Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5179049.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5179049.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5179049.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.32, per 1000 atoms: 0.35 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: 2.658 distance_ideal: 2.720 ideal - model: 0.062 slack: 0.000 delta_slack: 0.062 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.787 distance_ideal: 2.710 ideal - model: -0.077 slack: 0.000 delta_slack: -0.077 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 128.5 milliseconds Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.01: 671 1.01 - 1.26: 2642 1.26 - 1.50: 1585 1.50 - 1.74: 1024 1.74 - 1.98: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 55 " pdb=" H ALA B 55 " ideal model delta sigma weight residual 0.860 1.246 -0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" N GLY A 157 " pdb=" H GLY A 157 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.67e+02 bond pdb=" N ALA A 57 " pdb=" CA ALA A 57 " ideal model delta sigma weight residual 1.455 1.637 -0.182 9.60e-03 1.09e+04 3.59e+02 bond pdb=" C GLY B 126 " pdb=" O GLY B 126 " ideal model delta sigma weight residual 1.232 1.444 -0.211 1.13e-02 7.83e+03 3.49e+02 bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.453 1.284 0.169 9.20e-03 1.18e+04 3.37e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 5928 4.43 - 8.85: 3528 8.85 - 13.28: 1163 13.28 - 17.71: 179 17.71 - 22.14: 12 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 121.54 104.90 16.64 8.50e-01 1.38e+00 3.83e+02 angle pdb=" CE2 TRP A 139 " pdb=" CD2 TRP A 139 " pdb=" CE3 TRP A 139 " ideal model delta sigma weight residual 118.80 135.22 -16.42 1.00e+00 1.00e+00 2.70e+02 angle pdb=" N LEU A 185 " pdb=" CA LEU A 185 " pdb=" C LEU A 185 " ideal model delta sigma weight residual 113.28 131.55 -18.27 1.22e+00 6.72e-01 2.24e+02 angle pdb=" CA LYS B 52 " pdb=" C LYS B 52 " pdb=" O LYS B 52 " ideal model delta sigma weight residual 120.32 136.30 -15.98 1.10e+00 8.26e-01 2.11e+02 angle pdb=" NE ARG B 97 " pdb=" CZ ARG B 97 " pdb=" NH2 ARG B 97 " ideal model delta sigma weight residual 119.20 131.47 -12.27 9.00e-01 1.23e+00 1.86e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 1866 17.73 - 35.46: 119 35.46 - 53.18: 48 53.18 - 70.91: 12 70.91 - 88.64: 5 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 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 198 0.202 - 0.404: 134 0.404 - 0.605: 112 0.605 - 0.807: 32 0.807 - 1.008: 16 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA CYS A 8 " pdb=" N CYS A 8 " pdb=" C CYS A 8 " pdb=" CB CYS A 8 " both_signs ideal model delta sigma weight residual False 2.51 3.52 -1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CA ARG A 49 " pdb=" N ARG A 49 " pdb=" C ARG A 49 " pdb=" CB ARG A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 1.60 0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.113 2.00e-02 2.50e+03 6.79e-02 1.84e+02 pdb=" CG TRP A 146 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.085 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.102 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.110 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.082 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.074 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.097 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.061 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " 0.055 9.50e-02 1.11e+02 8.44e-02 1.53e+02 pdb=" NE ARG B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " 0.173 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " -0.131 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " -0.021 2.00e-02 2.50e+03 pdb="HH11 ARG B 143 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG B 143 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG B 143 " -0.096 2.00e-02 2.50e+03 pdb="HH22 ARG B 143 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 179 " -0.026 2.00e-02 2.50e+03 8.19e-02 1.51e+02 pdb=" CG HIS B 179 " 0.153 2.00e-02 2.50e+03 pdb=" ND1 HIS B 179 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS B 179 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS B 179 " 0.062 2.00e-02 2.50e+03 pdb=" NE2 HIS B 179 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 HIS B 179 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS B 179 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS B 179 " -0.073 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 24 1.60 - 2.35: 2248 2.35 - 3.10: 22167 3.10 - 3.85: 33063 3.85 - 4.60: 52810 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110312 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.850 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.920 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.017 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.124 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.155 2.620 ... (remaining 110307 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_5179049_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= 0.2039 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303375 | | target function (ml) not normalized (work): 806078.169425 | | target function (ml) not normalized (free): 16596.681187 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2145 0.1826 6.72 6.2864| | 2: 2.94 - 2.33 1.00 7339 128 0.1628 0.1401 5.5293 5.5283| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1694 5.1433 5.2108| | 4: 2.04 - 1.85 1.00 7170 155 0.1768 0.1691 4.9648 5.0895| | 5: 1.85 - 1.72 0.99 7113 159 0.1914 0.1593 4.7906 4.7431| | 6: 1.72 - 1.62 0.99 7102 142 0.2006 0.1796 4.6707 4.7023| | 7: 1.62 - 1.54 0.99 7104 148 0.2054 0.1840 4.5765 4.5969| | 8: 1.54 - 1.47 0.96 6798 152 0.2031 0.2218 4.4722 4.5209| | 9: 1.47 - 1.41 0.98 6938 155 0.2105 0.2117 4.393 4.4348| | 10: 1.41 - 1.36 0.99 7022 150 0.2063 0.2057 4.2925 4.3668| | 11: 1.36 - 1.32 0.99 6997 151 0.2100 0.2236 4.2281 4.2904| | 12: 1.32 - 1.28 0.98 6976 149 0.2098 0.2025 4.192 4.28| | 13: 1.28 - 1.25 0.98 6907 166 0.2055 0.2172 4.1333 4.1471| | 14: 1.25 - 1.22 0.98 7015 113 0.2109 0.2541 4.0951 4.329| | 15: 1.22 - 1.19 0.98 6957 137 0.2092 0.1933 4.0514 4.0261| | 16: 1.19 - 1.17 0.93 6604 132 0.2156 0.2175 4.0213 3.9987| | 17: 1.17 - 1.14 0.98 6941 135 0.2185 0.2075 3.9649 4.0634| | 18: 1.14 - 1.12 0.98 6875 142 0.2205 0.2381 3.9277 3.965| | 19: 1.12 - 1.10 0.97 6949 106 0.2283 0.2589 3.8833 4.0485| | 20: 1.10 - 1.08 0.97 6884 147 0.2325 0.2325 3.8303 3.874| | 21: 1.08 - 1.07 0.97 6852 152 0.2396 0.2756 3.7841 3.8323| | 22: 1.07 - 1.05 0.97 6838 135 0.2543 0.2549 3.7516 3.7501| | 23: 1.05 - 1.03 0.97 6829 159 0.2713 0.2878 3.7302 3.8944| | 24: 1.03 - 1.02 0.96 6785 133 0.2843 0.2982 3.6933 3.8022| | 25: 1.02 - 1.01 0.93 6552 130 0.3052 0.2918 3.6727 3.7103| | 26: 1.01 - 0.99 0.96 6767 158 0.3181 0.2919 3.6309 3.5775| | 27: 0.99 - 0.98 0.94 6648 131 0.3399 0.3382 3.6329 3.6208| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.77 0.91 0.98 33347.99| | 2: 2.94 - 2.33 7339 128 0.86 20.72 1.08 1.02 14451.52| | 3: 2.33 - 2.04 6939 150 0.93 12.55 1.11 1.06 4155.10| | 4: 2.04 - 1.85 7170 155 0.93 13.31 1.12 1.07 2705.92| | 5: 1.85 - 1.72 7113 159 0.91 14.97 1.11 1.07 1934.41| | 6: 1.72 - 1.62 7102 142 0.90 16.35 1.12 1.07 1569.56| | 7: 1.62 - 1.54 7104 148 0.89 17.41 1.11 1.06 1294.49| | 8: 1.54 - 1.47 6798 152 0.89 18.15 1.10 1.06 1128.61| | 9: 1.47 - 1.41 6938 155 0.88 18.73 1.10 1.05 952.59| | 10: 1.41 - 1.36 7022 150 0.87 20.46 1.09 1.04 882.71| | 11: 1.36 - 1.32 6997 151 0.86 20.94 1.09 1.04 786.18| | 12: 1.32 - 1.28 6976 149 0.87 20.71 1.08 1.05 715.35| | 13: 1.28 - 1.25 6907 166 0.87 20.35 1.07 1.05 636.26| | 14: 1.25 - 1.22 7015 113 0.86 21.02 1.08 1.05 594.31| | 15: 1.22 - 1.19 6957 137 0.86 21.18 1.07 1.04 561.04| | 16: 1.19 - 1.17 6604 132 0.86 21.07 1.07 1.03 509.92| | 17: 1.17 - 1.14 6941 135 0.85 21.97 1.08 1.01 473.22| | 18: 1.14 - 1.12 6875 142 0.85 22.05 1.08 1.00 430.17| | 19: 1.12 - 1.10 6949 106 0.84 23.35 1.07 0.98 412.28| | 20: 1.10 - 1.08 6884 147 0.84 23.78 1.06 0.96 371.87| | 21: 1.08 - 1.07 6852 152 0.83 24.93 1.06 0.96 358.93| | 22: 1.07 - 1.05 6838 135 0.81 26.66 1.05 0.97 353.42| | 23: 1.05 - 1.03 6829 159 0.78 29.02 1.05 0.96 358.71| | 24: 1.03 - 1.02 6785 133 0.77 30.34 1.05 0.96 343.21| | 25: 1.02 - 1.01 6552 130 0.77 30.32 1.03 0.93 306.43| | 26: 1.01 - 0.99 6767 158 0.76 31.08 1.03 0.93 281.99| | 27: 0.99 - 0.98 6648 131 0.75 32.22 1.04 0.93 280.26| |alpha: min = 0.93 max = 1.07 mean = 1.01| |beta: min = 280.26 max = 33347.99 mean = 2719.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.89| |phase err.(test): min = 0.00 max = 87.06 mean = 21.85| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.246 2950 Z= 5.428 Angle : 5.225 18.269 4018 Z= 3.683 Chirality : 0.379 1.008 492 Planarity : 0.032 0.110 512 Dihedral : 12.745 88.638 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.40 % Favored : 95.08 % Rotamer: Outliers : 1.29 % Allowed : 5.16 % Favored : 93.55 % Cbeta Deviations : 28.65 % 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: -1.84 (0.40), residues: 386 helix: -2.35 (0.32), residues: 142 sheet: -0.32 (0.56), residues: 82 loop : -0.34 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.167 0.022 ARG B 143 TYR 0.101 0.029 TYR B 194 PHE 0.124 0.043 PHE B 95 TRP 0.117 0.039 TRP A 146 HIS 0.076 0.032 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303375 | | target function (ml) not normalized (work): 806078.169425 | | target function (ml) not normalized (free): 16596.681187 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2037 0.2039 0.1957 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2037 0.2039 0.1957 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2039 0.1957 n_refl.: 191145 overall B=-0.01 to atoms: r(all,work,free)=0.2035 0.2038 0.1956 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1807 0.1898 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1804 0.1898 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 94.06 92 3 0.4068 398.008 291.732 0.419 0.933 0.297 13.296-10.522 99.01 99 1 0.2491 528.187 518.333 0.764 0.935 0.250 10.503-8.327 99.45 178 3 0.2516 565.118 554.965 0.938 0.935 0.230 8.318-6.595 100.00 360 8 0.2466 414.736 404.263 0.947 0.935 0.169 6.588-5.215 100.00 711 7 0.2305 381.101 364.115 0.922 0.935 0.140 5.214-4.128 98.38 1367 28 0.1477 557.435 549.477 1.039 0.936 0.090 4.126-3.266 94.74 2603 46 0.1349 508.132 498.600 1.108 0.936 0.023 3.266-2.585 99.86 5447 97 0.1472 342.774 337.307 1.081 0.936 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.280 1.085 0.936 0.000 2.046-1.619 99.39 21536 464 0.1624 153.054 149.929 1.107 0.935 0.000 1.619-1.281 98.00 42464 925 0.1923 82.395 80.444 1.091 0.935 0.000 1.281-0.980 96.53 101826 2056 0.2321 44.203 41.976 1.076 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0317 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1898 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1898 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.281482 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.132835 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 0.1268 0.1494 0.0226 0.038 1.1 11.0 0.0 0.3 0 11.141 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 14.94 2.26 1.118 13.099 567.133 0.018 12.96 15.67 2.71 1.248 13.350 567.133 0.017 Individual atomic B min max mean iso aniso Overall: 5.27 73.03 15.04 1.40 435 3274 Protein: 5.27 40.30 11.03 1.40 0 2902 Water: 6.38 73.03 29.50 N/A 435 370 Other: 16.06 30.51 23.28 N/A 0 2 Chain A: 5.38 59.91 13.07 N/A 0 1626 Chain B: 5.27 73.03 12.80 N/A 0 1648 Chain S: 12.35 62.50 30.90 N/A 435 0 Histogram: Values Number of atoms 5.27 - 12.05 2179 12.05 - 18.82 634 18.82 - 25.60 310 25.60 - 32.38 255 32.38 - 39.15 162 39.15 - 45.93 106 45.93 - 52.70 39 52.70 - 59.48 19 59.48 - 66.26 4 66.26 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1567 r_work=0.1296 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1561 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1551 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015546 | | target function (ls_wunit_k1) not normalized (work): 2911.746294 | | target function (ls_wunit_k1) not normalized (free): 115.890257 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1280 0.1551 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1631 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1467 0.1631 n_refl.: 191138 overall B=0.14 to atoms: r(all,work,free)=0.1491 0.1488 0.1640 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1273 0.1543 n_refl.: 191138 remove outliers: r(all,work,free)=0.1278 0.1273 0.1542 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3562 398.008 379.676 0.484 0.963 0.270 13.296-10.522 99.01 99 1 0.2086 528.187 520.041 0.735 0.965 0.240 10.503-8.327 99.45 178 3 0.1765 565.118 561.010 0.887 0.965 0.198 8.318-6.595 100.00 360 8 0.1697 414.736 412.827 0.909 0.965 0.150 6.588-5.215 100.00 711 7 0.1533 381.101 373.727 0.885 0.965 0.140 5.214-4.128 98.38 1367 28 0.0906 557.435 554.175 0.975 0.965 0.080 4.126-3.266 94.74 2603 46 0.0832 508.132 504.322 1.042 0.966 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.348 1.024 0.966 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.398 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.420 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1275 82.395 81.422 1.046 0.967 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.149 1.023 0.967 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0326 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1542 | n_water=805 | time (s): 2.900 (total time: 2.900) Filter (dist) r_work=0.1279 r_free=0.1548 | n_water=793 | time (s): 99.000 (total time: 101.900) Filter (q & B) r_work=0.1279 r_free=0.1547 | n_water=788 | time (s): 4.030 (total time: 105.930) Compute maps r_work=0.1279 r_free=0.1547 | n_water=788 | time (s): 2.050 (total time: 107.980) Filter (map) r_work=0.1304 r_free=0.1532 | n_water=650 | time (s): 4.270 (total time: 112.250) Find peaks r_work=0.1304 r_free=0.1532 | n_water=650 | time (s): 0.680 (total time: 112.930) Add new water r_work=0.1328 r_free=0.1557 | n_water=965 | time (s): 4.400 (total time: 117.330) Refine new water occ: r_work=0.1284 r_free=0.1513 adp: r_work=0.1271 r_free=0.1510 occ: r_work=0.1273 r_free=0.1509 adp: r_work=0.1266 r_free=0.1507 occ: r_work=0.1267 r_free=0.1507 adp: r_work=0.1264 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1506 r_work=0.1264 r_free=0.1506 | n_water=965 | time (s): 83.230 (total time: 200.560) Filter (q & B) r_work=0.1268 r_free=0.1511 | n_water=887 | time (s): 5.450 (total time: 206.010) Filter (dist only) r_work=0.1269 r_free=0.1510 | n_water=885 | time (s): 110.870 (total time: 316.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.720373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 601.492101 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 0.1253 0.1518 0.0265 0.041 1.1 17.7 0.0 0.3 0 11.860 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.18 2.65 2.046 15.212 601.492 0.014 12.30 15.06 2.76 2.417 15.285 601.492 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 68.91 16.41 1.21 517 3272 Protein: 5.41 40.90 10.99 1.21 0 2902 Water: 6.59 68.91 34.17 N/A 517 368 Other: 16.30 31.99 24.14 N/A 0 2 Chain A: 5.49 56.15 13.01 N/A 0 1624 Chain B: 5.41 68.18 12.85 N/A 0 1648 Chain S: 12.98 68.91 38.45 N/A 517 0 Histogram: Values Number of atoms 5.41 - 11.76 2082 11.76 - 18.11 697 18.11 - 24.46 261 24.46 - 30.81 200 30.81 - 37.16 184 37.16 - 43.51 164 43.51 - 49.86 96 49.86 - 56.21 56 56.21 - 62.56 36 62.56 - 68.91 13 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1506 r_work=0.1230 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1507 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1503 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013383 | | target function (ls_wunit_k1) not normalized (work): 2506.575638 | | target function (ls_wunit_k1) not normalized (free): 98.310905 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1224 0.1503 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1602 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1432 0.1602 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1600 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1513 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1231 0.1513 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3215 398.008 373.734 0.483 0.962 0.261 13.296-10.522 99.01 99 1 0.1826 528.187 519.816 0.753 0.964 0.208 10.503-8.327 99.45 178 3 0.1410 565.118 566.072 0.918 0.963 0.166 8.318-6.595 100.00 360 8 0.1544 414.736 414.630 0.935 0.963 0.140 6.588-5.215 100.00 711 7 0.1345 381.101 377.097 0.910 0.963 0.126 5.214-4.128 98.38 1367 28 0.0831 557.435 556.066 0.996 0.963 0.099 4.126-3.266 94.74 2603 46 0.0764 508.132 505.662 1.061 0.963 0.014 3.266-2.585 99.86 5447 97 0.0858 342.774 341.315 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.791 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.614 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.354 1.074 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.219 1.060 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0636 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1513 | n_water=885 | time (s): 3.440 (total time: 3.440) Filter (dist) r_work=0.1232 r_free=0.1514 | n_water=882 | time (s): 117.640 (total time: 121.080) Filter (q & B) r_work=0.1232 r_free=0.1514 | n_water=880 | time (s): 4.840 (total time: 125.920) Compute maps r_work=0.1232 r_free=0.1514 | n_water=880 | time (s): 1.870 (total time: 127.790) Filter (map) r_work=0.1275 r_free=0.1521 | n_water=684 | time (s): 3.870 (total time: 131.660) Find peaks r_work=0.1275 r_free=0.1521 | n_water=684 | time (s): 0.540 (total time: 132.200) Add new water r_work=0.1297 r_free=0.1551 | n_water=996 | time (s): 4.050 (total time: 136.250) Refine new water occ: r_work=0.1251 r_free=0.1505 adp: r_work=0.1252 r_free=0.1506 occ: r_work=0.1247 r_free=0.1502 adp: r_work=0.1247 r_free=0.1503 occ: r_work=0.1244 r_free=0.1499 adp: r_work=0.1244 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1499 r_work=0.1244 r_free=0.1499 | n_water=996 | time (s): 251.950 (total time: 388.200) Filter (q & B) r_work=0.1247 r_free=0.1508 | n_water=871 | time (s): 5.240 (total time: 393.440) Filter (dist only) r_work=0.1248 r_free=0.1506 | n_water=869 | time (s): 119.500 (total time: 512.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.713017 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.969891 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1431 0.0194 0.035 1.1 8.3 0.0 0.0 0 0.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.31 1.94 1.935 14.594 16.970 3.937 12.32 13.89 1.57 2.245 14.498 16.970 3.895 Individual atomic B min max mean iso aniso Overall: 5.56 67.67 15.27 1.06 503 3270 Protein: 5.56 36.72 10.74 1.06 0 2902 Water: 6.72 67.67 30.39 N/A 503 366 Other: 13.92 28.12 21.02 N/A 0 2 Chain A: 5.58 55.11 12.77 N/A 0 1624 Chain B: 5.56 67.67 12.54 N/A 0 1646 Chain S: 13.95 65.38 32.32 N/A 503 0 Histogram: Values Number of atoms 5.56 - 11.77 2130 11.77 - 17.99 688 17.99 - 24.20 294 24.20 - 30.41 235 30.41 - 36.62 173 36.62 - 42.83 140 42.83 - 49.04 70 49.04 - 55.25 31 55.25 - 61.46 7 61.46 - 67.67 5 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1390 r_work=0.1233 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1391 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1381 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889222 | | target function (ml) not normalized (work): 728435.683006 | | target function (ml) not normalized (free): 15212.341613 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1381 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1480 n_refl.: 191137 remove outliers: r(all,work,free)=0.1442 0.1442 0.1480 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1435 0.1435 0.1476 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1375 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1375 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 398.008 359.538 0.426 0.946 0.255 13.296-10.522 99.01 99 1 0.2388 528.187 509.686 0.704 0.947 0.210 10.503-8.327 98.35 176 3 0.1998 555.265 556.258 0.885 0.948 0.187 8.318-6.595 100.00 360 8 0.2061 414.736 410.453 0.899 0.947 0.130 6.588-5.215 100.00 711 7 0.1842 381.101 370.903 0.887 0.947 0.130 5.214-4.128 98.38 1367 28 0.1170 557.435 552.022 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1091 508.132 501.374 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1085 342.774 339.049 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0969 258.603 255.726 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.401 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.498 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.317 1.040 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1120 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1374 | n_water=869 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1223 r_free=0.1375 | n_water=867 | time (s): 106.280 (total time: 109.340) Filter (q & B) r_work=0.1224 r_free=0.1375 | n_water=859 | time (s): 4.980 (total time: 114.320) Compute maps r_work=0.1224 r_free=0.1375 | n_water=859 | time (s): 1.830 (total time: 116.150) Filter (map) r_work=0.1246 r_free=0.1377 | n_water=718 | time (s): 4.420 (total time: 120.570) Find peaks r_work=0.1246 r_free=0.1377 | n_water=718 | time (s): 0.770 (total time: 121.340) Add new water r_work=0.1261 r_free=0.1392 | n_water=944 | time (s): 4.240 (total time: 125.580) Refine new water occ: r_work=0.1215 r_free=0.1355 adp: r_work=0.1207 r_free=0.1352 occ: r_work=0.1204 r_free=0.1351 adp: r_work=0.1204 r_free=0.1351 occ: r_work=0.1204 r_free=0.1351 adp: r_work=0.1204 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1351 r_work=0.1204 r_free=0.1351 | n_water=944 | time (s): 151.690 (total time: 277.270) Filter (q & B) r_work=0.1208 r_free=0.1358 | n_water=846 | time (s): 4.470 (total time: 281.740) Filter (dist only) r_work=0.1209 r_free=0.1358 | n_water=845 | time (s): 111.660 (total time: 393.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541939 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.471855 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 0.1208 0.1358 0.0150 0.032 1.1 6.0 0.0 0.0 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.58 1.50 1.830 14.102 15.472 3.873 12.03 13.57 1.54 1.921 14.070 15.472 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.22 14.81 1.00 479 3270 Protein: 5.52 33.58 10.67 1.00 0 2902 Water: 5.93 67.22 29.00 N/A 479 366 Other: 14.00 27.24 20.62 N/A 0 2 Chain A: 5.56 54.06 12.64 N/A 0 1624 Chain B: 5.52 67.22 12.44 N/A 0 1646 Chain S: 5.93 65.19 30.26 N/A 479 0 Histogram: Values Number of atoms 5.52 - 11.69 2114 11.69 - 17.86 724 17.86 - 24.03 340 24.03 - 30.20 209 30.20 - 36.37 145 36.37 - 42.54 114 42.54 - 48.71 67 48.71 - 54.88 28 54.88 - 61.05 5 61.05 - 67.22 3 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1358 r_work=0.1203 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1358 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1357 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864854 | | target function (ml) not normalized (work): 723864.003691 | | target function (ml) not normalized (free): 15137.202373 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1357 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1435 0.1434 0.1493 n_refl.: 191135 remove outliers: r(all,work,free)=0.1435 0.1434 0.1493 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1426 0.1425 0.1487 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1355 n_refl.: 191135 remove outliers: r(all,work,free)=0.1202 0.1199 0.1355 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3744 356.373 323.750 0.410 0.947 0.240 13.296-10.522 98.02 98 1 0.2471 480.567 455.747 0.689 0.949 0.183 10.503-8.327 98.35 176 3 0.2145 502.844 495.284 0.861 0.949 0.160 8.318-6.595 100.00 360 8 0.2213 375.582 370.583 0.889 0.948 0.115 6.588-5.215 100.00 711 7 0.1918 345.122 335.343 0.882 0.949 0.090 5.214-4.128 98.38 1367 28 0.1225 504.809 499.838 0.971 0.949 0.080 4.126-3.266 94.74 2603 46 0.1129 460.161 453.429 1.034 0.949 0.000 3.266-2.585 99.86 5447 97 0.1081 310.413 307.259 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0935 234.189 231.798 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0918 138.605 137.274 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.617 73.896 1.056 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.029 38.360 1.045 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1319 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1355 | n_water=845 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1199 r_free=0.1355 | n_water=845 | time (s): 110.150 (total time: 112.390) Filter (q & B) r_work=0.1199 r_free=0.1355 | n_water=838 | time (s): 4.380 (total time: 116.770) Compute maps r_work=0.1199 r_free=0.1355 | n_water=838 | time (s): 2.380 (total time: 119.150) Filter (map) r_work=0.1221 r_free=0.1370 | n_water=717 | time (s): 3.760 (total time: 122.910) Find peaks r_work=0.1221 r_free=0.1370 | n_water=717 | time (s): 0.550 (total time: 123.460) Add new water r_work=0.1232 r_free=0.1385 | n_water=933 | time (s): 3.780 (total time: 127.240) Refine new water occ: r_work=0.1196 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 occ: r_work=0.1194 r_free=0.1349 adp: r_work=0.1194 r_free=0.1349 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1192 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1348 r_work=0.1192 r_free=0.1348 | n_water=933 | time (s): 243.320 (total time: 370.560) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=867 | time (s): 4.390 (total time: 374.950) Filter (dist only) r_work=0.1195 r_free=0.1347 | n_water=866 | time (s): 113.420 (total time: 488.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563588 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.761570 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 0.1356 0.0159 0.035 1.1 6.0 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.56 1.59 1.791 14.089 14.762 3.765 12.01 13.59 1.59 1.832 14.072 14.762 3.763 Individual atomic B min max mean iso aniso Overall: 5.60 66.96 14.89 0.96 500 3270 Protein: 5.60 32.50 10.62 0.96 0 2902 Water: 5.96 66.96 29.20 N/A 500 366 Other: 13.83 26.49 20.16 N/A 0 2 Chain A: 5.62 53.53 12.57 N/A 0 1624 Chain B: 5.60 66.96 12.37 N/A 0 1646 Chain S: 5.96 65.05 30.72 N/A 500 0 Histogram: Values Number of atoms 5.60 - 11.74 2143 11.74 - 17.88 717 17.88 - 24.01 302 24.01 - 30.15 219 30.15 - 36.28 157 36.28 - 42.42 127 42.42 - 48.56 72 48.56 - 54.69 25 54.69 - 60.83 4 60.83 - 66.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1359 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761893 | | target function (ml) not normalized (work): 704572.432666 | | target function (ml) not normalized (free): 14747.926944 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1428 0.1427 0.1506 n_refl.: 191133 remove outliers: r(all,work,free)=0.1428 0.1427 0.1506 n_refl.: 191133 overall B=-0.24 to atoms: r(all,work,free)=0.1385 0.1384 0.1477 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191133 remove outliers: r(all,work,free)=0.1201 0.1198 0.1362 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 0.3412 347.432 309.387 0.414 0.946 0.239 13.296-10.522 96.04 96 1 0.2379 480.479 451.447 0.714 0.947 0.181 10.503-8.327 97.80 175 3 0.2096 501.957 497.155 0.885 0.948 0.157 8.318-6.595 100.00 360 8 0.2172 375.582 370.980 0.916 0.947 0.110 6.588-5.215 100.00 711 7 0.1905 345.122 335.379 0.912 0.948 0.100 5.214-4.128 98.38 1367 28 0.1209 504.809 499.849 0.999 0.948 0.060 4.126-3.266 94.74 2603 46 0.1134 460.161 453.612 1.061 0.949 0.000 3.266-2.585 99.86 5447 97 0.1102 310.413 307.291 1.045 0.948 0.000 2.585-2.046 97.45 10613 204 0.0943 234.189 231.810 1.052 0.949 0.000 2.046-1.619 99.39 21536 464 0.0918 138.605 137.312 1.069 0.949 0.000 1.619-1.281 98.00 42464 925 0.0981 74.617 73.913 1.054 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.029 38.362 1.022 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9912 b_overall=0.0540 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1362 | n_water=866 | time (s): 3.050 (total time: 3.050) Filter (dist) r_work=0.1198 r_free=0.1362 | n_water=866 | time (s): 102.120 (total time: 105.170) Filter (q & B) r_work=0.1199 r_free=0.1361 | n_water=857 | time (s): 5.030 (total time: 110.200) Compute maps r_work=0.1199 r_free=0.1361 | n_water=857 | time (s): 2.340 (total time: 112.540) Filter (map) r_work=0.1220 r_free=0.1364 | n_water=742 | time (s): 4.530 (total time: 117.070) Find peaks r_work=0.1220 r_free=0.1364 | n_water=742 | time (s): 0.680 (total time: 117.750) Add new water r_work=0.1230 r_free=0.1371 | n_water=943 | time (s): 4.260 (total time: 122.010) Refine new water occ: r_work=0.1197 r_free=0.1352 adp: r_work=0.1197 r_free=0.1352 occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1352 r_work=0.1193 r_free=0.1352 | n_water=943 | time (s): 206.290 (total time: 328.300) Filter (q & B) r_work=0.1196 r_free=0.1351 | n_water=882 | time (s): 4.840 (total time: 333.140) Filter (dist only) r_work=0.1196 r_free=0.1350 | n_water=881 | time (s): 111.660 (total time: 444.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.858172 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1353 0.0154 0.035 1.1 6.5 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.53 1.54 1.767 13.818 14.858 3.763 12.01 13.53 1.52 1.916 13.772 14.858 3.760 Individual atomic B min max mean iso aniso Overall: 5.38 65.47 14.58 0.91 516 3269 Protein: 5.38 29.38 10.30 0.91 0 2902 Water: 5.82 65.47 28.69 N/A 516 365 Other: 13.68 23.49 18.58 N/A 0 2 Chain A: 5.42 52.80 12.21 N/A 0 1624 Chain B: 5.38 65.47 12.01 N/A 0 1645 Chain S: 5.82 64.20 30.24 N/A 516 0 Histogram: Values Number of atoms 5.38 - 11.39 2109 11.39 - 17.40 769 17.40 - 23.41 286 23.41 - 29.42 220 29.42 - 35.43 170 35.43 - 41.44 118 41.44 - 47.45 75 47.45 - 53.46 28 53.46 - 59.47 6 59.47 - 65.47 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1353 r_work=0.1202 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1354 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1356 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758981 | | target function (ml) not normalized (work): 704008.206661 | | target function (ml) not normalized (free): 14735.605615 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1381 0.1379 0.1471 n_refl.: 191128 remove outliers: r(all,work,free)=0.1381 0.1379 0.1471 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1390 0.1389 0.1477 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1345 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 0.3435 347.432 321.663 0.418 0.970 0.237 13.296-10.522 96.04 96 1 0.2363 480.479 462.082 0.715 0.971 0.173 10.503-8.327 97.80 175 3 0.2114 501.957 495.206 0.866 0.971 0.146 8.318-6.595 100.00 360 8 0.2216 375.582 370.356 0.899 0.971 0.100 6.588-5.215 100.00 711 7 0.1909 345.122 335.028 0.897 0.972 0.100 5.214-4.128 98.38 1367 28 0.1211 504.809 499.277 0.982 0.972 0.029 4.126-3.266 94.74 2603 46 0.1138 460.161 452.891 1.047 0.973 0.000 3.266-2.585 99.86 5447 97 0.1107 310.413 306.930 1.030 0.974 0.000 2.585-2.046 97.45 10613 204 0.0956 234.189 231.624 1.037 0.975 0.000 2.046-1.619 99.39 21536 464 0.0914 138.605 137.191 1.054 0.978 0.000 1.619-1.281 98.00 42464 925 0.0958 74.617 73.936 1.042 0.982 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.029 38.340 1.008 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0612 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1345 | n_water=881 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1189 r_free=0.1345 | n_water=881 | time (s): 104.850 (total time: 107.290) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=871 | time (s): 4.140 (total time: 111.430) Compute maps r_work=0.1190 r_free=0.1345 | n_water=871 | time (s): 1.830 (total time: 113.260) Filter (map) r_work=0.1213 r_free=0.1358 | n_water=752 | time (s): 4.930 (total time: 118.190) Find peaks r_work=0.1213 r_free=0.1358 | n_water=752 | time (s): 0.680 (total time: 118.870) Add new water r_work=0.1222 r_free=0.1369 | n_water=960 | time (s): 4.500 (total time: 123.370) Refine new water occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1186 r_free=0.1343 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1184 r_free=0.1344 adp: r_work=0.1184 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1344 r_work=0.1184 r_free=0.1344 | n_water=960 | time (s): 292.190 (total time: 415.560) Filter (q & B) r_work=0.1187 r_free=0.1346 | n_water=891 | time (s): 4.670 (total time: 420.230) Filter (dist only) r_work=0.1187 r_free=0.1344 | n_water=890 | time (s): 117.390 (total time: 537.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.639426 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1352 0.0161 0.037 1.1 7.2 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.52 1.61 1.697 13.789 14.639 3.758 11.91 13.51 1.60 1.739 13.767 14.639 3.755 Individual atomic B min max mean iso aniso Overall: 5.49 64.53 14.65 0.89 525 3269 Protein: 5.49 28.84 10.35 0.89 0 2902 Water: 5.91 64.53 28.67 N/A 525 365 Other: 13.75 22.42 18.09 N/A 0 2 Chain A: 5.54 52.58 12.23 N/A 0 1624 Chain B: 5.49 64.53 12.04 N/A 0 1645 Chain S: 5.91 63.84 30.34 N/A 525 0 Histogram: Values Number of atoms 5.49 - 11.40 2084 11.40 - 17.30 790 17.30 - 23.20 293 23.20 - 29.11 209 29.11 - 35.01 175 35.01 - 40.91 125 40.91 - 46.82 78 46.82 - 52.72 27 52.72 - 58.62 8 58.62 - 64.53 5 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1351 r_work=0.1191 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1351 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754861 | | target function (ml) not normalized (work): 703236.605130 | | target function (ml) not normalized (free): 14732.765288 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1354 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1395 0.1394 0.1494 n_refl.: 191128 remove outliers: r(all,work,free)=0.1395 0.1394 0.1494 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1398 0.1396 0.1496 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1353 n_refl.: 191128 remove outliers: r(all,work,free)=0.1191 0.1188 0.1353 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 0.3335 348.119 318.910 0.408 0.970 0.225 13.296-10.522 96.04 96 1 0.2333 480.479 462.472 0.708 0.971 0.160 10.503-8.327 97.80 175 3 0.2139 501.957 495.192 0.863 0.972 0.133 8.318-6.595 100.00 360 8 0.2181 375.582 371.065 0.895 0.971 0.090 6.588-5.215 100.00 711 7 0.1912 345.122 335.182 0.897 0.972 0.090 5.214-4.128 98.38 1367 28 0.1225 504.809 499.669 0.981 0.973 0.034 4.126-3.266 94.74 2603 46 0.1151 460.161 452.700 1.045 0.974 0.000 3.266-2.585 99.86 5447 97 0.1119 310.413 306.845 1.028 0.975 0.000 2.585-2.046 97.45 10613 204 0.0958 234.189 231.577 1.037 0.976 0.000 2.046-1.619 99.39 21536 464 0.0908 138.605 137.225 1.054 0.979 0.000 1.619-1.281 98.00 42464 925 0.0949 74.617 73.960 1.045 0.984 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.029 38.327 1.013 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1353 | n_water=890 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1188 r_free=0.1353 | n_water=890 | time (s): 105.680 (total time: 108.870) Filter (q & B) r_work=0.1189 r_free=0.1356 | n_water=879 | time (s): 4.140 (total time: 113.010) Compute maps r_work=0.1189 r_free=0.1356 | n_water=879 | time (s): 1.660 (total time: 114.670) Filter (map) r_work=0.1211 r_free=0.1362 | n_water=767 | time (s): 4.030 (total time: 118.700) Find peaks r_work=0.1211 r_free=0.1362 | n_water=767 | time (s): 0.640 (total time: 119.340) Add new water r_work=0.1218 r_free=0.1367 | n_water=986 | time (s): 4.920 (total time: 124.260) Refine new water occ: r_work=0.1185 r_free=0.1342 adp: r_work=0.1185 r_free=0.1342 occ: r_work=0.1183 r_free=0.1343 adp: r_work=0.1183 r_free=0.1342 occ: r_work=0.1181 r_free=0.1343 adp: r_work=0.1181 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1342 r_work=0.1181 r_free=0.1342 | n_water=986 | time (s): 175.770 (total time: 300.030) Filter (q & B) r_work=0.1185 r_free=0.1345 | n_water=910 | time (s): 5.180 (total time: 305.210) Filter (dist only) r_work=0.1186 r_free=0.1345 | n_water=909 | time (s): 116.810 (total time: 422.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540627 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.089635 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 0.1189 0.1346 0.0158 0.037 1.1 5.5 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.46 1.58 1.692 13.807 14.090 3.755 11.91 13.49 1.59 1.720 13.792 14.090 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 63.60 14.69 0.87 544 3269 Protein: 5.55 28.27 10.36 0.87 0 2902 Water: 6.01 63.60 28.50 N/A 544 365 Other: 13.82 22.29 18.06 N/A 0 2 Chain A: 5.61 52.16 12.20 N/A 0 1624 Chain B: 5.55 63.60 12.03 N/A 0 1645 Chain S: 6.01 63.45 30.19 N/A 544 0 Histogram: Values Number of atoms 5.55 - 11.35 2063 11.35 - 17.16 817 17.16 - 22.96 280 22.96 - 28.77 225 28.77 - 34.57 182 34.57 - 40.38 124 40.38 - 46.18 76 46.18 - 51.99 32 51.99 - 57.79 8 57.79 - 63.60 6 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1350 r_work=0.1191 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1350 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753591 | | target function (ml) not normalized (work): 702994.978989 | | target function (ml) not normalized (free): 14727.760256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1350 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1497 n_refl.: 191127 remove outliers: r(all,work,free)=0.1390 0.1388 0.1497 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1390 0.1388 0.1496 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1188 0.1349 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1188 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 0.3457 348.119 321.165 0.421 0.915 0.205 13.296-10.522 96.04 96 1 0.2343 480.479 462.977 0.739 0.916 0.137 10.503-8.327 97.80 175 3 0.2157 501.957 494.668 0.912 0.917 0.107 8.318-6.595 100.00 360 8 0.2180 375.582 370.465 0.947 0.917 0.083 6.588-5.215 100.00 711 7 0.1944 345.122 334.984 0.945 0.917 0.067 5.214-4.128 98.38 1367 28 0.1226 504.809 499.388 1.039 0.918 0.029 4.126-3.266 94.74 2603 46 0.1157 460.161 452.630 1.108 0.919 0.000 3.266-2.585 99.86 5447 97 0.1120 310.413 306.896 1.090 0.920 0.000 2.585-2.046 97.45 10613 204 0.0958 234.189 231.563 1.100 0.922 0.000 2.046-1.619 99.39 21536 464 0.0908 138.605 137.223 1.118 0.926 0.000 1.619-1.281 98.00 42464 925 0.0944 74.617 73.967 1.109 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.029 38.317 1.078 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1349 | n_water=909 | time (s): 2.190 (total time: 2.190) Filter (dist) r_work=0.1188 r_free=0.1349 | n_water=909 | time (s): 107.270 (total time: 109.460) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=897 | time (s): 4.960 (total time: 114.420) Compute maps r_work=0.1189 r_free=0.1348 | n_water=897 | time (s): 1.990 (total time: 116.410) Filter (map) r_work=0.1211 r_free=0.1361 | n_water=778 | time (s): 5.420 (total time: 121.830) Find peaks r_work=0.1211 r_free=0.1361 | n_water=778 | time (s): 0.760 (total time: 122.590) Add new water r_work=0.1218 r_free=0.1367 | n_water=989 | time (s): 4.980 (total time: 127.570) Refine new water occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1184 r_free=0.1342 adp: r_work=0.1184 r_free=0.1341 occ: r_work=0.1183 r_free=0.1342 adp: r_work=0.1182 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1341 r_work=0.1182 r_free=0.1341 | n_water=989 | time (s): 207.320 (total time: 334.890) Filter (q & B) r_work=0.1187 r_free=0.1347 | n_water=911 | time (s): 4.250 (total time: 339.140) Filter (dist only) r_work=0.1187 r_free=0.1347 | n_water=910 | time (s): 118.570 (total time: 457.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.523263 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.816119 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1351 0.0161 0.038 1.1 5.3 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.51 1.61 1.684 13.777 14.816 3.755 11.89 13.53 1.64 1.690 13.774 14.816 3.752 Individual atomic B min max mean iso aniso Overall: 5.57 62.93 14.67 0.87 545 3269 Protein: 5.57 28.29 10.38 0.87 0 2902 Water: 6.03 62.93 28.36 N/A 545 365 Other: 13.86 22.32 18.09 N/A 0 2 Chain A: 5.60 51.66 12.18 N/A 0 1624 Chain B: 5.57 62.24 12.01 N/A 0 1645 Chain S: 6.03 62.93 30.13 N/A 545 0 Histogram: Values Number of atoms 5.57 - 11.31 2051 11.31 - 17.04 829 17.04 - 22.78 281 22.78 - 28.51 214 28.51 - 34.25 189 34.25 - 39.99 122 39.99 - 45.72 77 45.72 - 51.46 35 51.46 - 57.19 9 57.19 - 62.93 7 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1354 r_work=0.1190 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1354 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1357 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** 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= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751713 | | target function (ml) not normalized (work): 702643.271464 | | target function (ml) not normalized (free): 14728.008687 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1357 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1511 n_refl.: 191127 remove outliers: r(all,work,free)=0.1398 0.1396 0.1511 n_refl.: 191127 overall B=-0.06 to atoms: r(all,work,free)=0.1388 0.1386 0.1503 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1356 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 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 0.3434 348.119 321.052 0.392 0.973 0.215 13.296-10.522 96.04 96 1 0.2335 480.479 461.836 0.680 0.975 0.145 10.503-8.327 97.80 175 3 0.2155 501.957 495.293 0.834 0.975 0.113 8.318-6.595 100.00 360 8 0.2176 375.582 370.736 0.865 0.975 0.076 6.588-5.215 100.00 711 7 0.1955 345.122 335.326 0.865 0.976 0.060 5.214-4.128 98.38 1367 28 0.1227 504.809 499.452 0.953 0.977 0.024 4.126-3.266 94.74 2603 46 0.1163 460.161 452.619 1.017 0.978 0.000 3.266-2.585 99.86 5447 97 0.1124 310.413 306.898 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0957 234.189 231.602 1.007 0.982 0.000 2.046-1.619 99.39 21536 464 0.0905 138.605 137.221 1.022 0.986 0.000 1.619-1.281 98.00 42464 925 0.0939 74.617 73.971 1.012 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.029 38.310 0.980 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0139 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1357 After: r_work=0.1188 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1357 | n_water=910 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1188 r_free=0.1357 | n_water=910 | time (s): 112.980 (total time: 115.330) Filter (q & B) r_work=0.1189 r_free=0.1355 | n_water=901 | time (s): 5.490 (total time: 120.820) Compute maps r_work=0.1189 r_free=0.1355 | n_water=901 | time (s): 2.070 (total time: 122.890) Filter (map) r_work=0.1210 r_free=0.1360 | n_water=786 | time (s): 4.760 (total time: 127.650) Find peaks r_work=0.1210 r_free=0.1360 | n_water=786 | time (s): 0.560 (total time: 128.210) Add new water r_work=0.1215 r_free=0.1369 | n_water=994 | time (s): 4.570 (total time: 132.780) Refine new water occ: r_work=0.1184 r_free=0.1350 adp: r_work=0.1184 r_free=0.1350 occ: r_work=0.1183 r_free=0.1351 adp: r_work=0.1183 r_free=0.1350 occ: r_work=0.1181 r_free=0.1351 adp: r_work=0.1181 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1351 r_work=0.1181 r_free=0.1351 | n_water=994 | time (s): 222.610 (total time: 355.390) Filter (q & B) r_work=0.1186 r_free=0.1353 | n_water=912 | time (s): 4.480 (total time: 359.870) Filter (dist only) r_work=0.1187 r_free=0.1352 | n_water=911 | time (s): 117.670 (total time: 477.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.776415 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 0.1189 0.1356 0.0167 0.038 1.2 7.8 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.56 1.67 1.684 13.720 13.776 3.754 11.91 13.60 1.68 1.684 13.717 13.776 3.754 Individual atomic B min max mean iso aniso Overall: 5.52 62.78 14.61 0.85 546 3269 Protein: 5.52 28.05 10.32 0.85 0 2902 Water: 6.00 62.78 28.23 N/A 546 365 Other: 13.79 22.26 18.03 N/A 0 2 Chain A: 5.58 51.53 12.10 N/A 0 1624 Chain B: 5.52 61.94 11.94 N/A 0 1645 Chain S: 6.00 62.78 30.06 N/A 546 0 Histogram: Values Number of atoms 5.52 - 11.25 2046 11.25 - 16.97 844 16.97 - 22.70 274 22.70 - 28.42 213 28.42 - 34.15 190 34.15 - 39.88 119 39.88 - 45.60 76 45.60 - 51.33 36 51.33 - 57.06 10 57.06 - 62.78 7 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1360 r_work=0.1191 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1362 target_work(ml) = 3.754 | | 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= 0.1191 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754426 | | target function (ml) not normalized (work): 703151.385891 | | target function (ml) not normalized (free): 14734.229859 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1346 0.1474 5.6797 5.7559| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1341 5.0758 5.1751| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1221 4.6611 4.7633| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1031 4.3949 4.5515| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.1026 4.1566 4.2695| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1110 3.9502 4.0817| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0970 3.8026 3.9404| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1326 3.7025 3.9126| | 9: 1.47 - 1.41 0.98 6938 155 0.0926 0.1132 3.6226 3.7528| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1188 3.5559 3.6784| | 11: 1.36 - 1.32 0.99 6997 151 0.0992 0.1137 3.4839 3.5859| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1122 3.4593 3.5833| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1251 3.437 3.5696| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1587 3.4331 3.6789| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1249 3.4474 3.4861| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1536 3.4645 3.6502| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1230 3.4322 3.4458| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1701 3.4382 3.5284| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1751 3.4191 3.5939| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1593 3.41 3.4373| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2126 3.418 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1936 3.4127 3.4131| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2018 3.4333 3.4882| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2254 3.4358 3.513| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2520 3.4494 3.524| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2854 3.4159 3.4218| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2811 3.4677 3.3981| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.50 1.00 0.97 10972.09| | 2: 2.94 - 2.33 7339 128 0.93 12.66 0.99 0.97 5057.79| | 3: 2.33 - 2.04 6939 150 0.96 7.69 1.01 0.98 1714.30| | 4: 2.04 - 1.85 7170 155 0.96 7.73 1.00 0.98 1017.30| | 5: 1.85 - 1.72 7113 159 0.96 8.22 1.00 0.98 648.75| | 6: 1.72 - 1.62 7102 142 0.96 8.13 1.00 0.99 449.86| | 7: 1.62 - 1.54 7104 148 0.96 8.22 1.01 0.99 342.76| | 8: 1.54 - 1.47 6798 152 0.96 8.36 1.01 0.99 283.22| | 9: 1.47 - 1.41 6938 155 0.96 8.55 1.00 1.00 233.60| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.99 203.88| | 11: 1.36 - 1.32 6997 151 0.96 8.95 0.99 0.98 175.10| | 12: 1.32 - 1.28 6975 149 0.96 9.00 0.98 0.97 160.84| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.98 158.03| | 14: 1.25 - 1.22 7015 112 0.95 10.71 1.01 0.99 163.19| | 15: 1.22 - 1.19 6956 137 0.95 11.22 1.01 1.00 166.30| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.98 159.80| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.98 153.23| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.97 147.21| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.97 150.99| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.96 150.28| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.95 153.38| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.95 155.00| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.94 165.04| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.95 179.52| | 25: 1.02 - 1.01 6552 130 0.83 25.21 0.98 0.92 182.61| | 26: 1.01 - 0.99 6767 158 0.81 26.69 0.98 0.91 177.39| | 27: 0.99 - 0.98 6647 131 0.82 26.44 0.99 0.89 162.52| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.21 max = 10972.09 mean = 916.01| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.31| |phase err.(test): min = 0.00 max = 89.27 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1362 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1398 0.1395 0.1519 n_refl.: 191127 remove outliers: r(all,work,free)=0.1398 0.1395 0.1519 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1393 0.1390 0.1514 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1361 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1190 0.1361 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 0.3449 348.119 319.647 0.388 0.974 0.212 13.296-10.522 96.04 96 1 0.2359 480.479 462.017 0.680 0.975 0.148 10.503-8.327 97.80 175 3 0.2157 501.957 495.402 0.834 0.976 0.108 8.318-6.595 100.00 360 8 0.2175 375.582 371.514 0.867 0.976 0.079 6.588-5.215 100.00 711 7 0.1936 345.122 335.558 0.867 0.976 0.060 5.214-4.128 98.38 1367 28 0.1228 504.809 499.374 0.954 0.977 0.024 4.126-3.266 94.74 2603 46 0.1160 460.161 452.605 1.018 0.979 0.000 3.266-2.585 99.86 5447 97 0.1121 310.413 307.012 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0964 234.189 231.610 1.007 0.983 0.000 2.046-1.619 99.39 21536 464 0.0912 138.605 137.217 1.022 0.988 0.000 1.619-1.281 98.00 42464 925 0.0946 74.617 73.962 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.029 38.306 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0079 ================= 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 : 0.2039 0.1957 0.081 5.225 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1898 0.081 5.225 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1898 0.081 5.225 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1898 0.081 5.225 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1898 0.081 5.225 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1268 0.1494 0.038 1.148 5.2 78.0 14.6 805 0.155 1_adp: 0.1297 0.1567 0.038 1.148 5.3 73.0 15.0 805 0.155 1_regHadp: 0.1296 0.1561 0.038 1.148 5.3 73.0 15.0 805 0.155 1_occ: 0.1280 0.1551 0.038 1.148 5.3 73.0 15.0 805 0.155 2_bss: 0.1273 0.1542 0.038 1.148 5.4 73.2 15.2 805 0.155 2_settarget: 0.1273 0.1542 0.038 1.148 5.4 73.2 15.2 805 0.155 2_updatecdl: 0.1273 0.1542 0.038 1.160 5.4 73.2 15.2 805 0.155 2_nqh: 0.1273 0.1542 0.038 1.160 5.4 73.2 15.2 805 0.155 2_sol: 0.1269 0.1510 0.038 1.160 5.4 73.2 16.3 885 n/a 2_weight: 0.1269 0.1510 0.038 1.160 5.4 73.2 16.3 885 n/a 2_xyzrec: 0.1253 0.1518 0.041 1.150 5.4 73.2 16.3 885 n/a 2_adp: 0.1230 0.1506 0.041 1.150 5.4 68.9 16.4 885 n/a 2_regHadp: 0.1230 0.1507 0.041 1.150 5.4 68.9 16.4 885 n/a 2_occ: 0.1224 0.1503 0.041 1.150 5.4 68.9 16.4 885 n/a 3_bss: 0.1231 0.1513 0.041 1.150 5.4 68.9 16.4 885 n/a 3_settarget: 0.1231 0.1513 0.041 1.150 5.4 68.9 16.4 885 n/a 3_updatecdl: 0.1231 0.1513 0.041 1.156 5.4 68.9 16.4 885 n/a 3_nqh: 0.1231 0.1513 0.041 1.156 5.4 68.9 16.4 885 n/a 3_sol: 0.1248 0.1506 0.041 1.156 5.4 68.2 15.4 869 n/a 3_weight: 0.1248 0.1506 0.041 1.156 5.4 68.2 15.4 869 n/a 3_xyzrec: 0.1237 0.1431 0.035 1.113 5.4 68.2 15.4 869 n/a 3_adp: 0.1233 0.1390 0.035 1.113 5.6 67.7 15.3 869 n/a 3_regHadp: 0.1233 0.1391 0.035 1.113 5.6 67.7 15.3 869 n/a 3_occ: 0.1227 0.1381 0.035 1.113 5.6 67.7 15.3 869 n/a 4_bss: 0.1223 0.1374 0.035 1.113 5.5 67.6 15.2 869 n/a 4_settarget: 0.1223 0.1374 0.035 1.113 5.5 67.6 15.2 869 n/a 4_updatecdl: 0.1223 0.1374 0.035 1.114 5.5 67.6 15.2 869 n/a 4_nqh: 0.1223 0.1374 0.035 1.114 5.5 67.6 15.2 869 n/a 4_sol: 0.1209 0.1358 0.035 1.114 5.5 67.6 14.9 845 n/a 4_weight: 0.1209 0.1358 0.035 1.114 5.5 67.6 14.9 845 n/a 4_xyzrec: 0.1208 0.1358 0.032 1.119 5.5 67.6 14.9 845 n/a 4_adp: 0.1203 0.1358 0.032 1.119 5.5 67.2 14.8 845 n/a 4_regHadp: 0.1203 0.1358 0.032 1.119 5.5 67.2 14.8 845 n/a 4_occ: 0.1202 0.1357 0.032 1.119 5.5 67.2 14.8 845 n/a 5_bss: 0.1199 0.1355 0.032 1.119 5.5 67.2 14.8 845 n/a 5_settarget: 0.1199 0.1355 0.032 1.119 5.5 67.2 14.8 845 n/a 5_updatecdl: 0.1199 0.1355 0.032 1.120 5.5 67.2 14.8 845 n/a 5_nqh: 0.1199 0.1355 0.032 1.120 5.5 67.2 14.8 845 n/a 5_sol: 0.1195 0.1347 0.032 1.120 5.5 67.2 14.9 866 n/a 5_weight: 0.1195 0.1347 0.032 1.120 5.5 67.2 14.9 866 n/a 5_xyzrec: 0.1197 0.1356 0.035 1.127 5.5 67.2 14.9 866 n/a 5_adp: 0.1201 0.1359 0.035 1.127 5.6 67.0 14.9 866 n/a 5_regHadp: 0.1201 0.1360 0.035 1.127 5.6 67.0 14.9 866 n/a 5_occ: 0.1199 0.1362 0.035 1.127 5.6 67.0 14.9 866 n/a 6_bss: 0.1198 0.1362 0.035 1.127 5.4 66.7 14.6 866 n/a 6_settarget: 0.1198 0.1362 0.035 1.127 5.4 66.7 14.6 866 n/a 6_updatecdl: 0.1198 0.1362 0.035 1.127 5.4 66.7 14.6 866 n/a 6_nqh: 0.1198 0.1362 0.035 1.127 5.4 66.7 14.6 866 n/a 6_sol: 0.1196 0.1350 0.035 1.127 5.4 66.7 14.7 881 n/a 6_weight: 0.1196 0.1350 0.035 1.127 5.4 66.7 14.7 881 n/a 6_xyzrec: 0.1199 0.1353 0.035 1.131 5.4 66.7 14.7 881 n/a 6_adp: 0.1202 0.1353 0.035 1.131 5.4 65.5 14.6 881 n/a 6_regHadp: 0.1202 0.1354 0.035 1.131 5.4 65.5 14.6 881 n/a 6_occ: 0.1199 0.1356 0.035 1.131 5.4 65.5 14.6 881 n/a 7_bss: 0.1189 0.1345 0.035 1.131 5.4 65.5 14.6 881 n/a 7_settarget: 0.1189 0.1345 0.035 1.131 5.4 65.5 14.6 881 n/a 7_updatecdl: 0.1189 0.1345 0.035 1.131 5.4 65.5 14.6 881 n/a 7_nqh: 0.1189 0.1345 0.035 1.131 5.4 65.5 14.6 881 n/a 7_sol: 0.1187 0.1344 0.035 1.131 5.4 65.5 14.7 890 n/a 7_weight: 0.1187 0.1344 0.035 1.131 5.4 65.5 14.7 890 n/a 7_xyzrec: 0.1191 0.1352 0.037 1.119 5.4 65.5 14.7 890 n/a 7_adp: 0.1191 0.1351 0.037 1.119 5.5 64.5 14.7 890 n/a 7_regHadp: 0.1191 0.1351 0.037 1.119 5.5 64.5 14.7 890 n/a 7_occ: 0.1190 0.1354 0.037 1.119 5.5 64.5 14.7 890 n/a 8_bss: 0.1188 0.1353 0.037 1.119 5.5 64.5 14.7 890 n/a 8_settarget: 0.1188 0.1353 0.037 1.119 5.5 64.5 14.7 890 n/a 8_updatecdl: 0.1188 0.1353 0.037 1.119 5.5 64.5 14.7 890 n/a 8_nqh: 0.1188 0.1353 0.037 1.119 5.5 64.5 14.7 890 n/a 8_sol: 0.1186 0.1345 0.037 1.119 5.5 64.5 14.7 909 n/a 8_weight: 0.1186 0.1345 0.037 1.119 5.5 64.5 14.7 909 n/a 8_xyzrec: 0.1189 0.1346 0.037 1.115 5.5 64.5 14.7 909 n/a 8_adp: 0.1191 0.1350 0.037 1.115 5.5 63.6 14.7 909 n/a 8_regHadp: 0.1191 0.1350 0.037 1.115 5.5 63.6 14.7 909 n/a 8_occ: 0.1190 0.1350 0.037 1.115 5.5 63.6 14.7 909 n/a 9_bss: 0.1188 0.1349 0.037 1.115 5.5 63.6 14.7 909 n/a 9_settarget: 0.1188 0.1349 0.037 1.115 5.5 63.6 14.7 909 n/a 9_updatecdl: 0.1188 0.1349 0.037 1.115 5.5 63.6 14.7 909 n/a 9_nqh: 0.1188 0.1349 0.037 1.115 5.5 63.6 14.7 909 n/a 9_sol: 0.1187 0.1347 0.037 1.115 5.5 63.6 14.7 910 n/a 9_weight: 0.1187 0.1347 0.037 1.115 5.5 63.6 14.7 910 n/a 9_xyzrec: 0.1191 0.1351 0.038 1.110 5.5 63.6 14.7 910 n/a 9_adp: 0.1190 0.1354 0.038 1.110 5.6 62.9 14.7 910 n/a 9_regHadp: 0.1190 0.1354 0.038 1.110 5.6 62.9 14.7 910 n/a 9_occ: 0.1188 0.1357 0.038 1.110 5.6 62.9 14.7 910 n/a 10_bss: 0.1187 0.1357 0.038 1.110 5.5 62.9 14.6 910 n/a 10_settarget: 0.1187 0.1357 0.038 1.110 5.5 62.9 14.6 910 n/a 10_updatecdl: 0.1187 0.1357 0.038 1.110 5.5 62.9 14.6 910 n/a 10_setrh: 0.1188 0.1357 0.038 1.110 5.5 62.9 14.6 910 n/a 10_nqh: 0.1188 0.1357 0.038 1.110 5.5 62.9 14.6 910 n/a 10_sol: 0.1187 0.1352 0.038 1.110 5.5 62.9 14.6 911 n/a 10_weight: 0.1187 0.1352 0.038 1.110 5.5 62.9 14.6 911 n/a 10_xyzrec: 0.1189 0.1356 0.038 1.158 5.5 62.9 14.6 911 n/a 10_adp: 0.1191 0.1360 0.038 1.158 5.5 62.8 14.6 911 n/a 10_regHadp: 0.1191 0.1360 0.038 1.158 5.5 62.8 14.6 911 n/a 10_occ: 0.1191 0.1362 0.038 1.158 5.5 62.8 14.6 911 n/a end: 0.1190 0.1361 0.038 1.158 5.5 62.7 14.6 911 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5179049_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5179049_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.7200 Refinement macro-cycles (run) : 11785.8600 Write final files (write_after_run_outputs) : 176.2400 Total : 11968.8200 Total CPU time: 3.34 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:42 PST -0800 (1736735802.84 s) Start R-work = 0.1804, R-free = 0.1898 Final R-work = 0.1190, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12315.29 seconds wall clock time: 206 minutes 15.80 seconds (12375.80 seconds total)