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_5354978.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5354978.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5354978.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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.59, per 1000 atoms: 0.39 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: 2.764 distance_ideal: 2.720 ideal - model: -0.044 slack: 0.000 delta_slack: -0.044 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: 2.812 distance_ideal: 2.710 ideal - model: -0.102 slack: 0.000 delta_slack: -0.102 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: 0.82 Conformation dependent library (CDL) restraints added in 115.5 milliseconds Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 850 1.03 - 1.27: 2512 1.27 - 1.51: 1643 1.51 - 1.75: 920 1.75 - 2.00: 9 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 57 " pdb=" CA ALA B 57 " ideal model delta sigma weight residual 1.456 1.671 -0.215 1.04e-02 9.25e+03 4.26e+02 bond pdb=" CA GLY A 122 " pdb=" C GLY A 122 " ideal model delta sigma weight residual 1.516 1.748 -0.232 1.18e-02 7.18e+03 3.85e+02 bond pdb=" CA GLU B 15 " pdb=" HA GLU B 15 " ideal model delta sigma weight residual 0.970 1.358 -0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" CA GLY A 165 " pdb=" C GLY A 165 " ideal model delta sigma weight residual 1.516 1.727 -0.210 1.09e-02 8.42e+03 3.72e+02 bond pdb=" N ILE B 76 " pdb=" H ILE B 76 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.67e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 5817 4.29 - 8.58: 3511 8.58 - 12.87: 1255 12.87 - 17.16: 210 17.16 - 21.45: 17 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.85 110.01 11.84 7.00e-01 2.04e+00 2.86e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 130.12 -10.74 6.80e-01 2.16e+00 2.49e+02 angle pdb=" O ALA B 182 " pdb=" C ALA B 182 " pdb=" N SER B 183 " ideal model delta sigma weight residual 122.12 137.09 -14.97 1.06e+00 8.90e-01 1.99e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N LYS A 52 " ideal model delta sigma weight residual 122.61 137.80 -15.19 1.09e+00 8.42e-01 1.94e+02 angle pdb=" CA CYS B 81 " pdb=" C CYS B 81 " pdb=" O CYS B 81 " ideal model delta sigma weight residual 120.55 106.20 14.35 1.06e+00 8.90e-01 1.83e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1852 17.15 - 34.30: 133 34.30 - 51.45: 43 51.45 - 68.60: 18 68.60 - 85.75: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -150.23 -29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -150.94 -29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.237: 212 0.237 - 0.473: 154 0.473 - 0.708: 86 0.708 - 0.944: 33 0.944 - 1.179: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA B 182 " pdb=" N ALA B 182 " pdb=" C ALA B 182 " pdb=" CB ALA B 182 " both_signs ideal model delta sigma weight residual False 2.48 3.66 -1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CB VAL B 51 " pdb=" CA VAL B 51 " pdb=" CG1 VAL B 51 " pdb=" CG2 VAL B 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.45 -1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" CA THR B 20 " pdb=" N THR B 20 " pdb=" C THR B 20 " pdb=" CB THR B 20 " both_signs ideal model delta sigma weight residual False 2.53 3.65 -1.13 2.00e-01 2.50e+01 3.17e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " -0.052 2.00e-02 2.50e+03 6.97e-02 1.46e+02 pdb=" CG TYR A 67 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.095 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " 0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.003 2.00e-02 2.50e+03 5.95e-02 1.42e+02 pdb=" CG TRP B 139 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.065 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.111 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " -0.052 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.058 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.056 2.00e-02 2.50e+03 6.65e-02 1.33e+02 pdb=" CG PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.073 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.034 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 26 1.61 - 2.36: 2363 2.36 - 3.10: 22248 3.10 - 3.85: 32906 3.85 - 4.60: 52798 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110341 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.861 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.902 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.913 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.133 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.185 2.620 ... (remaining 110336 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_5354978_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303112 | | target function (ml) not normalized (work): 806028.895146 | | target function (ml) not normalized (free): 16526.615592 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2152 0.1981 6.6825 6.326| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1563 5.5447 5.5717| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1532 5.1438 5.0964| | 4: 2.04 - 1.85 1.00 7170 155 0.1766 0.1576 4.9705 5.0582| | 5: 1.85 - 1.72 0.99 7113 159 0.1901 0.1687 4.7952 4.7671| | 6: 1.72 - 1.62 0.99 7102 142 0.1996 0.1889 4.6684 4.65| | 7: 1.62 - 1.54 0.99 7104 148 0.2013 0.1687 4.5567 4.561| | 8: 1.54 - 1.47 0.96 6798 152 0.2037 0.2139 4.4678 4.4689| | 9: 1.47 - 1.41 0.98 6938 155 0.2108 0.2205 4.4055 4.4456| | 10: 1.41 - 1.36 0.99 7022 150 0.2121 0.2164 4.3034 4.3223| | 11: 1.36 - 1.32 0.99 6997 151 0.2116 0.2039 4.2442 4.2012| | 12: 1.32 - 1.28 0.98 6976 149 0.2090 0.1894 4.1755 4.211| | 13: 1.28 - 1.25 0.98 6907 166 0.1981 0.2130 4.1276 4.1786| | 14: 1.25 - 1.22 0.98 7015 113 0.2102 0.2632 4.0934 4.3194| | 15: 1.22 - 1.19 0.98 6957 137 0.2117 0.1847 4.056 4.0067| | 16: 1.19 - 1.17 0.93 6604 132 0.2073 0.2185 3.9928 4.0804| | 17: 1.17 - 1.14 0.98 6941 135 0.2173 0.1984 3.9583 4.0024| | 18: 1.14 - 1.12 0.98 6875 142 0.2255 0.2276 3.932 3.9179| | 19: 1.12 - 1.10 0.97 6949 106 0.2268 0.2468 3.8773 4.0054| | 20: 1.10 - 1.08 0.97 6884 147 0.2365 0.2325 3.8331 3.8799| | 21: 1.08 - 1.07 0.97 6852 152 0.2454 0.2729 3.7994 3.8379| | 22: 1.07 - 1.05 0.97 6838 135 0.2569 0.2583 3.7605 3.754| | 23: 1.05 - 1.03 0.97 6829 159 0.2705 0.2545 3.7254 3.8102| | 24: 1.03 - 1.02 0.96 6785 133 0.2860 0.2841 3.6997 3.7633| | 25: 1.02 - 1.01 0.93 6552 130 0.3063 0.2965 3.6804 3.7297| | 26: 1.01 - 0.99 0.96 6767 158 0.3211 0.3251 3.633 3.6146| | 27: 0.99 - 0.98 0.94 6648 131 0.3430 0.3187 3.6433 3.6367| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.74 0.91 0.98 36489.41| | 2: 2.94 - 2.33 7339 128 0.85 21.37 1.08 1.02 15355.28| | 3: 2.33 - 2.04 6939 150 0.93 12.23 1.10 1.05 3949.80| | 4: 2.04 - 1.85 7170 155 0.93 12.81 1.11 1.06 2552.46| | 5: 1.85 - 1.72 7113 159 0.92 14.45 1.11 1.07 1840.65| | 6: 1.72 - 1.62 7102 142 0.91 15.65 1.11 1.07 1486.15| | 7: 1.62 - 1.54 7104 148 0.90 16.84 1.11 1.08 1243.49| | 8: 1.54 - 1.47 6798 152 0.89 17.81 1.10 1.07 1093.70| | 9: 1.47 - 1.41 6938 155 0.88 18.65 1.10 1.08 949.46| | 10: 1.41 - 1.36 7022 150 0.88 19.42 1.09 1.06 804.61| | 11: 1.36 - 1.32 6997 151 0.88 18.81 1.08 1.05 667.70| | 12: 1.32 - 1.28 6976 149 0.88 19.20 1.08 1.05 618.45| | 13: 1.28 - 1.25 6907 166 0.88 19.68 1.06 1.05 613.04| | 14: 1.25 - 1.22 7015 113 0.86 21.04 1.08 1.06 595.97| | 15: 1.22 - 1.19 6957 137 0.86 20.92 1.07 1.05 548.78| | 16: 1.19 - 1.17 6604 132 0.88 19.92 1.07 1.02 469.87| | 17: 1.17 - 1.14 6941 135 0.86 20.94 1.08 1.01 432.24| | 18: 1.14 - 1.12 6875 142 0.86 21.34 1.09 0.99 395.00| | 19: 1.12 - 1.10 6949 106 0.85 22.52 1.07 1.01 396.65| | 20: 1.10 - 1.08 6884 147 0.84 23.22 1.06 0.98 362.27| | 21: 1.08 - 1.07 6852 152 0.83 24.44 1.06 0.98 350.80| | 22: 1.07 - 1.05 6838 135 0.82 25.64 1.05 0.97 330.19| | 23: 1.05 - 1.03 6829 159 0.80 27.63 1.05 0.98 334.66| | 24: 1.03 - 1.02 6785 133 0.78 29.31 1.05 0.98 329.83| | 25: 1.02 - 1.01 6552 130 0.77 30.87 1.02 0.94 317.74| | 26: 1.01 - 0.99 6767 158 0.74 32.89 1.03 0.91 305.85| | 27: 0.99 - 0.98 6648 131 0.74 33.56 1.03 0.90 295.31| |alpha: min = 0.90 max = 1.08 mean = 1.02| |beta: min = 295.31 max = 36489.41 mean = 2838.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.46| |phase err.(test): min = 0.00 max = 89.25 mean = 21.64| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.261 2950 Z= 5.540 Angle : 5.223 17.907 4018 Z= 3.726 Chirality : 0.405 1.179 492 Planarity : 0.032 0.125 512 Dihedral : 12.862 85.747 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.63 % Favored : 95.60 % Rotamer: Outliers : 1.29 % Allowed : 4.84 % Favored : 93.87 % Cbeta Deviations : 34.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.41), residues: 386 helix: -2.01 (0.36), residues: 146 sheet: -0.73 (0.52), residues: 86 loop : -0.35 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.029 ARG A 143 TYR 0.107 0.038 TYR B 195 PHE 0.097 0.033 PHE A 119 TRP 0.139 0.045 TRP B 146 HIS 0.086 0.037 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303112 | | target function (ml) not normalized (work): 806028.895146 | | target function (ml) not normalized (free): 16526.615592 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2039 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2039 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2039 0.1961 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2037 0.2039 0.1961 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1808 0.1890 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1806 0.1890 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 0.4066 402.814 291.989 0.434 0.912 0.301 13.296-10.522 99.01 99 1 0.2513 528.187 519.392 0.787 0.913 0.253 10.503-8.327 99.45 178 3 0.2528 565.118 555.451 0.973 0.914 0.230 8.318-6.595 100.00 360 8 0.2485 414.736 404.146 0.967 0.913 0.159 6.588-5.215 100.00 711 7 0.2238 381.101 366.617 0.957 0.913 0.140 5.214-4.128 98.38 1367 28 0.1493 557.435 550.714 1.079 0.914 0.090 4.126-3.266 94.74 2603 46 0.1353 508.132 499.120 1.148 0.914 0.018 3.266-2.585 99.86 5447 97 0.1458 342.774 337.518 1.118 0.913 0.000 2.585-2.046 97.45 10613 204 0.1406 258.603 254.001 1.123 0.913 0.000 2.046-1.619 99.39 21536 464 0.1625 153.054 150.005 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1927 82.395 80.158 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2323 44.203 41.660 1.111 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0042 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1806 r_free=0.1890 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1806 r_free=0.1890 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.406925 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 566.911466 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 0.1270 0.1497 0.0227 0.038 1.1 11.2 0.0 0.3 0 11.203 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.97 2.27 1.118 13.113 566.911 0.018 12.95 15.62 2.66 1.211 13.277 566.911 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.05 14.90 1.39 435 3274 Protein: 5.15 40.32 10.95 1.39 0 2902 Water: 6.33 73.05 29.12 N/A 435 370 Other: 16.05 31.07 23.56 N/A 0 2 Chain A: 5.38 60.12 12.96 N/A 0 1626 Chain B: 5.15 73.05 12.69 N/A 0 1648 Chain S: 11.69 60.83 30.50 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2171 11.94 - 18.73 636 18.73 - 25.52 331 25.52 - 32.31 260 32.31 - 39.10 151 39.10 - 45.89 101 45.89 - 52.68 35 52.68 - 59.47 20 59.47 - 66.26 3 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1562 r_work=0.1295 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1557 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1544 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015612 | | target function (ls_wunit_k1) not normalized (work): 2924.163758 | | target function (ls_wunit_k1) not normalized (free): 115.418250 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1280 0.1544 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1464 0.1461 0.1621 n_refl.: 191139 remove outliers: r(all,work,free)=0.1464 0.1461 0.1621 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1486 0.1484 0.1630 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1277 0.1272 0.1533 n_refl.: 191139 remove outliers: r(all,work,free)=0.1277 0.1272 0.1532 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 0.3591 402.814 368.166 0.472 0.964 0.275 13.296-10.522 99.01 99 1 0.2094 528.187 519.471 0.737 0.965 0.243 10.503-8.327 99.45 178 3 0.1782 565.118 565.025 0.890 0.965 0.238 8.318-6.595 100.00 360 8 0.1717 414.736 412.217 0.908 0.965 0.150 6.588-5.215 100.00 711 7 0.1538 381.101 374.453 0.889 0.965 0.140 5.214-4.128 98.38 1367 28 0.0905 557.435 554.358 0.979 0.965 0.080 4.126-3.266 94.74 2603 46 0.0836 508.132 504.181 1.044 0.966 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.456 1.026 0.966 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.343 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1083 153.054 151.425 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.393 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.230 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0375 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1532 | n_water=805 | time (s): 2.930 (total time: 2.930) Filter (dist) r_work=0.1277 r_free=0.1540 | n_water=793 | time (s): 101.810 (total time: 104.740) Filter (q & B) r_work=0.1278 r_free=0.1540 | n_water=790 | time (s): 4.230 (total time: 108.970) Compute maps r_work=0.1278 r_free=0.1540 | n_water=790 | time (s): 1.900 (total time: 110.870) Filter (map) r_work=0.1303 r_free=0.1525 | n_water=654 | time (s): 4.300 (total time: 115.170) Find peaks r_work=0.1303 r_free=0.1525 | n_water=654 | time (s): 0.790 (total time: 115.960) Add new water r_work=0.1326 r_free=0.1552 | n_water=936 | time (s): 4.700 (total time: 120.660) Refine new water occ: r_work=0.1284 r_free=0.1495 adp: r_work=0.1272 r_free=0.1492 occ: r_work=0.1275 r_free=0.1489 adp: r_work=0.1268 r_free=0.1488 occ: r_work=0.1270 r_free=0.1486 adp: r_work=0.1267 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1487 r_work=0.1267 r_free=0.1487 | n_water=936 | time (s): 88.700 (total time: 209.360) Filter (q & B) r_work=0.1270 r_free=0.1492 | n_water=882 | time (s): 4.600 (total time: 213.960) Filter (dist only) r_work=0.1270 r_free=0.1492 | n_water=881 | time (s): 107.470 (total time: 321.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.927692 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 588.232188 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 0.1257 0.1508 0.0251 0.041 1.1 17.7 0.0 0.3 0 11.464 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.08 2.51 2.026 15.082 588.232 0.015 12.35 14.97 2.62 2.364 15.147 588.232 0.014 Individual atomic B min max mean iso aniso Overall: 5.37 68.25 16.23 1.20 513 3272 Protein: 5.37 40.02 10.97 1.20 0 2902 Water: 6.66 68.25 33.54 N/A 513 368 Other: 16.49 33.25 24.87 N/A 0 2 Chain A: 5.52 56.79 12.95 N/A 0 1624 Chain B: 5.37 68.21 12.78 N/A 0 1648 Chain S: 13.44 68.25 37.71 N/A 513 0 Histogram: Values Number of atoms 5.37 - 11.66 2056 11.66 - 17.95 715 17.95 - 24.24 267 24.24 - 30.52 219 30.52 - 36.81 170 36.81 - 43.10 161 43.10 - 49.39 105 49.39 - 55.68 40 55.68 - 61.96 40 61.96 - 68.25 12 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1497 r_work=0.1235 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1499 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1498 target_work(ls_wunit_k1) = 0.014 | | 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= 0.1228 r_free= 0.1498 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013593 | | target function (ls_wunit_k1) not normalized (work): 2546.005637 | | target function (ls_wunit_k1) not normalized (free): 97.715740 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1228 0.1498 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1437 0.1594 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1437 0.1594 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1434 0.1592 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1235 0.1503 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1235 0.1503 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 0.3308 402.814 377.189 0.491 0.962 0.271 13.296-10.522 99.01 99 1 0.1897 528.187 518.932 0.753 0.963 0.223 10.503-8.327 99.45 178 3 0.1488 565.118 566.459 0.923 0.963 0.179 8.318-6.595 100.00 360 8 0.1558 414.736 414.741 0.939 0.962 0.160 6.588-5.215 100.00 711 7 0.1346 381.101 376.802 0.913 0.962 0.150 5.214-4.128 98.38 1367 28 0.0841 557.435 555.982 0.997 0.962 0.100 4.126-3.266 94.74 2603 46 0.0773 508.132 505.395 1.060 0.962 0.009 3.266-2.585 99.86 5447 97 0.0862 342.774 341.256 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.714 1.059 0.960 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.621 1.080 0.958 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.351 1.073 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.223 1.058 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0435 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1503 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1503 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1503 | n_water=881 | time (s): 3.450 (total time: 3.450) Filter (dist) r_work=0.1235 r_free=0.1504 | n_water=878 | time (s): 118.550 (total time: 122.000) Filter (q & B) r_work=0.1236 r_free=0.1504 | n_water=874 | time (s): 4.340 (total time: 126.340) Compute maps r_work=0.1236 r_free=0.1504 | n_water=874 | time (s): 2.180 (total time: 128.520) Filter (map) r_work=0.1273 r_free=0.1517 | n_water=688 | time (s): 5.230 (total time: 133.750) Find peaks r_work=0.1273 r_free=0.1517 | n_water=688 | time (s): 0.700 (total time: 134.450) Add new water r_work=0.1299 r_free=0.1548 | n_water=998 | time (s): 3.810 (total time: 138.260) Refine new water occ: r_work=0.1254 r_free=0.1500 adp: r_work=0.1254 r_free=0.1501 occ: r_work=0.1250 r_free=0.1497 adp: r_work=0.1249 r_free=0.1498 occ: r_work=0.1247 r_free=0.1494 adp: r_work=0.1245 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1495 r_work=0.1245 r_free=0.1495 | n_water=998 | time (s): 282.700 (total time: 420.960) Filter (q & B) r_work=0.1250 r_free=0.1502 | n_water=870 | time (s): 4.350 (total time: 425.310) Filter (dist only) r_work=0.1251 r_free=0.1502 | n_water=868 | time (s): 109.350 (total time: 534.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.656856 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.972621 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 0.1238 0.1428 0.0190 0.036 1.1 7.8 0.0 0.0 0 0.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.28 1.90 1.926 14.535 15.973 3.938 12.33 13.90 1.57 2.214 14.441 15.973 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.76 15.20 1.05 501 3271 Protein: 5.53 36.42 10.73 1.05 0 2902 Water: 6.66 67.76 30.11 N/A 501 367 Other: 14.15 28.94 21.55 N/A 0 2 Chain A: 5.54 55.96 12.73 N/A 0 1624 Chain B: 5.53 67.76 12.50 N/A 0 1647 Chain S: 13.55 61.03 32.07 N/A 501 0 Histogram: Values Number of atoms 5.53 - 11.75 2138 11.75 - 17.97 681 17.97 - 24.20 285 24.20 - 30.42 247 30.42 - 36.64 185 36.64 - 42.87 133 42.87 - 49.09 74 49.09 - 55.31 20 55.31 - 61.54 8 61.54 - 67.76 1 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1390 r_work=0.1234 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1390 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1383 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890945 | | target function (ml) not normalized (work): 728762.317506 | | target function (ml) not normalized (free): 15217.474241 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1382 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1477 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1477 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1436 0.1474 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1378 n_refl.: 191138 remove outliers: r(all,work,free)=0.1226 0.1223 0.1378 n_refl.: 191134 ======================== 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 0.3734 393.525 361.005 0.424 0.947 0.253 13.296-10.522 99.01 99 1 0.2438 528.187 510.070 0.704 0.948 0.216 10.503-8.327 98.35 176 3 0.2016 555.265 555.596 0.887 0.948 0.169 8.318-6.595 100.00 360 8 0.2083 414.736 409.587 0.897 0.947 0.130 6.588-5.215 100.00 711 7 0.1780 381.101 371.477 0.889 0.947 0.120 5.214-4.128 98.38 1367 28 0.1170 557.435 552.039 0.971 0.948 0.059 4.126-3.266 94.74 2603 46 0.1085 508.132 501.372 1.033 0.948 0.014 3.266-2.585 99.86 5447 97 0.1083 342.774 339.049 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0968 258.603 255.713 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.403 1.055 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.484 1.051 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.311 1.036 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0916 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1378 | n_water=868 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1223 r_free=0.1377 | n_water=866 | time (s): 116.590 (total time: 119.740) Filter (q & B) r_work=0.1224 r_free=0.1379 | n_water=857 | time (s): 4.400 (total time: 124.140) Compute maps r_work=0.1224 r_free=0.1379 | n_water=857 | time (s): 1.630 (total time: 125.770) Filter (map) r_work=0.1248 r_free=0.1377 | n_water=707 | time (s): 5.360 (total time: 131.130) Find peaks r_work=0.1248 r_free=0.1377 | n_water=707 | time (s): 0.710 (total time: 131.840) Add new water r_work=0.1263 r_free=0.1388 | n_water=958 | time (s): 5.190 (total time: 137.030) Refine new water occ: r_work=0.1214 r_free=0.1354 adp: r_work=0.1206 r_free=0.1349 occ: r_work=0.1204 r_free=0.1350 adp: r_work=0.1204 r_free=0.1349 occ: r_work=0.1202 r_free=0.1349 adp: r_work=0.1201 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1349 r_work=0.1201 r_free=0.1349 | n_water=958 | time (s): 378.340 (total time: 515.370) Filter (q & B) r_work=0.1206 r_free=0.1359 | n_water=865 | time (s): 4.580 (total time: 519.950) Filter (dist only) r_work=0.1207 r_free=0.1358 | n_water=863 | time (s): 109.970 (total time: 629.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.650329 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.982913 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 0.1205 0.1361 0.0155 0.035 1.1 6.8 0.0 0.3 0 0.825 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.61 1.55 1.828 14.161 14.983 3.873 11.99 13.59 1.60 1.906 14.130 14.983 3.865 Individual atomic B min max mean iso aniso Overall: 5.53 67.41 14.92 1.00 497 3270 Protein: 5.53 33.60 10.67 1.00 0 2902 Water: 5.90 67.41 29.22 N/A 497 366 Other: 13.95 28.33 21.14 N/A 0 2 Chain A: 5.53 55.21 12.62 N/A 0 1624 Chain B: 5.53 67.41 12.41 N/A 0 1646 Chain S: 5.90 61.09 30.78 N/A 497 0 Histogram: Values Number of atoms 5.53 - 11.72 2132 11.72 - 17.90 710 17.90 - 24.09 299 24.09 - 30.28 238 30.28 - 36.47 181 36.47 - 42.66 123 42.66 - 48.85 63 48.85 - 55.03 14 55.03 - 61.22 6 61.22 - 67.41 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 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) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863363 | | target function (ml) not normalized (work): 723580.924308 | | target function (ml) not normalized (free): 15132.334612 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1358 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1426 0.1426 0.1471 n_refl.: 191134 remove outliers: r(all,work,free)=0.1426 0.1426 0.1471 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1419 0.1466 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1356 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1195 0.1356 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3614 348.644 314.657 0.402 0.946 0.235 13.296-10.522 97.03 97 1 0.2355 481.345 455.226 0.699 0.947 0.205 10.503-8.327 98.35 176 3 0.2088 502.951 495.705 0.871 0.947 0.175 8.318-6.595 100.00 360 8 0.2199 375.662 369.794 0.893 0.947 0.128 6.588-5.215 100.00 711 7 0.1906 345.196 335.474 0.888 0.947 0.107 5.214-4.128 98.38 1367 28 0.1195 504.917 499.807 0.974 0.947 0.070 4.126-3.266 94.74 2603 46 0.1121 460.259 453.674 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1088 310.480 307.262 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0933 234.239 231.804 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0912 138.634 137.368 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.633 73.920 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.037 38.376 1.037 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1119 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1356 | n_water=863 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1195 r_free=0.1356 | n_water=863 | time (s): 100.710 (total time: 102.970) Filter (q & B) r_work=0.1196 r_free=0.1355 | n_water=855 | time (s): 5.010 (total time: 107.980) Compute maps r_work=0.1196 r_free=0.1355 | n_water=855 | time (s): 2.380 (total time: 110.360) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=730 | time (s): 5.140 (total time: 115.500) Find peaks r_work=0.1219 r_free=0.1365 | n_water=730 | time (s): 0.660 (total time: 116.160) Add new water r_work=0.1234 r_free=0.1378 | n_water=951 | time (s): 3.930 (total time: 120.090) Refine new water occ: r_work=0.1195 r_free=0.1337 adp: r_work=0.1196 r_free=0.1336 occ: r_work=0.1192 r_free=0.1334 adp: r_work=0.1192 r_free=0.1334 occ: r_work=0.1190 r_free=0.1332 adp: r_work=0.1189 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1332 r_work=0.1189 r_free=0.1332 | n_water=951 | time (s): 245.110 (total time: 365.200) Filter (q & B) r_work=0.1193 r_free=0.1342 | n_water=882 | time (s): 4.680 (total time: 369.880) Filter (dist only) r_work=0.1194 r_free=0.1342 | n_water=881 | time (s): 110.060 (total time: 479.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.592494 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.944190 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1347 0.0151 0.036 1.1 6.3 0.0 0.3 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.47 1.51 1.795 14.127 14.944 3.764 12.00 13.50 1.50 1.884 14.092 14.944 3.761 Individual atomic B min max mean iso aniso Overall: 5.55 66.97 14.92 0.95 515 3270 Protein: 5.55 32.08 10.58 0.95 0 2902 Water: 6.15 66.97 29.20 N/A 515 366 Other: 13.84 26.88 20.36 N/A 0 2 Chain A: 5.56 54.26 12.51 N/A 0 1624 Chain B: 5.55 66.97 12.30 N/A 0 1646 Chain S: 6.15 61.18 30.90 N/A 515 0 Histogram: Values Number of atoms 5.55 - 11.69 2133 11.69 - 17.83 724 17.83 - 23.98 297 23.98 - 30.12 234 30.12 - 36.26 172 36.26 - 42.40 131 42.40 - 48.54 68 48.54 - 54.68 20 54.68 - 60.83 4 60.83 - 66.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1350 r_work=0.1200 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1350 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1349 target_work(ml) = 3.760 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760153 | | target function (ml) not normalized (work): 704235.257504 | | target function (ml) not normalized (free): 14740.603565 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1349 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1470 n_refl.: 191130 remove outliers: r(all,work,free)=0.1402 0.1401 0.1470 n_refl.: 191130 overall B=-0.03 to atoms: r(all,work,free)=0.1395 0.1394 0.1465 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1347 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1347 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 90.10 88 3 0.3624 343.876 314.119 0.383 0.952 0.215 13.296-10.522 97.03 97 1 0.2384 481.345 462.324 0.689 0.953 0.163 10.503-8.327 98.35 176 3 0.2125 502.951 495.101 0.863 0.954 0.140 8.318-6.595 100.00 360 8 0.2142 375.662 370.930 0.886 0.953 0.108 6.588-5.215 100.00 711 7 0.1878 345.196 335.430 0.881 0.953 0.087 5.214-4.128 98.38 1367 28 0.1198 504.917 499.628 0.967 0.954 0.060 4.126-3.266 94.74 2603 46 0.1137 460.259 453.371 1.029 0.954 0.009 3.266-2.585 99.86 5447 97 0.1108 310.480 307.149 1.015 0.953 0.000 2.585-2.046 97.45 10613 204 0.0946 234.239 231.730 1.027 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.634 137.324 1.051 0.951 0.000 1.619-1.281 98.00 42464 925 0.0978 74.633 73.913 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.037 38.363 1.037 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1213 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1347 | n_water=881 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1196 r_free=0.1347 | n_water=880 | time (s): 106.400 (total time: 109.050) Filter (q & B) r_work=0.1196 r_free=0.1348 | n_water=872 | time (s): 4.450 (total time: 113.500) Compute maps r_work=0.1196 r_free=0.1348 | n_water=872 | time (s): 2.470 (total time: 115.970) Filter (map) r_work=0.1218 r_free=0.1366 | n_water=750 | time (s): 4.740 (total time: 120.710) Find peaks r_work=0.1218 r_free=0.1366 | n_water=750 | time (s): 0.680 (total time: 121.390) Add new water r_work=0.1229 r_free=0.1376 | n_water=964 | time (s): 5.570 (total time: 126.960) Refine new water occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1196 r_free=0.1343 occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1342 r_work=0.1191 r_free=0.1342 | n_water=964 | time (s): 231.920 (total time: 358.880) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=897 | time (s): 5.300 (total time: 364.180) Filter (dist only) r_work=0.1194 r_free=0.1350 | n_water=896 | time (s): 114.870 (total time: 479.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566709 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.004198 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0159 0.036 1.1 7.7 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.59 1.760 14.038 15.004 3.762 12.00 13.61 1.60 1.893 13.995 15.004 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 65.90 14.84 0.90 530 3270 Protein: 5.56 29.32 10.48 0.90 0 2902 Water: 5.99 65.90 28.96 N/A 530 366 Other: 13.86 24.14 19.00 N/A 0 2 Chain A: 5.63 51.60 12.37 N/A 0 1624 Chain B: 5.56 65.90 12.18 N/A 0 1646 Chain S: 5.99 61.46 30.70 N/A 530 0 Histogram: Values Number of atoms 5.56 - 11.59 2117 11.59 - 17.63 772 17.63 - 23.66 280 23.66 - 29.69 209 29.69 - 35.73 188 35.73 - 41.76 129 41.76 - 47.80 73 47.80 - 53.83 26 53.83 - 59.87 4 59.87 - 65.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1361 r_work=0.1201 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757858 | | target function (ml) not normalized (work): 703801.789024 | | target function (ml) not normalized (free): 14743.625332 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1363 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1480 n_refl.: 191129 remove outliers: r(all,work,free)=0.1403 0.1402 0.1480 n_refl.: 191129 overall B=-0.22 to atoms: r(all,work,free)=0.1368 0.1367 0.1457 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191129 remove outliers: r(all,work,free)=0.1201 0.1198 0.1360 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 90.10 88 3 0.3709 343.876 309.335 0.379 0.952 0.205 13.296-10.522 97.03 97 1 0.2377 481.345 462.174 0.702 0.953 0.151 10.503-8.327 98.35 176 3 0.2124 502.951 494.671 0.886 0.953 0.123 8.318-6.595 100.00 360 8 0.2190 375.662 370.412 0.906 0.953 0.100 6.588-5.215 100.00 711 7 0.1905 345.196 335.389 0.902 0.953 0.080 5.214-4.128 98.38 1367 28 0.1205 504.917 499.836 0.993 0.954 0.040 4.126-3.266 94.74 2603 46 0.1152 460.259 453.242 1.055 0.954 0.009 3.266-2.585 99.86 5447 97 0.1122 310.480 307.115 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0954 234.239 231.680 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0912 138.634 137.331 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0969 74.633 73.924 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.037 38.362 1.026 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1361 | n_water=896 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1198 r_free=0.1361 | n_water=896 | time (s): 107.420 (total time: 110.220) Filter (q & B) r_work=0.1199 r_free=0.1361 | n_water=888 | time (s): 4.320 (total time: 114.540) Compute maps r_work=0.1199 r_free=0.1361 | n_water=888 | time (s): 2.420 (total time: 116.960) Filter (map) r_work=0.1223 r_free=0.1365 | n_water=758 | time (s): 5.030 (total time: 121.990) Find peaks r_work=0.1223 r_free=0.1365 | n_water=758 | time (s): 0.700 (total time: 122.690) Add new water r_work=0.1231 r_free=0.1373 | n_water=965 | time (s): 4.490 (total time: 127.180) Refine new water occ: r_work=0.1199 r_free=0.1343 adp: r_work=0.1199 r_free=0.1343 occ: r_work=0.1197 r_free=0.1343 adp: r_work=0.1197 r_free=0.1343 occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1195 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1343 r_work=0.1195 r_free=0.1343 | n_water=965 | time (s): 202.470 (total time: 329.650) Filter (q & B) r_work=0.1199 r_free=0.1354 | n_water=894 | time (s): 4.910 (total time: 334.560) Filter (dist only) r_work=0.1199 r_free=0.1353 | n_water=893 | time (s): 115.140 (total time: 449.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603303 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.681205 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1357 0.0154 0.037 1.1 5.1 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.57 1.54 1.719 13.708 13.681 3.759 12.05 13.60 1.56 1.725 13.703 13.681 3.759 Individual atomic B min max mean iso aniso Overall: 5.39 65.49 14.59 0.88 527 3270 Protein: 5.39 28.92 10.27 0.88 0 2902 Water: 5.83 65.49 28.59 N/A 527 366 Other: 13.62 23.66 18.64 N/A 0 2 Chain A: 5.43 51.17 12.14 N/A 0 1624 Chain B: 5.39 65.49 11.96 N/A 0 1646 Chain S: 5.83 61.31 30.35 N/A 527 0 Histogram: Values Number of atoms 5.39 - 11.40 2121 11.40 - 17.41 773 17.41 - 23.42 270 23.42 - 29.43 225 29.43 - 35.44 178 35.44 - 41.45 127 41.45 - 47.46 71 47.46 - 53.47 26 53.47 - 59.48 4 59.48 - 65.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1360 r_work=0.1205 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758942 | | target function (ml) not normalized (work): 704004.652048 | | target function (ml) not normalized (free): 14745.928134 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1379 0.1377 0.1472 n_refl.: 191129 remove outliers: r(all,work,free)=0.1379 0.1377 0.1472 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1387 0.1386 0.1478 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1356 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 90.10 88 3 0.3772 343.876 306.795 0.362 0.976 0.191 13.296-10.522 97.03 97 1 0.2411 481.345 461.728 0.689 0.978 0.146 10.503-8.327 98.35 176 3 0.2166 502.951 493.942 0.867 0.978 0.132 8.318-6.595 100.00 360 8 0.2204 375.662 369.469 0.890 0.978 0.096 6.588-5.215 100.00 711 7 0.1936 345.196 334.616 0.887 0.979 0.087 5.214-4.128 98.38 1367 28 0.1227 504.917 499.171 0.978 0.979 0.044 4.126-3.266 94.74 2603 46 0.1168 460.259 452.573 1.039 0.980 0.009 3.266-2.585 99.86 5447 97 0.1126 310.480 306.803 1.022 0.981 0.000 2.585-2.046 97.45 10613 204 0.0961 234.239 231.550 1.030 0.982 0.000 2.046-1.619 99.39 21536 464 0.0911 138.634 137.252 1.047 0.985 0.000 1.619-1.281 98.00 42464 925 0.0951 74.633 73.960 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.037 38.334 1.003 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1356 | n_water=893 | time (s): 3.430 (total time: 3.430) Filter (dist) r_work=0.1194 r_free=0.1356 | n_water=892 | time (s): 114.910 (total time: 118.340) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=882 | time (s): 5.460 (total time: 123.800) Compute maps r_work=0.1194 r_free=0.1356 | n_water=882 | time (s): 2.150 (total time: 125.950) Filter (map) r_work=0.1216 r_free=0.1354 | n_water=761 | time (s): 4.600 (total time: 130.550) Find peaks r_work=0.1216 r_free=0.1354 | n_water=761 | time (s): 0.830 (total time: 131.380) Add new water r_work=0.1224 r_free=0.1364 | n_water=973 | time (s): 4.940 (total time: 136.320) Refine new water occ: r_work=0.1191 r_free=0.1332 adp: r_work=0.1191 r_free=0.1333 occ: r_work=0.1189 r_free=0.1331 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1332 r_work=0.1187 r_free=0.1332 | n_water=973 | time (s): 229.590 (total time: 365.910) Filter (q & B) r_work=0.1192 r_free=0.1342 | n_water=902 | time (s): 5.240 (total time: 371.150) Filter (dist only) r_work=0.1192 r_free=0.1341 | n_water=901 | time (s): 118.040 (total time: 489.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.559137 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.429189 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 0.1344 0.0149 0.038 1.1 7.2 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.44 1.49 1.684 13.766 14.429 3.757 11.94 13.45 1.51 1.709 13.758 14.429 3.754 Individual atomic B min max mean iso aniso Overall: 5.47 64.81 14.67 0.88 535 3270 Protein: 5.47 28.60 10.34 0.88 0 2902 Water: 5.90 64.81 28.60 N/A 535 366 Other: 13.76 22.61 18.18 N/A 0 2 Chain A: 5.57 50.89 12.17 N/A 0 1624 Chain B: 5.47 64.81 12.00 N/A 0 1646 Chain S: 5.90 61.54 30.45 N/A 535 0 Histogram: Values Number of atoms 5.47 - 11.41 2092 11.41 - 17.34 804 17.34 - 23.27 264 23.27 - 29.21 218 29.21 - 35.14 190 35.14 - 41.08 128 41.08 - 47.01 74 47.01 - 52.94 29 52.94 - 58.88 4 58.88 - 64.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1345 r_work=0.1194 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1345 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 = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753195 | | target function (ml) not normalized (work): 702928.429103 | | target function (ml) not normalized (free): 14721.609949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1344 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1466 n_refl.: 191129 remove outliers: r(all,work,free)=0.1391 0.1390 0.1466 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1393 0.1392 0.1468 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1340 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1340 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 90.10 88 3 0.3889 343.876 306.572 0.324 0.981 0.126 13.296-10.522 97.03 97 1 0.2408 481.345 460.781 0.675 0.983 0.117 10.503-8.327 98.35 176 3 0.2178 502.951 493.300 0.862 0.983 0.105 8.318-6.595 100.00 360 8 0.2196 375.662 369.848 0.882 0.983 0.091 6.588-5.215 100.00 711 7 0.1930 345.196 334.730 0.881 0.983 0.083 5.214-4.128 98.38 1367 28 0.1230 504.917 499.149 0.972 0.984 0.049 4.126-3.266 94.74 2603 46 0.1163 460.259 452.543 1.034 0.985 0.009 3.266-2.585 99.86 5447 97 0.1125 310.480 306.867 1.018 0.986 0.000 2.585-2.046 97.45 10613 204 0.0962 234.239 231.547 1.026 0.988 0.000 2.046-1.619 99.39 21536 464 0.0908 138.634 137.278 1.043 0.991 0.000 1.619-1.281 98.00 42464 925 0.0945 74.633 73.973 1.033 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.037 38.326 1.003 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0191 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1340 | n_water=901 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1191 r_free=0.1340 | n_water=901 | time (s): 106.060 (total time: 108.640) Filter (q & B) r_work=0.1192 r_free=0.1341 | n_water=888 | time (s): 5.830 (total time: 114.470) Compute maps r_work=0.1192 r_free=0.1341 | n_water=888 | time (s): 1.750 (total time: 116.220) Filter (map) r_work=0.1213 r_free=0.1349 | n_water=770 | time (s): 4.640 (total time: 120.860) Find peaks r_work=0.1213 r_free=0.1349 | n_water=770 | time (s): 0.710 (total time: 121.570) Add new water r_work=0.1220 r_free=0.1357 | n_water=971 | time (s): 4.900 (total time: 126.470) Refine new water occ: r_work=0.1190 r_free=0.1323 adp: r_work=0.1190 r_free=0.1323 occ: r_work=0.1188 r_free=0.1322 adp: r_work=0.1188 r_free=0.1323 occ: r_work=0.1186 r_free=0.1322 adp: r_work=0.1186 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1323 r_work=0.1186 r_free=0.1323 | n_water=971 | time (s): 217.200 (total time: 343.670) Filter (q & B) r_work=0.1191 r_free=0.1340 | n_water=898 | time (s): 4.400 (total time: 348.070) Filter (dist only) r_work=0.1191 r_free=0.1338 | n_water=897 | time (s): 113.330 (total time: 461.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.792899 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 0.1342 0.0146 0.038 1.1 7.0 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.42 1.46 1.687 13.765 14.793 3.755 11.94 13.45 1.50 1.701 13.762 14.793 3.752 Individual atomic B min max mean iso aniso Overall: 5.54 63.92 14.66 0.88 531 3270 Protein: 5.54 28.39 10.36 0.88 0 2902 Water: 5.98 63.92 28.56 N/A 531 366 Other: 13.82 22.17 17.99 N/A 0 2 Chain A: 5.62 50.53 12.16 N/A 0 1624 Chain B: 5.54 63.92 12.00 N/A 0 1646 Chain S: 5.98 61.72 30.54 N/A 531 0 Histogram: Values Number of atoms 5.54 - 11.38 2079 11.38 - 17.22 815 17.22 - 23.06 255 23.06 - 28.89 221 28.89 - 34.73 188 34.73 - 40.57 122 40.57 - 46.40 79 46.40 - 52.24 34 52.24 - 58.08 4 58.08 - 63.92 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1345 r_work=0.1195 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1345 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1344 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751880 | | target function (ml) not normalized (work): 702682.083758 | | target function (ml) not normalized (free): 14720.179498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1344 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1481 n_refl.: 191129 remove outliers: r(all,work,free)=0.1403 0.1402 0.1481 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1403 0.1401 0.1481 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1342 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1342 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 90.10 88 3 0.3890 343.876 306.070 0.314 0.995 0.118 13.296-10.522 97.03 97 1 0.2426 481.345 460.438 0.662 0.996 0.111 10.503-8.327 98.35 176 3 0.2186 502.951 493.968 0.847 0.997 0.100 8.318-6.595 100.00 360 8 0.2205 375.662 369.925 0.867 0.997 0.087 6.588-5.215 100.00 711 7 0.1950 345.196 334.666 0.867 0.997 0.080 5.214-4.128 98.38 1367 28 0.1239 504.917 498.926 0.958 0.998 0.050 4.126-3.266 94.74 2603 46 0.1178 460.259 452.446 1.020 0.999 0.014 3.266-2.585 99.86 5447 97 0.1132 310.480 306.899 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0964 234.239 231.510 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0905 138.634 137.280 1.029 1.006 0.000 1.619-1.281 98.00 42464 925 0.0940 74.633 73.983 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.037 38.319 0.991 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0076 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1342 After: r_work=0.1193 r_free=0.1342 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1342 | n_water=897 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1193 r_free=0.1342 | n_water=897 | time (s): 109.600 (total time: 112.430) Filter (q & B) r_work=0.1193 r_free=0.1342 | n_water=886 | time (s): 4.740 (total time: 117.170) Compute maps r_work=0.1193 r_free=0.1342 | n_water=886 | time (s): 2.200 (total time: 119.370) Filter (map) r_work=0.1215 r_free=0.1343 | n_water=772 | time (s): 5.540 (total time: 124.910) Find peaks r_work=0.1215 r_free=0.1343 | n_water=772 | time (s): 0.670 (total time: 125.580) Add new water r_work=0.1221 r_free=0.1349 | n_water=969 | time (s): 4.880 (total time: 130.460) Refine new water occ: r_work=0.1191 r_free=0.1322 adp: r_work=0.1191 r_free=0.1322 occ: r_work=0.1189 r_free=0.1322 adp: r_work=0.1189 r_free=0.1322 occ: r_work=0.1188 r_free=0.1322 adp: r_work=0.1187 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1322 r_work=0.1187 r_free=0.1322 | n_water=969 | time (s): 230.540 (total time: 361.000) Filter (q & B) r_work=0.1191 r_free=0.1334 | n_water=897 | time (s): 4.520 (total time: 365.520) Filter (dist only) r_work=0.1192 r_free=0.1334 | n_water=895 | time (s): 115.730 (total time: 481.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579489 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.077515 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 0.1339 0.0144 0.038 1.2 8.9 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.39 1.44 1.685 13.751 14.078 3.754 11.96 13.41 1.45 1.682 13.751 14.078 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 63.63 14.64 0.87 530 3269 Protein: 5.54 28.30 10.37 0.87 0 2902 Water: 5.99 63.63 28.45 N/A 530 365 Other: 13.83 22.21 18.02 N/A 0 2 Chain A: 5.64 50.42 12.14 N/A 0 1623 Chain B: 5.54 63.63 12.00 N/A 0 1646 Chain S: 5.99 61.75 30.46 N/A 530 0 Histogram: Values Number of atoms 5.54 - 11.35 2064 11.35 - 17.16 832 17.16 - 22.97 254 22.97 - 28.78 217 28.78 - 34.59 191 34.59 - 40.40 118 40.40 - 46.21 79 46.21 - 52.02 36 52.02 - 57.82 4 57.82 - 63.63 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1341 r_work=0.1196 r_free=0.1341 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1341 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1342 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753952 | | target function (ml) not normalized (work): 703070.252204 | | target function (ml) not normalized (free): 14721.642941 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1368 0.1410 5.6904 5.7392| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1357 5.0752 5.1759| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1172 4.6617 4.761| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1054 4.3933 4.5719| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0974 4.1465 4.2178| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1045 3.9379 4.0517| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0953 3.794 3.9242| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1329 3.6988 3.9115| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1124 3.6212 3.7605| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1176 3.5567 3.667| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1136 3.4852 3.596| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1130 3.4607 3.5831| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1247 3.4393 3.5669| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1585 3.4332 3.6854| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1240 3.4493 3.4917| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1552 3.4649 3.6529| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1221 3.4327 3.4365| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1713 3.4379 3.5345| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1756 3.4202 3.5941| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1578 3.4105 3.4347| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2138 3.4191 3.5031| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1945 3.4132 3.4156| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2020 3.4339 3.4873| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2258 3.436 3.5131| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2503 3.4495 3.5227| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2858 3.4163 3.4221| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2808 3.4684 3.3991| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.93 11.31 1.00 0.96 10716.64| | 2: 2.94 - 2.33 7339 128 0.93 12.55 0.99 0.96 4993.23| | 3: 2.33 - 2.04 6939 150 0.96 7.72 1.01 0.95 1721.43| | 4: 2.04 - 1.85 7170 155 0.96 7.62 1.00 0.95 1004.10| | 5: 1.85 - 1.72 7113 159 0.96 7.92 1.00 0.96 618.13| | 6: 1.72 - 1.62 7102 142 0.96 7.82 1.00 0.96 429.85| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.97 331.20| | 8: 1.54 - 1.47 6798 152 0.96 8.28 1.01 0.97 278.91| | 9: 1.47 - 1.41 6938 155 0.96 8.50 1.00 0.98 232.17| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.97 203.59| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.96 176.06| | 12: 1.32 - 1.28 6975 149 0.96 9.04 0.98 0.95 161.88| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.96 159.38| | 14: 1.25 - 1.22 7015 112 0.95 10.74 1.01 0.97 163.92| | 15: 1.22 - 1.19 6956 137 0.95 11.26 1.01 0.98 167.00| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 160.06| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.96 153.33| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.26| | 19: 1.12 - 1.10 6948 106 0.93 14.12 1.00 0.95 150.79| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.94 150.15| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.34| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.93 155.33| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.92 165.34| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.60| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.57| | 26: 1.01 - 0.99 6767 158 0.81 26.71 0.98 0.88 177.52| | 27: 0.99 - 0.98 6647 131 0.82 26.51 0.99 0.87 163.00| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.26 max = 10716.64 mean = 900.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 13.27| |phase err.(test): min = 0.00 max = 88.66 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1342 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1413 0.1412 0.1487 n_refl.: 191129 remove outliers: r(all,work,free)=0.1413 0.1412 0.1487 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1405 0.1403 0.1481 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1341 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1341 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 90.10 88 3 0.3890 343.876 305.425 0.330 0.914 0.112 13.296-10.522 97.03 97 1 0.2408 481.345 461.293 0.697 0.915 0.100 10.503-8.327 98.35 176 3 0.2173 502.951 493.504 0.899 0.916 0.089 8.318-6.595 100.00 360 8 0.2188 375.662 370.246 0.919 0.915 0.080 6.588-5.215 100.00 711 7 0.1958 345.196 334.862 0.920 0.916 0.077 5.214-4.128 98.38 1367 28 0.1244 504.917 498.922 1.017 0.917 0.044 4.126-3.266 94.74 2603 46 0.1174 460.259 452.520 1.085 0.918 0.009 3.266-2.585 99.86 5447 97 0.1131 310.480 307.047 1.066 0.919 0.000 2.585-2.046 97.45 10613 204 0.0968 234.239 231.530 1.073 0.921 0.000 2.046-1.619 99.39 21536 464 0.0909 138.634 137.279 1.091 0.925 0.000 1.619-1.281 98.00 42464 925 0.0944 74.633 73.981 1.080 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.037 38.311 1.046 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0113 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2039 0.1961 0.083 5.223 5.2 78.0 14.6 805 0.000 1_bss: 0.1806 0.1890 0.083 5.223 5.2 78.0 14.6 805 0.000 1_settarget: 0.1806 0.1890 0.083 5.223 5.2 78.0 14.6 805 0.000 1_nqh: 0.1806 0.1890 0.083 5.223 5.2 78.0 14.6 805 0.000 1_weight: 0.1806 0.1890 0.083 5.223 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1497 0.038 1.150 5.2 78.0 14.6 805 0.154 1_adp: 0.1296 0.1562 0.038 1.150 5.1 73.0 14.9 805 0.154 1_regHadp: 0.1295 0.1557 0.038 1.150 5.1 73.0 14.9 805 0.154 1_occ: 0.1280 0.1544 0.038 1.150 5.1 73.0 14.9 805 0.154 2_bss: 0.1272 0.1532 0.038 1.150 5.3 73.2 15.1 805 0.154 2_settarget: 0.1272 0.1532 0.038 1.150 5.3 73.2 15.1 805 0.154 2_updatecdl: 0.1272 0.1532 0.038 1.154 5.3 73.2 15.1 805 0.154 2_nqh: 0.1272 0.1532 0.038 1.154 5.3 73.2 15.1 805 0.154 2_sol: 0.1270 0.1492 0.038 1.154 5.3 73.2 16.1 881 n/a 2_weight: 0.1270 0.1492 0.038 1.154 5.3 73.2 16.1 881 n/a 2_xyzrec: 0.1257 0.1508 0.041 1.117 5.3 73.2 16.1 881 n/a 2_adp: 0.1235 0.1497 0.041 1.117 5.4 68.3 16.2 881 n/a 2_regHadp: 0.1235 0.1499 0.041 1.117 5.4 68.3 16.2 881 n/a 2_occ: 0.1228 0.1498 0.041 1.117 5.4 68.3 16.2 881 n/a 3_bss: 0.1235 0.1503 0.041 1.117 5.4 68.2 16.2 881 n/a 3_settarget: 0.1235 0.1503 0.041 1.117 5.4 68.2 16.2 881 n/a 3_updatecdl: 0.1235 0.1503 0.041 1.126 5.4 68.2 16.2 881 n/a 3_nqh: 0.1235 0.1503 0.041 1.126 5.4 68.2 16.2 881 n/a 3_sol: 0.1251 0.1502 0.041 1.126 5.4 68.2 15.4 868 n/a 3_weight: 0.1251 0.1502 0.041 1.126 5.4 68.2 15.4 868 n/a 3_xyzrec: 0.1238 0.1428 0.036 1.097 5.4 68.2 15.4 868 n/a 3_adp: 0.1233 0.1390 0.036 1.097 5.5 67.8 15.2 868 n/a 3_regHadp: 0.1234 0.1390 0.036 1.097 5.5 67.8 15.2 868 n/a 3_occ: 0.1228 0.1383 0.036 1.097 5.5 67.8 15.2 868 n/a 4_bss: 0.1223 0.1378 0.036 1.097 5.5 67.7 15.2 868 n/a 4_settarget: 0.1223 0.1378 0.036 1.097 5.5 67.7 15.2 868 n/a 4_updatecdl: 0.1223 0.1378 0.036 1.102 5.5 67.7 15.2 868 n/a 4_nqh: 0.1223 0.1378 0.036 1.102 5.5 67.7 15.2 868 n/a 4_sol: 0.1207 0.1358 0.036 1.102 5.5 67.7 15.0 863 n/a 4_weight: 0.1207 0.1358 0.036 1.102 5.5 67.7 15.0 863 n/a 4_xyzrec: 0.1205 0.1361 0.035 1.126 5.5 67.7 15.0 863 n/a 4_adp: 0.1199 0.1359 0.035 1.126 5.5 67.4 14.9 863 n/a 4_regHadp: 0.1199 0.1360 0.035 1.126 5.5 67.4 14.9 863 n/a 4_occ: 0.1198 0.1358 0.035 1.126 5.5 67.4 14.9 863 n/a 5_bss: 0.1195 0.1356 0.035 1.126 5.5 67.4 14.9 863 n/a 5_settarget: 0.1195 0.1356 0.035 1.126 5.5 67.4 14.9 863 n/a 5_updatecdl: 0.1195 0.1356 0.035 1.126 5.5 67.4 14.9 863 n/a 5_nqh: 0.1195 0.1356 0.035 1.126 5.5 67.4 14.9 863 n/a 5_sol: 0.1194 0.1342 0.035 1.126 5.5 67.4 15.0 881 n/a 5_weight: 0.1194 0.1342 0.035 1.126 5.5 67.4 15.0 881 n/a 5_xyzrec: 0.1196 0.1347 0.036 1.131 5.5 67.4 15.0 881 n/a 5_adp: 0.1200 0.1350 0.036 1.131 5.6 67.0 14.9 881 n/a 5_regHadp: 0.1200 0.1350 0.036 1.131 5.6 67.0 14.9 881 n/a 5_occ: 0.1198 0.1349 0.036 1.131 5.6 67.0 14.9 881 n/a 6_bss: 0.1196 0.1347 0.036 1.131 5.5 66.9 14.9 881 n/a 6_settarget: 0.1196 0.1347 0.036 1.131 5.5 66.9 14.9 881 n/a 6_updatecdl: 0.1196 0.1347 0.036 1.130 5.5 66.9 14.9 881 n/a 6_nqh: 0.1196 0.1347 0.036 1.130 5.5 66.9 14.9 881 n/a 6_sol: 0.1194 0.1350 0.036 1.130 5.5 66.9 14.9 896 n/a 6_weight: 0.1194 0.1350 0.036 1.130 5.5 66.9 14.9 896 n/a 6_xyzrec: 0.1199 0.1357 0.036 1.131 5.5 66.9 14.9 896 n/a 6_adp: 0.1200 0.1361 0.036 1.131 5.6 65.9 14.8 896 n/a 6_regHadp: 0.1201 0.1361 0.036 1.131 5.6 65.9 14.8 896 n/a 6_occ: 0.1199 0.1362 0.036 1.131 5.6 65.9 14.8 896 n/a 7_bss: 0.1198 0.1361 0.036 1.131 5.3 65.7 14.6 896 n/a 7_settarget: 0.1198 0.1361 0.036 1.131 5.3 65.7 14.6 896 n/a 7_updatecdl: 0.1198 0.1361 0.036 1.132 5.3 65.7 14.6 896 n/a 7_nqh: 0.1198 0.1361 0.036 1.132 5.3 65.7 14.6 896 n/a 7_sol: 0.1199 0.1353 0.036 1.132 5.3 65.7 14.6 893 n/a 7_weight: 0.1199 0.1353 0.036 1.132 5.3 65.7 14.6 893 n/a 7_xyzrec: 0.1203 0.1357 0.037 1.136 5.3 65.7 14.6 893 n/a 7_adp: 0.1205 0.1360 0.037 1.136 5.4 65.5 14.6 893 n/a 7_regHadp: 0.1205 0.1361 0.037 1.136 5.4 65.5 14.6 893 n/a 7_occ: 0.1203 0.1366 0.037 1.136 5.4 65.5 14.6 893 n/a 8_bss: 0.1194 0.1356 0.037 1.136 5.5 65.5 14.6 893 n/a 8_settarget: 0.1194 0.1356 0.037 1.136 5.5 65.5 14.6 893 n/a 8_updatecdl: 0.1194 0.1356 0.037 1.136 5.5 65.5 14.6 893 n/a 8_nqh: 0.1194 0.1356 0.037 1.136 5.5 65.5 14.6 893 n/a 8_sol: 0.1192 0.1341 0.037 1.136 5.5 65.5 14.7 901 n/a 8_weight: 0.1192 0.1341 0.037 1.136 5.5 65.5 14.7 901 n/a 8_xyzrec: 0.1195 0.1344 0.038 1.127 5.5 65.5 14.7 901 n/a 8_adp: 0.1194 0.1345 0.038 1.127 5.5 64.8 14.7 901 n/a 8_regHadp: 0.1194 0.1345 0.038 1.127 5.5 64.8 14.7 901 n/a 8_occ: 0.1192 0.1344 0.038 1.127 5.5 64.8 14.7 901 n/a 9_bss: 0.1191 0.1340 0.038 1.127 5.5 64.8 14.7 901 n/a 9_settarget: 0.1191 0.1340 0.038 1.127 5.5 64.8 14.7 901 n/a 9_updatecdl: 0.1191 0.1340 0.038 1.128 5.5 64.8 14.7 901 n/a 9_nqh: 0.1191 0.1340 0.038 1.128 5.5 64.8 14.7 901 n/a 9_sol: 0.1191 0.1338 0.038 1.128 5.5 64.8 14.7 897 n/a 9_weight: 0.1191 0.1338 0.038 1.128 5.5 64.8 14.7 897 n/a 9_xyzrec: 0.1195 0.1342 0.038 1.117 5.5 64.8 14.7 897 n/a 9_adp: 0.1194 0.1345 0.038 1.117 5.5 63.9 14.7 897 n/a 9_regHadp: 0.1195 0.1345 0.038 1.117 5.5 63.9 14.7 897 n/a 9_occ: 0.1193 0.1344 0.038 1.117 5.5 63.9 14.7 897 n/a 10_bss: 0.1192 0.1342 0.038 1.117 5.5 63.9 14.7 897 n/a 10_settarget: 0.1192 0.1342 0.038 1.117 5.5 63.9 14.7 897 n/a 10_updatecdl: 0.1192 0.1342 0.038 1.117 5.5 63.9 14.7 897 n/a 10_setrh: 0.1193 0.1342 0.038 1.117 5.5 63.9 14.7 897 n/a 10_nqh: 0.1193 0.1342 0.038 1.117 5.5 63.9 14.7 897 n/a 10_sol: 0.1192 0.1334 0.038 1.117 5.5 63.9 14.6 895 n/a 10_weight: 0.1192 0.1334 0.038 1.117 5.5 63.9 14.6 895 n/a 10_xyzrec: 0.1194 0.1339 0.038 1.179 5.5 63.9 14.6 895 n/a 10_adp: 0.1196 0.1341 0.038 1.179 5.5 63.6 14.6 895 n/a 10_regHadp: 0.1196 0.1341 0.038 1.179 5.5 63.6 14.6 895 n/a 10_occ: 0.1195 0.1342 0.038 1.179 5.5 63.6 14.6 895 n/a end: 0.1194 0.1341 0.038 1.179 5.5 63.6 14.6 895 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5354978_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5354978_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3700 Refinement macro-cycles (run) : 12216.6800 Write final files (write_after_run_outputs) : 151.7100 Total : 12374.7600 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:30 PST -0800 (1736736210.16 s) Start R-work = 0.1806, R-free = 0.1890 Final R-work = 0.1194, R-free = 0.1341 =============================================================================== Job complete usr+sys time: 12650.52 seconds wall clock time: 211 minutes 50.27 seconds (12710.27 seconds total)