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_4119100.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4119100.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4119100.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.18, per 1000 atoms: 0.33 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: 2.731 distance_ideal: 2.720 ideal - model: -0.011 slack: 0.000 delta_slack: -0.011 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: 2.768 distance_ideal: 2.710 ideal - model: -0.058 slack: 0.000 delta_slack: -0.058 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 136.5 milliseconds Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 857 1.03 - 1.26: 2465 1.26 - 1.48: 1415 1.48 - 1.70: 1168 1.70 - 1.93: 29 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.623 -0.168 7.00e-03 2.04e+04 5.79e+02 bond pdb=" C THR B 91 " pdb=" O THR B 91 " ideal model delta sigma weight residual 1.236 1.485 -0.249 1.15e-02 7.56e+03 4.69e+02 bond pdb=" NZ LYS A 77 " pdb=" HZ3 LYS A 77 " ideal model delta sigma weight residual 0.890 1.277 -0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" C SER B 36 " pdb=" N VAL B 37 " ideal model delta sigma weight residual 1.333 1.529 -0.196 1.07e-02 8.73e+03 3.35e+02 bond pdb=" C VAL B 51 " pdb=" O VAL B 51 " ideal model delta sigma weight residual 1.238 1.044 0.194 1.06e-02 8.90e+03 3.34e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 6163 4.59 - 9.18: 3469 9.18 - 13.77: 1027 13.77 - 18.37: 141 18.37 - 22.96: 10 Bond angle restraints: 10810 Sorted by residual: angle pdb=" OE1 GLN B 184 " pdb=" CD GLN B 184 " pdb=" NE2 GLN B 184 " ideal model delta sigma weight residual 122.60 106.56 16.04 1.00e+00 1.00e+00 2.57e+02 angle pdb=" O LYS A 52 " pdb=" C LYS A 52 " pdb=" N LEU A 53 " ideal model delta sigma weight residual 123.13 137.86 -14.73 1.15e+00 7.56e-01 1.64e+02 angle pdb=" O CYS B 8 " pdb=" C CYS B 8 " pdb=" N LEU B 9 " ideal model delta sigma weight residual 123.01 137.74 -14.73 1.18e+00 7.18e-01 1.56e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.32 107.05 14.27 1.15e+00 7.56e-01 1.54e+02 angle pdb=" O LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 120.68 133.55 -12.87 1.09e+00 8.42e-01 1.39e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1859 17.89 - 35.77: 117 35.77 - 53.66: 54 53.66 - 71.55: 14 71.55 - 89.43: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CB TRP A 146 " pdb=" CG TRP A 146 " pdb=" CD1 TRP A 146 " pdb=" HD1 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 25.44 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.34 -23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.245: 221 0.245 - 0.490: 167 0.490 - 0.735: 81 0.735 - 0.979: 19 0.979 - 1.224: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 130 " pdb=" CB LEU B 130 " pdb=" CD1 LEU B 130 " pdb=" CD2 LEU B 130 " both_signs ideal model delta sigma weight residual False -2.59 -1.37 -1.22 2.00e-01 2.50e+01 3.75e+01 chirality pdb=" CA ALA B 5 " pdb=" N ALA B 5 " pdb=" C ALA B 5 " pdb=" CB ALA B 5 " both_signs ideal model delta sigma weight residual False 2.48 3.67 -1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CA ALA A 108 " pdb=" N ALA A 108 " pdb=" C ALA A 108 " pdb=" CB ALA A 108 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.11 2.00e-01 2.50e+01 3.10e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.104 2.00e-02 2.50e+03 7.74e-02 2.39e+02 pdb=" CG TRP A 146 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.129 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.097 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.077 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.065 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.009 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.109 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.052 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.097 2.00e-02 2.50e+03 7.49e-02 1.68e+02 pdb=" CG TYR B 67 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.100 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " -0.072 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.042 2.00e-02 2.50e+03 7.22e-02 1.56e+02 pdb=" CG PHE B 164 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.120 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.035 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 22 1.59 - 2.34: 2189 2.34 - 3.10: 22053 3.10 - 3.85: 33155 3.85 - 4.60: 52822 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110241 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.840 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.941 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 0.969 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.012 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.189 2.620 ... (remaining 110236 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_4119100_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= 0.2017 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301898 | | target function (ml) not normalized (work): 805801.329040 | | target function (ml) not normalized (free): 16569.924989 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2137 0.1916 6.6942 6.3017| | 2: 2.94 - 2.33 1.00 7339 128 0.1616 0.1615 5.5466 5.5983| | 3: 2.33 - 2.04 0.96 6939 150 0.1629 0.1834 5.1577 5.2554| | 4: 2.04 - 1.85 1.00 7170 155 0.1747 0.1662 4.9699 5.0652| | 5: 1.85 - 1.72 0.99 7113 159 0.1937 0.1788 4.8036 4.8784| | 6: 1.72 - 1.62 0.99 7102 142 0.1977 0.2170 4.6715 4.7141| | 7: 1.62 - 1.54 0.99 7104 148 0.2034 0.1889 4.5749 4.6216| | 8: 1.54 - 1.47 0.96 6798 152 0.2055 0.2119 4.4762 4.5034| | 9: 1.47 - 1.41 0.98 6938 155 0.2105 0.2228 4.3986 4.4372| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.2188 4.3104 4.3721| | 11: 1.36 - 1.32 0.99 6997 151 0.2119 0.2298 4.2442 4.3075| | 12: 1.32 - 1.28 0.98 6976 149 0.2103 0.1951 4.1823 4.1967| | 13: 1.28 - 1.25 0.98 6907 166 0.1993 0.2203 4.106 4.2025| | 14: 1.25 - 1.22 0.98 7015 113 0.2085 0.2110 4.0803 4.1146| | 15: 1.22 - 1.19 0.98 6957 137 0.2084 0.1899 4.0319 3.9635| | 16: 1.19 - 1.17 0.93 6604 132 0.2090 0.2241 3.9972 4.082| | 17: 1.17 - 1.14 0.98 6941 135 0.2144 0.1936 3.9469 3.9735| | 18: 1.14 - 1.12 0.98 6875 142 0.2244 0.2347 3.9315 3.9476| | 19: 1.12 - 1.10 0.97 6949 106 0.2283 0.2176 3.8726 3.8574| | 20: 1.10 - 1.08 0.97 6884 147 0.2293 0.2271 3.8137 3.9039| | 21: 1.08 - 1.07 0.97 6852 152 0.2452 0.2645 3.7958 3.8047| | 22: 1.07 - 1.05 0.97 6838 135 0.2547 0.2528 3.7477 3.779| | 23: 1.05 - 1.03 0.97 6829 159 0.2711 0.2596 3.7288 3.7871| | 24: 1.03 - 1.02 0.96 6785 133 0.2883 0.2949 3.6989 3.8076| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.2892 3.6746 3.6815| | 26: 1.01 - 0.99 0.96 6767 158 0.3228 0.3218 3.634 3.632| | 27: 0.99 - 0.98 0.94 6648 131 0.3456 0.3203 3.6459 3.6113| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.36 0.91 0.97 35136.88| | 2: 2.94 - 2.33 7339 128 0.85 21.51 1.08 1.02 15486.97| | 3: 2.33 - 2.04 6939 150 0.92 13.80 1.11 1.04 4772.32| | 4: 2.04 - 1.85 7170 155 0.92 14.44 1.11 1.05 3047.12| | 5: 1.85 - 1.72 7113 159 0.90 16.45 1.11 1.07 2274.67| | 6: 1.72 - 1.62 7102 142 0.90 17.19 1.11 1.08 1728.59| | 7: 1.62 - 1.54 7104 148 0.89 18.17 1.11 1.07 1421.82| | 8: 1.54 - 1.47 6798 152 0.89 18.48 1.10 1.06 1161.96| | 9: 1.47 - 1.41 6938 155 0.88 19.11 1.11 1.06 989.88| | 10: 1.41 - 1.36 7022 150 0.87 20.14 1.10 1.06 865.77| | 11: 1.36 - 1.32 6997 151 0.87 20.15 1.08 1.05 748.97| | 12: 1.32 - 1.28 6976 149 0.87 20.29 1.08 1.04 674.26| | 13: 1.28 - 1.25 6907 166 0.87 19.94 1.07 1.04 611.53| | 14: 1.25 - 1.22 7015 113 0.87 20.34 1.07 1.03 554.27| | 15: 1.22 - 1.19 6957 137 0.87 20.01 1.07 1.03 502.48| | 16: 1.19 - 1.17 6604 132 0.88 19.72 1.07 1.01 456.83| | 17: 1.17 - 1.14 6941 135 0.87 20.50 1.08 1.01 421.87| | 18: 1.14 - 1.12 6875 142 0.87 20.79 1.08 1.00 386.83| | 19: 1.12 - 1.10 6949 106 0.86 21.66 1.07 1.01 368.79| | 20: 1.10 - 1.08 6884 147 0.85 22.42 1.07 0.99 348.59| | 21: 1.08 - 1.07 6852 152 0.84 23.87 1.06 1.00 342.17| | 22: 1.07 - 1.05 6838 135 0.82 25.85 1.06 0.98 333.28| | 23: 1.05 - 1.03 6829 159 0.80 27.67 1.05 0.98 335.99| | 24: 1.03 - 1.02 6785 133 0.78 29.62 1.05 0.97 331.97| | 25: 1.02 - 1.01 6552 130 0.77 30.54 1.03 0.95 314.79| | 26: 1.01 - 0.99 6767 158 0.75 32.04 1.03 0.93 295.24| | 27: 0.99 - 0.98 6648 131 0.75 32.57 1.04 0.92 279.10| |alpha: min = 0.92 max = 1.08 mean = 1.02| |beta: min = 279.10 max = 35136.88 mean = 2875.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.69| |phase err.(test): min = 0.00 max = 89.52 mean = 22.02| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.249 2950 Z= 5.378 Angle : 5.186 18.695 4018 Z= 3.630 Chirality : 0.383 1.224 492 Planarity : 0.034 0.127 512 Dihedral : 13.025 89.434 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 1.29 % Allowed : 4.19 % Favored : 94.52 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.38), residues: 386 helix: -2.66 (0.32), residues: 146 sheet: -1.16 (0.50), residues: 82 loop : -0.97 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.117 0.023 ARG B 83 TYR 0.127 0.036 TYR B 67 PHE 0.120 0.036 PHE B 164 TRP 0.141 0.044 TRP A 146 HIS 0.099 0.035 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.2017 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301898 | | target function (ml) not normalized (work): 805801.329040 | | target function (ml) not normalized (free): 16569.924989 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2035 0.2017 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2035 0.2017 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2035 0.2017 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2036 0.2037 0.2018 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1798 0.1946 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1946 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4225 400.535 295.365 0.423 0.933 0.299 13.296-10.522 99.01 99 1 0.2510 528.187 519.151 0.765 0.934 0.250 10.503-8.327 99.45 178 3 0.2524 565.118 554.185 0.951 0.934 0.227 8.318-6.595 100.00 360 8 0.2498 414.736 403.013 0.946 0.933 0.170 6.588-5.215 100.00 711 7 0.2307 381.101 365.066 0.931 0.933 0.160 5.214-4.128 98.38 1367 28 0.1446 557.435 550.183 1.053 0.933 0.090 4.126-3.266 94.74 2603 46 0.1343 508.132 499.225 1.121 0.932 0.018 3.266-2.585 99.86 5447 97 0.1445 342.774 337.392 1.094 0.929 0.000 2.585-2.046 97.45 10613 204 0.1391 258.603 254.143 1.105 0.926 0.000 2.046-1.619 99.39 21536 464 0.1619 153.054 149.641 1.127 0.921 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.206 1.124 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2308 44.203 41.689 1.121 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0163 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1946 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1953 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.973482 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.125320 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 0.1271 0.1506 0.0234 0.039 1.2 11.0 0.0 0.0 0 11.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.06 2.34 1.117 13.121 574.125 0.018 12.98 15.71 2.73 1.243 13.356 574.125 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.05 15.04 1.40 435 3274 Protein: 5.22 40.45 11.01 1.40 0 2902 Water: 6.37 73.05 29.54 N/A 435 370 Other: 16.17 30.46 23.32 N/A 0 2 Chain A: 5.33 60.59 13.06 N/A 0 1626 Chain B: 5.22 73.05 12.78 N/A 0 1648 Chain S: 11.78 66.25 30.96 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2172 12.00 - 18.78 631 18.78 - 25.57 312 25.57 - 32.35 266 32.35 - 39.14 154 39.14 - 45.92 108 45.92 - 52.70 42 52.70 - 59.49 17 59.49 - 66.27 6 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1571 r_work=0.1298 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1567 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 = 0.1283 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015620 | | target function (ls_wunit_k1) not normalized (work): 2925.680682 | | target function (ls_wunit_k1) not normalized (free): 116.010772 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1283 0.1556 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1476 0.1474 0.1635 n_refl.: 191140 remove outliers: r(all,work,free)=0.1476 0.1474 0.1635 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1500 0.1497 0.1645 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1552 n_refl.: 191140 remove outliers: r(all,work,free)=0.1283 0.1277 0.1551 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 0.3632 402.814 368.846 0.480 0.962 0.287 13.296-10.522 99.01 99 1 0.2061 528.187 527.745 0.748 0.963 0.248 10.503-8.327 99.45 178 3 0.1745 565.118 561.837 0.892 0.963 0.199 8.318-6.595 100.00 360 8 0.1689 414.736 413.538 0.911 0.963 0.160 6.588-5.215 100.00 711 7 0.1550 381.101 373.090 0.887 0.963 0.150 5.214-4.128 98.38 1367 28 0.0900 557.435 555.280 0.979 0.964 0.054 4.126-3.266 94.74 2603 46 0.0828 508.132 504.183 1.045 0.964 0.014 3.266-2.585 99.86 5447 97 0.0922 342.774 340.279 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.383 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1094 153.054 151.385 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1285 82.395 81.419 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.167 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=0.0373 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1551 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1551 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1551 | n_water=805 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1281 r_free=0.1558 | n_water=795 | time (s): 99.290 (total time: 101.970) Filter (q & B) r_work=0.1281 r_free=0.1559 | n_water=791 | time (s): 4.960 (total time: 106.930) Compute maps r_work=0.1281 r_free=0.1559 | n_water=791 | time (s): 1.550 (total time: 108.480) Filter (map) r_work=0.1308 r_free=0.1532 | n_water=653 | time (s): 5.390 (total time: 113.870) Find peaks r_work=0.1308 r_free=0.1532 | n_water=653 | time (s): 0.650 (total time: 114.520) Add new water r_work=0.1330 r_free=0.1563 | n_water=967 | time (s): 4.450 (total time: 118.970) Refine new water occ: r_work=0.1285 r_free=0.1522 adp: r_work=0.1273 r_free=0.1517 occ: r_work=0.1276 r_free=0.1518 adp: r_work=0.1269 r_free=0.1516 occ: r_work=0.1270 r_free=0.1516 adp: r_work=0.1268 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1516 r_work=0.1268 r_free=0.1516 | n_water=967 | time (s): 85.180 (total time: 204.150) Filter (q & B) r_work=0.1271 r_free=0.1514 | n_water=901 | time (s): 4.840 (total time: 208.990) Filter (dist only) r_work=0.1272 r_free=0.1513 | n_water=899 | time (s): 116.590 (total time: 325.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.868360 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.320568 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 0.1254 0.1524 0.0270 0.041 1.1 20.9 0.0 0.3 0 11.934 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.24 2.70 2.044 15.249 595.321 0.014 12.31 15.02 2.71 2.419 15.299 595.321 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 70.45 16.43 1.20 531 3272 Protein: 5.44 40.76 10.99 1.20 0 2902 Water: 6.62 70.45 33.99 N/A 531 368 Other: 16.24 34.20 25.22 N/A 0 2 Chain A: 5.56 56.63 13.01 N/A 0 1624 Chain B: 5.44 68.22 12.84 N/A 0 1648 Chain S: 9.10 70.45 38.08 N/A 531 0 Histogram: Values Number of atoms 5.44 - 11.94 2119 11.94 - 18.44 688 18.44 - 24.94 249 24.94 - 31.44 214 31.44 - 37.94 169 37.94 - 44.44 187 44.44 - 50.94 88 50.94 - 57.45 48 57.45 - 63.95 36 63.95 - 70.45 5 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1503 r_work=0.1232 r_free=0.1504 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1504 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 = 0.1225 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013337 | | target function (ls_wunit_k1) not normalized (work): 2497.976452 | | target function (ls_wunit_k1) not normalized (free): 100.328291 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1505 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1437 0.1434 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1437 0.1434 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1512 n_refl.: 191138 remove outliers: r(all,work,free)=0.1237 0.1231 0.1512 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 0.3191 402.814 382.244 0.492 0.963 0.277 13.296-10.522 99.01 99 1 0.1915 528.187 520.871 0.754 0.964 0.222 10.503-8.327 99.45 178 3 0.1401 565.118 564.705 0.921 0.963 0.169 8.318-6.595 100.00 360 8 0.1551 414.736 414.463 0.933 0.963 0.150 6.588-5.215 100.00 711 7 0.1335 381.101 376.650 0.911 0.963 0.150 5.214-4.128 98.38 1367 28 0.0816 557.435 556.180 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0765 508.132 505.519 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0856 342.774 341.360 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0895 258.603 256.826 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.626 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.362 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.210 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0469 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1512 | n_water=899 | time (s): 3.430 (total time: 3.430) Filter (dist) r_work=0.1233 r_free=0.1515 | n_water=893 | time (s): 119.930 (total time: 123.360) Filter (q & B) r_work=0.1233 r_free=0.1515 | n_water=891 | time (s): 5.340 (total time: 128.700) Compute maps r_work=0.1233 r_free=0.1515 | n_water=891 | time (s): 2.070 (total time: 130.770) Filter (map) r_work=0.1271 r_free=0.1521 | n_water=698 | time (s): 4.780 (total time: 135.550) Find peaks r_work=0.1271 r_free=0.1521 | n_water=698 | time (s): 0.600 (total time: 136.150) Add new water r_work=0.1293 r_free=0.1544 | n_water=1025 | time (s): 4.910 (total time: 141.060) Refine new water occ: r_work=0.1249 r_free=0.1509 adp: r_work=0.1249 r_free=0.1511 occ: r_work=0.1245 r_free=0.1506 adp: r_work=0.1244 r_free=0.1508 occ: r_work=0.1241 r_free=0.1504 adp: r_work=0.1241 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1505 r_work=0.1241 r_free=0.1505 | n_water=1025 | time (s): 295.180 (total time: 436.240) Filter (q & B) r_work=0.1246 r_free=0.1503 | n_water=895 | time (s): 6.080 (total time: 442.320) Filter (dist only) r_work=0.1246 r_free=0.1503 | n_water=894 | time (s): 118.870 (total time: 561.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.662508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.838530 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 0.1234 0.1426 0.0193 0.035 1.1 9.0 0.0 0.0 0 0.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.26 1.93 1.934 14.664 16.839 3.937 12.27 13.88 1.60 2.211 14.575 16.839 3.894 Individual atomic B min max mean iso aniso Overall: 5.54 67.86 15.40 1.08 527 3271 Protein: 5.54 37.31 10.76 1.08 0 2902 Water: 6.72 67.86 30.45 N/A 527 367 Other: 14.09 29.55 21.82 N/A 0 2 Chain A: 5.55 55.79 12.79 N/A 0 1624 Chain B: 5.54 67.86 12.56 N/A 0 1647 Chain S: 12.71 60.39 32.33 N/A 527 0 Histogram: Values Number of atoms 5.54 - 11.77 2137 11.77 - 18.00 677 18.00 - 24.24 299 24.24 - 30.47 230 30.47 - 36.70 182 36.70 - 42.93 157 42.93 - 49.17 79 49.17 - 55.40 28 55.40 - 61.63 8 61.63 - 67.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1388 r_work=0.1228 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1228 r_free = 0.1388 target_work(ml) = 3.894 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1222 r_free = 0.1384 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1222 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.888586 | | target function (ml) not normalized (work): 728320.525953 | | target function (ml) not normalized (free): 15210.700244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1225 0.1222 0.1383 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1503 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1439 0.1503 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1434 0.1433 0.1499 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1222 0.1218 0.1377 n_refl.: 191138 remove outliers: r(all,work,free)=0.1221 0.1218 0.1377 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 0.3761 398.008 364.719 0.424 0.947 0.251 13.296-10.522 99.01 99 1 0.2448 528.187 507.654 0.710 0.948 0.225 10.503-8.327 98.35 176 3 0.1895 556.299 558.661 0.887 0.948 0.220 8.318-6.595 100.00 360 8 0.1998 414.736 411.165 0.898 0.948 0.140 6.588-5.215 100.00 711 7 0.1786 381.101 371.480 0.888 0.948 0.140 5.214-4.128 98.38 1367 28 0.1142 557.435 552.712 0.971 0.948 0.080 4.126-3.266 94.74 2603 46 0.1076 508.132 501.520 1.034 0.948 0.030 3.266-2.585 99.86 5447 97 0.1074 342.774 339.101 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0963 258.603 255.765 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.387 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.485 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.315 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0975 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1218 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1218 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1218 r_free=0.1377 | n_water=894 | time (s): 2.970 (total time: 2.970) Filter (dist) r_work=0.1218 r_free=0.1377 | n_water=893 | time (s): 114.390 (total time: 117.360) Filter (q & B) r_work=0.1219 r_free=0.1378 | n_water=878 | time (s): 5.120 (total time: 122.480) Compute maps r_work=0.1219 r_free=0.1378 | n_water=878 | time (s): 2.040 (total time: 124.520) Filter (map) r_work=0.1239 r_free=0.1378 | n_water=741 | time (s): 4.380 (total time: 128.900) Find peaks r_work=0.1239 r_free=0.1378 | n_water=741 | time (s): 0.920 (total time: 129.820) Add new water r_work=0.1256 r_free=0.1396 | n_water=985 | time (s): 4.430 (total time: 134.250) Refine new water occ: r_work=0.1208 r_free=0.1362 adp: r_work=0.1201 r_free=0.1357 occ: r_work=0.1198 r_free=0.1355 adp: r_work=0.1198 r_free=0.1355 occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1355 r_work=0.1197 r_free=0.1355 | n_water=985 | time (s): 328.230 (total time: 462.480) Filter (q & B) r_work=0.1202 r_free=0.1358 | n_water=883 | time (s): 5.250 (total time: 467.730) Filter (dist only) r_work=0.1202 r_free=0.1357 | n_water=881 | time (s): 115.840 (total time: 583.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.473637 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.487664 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 0.1364 0.0162 0.036 1.1 6.5 0.0 0.3 0 0.737 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.64 1.62 1.843 14.285 15.488 3.872 11.97 13.62 1.65 1.947 14.245 15.488 3.866 Individual atomic B min max mean iso aniso Overall: 5.53 67.47 15.08 1.01 514 3271 Protein: 5.53 34.07 10.68 1.01 0 2902 Water: 5.88 67.47 29.57 N/A 514 367 Other: 13.98 28.91 21.45 N/A 0 2 Chain A: 5.54 55.46 12.66 N/A 0 1624 Chain B: 5.53 67.47 12.47 N/A 0 1647 Chain S: 5.88 60.19 31.12 N/A 514 0 Histogram: Values Number of atoms 5.53 - 11.72 2125 11.72 - 17.92 714 17.92 - 24.11 299 24.11 - 30.30 239 30.30 - 36.50 171 36.50 - 42.69 133 42.69 - 48.88 73 48.88 - 55.08 23 55.08 - 61.27 7 61.27 - 67.47 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1362 r_work=0.1197 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 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= 0.1195 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863902 | | target function (ml) not normalized (work): 723685.648141 | | target function (ml) not normalized (free): 15132.540436 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1362 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1423 0.1423 0.1477 n_refl.: 191135 remove outliers: r(all,work,free)=0.1423 0.1423 0.1477 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1415 0.1472 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1362 n_refl.: 191135 remove outliers: r(all,work,free)=0.1196 0.1193 0.1362 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 94.06 92 3 0.3773 360.355 326.095 0.414 0.946 0.240 13.296-10.522 97.03 97 1 0.2423 481.138 451.269 0.703 0.948 0.205 10.503-8.327 97.80 175 3 0.2003 501.849 497.750 0.868 0.948 0.172 8.318-6.595 100.00 360 8 0.2106 375.501 372.034 0.892 0.948 0.128 6.588-5.215 100.00 711 7 0.1871 345.048 335.363 0.886 0.948 0.100 5.214-4.128 98.38 1367 28 0.1181 504.701 500.085 0.975 0.948 0.090 4.126-3.266 94.74 2603 46 0.1100 460.062 453.912 1.033 0.948 0.005 3.266-2.585 99.86 5447 97 0.1083 310.347 307.114 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0932 234.139 231.699 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.575 137.289 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0991 74.601 73.882 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1666 40.020 38.353 1.037 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1173 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1362 | n_water=881 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1193 r_free=0.1362 | n_water=881 | time (s): 108.350 (total time: 111.510) Filter (q & B) r_work=0.1193 r_free=0.1363 | n_water=871 | time (s): 5.640 (total time: 117.150) Compute maps r_work=0.1193 r_free=0.1363 | n_water=871 | time (s): 2.630 (total time: 119.780) Filter (map) r_work=0.1214 r_free=0.1365 | n_water=756 | time (s): 4.650 (total time: 124.430) Find peaks r_work=0.1214 r_free=0.1365 | n_water=756 | time (s): 0.550 (total time: 124.980) Add new water r_work=0.1226 r_free=0.1381 | n_water=990 | time (s): 5.160 (total time: 130.140) Refine new water occ: r_work=0.1190 r_free=0.1352 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1350 occ: r_work=0.1186 r_free=0.1350 adp: r_work=0.1186 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1350 r_work=0.1186 r_free=0.1350 | n_water=990 | time (s): 378.390 (total time: 508.530) Filter (q & B) r_work=0.1189 r_free=0.1352 | n_water=906 | time (s): 4.840 (total time: 513.370) Filter (dist only) r_work=0.1190 r_free=0.1351 | n_water=905 | time (s): 116.570 (total time: 629.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568681 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.037813 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1354 0.0162 0.037 1.1 8.0 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.54 1.62 1.801 14.221 15.038 3.763 11.98 13.58 1.60 1.934 14.172 15.038 3.761 Individual atomic B min max mean iso aniso Overall: 5.54 66.86 15.04 0.95 538 3271 Protein: 5.54 31.70 10.57 0.95 0 2902 Water: 6.06 66.86 29.35 N/A 538 367 Other: 13.91 26.77 20.34 N/A 0 2 Chain A: 5.58 55.07 12.52 N/A 0 1624 Chain B: 5.54 66.86 12.34 N/A 0 1647 Chain S: 6.06 59.96 30.92 N/A 538 0 Histogram: Values Number of atoms 5.54 - 11.67 2131 11.67 - 17.80 730 17.80 - 23.94 303 23.94 - 30.07 224 30.07 - 36.20 179 36.20 - 42.33 135 42.33 - 48.46 75 48.46 - 54.59 24 54.59 - 60.72 7 60.72 - 66.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1358 r_work=0.1199 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759502 | | target function (ml) not normalized (work): 704120.822514 | | target function (ml) not normalized (free): 14739.282907 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1358 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1419 0.1418 0.1470 n_refl.: 191132 remove outliers: r(all,work,free)=0.1419 0.1418 0.1470 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1411 0.1411 0.1465 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1355 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1355 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 93.07 91 3 0.3836 361.159 317.920 0.390 0.949 0.223 13.296-10.522 96.04 96 1 0.2366 480.375 457.381 0.704 0.951 0.178 10.503-8.327 97.80 175 3 0.2090 501.849 495.830 0.859 0.951 0.157 8.318-6.595 100.00 360 8 0.2121 375.501 372.083 0.886 0.951 0.118 6.588-5.215 100.00 711 7 0.1882 345.048 335.529 0.885 0.951 0.097 5.214-4.128 98.38 1367 28 0.1196 504.701 500.209 0.972 0.951 0.044 4.126-3.266 94.74 2603 46 0.1127 460.062 453.866 1.032 0.951 0.009 3.266-2.585 99.86 5447 97 0.1096 310.347 307.152 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0947 234.139 231.640 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0913 138.575 137.283 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0978 74.601 73.893 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.020 38.357 1.041 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1281 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1356 | n_water=905 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1195 r_free=0.1356 | n_water=904 | time (s): 116.130 (total time: 118.580) Filter (q & B) r_work=0.1195 r_free=0.1356 | n_water=889 | time (s): 4.290 (total time: 122.870) Compute maps r_work=0.1195 r_free=0.1356 | n_water=889 | time (s): 1.760 (total time: 124.630) Filter (map) r_work=0.1217 r_free=0.1359 | n_water=773 | time (s): 5.260 (total time: 129.890) Find peaks r_work=0.1217 r_free=0.1359 | n_water=773 | time (s): 0.760 (total time: 130.650) Add new water r_work=0.1227 r_free=0.1372 | n_water=990 | time (s): 5.050 (total time: 135.700) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1349 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1189 r_free=0.1350 adp: r_work=0.1189 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1350 r_work=0.1189 r_free=0.1350 | n_water=990 | time (s): 160.900 (total time: 296.600) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=907 | time (s): 4.230 (total time: 300.830) Filter (dist only) r_work=0.1194 r_free=0.1352 | n_water=906 | time (s): 112.980 (total time: 413.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.503954 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.831739 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1360 0.0162 0.038 1.1 5.5 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.60 1.62 1.754 14.019 14.832 3.761 11.99 13.61 1.62 1.863 13.987 14.832 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 65.79 14.85 0.90 539 3271 Protein: 5.58 29.54 10.48 0.90 0 2902 Water: 6.01 65.79 28.82 N/A 539 367 Other: 13.85 23.88 18.86 N/A 0 2 Chain A: 5.64 54.47 12.39 N/A 0 1624 Chain B: 5.58 65.79 12.22 N/A 0 1647 Chain S: 6.01 59.67 30.28 N/A 539 0 Histogram: Values Number of atoms 5.58 - 11.60 2110 11.60 - 17.62 771 17.62 - 23.64 301 23.64 - 29.66 210 29.66 - 35.68 189 35.68 - 41.70 121 41.70 - 47.72 72 47.72 - 53.74 27 53.74 - 59.76 8 59.76 - 65.79 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1361 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757133 | | target function (ml) not normalized (work): 703669.734113 | | target function (ml) not normalized (free): 14735.368363 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1481 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1402 0.1481 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1395 0.1476 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1360 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 93.07 91 3 0.3861 361.159 323.129 0.384 0.951 0.207 13.296-10.522 96.04 96 1 0.2375 480.375 462.132 0.700 0.953 0.166 10.503-8.327 97.80 175 3 0.2161 501.849 494.697 0.854 0.953 0.147 8.318-6.595 100.00 360 8 0.2155 375.501 370.938 0.877 0.953 0.100 6.588-5.215 100.00 711 7 0.1910 345.048 335.496 0.882 0.953 0.100 5.214-4.128 98.38 1367 28 0.1223 504.701 499.721 0.968 0.953 0.034 4.126-3.266 94.74 2603 46 0.1140 460.062 453.455 1.031 0.954 0.005 3.266-2.585 99.86 5447 97 0.1107 310.347 307.081 1.017 0.953 0.000 2.585-2.046 97.45 10613 204 0.0952 234.139 231.585 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0908 138.575 137.272 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0970 74.601 73.896 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.020 38.351 1.036 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1352 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1360 | n_water=906 | time (s): 3.180 (total time: 3.180) Filter (dist) r_work=0.1197 r_free=0.1359 | n_water=905 | time (s): 125.850 (total time: 129.030) Filter (q & B) r_work=0.1198 r_free=0.1360 | n_water=889 | time (s): 4.330 (total time: 133.360) Compute maps r_work=0.1198 r_free=0.1360 | n_water=889 | time (s): 1.640 (total time: 135.000) Filter (map) r_work=0.1218 r_free=0.1359 | n_water=781 | time (s): 4.530 (total time: 139.530) Find peaks r_work=0.1218 r_free=0.1359 | n_water=781 | time (s): 0.630 (total time: 140.160) Add new water r_work=0.1226 r_free=0.1372 | n_water=980 | time (s): 3.980 (total time: 144.140) Refine new water occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1191 r_free=0.1351 adp: r_work=0.1191 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1350 r_work=0.1191 r_free=0.1350 | n_water=980 | time (s): 219.250 (total time: 363.390) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=911 | time (s): 5.150 (total time: 368.540) Filter (dist only) r_work=0.1195 r_free=0.1352 | n_water=910 | time (s): 116.730 (total time: 485.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.313512 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1357 0.0160 0.039 1.1 6.3 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.60 1.719 13.942 14.314 3.757 11.98 13.60 1.62 1.755 13.925 14.314 3.756 Individual atomic B min max mean iso aniso Overall: 5.58 64.98 14.84 0.88 543 3271 Protein: 5.58 28.90 10.43 0.88 0 2902 Water: 5.98 64.98 28.89 N/A 543 367 Other: 13.87 22.72 18.29 N/A 0 2 Chain A: 5.64 54.09 12.30 N/A 0 1624 Chain B: 5.58 64.98 12.15 N/A 0 1647 Chain S: 5.98 59.44 30.58 N/A 543 0 Histogram: Values Number of atoms 5.58 - 11.52 2103 11.52 - 17.46 782 17.46 - 23.40 285 23.40 - 29.34 205 29.34 - 35.28 196 35.28 - 41.22 120 41.22 - 47.16 85 47.16 - 53.10 29 53.10 - 59.04 6 59.04 - 64.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1361 r_work=0.1198 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755578 | | target function (ml) not normalized (work): 703378.452304 | | target function (ml) not normalized (free): 14733.391081 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1489 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1402 0.1489 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1369 0.1367 0.1468 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1358 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3743 356.307 317.383 0.357 0.952 0.140 13.296-10.522 96.04 96 1 0.2381 480.375 462.012 0.711 0.953 0.138 10.503-8.327 97.80 175 3 0.2144 501.849 495.039 0.878 0.953 0.137 8.318-6.595 100.00 360 8 0.2165 375.501 370.847 0.900 0.953 0.090 6.588-5.215 100.00 711 7 0.1923 345.048 335.256 0.905 0.953 0.090 5.214-4.128 98.38 1367 28 0.1217 504.701 499.672 0.995 0.953 0.040 4.126-3.266 94.74 2603 46 0.1145 460.062 453.459 1.057 0.954 0.009 3.266-2.585 99.86 5447 97 0.1113 310.347 307.129 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0956 234.139 231.603 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0906 138.575 137.299 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0965 74.601 73.908 1.051 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.020 38.350 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9912 b_overall=0.0506 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=910 | time (s): 2.790 (total time: 2.790) Filter (dist) r_work=0.1197 r_free=0.1358 | n_water=909 | time (s): 110.600 (total time: 113.390) Filter (q & B) r_work=0.1198 r_free=0.1358 | n_water=897 | time (s): 4.010 (total time: 117.400) Compute maps r_work=0.1198 r_free=0.1358 | n_water=897 | time (s): 1.690 (total time: 119.090) Filter (map) r_work=0.1218 r_free=0.1357 | n_water=786 | time (s): 5.440 (total time: 124.530) Find peaks r_work=0.1218 r_free=0.1357 | n_water=786 | time (s): 0.870 (total time: 125.400) Add new water r_work=0.1226 r_free=0.1366 | n_water=988 | time (s): 4.870 (total time: 130.270) Refine new water occ: r_work=0.1195 r_free=0.1348 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1347 r_work=0.1191 r_free=0.1347 | n_water=988 | time (s): 253.360 (total time: 383.630) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=916 | time (s): 4.780 (total time: 388.410) Filter (dist only) r_work=0.1196 r_free=0.1353 | n_water=915 | time (s): 118.520 (total time: 506.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.593070 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.889615 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1358 0.0158 0.039 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 12.00 13.58 1.58 1.701 13.689 14.890 3.757 11.99 13.59 1.61 1.718 13.683 14.890 3.754 Individual atomic B min max mean iso aniso Overall: 5.36 63.88 14.61 0.88 548 3271 Protein: 5.36 28.41 10.21 0.88 0 2902 Water: 5.77 63.88 28.56 N/A 548 367 Other: 13.67 22.01 17.84 N/A 0 2 Chain A: 5.43 53.48 12.04 N/A 0 1624 Chain B: 5.36 63.88 11.90 N/A 0 1647 Chain S: 5.77 58.94 30.36 N/A 548 0 Histogram: Values Number of atoms 5.36 - 11.21 2070 11.21 - 17.06 814 17.06 - 22.91 272 22.91 - 28.76 213 28.76 - 34.62 196 34.62 - 40.47 126 40.47 - 46.32 86 46.32 - 52.17 32 52.17 - 58.02 7 58.02 - 63.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1360 r_work=0.1199 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.753865 | | target function (ml) not normalized (work): 703050.200992 | | target function (ml) not normalized (free): 14727.898519 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1358 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1364 0.1362 0.1474 n_refl.: 191128 remove outliers: r(all,work,free)=0.1364 0.1362 0.1474 n_refl.: 191128 overall B=0.07 to atoms: r(all,work,free)=0.1372 0.1370 0.1478 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1347 n_refl.: 191128 remove outliers: r(all,work,free)=0.1191 0.1188 0.1347 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3670 356.074 321.428 0.322 0.986 0.070 13.296-10.522 96.04 96 1 0.2398 480.375 461.211 0.683 0.987 0.120 10.503-8.327 97.80 175 3 0.2167 501.849 493.509 0.853 0.988 0.120 8.318-6.595 100.00 360 8 0.2170 375.501 369.952 0.878 0.988 0.098 6.588-5.215 100.00 711 7 0.1943 345.048 334.709 0.881 0.988 0.080 5.214-4.128 98.38 1367 28 0.1232 504.701 498.941 0.970 0.989 0.049 4.126-3.266 94.74 2603 46 0.1150 460.062 452.934 1.031 0.990 0.014 3.266-2.585 99.86 5447 97 0.1117 310.347 306.835 1.013 0.991 0.000 2.585-2.046 97.45 10613 204 0.0958 234.139 231.484 1.020 0.993 0.000 2.046-1.619 99.39 21536 464 0.0901 138.575 137.226 1.036 0.996 0.000 1.619-1.281 98.00 42464 925 0.0945 74.601 73.945 1.023 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.020 38.320 0.989 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0616 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1347 | n_water=915 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1188 r_free=0.1347 | n_water=914 | time (s): 119.380 (total time: 121.890) Filter (q & B) r_work=0.1189 r_free=0.1346 | n_water=899 | time (s): 4.450 (total time: 126.340) Compute maps r_work=0.1189 r_free=0.1346 | n_water=899 | time (s): 2.240 (total time: 128.580) Filter (map) r_work=0.1209 r_free=0.1349 | n_water=796 | time (s): 4.290 (total time: 132.870) Find peaks r_work=0.1209 r_free=0.1349 | n_water=796 | time (s): 0.680 (total time: 133.550) Add new water r_work=0.1216 r_free=0.1358 | n_water=999 | time (s): 4.260 (total time: 137.810) Refine new water occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1183 r_free=0.1336 adp: r_work=0.1184 r_free=0.1334 occ: r_work=0.1182 r_free=0.1336 adp: r_work=0.1182 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1335 r_work=0.1182 r_free=0.1335 | n_water=999 | time (s): 186.770 (total time: 324.580) Filter (q & B) r_work=0.1185 r_free=0.1341 | n_water=921 | time (s): 5.680 (total time: 330.260) Filter (dist only) r_work=0.1186 r_free=0.1341 | n_water=920 | time (s): 116.300 (total time: 446.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.647592 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.227754 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 0.1188 0.1351 0.0163 0.039 1.1 7.7 0.0 0.3 0 0.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.51 1.63 1.669 13.740 14.228 3.752 11.90 13.53 1.64 1.671 13.736 14.228 3.752 Individual atomic B min max mean iso aniso Overall: 5.46 63.63 14.69 0.87 553 3271 Protein: 5.46 28.25 10.29 0.87 0 2902 Water: 5.91 63.63 28.56 N/A 553 367 Other: 13.73 22.05 17.89 N/A 0 2 Chain A: 5.53 53.42 12.10 N/A 0 1624 Chain B: 5.46 63.63 11.96 N/A 0 1647 Chain S: 5.91 58.92 30.41 N/A 553 0 Histogram: Values Number of atoms 5.46 - 11.28 2067 11.28 - 17.10 826 17.10 - 22.91 272 22.91 - 28.73 211 28.73 - 34.54 194 34.54 - 40.36 120 40.36 - 46.18 89 46.18 - 51.99 32 51.99 - 57.81 9 57.81 - 63.63 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1353 r_work=0.1190 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1353 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1351 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751530 | | target function (ml) not normalized (work): 702609.080934 | | target function (ml) not normalized (free): 14728.639080 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1351 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1481 n_refl.: 191127 remove outliers: r(all,work,free)=0.1371 0.1369 0.1481 n_refl.: 191127 overall B=0.01 to atoms: r(all,work,free)=0.1373 0.1371 0.1483 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1349 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 0.1349 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3680 356.074 326.648 0.327 0.986 0.070 13.296-10.522 96.04 96 1 0.2403 480.375 461.377 0.677 0.987 0.108 10.503-8.327 97.80 175 3 0.2192 501.849 493.658 0.853 0.988 0.109 8.318-6.595 100.00 360 8 0.2174 375.501 370.224 0.876 0.988 0.093 6.588-5.215 100.00 711 7 0.1939 345.048 334.871 0.880 0.988 0.077 5.214-4.128 98.38 1367 28 0.1225 504.701 499.054 0.968 0.989 0.044 4.126-3.266 94.74 2603 46 0.1155 460.062 452.863 1.030 0.990 0.009 3.266-2.585 99.86 5447 97 0.1115 310.347 306.837 1.013 0.991 0.000 2.585-2.046 97.45 10613 204 0.0960 234.139 231.420 1.020 0.993 0.000 2.046-1.619 99.39 21536 464 0.0902 138.575 137.223 1.036 0.997 0.000 1.619-1.281 98.00 42464 925 0.0942 74.601 73.947 1.026 1.002 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.020 38.304 0.994 1.012 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0223 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1349 After: r_work=0.1188 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1350 | n_water=920 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1188 r_free=0.1349 | n_water=918 | time (s): 121.560 (total time: 124.720) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=904 | time (s): 5.240 (total time: 129.960) Compute maps r_work=0.1189 r_free=0.1349 | n_water=904 | time (s): 1.940 (total time: 131.900) Filter (map) r_work=0.1209 r_free=0.1358 | n_water=799 | time (s): 5.550 (total time: 137.450) Find peaks r_work=0.1209 r_free=0.1358 | n_water=799 | time (s): 0.880 (total time: 138.330) Add new water r_work=0.1215 r_free=0.1364 | n_water=994 | time (s): 4.680 (total time: 143.010) Refine new water occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1333 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1334 occ: r_work=0.1183 r_free=0.1335 adp: r_work=0.1183 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1334 r_work=0.1183 r_free=0.1334 | n_water=994 | time (s): 202.350 (total time: 345.360) Filter (q & B) r_work=0.1187 r_free=0.1346 | n_water=917 | time (s): 4.500 (total time: 349.860) Filter (dist only) r_work=0.1187 r_free=0.1346 | n_water=916 | time (s): 120.730 (total time: 470.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.489489 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.854692 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1354 0.0159 0.040 1.2 8.9 0.0 0.3 0 0.745 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.54 1.59 1.673 13.738 13.855 3.758 11.97 13.57 1.60 1.680 13.733 13.855 3.758 Individual atomic B min max mean iso aniso Overall: 5.53 62.85 14.65 0.86 549 3271 Protein: 5.53 27.92 10.31 0.86 0 2902 Water: 5.97 62.85 28.40 N/A 549 367 Other: 13.80 21.93 17.86 N/A 0 2 Chain A: 5.60 53.14 12.10 N/A 0 1624 Chain B: 5.53 62.85 11.97 N/A 0 1647 Chain S: 5.97 58.83 30.28 N/A 549 0 Histogram: Values Number of atoms 5.53 - 11.27 2055 11.27 - 17.00 842 17.00 - 22.73 263 22.73 - 28.46 207 28.46 - 34.19 197 34.19 - 39.92 127 39.92 - 45.66 84 45.66 - 51.39 31 51.39 - 57.12 9 57.12 - 62.85 5 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1357 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757659 | | target function (ml) not normalized (work): 703756.966079 | | target function (ml) not normalized (free): 14743.679809 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1355 0.1433 5.6845 5.7558| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1409 5.0795 5.2045| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1151 4.6634 4.7415| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1080 4.3982 4.5883| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.0981 4.1551 4.2361| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1098 3.9485 4.0803| | 7: 1.62 - 1.54 0.99 7104 148 0.0899 0.0949 3.803 3.9203| | 8: 1.54 - 1.47 0.96 6798 152 0.0900 0.1341 3.7074 3.9175| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1118 3.6268 3.7511| | 10: 1.41 - 1.36 0.99 7022 150 0.0984 0.1215 3.565 3.6993| | 11: 1.36 - 1.32 0.99 6997 151 0.1004 0.1126 3.4944 3.5904| | 12: 1.32 - 1.28 0.98 6975 149 0.1041 0.1134 3.467 3.5927| | 13: 1.28 - 1.25 0.98 6907 166 0.1050 0.1267 3.4446 3.5777| | 14: 1.25 - 1.22 0.98 7015 112 0.1112 0.1575 3.4375 3.6788| | 15: 1.22 - 1.19 0.98 6956 137 0.1175 0.1245 3.452 3.4942| | 16: 1.19 - 1.17 0.93 6604 132 0.1254 0.1536 3.4668 3.6515| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1226 3.4341 3.4444| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1712 3.4401 3.5316| | 19: 1.12 - 1.10 0.97 6948 106 0.1475 0.1791 3.4225 3.6031| | 20: 1.10 - 1.08 0.97 6884 147 0.1589 0.1605 3.413 3.4453| | 21: 1.08 - 1.07 0.97 6852 152 0.1733 0.2150 3.4209 3.5074| | 22: 1.07 - 1.05 0.97 6836 135 0.1909 0.1973 3.415 3.4227| | 23: 1.05 - 1.03 0.97 6827 159 0.2125 0.2017 3.4347 3.4874| | 24: 1.03 - 1.02 0.96 6784 133 0.2336 0.2253 3.4367 3.5108| | 25: 1.02 - 1.01 0.93 6552 130 0.2621 0.2505 3.4502 3.5227| | 26: 1.01 - 0.99 0.96 6767 158 0.2762 0.2860 3.4162 3.4211| | 27: 0.99 - 0.98 0.94 6647 131 0.3046 0.2814 3.469 3.3976| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7395 127 0.93 11.61 1.00 0.95 11076.96| | 2: 2.94 - 2.33 7339 128 0.93 12.79 0.99 0.95 5123.65| | 3: 2.33 - 2.04 6939 150 0.96 7.79 1.01 0.95 1738.14| | 4: 2.04 - 1.85 7170 155 0.96 7.79 1.00 0.95 1028.03| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.96 635.88| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.96 442.86| | 7: 1.62 - 1.54 7104 148 0.96 8.07 1.01 0.97 334.30| | 8: 1.54 - 1.47 6798 152 0.96 8.31 1.01 0.97 280.67| | 9: 1.47 - 1.41 6938 155 0.96 8.56 1.00 0.97 233.30| | 10: 1.41 - 1.36 7022 150 0.96 9.07 1.00 0.97 207.00| | 11: 1.36 - 1.32 6997 151 0.96 9.11 0.99 0.96 178.96| | 12: 1.32 - 1.28 6975 149 0.96 9.14 0.98 0.95 164.55| | 13: 1.28 - 1.25 6907 166 0.95 9.69 1.01 0.96 161.14| | 14: 1.25 - 1.22 7015 112 0.95 10.81 1.01 0.96 165.26| | 15: 1.22 - 1.19 6956 137 0.95 11.31 1.01 0.98 167.75| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.96 160.64| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.96 154.17| | 18: 1.14 - 1.12 6875 142 0.94 12.80 1.01 0.94 148.60| | 19: 1.12 - 1.10 6948 106 0.93 14.26 1.00 0.94 153.03| | 20: 1.10 - 1.08 6884 147 0.92 15.42 1.00 0.93 152.94| | 21: 1.08 - 1.07 6852 152 0.91 16.83 1.00 0.93 155.78| | 22: 1.07 - 1.05 6836 135 0.89 18.44 0.99 0.92 156.80| | 23: 1.05 - 1.03 6827 159 0.87 20.58 0.99 0.92 165.66| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.92 179.37| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.97 0.89 181.92| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.88 176.67| | 27: 0.99 - 0.98 6647 131 0.82 26.37 0.99 0.87 161.78| |alpha: min = 0.87 max = 0.98 mean = 0.94| |beta: min = 148.60 max = 11076.96 mean = 923.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.37| |phase err.(test): min = 0.00 max = 89.28 mean = 13.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1387 0.1385 0.1496 n_refl.: 191127 remove outliers: r(all,work,free)=0.1387 0.1385 0.1496 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1387 0.1385 0.1496 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191127 remove outliers: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3690 356.074 326.093 0.319 0.995 0.060 13.296-10.522 96.04 96 1 0.2431 480.375 459.916 0.667 0.996 0.103 10.503-8.327 97.80 175 3 0.2184 501.849 493.469 0.844 0.996 0.103 8.318-6.595 100.00 360 8 0.2180 375.501 369.621 0.867 0.996 0.087 6.588-5.215 100.00 711 7 0.1943 345.048 334.597 0.870 0.997 0.077 5.214-4.128 98.38 1367 28 0.1236 504.701 499.046 0.960 0.998 0.039 4.126-3.266 94.74 2603 46 0.1162 460.062 452.764 1.022 0.999 0.005 3.266-2.585 99.86 5447 97 0.1118 310.347 306.858 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0968 234.139 231.424 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0913 138.575 137.195 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0954 74.601 73.934 1.018 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.020 38.292 0.988 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0048 ================= 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 0.2017 0.080 5.186 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1946 0.080 5.186 5.2 78.1 14.6 805 0.000 1_settarget: 0.1797 0.1946 0.080 5.186 5.2 78.1 14.6 805 0.000 1_nqh: 0.1801 0.1953 0.080 5.186 5.2 78.1 14.6 805 0.002 1_weight: 0.1801 0.1953 0.080 5.186 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1271 0.1506 0.039 1.155 5.2 78.1 14.6 805 0.159 1_adp: 0.1298 0.1571 0.039 1.155 5.2 73.1 15.0 805 0.159 1_regHadp: 0.1298 0.1567 0.039 1.155 5.2 73.1 15.0 805 0.159 1_occ: 0.1283 0.1556 0.039 1.155 5.2 73.1 15.0 805 0.159 2_bss: 0.1277 0.1551 0.039 1.155 5.4 73.2 15.2 805 0.159 2_settarget: 0.1277 0.1551 0.039 1.155 5.4 73.2 15.2 805 0.159 2_updatecdl: 0.1277 0.1551 0.039 1.184 5.4 73.2 15.2 805 0.159 2_nqh: 0.1277 0.1551 0.039 1.184 5.4 73.2 15.2 805 0.159 2_sol: 0.1272 0.1513 0.039 1.184 5.4 73.2 16.3 899 n/a 2_weight: 0.1272 0.1513 0.039 1.184 5.4 73.2 16.3 899 n/a 2_xyzrec: 0.1254 0.1524 0.041 1.144 5.4 73.2 16.3 899 n/a 2_adp: 0.1232 0.1503 0.041 1.144 5.4 70.4 16.4 899 n/a 2_regHadp: 0.1232 0.1504 0.041 1.144 5.4 70.4 16.4 899 n/a 2_occ: 0.1225 0.1505 0.041 1.144 5.4 70.4 16.4 899 n/a 3_bss: 0.1231 0.1512 0.041 1.144 5.4 70.4 16.4 899 n/a 3_settarget: 0.1231 0.1512 0.041 1.144 5.4 70.4 16.4 899 n/a 3_updatecdl: 0.1231 0.1512 0.041 1.147 5.4 70.4 16.4 899 n/a 3_nqh: 0.1231 0.1512 0.041 1.147 5.4 70.4 16.4 899 n/a 3_sol: 0.1246 0.1503 0.041 1.147 5.4 68.2 15.6 894 n/a 3_weight: 0.1246 0.1503 0.041 1.147 5.4 68.2 15.6 894 n/a 3_xyzrec: 0.1234 0.1426 0.035 1.098 5.4 68.2 15.6 894 n/a 3_adp: 0.1227 0.1388 0.035 1.098 5.5 67.9 15.4 894 n/a 3_regHadp: 0.1228 0.1388 0.035 1.098 5.5 67.9 15.4 894 n/a 3_occ: 0.1222 0.1384 0.035 1.098 5.5 67.9 15.4 894 n/a 4_bss: 0.1218 0.1377 0.035 1.098 5.5 67.8 15.4 894 n/a 4_settarget: 0.1218 0.1377 0.035 1.098 5.5 67.8 15.4 894 n/a 4_updatecdl: 0.1218 0.1377 0.035 1.098 5.5 67.8 15.4 894 n/a 4_nqh: 0.1218 0.1377 0.035 1.098 5.5 67.8 15.4 894 n/a 4_sol: 0.1202 0.1357 0.035 1.098 5.5 67.8 15.2 881 n/a 4_weight: 0.1202 0.1357 0.035 1.098 5.5 67.8 15.2 881 n/a 4_xyzrec: 0.1202 0.1364 0.036 1.104 5.5 67.8 15.2 881 n/a 4_adp: 0.1197 0.1362 0.036 1.104 5.5 67.5 15.1 881 n/a 4_regHadp: 0.1197 0.1362 0.036 1.104 5.5 67.5 15.1 881 n/a 4_occ: 0.1195 0.1362 0.036 1.104 5.5 67.5 15.1 881 n/a 5_bss: 0.1193 0.1362 0.036 1.104 5.5 67.4 15.1 881 n/a 5_settarget: 0.1193 0.1362 0.036 1.104 5.5 67.4 15.1 881 n/a 5_updatecdl: 0.1193 0.1362 0.036 1.105 5.5 67.4 15.1 881 n/a 5_nqh: 0.1193 0.1362 0.036 1.105 5.5 67.4 15.1 881 n/a 5_sol: 0.1190 0.1351 0.036 1.105 5.5 67.4 15.1 905 n/a 5_weight: 0.1190 0.1351 0.036 1.105 5.5 67.4 15.1 905 n/a 5_xyzrec: 0.1192 0.1354 0.037 1.125 5.5 67.4 15.1 905 n/a 5_adp: 0.1198 0.1358 0.037 1.125 5.5 66.9 15.0 905 n/a 5_regHadp: 0.1199 0.1359 0.037 1.125 5.5 66.9 15.0 905 n/a 5_occ: 0.1196 0.1359 0.037 1.125 5.5 66.9 15.0 905 n/a 6_bss: 0.1195 0.1356 0.037 1.125 5.5 66.8 15.0 905 n/a 6_settarget: 0.1195 0.1356 0.037 1.125 5.5 66.8 15.0 905 n/a 6_updatecdl: 0.1195 0.1356 0.037 1.125 5.5 66.8 15.0 905 n/a 6_nqh: 0.1195 0.1356 0.037 1.125 5.5 66.8 15.0 905 n/a 6_sol: 0.1194 0.1352 0.037 1.125 5.5 66.8 14.9 906 n/a 6_weight: 0.1194 0.1352 0.037 1.125 5.5 66.8 14.9 906 n/a 6_xyzrec: 0.1198 0.1360 0.038 1.120 5.5 66.8 14.9 906 n/a 6_adp: 0.1199 0.1361 0.038 1.120 5.6 65.8 14.8 906 n/a 6_regHadp: 0.1199 0.1362 0.038 1.120 5.6 65.8 14.8 906 n/a 6_occ: 0.1197 0.1362 0.038 1.120 5.6 65.8 14.8 906 n/a 7_bss: 0.1196 0.1360 0.038 1.120 5.5 65.7 14.8 906 n/a 7_settarget: 0.1196 0.1360 0.038 1.120 5.5 65.7 14.8 906 n/a 7_updatecdl: 0.1196 0.1360 0.038 1.120 5.5 65.7 14.8 906 n/a 7_nqh: 0.1196 0.1360 0.038 1.120 5.5 65.7 14.8 906 n/a 7_sol: 0.1195 0.1352 0.038 1.120 5.5 65.7 14.9 910 n/a 7_weight: 0.1195 0.1352 0.038 1.120 5.5 65.7 14.9 910 n/a 7_xyzrec: 0.1197 0.1357 0.039 1.120 5.5 65.7 14.9 910 n/a 7_adp: 0.1198 0.1361 0.039 1.120 5.6 65.0 14.8 910 n/a 7_regHadp: 0.1198 0.1361 0.039 1.120 5.6 65.0 14.8 910 n/a 7_occ: 0.1197 0.1361 0.039 1.120 5.6 65.0 14.8 910 n/a 8_bss: 0.1196 0.1359 0.039 1.120 5.4 64.8 14.6 910 n/a 8_settarget: 0.1196 0.1359 0.039 1.120 5.4 64.8 14.6 910 n/a 8_updatecdl: 0.1196 0.1359 0.039 1.121 5.4 64.8 14.6 910 n/a 8_nqh: 0.1196 0.1359 0.039 1.121 5.4 64.8 14.6 910 n/a 8_sol: 0.1196 0.1353 0.039 1.121 5.4 64.8 14.6 915 n/a 8_weight: 0.1196 0.1353 0.039 1.121 5.4 64.8 14.6 915 n/a 8_xyzrec: 0.1200 0.1358 0.039 1.129 5.4 64.8 14.6 915 n/a 8_adp: 0.1199 0.1360 0.039 1.129 5.4 63.9 14.6 915 n/a 8_regHadp: 0.1199 0.1360 0.039 1.129 5.4 63.9 14.6 915 n/a 8_occ: 0.1197 0.1358 0.039 1.129 5.4 63.9 14.6 915 n/a 9_bss: 0.1188 0.1347 0.039 1.129 5.4 63.9 14.7 915 n/a 9_settarget: 0.1188 0.1347 0.039 1.129 5.4 63.9 14.7 915 n/a 9_updatecdl: 0.1188 0.1347 0.039 1.129 5.4 63.9 14.7 915 n/a 9_nqh: 0.1188 0.1347 0.039 1.129 5.4 63.9 14.7 915 n/a 9_sol: 0.1186 0.1341 0.039 1.129 5.4 63.9 14.7 920 n/a 9_weight: 0.1186 0.1341 0.039 1.129 5.4 63.9 14.7 920 n/a 9_xyzrec: 0.1188 0.1351 0.039 1.124 5.4 63.9 14.7 920 n/a 9_adp: 0.1190 0.1353 0.039 1.124 5.5 63.6 14.7 920 n/a 9_regHadp: 0.1190 0.1353 0.039 1.124 5.5 63.6 14.7 920 n/a 9_occ: 0.1188 0.1351 0.039 1.124 5.5 63.6 14.7 920 n/a 10_bss: 0.1187 0.1349 0.039 1.124 5.5 63.6 14.7 920 n/a 10_settarget: 0.1187 0.1349 0.039 1.124 5.5 63.6 14.7 920 n/a 10_updatecdl: 0.1187 0.1349 0.039 1.124 5.5 63.6 14.7 920 n/a 10_setrh: 0.1188 0.1350 0.039 1.124 5.5 63.6 14.7 920 n/a 10_nqh: 0.1188 0.1350 0.039 1.124 5.5 63.6 14.7 920 n/a 10_sol: 0.1187 0.1346 0.039 1.124 5.5 63.6 14.7 916 n/a 10_weight: 0.1187 0.1346 0.039 1.124 5.5 63.6 14.7 916 n/a 10_xyzrec: 0.1195 0.1354 0.040 1.152 5.5 63.6 14.7 916 n/a 10_adp: 0.1197 0.1357 0.040 1.152 5.5 62.9 14.7 916 n/a 10_regHadp: 0.1197 0.1357 0.040 1.152 5.5 62.9 14.7 916 n/a 10_occ: 0.1196 0.1357 0.040 1.152 5.5 62.9 14.7 916 n/a end: 0.1195 0.1356 0.040 1.152 5.5 62.8 14.7 916 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4119100_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4119100_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1700 Refinement macro-cycles (run) : 12066.4500 Write final files (write_after_run_outputs) : 150.5200 Total : 12223.1400 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:54 PST -0800 (1736736054.26 s) Start R-work = 0.1797, R-free = 0.1946 Final R-work = 0.1195, R-free = 0.1356 =============================================================================== Job complete usr+sys time: 12490.86 seconds wall clock time: 209 minutes 10.49 seconds (12550.49 seconds total)