Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5578134.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5578134.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5578134.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.41, per 1000 atoms: 0.36 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: 2.655 distance_ideal: 2.720 ideal - model: 0.065 slack: 0.000 delta_slack: 0.065 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: 2.771 distance_ideal: 2.710 ideal - model: -0.061 slack: 0.000 delta_slack: -0.061 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: 0.92 Conformation dependent library (CDL) restraints added in 118.1 milliseconds Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 766 1.02 - 1.26: 2568 1.26 - 1.50: 1613 1.50 - 1.74: 975 1.74 - 1.99: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" CA PHE B 119 " pdb=" CB PHE B 119 " ideal model delta sigma weight residual 1.528 1.731 -0.203 1.07e-02 8.73e+03 3.61e+02 bond pdb=" CG2 THR A 111 " pdb="HG21 THR A 111 " ideal model delta sigma weight residual 0.970 1.339 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 1.522 1.743 -0.221 1.20e-02 6.94e+03 3.39e+02 bond pdb=" N ALA B 104 " pdb=" H ALA B 104 " ideal model delta sigma weight residual 0.860 1.223 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" CD PRO B 11 " pdb=" HD2 PRO B 11 " ideal model delta sigma weight residual 0.970 1.331 -0.361 2.00e-02 2.50e+03 3.25e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 5631 4.23 - 8.45: 3618 8.45 - 12.68: 1273 12.68 - 16.91: 272 16.91 - 21.13: 16 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 97 " pdb=" CZ ARG B 97 " pdb=" NH2 ARG B 97 " ideal model delta sigma weight residual 119.20 132.60 -13.40 9.00e-01 1.23e+00 2.22e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 110.19 9.19 6.80e-01 2.16e+00 1.83e+02 angle pdb=" CA ILE B 22 " pdb=" C ILE B 22 " pdb=" O ILE B 22 " ideal model delta sigma weight residual 121.17 135.46 -14.29 1.06e+00 8.90e-01 1.82e+02 angle pdb=" CA ASP B 68 " pdb=" CB ASP B 68 " pdb=" CG ASP B 68 " ideal model delta sigma weight residual 112.60 99.14 13.46 1.00e+00 1.00e+00 1.81e+02 angle pdb=" CA ALA A 148 " pdb=" C ALA A 148 " pdb=" O ALA A 148 " ideal model delta sigma weight residual 119.49 103.50 15.99 1.21e+00 6.83e-01 1.75e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 1866 17.81 - 35.61: 119 35.61 - 53.42: 38 53.42 - 71.23: 23 71.23 - 89.03: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -21.73 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.236: 207 0.236 - 0.471: 161 0.471 - 0.706: 85 0.706 - 0.942: 30 0.942 - 1.177: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 54 " pdb=" CB LEU B 54 " pdb=" CD1 LEU B 54 " pdb=" CD2 LEU B 54 " both_signs ideal model delta sigma weight residual False -2.59 -3.77 1.18 2.00e-01 2.50e+01 3.46e+01 chirality pdb=" CA VAL B 181 " pdb=" N VAL B 181 " pdb=" C VAL B 181 " pdb=" CB VAL B 181 " both_signs ideal model delta sigma weight residual False 2.44 1.31 1.13 2.00e-01 2.50e+01 3.17e+01 chirality pdb=" CA TYR B 67 " pdb=" N TYR B 67 " pdb=" C TYR B 67 " pdb=" CB TYR B 67 " both_signs ideal model delta sigma weight residual False 2.51 3.59 -1.08 2.00e-01 2.50e+01 2.90e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.014 2.00e-02 2.50e+03 6.08e-02 1.48e+02 pdb=" CG TRP A 146 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.048 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.088 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.052 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.116 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.074 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.062 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.036 2.00e-02 2.50e+03 6.03e-02 1.45e+02 pdb=" CG TRP A 139 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.075 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.090 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.092 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.083 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.049 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " 0.097 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 194 " -0.030 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG TYR B 194 " 0.140 2.00e-02 2.50e+03 pdb=" CD1 TYR B 194 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 194 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 194 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR B 194 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR B 194 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 194 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 TYR B 194 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR B 194 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 TYR B 194 " 0.080 2.00e-02 2.50e+03 pdb=" HE2 TYR B 194 " 0.073 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.61: 26 1.61 - 2.36: 2389 2.36 - 3.11: 22226 3.11 - 3.85: 33040 3.85 - 4.60: 52579 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110260 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.866 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.955 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.961 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.050 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.140 2.620 ... (remaining 110255 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_5578134_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= 0.2030 r_free= 0.1998 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298517 | | target function (ml) not normalized (work): 805168.189813 | | target function (ml) not normalized (free): 16560.083174 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2130 0.1899 6.6804 6.3066| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1781 5.5352 5.6165| | 3: 2.33 - 2.04 0.96 6939 150 0.1627 0.1489 5.1436 5.0894| | 4: 2.04 - 1.85 1.00 7170 155 0.1768 0.1612 4.9608 5.0177| | 5: 1.85 - 1.72 0.99 7113 159 0.1899 0.1878 4.7863 4.8459| | 6: 1.72 - 1.62 0.99 7102 142 0.1971 0.2038 4.6652 4.6965| | 7: 1.62 - 1.54 0.99 7104 148 0.2025 0.1742 4.549 4.6042| | 8: 1.54 - 1.47 0.96 6798 152 0.2014 0.2279 4.465 4.5633| | 9: 1.47 - 1.41 0.98 6938 155 0.2092 0.1958 4.378 4.3624| | 10: 1.41 - 1.36 0.99 7022 150 0.2110 0.2179 4.307 4.388| | 11: 1.36 - 1.32 0.99 6997 151 0.2084 0.2092 4.2464 4.2696| | 12: 1.32 - 1.28 0.98 6976 149 0.2114 0.2119 4.1911 4.2904| | 13: 1.28 - 1.25 0.98 6907 166 0.1999 0.1991 4.1137 4.1285| | 14: 1.25 - 1.22 0.98 7015 113 0.2113 0.2184 4.0868 4.1857| | 15: 1.22 - 1.19 0.98 6957 137 0.2095 0.2066 4.0375 4.0646| | 16: 1.19 - 1.17 0.93 6604 132 0.2101 0.2330 4.0015 4.0792| | 17: 1.17 - 1.14 0.98 6941 135 0.2146 0.1999 3.9476 3.9956| | 18: 1.14 - 1.12 0.98 6875 142 0.2231 0.2266 3.9175 3.8689| | 19: 1.12 - 1.10 0.97 6949 106 0.2261 0.2556 3.8712 4.0017| | 20: 1.10 - 1.08 0.97 6884 147 0.2329 0.2240 3.8288 3.8154| | 21: 1.08 - 1.07 0.97 6852 152 0.2441 0.2907 3.7993 3.8341| | 22: 1.07 - 1.05 0.97 6838 135 0.2560 0.2844 3.7611 3.7863| | 23: 1.05 - 1.03 0.97 6829 159 0.2679 0.2704 3.7228 3.8204| | 24: 1.03 - 1.02 0.96 6785 133 0.2860 0.2806 3.6995 3.7968| | 25: 1.02 - 1.01 0.93 6552 130 0.3096 0.2954 3.6806 3.7372| | 26: 1.01 - 0.99 0.96 6767 158 0.3228 0.3306 3.6316 3.656| | 27: 0.99 - 0.98 0.94 6648 131 0.3413 0.3161 3.6405 3.5955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.40 0.91 0.97 35273.52| | 2: 2.94 - 2.33 7339 128 0.86 21.17 1.08 1.02 15007.82| | 3: 2.33 - 2.04 6939 150 0.93 12.25 1.11 1.06 4063.87| | 4: 2.04 - 1.85 7170 155 0.93 13.02 1.12 1.08 2636.83| | 5: 1.85 - 1.72 7113 159 0.91 15.31 1.11 1.09 2033.84| | 6: 1.72 - 1.62 7102 142 0.90 16.87 1.11 1.08 1666.80| | 7: 1.62 - 1.54 7104 148 0.89 17.92 1.11 1.06 1355.11| | 8: 1.54 - 1.47 6798 152 0.89 18.08 1.10 1.06 1117.84| | 9: 1.47 - 1.41 6938 155 0.88 18.78 1.11 1.06 949.84| | 10: 1.41 - 1.36 7022 150 0.87 19.96 1.09 1.05 855.45| | 11: 1.36 - 1.32 6997 151 0.87 20.24 1.07 1.05 765.19| | 12: 1.32 - 1.28 6976 149 0.87 20.14 1.08 1.05 679.50| | 13: 1.28 - 1.25 6907 166 0.87 19.75 1.07 1.04 602.14| | 14: 1.25 - 1.22 7015 113 0.87 20.65 1.07 1.03 562.80| | 15: 1.22 - 1.19 6957 137 0.86 20.99 1.08 1.04 538.24| | 16: 1.19 - 1.17 6604 132 0.87 20.35 1.07 1.04 485.19| | 17: 1.17 - 1.14 6941 135 0.87 20.47 1.08 1.03 425.90| | 18: 1.14 - 1.12 6875 142 0.87 20.25 1.08 1.01 369.58| | 19: 1.12 - 1.10 6949 106 0.86 21.35 1.07 1.00 363.33| | 20: 1.10 - 1.08 6884 147 0.85 22.76 1.06 0.97 345.29| | 21: 1.08 - 1.07 6852 152 0.83 24.83 1.06 0.95 347.69| | 22: 1.07 - 1.05 6838 135 0.81 26.59 1.06 0.94 342.20| | 23: 1.05 - 1.03 6829 159 0.79 28.47 1.05 0.95 343.81| | 24: 1.03 - 1.02 6785 133 0.77 30.22 1.06 0.97 343.70| | 25: 1.02 - 1.01 6552 130 0.76 31.48 1.03 0.93 320.23| | 26: 1.01 - 0.99 6767 158 0.74 33.30 1.03 0.90 305.26| | 27: 0.99 - 0.98 6648 131 0.73 33.63 1.04 0.88 287.75| |alpha: min = 0.88 max = 1.09 mean = 1.01| |beta: min = 287.75 max = 35273.52 mean = 2807.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.95 mean = 21.73| |phase err.(test): min = 0.00 max = 89.63 mean = 21.64| |-----------------------------------------------------------------------------| ----------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 0.244 2950 Z= 5.386 Angle : 5.264 16.834 4018 Z= 3.723 Chirality : 0.405 1.177 492 Planarity : 0.033 0.159 512 Dihedral : 12.773 89.032 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.66 % Favored : 94.82 % Rotamer: Outliers : 0.97 % Allowed : 3.55 % Favored : 95.48 % Cbeta Deviations : 33.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.40), residues: 386 helix: -3.01 (0.30), residues: 144 sheet: -0.92 (0.61), residues: 66 loop : -0.20 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.024 ARG A 143 TYR 0.129 0.036 TYR B 194 PHE 0.106 0.036 PHE A 164 TRP 0.080 0.036 TRP A 139 HIS 0.085 0.032 HIS B 116 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= 0.2030 r_free= 0.1998 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298517 | | target function (ml) not normalized (work): 805168.189813 | | target function (ml) not normalized (free): 16560.083174 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2030 0.1998 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2030 0.1998 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2030 0.1998 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2029 0.2030 0.1998 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1800 0.1797 0.1926 n_refl.: 191145 remove outliers: r(all,work,free)=0.1798 0.1795 0.1926 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4217 400.535 296.002 0.436 0.913 0.301 13.296-10.522 99.01 99 1 0.2528 528.187 518.836 0.785 0.914 0.248 10.503-8.327 99.45 178 3 0.2517 565.118 555.966 0.972 0.914 0.220 8.318-6.595 100.00 360 8 0.2500 414.736 404.050 0.968 0.914 0.166 6.588-5.215 100.00 711 7 0.2273 381.101 366.328 0.955 0.914 0.133 5.214-4.128 98.38 1367 28 0.1485 557.435 550.486 1.074 0.914 0.080 4.126-3.266 94.74 2603 46 0.1334 508.132 499.273 1.144 0.915 0.028 3.266-2.585 99.86 5447 97 0.1436 342.774 337.843 1.119 0.914 0.005 2.585-2.046 97.45 10613 204 0.1399 258.603 254.255 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 149.846 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1916 82.395 80.242 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2316 44.203 41.620 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0035 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1795 r_free=0.1926 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1797 r_free=0.1931 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.073701 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 579.430503 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1508 0.0236 0.039 1.1 11.2 0.0 0.3 0 11.037 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.08 2.36 1.117 13.113 579.431 0.018 12.95 15.70 2.75 1.230 13.325 579.431 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.05 14.99 1.41 435 3274 Protein: 5.15 40.69 10.99 1.41 0 2902 Water: 6.32 73.05 29.38 N/A 435 370 Other: 15.96 29.78 22.87 N/A 0 2 Chain A: 5.35 59.50 13.03 N/A 0 1626 Chain B: 5.15 73.05 12.75 N/A 0 1648 Chain S: 12.51 62.75 30.77 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2167 11.94 - 18.73 635 18.73 - 25.52 320 25.52 - 32.31 261 32.31 - 39.10 159 39.10 - 45.89 103 45.89 - 52.68 42 52.68 - 59.47 16 59.47 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1570 r_work=0.1295 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1565 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 = 0.1562 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1562 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015632 | | target function (ls_wunit_k1) not normalized (work): 2927.763790 | | target function (ls_wunit_k1) not normalized (free): 117.331396 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1280 0.1562 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1637 n_refl.: 191140 remove outliers: r(all,work,free)=0.1470 0.1467 0.1637 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1493 0.1491 0.1647 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1278 0.1273 0.1552 n_refl.: 191140 remove outliers: r(all,work,free)=0.1278 0.1273 0.1551 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3585 402.814 377.817 0.480 0.963 0.269 13.296-10.522 99.01 99 1 0.2089 528.187 522.222 0.736 0.964 0.235 10.503-8.327 99.45 178 3 0.1761 565.118 562.150 0.891 0.964 0.193 8.318-6.595 100.00 360 8 0.1723 414.736 412.396 0.909 0.964 0.150 6.588-5.215 100.00 711 7 0.1553 381.101 372.752 0.887 0.964 0.140 5.214-4.128 98.38 1367 28 0.0903 557.435 555.089 0.977 0.964 0.054 4.126-3.266 94.74 2603 46 0.0836 508.132 504.155 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0926 342.774 340.232 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.332 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1086 153.054 151.376 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.428 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.191 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0374 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1551 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1551 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1551 | n_water=805 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1277 r_free=0.1555 | n_water=795 | time (s): 95.570 (total time: 97.870) Filter (q & B) r_work=0.1277 r_free=0.1555 | n_water=791 | time (s): 4.770 (total time: 102.640) Compute maps r_work=0.1277 r_free=0.1555 | n_water=791 | time (s): 1.960 (total time: 104.600) Filter (map) r_work=0.1301 r_free=0.1537 | n_water=663 | time (s): 4.480 (total time: 109.080) Find peaks r_work=0.1301 r_free=0.1537 | n_water=663 | time (s): 0.760 (total time: 109.840) Add new water r_work=0.1322 r_free=0.1561 | n_water=958 | time (s): 5.210 (total time: 115.050) Refine new water occ: r_work=0.1281 r_free=0.1523 adp: r_work=0.1269 r_free=0.1516 occ: r_work=0.1271 r_free=0.1516 adp: r_work=0.1265 r_free=0.1513 occ: r_work=0.1266 r_free=0.1510 adp: r_work=0.1263 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1512 r_work=0.1263 r_free=0.1512 | n_water=958 | time (s): 84.320 (total time: 199.370) Filter (q & B) r_work=0.1267 r_free=0.1514 | n_water=889 | time (s): 5.190 (total time: 204.560) Filter (dist only) r_work=0.1268 r_free=0.1512 | n_water=887 | time (s): 113.510 (total time: 318.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.775010 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 587.662262 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1252 0.1528 0.0276 0.042 1.1 18.4 0.0 0.3 0 11.888 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.28 2.76 2.043 15.211 587.662 0.014 12.30 15.17 2.87 2.426 15.321 587.662 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 70.01 16.50 1.21 519 3272 Protein: 5.38 40.88 10.97 1.21 0 2902 Water: 6.60 70.01 34.56 N/A 519 368 Other: 16.34 32.49 24.42 N/A 0 2 Chain A: 5.46 55.54 13.00 N/A 0 1624 Chain B: 5.38 68.21 12.83 N/A 0 1648 Chain S: 12.78 70.01 39.08 N/A 519 0 Histogram: Values Number of atoms 5.38 - 11.84 2095 11.84 - 18.30 696 18.30 - 24.77 260 24.77 - 31.23 200 31.23 - 37.69 176 37.69 - 44.16 159 44.16 - 50.62 94 50.62 - 57.08 59 57.08 - 63.55 39 63.55 - 70.01 13 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1517 r_work=0.1231 r_free=0.1518 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1518 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1512 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1223 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013333 | | target function (ls_wunit_k1) not normalized (work): 2497.239563 | | target function (ls_wunit_k1) not normalized (free): 100.814162 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1223 0.1512 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1610 n_refl.: 191138 remove outliers: r(all,work,free)=0.1433 0.1430 0.1610 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1608 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1230 0.1520 n_refl.: 191138 remove outliers: r(all,work,free)=0.1235 0.1230 0.1520 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3166 402.814 379.246 0.490 0.962 0.265 13.296-10.522 99.01 99 1 0.1818 528.187 520.382 0.757 0.963 0.213 10.503-8.327 99.45 178 3 0.1391 565.118 567.092 0.924 0.963 0.169 8.318-6.595 100.00 360 8 0.1556 414.736 413.856 0.936 0.963 0.150 6.588-5.215 100.00 711 7 0.1343 381.101 376.358 0.913 0.963 0.140 5.214-4.128 98.38 1367 28 0.0825 557.435 556.190 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0760 508.132 505.575 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0858 342.774 341.347 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.758 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.597 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.353 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.220 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1520 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1230 r_free=0.1520 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1520 | n_water=887 | time (s): 3.440 (total time: 3.440) Filter (dist) r_work=0.1232 r_free=0.1521 | n_water=880 | time (s): 111.690 (total time: 115.130) Filter (q & B) r_work=0.1233 r_free=0.1522 | n_water=874 | time (s): 5.210 (total time: 120.340) Compute maps r_work=0.1233 r_free=0.1522 | n_water=874 | time (s): 2.080 (total time: 122.420) Filter (map) r_work=0.1272 r_free=0.1530 | n_water=688 | time (s): 5.040 (total time: 127.460) Find peaks r_work=0.1272 r_free=0.1530 | n_water=688 | time (s): 0.750 (total time: 128.210) Add new water r_work=0.1296 r_free=0.1563 | n_water=1021 | time (s): 4.310 (total time: 132.520) Refine new water occ: r_work=0.1250 r_free=0.1524 adp: r_work=0.1250 r_free=0.1526 occ: r_work=0.1246 r_free=0.1521 adp: r_work=0.1245 r_free=0.1522 occ: r_work=0.1242 r_free=0.1518 adp: r_work=0.1242 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1519 r_work=0.1242 r_free=0.1519 | n_water=1021 | time (s): 298.570 (total time: 431.090) Filter (q & B) r_work=0.1246 r_free=0.1523 | n_water=887 | time (s): 5.330 (total time: 436.420) Filter (dist only) r_work=0.1247 r_free=0.1522 | n_water=886 | time (s): 114.550 (total time: 550.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.749124 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.070126 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 0.1236 0.1441 0.0204 0.035 1.1 7.5 0.0 0.0 0 0.875 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.41 2.04 1.931 14.639 16.070 3.938 12.33 13.98 1.66 2.280 14.523 16.070 3.896 Individual atomic B min max mean iso aniso Overall: 5.54 67.68 15.34 1.04 519 3271 Protein: 5.54 36.29 10.69 1.04 0 2902 Water: 6.71 67.68 30.53 N/A 519 367 Other: 13.82 28.16 20.99 N/A 0 2 Chain A: 5.60 54.22 12.73 N/A 0 1624 Chain B: 5.54 67.68 12.50 N/A 0 1647 Chain S: 14.41 65.65 32.48 N/A 519 0 Histogram: Values Number of atoms 5.54 - 11.75 2125 11.75 - 17.97 707 17.97 - 24.18 293 24.18 - 30.40 228 30.40 - 36.61 179 36.61 - 42.82 133 42.82 - 49.04 80 49.04 - 55.25 32 55.25 - 61.46 8 61.46 - 67.68 5 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1399 r_work=0.1233 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1400 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1388 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889814 | | target function (ml) not normalized (work): 728550.524513 | | target function (ml) not normalized (free): 15212.324847 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1387 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1439 0.1475 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1439 0.1475 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1432 0.1472 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1383 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1224 0.1383 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 0.3819 398.008 360.946 0.419 0.947 0.249 13.296-10.522 99.01 99 1 0.2435 528.187 509.698 0.709 0.948 0.206 10.503-8.327 99.45 178 3 0.2054 565.118 561.382 0.886 0.948 0.183 8.318-6.595 100.00 360 8 0.2086 414.736 411.342 0.897 0.948 0.115 6.588-5.215 100.00 711 7 0.1836 381.101 370.583 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1170 557.435 552.020 0.971 0.948 0.080 4.126-3.266 94.74 2603 46 0.1095 508.132 501.106 1.032 0.948 0.015 3.266-2.585 99.86 5447 97 0.1087 342.774 339.151 1.019 0.947 0.005 2.585-2.046 97.45 10613 204 0.0963 258.603 255.848 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.454 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.506 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.321 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1033 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1383 | n_water=886 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1224 r_free=0.1384 | n_water=885 | time (s): 110.570 (total time: 113.220) Filter (q & B) r_work=0.1225 r_free=0.1384 | n_water=877 | time (s): 4.700 (total time: 117.920) Compute maps r_work=0.1225 r_free=0.1384 | n_water=877 | time (s): 1.740 (total time: 119.660) Filter (map) r_work=0.1250 r_free=0.1381 | n_water=722 | time (s): 4.650 (total time: 124.310) Find peaks r_work=0.1250 r_free=0.1381 | n_water=722 | time (s): 0.750 (total time: 125.060) Add new water r_work=0.1264 r_free=0.1402 | n_water=959 | time (s): 5.400 (total time: 130.460) Refine new water occ: r_work=0.1215 r_free=0.1371 adp: r_work=0.1207 r_free=0.1366 occ: r_work=0.1205 r_free=0.1367 adp: r_work=0.1205 r_free=0.1366 occ: r_work=0.1203 r_free=0.1367 adp: r_work=0.1203 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1366 r_work=0.1203 r_free=0.1366 | n_water=959 | time (s): 291.960 (total time: 422.420) Filter (q & B) r_work=0.1209 r_free=0.1375 | n_water=863 | time (s): 4.930 (total time: 427.350) Filter (dist only) r_work=0.1209 r_free=0.1374 | n_water=862 | time (s): 109.410 (total time: 536.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.591052 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.806007 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 0.1207 0.1372 0.0165 0.035 1.1 6.5 0.0 0.0 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.72 1.65 1.813 14.151 15.806 3.874 12.00 13.72 1.72 1.899 14.119 15.806 3.865 Individual atomic B min max mean iso aniso Overall: 5.51 67.16 14.94 0.99 497 3269 Protein: 5.51 33.14 10.63 0.99 0 2902 Water: 6.04 67.16 29.44 N/A 497 365 Other: 13.95 26.71 20.33 N/A 0 2 Chain A: 5.56 52.98 12.60 N/A 0 1623 Chain B: 5.51 67.16 12.41 N/A 0 1646 Chain S: 6.04 65.49 31.01 N/A 497 0 Histogram: Values Number of atoms 5.51 - 11.67 2104 11.67 - 17.84 747 17.84 - 24.00 290 24.00 - 30.17 226 30.17 - 36.33 178 36.33 - 42.50 116 42.50 - 48.66 68 48.66 - 54.83 27 54.83 - 60.99 6 60.99 - 67.16 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1373 r_work=0.1200 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1373 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1372 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863250 | | target function (ml) not normalized (work): 723571.223464 | | target function (ml) not normalized (free): 15133.652421 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1371 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1481 n_refl.: 191137 remove outliers: r(all,work,free)=0.1425 0.1424 0.1481 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1417 0.1477 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1369 n_refl.: 191137 remove outliers: r(all,work,free)=0.1199 0.1196 0.1369 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 0.3768 360.418 322.854 0.411 0.948 0.246 13.296-10.522 98.02 98 1 0.2437 478.949 454.878 0.700 0.949 0.204 10.503-8.327 98.90 177 3 0.2122 504.631 502.905 0.876 0.949 0.190 8.318-6.595 100.00 360 8 0.2163 375.567 371.348 0.890 0.949 0.105 6.588-5.215 100.00 711 7 0.1903 345.109 335.187 0.880 0.949 0.084 5.214-4.128 98.38 1367 28 0.1204 504.789 499.253 0.969 0.949 0.070 4.126-3.266 94.74 2603 46 0.1113 460.143 453.459 1.032 0.949 0.000 3.266-2.585 99.86 5447 97 0.1087 310.401 307.077 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0941 234.180 231.648 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0917 138.599 137.249 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0982 74.614 73.877 1.055 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.027 38.344 1.043 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1099 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1369 | n_water=862 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1196 r_free=0.1369 | n_water=862 | time (s): 104.560 (total time: 107.240) Filter (q & B) r_work=0.1196 r_free=0.1370 | n_water=855 | time (s): 4.430 (total time: 111.670) Compute maps r_work=0.1196 r_free=0.1370 | n_water=855 | time (s): 1.880 (total time: 113.550) Filter (map) r_work=0.1217 r_free=0.1362 | n_water=736 | time (s): 5.090 (total time: 118.640) Find peaks r_work=0.1217 r_free=0.1362 | n_water=736 | time (s): 0.820 (total time: 119.460) Add new water r_work=0.1229 r_free=0.1385 | n_water=954 | time (s): 4.700 (total time: 124.160) Refine new water occ: r_work=0.1195 r_free=0.1354 adp: r_work=0.1195 r_free=0.1354 occ: r_work=0.1192 r_free=0.1354 adp: r_work=0.1192 r_free=0.1354 occ: r_work=0.1190 r_free=0.1355 adp: r_work=0.1190 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1354 r_work=0.1190 r_free=0.1354 | n_water=954 | time (s): 226.420 (total time: 350.580) Filter (q & B) r_work=0.1194 r_free=0.1363 | n_water=884 | time (s): 5.450 (total time: 356.030) Filter (dist only) r_work=0.1195 r_free=0.1362 | n_water=883 | time (s): 114.920 (total time: 470.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.611517 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.171887 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 0.1363 0.0166 0.035 1.1 7.5 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.63 1.66 1.782 14.120 15.172 3.763 12.00 13.67 1.67 1.839 14.094 15.172 3.762 Individual atomic B min max mean iso aniso Overall: 5.56 66.81 14.96 0.95 518 3269 Protein: 5.56 31.64 10.57 0.95 0 2902 Water: 5.96 66.81 29.39 N/A 518 365 Other: 13.85 25.62 19.73 N/A 0 2 Chain A: 5.58 52.52 12.50 N/A 0 1623 Chain B: 5.56 66.81 12.33 N/A 0 1646 Chain S: 5.96 65.39 31.05 N/A 518 0 Histogram: Values Number of atoms 5.56 - 11.68 2124 11.68 - 17.81 741 17.81 - 23.93 295 23.93 - 30.06 215 30.06 - 36.18 185 36.18 - 42.31 121 42.31 - 48.43 70 48.43 - 54.56 27 54.56 - 60.68 5 60.68 - 66.81 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1367 r_work=0.1200 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1367 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761078 | | target function (ml) not normalized (work): 704427.348450 | | target function (ml) not normalized (free): 14743.689565 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1367 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1423 0.1422 0.1481 n_refl.: 191135 remove outliers: r(all,work,free)=0.1423 0.1422 0.1481 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1415 0.1414 0.1475 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191135 remove outliers: r(all,work,free)=0.1201 0.1198 0.1364 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3750 357.128 316.778 0.388 0.947 0.219 13.296-10.522 97.03 97 1 0.2415 481.222 458.471 0.690 0.948 0.171 10.503-8.327 98.35 176 3 0.2161 502.824 496.278 0.868 0.948 0.150 8.318-6.595 100.00 360 8 0.2178 375.567 370.603 0.891 0.948 0.105 6.588-5.215 100.00 711 7 0.1914 345.109 335.352 0.885 0.948 0.090 5.214-4.128 98.38 1367 28 0.1212 504.789 499.292 0.971 0.948 0.039 4.126-3.266 94.74 2603 46 0.1132 460.143 453.498 1.035 0.949 0.000 3.266-2.585 99.86 5447 97 0.1099 310.401 307.215 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0950 234.180 231.700 1.034 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.599 137.298 1.056 0.948 0.000 1.619-1.281 98.00 42464 925 0.0976 74.614 73.901 1.052 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.027 38.349 1.038 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1290 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1199 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1367 | n_water=883 | time (s): 3.180 (total time: 3.180) Filter (dist) r_work=0.1199 r_free=0.1367 | n_water=883 | time (s): 103.940 (total time: 107.120) Filter (q & B) r_work=0.1199 r_free=0.1367 | n_water=874 | time (s): 4.300 (total time: 111.420) Compute maps r_work=0.1199 r_free=0.1367 | n_water=874 | time (s): 2.120 (total time: 113.540) Filter (map) r_work=0.1219 r_free=0.1360 | n_water=759 | time (s): 4.630 (total time: 118.170) Find peaks r_work=0.1219 r_free=0.1360 | n_water=759 | time (s): 0.540 (total time: 118.710) Add new water r_work=0.1227 r_free=0.1373 | n_water=967 | time (s): 4.270 (total time: 122.980) Refine new water occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1191 r_free=0.1353 adp: r_work=0.1191 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1352 r_work=0.1191 r_free=0.1352 | n_water=967 | time (s): 185.300 (total time: 308.280) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=893 | time (s): 5.150 (total time: 313.430) Filter (dist only) r_work=0.1196 r_free=0.1359 | n_water=892 | time (s): 117.520 (total time: 430.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599539 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.849121 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1365 0.0166 0.036 1.1 7.0 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.65 1.66 1.753 14.042 14.849 3.762 12.02 13.66 1.64 1.868 14.001 14.849 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 65.67 14.88 0.90 527 3269 Protein: 5.57 29.34 10.47 0.90 0 2902 Water: 6.04 65.67 29.19 N/A 527 365 Other: 13.87 23.00 18.44 N/A 0 2 Chain A: 5.65 52.00 12.37 N/A 0 1623 Chain B: 5.57 65.67 12.21 N/A 0 1646 Chain S: 6.04 65.52 30.93 N/A 527 0 Histogram: Values Number of atoms 5.57 - 11.58 2106 11.58 - 17.59 776 17.59 - 23.60 285 23.60 - 29.61 201 29.61 - 35.62 180 35.62 - 41.63 130 41.63 - 47.64 79 47.64 - 53.65 30 53.65 - 59.66 4 59.66 - 65.67 5 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1367 r_work=0.1202 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758133 | | target function (ml) not normalized (work): 703860.734037 | | target function (ml) not normalized (free): 14736.703339 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1484 n_refl.: 191131 remove outliers: r(all,work,free)=0.1403 0.1402 0.1484 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1368 0.1366 0.1463 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3812 357.128 318.933 0.387 0.952 0.199 13.296-10.522 97.03 97 1 0.2371 481.222 462.454 0.703 0.953 0.146 10.503-8.327 98.35 176 3 0.2216 502.824 494.882 0.881 0.954 0.120 8.318-6.595 100.00 360 8 0.2167 375.567 370.559 0.907 0.953 0.093 6.588-5.215 100.00 711 7 0.1929 345.109 335.241 0.901 0.953 0.073 5.214-4.128 98.38 1367 28 0.1215 504.789 499.332 0.991 0.954 0.035 4.126-3.266 94.74 2603 46 0.1154 460.143 453.229 1.055 0.954 0.005 3.266-2.585 99.86 5447 97 0.1116 310.401 307.157 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0951 234.180 231.673 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0909 138.599 137.302 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0971 74.614 73.907 1.054 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.027 38.355 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0482 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1366 | n_water=892 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1199 r_free=0.1366 | n_water=892 | time (s): 104.170 (total time: 106.700) Filter (q & B) r_work=0.1200 r_free=0.1366 | n_water=881 | time (s): 4.220 (total time: 110.920) Compute maps r_work=0.1200 r_free=0.1366 | n_water=881 | time (s): 1.680 (total time: 112.600) Filter (map) r_work=0.1223 r_free=0.1361 | n_water=762 | time (s): 4.340 (total time: 116.940) Find peaks r_work=0.1223 r_free=0.1361 | n_water=762 | time (s): 0.670 (total time: 117.610) Add new water r_work=0.1231 r_free=0.1369 | n_water=978 | time (s): 4.790 (total time: 122.400) Refine new water occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1196 r_free=0.1343 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1342 r_work=0.1192 r_free=0.1342 | n_water=978 | time (s): 174.710 (total time: 297.110) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=903 | time (s): 4.510 (total time: 301.620) Filter (dist only) r_work=0.1197 r_free=0.1351 | n_water=901 | time (s): 111.430 (total time: 413.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.575553 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.193146 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1360 0.0159 0.038 1.1 6.3 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.60 1.59 1.716 13.741 14.193 3.759 12.03 13.63 1.60 1.767 13.714 14.193 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 65.50 14.62 0.88 537 3268 Protein: 5.39 28.38 10.23 0.88 0 2902 Water: 5.79 65.50 28.72 N/A 537 364 Other: 13.67 22.10 17.88 N/A 0 2 Chain A: 5.42 51.37 12.09 N/A 0 1623 Chain B: 5.39 64.38 11.92 N/A 0 1645 Chain S: 5.79 65.50 30.50 N/A 537 0 Histogram: Values Number of atoms 5.39 - 11.40 2115 11.40 - 17.41 780 17.41 - 23.42 281 23.42 - 29.44 206 29.44 - 35.45 187 35.45 - 41.46 125 41.46 - 47.47 73 47.47 - 53.48 29 53.48 - 59.49 5 59.49 - 65.50 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1363 r_work=0.1203 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1363 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756949 | | target function (ml) not normalized (work): 703638.914354 | | target function (ml) not normalized (free): 14733.560442 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1374 0.1373 0.1466 n_refl.: 191131 remove outliers: r(all,work,free)=0.1374 0.1373 0.1466 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1383 0.1381 0.1470 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3899 357.128 316.250 0.400 0.908 0.191 13.296-10.522 97.03 97 1 0.2377 481.222 462.121 0.739 0.909 0.141 10.503-8.327 98.35 176 3 0.2224 502.824 494.294 0.931 0.910 0.117 8.318-6.595 100.00 360 8 0.2183 375.567 370.323 0.957 0.910 0.086 6.588-5.215 100.00 711 7 0.1929 345.109 334.585 0.951 0.910 0.070 5.214-4.128 98.38 1367 28 0.1231 504.789 498.726 1.050 0.911 0.034 4.126-3.266 94.74 2603 46 0.1163 460.143 452.459 1.118 0.912 0.005 3.266-2.585 99.86 5447 97 0.1124 310.401 306.860 1.099 0.912 0.000 2.585-2.046 97.45 10613 204 0.0956 234.180 231.564 1.108 0.914 0.000 2.046-1.619 99.39 21536 464 0.0904 138.599 137.246 1.126 0.916 0.000 1.619-1.281 98.00 42464 925 0.0950 74.614 73.951 1.113 0.919 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.027 38.331 1.078 0.926 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0575 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1354 | n_water=901 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1192 r_free=0.1354 | n_water=901 | time (s): 113.200 (total time: 116.160) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=891 | time (s): 4.210 (total time: 120.370) Compute maps r_work=0.1192 r_free=0.1354 | n_water=891 | time (s): 1.930 (total time: 122.300) Filter (map) r_work=0.1216 r_free=0.1354 | n_water=760 | time (s): 3.990 (total time: 126.290) Find peaks r_work=0.1216 r_free=0.1354 | n_water=760 | time (s): 0.690 (total time: 126.980) Add new water r_work=0.1224 r_free=0.1363 | n_water=987 | time (s): 4.910 (total time: 131.890) Refine new water occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1339 occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1186 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1336 r_work=0.1186 r_free=0.1336 | n_water=987 | time (s): 241.020 (total time: 372.910) Filter (q & B) r_work=0.1191 r_free=0.1346 | n_water=909 | time (s): 5.220 (total time: 378.130) Filter (dist only) r_work=0.1191 r_free=0.1347 | n_water=907 | time (s): 114.400 (total time: 492.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567143 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.868290 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1352 0.0158 0.038 1.1 7.7 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.52 1.58 1.672 13.753 13.868 3.756 11.94 13.53 1.59 1.681 13.745 13.868 3.754 Individual atomic B min max mean iso aniso Overall: 5.47 65.68 14.68 0.87 543 3268 Protein: 5.47 28.24 10.30 0.87 0 2902 Water: 5.91 65.68 28.69 N/A 543 364 Other: 13.71 22.17 17.94 N/A 0 2 Chain A: 5.56 51.22 12.13 N/A 0 1623 Chain B: 5.47 63.88 11.97 N/A 0 1645 Chain S: 5.91 65.68 30.56 N/A 543 0 Histogram: Values Number of atoms 5.47 - 11.49 2118 11.49 - 17.51 788 17.51 - 23.53 278 23.53 - 29.56 207 29.56 - 35.58 186 35.58 - 41.60 131 41.60 - 47.62 69 47.62 - 53.64 27 53.64 - 59.66 3 59.66 - 65.68 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1353 r_work=0.1194 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1351 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753299 | | target function (ml) not normalized (work): 702955.313270 | | target function (ml) not normalized (free): 14714.326646 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1351 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1388 0.1386 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1388 0.1386 0.1483 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1390 0.1389 0.1485 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1350 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1191 0.1350 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3858 357.128 317.100 0.369 0.977 0.189 13.296-10.522 97.03 97 1 0.2382 481.222 461.413 0.681 0.979 0.131 10.503-8.327 98.35 176 3 0.2226 502.824 494.421 0.862 0.979 0.107 8.318-6.595 100.00 360 8 0.2175 375.567 370.454 0.887 0.979 0.086 6.588-5.215 100.00 711 7 0.1932 345.109 334.962 0.884 0.979 0.070 5.214-4.128 98.38 1367 28 0.1227 504.789 498.680 0.975 0.980 0.040 4.126-3.266 94.74 2603 46 0.1169 460.143 452.471 1.040 0.981 0.009 3.266-2.585 99.86 5447 97 0.1123 310.401 306.889 1.021 0.982 0.000 2.585-2.046 97.45 10613 204 0.0961 234.180 231.557 1.030 0.984 0.000 2.046-1.619 99.39 21536 464 0.0907 138.599 137.238 1.047 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.614 73.957 1.037 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.027 38.314 1.006 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0220 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1350 | n_water=907 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1191 r_free=0.1350 | n_water=907 | time (s): 116.670 (total time: 119.390) Filter (q & B) r_work=0.1192 r_free=0.1351 | n_water=896 | time (s): 4.390 (total time: 123.780) Compute maps r_work=0.1192 r_free=0.1351 | n_water=896 | time (s): 1.650 (total time: 125.430) Filter (map) r_work=0.1213 r_free=0.1355 | n_water=784 | time (s): 4.820 (total time: 130.250) Find peaks r_work=0.1213 r_free=0.1355 | n_water=784 | time (s): 0.790 (total time: 131.040) Add new water r_work=0.1220 r_free=0.1363 | n_water=994 | time (s): 4.580 (total time: 135.620) Refine new water occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1189 r_free=0.1343 occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1186 r_free=0.1344 occ: r_work=0.1185 r_free=0.1342 adp: r_work=0.1185 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1344 r_work=0.1185 r_free=0.1344 | n_water=994 | time (s): 193.120 (total time: 328.740) Filter (q & B) r_work=0.1189 r_free=0.1350 | n_water=915 | time (s): 5.200 (total time: 333.940) Filter (dist only) r_work=0.1190 r_free=0.1348 | n_water=913 | time (s): 117.440 (total time: 451.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.240669 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1353 0.0160 0.038 1.1 7.3 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.53 1.60 1.676 13.777 14.241 3.754 11.93 13.55 1.63 1.687 13.770 14.241 3.752 Individual atomic B min max mean iso aniso Overall: 5.53 65.94 14.70 0.86 550 3267 Protein: 5.53 28.11 10.33 0.86 0 2902 Water: 5.98 65.94 28.61 N/A 550 363 Other: 13.79 22.14 17.97 N/A 0 2 Chain A: 5.58 50.89 12.12 N/A 0 1623 Chain B: 5.53 62.88 11.95 N/A 0 1644 Chain S: 5.98 65.94 30.56 N/A 550 0 Histogram: Values Number of atoms 5.53 - 11.57 2132 11.57 - 17.61 798 17.61 - 23.65 261 23.65 - 29.69 214 29.69 - 35.74 184 35.74 - 41.78 127 41.78 - 47.82 69 47.82 - 53.86 25 53.86 - 59.90 3 59.90 - 65.94 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1355 r_work=0.1193 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1356 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1355 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752077 | | target function (ml) not normalized (work): 702726.408297 | | target function (ml) not normalized (free): 14721.001345 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1497 n_refl.: 191131 remove outliers: r(all,work,free)=0.1398 0.1396 0.1497 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1397 0.1396 0.1497 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1352 n_refl.: 191131 remove outliers: r(all,work,free)=0.1193 0.1190 0.1352 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3910 352.506 316.957 0.335 0.995 0.138 13.296-10.522 97.03 97 1 0.2379 481.222 461.366 0.663 0.996 0.114 10.503-8.327 98.35 176 3 0.2231 502.824 495.201 0.844 0.997 0.098 8.318-6.595 100.00 360 8 0.2176 375.567 370.986 0.871 0.997 0.083 6.588-5.215 100.00 711 7 0.1948 345.109 334.865 0.867 0.997 0.070 5.214-4.128 98.38 1367 28 0.1231 504.789 498.857 0.957 0.998 0.039 4.126-3.266 94.74 2603 46 0.1168 460.143 452.575 1.021 0.999 0.005 3.266-2.585 99.86 5447 97 0.1130 310.401 306.829 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.180 231.558 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.599 137.245 1.029 1.006 0.000 1.619-1.281 98.00 42464 925 0.0939 74.614 73.963 1.021 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.027 38.306 0.991 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0068 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1352 After: r_work=0.1191 r_free=0.1353 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=913 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1191 r_free=0.1353 | n_water=913 | time (s): 120.800 (total time: 123.930) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=902 | time (s): 4.450 (total time: 128.380) Compute maps r_work=0.1192 r_free=0.1354 | n_water=902 | time (s): 2.280 (total time: 130.660) Filter (map) r_work=0.1216 r_free=0.1362 | n_water=784 | time (s): 4.970 (total time: 135.630) Find peaks r_work=0.1216 r_free=0.1362 | n_water=784 | time (s): 0.640 (total time: 136.270) Add new water r_work=0.1222 r_free=0.1370 | n_water=992 | time (s): 4.760 (total time: 141.030) Refine new water occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1341 occ: r_work=0.1187 r_free=0.1340 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=992 | time (s): 211.110 (total time: 352.140) Filter (q & B) r_work=0.1191 r_free=0.1351 | n_water=916 | time (s): 5.020 (total time: 357.160) Filter (dist only) r_work=0.1191 r_free=0.1351 | n_water=914 | time (s): 119.410 (total time: 476.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.344789 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1355 0.0161 0.038 1.2 11.1 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.55 1.61 1.675 13.758 13.345 3.755 11.96 13.57 1.61 1.671 13.758 13.345 3.756 Individual atomic B min max mean iso aniso Overall: 5.55 65.96 14.68 0.85 551 3267 Protein: 5.55 27.99 10.34 0.85 0 2902 Water: 6.01 65.96 28.44 N/A 551 363 Other: 13.83 22.16 17.99 N/A 0 2 Chain A: 5.63 50.81 12.11 N/A 0 1623 Chain B: 5.55 62.65 11.95 N/A 0 1644 Chain S: 6.01 65.96 30.37 N/A 551 0 Histogram: Values Number of atoms 5.55 - 11.59 2131 11.59 - 17.63 802 17.63 - 23.67 266 23.67 - 29.71 214 29.71 - 35.75 190 35.75 - 41.79 119 41.79 - 47.83 65 47.83 - 53.88 24 53.88 - 59.92 3 59.92 - 65.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755471 | | target function (ml) not normalized (work): 703358.425842 | | target function (ml) not normalized (free): 14726.802491 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1366 0.1478 5.6944 5.7836| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1363 5.0891 5.1888| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1204 4.6612 4.7662| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1038 4.3911 4.5379| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0986 4.1486 4.2296| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1086 3.9461 4.0762| | 7: 1.62 - 1.54 0.99 7104 148 0.0890 0.0968 3.7995 3.9379| | 8: 1.54 - 1.47 0.96 6798 152 0.0894 0.1300 3.702 3.8971| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1117 3.6208 3.7509| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1183 3.5563 3.6725| | 11: 1.36 - 1.32 0.99 6997 151 0.0996 0.1123 3.4866 3.5888| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1127 3.4618 3.5816| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1252 3.4386 3.5717| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1580 3.4333 3.6731| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1238 3.4473 3.4844| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1542 3.4653 3.653| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1224 3.4337 3.4402| | 18: 1.14 - 1.12 0.98 6875 142 0.1387 0.1702 3.4395 3.5306| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1763 3.4207 3.5974| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1584 3.4117 3.4354| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2133 3.4191 3.5047| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1949 3.4139 3.413| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2027 3.4338 3.4887| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2268 3.4364 3.5155| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2505 3.4495 3.5235| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2858 3.416 3.4222| | 27: 0.99 - 0.98 0.94 6647 131 0.3046 0.2802 3.4691 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.86 1.00 0.96 11539.07| | 2: 2.94 - 2.33 7339 128 0.92 12.95 0.99 0.95 5267.70| | 3: 2.33 - 2.04 6939 150 0.96 7.70 1.01 0.95 1717.14| | 4: 2.04 - 1.85 7170 155 0.96 7.52 1.00 0.95 986.46| | 5: 1.85 - 1.72 7113 159 0.96 7.92 1.00 0.96 621.54| | 6: 1.72 - 1.62 7102 142 0.96 7.95 1.00 0.96 439.35| | 7: 1.62 - 1.54 7104 148 0.96 8.13 1.01 0.97 336.63| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.97 278.61| | 9: 1.47 - 1.41 6938 155 0.96 8.44 1.00 0.98 229.91| | 10: 1.41 - 1.36 7022 150 0.96 8.89 1.00 0.97 201.99| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.96 175.09| | 12: 1.32 - 1.28 6975 149 0.96 9.04 0.98 0.95 161.55| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.96 158.44| | 14: 1.25 - 1.22 7015 112 0.95 10.67 1.01 0.97 162.63| | 15: 1.22 - 1.19 6956 137 0.95 11.15 1.01 0.98 165.13| | 16: 1.19 - 1.17 6604 132 0.95 11.36 1.01 0.96 158.87| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.96 152.99| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.95 147.53| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.95 151.43| | 20: 1.10 - 1.08 6884 147 0.92 15.25 1.00 0.94 150.68| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.93 153.70| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.36| | 23: 1.05 - 1.03 6827 159 0.87 20.55 0.99 0.92 165.38| | 24: 1.03 - 1.02 6784 133 0.85 23.22 0.99 0.93 179.78| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.46| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.89 176.80| | 27: 0.99 - 0.98 6647 131 0.82 26.32 0.99 0.87 161.33| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.53 max = 11539.07 mean = 943.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.29| |phase err.(test): min = 0.00 max = 89.39 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1410 0.1408 0.1510 n_refl.: 191130 remove outliers: r(all,work,free)=0.1410 0.1408 0.1510 n_refl.: 191130 overall B=-0.05 to atoms: r(all,work,free)=0.1402 0.1400 0.1504 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3836 352.506 313.727 0.368 0.915 0.167 13.296-10.522 97.03 97 1 0.2416 481.222 462.116 0.703 0.916 0.120 10.503-8.327 98.35 176 3 0.2229 502.824 494.062 0.895 0.916 0.084 8.318-6.595 100.00 360 8 0.2168 375.567 370.589 0.923 0.916 0.070 6.588-5.215 100.00 711 7 0.1965 345.109 334.569 0.919 0.917 0.070 5.214-4.128 98.38 1367 28 0.1246 504.789 498.860 1.016 0.918 0.034 4.126-3.266 94.74 2603 46 0.1167 460.143 452.464 1.084 0.919 0.000 3.266-2.585 99.86 5447 97 0.1128 310.401 306.896 1.065 0.920 0.000 2.585-2.046 97.45 10613 204 0.0968 234.180 231.556 1.073 0.922 0.000 2.046-1.619 99.39 21536 464 0.0911 138.599 137.242 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0947 74.614 73.960 1.080 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.027 38.299 1.046 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0110 ================= 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 : 0.2030 0.1998 0.081 5.264 5.2 78.0 14.6 805 0.000 1_bss: 0.1795 0.1926 0.081 5.264 5.2 78.0 14.6 805 0.000 1_settarget: 0.1795 0.1926 0.081 5.264 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1931 0.081 5.264 5.2 78.0 14.6 805 0.002 1_weight: 0.1797 0.1931 0.081 5.264 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1508 0.039 1.139 5.2 78.0 14.6 805 0.156 1_adp: 0.1296 0.1570 0.039 1.139 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1295 0.1565 0.039 1.139 5.2 73.0 15.0 805 0.156 1_occ: 0.1280 0.1562 0.039 1.139 5.2 73.0 15.0 805 0.156 2_bss: 0.1273 0.1551 0.039 1.139 5.3 73.2 15.1 805 0.156 2_settarget: 0.1273 0.1551 0.039 1.139 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1273 0.1551 0.039 1.155 5.3 73.2 15.1 805 0.156 2_nqh: 0.1273 0.1551 0.039 1.155 5.3 73.2 15.1 805 0.156 2_sol: 0.1268 0.1512 0.039 1.155 5.3 73.2 16.3 887 n/a 2_weight: 0.1268 0.1512 0.039 1.155 5.3 73.2 16.3 887 n/a 2_xyzrec: 0.1252 0.1528 0.042 1.135 5.3 73.2 16.3 887 n/a 2_adp: 0.1230 0.1517 0.042 1.135 5.4 70.0 16.5 887 n/a 2_regHadp: 0.1231 0.1518 0.042 1.135 5.4 70.0 16.5 887 n/a 2_occ: 0.1223 0.1512 0.042 1.135 5.4 70.0 16.5 887 n/a 3_bss: 0.1230 0.1520 0.042 1.135 5.4 70.0 16.5 887 n/a 3_settarget: 0.1230 0.1520 0.042 1.135 5.4 70.0 16.5 887 n/a 3_updatecdl: 0.1230 0.1520 0.042 1.140 5.4 70.0 16.5 887 n/a 3_nqh: 0.1230 0.1520 0.042 1.140 5.4 70.0 16.5 887 n/a 3_sol: 0.1247 0.1522 0.042 1.140 5.4 68.2 15.5 886 n/a 3_weight: 0.1247 0.1522 0.042 1.140 5.4 68.2 15.5 886 n/a 3_xyzrec: 0.1236 0.1441 0.035 1.102 5.4 68.2 15.5 886 n/a 3_adp: 0.1233 0.1399 0.035 1.102 5.5 67.7 15.3 886 n/a 3_regHadp: 0.1233 0.1400 0.035 1.102 5.5 67.7 15.3 886 n/a 3_occ: 0.1228 0.1388 0.035 1.102 5.5 67.7 15.3 886 n/a 4_bss: 0.1224 0.1383 0.035 1.102 5.5 67.6 15.3 886 n/a 4_settarget: 0.1224 0.1383 0.035 1.102 5.5 67.6 15.3 886 n/a 4_updatecdl: 0.1224 0.1383 0.035 1.102 5.5 67.6 15.3 886 n/a 4_nqh: 0.1224 0.1383 0.035 1.102 5.5 67.6 15.3 886 n/a 4_sol: 0.1209 0.1374 0.035 1.102 5.5 67.6 15.0 862 n/a 4_weight: 0.1209 0.1374 0.035 1.102 5.5 67.6 15.0 862 n/a 4_xyzrec: 0.1207 0.1372 0.035 1.139 5.5 67.6 15.0 862 n/a 4_adp: 0.1200 0.1373 0.035 1.139 5.5 67.2 14.9 862 n/a 4_regHadp: 0.1200 0.1373 0.035 1.139 5.5 67.2 14.9 862 n/a 4_occ: 0.1198 0.1372 0.035 1.139 5.5 67.2 14.9 862 n/a 5_bss: 0.1196 0.1369 0.035 1.139 5.5 67.1 14.9 862 n/a 5_settarget: 0.1196 0.1369 0.035 1.139 5.5 67.1 14.9 862 n/a 5_updatecdl: 0.1196 0.1369 0.035 1.139 5.5 67.1 14.9 862 n/a 5_nqh: 0.1196 0.1369 0.035 1.139 5.5 67.1 14.9 862 n/a 5_sol: 0.1195 0.1362 0.035 1.139 5.5 67.1 15.0 883 n/a 5_weight: 0.1195 0.1362 0.035 1.139 5.5 67.1 15.0 883 n/a 5_xyzrec: 0.1197 0.1363 0.035 1.138 5.5 67.1 15.0 883 n/a 5_adp: 0.1200 0.1367 0.035 1.138 5.6 66.8 15.0 883 n/a 5_regHadp: 0.1200 0.1367 0.035 1.138 5.6 66.8 15.0 883 n/a 5_occ: 0.1199 0.1367 0.035 1.138 5.6 66.8 15.0 883 n/a 6_bss: 0.1198 0.1364 0.035 1.138 5.5 66.8 14.9 883 n/a 6_settarget: 0.1198 0.1364 0.035 1.138 5.5 66.8 14.9 883 n/a 6_updatecdl: 0.1198 0.1364 0.035 1.139 5.5 66.8 14.9 883 n/a 6_nqh: 0.1199 0.1367 0.035 1.139 5.5 66.8 14.9 883 n/a 6_sol: 0.1196 0.1359 0.035 1.139 5.5 66.8 14.9 892 n/a 6_weight: 0.1196 0.1359 0.035 1.139 5.5 66.8 14.9 892 n/a 6_xyzrec: 0.1200 0.1365 0.036 1.138 5.5 66.8 14.9 892 n/a 6_adp: 0.1202 0.1367 0.036 1.138 5.6 65.7 14.9 892 n/a 6_regHadp: 0.1202 0.1367 0.036 1.138 5.6 65.7 14.9 892 n/a 6_occ: 0.1200 0.1367 0.036 1.138 5.6 65.7 14.9 892 n/a 7_bss: 0.1199 0.1366 0.036 1.138 5.3 65.4 14.7 892 n/a 7_settarget: 0.1199 0.1366 0.036 1.138 5.3 65.4 14.7 892 n/a 7_updatecdl: 0.1199 0.1366 0.036 1.138 5.3 65.4 14.7 892 n/a 7_nqh: 0.1199 0.1366 0.036 1.138 5.3 65.4 14.7 892 n/a 7_sol: 0.1197 0.1351 0.036 1.138 5.3 65.4 14.7 901 n/a 7_weight: 0.1197 0.1351 0.036 1.138 5.3 65.4 14.7 901 n/a 7_xyzrec: 0.1201 0.1360 0.038 1.135 5.3 65.4 14.7 901 n/a 7_adp: 0.1203 0.1363 0.038 1.135 5.4 65.5 14.6 901 n/a 7_regHadp: 0.1203 0.1363 0.038 1.135 5.4 65.5 14.6 901 n/a 7_occ: 0.1201 0.1363 0.038 1.135 5.4 65.5 14.6 901 n/a 8_bss: 0.1192 0.1354 0.038 1.135 5.5 65.6 14.7 901 n/a 8_settarget: 0.1192 0.1354 0.038 1.135 5.5 65.6 14.7 901 n/a 8_updatecdl: 0.1192 0.1354 0.038 1.135 5.5 65.6 14.7 901 n/a 8_nqh: 0.1192 0.1354 0.038 1.135 5.5 65.6 14.7 901 n/a 8_sol: 0.1191 0.1347 0.038 1.135 5.5 65.6 14.7 907 n/a 8_weight: 0.1191 0.1347 0.038 1.135 5.5 65.6 14.7 907 n/a 8_xyzrec: 0.1194 0.1352 0.038 1.135 5.5 65.6 14.7 907 n/a 8_adp: 0.1194 0.1353 0.038 1.135 5.5 65.7 14.7 907 n/a 8_regHadp: 0.1194 0.1353 0.038 1.135 5.5 65.7 14.7 907 n/a 8_occ: 0.1193 0.1351 0.038 1.135 5.5 65.7 14.7 907 n/a 9_bss: 0.1191 0.1350 0.038 1.135 5.5 65.7 14.7 907 n/a 9_settarget: 0.1191 0.1350 0.038 1.135 5.5 65.7 14.7 907 n/a 9_updatecdl: 0.1191 0.1350 0.038 1.135 5.5 65.7 14.7 907 n/a 9_nqh: 0.1191 0.1350 0.038 1.135 5.5 65.7 14.7 907 n/a 9_sol: 0.1190 0.1348 0.038 1.135 5.5 65.7 14.7 913 n/a 9_weight: 0.1190 0.1348 0.038 1.135 5.5 65.7 14.7 913 n/a 9_xyzrec: 0.1193 0.1353 0.038 1.129 5.5 65.7 14.7 913 n/a 9_adp: 0.1193 0.1355 0.038 1.129 5.5 65.9 14.7 913 n/a 9_regHadp: 0.1193 0.1356 0.038 1.129 5.5 65.9 14.7 913 n/a 9_occ: 0.1191 0.1355 0.038 1.129 5.5 65.9 14.7 913 n/a 10_bss: 0.1190 0.1352 0.038 1.129 5.5 65.9 14.7 913 n/a 10_settarget: 0.1190 0.1352 0.038 1.129 5.5 65.9 14.7 913 n/a 10_updatecdl: 0.1190 0.1352 0.038 1.129 5.5 65.9 14.7 913 n/a 10_setrh: 0.1191 0.1353 0.038 1.129 5.5 65.9 14.7 913 n/a 10_nqh: 0.1191 0.1353 0.038 1.129 5.5 65.9 14.7 913 n/a 10_sol: 0.1191 0.1351 0.038 1.129 5.5 65.9 14.7 914 n/a 10_weight: 0.1191 0.1351 0.038 1.129 5.5 65.9 14.7 914 n/a 10_xyzrec: 0.1195 0.1355 0.038 1.171 5.5 65.9 14.7 914 n/a 10_adp: 0.1197 0.1357 0.038 1.171 5.5 66.0 14.7 914 n/a 10_regHadp: 0.1197 0.1357 0.038 1.171 5.5 66.0 14.7 914 n/a 10_occ: 0.1196 0.1358 0.038 1.171 5.5 66.0 14.7 914 n/a end: 0.1195 0.1359 0.038 1.171 5.5 65.9 14.6 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5578134_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5578134_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.5300 Refinement macro-cycles (run) : 11785.3600 Write final files (write_after_run_outputs) : 172.2400 Total : 11964.1300 Total CPU time: 3.33 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:32 PST -0800 (1736735792.76 s) Start R-work = 0.1795, R-free = 0.1926 Final R-work = 0.1195, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12296.14 seconds wall clock time: 205 minutes 54.43 seconds (12354.43 seconds total)