 (total time: 503.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.517119 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.969786 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 0.1364 0.0158 0.036 1.1 6.5 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.64 1.58 1.809 14.188 14.970 3.873 12.00 13.64 1.63 1.880 14.158 14.970 3.865 Individual atomic B min max mean iso aniso Overall: 5.53 67.11 15.02 0.98 518 3271 Protein: 5.53 32.76 10.63 0.98 0 2902 Water: 5.68 67.11 29.42 N/A 518 367 Other: 13.95 26.66 20.31 N/A 0 2 Chain A: 5.53 54.24 12.56 N/A 0 1624 Chain B: 5.54 67.11 12.37 N/A 0 1647 Chain S: 5.68 62.92 31.17 N/A 518 0 Histogram: Values Number of atoms 5.53 - 11.69 2114 11.69 - 17.85 738 17.85 - 24.00 302 24.00 - 30.16 233 30.16 - 36.32 167 36.32 - 42.48 131 42.48 - 48.63 72 48.63 - 54.79 21 54.79 - 60.95 8 60.95 - 67.11 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1364 r_work=0.1200 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1364 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1365 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863731 | | target function (ml) not normalized (work): 723653.604470 | | target function (ml) not normalized (free): 15142.530441 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1479 n_refl.: 191135 remove outliers: r(all,work,free)=0.1425 0.1424 0.1479 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1416 0.1475 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191135 remove outliers: r(all,work,free)=0.1200 0.1196 0.1363 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3783 361.355 318.188 0.402 0.948 0.239 13.296-10.522 98.02 98 1 0.2414 479.125 456.552 0.695 0.950 0.196 10.503-8.327 97.80 175 3 0.2050 502.122 499.622 0.865 0.950 0.173 8.318-6.595 100.00 360 8 0.2187 375.705 370.868 0.884 0.950 0.100 6.588-5.215 100.00 711 7 0.1922 345.235 335.044 0.881 0.950 0.085 5.214-4.128 98.38 1367 28 0.1201 504.974 499.886 0.972 0.950 0.080 4.126-3.266 94.74 2603 46 0.1126 460.312 453.635 1.032 0.950 0.005 3.266-2.585 99.86 5447 97 0.1089 310.515 307.343 1.019 0.949 0.000 2.585-2.046 97.45 10613 204 0.0941 234.266 231.824 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0912 138.650 137.349 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0984 74.641 73.923 1.055 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.042 38.373 1.044 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1363 | n_water=885 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1197 r_free=0.1364 | n_water=884 | time (s): 111.790 (total time: 114.780) Filter (q & B) r_work=0.1197 r_free=0.1364 | n_water=871 | time (s): 5.210 (total time: 119.990) Compute maps r_work=0.1197 r_free=0.1364 | n_water=871 | time (s): 2.130 (total time: 122.120) Filter (map) r_work=0.1222 r_free=0.1353 | n_water=738 | time (s): 4.930 (total time: 127.050) Find peaks r_work=0.1222 r_free=0.1353 | n_water=738 | time (s): 0.690 (total time: 127.740) Add new water r_work=0.1234 r_free=0.1378 | n_water=969 | time (s): 4.980 (total time: 132.720) Refine new water occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1354 occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1194 r_free=0.1355 occ: r_work=0.1193 r_free=0.1358 adp: r_work=0.1192 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1357 r_work=0.1192 r_free=0.1357 | n_water=969 | time (s): 198.320 (total time: 331.040) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=889 | time (s): 5.760 (total time: 336.800) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=888 | time (s): 111.600 (total time: 448.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558781 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.662134 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 0.1365 0.0166 0.036 1.1 6.8 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.65 1.66 1.777 14.082 14.662 3.764 12.03 13.68 1.65 1.855 14.047 14.662 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 66.66 14.89 0.93 524 3268 Protein: 5.57 31.11 10.55 0.93 0 2902 Water: 5.77 66.66 29.05 N/A 524 364 Other: 13.81 25.52 19.67 N/A 0 2 Chain A: 5.58 53.22 12.44 N/A 0 1623 Chain B: 5.57 66.66 12.24 N/A 0 1645 Chain S: 5.77 62.96 30.79 N/A 524 0 Histogram: Values Number of atoms 5.57 - 11.68 2134 11.68 - 17.79 737 17.79 - 23.90 300 23.90 - 30.01 223 30.01 - 36.12 171 36.12 - 42.22 128 42.22 - 48.33 69 48.33 - 54.44 20 54.44 - 60.55 7 60.55 - 66.66 3 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1368 r_work=0.1204 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1371 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761654 | | target function (ml) not normalized (work): 704523.987521 | | target function (ml) not normalized (free): 14756.383563 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1201 0.1372 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1486 n_refl.: 191132 remove outliers: r(all,work,free)=0.1409 0.1408 0.1486 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1480 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 remove outliers: r(all,work,free)=0.1203 0.1200 0.1368 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3725 361.051 311.448 0.395 0.951 0.224 13.296-10.522 97.03 97 1 0.2348 481.399 459.201 0.696 0.953 0.186 10.503-8.327 97.80 175 3 0.2106 502.122 498.735 0.856 0.953 0.163 8.318-6.595 100.00 360 8 0.2176 375.705 371.170 0.883 0.952 0.106 6.588-5.215 100.00 711 7 0.1930 345.235 335.242 0.881 0.953 0.083 5.214-4.128 98.38 1367 28 0.1206 504.974 499.913 0.969 0.953 0.039 4.126-3.266 94.74 2603 46 0.1149 460.312 453.452 1.031 0.953 0.005 3.266-2.585 99.86 5447 97 0.1116 310.515 307.264 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0957 234.266 231.775 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.650 137.361 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0974 74.641 73.945 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.042 38.373 1.040 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1356 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1368 | n_water=888 | time (s): 3.000 (total time: 3.000) Filter (dist) r_work=0.1200 r_free=0.1367 | n_water=887 | time (s): 111.850 (total time: 114.850) Filter (q & B) r_work=0.1201 r_free=0.1365 | n_water=875 | time (s): 4.640 (total time: 119.490) Compute maps r_work=0.1201 r_free=0.1365 | n_water=875 | time (s): 2.350 (total time: 121.840) Filter (map) r_work=0.1224 r_free=0.1362 | n_water=756 | time (s): 5.790 (total time: 127.630) Find peaks r_work=0.1224 r_free=0.1362 | n_water=756 | time (s): 0.830 (total time: 128.460) Add new water r_work=0.1234 r_free=0.1368 | n_water=977 | time (s): 4.350 (total time: 132.810) Refine new water occ: r_work=0.1199 r_free=0.1347 adp: r_work=0.1199 r_free=0.1347 occ: r_work=0.1197 r_free=0.1348 adp: r_work=0.1196 r_free=0.1348 occ: r_work=0.1195 r_free=0.1350 adp: r_work=0.1195 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 | n_water=977 | time (s): 302.550 (total time: 435.360) Filter (q & B) r_work=0.1199 r_free=0.1358 | n_water=899 | time (s): 4.480 (total time: 439.840) Filter (dist only) r_work=0.1199 r_free=0.1358 | n_water=898 | time (s): 108.590 (total time: 548.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573972 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.532775 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 0.1202 0.1360 0.0158 0.037 1.1 6.0 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.60 1.58 1.743 13.983 13.533 3.761 12.05 13.65 1.59 1.867 13.943 13.533 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 65.52 14.80 0.88 534 3268 Protein: 5.58 28.66 10.45 0.88 0 2902 Water: 5.83 65.52 28.85 N/A 534 364 Other: 13.86 23.06 18.46 N/A 0 2 Chain A: 5.63 51.72 12.30 N/A 0 1623 Chain B: 5.58 65.52 12.11 N/A 0 1645 Chain S: 5.83 63.15 30.66 N/A 534 0 Histogram: Values Number of atoms 5.58 - 11.57 2109 11.57 - 17.57 780 17.57 - 23.56 278 23.56 - 29.56 216 29.56 - 35.55 187 35.55 - 41.54 122 41.54 - 47.54 75 47.54 - 53.53 24 53.53 - 59.53 8 59.53 - 65.52 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1365 r_work=0.1206 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1365 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1367 target_work(ml) = 3.760 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759893 | | target function (ml) not normalized (work): 704186.518421 | | target function (ml) not normalized (free): 14742.214542 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1367 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1487 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1400 0.1487 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1364 0.1363 0.1463 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191130 remove outliers: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3691 361.051 330.723 0.426 0.952 0.217 13.296-10.522 97.03 97 1 0.2318 481.399 464.046 0.711 0.954 0.160 10.503-8.327 97.80 175 3 0.2153 502.122 497.505 0.876 0.954 0.133 8.318-6.595 100.00 360 8 0.2186 375.705 371.371 0.902 0.954 0.094 6.588-5.215 100.00 711 7 0.1945 345.235 335.791 0.901 0.954 0.073 5.214-4.128 98.38 1367 28 0.1232 504.974 499.618 0.992 0.954 0.039 4.126-3.266 94.74 2603 46 0.1160 460.312 453.262 1.055 0.955 0.005 3.266-2.585 99.86 5447 97 0.1122 310.515 307.116 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0962 234.266 231.710 1.046 0.954 0.000 2.046-1.619 99.39 21536 464 0.0916 138.650 137.348 1.063 0.953 0.000 1.619-1.281 98.00 42464 925 0.0969 74.641 73.942 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.042 38.376 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0521 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1366 | n_water=898 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1203 r_free=0.1366 | n_water=898 | time (s): 112.620 (total time: 115.820) Filter (q & B) r_work=0.1204 r_free=0.1366 | n_water=889 | time (s): 5.500 (total time: 121.320) Compute maps r_work=0.1204 r_free=0.1366 | n_water=889 | time (s): 1.910 (total time: 123.230) Filter (map) r_work=0.1226 r_free=0.1374 | n_water=770 | time (s): 5.230 (total time: 128.460) Find peaks r_work=0.1226 r_free=0.1374 | n_water=770 | time (s): 0.700 (total time: 129.160) Add new water r_work=0.1235 r_free=0.1384 | n_water=989 | time (s): 5.070 (total time: 134.230) Refine new water occ: r_work=0.1202 r_free=0.1356 adp: r_work=0.1202 r_free=0.1356 occ: r_work=0.1200 r_free=0.1356 adp: r_work=0.1200 r_free=0.1357 occ: r_work=0.1198 r_free=0.1357 adp: r_work=0.1198 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1357 r_work=0.1198 r_free=0.1357 | n_water=989 | time (s): 224.340 (total time: 358.570) Filter (q & B) r_work=0.1202 r_free=0.1369 | n_water=903 | time (s): 4.130 (total time: 362.700) Filter (dist only) r_work=0.1203 r_free=0.1368 | n_water=902 | time (s): 114.170 (total time: 476.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.545981 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.938527 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 0.1375 0.0169 0.037 1.1 6.8 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.75 1.69 1.702 13.660 14.939 3.762 12.03 13.74 1.71 1.718 13.655 14.939 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.28 14.56 0.89 538 3268 Protein: 5.39 28.49 10.22 0.89 0 2902 Water: 5.71 64.28 28.50 N/A 538 364 Other: 13.65 22.10 17.88 N/A 0 2 Chain A: 5.43 51.00 12.03 N/A 0 1623 Chain B: 5.39 64.28 11.87 N/A 0 1645 Chain S: 5.71 63.11 30.40 N/A 538 0 Histogram: Values Number of atoms 5.39 - 11.28 2078 11.28 - 17.16 809 17.16 - 23.05 275 23.05 - 28.94 218 28.94 - 34.83 186 34.83 - 40.72 122 40.72 - 46.61 75 46.61 - 52.50 32 52.50 - 58.39 6 58.39 - 64.28 5 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1374 r_work=0.1203 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1375 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1374 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756374 | | target function (ml) not normalized (work): 703527.604131 | | target function (ml) not normalized (free): 14737.632666 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1374 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1483 n_refl.: 191130 remove outliers: r(all,work,free)=0.1371 0.1369 0.1483 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1371 0.1369 0.1483 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1192 0.1365 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3652 361.051 330.304 0.415 0.974 0.223 13.296-10.522 97.03 97 1 0.2351 481.399 463.185 0.685 0.976 0.153 10.503-8.327 97.80 175 3 0.2191 502.122 495.231 0.845 0.976 0.123 8.318-6.595 100.00 360 8 0.2216 375.705 370.372 0.872 0.976 0.096 6.588-5.215 100.00 711 7 0.1964 345.235 335.190 0.873 0.976 0.077 5.214-4.128 98.38 1367 28 0.1242 504.974 499.052 0.962 0.977 0.034 4.126-3.266 94.74 2603 46 0.1166 460.312 452.609 1.023 0.978 0.005 3.266-2.585 99.86 5447 97 0.1124 310.515 306.876 1.006 0.979 0.000 2.585-2.046 97.45 10613 204 0.0964 234.266 231.603 1.012 0.980 0.000 2.046-1.619 99.39 21536 464 0.0907 138.650 137.268 1.025 0.983 0.000 1.619-1.281 98.00 42464 925 0.0943 74.641 73.991 1.011 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.042 38.356 0.972 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1228 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1365 | n_water=902 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1192 r_free=0.1365 | n_water=902 | time (s): 114.810 (total time: 117.570) Filter (q & B) r_work=0.1193 r_free=0.1363 | n_water=894 | time (s): 4.460 (total time: 122.030) Compute maps r_work=0.1193 r_free=0.1363 | n_water=894 | time (s): 2.530 (total time: 124.560) Filter (map) r_work=0.1215 r_free=0.1372 | n_water=778 | time (s): 5.180 (total time: 129.740) Find peaks r_work=0.1215 r_free=0.1372 | n_water=778 | time (s): 0.820 (total time: 130.560) Add new water r_work=0.1223 r_free=0.1383 | n_water=990 | time (s): 5.040 (total time: 135.600) Refine new water occ: r_work=0.1189 r_free=0.1351 adp: r_work=0.1189 r_free=0.1351 occ: r_work=0.1188 r_free=0.1351 adp: r_work=0.1188 r_free=0.1351 occ: r_work=0.1186 r_free=0.1351 adp: r_work=0.1186 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1351 r_work=0.1186 r_free=0.1351 | n_water=990 | time (s): 201.470 (total time: 337.070) Filter (q & B) r_work=0.1190 r_free=0.1363 | n_water=906 | time (s): 5.090 (total time: 342.160) Filter (dist only) r_work=0.1191 r_free=0.1362 | n_water=905 | time (s): 119.660 (total time: 461.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.611219 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.130109 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1366 0.0173 0.037 1.1 7.5 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.66 1.73 1.673 13.631 14.130 3.755 11.95 13.69 1.74 1.673 13.631 14.130 3.755 Individual atomic B min max mean iso aniso Overall: 5.40 64.05 14.54 0.87 541 3268 Protein: 5.40 28.27 10.24 0.87 0 2902 Water: 5.83 64.05 28.33 N/A 541 364 Other: 13.66 22.09 17.87 N/A 0 2 Chain A: 5.46 50.88 12.03 N/A 0 1623 Chain B: 5.40 64.05 11.87 N/A 0 1645 Chain S: 5.83 63.15 30.22 N/A 541 0 Histogram: Values Number of atoms 5.40 - 11.26 2076 11.26 - 17.13 812 17.13 - 22.99 282 22.99 - 28.86 219 28.86 - 34.72 184 34.72 - 40.59 115 40.59 - 46.45 76 46.45 - 52.32 34 52.32 - 58.18 6 58.18 - 64.05 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1369 r_work=0.1195 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1369 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1370 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754388 | | target function (ml) not normalized (work): 703155.636704 | | target function (ml) not normalized (free): 14729.023525 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1370 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1379 0.1377 0.1495 n_refl.: 191130 remove outliers: r(all,work,free)=0.1379 0.1377 0.1495 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1379 0.1377 0.1495 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1369 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1193 0.1369 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3663 361.051 329.209 0.401 0.995 0.217 13.296-10.522 97.03 97 1 0.2354 481.399 463.831 0.669 0.997 0.150 10.503-8.327 97.80 175 3 0.2196 502.122 495.391 0.826 0.997 0.120 8.318-6.595 100.00 360 8 0.2214 375.705 370.157 0.853 0.997 0.096 6.588-5.215 100.00 711 7 0.1975 345.235 334.823 0.853 0.997 0.080 5.214-4.128 98.38 1367 28 0.1251 504.974 499.031 0.943 0.998 0.044 4.126-3.266 94.74 2603 46 0.1168 460.312 452.748 1.002 0.999 0.005 3.266-2.585 99.86 5447 97 0.1128 310.515 306.854 0.985 1.000 0.000 2.585-2.046 97.45 10613 204 0.0966 234.266 231.605 0.991 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.650 137.282 1.005 1.006 0.000 1.619-1.281 98.00 42464 925 0.0941 74.641 73.994 0.992 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.042 38.341 0.956 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0859 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1369 | n_water=905 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1193 r_free=0.1369 | n_water=905 | time (s): 113.580 (total time: 116.150) Filter (q & B) r_work=0.1194 r_free=0.1368 | n_water=894 | time (s): 4.970 (total time: 121.120) Compute maps r_work=0.1194 r_free=0.1368 | n_water=894 | time (s): 1.990 (total time: 123.110) Filter (map) r_work=0.1215 r_free=0.1370 | n_water=782 | time (s): 4.290 (total time: 127.400) Find peaks r_work=0.1215 r_free=0.1370 | n_water=782 | time (s): 0.630 (total time: 128.030) Add new water r_work=0.1223 r_free=0.1380 | n_water=997 | time (s): 4.710 (total time: 132.740) Refine new water occ: r_work=0.1191 r_free=0.1354 adp: r_work=0.1191 r_free=0.1354 occ: r_work=0.1189 r_free=0.1356 adp: r_work=0.1189 r_free=0.1356 occ: r_work=0.1188 r_free=0.1357 adp: r_work=0.1188 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1356 r_work=0.1188 r_free=0.1356 | n_water=997 | time (s): 217.170 (total time: 349.910) Filter (q & B) r_work=0.1192 r_free=0.1371 | n_water=908 | time (s): 5.440 (total time: 355.350) Filter (dist only) r_work=0.1192 r_free=0.1370 | n_water=907 | time (s): 122.270 (total time: 477.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594828 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.261249 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1374 0.0178 0.037 1.1 6.8 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.74 1.78 1.669 13.642 14.261 3.756 11.96 13.77 1.81 1.679 13.638 14.261 3.755 Individual atomic B min max mean iso aniso Overall: 5.45 63.28 14.54 0.86 543 3268 Protein: 5.45 27.92 10.25 0.86 0 2902 Water: 5.88 63.28 28.28 N/A 543 364 Other: 13.70 22.04 17.87 N/A 0 2 Chain A: 5.53 50.44 12.01 N/A 0 1623 Chain B: 5.45 63.20 11.86 N/A 0 1645 Chain S: 5.88 63.28 30.25 N/A 543 0 Histogram: Values Number of atoms 5.45 - 11.23 2060 11.23 - 17.01 827 17.01 - 22.80 275 22.80 - 28.58 220 28.58 - 34.36 185 34.36 - 40.14 118 40.14 - 45.93 80 45.93 - 51.71 35 51.71 - 57.49 5 57.49 - 63.28 6 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1378 r_work=0.1197 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1378 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1380 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754739 | | target function (ml) not normalized (work): 703221.324667 | | target function (ml) not normalized (free): 14738.012435 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1380 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1389 0.1386 0.1511 n_refl.: 191130 remove outliers: r(all,work,free)=0.1389 0.1386 0.1511 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1389 0.1386 0.1511 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1379 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1195 0.1379 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3694 361.051 327.947 0.395 0.974 0.203 13.296-10.522 97.03 97 1 0.2382 481.399 463.745 0.675 0.976 0.144 10.503-8.327 97.80 175 3 0.2212 502.122 495.736 0.837 0.977 0.117 8.318-6.595 100.00 360 8 0.2214 375.705 370.153 0.864 0.976 0.095 6.588-5.215 100.00 711 7 0.1987 345.235 334.682 0.864 0.977 0.080 5.214-4.128 98.38 1367 28 0.1262 504.974 498.898 0.958 0.978 0.080 4.126-3.266 94.74 2603 46 0.1178 460.312 452.624 1.017 0.979 0.000 3.266-2.585 99.86 5447 97 0.1134 310.515 306.800 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0969 234.266 231.602 1.006 0.982 0.000 2.046-1.619 99.39 21536 464 0.0909 138.650 137.286 1.021 0.986 0.000 1.619-1.281 98.00 42464 925 0.0940 74.641 73.994 1.008 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.042 38.335 0.974 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1379 After: r_work=0.1196 r_free=0.1379 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1379 | n_water=907 | time (s): 3.210 (total time: 3.210) Filter (dist) r_work=0.1196 r_free=0.1379 | n_water=907 | time (s): 113.190 (total time: 116.400) Filter (q & B) r_work=0.1197 r_free=0.1377 | n_water=898 | time (s): 4.820 (total time: 121.220) Compute maps r_work=0.1197 r_free=0.1377 | n_water=898 | time (s): 1.930 (total time: 123.150) Filter (map) r_work=0.1217 r_free=0.1381 | n_water=782 | time (s): 4.550 (total time: 127.700) Find peaks r_work=0.1217 r_free=0.1381 | n_water=782 | time (s): 0.870 (total time: 128.570) Add new water r_work=0.1226 r_free=0.1396 | n_water=991 | time (s): 4.620 (total time: 133.190) Refine new water occ: r_work=0.1194 r_free=0.1364 adp: r_work=0.1194 r_free=0.1365 occ: r_work=0.1192 r_free=0.1363 adp: r_work=0.1193 r_free=0.1364 occ: r_work=0.1191 r_free=0.1362 adp: r_work=0.1191 r_free=0.1363 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1363 r_work=0.1191 r_free=0.1363 | n_water=991 | time (s): 270.080 (total time: 403.270) Filter (q & B) r_work=0.1195 r_free=0.1374 | n_water=908 | time (s): 5.620 (total time: 408.890) Filter (dist only) r_work=0.1195 r_free=0.1375 | n_water=906 | time (s): 122.740 (total time: 531.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557384 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.453562 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 0.1203 0.1383 0.0180 0.038 1.2 8.4 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.83 1.80 1.665 13.625 13.454 3.761 12.05 13.88 1.83 1.660 13.627 13.454 3.762 Individual atomic B min max mean iso aniso Overall: 5.46 63.29 14.52 0.85 542 3268 Protein: 5.46 27.83 10.27 0.85 0 2902 Water: 5.96 63.29 28.13 N/A 542 364 Other: 13.72 22.05 17.88 N/A 0 2 Chain A: 5.57 50.34 12.01 N/A 0 1623 Chain B: 5.46 62.97 11.86 N/A 0 1645 Chain S: 5.96 63.29 30.09 N/A 542 0 Histogram: Values Number of atoms 5.46 - 11.25 2059 11.25 - 17.03 838 17.03 - 22.81 274 22.81 - 28.60 218 28.60 - 34.38 184 34.38 - 40.16 116 40.16 - 45.95 76 45.95 - 51.73 34 51.73 - 57.51 5 57.51 - 63.29 6 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1388 r_work=0.1205 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1388 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1388 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.761546 | | target function (ml) not normalized (work): 704496.097370 | | target function (ml) not normalized (free): 14756.432866 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1381 0.1580 5.7103 5.828| | 2: 2.94 - 2.33 1.00 7339 128 0.1088 0.1367 5.1093 5.1895| | 3: 2.33 - 2.04 0.96 6939 150 0.0917 0.1232 4.6697 4.7684| | 4: 2.04 - 1.85 1.00 7170 155 0.0908 0.1048 4.4052 4.5644| | 5: 1.85 - 1.72 0.99 7113 159 0.0944 0.1032 4.1659 4.2614| | 6: 1.72 - 1.62 0.99 7102 142 0.0905 0.1120 3.9568 4.0953| | 7: 1.62 - 1.54 0.99 7104 148 0.0901 0.0963 3.8091 3.9282| | 8: 1.54 - 1.47 0.96 6798 152 0.0900 0.1328 3.7094 3.9108| | 9: 1.47 - 1.41 0.98 6938 155 0.0931 0.1165 3.629 3.7721| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1183 3.5628 3.6749| | 11: 1.36 - 1.32 0.99 6997 151 0.0998 0.1130 3.4893 3.5869| | 12: 1.32 - 1.28 0.98 6975 149 0.1041 0.1130 3.4648 3.5893| | 13: 1.28 - 1.25 0.98 6907 166 0.1055 0.1277 3.4469 3.5856| | 14: 1.25 - 1.22 0.98 7015 112 0.1115 0.1589 3.4402 3.6811| | 15: 1.22 - 1.19 0.98 6956 137 0.1176 0.1257 3.453 3.4936| | 16: 1.19 - 1.17 0.93 6604 132 0.1256 0.1531 3.4673 3.6459| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1219 3.4352 3.4436| | 18: 1.14 - 1.12 0.98 6875 142 0.1390 0.1714 3.4417 3.538| | 19: 1.12 - 1.10 0.97 6948 106 0.1475 0.1783 3.423 3.5971| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1588 3.4125 3.4405| | 21: 1.08 - 1.07 0.97 6852 152 0.1733 0.2139 3.42 3.5055| | 22: 1.07 - 1.05 0.97 6836 135 0.1909 0.1938 3.4151 3.415| | 23: 1.05 - 1.03 0.97 6827 159 0.2124 0.2021 3.4349 3.4888| | 24: 1.03 - 1.02 0.96 6784 133 0.2337 0.2275 3.4377 3.5155| | 25: 1.02 - 1.01 0.93 6552 130 0.2620 0.2515 3.4506 3.5239| | 26: 1.01 - 0.99 0.96 6767 158 0.2761 0.2867 3.4166 3.4235| | 27: 0.99 - 0.98 0.94 6647 131 0.3047 0.2805 3.4699 3.398| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.92 12.58 1.00 0.97 12577.65| | 2: 2.94 - 2.33 7339 128 0.92 13.52 0.99 0.97 5625.39| | 3: 2.33 - 2.04 6939 150 0.96 7.82 1.01 0.97 1747.55| | 4: 2.04 - 1.85 7170 155 0.96 7.81 1.00 0.97 1034.19| | 5: 1.85 - 1.72 7113 159 0.96 8.26 1.00 0.98 654.52| | 6: 1.72 - 1.62 7102 142 0.96 8.18 1.00 0.98 454.85| | 7: 1.62 - 1.54 7104 148 0.96 8.21 1.01 0.99 342.67| | 8: 1.54 - 1.47 6798 152 0.96 8.37 1.01 0.99 284.00| | 9: 1.47 - 1.41 6938 155 0.96 8.56 1.00 1.00 234.65| | 10: 1.41 - 1.36 7022 150 0.96 9.00 1.00 0.99 205.23| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.98 176.33| | 12: 1.32 - 1.28 6975 149 0.96 9.08 0.98 0.97 163.02| | 13: 1.28 - 1.25 6907 166 0.95 9.70 1.01 0.98 161.58| | 14: 1.25 - 1.22 7015 112 0.95 10.87 1.01 0.99 166.35| | 15: 1.22 - 1.19 6956 137 0.95 11.32 1.01 1.00 168.39| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.01 0.98 160.64| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.98 154.15| | 18: 1.14 - 1.12 6875 142 0.94 12.81 1.01 0.97 148.63| | 19: 1.12 - 1.10 6948 106 0.93 14.24 1.00 0.97 152.53| | 20: 1.10 - 1.08 6884 147 0.92 15.32 1.00 0.96 151.70| | 21: 1.08 - 1.07 6852 152 0.91 16.70 1.00 0.95 154.28| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.95 155.73| | 23: 1.05 - 1.03 6827 159 0.87 20.56 0.99 0.94 165.71| | 24: 1.03 - 1.02 6784 133 0.85 23.24 0.99 0.95 180.25| | 25: 1.02 - 1.01 6552 130 0.83 25.22 0.97 0.92 183.18| | 26: 1.01 - 0.99 6767 158 0.81 26.71 0.98 0.90 177.57| | 27: 0.99 - 0.98 6647 131 0.82 26.39 0.98 0.89 162.02| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 148.63 max = 12577.65 mean = 1005.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.44| |phase err.(test): min = 0.00 max = 89.67 mean = 13.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1204 0.1388 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1528 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1402 0.1528 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1404 0.1402 0.1528 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1203 0.1386 n_refl.: 191130 remove outliers: r(all,work,free)=0.1207 0.1203 0.1386 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3670 361.051 328.566 0.404 0.973 0.215 13.296-10.522 97.03 97 1 0.2410 481.399 463.229 0.674 0.974 0.147 10.503-8.327 97.80 175 3 0.2200 502.122 495.645 0.837 0.975 0.117 8.318-6.595 100.00 360 8 0.2192 375.705 370.555 0.865 0.975 0.095 6.588-5.215 100.00 711 7 0.1981 345.235 334.394 0.866 0.975 0.087 5.214-4.128 98.38 1367 28 0.1262 504.974 498.867 0.959 0.976 0.052 4.126-3.266 94.74 2603 46 0.1184 460.312 452.590 1.020 0.978 0.000 3.266-2.585 99.86 5447 97 0.1140 310.515 306.947 1.002 0.979 0.000 2.585-2.046 97.45 10613 204 0.0978 234.266 231.610 1.008 0.982 0.000 2.046-1.619 99.39 21536 464 0.0920 138.650 137.271 1.023 0.986 0.000 1.619-1.281 98.00 42464 925 0.0953 74.641 73.984 1.012 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.042 38.321 0.979 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0150 ================= 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 : 0.2035 0.1964 0.082 5.195 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1900 0.082 5.195 5.2 78.1 14.6 805 0.000 1_settarget: 0.1801 0.1900 0.082 5.195 5.2 78.1 14.6 805 0.000 1_nqh: 0.1810 0.1905 0.082 5.195 5.2 78.1 14.6 805 0.003 1_weight: 0.1810 0.1905 0.082 5.195 5.2 78.1 14.6 805 0.003 1_xyzrec: 0.1274 0.1502 0.039 1.158 5.2 78.1 14.6 805 0.159 1_adp: 0.1290 0.1553 0.039 1.158 5.2 73.1 14.9 805 0.159 1_regHadp: 0.1289 0.1550 0.039 1.158 5.2 73.1 14.9 805 0.159 1_occ: 0.1275 0.1541 0.039 1.158 5.2 73.1 14.9 805 0.159 2_bss: 0.1269 0.1536 0.039 1.158 5.4 73.2 15.0 805 0.159 2_settarget: 0.1269 0.1536 0.039 1.158 5.4 73.2 15.0 805 0.159 2_updatecdl: 0.1269 0.1536 0.039 1.164 5.4 73.2 15.0 805 0.159 2_nqh: 0.1272 0.1543 0.039 1.164 5.4 73.2 15.0 805 0.157 2_sol: 0.1267 0.1507 0.039 1.164 5.4 73.2 16.1 882 n/a 2_weight: 0.1267 0.1507 0.039 1.164 5.4 73.2 16.1 882 n/a 2_xyzrec: 0.1252 0.1526 0.042 1.136 5.4 73.2 16.1 882 n/a 2_adp: 0.1233 0.1511 0.042 1.136 5.4 68.2 16.2 882 n/a 2_regHadp: 0.1234 0.1512 0.042 1.136 5.4 68.2 16.2 882 n/a 2_occ: 0.1228 0.1511 0.042 1.136 5.4 68.2 16.2 882 n/a 3_bss: 0.1235 0.1519 0.042 1.136 5.4 68.2 16.1 882 n/a 3_settarget: 0.1235 0.1519 0.042 1.136 5.4 68.2 16.1 882 n/a 3_updatecdl: 0.1235 0.1519 0.042 1.143 5.4 68.2 16.1 882 n/a 3_nqh: 0.1235 0.1519 0.042 1.143 5.4 68.2 16.1 882 n/a 3_sol: 0.1238 0.1506 0.042 1.143 5.4 68.2 15.2 851 n/a 3_weight: 0.1238 0.1506 0.042 1.143 5.4 68.2 15.2 851 n/a 3_xyzrec: 0.1225 0.1434 0.034 1.100 5.4 68.2 15.2 851 n/a 3_adp: 0.1221 0.1397 0.034 1.100 5.6 67.5 15.0 851 n/a 3_regHadp: 0.1222 0.1397 0.034 1.100 5.6 67.5 15.0 851 n/a 3_occ: 0.1214 0.1389 0.034 1.100 5.6 67.5 15.0 851 n/a 4_bss: 0.1210 0.1383 0.034 1.100 5.5 67.5 15.0 851 n/a 4_settarget: 0.1210 0.1383 0.034 1.100 5.5 67.5 15.0 851 n/a 4_updatecdl: 0.1210 0.1383 0.034 1.101 5.5 67.5 15.0 851 n/a 4_nqh: 0.1210 0.1383 0.034 1.101 5.5 67.5 15.0 851 n/a 4_sol: 0.1205 0.1361 0.034 1.101 5.5 67.5 15.1 885 n/a 4_weight: 0.1205 0.1361 0.034 1.101 5.5 67.5 15.1 885 n/a 4_xyzrec: 0.1206 0.1364 0.036 1.113 5.5 67.5 15.1 885 n/a 4_adp: 0.1200 0.1364 0.036 1.113 5.5 67.1 15.0 885 n/a 4_regHadp: 0.1200 0.1364 0.036 1.113 5.5 67.1 15.0 885 n/a 4_occ: 0.1199 0.1365 0.036 1.113 5.5 67.1 15.0 885 n/a 5_bss: 0.1196 0.1363 0.036 1.113 5.5 67.1 15.0 885 n/a 5_settarget: 0.1196 0.1363 0.036 1.113 5.5 67.1 15.0 885 n/a 5_updatecdl: 0.1196 0.1363 0.036 1.113 5.5 67.1 15.0 885 n/a 5_nqh: 0.1196 0.1363 0.036 1.113 5.5 67.1 15.0 885 n/a 5_sol: 0.1196 0.1356 0.036 1.113 5.5 67.1 14.9 888 n/a 5_weight: 0.1196 0.1356 0.036 1.113 5.5 67.1 14.9 888 n/a 5_xyzrec: 0.1199 0.1365 0.036 1.124 5.5 67.1 14.9 888 n/a 5_adp: 0.1203 0.1368 0.036 1.124 5.6 66.7 14.9 888 n/a 5_regHadp: 0.1204 0.1368 0.036 1.124 5.6 66.7 14.9 888 n/a 5_occ: 0.1201 0.1371 0.036 1.124 5.6 66.7 14.9 888 n/a 6_bss: 0.1200 0.1368 0.036 1.124 5.5 66.6 14.8 888 n/a 6_settarget: 0.1200 0.1368 0.036 1.124 5.5 66.6 14.8 888 n/a 6_updatecdl: 0.1200 0.1368 0.036 1.124 5.5 66.6 14.8 888 n/a 6_nqh: 0.1200 0.1368 0.036 1.124 5.5 66.6 14.8 888 n/a 6_sol: 0.1199 0.1358 0.036 1.124 5.5 66.6 14.9 898 n/a 6_weight: 0.1199 0.1358 0.036 1.124 5.5 66.6 14.9 898 n/a 6_xyzrec: 0.1202 0.1360 0.037 1.135 5.5 66.6 14.9 898 n/a 6_adp: 0.1206 0.1365 0.037 1.135 5.6 65.5 14.8 898 n/a 6_regHadp: 0.1206 0.1365 0.037 1.135 5.6 65.5 14.8 898 n/a 6_occ: 0.1204 0.1367 0.037 1.135 5.6 65.5 14.8 898 n/a 7_bss: 0.1203 0.1366 0.037 1.135 5.3 65.3 14.6 898 n/a 7_settarget: 0.1203 0.1366 0.037 1.135 5.3 65.3 14.6 898 n/a 7_updatecdl: 0.1203 0.1366 0.037 1.136 5.3 65.3 14.6 898 n/a 7_nqh: 0.1203 0.1366 0.037 1.136 5.3 65.3 14.6 898 n/a 7_sol: 0.1203 0.1368 0.037 1.136 5.3 65.3 14.6 902 n/a 7_weight: 0.1203 0.1368 0.037 1.136 5.3 65.3 14.6 902 n/a 7_xyzrec: 0.1206 0.1375 0.037 1.130 5.3 65.3 14.6 902 n/a 7_adp: 0.1203 0.1374 0.037 1.130 5.4 64.3 14.6 902 n/a 7_regHadp: 0.1203 0.1375 0.037 1.130 5.4 64.3 14.6 902 n/a 7_occ: 0.1202 0.1374 0.037 1.130 5.4 64.3 14.6 902 n/a 8_bss: 0.1192 0.1365 0.037 1.130 5.4 64.3 14.6 902 n/a 8_settarget: 0.1192 0.1365 0.037 1.130 5.4 64.3 14.6 902 n/a 8_updatecdl: 0.1192 0.1365 0.037 1.130 5.4 64.3 14.6 902 n/a 8_nqh: 0.1192 0.1365 0.037 1.130 5.4 64.3 14.6 902 n/a 8_sol: 0.1191 0.1362 0.037 1.130 5.4 64.3 14.5 905 n/a 8_weight: 0.1191 0.1362 0.037 1.130 5.4 64.3 14.5 905 n/a 8_xyzrec: 0.1193 0.1366 0.037 1.134 5.4 64.3 14.5 905 n/a 8_adp: 0.1195 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 8_regHadp: 0.1195 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 8_occ: 0.1195 0.1370 0.037 1.134 5.4 64.0 14.5 905 n/a 9_bss: 0.1193 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 9_settarget: 0.1193 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 9_updatecdl: 0.1193 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 9_nqh: 0.1193 0.1369 0.037 1.134 5.4 64.0 14.5 905 n/a 9_sol: 0.1192 0.1370 0.037 1.134 5.4 64.0 14.6 907 n/a 9_weight: 0.1192 0.1370 0.037 1.134 5.4 64.0 14.6 907 n/a 9_xyzrec: 0.1196 0.1374 0.037 1.131 5.4 64.0 14.6 907 n/a 9_adp: 0.1197 0.1378 0.037 1.131 5.4 63.3 14.5 907 n/a 9_regHadp: 0.1197 0.1378 0.037 1.131 5.4 63.3 14.5 907 n/a 9_occ: 0.1196 0.1380 0.037 1.131 5.4 63.3 14.5 907 n/a 10_bss: 0.1195 0.1379 0.037 1.131 5.4 63.3 14.5 907 n/a 10_settarget: 0.1195 0.1379 0.037 1.131 5.4 63.3 14.5 907 n/a 10_updatecdl: 0.1195 0.1379 0.037 1.132 5.4 63.3 14.5 907 n/a 10_setrh: 0.1196 0.1379 0.037 1.132 5.4 63.3 14.5 907 n/a 10_nqh: 0.1196 0.1379 0.037 1.132 5.4 63.3 14.5 907 n/a 10_sol: 0.1195 0.1375 0.037 1.132 5.4 63.3 14.5 906 n/a 10_weight: 0.1195 0.1375 0.037 1.132 5.4 63.3 14.5 906 n/a 10_xyzrec: 0.1203 0.1383 0.038 1.194 5.4 63.3 14.5 906 n/a 10_adp: 0.1205 0.1388 0.038 1.194 5.5 63.3 14.5 906 n/a 10_regHadp: 0.1205 0.1388 0.038 1.194 5.5 63.3 14.5 906 n/a 10_occ: 0.1204 0.1388 0.038 1.194 5.5 63.3 14.5 906 n/a end: 0.1203 0.1386 0.038 1.194 5.5 63.3 14.5 906 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4328694_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4328694_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.8300 Refinement macro-cycles (run) : 12048.9500 Write final files (write_after_run_outputs) : 156.2500 Total : 12212.0300 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:43 PST -0800 (1736736043.96 s) Start R-work = 0.1801, R-free = 0.1900 Final R-work = 0.1203, R-free = 0.1386 =============================================================================== Job complete usr+sys time: 12496.10 seconds wall clock time: 209 minutes 15.46 seconds (12555.46 seconds total)