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_6200443.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/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6200443.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6200443.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.61, per 1000 atoms: 0.24 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: 2.798 distance_ideal: 2.720 ideal - model: -0.078 slack: 0.000 delta_slack: -0.078 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: 2.621 distance_ideal: 2.710 ideal - model: 0.089 slack: 0.000 delta_slack: 0.089 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: 0.70 Conformation dependent library (CDL) restraints added in 111.3 milliseconds Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.06: 1175 1.06 - 1.32: 2483 1.32 - 1.58: 1894 1.58 - 1.84: 376 1.84 - 2.10: 6 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.622 -0.167 7.00e-03 2.04e+04 5.66e+02 bond pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 1.459 1.685 -0.227 1.16e-02 7.43e+03 3.82e+02 bond pdb=" NE1 TRP A 146 " pdb=" HE1 TRP A 146 " ideal model delta sigma weight residual 0.860 1.250 -0.390 2.00e-02 2.50e+03 3.81e+02 bond pdb=" NH1 ARG A 49 " pdb="HH12 ARG A 49 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.55e+02 bond pdb=" N ARG B 149 " pdb=" H ARG B 149 " ideal model delta sigma weight residual 0.860 1.229 -0.369 2.00e-02 2.50e+03 3.40e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 5472 3.97 - 7.93: 3483 7.93 - 11.90: 1473 11.90 - 15.86: 331 15.86 - 19.83: 51 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE B 121 " pdb=" C ILE B 121 " pdb=" O ILE B 121 " ideal model delta sigma weight residual 120.43 139.35 -18.92 1.09e+00 8.42e-01 3.01e+02 angle pdb=" CG TRP B 139 " pdb=" CD2 TRP B 139 " pdb=" CE3 TRP B 139 " ideal model delta sigma weight residual 133.90 150.36 -16.46 1.00e+00 1.00e+00 2.71e+02 angle pdb=" O VAL A 144 " pdb=" C VAL A 144 " pdb=" N VAL A 145 " ideal model delta sigma weight residual 123.05 140.42 -17.37 1.11e+00 8.12e-01 2.45e+02 angle pdb=" CA ASN B 42 " pdb=" C ASN B 42 " pdb=" O ASN B 42 " ideal model delta sigma weight residual 120.88 107.31 13.57 9.40e-01 1.13e+00 2.08e+02 angle pdb=" CA ASN A 193 " pdb=" CB ASN A 193 " pdb=" CG ASN A 193 " ideal model delta sigma weight residual 112.60 126.54 -13.94 1.00e+00 1.00e+00 1.94e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.85: 1832 16.85 - 33.68: 145 33.68 - 50.52: 45 50.52 - 67.35: 24 67.35 - 84.19: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 207 0.224 - 0.448: 151 0.448 - 0.672: 97 0.672 - 0.895: 31 0.895 - 1.119: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB THR A 86 " pdb=" CA THR A 86 " pdb=" OG1 THR A 86 " pdb=" CG2 THR A 86 " both_signs ideal model delta sigma weight residual False 2.55 3.67 -1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CA GLN A 138 " pdb=" N GLN A 138 " pdb=" C GLN A 138 " pdb=" CB GLN A 138 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB THR B 160 " pdb=" CA THR B 160 " pdb=" OG1 THR B 160 " pdb=" CG2 THR B 160 " both_signs ideal model delta sigma weight residual False 2.55 1.56 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.191 2.00e-02 2.50e+03 9.20e-02 2.54e+02 pdb=" CG PHE A 164 " 0.122 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.127 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " 0.071 2.00e-02 2.50e+03 7.74e-02 1.80e+02 pdb=" CG PHE B 119 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " -0.105 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " -0.071 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " 0.148 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " 0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.046 2.00e-02 2.50e+03 6.43e-02 1.65e+02 pdb=" CG TRP B 146 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.106 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.073 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.043 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.054 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.105 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.111 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.72 - 1.50: 17 1.50 - 2.27: 1527 2.27 - 3.05: 21152 3.05 - 3.82: 33214 3.82 - 4.60: 54383 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110293 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.720 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.913 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.963 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.012 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.149 2.620 ... (remaining 110288 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_6200443_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= 0.2042 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.304921 | | target function (ml) not normalized (work): 806367.624798 | | target function (ml) not normalized (free): 16562.419012 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2150 0.1926 6.6933 6.3043| | 2: 2.94 - 2.33 1.00 7339 128 0.1618 0.1626 5.5361 5.591| | 3: 2.33 - 2.04 0.96 6939 150 0.1650 0.1558 5.1541 5.1562| | 4: 2.04 - 1.85 1.00 7170 155 0.1761 0.1698 4.9711 5.0463| | 5: 1.85 - 1.72 0.99 7113 159 0.1886 0.1725 4.784 4.8439| | 6: 1.72 - 1.62 0.99 7102 142 0.1983 0.1852 4.6601 4.6242| | 7: 1.62 - 1.54 0.99 7104 148 0.2013 0.1661 4.5486 4.4955| | 8: 1.54 - 1.47 0.96 6798 152 0.2025 0.2178 4.4652 4.5166| | 9: 1.47 - 1.41 0.98 6938 155 0.2131 0.2208 4.4116 4.4729| | 10: 1.41 - 1.36 0.99 7022 150 0.2193 0.2159 4.3348 4.3297| | 11: 1.36 - 1.32 0.99 6997 151 0.2100 0.2305 4.2454 4.3327| | 12: 1.32 - 1.28 0.98 6976 149 0.2108 0.2219 4.2014 4.3137| | 13: 1.28 - 1.25 0.98 6907 166 0.2020 0.2302 4.1305 4.2509| | 14: 1.25 - 1.22 0.98 7015 113 0.2087 0.2204 4.0834 4.1927| | 15: 1.22 - 1.19 0.98 6957 137 0.2117 0.1962 4.0401 3.9926| | 16: 1.19 - 1.17 0.93 6604 132 0.2116 0.2141 4.0115 4.0647| | 17: 1.17 - 1.14 0.98 6941 135 0.2162 0.2074 3.9538 4.0422| | 18: 1.14 - 1.12 0.98 6875 142 0.2248 0.2391 3.9304 3.9003| | 19: 1.12 - 1.10 0.97 6949 106 0.2299 0.2523 3.8817 3.9722| | 20: 1.10 - 1.08 0.97 6884 147 0.2329 0.2609 3.8268 3.9653| | 21: 1.08 - 1.07 0.97 6852 152 0.2444 0.2585 3.7972 3.7886| | 22: 1.07 - 1.05 0.97 6838 135 0.2558 0.2450 3.7495 3.7055| | 23: 1.05 - 1.03 0.97 6829 159 0.2713 0.2812 3.7282 3.8205| | 24: 1.03 - 1.02 0.96 6785 133 0.2891 0.2679 3.7119 3.7596| | 25: 1.02 - 1.01 0.93 6552 130 0.3088 0.2945 3.6814 3.7311| | 26: 1.01 - 0.99 0.96 6767 158 0.3201 0.3181 3.6293 3.6047| | 27: 0.99 - 0.98 0.94 6648 131 0.3452 0.3069 3.6596 3.5689| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.35 0.91 0.97 35217.72| | 2: 2.94 - 2.33 7339 128 0.86 21.17 1.09 1.02 14986.99| | 3: 2.33 - 2.04 6939 150 0.93 12.60 1.11 1.05 4158.90| | 4: 2.04 - 1.85 7170 155 0.92 13.54 1.12 1.05 2764.32| | 5: 1.85 - 1.72 7113 159 0.91 15.32 1.11 1.06 1991.36| | 6: 1.72 - 1.62 7102 142 0.91 15.98 1.11 1.05 1475.38| | 7: 1.62 - 1.54 7104 148 0.90 16.84 1.11 1.05 1211.58| | 8: 1.54 - 1.47 6798 152 0.89 17.69 1.10 1.05 1076.82| | 9: 1.47 - 1.41 6938 155 0.88 19.09 1.10 1.05 979.40| | 10: 1.41 - 1.36 7022 150 0.86 20.79 1.10 1.04 889.99| | 11: 1.36 - 1.32 6997 151 0.86 21.18 1.08 1.05 816.30| | 12: 1.32 - 1.28 6976 149 0.86 21.39 1.08 1.04 753.85| | 13: 1.28 - 1.25 6907 166 0.86 21.29 1.07 1.03 683.87| | 14: 1.25 - 1.22 7015 113 0.86 21.43 1.08 1.03 608.54| | 15: 1.22 - 1.19 6957 137 0.87 20.52 1.08 1.04 532.77| | 16: 1.19 - 1.17 6604 132 0.87 20.26 1.08 1.05 489.10| | 17: 1.17 - 1.14 6941 135 0.86 20.95 1.08 1.03 447.61| | 18: 1.14 - 1.12 6875 142 0.85 21.96 1.08 1.01 426.63| | 19: 1.12 - 1.10 6949 106 0.85 22.94 1.07 0.99 402.16| | 20: 1.10 - 1.08 6884 147 0.84 23.61 1.06 0.97 371.00| | 21: 1.08 - 1.07 6852 152 0.84 23.84 1.06 0.98 334.83| | 22: 1.07 - 1.05 6838 135 0.83 24.75 1.05 0.99 315.40| | 23: 1.05 - 1.03 6829 159 0.81 26.60 1.05 0.99 314.73| | 24: 1.03 - 1.02 6785 133 0.79 28.57 1.04 0.99 320.28| | 25: 1.02 - 1.01 6552 130 0.77 30.12 1.03 0.94 304.55| | 26: 1.01 - 0.99 6767 158 0.76 31.23 1.03 0.92 278.04| | 27: 0.99 - 0.98 6648 131 0.77 30.37 1.03 0.90 244.33| |alpha: min = 0.90 max = 1.06 mean = 1.01| |beta: min = 244.33 max = 35217.72 mean = 2807.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.93 mean = 21.57| |phase err.(test): min = 0.00 max = 89.42 mean = 21.56| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.294 2950 Z= 5.587 Angle : 5.066 18.923 4018 Z= 3.600 Chirality : 0.385 1.119 492 Planarity : 0.032 0.146 512 Dihedral : 12.854 84.189 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Cbeta Deviations : 30.90 % 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: -2.21 (0.37), residues: 386 helix: -2.41 (0.32), residues: 148 sheet: -0.92 (0.51), residues: 82 loop : -0.47 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.104 0.028 ARG B 83 TYR 0.084 0.031 TYR A 67 PHE 0.149 0.041 PHE A 164 TRP 0.120 0.036 TRP A 146 HIS 0.082 0.031 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2042 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.304921 | | target function (ml) not normalized (work): 806367.624798 | | target function (ml) not normalized (free): 16562.419012 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2040 0.2042 0.1992 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2040 0.2042 0.1992 n_refl.: 191155 remove outliers: r(all,work,free)=0.2040 0.2042 0.1992 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2042 0.2044 0.1993 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1806 0.1929 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1804 0.1929 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4076 402.814 296.836 0.433 0.933 0.307 13.296-10.522 99.01 99 1 0.2497 528.187 520.280 0.765 0.934 0.256 10.503-8.327 99.45 178 3 0.2501 565.118 555.071 0.947 0.934 0.233 8.318-6.595 100.00 360 8 0.2489 414.736 403.656 0.940 0.934 0.180 6.588-5.215 100.00 711 7 0.2246 381.101 366.065 0.932 0.934 0.170 5.214-4.128 98.38 1367 28 0.1471 557.435 549.704 1.049 0.933 0.070 4.126-3.266 94.74 2603 46 0.1351 508.132 499.161 1.118 0.932 0.018 3.266-2.585 99.86 5447 97 0.1459 342.774 337.528 1.096 0.930 0.000 2.585-2.046 97.45 10613 204 0.1409 258.603 254.201 1.105 0.927 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 150.022 1.128 0.921 0.000 1.619-1.281 98.00 42464 925 0.1934 82.395 80.192 1.122 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.699 1.122 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0177 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1929 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=0.1805 r_free=0.1931 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.347995 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.622306 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 0.1492 0.0220 0.039 1.2 11.2 0.0 0.3 0 11.674 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 14.92 2.20 1.118 13.122 574.622 0.019 12.98 15.63 2.66 1.227 13.319 574.622 0.017 Individual atomic B min max mean iso aniso Overall: 5.09 73.05 14.97 1.40 435 3274 Protein: 5.09 40.33 11.00 1.40 0 2902 Water: 6.39 73.05 29.26 N/A 435 370 Other: 15.88 30.94 23.41 N/A 0 2 Chain A: 5.41 60.33 13.02 N/A 0 1626 Chain B: 5.09 73.05 12.74 N/A 0 1648 Chain S: 11.61 61.55 30.67 N/A 435 0 Histogram: Values Number of atoms 5.09 - 11.88 2150 11.88 - 18.68 650 18.68 - 25.48 322 25.48 - 32.27 263 32.27 - 39.07 159 39.07 - 45.87 100 45.87 - 52.66 44 52.66 - 59.46 16 59.46 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1563 r_work=0.1297 r_free=0.1558 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1558 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 = 0.1282 r_free = 0.1547 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015649 | | target function (ls_wunit_k1) not normalized (work): 2930.948068 | | target function (ls_wunit_k1) not normalized (free): 115.514182 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1547 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1472 0.1470 0.1626 n_refl.: 191139 remove outliers: r(all,work,free)=0.1472 0.1470 0.1626 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1495 0.1493 0.1637 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1276 0.1540 n_refl.: 191139 remove outliers: r(all,work,free)=0.1282 0.1276 0.1539 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 0.3621 402.814 380.808 0.486 0.963 0.275 13.296-10.522 99.01 99 1 0.2103 528.187 520.723 0.739 0.964 0.250 10.503-8.327 99.45 178 3 0.1766 565.118 560.920 0.886 0.964 0.208 8.318-6.595 100.00 360 8 0.1730 414.736 412.095 0.908 0.964 0.165 6.588-5.215 100.00 711 7 0.1543 381.101 373.601 0.887 0.965 0.160 5.214-4.128 98.38 1367 28 0.0904 557.435 555.157 0.976 0.965 0.049 4.126-3.266 94.74 2603 46 0.0841 508.132 504.080 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.253 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.413 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.376 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.417 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.160 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0361 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1539 | n_water=805 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1279 r_free=0.1537 | n_water=797 | time (s): 101.180 (total time: 103.600) Filter (q & B) r_work=0.1280 r_free=0.1537 | n_water=793 | time (s): 4.150 (total time: 107.750) Compute maps r_work=0.1280 r_free=0.1537 | n_water=793 | time (s): 2.320 (total time: 110.070) Filter (map) r_work=0.1306 r_free=0.1529 | n_water=658 | time (s): 4.950 (total time: 115.020) Find peaks r_work=0.1306 r_free=0.1529 | n_water=658 | time (s): 0.800 (total time: 115.820) Add new water r_work=0.1328 r_free=0.1554 | n_water=952 | time (s): 5.090 (total time: 120.910) Refine new water occ: r_work=0.1287 r_free=0.1508 adp: r_work=0.1274 r_free=0.1506 occ: r_work=0.1276 r_free=0.1501 adp: r_work=0.1269 r_free=0.1502 occ: r_work=0.1271 r_free=0.1498 adp: r_work=0.1268 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1500 r_work=0.1268 r_free=0.1500 | n_water=952 | time (s): 79.430 (total time: 200.340) Filter (q & B) r_work=0.1272 r_free=0.1504 | n_water=885 | time (s): 4.280 (total time: 204.620) Filter (dist only) r_work=0.1272 r_free=0.1503 | n_water=884 | time (s): 110.340 (total time: 314.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.051092 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.540304 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 0.1255 0.1520 0.0264 0.040 1.1 17.7 0.0 0.3 0 11.526 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.20 2.64 2.036 15.156 595.540 0.015 12.33 15.06 2.73 2.383 15.220 595.540 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.65 16.31 1.20 516 3272 Protein: 5.38 40.11 10.99 1.20 0 2902 Water: 6.63 68.65 33.77 N/A 516 368 Other: 16.37 32.11 24.24 N/A 0 2 Chain A: 5.49 57.05 12.98 N/A 0 1624 Chain B: 5.38 68.52 12.81 N/A 0 1648 Chain S: 13.23 68.65 38.01 N/A 516 0 Histogram: Values Number of atoms 5.38 - 11.71 2069 11.71 - 18.04 705 18.04 - 24.36 268 24.36 - 30.69 213 30.69 - 37.02 172 37.02 - 43.34 168 43.34 - 49.67 92 49.67 - 56.00 52 56.00 - 62.32 38 62.32 - 68.65 11 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1506 r_work=0.1233 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1507 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1504 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1504 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013498 | | target function (ls_wunit_k1) not normalized (work): 2528.223936 | | target function (ls_wunit_k1) not normalized (free): 100.358359 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1504 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1600 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1600 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1598 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1510 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1233 0.1510 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 0.3222 402.814 380.874 0.494 0.962 0.271 13.296-10.522 99.01 99 1 0.1874 528.187 519.124 0.753 0.963 0.223 10.503-8.327 99.45 178 3 0.1422 565.118 567.587 0.924 0.963 0.174 8.318-6.595 100.00 360 8 0.1540 414.736 414.851 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1341 381.101 377.065 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0842 557.435 556.232 0.994 0.963 0.070 4.126-3.266 94.74 2603 46 0.0771 508.132 505.253 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0865 342.774 341.261 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0896 258.603 256.733 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.623 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.351 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.216 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=0.1233 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1510 | n_water=884 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1234 r_free=0.1512 | n_water=882 | time (s): 116.410 (total time: 119.180) Filter (q & B) r_work=0.1235 r_free=0.1512 | n_water=879 | time (s): 5.320 (total time: 124.500) Compute maps r_work=0.1235 r_free=0.1512 | n_water=879 | time (s): 2.230 (total time: 126.730) Filter (map) r_work=0.1269 r_free=0.1516 | n_water=703 | time (s): 5.290 (total time: 132.020) Find peaks r_work=0.1269 r_free=0.1516 | n_water=703 | time (s): 0.770 (total time: 132.790) Add new water r_work=0.1292 r_free=0.1543 | n_water=1016 | time (s): 4.830 (total time: 137.620) Refine new water occ: r_work=0.1251 r_free=0.1503 adp: r_work=0.1251 r_free=0.1504 occ: r_work=0.1247 r_free=0.1501 adp: r_work=0.1247 r_free=0.1501 occ: r_work=0.1244 r_free=0.1499 adp: r_work=0.1244 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1500 r_work=0.1244 r_free=0.1500 | n_water=1016 | time (s): 305.780 (total time: 443.400) Filter (q & B) r_work=0.1248 r_free=0.1512 | n_water=883 | time (s): 4.360 (total time: 447.760) Filter (dist only) r_work=0.1248 r_free=0.1512 | n_water=882 | time (s): 112.930 (total time: 560.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.762300 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.957086 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 0.1235 0.1434 0.0199 0.034 1.1 8.3 0.0 0.0 0 0.881 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.34 1.99 1.931 14.627 16.957 3.938 12.30 13.95 1.66 2.237 14.526 16.957 3.895 Individual atomic B min max mean iso aniso Overall: 5.54 68.13 15.32 1.06 516 3270 Protein: 5.54 36.37 10.74 1.06 0 2902 Water: 6.69 68.13 30.38 N/A 516 366 Other: 14.13 27.65 20.89 N/A 0 2 Chain A: 5.55 56.11 12.71 N/A 0 1623 Chain B: 5.54 68.13 12.51 N/A 0 1647 Chain S: 13.59 62.54 32.48 N/A 516 0 Histogram: Values Number of atoms 5.54 - 11.80 2141 11.80 - 18.05 683 18.05 - 24.31 292 24.31 - 30.57 249 30.57 - 36.83 160 36.83 - 43.09 160 43.09 - 49.35 61 49.35 - 55.61 27 55.61 - 61.87 11 61.87 - 68.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1396 r_work=0.1230 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1396 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1390 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.888923 | | target function (ml) not normalized (work): 728383.676466 | | target function (ml) not normalized (free): 15216.139240 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1225 0.1390 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1440 0.1498 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1440 0.1498 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1434 0.1433 0.1494 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1386 n_refl.: 191138 remove outliers: r(all,work,free)=0.1224 0.1221 0.1386 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 93.07 91 3 0.3796 398.895 358.914 0.416 0.946 0.243 13.296-10.522 99.01 99 1 0.2431 528.187 507.451 0.707 0.947 0.209 10.503-8.327 98.90 177 3 0.2043 557.261 557.606 0.888 0.947 0.164 8.318-6.595 100.00 360 8 0.2048 414.736 411.475 0.899 0.947 0.135 6.588-5.215 100.00 711 7 0.1833 381.101 370.556 0.886 0.947 0.130 5.214-4.128 98.38 1367 28 0.1167 557.435 552.169 0.972 0.947 0.090 4.126-3.266 94.74 2603 46 0.1085 508.132 501.387 1.033 0.947 0.009 3.266-2.585 99.86 5447 97 0.1082 342.774 339.237 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0963 258.603 255.727 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.423 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.498 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1684 44.202 42.324 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1010 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1221 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1386 | n_water=882 | time (s): 3.270 (total time: 3.270) Filter (dist) r_work=0.1223 r_free=0.1390 | n_water=879 | time (s): 112.870 (total time: 116.140) Filter (q & B) r_work=0.1223 r_free=0.1387 | n_water=867 | time (s): 4.390 (total time: 120.530) Compute maps r_work=0.1223 r_free=0.1387 | n_water=867 | time (s): 1.820 (total time: 122.350) Filter (map) r_work=0.1240 r_free=0.1381 | n_water=742 | time (s): 4.680 (total time: 127.030) Find peaks r_work=0.1240 r_free=0.1381 | n_water=742 | time (s): 0.580 (total time: 127.610) Add new water r_work=0.1255 r_free=0.1395 | n_water=976 | time (s): 4.560 (total time: 132.170) Refine new water occ: r_work=0.1211 r_free=0.1356 adp: r_work=0.1204 r_free=0.1352 occ: r_work=0.1201 r_free=0.1351 adp: r_work=0.1201 r_free=0.1351 occ: r_work=0.1201 r_free=0.1351 adp: r_work=0.1201 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1351 r_work=0.1201 r_free=0.1351 | n_water=976 | time (s): 201.210 (total time: 333.380) Filter (q & B) r_work=0.1207 r_free=0.1359 | n_water=864 | time (s): 4.630 (total time: 338.010) Filter (dist only) r_work=0.1207 r_free=0.1357 | n_water=862 | time (s): 109.450 (total time: 447.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.625884 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.924377 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1359 0.0153 0.035 1.1 6.0 0.0 0.3 0 0.813 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.59 1.53 1.831 14.152 15.924 3.872 11.99 13.56 1.57 1.924 14.120 15.924 3.865 Individual atomic B min max mean iso aniso Overall: 5.50 67.73 14.90 1.00 496 3270 Protein: 5.50 33.37 10.67 1.00 0 2902 Water: 5.94 67.73 29.12 N/A 496 366 Other: 14.03 27.06 20.54 N/A 0 2 Chain A: 5.53 55.06 12.59 N/A 0 1623 Chain B: 5.50 67.73 12.43 N/A 0 1647 Chain S: 5.94 60.94 30.63 N/A 496 0 Histogram: Values Number of atoms 5.50 - 11.72 2119 11.72 - 17.94 730 17.94 - 24.17 327 24.17 - 30.39 223 30.39 - 36.62 143 36.62 - 42.84 137 42.84 - 49.06 55 49.06 - 55.29 24 55.29 - 61.51 7 61.51 - 67.73 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1356 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862846 | | target function (ml) not normalized (work): 723487.858672 | | target function (ml) not normalized (free): 15134.620239 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1460 n_refl.: 191135 remove outliers: r(all,work,free)=0.1410 0.1409 0.1460 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1403 0.1402 0.1456 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1351 n_refl.: 191135 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3587 356.872 311.823 0.410 0.949 0.245 13.296-10.522 96.04 96 1 0.2322 480.589 448.408 0.695 0.950 0.199 10.503-8.327 98.35 176 3 0.2146 502.784 492.349 0.864 0.951 0.177 8.318-6.595 100.00 360 8 0.2202 375.668 370.001 0.891 0.950 0.129 6.588-5.215 100.00 711 7 0.1928 345.201 335.378 0.879 0.950 0.107 5.214-4.128 98.38 1367 28 0.1210 504.924 500.036 0.969 0.951 0.070 4.126-3.266 94.74 2603 46 0.1115 460.266 454.111 1.031 0.951 0.000 3.266-2.585 99.86 5447 97 0.1090 310.484 307.457 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0930 234.243 231.951 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0913 138.636 137.407 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.0985 74.634 73.954 1.049 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.038 38.390 1.034 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1153 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1351 | n_water=862 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1195 r_free=0.1351 | n_water=862 | time (s): 107.570 (total time: 110.930) Filter (q & B) r_work=0.1195 r_free=0.1350 | n_water=857 | time (s): 4.260 (total time: 115.190) Compute maps r_work=0.1195 r_free=0.1350 | n_water=857 | time (s): 1.740 (total time: 116.930) Filter (map) r_work=0.1215 r_free=0.1364 | n_water=741 | time (s): 4.140 (total time: 121.070) Find peaks r_work=0.1215 r_free=0.1364 | n_water=741 | time (s): 0.810 (total time: 121.880) Add new water r_work=0.1227 r_free=0.1375 | n_water=972 | time (s): 5.270 (total time: 127.150) Refine new water occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1186 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1340 r_work=0.1186 r_free=0.1340 | n_water=972 | time (s): 213.200 (total time: 340.350) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=889 | time (s): 4.960 (total time: 345.310) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=888 | time (s): 116.000 (total time: 461.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533257 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.876662 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 0.1356 0.0161 0.036 1.1 5.8 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.56 1.61 1.794 14.146 15.877 3.763 11.98 13.59 1.61 1.876 14.114 15.877 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 67.30 14.96 0.96 523 3269 Protein: 5.56 31.85 10.59 0.96 0 2902 Water: 6.05 67.30 29.23 N/A 523 365 Other: 13.85 25.59 19.72 N/A 0 2 Chain A: 5.57 54.01 12.47 N/A 0 1622 Chain B: 5.56 67.30 12.33 N/A 0 1647 Chain S: 6.05 60.93 30.98 N/A 523 0 Histogram: Values Number of atoms 5.56 - 11.73 2144 11.73 - 17.91 720 17.91 - 24.08 309 24.08 - 30.25 228 30.25 - 36.43 164 36.43 - 42.60 131 42.60 - 48.78 64 48.78 - 54.95 24 54.95 - 61.12 7 61.12 - 67.30 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1359 r_work=0.1199 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758565 | | target function (ml) not normalized (work): 703934.079646 | | target function (ml) not normalized (free): 14738.270963 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1360 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1462 n_refl.: 191129 remove outliers: r(all,work,free)=0.1392 0.1391 0.1462 n_refl.: 191129 overall B=-0.03 to atoms: r(all,work,free)=0.1386 0.1385 0.1458 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3545 356.872 329.594 0.406 0.976 0.225 13.296-10.522 96.04 96 1 0.2337 480.589 462.290 0.685 0.977 0.176 10.503-8.327 98.35 176 3 0.2163 502.784 494.314 0.843 0.977 0.157 8.318-6.595 100.00 360 8 0.2174 375.668 370.966 0.863 0.977 0.125 6.588-5.215 100.00 711 7 0.1913 345.201 335.089 0.855 0.976 0.120 5.214-4.128 98.38 1367 28 0.1217 504.924 499.301 0.940 0.976 0.060 4.126-3.266 94.74 2603 46 0.1130 460.266 453.563 1.004 0.975 0.005 3.266-2.585 99.86 5447 97 0.1105 310.484 307.129 0.992 0.972 0.000 2.585-2.046 97.45 10613 204 0.0944 234.243 231.750 1.007 0.968 0.000 2.046-1.619 99.39 21536 464 0.0913 138.636 137.301 1.035 0.962 0.000 1.619-1.281 98.00 42464 925 0.0968 74.634 73.938 1.043 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1642 40.038 38.371 1.047 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1054 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1352 | n_water=888 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1192 r_free=0.1355 | n_water=886 | time (s): 108.790 (total time: 111.680) Filter (q & B) r_work=0.1193 r_free=0.1355 | n_water=878 | time (s): 5.820 (total time: 117.500) Compute maps r_work=0.1193 r_free=0.1355 | n_water=878 | time (s): 1.790 (total time: 119.290) Filter (map) r_work=0.1213 r_free=0.1357 | n_water=761 | time (s): 5.140 (total time: 124.430) Find peaks r_work=0.1213 r_free=0.1357 | n_water=761 | time (s): 0.800 (total time: 125.230) Add new water r_work=0.1225 r_free=0.1369 | n_water=982 | time (s): 4.230 (total time: 129.460) Refine new water occ: r_work=0.1189 r_free=0.1336 adp: r_work=0.1189 r_free=0.1336 occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1335 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1334 r_work=0.1185 r_free=0.1334 | n_water=982 | time (s): 288.240 (total time: 417.700) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=908 | time (s): 5.000 (total time: 422.700) Filter (dist only) r_work=0.1189 r_free=0.1340 | n_water=907 | time (s): 115.090 (total time: 537.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.561549 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.743400 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1353 0.0161 0.037 1.1 6.3 0.0 0.3 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.53 1.61 1.762 14.084 14.743 3.758 11.95 13.55 1.60 1.889 14.037 14.743 3.756 Individual atomic B min max mean iso aniso Overall: 5.59 66.18 14.91 0.90 542 3269 Protein: 5.59 29.07 10.49 0.90 0 2902 Water: 5.89 66.18 29.03 N/A 542 365 Other: 13.86 23.09 18.48 N/A 0 2 Chain A: 5.65 51.55 12.34 N/A 0 1622 Chain B: 5.59 66.18 12.21 N/A 0 1647 Chain S: 5.89 60.99 30.81 N/A 542 0 Histogram: Values Number of atoms 5.59 - 11.65 2126 11.65 - 17.71 765 17.71 - 23.77 289 23.77 - 29.83 221 29.83 - 35.89 166 35.89 - 41.94 137 41.94 - 48.00 70 48.00 - 54.06 28 54.06 - 60.12 6 60.12 - 66.18 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1355 r_work=0.1196 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1356 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755492 | | target function (ml) not normalized (work): 703358.496123 | | target function (ml) not normalized (free): 14728.299747 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1394 0.1393 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1394 0.1393 0.1475 n_refl.: 191129 overall B=-0.24 to atoms: r(all,work,free)=0.1357 0.1356 0.1451 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1357 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1195 0.1357 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3652 356.872 328.203 0.415 0.954 0.207 13.296-10.522 96.04 96 1 0.2324 480.589 461.706 0.718 0.955 0.158 10.503-8.327 98.35 176 3 0.2183 502.784 494.671 0.889 0.956 0.137 8.318-6.595 100.00 360 8 0.2155 375.668 371.517 0.907 0.955 0.110 6.588-5.215 100.00 711 7 0.1924 345.201 335.478 0.899 0.955 0.090 5.214-4.128 98.38 1367 28 0.1229 504.924 499.768 0.990 0.956 0.060 4.126-3.266 94.74 2603 46 0.1138 460.266 453.473 1.054 0.956 0.009 3.266-2.585 99.86 5447 97 0.1113 310.484 307.138 1.036 0.955 0.000 2.585-2.046 97.45 10613 204 0.0947 234.243 231.755 1.044 0.955 0.000 2.046-1.619 99.39 21536 464 0.0911 138.636 137.340 1.062 0.954 0.000 1.619-1.281 98.00 42464 925 0.0968 74.634 73.935 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.038 38.372 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0529 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1357 | n_water=907 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1196 r_free=0.1357 | n_water=907 | time (s): 110.380 (total time: 113.570) Filter (q & B) r_work=0.1197 r_free=0.1357 | n_water=897 | time (s): 5.090 (total time: 118.660) Compute maps r_work=0.1197 r_free=0.1357 | n_water=897 | time (s): 1.860 (total time: 120.520) Filter (map) r_work=0.1218 r_free=0.1363 | n_water=774 | time (s): 4.200 (total time: 124.720) Find peaks r_work=0.1218 r_free=0.1363 | n_water=774 | time (s): 0.710 (total time: 125.430) Add new water r_work=0.1228 r_free=0.1377 | n_water=984 | time (s): 4.180 (total time: 129.610) Refine new water occ: r_work=0.1196 r_free=0.1344 adp: r_work=0.1196 r_free=0.1344 occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1343 occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1343 r_work=0.1193 r_free=0.1343 | n_water=984 | time (s): 208.120 (total time: 337.730) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=908 | time (s): 4.490 (total time: 342.220) Filter (dist only) r_work=0.1197 r_free=0.1352 | n_water=906 | time (s): 118.650 (total time: 460.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.578856 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.110369 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 0.1360 0.0160 0.037 1.1 6.6 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.60 1.60 1.719 13.733 14.110 3.758 12.02 13.62 1.61 1.764 13.713 14.110 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 64.87 14.61 0.88 542 3268 Protein: 5.40 28.19 10.24 0.88 0 2902 Water: 5.71 64.87 28.60 N/A 542 364 Other: 13.69 22.02 17.86 N/A 0 2 Chain A: 5.44 50.97 12.04 N/A 0 1622 Chain B: 5.40 64.87 11.92 N/A 0 1646 Chain S: 5.71 60.75 30.46 N/A 542 0 Histogram: Values Number of atoms 5.40 - 11.35 2110 11.35 - 17.30 777 17.30 - 23.24 283 23.24 - 29.19 233 29.19 - 35.14 165 35.14 - 41.08 127 41.08 - 47.03 72 47.03 - 52.98 31 52.98 - 58.92 8 58.92 - 64.87 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1363 r_work=0.1202 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756719 | | target function (ml) not normalized (work): 703588.370522 | | target function (ml) not normalized (free): 14733.777823 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1362 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1367 0.1365 0.1458 n_refl.: 191129 remove outliers: r(all,work,free)=0.1367 0.1365 0.1458 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1374 0.1372 0.1462 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1352 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3579 352.195 328.383 0.405 0.975 0.203 13.296-10.522 96.04 96 1 0.2355 480.589 461.768 0.705 0.976 0.149 10.503-8.327 98.35 176 3 0.2211 502.784 493.820 0.875 0.977 0.127 8.318-6.595 100.00 360 8 0.2162 375.668 370.586 0.893 0.977 0.103 6.588-5.215 100.00 711 7 0.1941 345.201 334.815 0.887 0.977 0.087 5.214-4.128 98.38 1367 28 0.1246 504.924 499.021 0.979 0.978 0.070 4.126-3.266 94.74 2603 46 0.1152 460.266 452.712 1.041 0.979 0.005 3.266-2.585 99.86 5447 97 0.1122 310.484 306.852 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0955 234.243 231.615 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0911 138.636 137.240 1.046 0.984 0.000 1.619-1.281 98.00 42464 925 0.0949 74.634 73.969 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.038 38.348 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0621 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1352 | n_water=906 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1191 r_free=0.1352 | n_water=906 | time (s): 108.580 (total time: 111.180) Filter (q & B) r_work=0.1191 r_free=0.1352 | n_water=898 | time (s): 4.850 (total time: 116.030) Compute maps r_work=0.1191 r_free=0.1352 | n_water=898 | time (s): 2.090 (total time: 118.120) Filter (map) r_work=0.1210 r_free=0.1354 | n_water=780 | time (s): 4.500 (total time: 122.620) Find peaks r_work=0.1210 r_free=0.1354 | n_water=780 | time (s): 0.870 (total time: 123.490) Add new water r_work=0.1219 r_free=0.1368 | n_water=983 | time (s): 4.690 (total time: 128.180) Refine new water occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1187 r_free=0.1337 occ: r_work=0.1185 r_free=0.1336 adp: r_work=0.1185 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1336 r_work=0.1185 r_free=0.1336 | n_water=983 | time (s): 282.750 (total time: 410.930) Filter (q & B) r_work=0.1190 r_free=0.1347 | n_water=910 | time (s): 5.570 (total time: 416.500) Filter (dist only) r_work=0.1190 r_free=0.1346 | n_water=909 | time (s): 116.890 (total time: 533.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579339 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.262364 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 0.1359 0.0167 0.038 1.1 7.5 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.59 1.67 1.674 13.737 14.262 3.756 11.93 13.61 1.68 1.694 13.724 14.262 3.754 Individual atomic B min max mean iso aniso Overall: 5.48 64.02 14.65 0.87 545 3268 Protein: 5.48 27.91 10.30 0.87 0 2902 Water: 5.88 64.02 28.53 N/A 545 364 Other: 13.77 22.09 17.93 N/A 0 2 Chain A: 5.55 50.77 12.07 N/A 0 1622 Chain B: 5.48 64.02 11.95 N/A 0 1646 Chain S: 5.88 60.93 30.44 N/A 545 0 Histogram: Values Number of atoms 5.48 - 11.33 2073 11.33 - 17.19 816 17.19 - 23.04 269 23.04 - 28.90 236 28.90 - 34.75 171 34.75 - 40.60 125 40.60 - 46.46 77 46.46 - 52.31 32 52.31 - 58.16 10 58.16 - 64.02 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1361 r_work=0.1194 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753812 | | target function (ml) not normalized (work): 703040.124964 | | target function (ml) not normalized (free): 14734.480769 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1361 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1476 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1380 0.1476 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1384 0.1383 0.1477 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1359 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1359 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3645 352.195 324.009 0.386 0.995 0.195 13.296-10.522 96.04 96 1 0.2347 480.589 462.085 0.687 0.996 0.143 10.503-8.327 97.80 175 3 0.2204 500.954 493.536 0.854 0.997 0.120 8.318-6.595 100.00 360 8 0.2164 375.668 370.484 0.873 0.997 0.103 6.588-5.215 100.00 711 7 0.1951 345.201 334.749 0.867 0.997 0.090 5.214-4.128 98.38 1367 28 0.1255 504.924 498.914 0.959 0.998 0.080 4.126-3.266 94.74 2603 46 0.1159 460.266 452.663 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1131 310.484 306.821 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.243 231.609 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0910 138.636 137.251 1.026 1.006 0.000 1.619-1.281 98.00 42464 925 0.0943 74.634 73.980 1.017 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.332 0.986 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0221 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1359 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=0.1192 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1362 | n_water=909 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1192 r_free=0.1362 | n_water=908 | time (s): 117.850 (total time: 120.460) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=898 | time (s): 5.230 (total time: 125.690) Compute maps r_work=0.1193 r_free=0.1361 | n_water=898 | time (s): 2.500 (total time: 128.190) Filter (map) r_work=0.1213 r_free=0.1359 | n_water=779 | time (s): 4.600 (total time: 132.790) Find peaks r_work=0.1213 r_free=0.1359 | n_water=779 | time (s): 0.720 (total time: 133.510) Add new water r_work=0.1222 r_free=0.1373 | n_water=992 | time (s): 4.160 (total time: 137.670) Refine new water occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1185 r_free=0.1338 adp: r_work=0.1185 r_free=0.1339 occ: r_work=0.1183 r_free=0.1338 adp: r_work=0.1183 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1339 r_work=0.1183 r_free=0.1339 | n_water=992 | time (s): 267.280 (total time: 404.950) Filter (q & B) r_work=0.1187 r_free=0.1351 | n_water=922 | time (s): 4.410 (total time: 409.360) Filter (dist only) r_work=0.1188 r_free=0.1351 | n_water=921 | time (s): 119.280 (total time: 528.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500526 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.148476 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 0.1358 0.0165 0.039 1.1 7.0 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.65 1.675 13.760 14.148 3.755 11.93 13.60 1.67 1.683 13.758 14.148 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 62.91 14.69 0.86 557 3268 Protein: 5.55 27.80 10.32 0.86 0 2902 Water: 5.94 62.91 28.43 N/A 557 364 Other: 13.84 22.17 18.00 N/A 0 2 Chain A: 5.63 50.44 12.07 N/A 0 1622 Chain B: 5.55 62.91 11.96 N/A 0 1646 Chain S: 5.94 61.26 30.37 N/A 557 0 Histogram: Values Number of atoms 5.55 - 11.29 2060 11.29 - 17.02 825 17.02 - 22.76 279 22.76 - 28.49 217 28.49 - 34.23 187 34.23 - 39.97 122 39.97 - 45.70 77 45.70 - 51.44 41 51.44 - 57.17 13 57.17 - 62.91 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1360 r_work=0.1193 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1360 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1359 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753303 | | target function (ml) not normalized (work): 702941.067193 | | target function (ml) not normalized (free): 14732.511343 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1359 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1485 n_refl.: 191127 remove outliers: r(all,work,free)=0.1391 0.1390 0.1485 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1391 0.1389 0.1485 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1357 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1190 0.1357 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3657 352.195 322.780 0.379 0.995 0.187 13.296-10.522 96.04 96 1 0.2363 480.589 461.336 0.682 0.996 0.138 10.503-8.327 97.80 175 3 0.2183 500.954 492.368 0.850 0.997 0.115 8.318-6.595 100.00 360 8 0.2147 375.668 370.030 0.872 0.997 0.101 6.588-5.215 100.00 711 7 0.1949 345.201 334.976 0.867 0.997 0.090 5.214-4.128 98.38 1367 28 0.1255 504.924 499.115 0.959 0.998 0.080 4.126-3.266 94.74 2603 46 0.1156 460.266 452.678 1.021 0.999 0.005 3.266-2.585 99.86 5447 97 0.1131 310.484 306.800 1.003 1.001 0.000 2.585-2.046 97.45 10613 204 0.0958 234.243 231.614 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0909 138.636 137.260 1.027 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.634 73.987 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.324 0.989 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0088 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1357 After: r_work=0.1191 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1357 | n_water=921 | time (s): 2.790 (total time: 2.790) Filter (dist) r_work=0.1191 r_free=0.1357 | n_water=921 | time (s): 110.240 (total time: 113.030) Filter (q & B) r_work=0.1192 r_free=0.1360 | n_water=902 | time (s): 4.220 (total time: 117.250) Compute maps r_work=0.1192 r_free=0.1360 | n_water=902 | time (s): 2.010 (total time: 119.260) Filter (map) r_work=0.1215 r_free=0.1364 | n_water=781 | time (s): 5.240 (total time: 124.500) Find peaks r_work=0.1215 r_free=0.1364 | n_water=781 | time (s): 0.870 (total time: 125.370) Add new water r_work=0.1223 r_free=0.1380 | n_water=976 | time (s): 5.290 (total time: 130.660) Refine new water occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1349 occ: r_work=0.1190 r_free=0.1349 adp: r_work=0.1190 r_free=0.1349 occ: r_work=0.1189 r_free=0.1349 adp: r_work=0.1189 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1349 r_work=0.1189 r_free=0.1349 | n_water=976 | time (s): 227.600 (total time: 358.260) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=910 | time (s): 5.370 (total time: 363.630) Filter (dist only) r_work=0.1193 r_free=0.1356 | n_water=908 | time (s): 114.820 (total time: 478.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.484740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.630065 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 0.1360 0.0166 0.039 1.1 9.4 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.60 1.66 1.674 13.721 14.630 3.755 11.93 13.62 1.69 1.664 13.723 14.630 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 62.52 14.62 0.86 544 3268 Protein: 5.55 27.85 10.35 0.86 0 2902 Water: 6.02 62.52 28.27 N/A 544 364 Other: 13.85 22.13 17.99 N/A 0 2 Chain A: 5.62 50.32 12.07 N/A 0 1622 Chain B: 5.55 62.52 11.97 N/A 0 1646 Chain S: 6.02 61.35 30.27 N/A 544 0 Histogram: Values Number of atoms 5.55 - 11.25 2045 11.25 - 16.95 832 16.95 - 22.64 288 22.64 - 28.34 214 28.34 - 34.04 182 34.04 - 39.73 116 39.73 - 45.43 75 45.43 - 51.13 43 51.13 - 56.82 12 56.82 - 62.52 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1362 r_work=0.1193 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1362 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1363 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753146 | | target function (ml) not normalized (work): 702911.701556 | | target function (ml) not normalized (free): 14726.440185 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1366 0.1505 5.6925 5.7851| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1334 5.0863 5.1751| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1202 4.6611 4.7612| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1060 4.3942 4.5679| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.1012 4.15 4.2474| | 6: 1.72 - 1.62 0.99 7102 142 0.0893 0.1085 3.9431 4.074| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0958 3.7935 3.9154| | 8: 1.54 - 1.47 0.96 6798 152 0.0884 0.1317 3.6924 3.8979| | 9: 1.47 - 1.41 0.98 6938 155 0.0920 0.1113 3.6168 3.7474| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1192 3.5533 3.6774| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1126 3.4829 3.5859| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1135 3.4562 3.5814| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1245 3.434 3.5591| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1583 3.4298 3.6714| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1252 3.4469 3.4933| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1564 3.4641 3.6629| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1218 3.4321 3.4402| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1702 3.4371 3.5303| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1754 3.4179 3.5936| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1579 3.4092 3.434| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2124 3.4172 3.4988| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1948 3.4128 3.4149| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2032 3.433 3.4882| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2250 3.4356 3.511| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2507 3.4486 3.5234| | 26: 1.01 - 0.99 0.96 6767 158 0.2751 0.2864 3.4153 3.4244| | 27: 0.99 - 0.98 0.94 6647 131 0.3036 0.2795 3.468 3.3946| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.87 1.00 0.95 11482.07| | 2: 2.94 - 2.33 7339 128 0.92 12.98 0.99 0.95 5249.14| | 3: 2.33 - 2.04 6939 150 0.96 7.75 1.01 0.95 1729.91| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.95 1016.18| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.96 636.41| | 6: 1.72 - 1.62 7102 142 0.96 7.95 1.00 0.96 439.11| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.97 331.65| | 8: 1.54 - 1.47 6798 152 0.96 8.17 1.01 0.97 275.84| | 9: 1.47 - 1.41 6938 155 0.96 8.45 1.00 0.98 230.32| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.97 202.81| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.96 175.13| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.95 160.40| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.96 156.85| | 14: 1.25 - 1.22 7015 112 0.95 10.62 1.01 0.97 161.67| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 0.98 165.67| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 160.10| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.96 153.77| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.95 147.21| | 19: 1.12 - 1.10 6948 106 0.93 14.07 1.00 0.95 150.24| | 20: 1.10 - 1.08 6884 147 0.92 15.16 1.00 0.94 149.43| | 21: 1.08 - 1.07 6852 152 0.91 16.59 1.00 0.93 152.63| | 22: 1.07 - 1.05 6836 135 0.89 18.27 0.99 0.93 154.82| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.92 164.98| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.93 179.33| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.98 0.90 182.09| | 26: 1.01 - 0.99 6767 158 0.81 26.58 0.98 0.88 176.38| | 27: 0.99 - 0.98 6647 131 0.82 26.24 0.99 0.87 160.78| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.21 max = 11482.07 mean = 942.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 13.28| |phase err.(test): min = 0.00 max = 87.88 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1363 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1489 n_refl.: 191127 remove outliers: r(all,work,free)=0.1401 0.1400 0.1489 n_refl.: 191127 overall B=-0.05 to atoms: r(all,work,free)=0.1393 0.1392 0.1484 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1360 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1192 0.1360 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3532 352.195 323.865 0.383 0.975 0.194 13.296-10.522 96.04 96 1 0.2386 480.589 462.130 0.678 0.976 0.141 10.503-8.327 97.80 175 3 0.2200 500.954 492.904 0.844 0.976 0.113 8.318-6.595 100.00 360 8 0.2148 375.668 369.837 0.866 0.976 0.098 6.588-5.215 100.00 711 7 0.1982 345.201 334.262 0.861 0.977 0.093 5.214-4.128 98.38 1367 28 0.1269 504.924 498.888 0.954 0.978 0.049 4.126-3.266 94.74 2603 46 0.1165 460.266 452.432 1.017 0.979 0.005 3.266-2.585 99.86 5447 97 0.1131 310.484 306.878 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0962 234.243 231.586 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.636 137.255 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0941 74.634 73.985 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.038 38.316 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0114 ================= 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 : 0.2042 0.1992 0.083 5.066 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1929 0.083 5.066 5.2 78.1 14.6 805 0.000 1_settarget: 0.1804 0.1929 0.083 5.066 5.2 78.1 14.6 805 0.000 1_nqh: 0.1805 0.1931 0.083 5.066 5.2 78.1 14.6 805 0.002 1_weight: 0.1805 0.1931 0.083 5.066 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1272 0.1492 0.039 1.191 5.2 78.1 14.6 805 0.154 1_adp: 0.1298 0.1563 0.039 1.191 5.1 73.1 15.0 805 0.154 1_regHadp: 0.1297 0.1558 0.039 1.191 5.1 73.1 15.0 805 0.154 1_occ: 0.1282 0.1547 0.039 1.191 5.1 73.1 15.0 805 0.154 2_bss: 0.1276 0.1539 0.039 1.191 5.2 73.2 15.1 805 0.154 2_settarget: 0.1276 0.1539 0.039 1.191 5.2 73.2 15.1 805 0.154 2_updatecdl: 0.1276 0.1539 0.039 1.198 5.2 73.2 15.1 805 0.154 2_nqh: 0.1276 0.1539 0.039 1.198 5.2 73.2 15.1 805 0.154 2_sol: 0.1272 0.1503 0.039 1.198 5.2 73.2 16.2 884 n/a 2_weight: 0.1272 0.1503 0.039 1.198 5.2 73.2 16.2 884 n/a 2_xyzrec: 0.1255 0.1520 0.040 1.149 5.2 73.2 16.2 884 n/a 2_adp: 0.1233 0.1506 0.040 1.149 5.4 68.6 16.3 884 n/a 2_regHadp: 0.1233 0.1507 0.040 1.149 5.4 68.6 16.3 884 n/a 2_occ: 0.1227 0.1504 0.040 1.149 5.4 68.6 16.3 884 n/a 3_bss: 0.1233 0.1510 0.040 1.149 5.4 68.6 16.3 884 n/a 3_settarget: 0.1233 0.1510 0.040 1.149 5.4 68.6 16.3 884 n/a 3_updatecdl: 0.1233 0.1510 0.040 1.153 5.4 68.6 16.3 884 n/a 3_nqh: 0.1233 0.1510 0.040 1.153 5.4 68.6 16.3 884 n/a 3_sol: 0.1248 0.1512 0.040 1.153 5.4 68.5 15.5 882 n/a 3_weight: 0.1248 0.1512 0.040 1.153 5.4 68.5 15.5 882 n/a 3_xyzrec: 0.1235 0.1434 0.034 1.103 5.4 68.5 15.5 882 n/a 3_adp: 0.1230 0.1396 0.034 1.103 5.5 68.1 15.3 882 n/a 3_regHadp: 0.1230 0.1396 0.034 1.103 5.5 68.1 15.3 882 n/a 3_occ: 0.1225 0.1390 0.034 1.103 5.5 68.1 15.3 882 n/a 4_bss: 0.1221 0.1386 0.034 1.103 5.5 68.1 15.3 882 n/a 4_settarget: 0.1221 0.1386 0.034 1.103 5.5 68.1 15.3 882 n/a 4_updatecdl: 0.1221 0.1386 0.034 1.109 5.5 68.1 15.3 882 n/a 4_nqh: 0.1221 0.1386 0.034 1.109 5.5 68.1 15.3 882 n/a 4_sol: 0.1207 0.1357 0.034 1.109 5.5 68.1 15.0 862 n/a 4_weight: 0.1207 0.1357 0.034 1.109 5.5 68.1 15.0 862 n/a 4_xyzrec: 0.1206 0.1359 0.035 1.124 5.5 68.1 15.0 862 n/a 4_adp: 0.1199 0.1356 0.035 1.124 5.5 67.7 14.9 862 n/a 4_regHadp: 0.1200 0.1357 0.035 1.124 5.5 67.7 14.9 862 n/a 4_occ: 0.1197 0.1353 0.035 1.124 5.5 67.7 14.9 862 n/a 5_bss: 0.1195 0.1351 0.035 1.124 5.5 67.7 14.9 862 n/a 5_settarget: 0.1195 0.1351 0.035 1.124 5.5 67.7 14.9 862 n/a 5_updatecdl: 0.1195 0.1351 0.035 1.124 5.5 67.7 14.9 862 n/a 5_nqh: 0.1195 0.1351 0.035 1.124 5.5 67.7 14.9 862 n/a 5_sol: 0.1191 0.1348 0.035 1.124 5.5 67.7 15.0 888 n/a 5_weight: 0.1191 0.1348 0.035 1.124 5.5 67.7 15.0 888 n/a 5_xyzrec: 0.1195 0.1356 0.036 1.130 5.5 67.7 15.0 888 n/a 5_adp: 0.1198 0.1359 0.036 1.130 5.6 67.3 15.0 888 n/a 5_regHadp: 0.1199 0.1360 0.036 1.130 5.6 67.3 15.0 888 n/a 5_occ: 0.1197 0.1360 0.036 1.130 5.6 67.3 15.0 888 n/a 6_bss: 0.1192 0.1352 0.036 1.130 5.5 67.3 14.9 888 n/a 6_settarget: 0.1192 0.1352 0.036 1.130 5.5 67.3 14.9 888 n/a 6_updatecdl: 0.1192 0.1352 0.036 1.130 5.5 67.3 14.9 888 n/a 6_nqh: 0.1192 0.1352 0.036 1.130 5.5 67.3 14.9 888 n/a 6_sol: 0.1189 0.1340 0.036 1.130 5.5 67.3 15.0 907 n/a 6_weight: 0.1189 0.1340 0.036 1.130 5.5 67.3 15.0 907 n/a 6_xyzrec: 0.1192 0.1353 0.037 1.122 5.5 67.3 15.0 907 n/a 6_adp: 0.1195 0.1355 0.037 1.122 5.6 66.2 14.9 907 n/a 6_regHadp: 0.1196 0.1356 0.037 1.122 5.6 66.2 14.9 907 n/a 6_occ: 0.1193 0.1354 0.037 1.122 5.6 66.2 14.9 907 n/a 7_bss: 0.1196 0.1357 0.037 1.122 5.4 65.9 14.7 907 n/a 7_settarget: 0.1196 0.1357 0.037 1.122 5.4 65.9 14.7 907 n/a 7_updatecdl: 0.1196 0.1357 0.037 1.122 5.4 65.9 14.7 907 n/a 7_nqh: 0.1196 0.1357 0.037 1.122 5.4 65.9 14.7 907 n/a 7_sol: 0.1197 0.1352 0.037 1.122 5.4 65.9 14.6 906 n/a 7_weight: 0.1197 0.1352 0.037 1.122 5.4 65.9 14.6 906 n/a 7_xyzrec: 0.1200 0.1360 0.037 1.132 5.4 65.9 14.6 906 n/a 7_adp: 0.1202 0.1363 0.037 1.132 5.4 64.9 14.6 906 n/a 7_regHadp: 0.1202 0.1363 0.037 1.132 5.4 64.9 14.6 906 n/a 7_occ: 0.1200 0.1362 0.037 1.132 5.4 64.9 14.6 906 n/a 8_bss: 0.1191 0.1352 0.037 1.132 5.5 64.9 14.7 906 n/a 8_settarget: 0.1191 0.1352 0.037 1.132 5.5 64.9 14.7 906 n/a 8_updatecdl: 0.1191 0.1352 0.037 1.133 5.5 64.9 14.7 906 n/a 8_nqh: 0.1191 0.1352 0.037 1.133 5.5 64.9 14.7 906 n/a 8_sol: 0.1190 0.1346 0.037 1.133 5.5 64.9 14.7 909 n/a 8_weight: 0.1190 0.1346 0.037 1.133 5.5 64.9 14.7 909 n/a 8_xyzrec: 0.1193 0.1359 0.038 1.119 5.5 64.9 14.7 909 n/a 8_adp: 0.1193 0.1361 0.038 1.119 5.5 64.0 14.6 909 n/a 8_regHadp: 0.1194 0.1361 0.038 1.119 5.5 64.0 14.6 909 n/a 8_occ: 0.1192 0.1361 0.038 1.119 5.5 64.0 14.6 909 n/a 9_bss: 0.1191 0.1359 0.038 1.119 5.5 64.0 14.7 909 n/a 9_settarget: 0.1191 0.1359 0.038 1.119 5.5 64.0 14.7 909 n/a 9_updatecdl: 0.1191 0.1359 0.038 1.119 5.5 64.0 14.7 909 n/a 9_nqh: 0.1192 0.1362 0.038 1.119 5.5 64.0 14.7 909 n/a 9_sol: 0.1188 0.1351 0.038 1.119 5.5 64.0 14.7 921 n/a 9_weight: 0.1188 0.1351 0.038 1.119 5.5 64.0 14.7 921 n/a 9_xyzrec: 0.1193 0.1358 0.039 1.114 5.5 64.0 14.7 921 n/a 9_adp: 0.1193 0.1360 0.039 1.114 5.6 62.9 14.7 921 n/a 9_regHadp: 0.1193 0.1360 0.039 1.114 5.6 62.9 14.7 921 n/a 9_occ: 0.1191 0.1359 0.039 1.114 5.6 62.9 14.7 921 n/a 10_bss: 0.1190 0.1357 0.039 1.114 5.5 62.9 14.7 921 n/a 10_settarget: 0.1190 0.1357 0.039 1.114 5.5 62.9 14.7 921 n/a 10_updatecdl: 0.1190 0.1357 0.039 1.115 5.5 62.9 14.7 921 n/a 10_setrh: 0.1191 0.1357 0.039 1.115 5.5 62.9 14.7 921 n/a 10_nqh: 0.1191 0.1357 0.039 1.115 5.5 62.9 14.7 921 n/a 10_sol: 0.1193 0.1356 0.039 1.115 5.5 62.9 14.6 908 n/a 10_weight: 0.1193 0.1356 0.039 1.115 5.5 62.9 14.6 908 n/a 10_xyzrec: 0.1194 0.1360 0.039 1.145 5.5 62.9 14.6 908 n/a 10_adp: 0.1193 0.1362 0.039 1.145 5.6 62.5 14.6 908 n/a 10_regHadp: 0.1193 0.1362 0.039 1.145 5.6 62.5 14.6 908 n/a 10_occ: 0.1193 0.1363 0.039 1.145 5.6 62.5 14.6 908 n/a end: 0.1192 0.1360 0.039 1.145 5.5 62.5 14.6 908 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6200443_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6200443_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.5200 Refinement macro-cycles (run) : 12390.9600 Write final files (write_after_run_outputs) : 127.3500 Total : 12524.8300 Total CPU time: 3.49 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:57 PST -0800 (1736736357.44 s) Start R-work = 0.1804, R-free = 0.1929 Final R-work = 0.1192, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12772.86 seconds wall clock time: 213 minutes 53.35 seconds (12833.35 seconds total)