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_5473392.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" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5473392.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5473392.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.64, 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: 2.758 distance_ideal: 2.720 ideal - model: -0.038 slack: 0.000 delta_slack: -0.038 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: 2.722 distance_ideal: 2.710 ideal - model: -0.012 slack: 0.000 delta_slack: -0.012 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: 0.76 Conformation dependent library (CDL) restraints added in 153.6 milliseconds Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 875 1.03 - 1.27: 2499 1.27 - 1.50: 1573 1.50 - 1.74: 970 1.74 - 1.97: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" C ASP A 170 " pdb=" O ASP A 170 " ideal model delta sigma weight residual 1.236 1.490 -0.253 1.15e-02 7.56e+03 4.85e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.235 1.443 -0.208 1.02e-02 9.61e+03 4.15e+02 bond pdb=" CG HIS B 96 " pdb=" CD2 HIS B 96 " ideal model delta sigma weight residual 1.354 1.135 0.219 1.10e-02 8.26e+03 3.95e+02 bond pdb=" N GLY B 174 " pdb=" CA GLY B 174 " ideal model delta sigma weight residual 1.448 1.622 -0.174 9.00e-03 1.23e+04 3.74e+02 bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.435 0.104 5.40e-03 3.43e+04 3.70e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 5467 4.11 - 8.22: 3597 8.22 - 12.34: 1432 12.34 - 16.45: 277 16.45 - 20.56: 37 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ALA B 18 " pdb=" C ALA B 18 " pdb=" O ALA B 18 " ideal model delta sigma weight residual 121.00 136.25 -15.25 1.05e+00 9.07e-01 2.11e+02 angle pdb=" O ILE B 118 " pdb=" C ILE B 118 " pdb=" N PHE B 119 " ideal model delta sigma weight residual 121.87 136.46 -14.59 1.01e+00 9.80e-01 2.09e+02 angle pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " pdb=" CG ASP B 132 " ideal model delta sigma weight residual 112.60 126.69 -14.09 1.00e+00 1.00e+00 1.98e+02 angle pdb=" OD1 ASN A 193 " pdb=" CG ASN A 193 " pdb=" ND2 ASN A 193 " ideal model delta sigma weight residual 122.60 135.79 -13.19 1.00e+00 1.00e+00 1.74e+02 angle pdb=" O THR B 21 " pdb=" C THR B 21 " pdb=" N ILE B 22 " ideal model delta sigma weight residual 122.07 108.57 13.50 1.03e+00 9.43e-01 1.72e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 1810 16.14 - 32.27: 158 32.27 - 48.41: 51 48.41 - 64.54: 26 64.54 - 80.68: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.275: 250 0.275 - 0.546: 151 0.546 - 0.817: 71 0.817 - 1.088: 17 1.088 - 1.359: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.23 -1.36 2.00e-01 2.50e+01 4.62e+01 chirality pdb=" CA LEU B 153 " pdb=" N LEU B 153 " pdb=" C LEU B 153 " pdb=" CB LEU B 153 " both_signs ideal model delta sigma weight residual False 2.51 3.78 -1.27 2.00e-01 2.50e+01 4.04e+01 chirality pdb=" CB VAL B 150 " pdb=" CA VAL B 150 " pdb=" CG1 VAL B 150 " pdb=" CG2 VAL B 150 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.98e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.129 2.00e-02 2.50e+03 7.91e-02 1.88e+02 pdb=" CG PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.081 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.093 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.053 2.00e-02 2.50e+03 5.72e-02 1.31e+02 pdb=" CG TRP B 146 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.068 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.126 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.062 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.022 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.066 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.063 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " -0.077 2.00e-02 2.50e+03 6.59e-02 1.30e+02 pdb=" CG PHE B 95 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.111 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " 0.133 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " -0.030 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " -0.052 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.66: 37 1.66 - 2.39: 2950 2.39 - 3.13: 22543 3.13 - 3.86: 32714 3.86 - 4.60: 51984 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110228 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.924 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.941 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 0.958 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.987 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.082 2.620 ... (remaining 110223 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_5473392_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2030 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298936 | | target function (ml) not normalized (work): 805246.625120 | | target function (ml) not normalized (free): 16554.896746 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2123 0.1938 6.6963 6.3069| | 2: 2.94 - 2.33 1.00 7339 128 0.1609 0.1392 5.5252 5.5343| | 3: 2.33 - 2.04 0.96 6939 150 0.1622 0.1641 5.1305 5.1762| | 4: 2.04 - 1.85 1.00 7170 155 0.1758 0.1689 4.9596 5.0909| | 5: 1.85 - 1.72 0.99 7113 159 0.1903 0.1780 4.7845 4.8339| | 6: 1.72 - 1.62 0.99 7102 142 0.1985 0.1779 4.6652 4.6314| | 7: 1.62 - 1.54 0.99 7104 148 0.2012 0.1736 4.56 4.5469| | 8: 1.54 - 1.47 0.96 6798 152 0.2067 0.2067 4.4873 4.4643| | 9: 1.47 - 1.41 0.98 6938 155 0.2114 0.2273 4.4011 4.4877| | 10: 1.41 - 1.36 0.99 7022 150 0.2144 0.2076 4.3174 4.3292| | 11: 1.36 - 1.32 0.99 6997 151 0.2102 0.2192 4.2382 4.2926| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.2148 4.1864 4.3018| | 13: 1.28 - 1.25 0.98 6907 166 0.2025 0.2314 4.1278 4.2652| | 14: 1.25 - 1.22 0.98 7015 113 0.2045 0.2377 4.0743 4.2055| | 15: 1.22 - 1.19 0.98 6957 137 0.2097 0.1953 4.0373 4.0157| | 16: 1.19 - 1.17 0.93 6604 132 0.2101 0.2164 4.0015 4.0664| | 17: 1.17 - 1.14 0.98 6941 135 0.2210 0.1960 3.9762 4.0077| | 18: 1.14 - 1.12 0.98 6875 142 0.2219 0.2583 3.9185 3.989| | 19: 1.12 - 1.10 0.97 6949 106 0.2264 0.2398 3.8571 3.9213| | 20: 1.10 - 1.08 0.97 6884 147 0.2285 0.2221 3.8072 3.8003| | 21: 1.08 - 1.07 0.97 6852 152 0.2418 0.2401 3.7848 3.7466| | 22: 1.07 - 1.05 0.97 6838 135 0.2513 0.2518 3.7421 3.7604| | 23: 1.05 - 1.03 0.97 6829 159 0.2712 0.2767 3.725 3.8262| | 24: 1.03 - 1.02 0.96 6785 133 0.2910 0.2671 3.7056 3.7066| | 25: 1.02 - 1.01 0.93 6552 130 0.3077 0.3124 3.6757 3.8052| | 26: 1.01 - 0.99 0.96 6767 158 0.3260 0.3362 3.6362 3.6112| | 27: 0.99 - 0.98 0.94 6648 131 0.3394 0.3170 3.6376 3.6065| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.16 0.91 0.97 34642.20| | 2: 2.94 - 2.33 7339 128 0.86 20.97 1.09 1.02 14643.18| | 3: 2.33 - 2.04 6939 150 0.93 12.31 1.11 1.05 4036.48| | 4: 2.04 - 1.85 7170 155 0.92 13.64 1.12 1.07 2808.27| | 5: 1.85 - 1.72 7113 159 0.91 15.70 1.12 1.07 2078.52| | 6: 1.72 - 1.62 7102 142 0.90 16.11 1.11 1.06 1522.05| | 7: 1.62 - 1.54 7104 148 0.90 16.81 1.11 1.06 1231.02| | 8: 1.54 - 1.47 6798 152 0.89 17.58 1.10 1.06 1060.04| | 9: 1.47 - 1.41 6938 155 0.88 18.84 1.11 1.06 967.29| | 10: 1.41 - 1.36 7022 150 0.87 20.37 1.09 1.05 871.22| | 11: 1.36 - 1.32 6997 151 0.86 20.78 1.08 1.05 789.24| | 12: 1.32 - 1.28 6976 149 0.86 21.12 1.08 1.03 722.88| | 13: 1.28 - 1.25 6907 166 0.86 21.05 1.07 1.03 662.93| | 14: 1.25 - 1.22 7015 113 0.86 21.70 1.07 1.02 619.11| | 15: 1.22 - 1.19 6957 137 0.86 21.34 1.08 1.02 551.29| | 16: 1.19 - 1.17 6604 132 0.87 20.89 1.07 1.02 500.88| | 17: 1.17 - 1.14 6941 135 0.86 21.14 1.08 1.01 443.96| | 18: 1.14 - 1.12 6875 142 0.86 21.45 1.09 0.99 404.79| | 19: 1.12 - 1.10 6949 106 0.86 21.58 1.08 1.00 360.51| | 20: 1.10 - 1.08 6884 147 0.86 21.60 1.06 0.99 326.52| | 21: 1.08 - 1.07 6852 152 0.85 22.70 1.06 0.99 313.40| | 22: 1.07 - 1.05 6838 135 0.83 24.79 1.06 0.98 314.37| | 23: 1.05 - 1.03 6829 159 0.80 27.53 1.06 0.97 326.28| | 24: 1.03 - 1.02 6785 133 0.78 29.49 1.05 0.98 328.15| | 25: 1.02 - 1.01 6552 130 0.76 31.05 1.04 0.93 317.45| | 26: 1.01 - 0.99 6767 158 0.75 32.43 1.02 0.91 295.40| | 27: 0.99 - 0.98 6648 131 0.75 32.54 1.03 0.88 273.09| |alpha: min = 0.88 max = 1.07 mean = 1.01| |beta: min = 273.09 max = 34642.20 mean = 2768.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.61| |phase err.(test): min = 0.00 max = 89.78 mean = 21.52| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.258 2950 Z= 5.431 Angle : 5.213 18.065 4018 Z= 3.691 Chirality : 0.408 1.359 492 Planarity : 0.034 0.173 512 Dihedral : 13.086 80.677 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 0.65 % Allowed : 6.13 % Favored : 93.23 % Cbeta Deviations : 33.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.37), residues: 386 helix: -2.71 (0.31), residues: 144 sheet: -0.40 (0.57), residues: 66 loop : -0.82 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.110 0.021 ARG A 97 TYR 0.093 0.034 TYR B 194 PHE 0.140 0.039 PHE A 164 TRP 0.114 0.033 TRP B 146 HIS 0.058 0.025 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2030 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298936 | | target function (ml) not normalized (work): 805246.625120 | | target function (ml) not normalized (free): 16554.896746 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2030 0.1971 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2030 0.1971 n_refl.: 191155 remove outliers: r(all,work,free)=0.2028 0.2030 0.1971 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2029 0.2031 0.1971 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1796 0.1794 0.1904 n_refl.: 191145 remove outliers: r(all,work,free)=0.1794 0.1792 0.1904 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4035 402.814 291.751 0.424 0.933 0.298 13.296-10.522 98.02 98 1 0.2477 527.329 513.814 0.764 0.934 0.249 10.503-8.327 98.90 177 3 0.2479 564.205 559.170 0.947 0.934 0.227 8.318-6.595 100.00 360 8 0.2479 414.736 403.207 0.946 0.934 0.164 6.588-5.215 100.00 711 7 0.2284 381.101 366.384 0.932 0.933 0.140 5.214-4.128 98.38 1367 28 0.1474 557.435 550.094 1.049 0.933 0.080 4.126-3.266 94.74 2603 46 0.1356 508.132 498.609 1.119 0.932 0.050 3.266-2.585 99.86 5447 97 0.1426 342.774 337.987 1.097 0.929 0.000 2.585-2.046 97.45 10613 204 0.1377 258.603 254.226 1.105 0.926 0.000 2.046-1.619 99.39 21536 464 0.1605 153.054 149.876 1.130 0.920 0.000 1.619-1.281 98.00 42464 925 0.1933 82.395 80.155 1.122 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2308 44.203 41.694 1.122 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0160 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1792 r_free=0.1904 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1793 r_free=0.1904 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.544564 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.327580 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 0.1265 0.1494 0.0229 0.038 1.2 10.5 0.0 0.3 0 11.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.65 14.94 2.29 1.117 13.121 575.328 0.018 12.96 15.63 2.68 1.266 13.365 575.328 0.017 Individual atomic B min max mean iso aniso Overall: 5.08 73.05 15.05 1.41 435 3274 Protein: 5.08 40.33 11.04 1.41 0 2902 Water: 6.34 73.05 29.50 N/A 435 370 Other: 16.02 30.71 23.36 N/A 0 2 Chain A: 5.34 60.64 13.09 N/A 0 1626 Chain B: 5.08 73.05 12.81 N/A 0 1648 Chain S: 11.36 61.05 30.89 N/A 435 0 Histogram: Values Number of atoms 5.08 - 11.88 2150 11.88 - 18.68 644 18.68 - 25.47 315 25.47 - 32.27 272 32.27 - 39.07 156 39.07 - 45.86 107 45.86 - 52.66 42 52.66 - 59.46 16 59.46 - 66.26 6 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1564 r_work=0.1295 r_free=0.1558 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1558 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015462 | | target function (ls_wunit_k1) not normalized (work): 2895.892895 | | target function (ls_wunit_k1) not normalized (free): 114.590580 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1280 0.1548 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1628 n_refl.: 191137 remove outliers: r(all,work,free)=0.1469 0.1467 0.1628 n_refl.: 191137 overall B=0.15 to atoms: r(all,work,free)=0.1492 0.1490 0.1638 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1542 n_refl.: 191137 remove outliers: r(all,work,free)=0.1279 0.1274 0.1541 n_refl.: 191136 ======================== 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 0.3625 402.814 378.621 0.485 0.963 0.281 13.296-10.522 98.02 98 1 0.2016 527.329 525.644 0.749 0.964 0.244 10.503-8.327 98.90 177 3 0.1734 564.205 562.303 0.888 0.964 0.193 8.318-6.595 100.00 360 8 0.1717 414.736 412.824 0.907 0.964 0.155 6.588-5.215 100.00 711 7 0.1535 381.101 373.726 0.887 0.964 0.150 5.214-4.128 98.38 1367 28 0.0909 557.435 555.009 0.975 0.965 0.055 4.126-3.266 94.74 2603 46 0.0832 508.132 503.974 1.043 0.965 0.040 3.266-2.585 99.86 5447 97 0.0917 342.774 340.333 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0946 258.603 256.398 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1087 153.054 151.384 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.408 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.161 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0351 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1541 | n_water=805 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1278 r_free=0.1545 | n_water=794 | time (s): 98.560 (total time: 101.630) Filter (q & B) r_work=0.1278 r_free=0.1544 | n_water=789 | time (s): 5.180 (total time: 106.810) Compute maps r_work=0.1278 r_free=0.1544 | n_water=789 | time (s): 2.300 (total time: 109.110) Filter (map) r_work=0.1303 r_free=0.1532 | n_water=662 | time (s): 4.680 (total time: 113.790) Find peaks r_work=0.1303 r_free=0.1532 | n_water=662 | time (s): 0.580 (total time: 114.370) Add new water r_work=0.1326 r_free=0.1556 | n_water=960 | time (s): 4.440 (total time: 118.810) Refine new water occ: r_work=0.1283 r_free=0.1515 adp: r_work=0.1271 r_free=0.1511 occ: r_work=0.1274 r_free=0.1510 adp: r_work=0.1267 r_free=0.1508 occ: r_work=0.1268 r_free=0.1506 adp: r_work=0.1266 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1508 r_work=0.1266 r_free=0.1508 | n_water=960 | time (s): 82.000 (total time: 200.810) Filter (q & B) r_work=0.1270 r_free=0.1510 | n_water=885 | time (s): 5.090 (total time: 205.900) Filter (dist only) r_work=0.1270 r_free=0.1510 | n_water=884 | time (s): 112.890 (total time: 318.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.722226 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.177527 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1255 0.1531 0.0276 0.040 1.1 16.0 0.0 0.3 0 11.861 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.31 2.76 2.051 15.188 595.178 0.014 12.29 15.11 2.82 2.442 15.234 595.178 0.014 Individual atomic B min max mean iso aniso Overall: 5.37 68.21 16.30 1.21 516 3272 Protein: 5.37 40.87 10.98 1.21 0 2902 Water: 6.62 68.21 33.73 N/A 516 368 Other: 16.19 33.95 25.07 N/A 0 2 Chain A: 5.58 56.71 13.00 N/A 0 1624 Chain B: 5.37 68.21 12.84 N/A 0 1648 Chain S: 8.92 68.02 37.72 N/A 516 0 Histogram: Values Number of atoms 5.37 - 11.65 2056 11.65 - 17.94 710 17.94 - 24.22 264 24.22 - 30.50 212 30.50 - 36.79 181 36.79 - 43.07 166 43.07 - 49.36 100 49.36 - 55.64 51 55.64 - 61.92 33 61.92 - 68.21 15 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1511 r_work=0.1230 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1512 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013395 | | target function (ls_wunit_k1) not normalized (work): 2508.829761 | | target function (ls_wunit_k1) not normalized (free): 100.390972 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1224 0.1512 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1608 n_refl.: 191136 remove outliers: r(all,work,free)=0.1434 0.1431 0.1608 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1605 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1231 0.1520 n_refl.: 191136 remove outliers: r(all,work,free)=0.1236 0.1231 0.1520 n_refl.: 191136 ======================== 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 0.3357 402.814 379.910 0.490 0.963 0.278 13.296-10.522 98.02 98 1 0.1847 527.329 520.735 0.763 0.964 0.227 10.503-8.327 98.90 177 3 0.1419 564.205 566.821 0.921 0.964 0.174 8.318-6.595 100.00 360 8 0.1540 414.736 414.693 0.932 0.964 0.155 6.588-5.215 100.00 711 7 0.1346 381.101 377.081 0.912 0.964 0.150 5.214-4.128 98.38 1367 28 0.0818 557.435 556.300 0.992 0.964 0.054 4.126-3.266 94.74 2603 46 0.0761 508.132 505.587 1.059 0.964 0.019 3.266-2.585 99.86 5447 97 0.0859 342.774 341.390 1.046 0.963 0.010 2.585-2.046 97.45 10613 204 0.0898 258.603 256.764 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.633 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.356 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.215 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0560 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1521 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1521 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1521 | n_water=884 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1231 r_free=0.1522 | n_water=881 | time (s): 109.910 (total time: 113.190) Filter (q & B) r_work=0.1231 r_free=0.1521 | n_water=878 | time (s): 5.400 (total time: 118.590) Compute maps r_work=0.1231 r_free=0.1521 | n_water=878 | time (s): 2.120 (total time: 120.710) Filter (map) r_work=0.1269 r_free=0.1521 | n_water=696 | time (s): 4.690 (total time: 125.400) Find peaks r_work=0.1269 r_free=0.1521 | n_water=696 | time (s): 0.570 (total time: 125.970) Add new water r_work=0.1290 r_free=0.1560 | n_water=1011 | time (s): 5.090 (total time: 131.060) Refine new water occ: r_work=0.1249 r_free=0.1516 adp: r_work=0.1250 r_free=0.1517 occ: r_work=0.1246 r_free=0.1512 adp: r_work=0.1246 r_free=0.1513 occ: r_work=0.1243 r_free=0.1510 adp: r_work=0.1242 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1509 r_work=0.1242 r_free=0.1509 | n_water=1011 | time (s): 363.110 (total time: 494.170) Filter (q & B) r_work=0.1248 r_free=0.1514 | n_water=867 | time (s): 4.220 (total time: 498.390) Filter (dist only) r_work=0.1249 r_free=0.1516 | n_water=865 | time (s): 110.300 (total time: 608.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.676818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.846450 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 0.1440 0.0202 0.035 1.1 7.3 0.0 0.0 0 0.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.40 2.02 1.935 14.579 16.846 3.938 12.34 14.04 1.70 2.249 14.479 16.846 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 67.70 15.24 1.05 499 3270 Protein: 5.55 36.71 10.74 1.05 0 2902 Water: 6.73 67.70 30.34 N/A 499 366 Other: 13.95 29.37 21.66 N/A 0 2 Chain A: 5.56 55.62 12.75 N/A 0 1623 Chain B: 5.55 67.70 12.54 N/A 0 1647 Chain S: 12.84 62.37 32.27 N/A 499 0 Histogram: Values Number of atoms 5.55 - 11.77 2131 11.77 - 17.98 696 17.98 - 24.20 279 24.20 - 30.41 228 30.41 - 36.62 186 36.62 - 42.84 141 42.84 - 49.05 69 49.05 - 55.27 28 55.27 - 61.48 8 61.48 - 67.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1404 r_work=0.1234 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1405 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1393 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890292 | | target function (ml) not normalized (work): 728632.206977 | | target function (ml) not normalized (free): 15217.736334 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1393 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1448 0.1447 0.1498 n_refl.: 191136 remove outliers: r(all,work,free)=0.1448 0.1447 0.1498 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1441 0.1494 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1384 n_refl.: 191136 remove outliers: r(all,work,free)=0.1228 0.1224 0.1384 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3789 398.895 358.588 0.422 0.945 0.248 13.296-10.522 98.02 98 1 0.2410 527.329 510.890 0.717 0.947 0.229 10.503-8.327 97.80 175 3 0.1982 554.286 559.328 0.885 0.947 0.178 8.318-6.595 100.00 360 8 0.2107 414.736 410.047 0.898 0.946 0.140 6.588-5.215 100.00 711 7 0.1821 381.101 370.685 0.888 0.947 0.140 5.214-4.128 98.38 1367 28 0.1174 557.435 552.347 0.971 0.947 0.054 4.126-3.266 94.74 2603 46 0.1103 508.132 501.394 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1095 342.774 339.165 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0964 258.603 255.677 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.413 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.491 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.320 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1049 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1384 | n_water=865 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1226 r_free=0.1389 | n_water=862 | time (s): 112.060 (total time: 114.800) Filter (q & B) r_work=0.1227 r_free=0.1388 | n_water=853 | time (s): 5.070 (total time: 119.870) Compute maps r_work=0.1227 r_free=0.1388 | n_water=853 | time (s): 1.930 (total time: 121.800) Filter (map) r_work=0.1247 r_free=0.1390 | n_water=722 | time (s): 4.480 (total time: 126.280) Find peaks r_work=0.1247 r_free=0.1390 | n_water=722 | time (s): 0.570 (total time: 126.850) Add new water r_work=0.1261 r_free=0.1408 | n_water=964 | time (s): 4.150 (total time: 131.000) Refine new water occ: r_work=0.1213 r_free=0.1364 adp: r_work=0.1205 r_free=0.1357 occ: r_work=0.1203 r_free=0.1360 adp: r_work=0.1203 r_free=0.1358 occ: r_work=0.1201 r_free=0.1361 adp: r_work=0.1201 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1361 r_work=0.1201 r_free=0.1361 | n_water=964 | time (s): 222.130 (total time: 353.130) Filter (q & B) r_work=0.1205 r_free=0.1370 | n_water=873 | time (s): 5.390 (total time: 358.520) Filter (dist only) r_work=0.1206 r_free=0.1370 | n_water=872 | time (s): 109.880 (total time: 468.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.623347 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.161320 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 0.1204 0.1374 0.0170 0.036 1.1 7.3 0.0 0.0 0 0.812 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.74 1.70 1.828 14.180 15.161 3.873 12.00 13.72 1.72 1.922 14.145 15.161 3.867 Individual atomic B min max mean iso aniso Overall: 5.53 67.26 14.94 0.99 506 3270 Protein: 5.53 33.65 10.66 0.99 0 2902 Water: 5.80 67.26 29.17 N/A 506 366 Other: 13.97 28.29 21.13 N/A 0 2 Chain A: 5.54 54.61 12.62 N/A 0 1623 Chain B: 5.53 67.26 12.45 N/A 0 1647 Chain S: 5.80 62.35 30.48 N/A 506 0 Histogram: Values Number of atoms 5.53 - 11.71 2117 11.71 - 17.88 733 17.88 - 24.05 308 24.05 - 30.23 238 30.23 - 36.40 161 36.40 - 42.57 124 42.57 - 48.74 59 48.74 - 54.92 27 54.92 - 61.09 7 61.09 - 67.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1372 r_work=0.1200 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1372 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1370 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864727 | | target function (ml) not normalized (work): 723828.533479 | | target function (ml) not normalized (free): 15148.766120 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1370 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1412 0.1411 0.1481 n_refl.: 191132 remove outliers: r(all,work,free)=0.1412 0.1411 0.1481 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1404 0.1403 0.1476 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3825 361.203 324.843 0.408 0.948 0.239 13.296-10.522 96.04 96 1 0.2339 480.434 452.412 0.702 0.950 0.198 10.503-8.327 97.80 175 3 0.2136 501.911 497.151 0.863 0.950 0.177 8.318-6.595 100.00 360 8 0.2176 375.547 370.635 0.890 0.950 0.120 6.588-5.215 100.00 711 7 0.1911 345.090 334.786 0.881 0.950 0.094 5.214-4.128 98.38 1367 28 0.1202 504.762 499.996 0.969 0.950 0.034 4.126-3.266 94.74 2603 46 0.1116 460.118 454.031 1.033 0.951 0.000 3.266-2.585 99.86 5447 97 0.1092 310.384 307.143 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0935 234.167 231.703 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0915 138.592 137.309 1.054 0.949 0.000 1.619-1.281 98.00 42464 925 0.0988 74.610 73.893 1.050 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.025 38.366 1.037 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1281 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1368 | n_water=872 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1197 r_free=0.1367 | n_water=871 | time (s): 109.790 (total time: 112.180) Filter (q & B) r_work=0.1197 r_free=0.1368 | n_water=859 | time (s): 4.030 (total time: 116.210) Compute maps r_work=0.1197 r_free=0.1368 | n_water=859 | time (s): 1.760 (total time: 117.970) Filter (map) r_work=0.1222 r_free=0.1384 | n_water=728 | time (s): 5.130 (total time: 123.100) Find peaks r_work=0.1222 r_free=0.1384 | n_water=728 | time (s): 0.540 (total time: 123.640) Add new water r_work=0.1233 r_free=0.1398 | n_water=954 | time (s): 4.290 (total time: 127.930) Refine new water occ: r_work=0.1195 r_free=0.1359 adp: r_work=0.1195 r_free=0.1358 occ: r_work=0.1192 r_free=0.1358 adp: r_work=0.1192 r_free=0.1357 occ: r_work=0.1190 r_free=0.1357 adp: r_work=0.1190 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1357 r_work=0.1190 r_free=0.1357 | n_water=954 | time (s): 252.620 (total time: 380.550) Filter (q & B) r_work=0.1195 r_free=0.1367 | n_water=877 | time (s): 4.450 (total time: 385.000) Filter (dist only) r_work=0.1195 r_free=0.1366 | n_water=876 | time (s): 114.160 (total time: 499.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.584516 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 0.1369 0.0170 0.036 1.1 6.6 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.69 1.70 1.788 14.106 14.585 3.766 12.03 13.73 1.70 1.854 14.080 14.585 3.763 Individual atomic B min max mean iso aniso Overall: 5.59 66.89 14.91 0.94 511 3269 Protein: 5.59 32.12 10.59 0.94 0 2902 Water: 5.99 66.89 29.20 N/A 511 365 Other: 13.80 27.19 20.50 N/A 0 2 Chain A: 5.59 53.77 12.51 N/A 0 1622 Chain B: 5.59 66.89 12.36 N/A 0 1647 Chain S: 5.99 62.29 30.75 N/A 511 0 Histogram: Values Number of atoms 5.59 - 11.72 2138 11.72 - 17.85 729 17.85 - 23.98 295 23.98 - 30.11 228 30.11 - 36.24 164 36.24 - 42.37 129 42.37 - 48.50 61 48.50 - 54.63 27 54.63 - 60.76 7 60.76 - 66.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1373 r_work=0.1203 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1373 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1371 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762446 | | target function (ml) not normalized (work): 704664.840515 | | target function (ml) not normalized (free): 14755.710734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1371 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1408 0.1407 0.1492 n_refl.: 191130 remove outliers: r(all,work,free)=0.1408 0.1407 0.1492 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1400 0.1399 0.1486 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1370 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1370 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3811 361.203 324.828 0.395 0.952 0.225 13.296-10.522 96.04 96 1 0.2377 480.434 461.905 0.701 0.953 0.179 10.503-8.327 97.80 175 3 0.2178 501.911 495.793 0.855 0.954 0.157 8.318-6.595 100.00 360 8 0.2169 375.547 370.483 0.886 0.953 0.116 6.588-5.215 100.00 711 7 0.1909 345.090 335.073 0.879 0.953 0.093 5.214-4.128 98.38 1367 28 0.1217 504.762 499.528 0.969 0.954 0.070 4.126-3.266 94.74 2603 46 0.1133 460.118 453.663 1.030 0.954 0.000 3.266-2.585 99.86 5447 97 0.1104 310.384 307.032 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0947 234.167 231.642 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0916 138.592 137.273 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0981 74.610 73.886 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.025 38.350 1.040 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1361 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1370 | n_water=876 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1200 r_free=0.1371 | n_water=875 | time (s): 109.490 (total time: 112.510) Filter (q & B) r_work=0.1200 r_free=0.1372 | n_water=865 | time (s): 5.280 (total time: 117.790) Compute maps r_work=0.1200 r_free=0.1372 | n_water=865 | time (s): 2.480 (total time: 120.270) Filter (map) r_work=0.1223 r_free=0.1370 | n_water=741 | time (s): 4.510 (total time: 124.780) Find peaks r_work=0.1223 r_free=0.1370 | n_water=741 | time (s): 0.640 (total time: 125.420) Add new water r_work=0.1234 r_free=0.1386 | n_water=960 | time (s): 5.070 (total time: 130.490) Refine new water occ: r_work=0.1198 r_free=0.1359 adp: r_work=0.1198 r_free=0.1359 occ: r_work=0.1196 r_free=0.1357 adp: r_work=0.1196 r_free=0.1357 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1194 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1355 r_work=0.1194 r_free=0.1355 | n_water=960 | time (s): 155.560 (total time: 286.050) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=887 | time (s): 4.250 (total time: 290.300) Filter (dist only) r_work=0.1199 r_free=0.1361 | n_water=885 | time (s): 113.760 (total time: 404.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.642681 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1367 0.0165 0.037 1.1 6.8 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.67 1.65 1.758 14.009 14.643 3.763 12.03 13.69 1.66 1.891 13.967 14.643 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 65.65 14.79 0.90 520 3269 Protein: 5.59 29.31 10.49 0.90 0 2902 Water: 6.03 65.65 28.89 N/A 520 365 Other: 13.88 24.16 19.02 N/A 0 2 Chain A: 5.65 52.71 12.37 N/A 0 1622 Chain B: 5.59 65.65 12.24 N/A 0 1647 Chain S: 6.03 62.10 30.44 N/A 520 0 Histogram: Values Number of atoms 5.59 - 11.60 2111 11.60 - 17.60 780 17.60 - 23.61 280 23.61 - 29.61 205 29.61 - 35.62 179 35.62 - 41.63 125 41.63 - 47.63 67 47.63 - 53.64 32 53.64 - 59.64 8 59.64 - 65.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1369 r_work=0.1204 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1370 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758937 | | target function (ml) not normalized (work): 704007.472979 | | target function (ml) not normalized (free): 14741.656468 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1367 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1408 0.1407 0.1484 n_refl.: 191130 remove outliers: r(all,work,free)=0.1408 0.1407 0.1484 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1370 0.1368 0.1462 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1204 0.1201 0.1365 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3927 361.203 322.785 0.394 0.951 0.211 13.296-10.522 96.04 96 1 0.2397 480.434 462.097 0.718 0.953 0.175 10.503-8.327 97.80 175 3 0.2185 501.911 495.217 0.874 0.953 0.157 8.318-6.595 100.00 360 8 0.2161 375.547 370.513 0.908 0.953 0.110 6.588-5.215 100.00 711 7 0.1917 345.090 335.319 0.901 0.953 0.084 5.214-4.128 98.38 1367 28 0.1241 504.762 499.483 0.994 0.953 0.060 4.126-3.266 94.74 2603 46 0.1153 460.118 453.394 1.056 0.954 0.000 3.266-2.585 99.86 5447 97 0.1119 310.384 307.121 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0951 234.167 231.615 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0911 138.592 137.293 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0973 74.610 73.899 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.025 38.356 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0523 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1365 | n_water=885 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1201 r_free=0.1365 | n_water=885 | time (s): 105.760 (total time: 109.040) Filter (q & B) r_work=0.1201 r_free=0.1365 | n_water=878 | time (s): 5.130 (total time: 114.170) Compute maps r_work=0.1201 r_free=0.1365 | n_water=878 | time (s): 2.110 (total time: 116.280) Filter (map) r_work=0.1224 r_free=0.1374 | n_water=749 | time (s): 4.410 (total time: 120.690) Find peaks r_work=0.1224 r_free=0.1374 | n_water=749 | time (s): 0.600 (total time: 121.290) Add new water r_work=0.1234 r_free=0.1388 | n_water=966 | time (s): 3.910 (total time: 125.200) Refine new water occ: r_work=0.1197 r_free=0.1356 adp: r_work=0.1198 r_free=0.1356 occ: r_work=0.1195 r_free=0.1353 adp: r_work=0.1195 r_free=0.1353 occ: r_work=0.1194 r_free=0.1351 adp: r_work=0.1194 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1351 r_work=0.1194 r_free=0.1351 | n_water=966 | time (s): 224.910 (total time: 350.110) Filter (q & B) r_work=0.1198 r_free=0.1359 | n_water=894 | time (s): 4.450 (total time: 354.560) Filter (dist only) r_work=0.1199 r_free=0.1360 | n_water=892 | time (s): 111.810 (total time: 466.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.609117 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.883217 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1369 0.0168 0.037 1.1 6.0 0.0 0.3 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.69 1.68 1.718 13.701 14.883 3.760 12.02 13.71 1.69 1.763 13.680 14.883 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 64.19 14.55 0.89 527 3269 Protein: 5.40 28.50 10.24 0.89 0 2902 Water: 5.84 64.19 28.59 N/A 527 365 Other: 13.69 22.20 17.95 N/A 0 2 Chain A: 5.47 51.99 12.08 N/A 0 1622 Chain B: 5.40 64.19 11.96 N/A 0 1647 Chain S: 5.84 61.77 30.29 N/A 527 0 Histogram: Values Number of atoms 5.40 - 11.27 2078 11.27 - 17.15 803 17.15 - 23.03 282 23.03 - 28.91 206 28.91 - 34.79 182 34.79 - 40.67 122 40.67 - 46.55 77 46.55 - 52.43 35 52.43 - 58.31 8 58.31 - 64.19 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1371 r_work=0.1202 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1371 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1371 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756284 | | target function (ml) not normalized (work): 703510.701537 | | target function (ml) not normalized (free): 14737.290292 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1371 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1374 0.1373 0.1468 n_refl.: 191130 remove outliers: r(all,work,free)=0.1374 0.1373 0.1468 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1374 0.1373 0.1468 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3901 361.203 320.724 0.380 0.974 0.207 13.296-10.522 96.04 96 1 0.2370 480.434 461.156 0.691 0.976 0.161 10.503-8.327 97.80 175 3 0.2187 501.911 494.421 0.846 0.977 0.137 8.318-6.595 100.00 360 8 0.2161 375.547 369.637 0.876 0.977 0.099 6.588-5.215 100.00 711 7 0.1925 345.090 334.873 0.872 0.977 0.077 5.214-4.128 98.38 1367 28 0.1241 504.762 499.034 0.960 0.978 0.029 4.126-3.266 94.74 2603 46 0.1166 460.118 452.736 1.022 0.979 0.000 3.266-2.585 99.86 5447 97 0.1122 310.384 306.874 1.004 0.980 0.000 2.585-2.046 97.45 10613 204 0.0956 234.167 231.513 1.011 0.981 0.000 2.046-1.619 99.39 21536 464 0.0905 138.592 137.227 1.025 0.984 0.000 1.619-1.281 98.00 42464 925 0.0949 74.610 73.949 1.011 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.025 38.333 0.972 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1210 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1362 | n_water=892 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1191 r_free=0.1362 | n_water=892 | time (s): 117.850 (total time: 120.050) Filter (q & B) r_work=0.1191 r_free=0.1362 | n_water=887 | time (s): 4.370 (total time: 124.420) Compute maps r_work=0.1191 r_free=0.1362 | n_water=887 | time (s): 1.870 (total time: 126.290) Filter (map) r_work=0.1215 r_free=0.1354 | n_water=758 | time (s): 4.930 (total time: 131.220) Find peaks r_work=0.1215 r_free=0.1354 | n_water=758 | time (s): 0.660 (total time: 131.880) Add new water r_work=0.1223 r_free=0.1362 | n_water=972 | time (s): 5.200 (total time: 137.080) Refine new water occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1186 r_free=0.1338 adp: r_work=0.1186 r_free=0.1338 occ: r_work=0.1185 r_free=0.1336 adp: r_work=0.1185 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1337 r_work=0.1185 r_free=0.1337 | n_water=972 | time (s): 216.400 (total time: 353.480) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=902 | time (s): 5.090 (total time: 358.570) Filter (dist only) r_work=0.1189 r_free=0.1344 | n_water=900 | time (s): 114.010 (total time: 472.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.376143 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1350 0.0158 0.038 1.1 7.3 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.50 1.58 1.677 13.669 15.376 3.755 11.90 13.52 1.61 1.685 13.668 15.376 3.751 Individual atomic B min max mean iso aniso Overall: 5.43 63.13 14.59 0.89 535 3269 Protein: 5.43 28.38 10.26 0.89 0 2902 Water: 5.88 63.13 28.54 N/A 535 365 Other: 13.70 22.01 17.85 N/A 0 2 Chain A: 5.51 51.61 12.06 N/A 0 1622 Chain B: 5.43 63.13 11.95 N/A 0 1647 Chain S: 5.88 61.62 30.38 N/A 535 0 Histogram: Values Number of atoms 5.43 - 11.20 2047 11.20 - 16.97 829 16.97 - 22.74 280 22.74 - 28.51 207 28.51 - 34.28 182 34.28 - 40.05 127 40.05 - 45.82 85 45.82 - 51.59 30 51.59 - 57.36 14 57.36 - 63.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1352 r_work=0.1191 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1352 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1349 target_work(ml) = 3.751 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751058 | | target function (ml) not normalized (work): 702531.865001 | | target function (ml) not normalized (free): 14717.961886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1349 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1379 0.1378 0.1460 n_refl.: 191130 remove outliers: r(all,work,free)=0.1379 0.1378 0.1460 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1379 0.1378 0.1460 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3917 361.203 320.233 0.372 0.975 0.199 13.296-10.522 96.04 96 1 0.2334 480.434 461.927 0.689 0.977 0.157 10.503-8.327 97.80 175 3 0.2186 501.911 494.874 0.844 0.978 0.136 8.318-6.595 100.00 360 8 0.2154 375.547 369.634 0.870 0.977 0.080 6.588-5.215 100.00 711 7 0.1898 345.090 335.332 0.872 0.978 0.080 5.214-4.128 98.38 1367 28 0.1238 504.762 499.138 0.959 0.979 0.029 4.126-3.266 94.74 2603 46 0.1165 460.118 452.744 1.022 0.980 0.000 3.266-2.585 99.86 5447 97 0.1118 310.384 306.919 1.004 0.981 0.000 2.585-2.046 97.45 10613 204 0.0957 234.167 231.516 1.011 0.983 0.000 2.046-1.619 99.39 21536 464 0.0903 138.592 137.244 1.026 0.986 0.000 1.619-1.281 98.00 42464 925 0.0941 74.610 73.959 1.013 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.025 38.319 0.977 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0827 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1351 | n_water=900 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1189 r_free=0.1350 | n_water=899 | time (s): 122.890 (total time: 126.090) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=891 | time (s): 5.470 (total time: 131.560) Compute maps r_work=0.1189 r_free=0.1349 | n_water=891 | time (s): 2.460 (total time: 134.020) Filter (map) r_work=0.1212 r_free=0.1353 | n_water=771 | time (s): 5.090 (total time: 139.110) Find peaks r_work=0.1212 r_free=0.1353 | n_water=771 | time (s): 0.540 (total time: 139.650) Add new water r_work=0.1219 r_free=0.1365 | n_water=986 | time (s): 3.940 (total time: 143.590) Refine new water occ: r_work=0.1187 r_free=0.1343 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1185 r_free=0.1341 adp: r_work=0.1185 r_free=0.1341 occ: r_work=0.1184 r_free=0.1340 adp: r_work=0.1184 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1340 r_work=0.1184 r_free=0.1340 | n_water=986 | time (s): 203.690 (total time: 347.280) Filter (q & B) r_work=0.1188 r_free=0.1349 | n_water=906 | time (s): 4.470 (total time: 351.750) Filter (dist only) r_work=0.1189 r_free=0.1350 | n_water=904 | time (s): 114.050 (total time: 465.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.597395 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.894732 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1355 0.0163 0.038 1.1 5.8 0.0 0.3 0 0.799 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.55 1.63 1.676 13.663 13.895 3.753 11.95 13.58 1.64 1.677 13.661 13.895 3.754 Individual atomic B min max mean iso aniso Overall: 5.47 62.92 14.56 0.86 539 3269 Protein: 5.47 28.16 10.27 0.86 0 2902 Water: 5.92 62.92 28.33 N/A 539 365 Other: 13.73 22.01 17.87 N/A 0 2 Chain A: 5.52 51.55 12.05 N/A 0 1622 Chain B: 5.47 62.92 11.95 N/A 0 1647 Chain S: 5.92 61.57 30.11 N/A 539 0 Histogram: Values Number of atoms 5.47 - 11.22 2057 11.22 - 16.96 831 16.96 - 22.71 276 22.71 - 28.45 205 28.45 - 34.20 188 34.20 - 39.94 123 39.94 - 45.69 79 45.69 - 51.43 32 51.43 - 57.18 14 57.18 - 62.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1359 r_work=0.1195 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753254 | | target function (ml) not normalized (work): 702943.195666 | | target function (ml) not normalized (free): 14730.556394 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1481 n_refl.: 191130 remove outliers: r(all,work,free)=0.1391 0.1389 0.1481 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1391 0.1389 0.1481 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3943 361.203 318.796 0.361 0.994 0.199 13.296-10.522 96.04 96 1 0.2300 480.434 462.499 0.669 0.996 0.154 10.503-8.327 97.80 175 3 0.2225 501.911 494.293 0.821 0.997 0.130 8.318-6.595 100.00 360 8 0.2165 375.547 368.960 0.848 0.997 0.086 6.588-5.215 100.00 711 7 0.1944 345.090 334.772 0.847 0.997 0.067 5.214-4.128 98.38 1367 28 0.1259 504.762 498.808 0.935 0.998 0.029 4.126-3.266 94.74 2603 46 0.1177 460.118 452.597 0.996 0.999 0.000 3.266-2.585 99.86 5447 97 0.1127 310.384 306.812 0.979 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.167 231.486 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0907 138.592 137.235 1.001 1.006 0.000 1.619-1.281 98.00 42464 925 0.0943 74.610 73.958 0.989 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.025 38.312 0.956 1.023 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0447 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1360 After: r_work=0.1194 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1361 | n_water=904 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1194 r_free=0.1361 | n_water=903 | time (s): 119.070 (total time: 121.410) Filter (q & B) r_work=0.1195 r_free=0.1362 | n_water=894 | time (s): 4.330 (total time: 125.740) Compute maps r_work=0.1195 r_free=0.1362 | n_water=894 | time (s): 1.660 (total time: 127.400) Filter (map) r_work=0.1220 r_free=0.1361 | n_water=769 | time (s): 4.240 (total time: 131.640) Find peaks r_work=0.1220 r_free=0.1361 | n_water=769 | time (s): 0.530 (total time: 132.170) Add new water r_work=0.1227 r_free=0.1372 | n_water=994 | time (s): 5.180 (total time: 137.350) Refine new water occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1346 occ: r_work=0.1189 r_free=0.1346 adp: r_work=0.1189 r_free=0.1345 occ: r_work=0.1187 r_free=0.1346 adp: r_work=0.1187 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1345 r_work=0.1187 r_free=0.1345 | n_water=994 | time (s): 160.290 (total time: 297.640) Filter (q & B) r_work=0.1192 r_free=0.1355 | n_water=915 | time (s): 5.810 (total time: 303.450) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=913 | time (s): 119.410 (total time: 422.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.517013 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.670889 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 0.1360 0.0164 0.038 1.2 10.6 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.60 1.64 1.669 13.679 13.671 3.757 11.98 13.63 1.65 1.668 13.678 13.671 3.757 Individual atomic B min max mean iso aniso Overall: 5.48 62.58 14.59 0.85 548 3269 Protein: 5.48 27.93 10.29 0.85 0 2902 Water: 5.93 62.58 28.24 N/A 548 365 Other: 13.76 22.02 17.89 N/A 0 2 Chain A: 5.58 51.44 12.04 N/A 0 1622 Chain B: 5.48 62.58 11.95 N/A 0 1647 Chain S: 5.93 61.46 30.04 N/A 548 0 Histogram: Values Number of atoms 5.48 - 11.19 2042 11.19 - 16.90 847 16.90 - 22.61 277 22.61 - 28.32 209 28.32 - 34.03 187 34.03 - 39.74 125 39.74 - 45.45 80 45.45 - 51.16 32 51.16 - 56.87 14 56.87 - 62.58 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1363 r_work=0.1198 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756583 | | target function (ml) not normalized (work): 703566.652079 | | target function (ml) not normalized (free): 14739.127880 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1369 0.1488 5.697 5.7861| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1355 5.089 5.1802| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1209 4.6566 4.756| | 4: 2.04 - 1.85 1.00 7170 155 0.0904 0.1046 4.3986 4.5818| | 5: 1.85 - 1.72 0.99 7113 159 0.0936 0.0990 4.1542 4.2381| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1091 3.9497 4.0834| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0956 3.8023 3.9259| | 8: 1.54 - 1.47 0.96 6798 152 0.0897 0.1342 3.7058 3.9234| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1144 3.6274 3.7601| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1205 3.5624 3.6803| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1132 3.4882 3.5957| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1127 3.4615 3.5797| | 13: 1.28 - 1.25 0.98 6907 166 0.1046 0.1251 3.4395 3.5702| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1589 3.4325 3.6777| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1241 3.448 3.4877| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1543 3.4651 3.6553| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1236 3.434 3.4459| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1702 3.4384 3.5303| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1762 3.4206 3.6| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1583 3.4096 3.4326| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2129 3.4183 3.5026| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1952 3.4129 3.4171| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2011 3.4331 3.4846| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2253 3.4359 3.5115| | 25: 1.02 - 1.01 0.93 6552 130 0.2617 0.2508 3.4497 3.5217| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2844 3.4159 3.4196| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2810 3.4688 3.3962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.93 1.00 0.97 11636.33| | 2: 2.94 - 2.33 7339 128 0.92 13.06 0.99 0.98 5298.89| | 3: 2.33 - 2.04 6939 150 0.96 7.75 1.01 0.98 1727.59| | 4: 2.04 - 1.85 7170 155 0.96 7.76 1.00 0.98 1020.99| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.98 638.55| | 6: 1.72 - 1.62 7102 142 0.96 8.06 1.00 0.98 445.97| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.99 337.83| | 8: 1.54 - 1.47 6798 152 0.96 8.37 1.01 0.99 283.38| | 9: 1.47 - 1.41 6938 155 0.96 8.57 1.00 1.00 234.53| | 10: 1.41 - 1.36 7022 150 0.96 9.03 1.00 0.99 206.19| | 11: 1.36 - 1.32 6997 151 0.96 8.99 0.99 0.98 176.48| | 12: 1.32 - 1.28 6975 149 0.96 9.00 0.98 0.97 161.56| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.98 158.77| | 14: 1.25 - 1.22 7015 112 0.95 10.71 1.01 0.99 163.12| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 1.00 166.48| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.98 160.04| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.98 154.33| | 18: 1.14 - 1.12 6875 142 0.94 12.77 1.01 0.97 148.10| | 19: 1.12 - 1.10 6948 106 0.93 14.17 1.00 0.97 151.33| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.96 150.23| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.95 153.20| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.95 154.96| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.94 164.68| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.95 178.81| | 25: 1.02 - 1.01 6552 130 0.83 25.11 0.97 0.92 181.56| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.98 0.90 176.22| | 27: 0.99 - 0.98 6647 131 0.82 26.33 0.98 0.89 161.22| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 148.10 max = 11636.33 mean = 951.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.34| |phase err.(test): min = 0.00 max = 89.45 mean = 13.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1490 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1400 0.1490 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1401 0.1400 0.1490 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3919 361.203 319.836 0.360 0.994 0.199 13.296-10.522 96.04 96 1 0.2347 480.434 461.224 0.664 0.996 0.146 10.503-8.327 97.80 175 3 0.2200 501.911 494.508 0.823 0.996 0.111 8.318-6.595 100.00 360 8 0.2147 375.547 369.450 0.847 0.996 0.086 6.588-5.215 100.00 711 7 0.1930 345.090 334.954 0.847 0.997 0.070 5.214-4.128 98.38 1367 28 0.1260 504.762 498.722 0.936 0.998 0.029 4.126-3.266 94.74 2603 46 0.1173 460.118 452.699 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1125 310.384 306.887 0.980 1.001 0.000 2.585-2.046 97.45 10613 204 0.0966 234.167 231.479 0.987 1.003 0.000 2.046-1.619 99.39 21536 464 0.0914 138.592 137.219 1.002 1.007 0.000 1.619-1.281 98.00 42464 925 0.0950 74.610 73.951 0.991 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.025 38.303 0.960 1.026 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0114 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2030 0.1971 0.081 5.213 5.2 78.0 14.6 805 0.000 1_bss: 0.1792 0.1904 0.081 5.213 5.2 78.1 14.6 805 0.000 1_settarget: 0.1792 0.1904 0.081 5.213 5.2 78.1 14.6 805 0.000 1_nqh: 0.1793 0.1904 0.081 5.213 5.2 78.1 14.6 805 0.002 1_weight: 0.1793 0.1904 0.081 5.213 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1265 0.1494 0.038 1.184 5.2 78.1 14.6 805 0.152 1_adp: 0.1296 0.1564 0.038 1.184 5.1 73.1 15.1 805 0.152 1_regHadp: 0.1295 0.1558 0.038 1.184 5.1 73.1 15.1 805 0.152 1_occ: 0.1280 0.1548 0.038 1.184 5.1 73.1 15.1 805 0.152 2_bss: 0.1274 0.1541 0.038 1.184 5.2 73.2 15.2 805 0.152 2_settarget: 0.1274 0.1541 0.038 1.184 5.2 73.2 15.2 805 0.152 2_updatecdl: 0.1274 0.1541 0.038 1.197 5.2 73.2 15.2 805 0.152 2_nqh: 0.1274 0.1541 0.038 1.197 5.2 73.2 15.2 805 0.152 2_sol: 0.1270 0.1510 0.038 1.197 5.2 73.2 16.2 884 n/a 2_weight: 0.1270 0.1510 0.038 1.197 5.2 73.2 16.2 884 n/a 2_xyzrec: 0.1255 0.1531 0.040 1.149 5.2 73.2 16.2 884 n/a 2_adp: 0.1230 0.1511 0.040 1.149 5.4 68.2 16.3 884 n/a 2_regHadp: 0.1230 0.1512 0.040 1.149 5.4 68.2 16.3 884 n/a 2_occ: 0.1224 0.1512 0.040 1.149 5.4 68.2 16.3 884 n/a 3_bss: 0.1231 0.1521 0.040 1.149 5.3 68.2 16.3 884 n/a 3_settarget: 0.1231 0.1521 0.040 1.149 5.3 68.2 16.3 884 n/a 3_updatecdl: 0.1231 0.1521 0.040 1.154 5.3 68.2 16.3 884 n/a 3_nqh: 0.1231 0.1521 0.040 1.154 5.3 68.2 16.3 884 n/a 3_sol: 0.1249 0.1516 0.040 1.154 5.3 68.2 15.4 865 n/a 3_weight: 0.1249 0.1516 0.040 1.154 5.3 68.2 15.4 865 n/a 3_xyzrec: 0.1238 0.1440 0.035 1.099 5.3 68.2 15.4 865 n/a 3_adp: 0.1234 0.1404 0.035 1.099 5.6 67.7 15.2 865 n/a 3_regHadp: 0.1234 0.1405 0.035 1.099 5.6 67.7 15.2 865 n/a 3_occ: 0.1229 0.1393 0.035 1.099 5.6 67.7 15.2 865 n/a 4_bss: 0.1225 0.1384 0.035 1.099 5.5 67.7 15.2 865 n/a 4_settarget: 0.1225 0.1384 0.035 1.099 5.5 67.7 15.2 865 n/a 4_updatecdl: 0.1225 0.1384 0.035 1.104 5.5 67.7 15.2 865 n/a 4_nqh: 0.1225 0.1384 0.035 1.104 5.5 67.7 15.2 865 n/a 4_sol: 0.1206 0.1370 0.035 1.104 5.5 67.7 15.0 872 n/a 4_weight: 0.1206 0.1370 0.035 1.104 5.5 67.7 15.0 872 n/a 4_xyzrec: 0.1204 0.1374 0.036 1.126 5.5 67.7 15.0 872 n/a 4_adp: 0.1200 0.1372 0.036 1.126 5.5 67.3 14.9 872 n/a 4_regHadp: 0.1200 0.1372 0.036 1.126 5.5 67.3 14.9 872 n/a 4_occ: 0.1198 0.1370 0.036 1.126 5.5 67.3 14.9 872 n/a 5_bss: 0.1197 0.1368 0.036 1.126 5.5 67.2 14.9 872 n/a 5_settarget: 0.1197 0.1368 0.036 1.126 5.5 67.2 14.9 872 n/a 5_updatecdl: 0.1197 0.1368 0.036 1.127 5.5 67.2 14.9 872 n/a 5_nqh: 0.1197 0.1368 0.036 1.127 5.5 67.2 14.9 872 n/a 5_sol: 0.1195 0.1366 0.036 1.127 5.5 67.2 15.0 876 n/a 5_weight: 0.1195 0.1366 0.036 1.127 5.5 67.2 15.0 876 n/a 5_xyzrec: 0.1199 0.1369 0.036 1.118 5.5 67.2 15.0 876 n/a 5_adp: 0.1203 0.1373 0.036 1.118 5.6 66.9 14.9 876 n/a 5_regHadp: 0.1203 0.1373 0.036 1.118 5.6 66.9 14.9 876 n/a 5_occ: 0.1201 0.1371 0.036 1.118 5.6 66.9 14.9 876 n/a 6_bss: 0.1199 0.1370 0.036 1.118 5.6 66.9 14.9 876 n/a 6_settarget: 0.1199 0.1370 0.036 1.118 5.6 66.9 14.9 876 n/a 6_updatecdl: 0.1199 0.1370 0.036 1.118 5.6 66.9 14.9 876 n/a 6_nqh: 0.1199 0.1370 0.036 1.118 5.6 66.9 14.9 876 n/a 6_sol: 0.1199 0.1361 0.036 1.118 5.6 66.9 14.9 885 n/a 6_weight: 0.1199 0.1361 0.036 1.118 5.6 66.9 14.9 885 n/a 6_xyzrec: 0.1202 0.1367 0.037 1.127 5.6 66.9 14.9 885 n/a 6_adp: 0.1203 0.1369 0.037 1.127 5.6 65.7 14.8 885 n/a 6_regHadp: 0.1204 0.1370 0.037 1.127 5.6 65.7 14.8 885 n/a 6_occ: 0.1202 0.1367 0.037 1.127 5.6 65.7 14.8 885 n/a 7_bss: 0.1201 0.1365 0.037 1.127 5.4 65.4 14.6 885 n/a 7_settarget: 0.1201 0.1365 0.037 1.127 5.4 65.4 14.6 885 n/a 7_updatecdl: 0.1201 0.1365 0.037 1.127 5.4 65.4 14.6 885 n/a 7_nqh: 0.1201 0.1365 0.037 1.127 5.4 65.4 14.6 885 n/a 7_sol: 0.1199 0.1360 0.037 1.127 5.4 65.4 14.6 892 n/a 7_weight: 0.1199 0.1360 0.037 1.127 5.4 65.4 14.6 892 n/a 7_xyzrec: 0.1201 0.1369 0.037 1.127 5.4 65.4 14.6 892 n/a 7_adp: 0.1202 0.1371 0.037 1.127 5.4 64.2 14.6 892 n/a 7_regHadp: 0.1202 0.1371 0.037 1.127 5.4 64.2 14.6 892 n/a 7_occ: 0.1200 0.1371 0.037 1.127 5.4 64.2 14.6 892 n/a 8_bss: 0.1191 0.1362 0.037 1.127 5.4 64.2 14.6 892 n/a 8_settarget: 0.1191 0.1362 0.037 1.127 5.4 64.2 14.6 892 n/a 8_updatecdl: 0.1191 0.1362 0.037 1.127 5.4 64.2 14.6 892 n/a 8_nqh: 0.1191 0.1362 0.037 1.127 5.4 64.2 14.6 892 n/a 8_sol: 0.1189 0.1344 0.037 1.127 5.4 64.2 14.6 900 n/a 8_weight: 0.1189 0.1344 0.037 1.127 5.4 64.2 14.6 900 n/a 8_xyzrec: 0.1192 0.1350 0.038 1.123 5.4 64.2 14.6 900 n/a 8_adp: 0.1191 0.1352 0.038 1.123 5.4 63.1 14.6 900 n/a 8_regHadp: 0.1191 0.1352 0.038 1.123 5.4 63.1 14.6 900 n/a 8_occ: 0.1189 0.1349 0.038 1.123 5.4 63.1 14.6 900 n/a 9_bss: 0.1188 0.1348 0.038 1.123 5.4 63.1 14.6 900 n/a 9_settarget: 0.1188 0.1348 0.038 1.123 5.4 63.1 14.6 900 n/a 9_updatecdl: 0.1188 0.1348 0.038 1.124 5.4 63.1 14.6 900 n/a 9_nqh: 0.1189 0.1351 0.038 1.124 5.4 63.1 14.6 900 n/a 9_sol: 0.1189 0.1350 0.038 1.124 5.4 63.1 14.6 904 n/a 9_weight: 0.1189 0.1350 0.038 1.124 5.4 63.1 14.6 904 n/a 9_xyzrec: 0.1192 0.1355 0.038 1.118 5.4 63.1 14.6 904 n/a 9_adp: 0.1195 0.1359 0.038 1.118 5.5 62.9 14.6 904 n/a 9_regHadp: 0.1195 0.1359 0.038 1.118 5.5 62.9 14.6 904 n/a 9_occ: 0.1194 0.1360 0.038 1.118 5.5 62.9 14.6 904 n/a 10_bss: 0.1193 0.1360 0.038 1.118 5.5 62.9 14.6 904 n/a 10_settarget: 0.1193 0.1360 0.038 1.118 5.5 62.9 14.6 904 n/a 10_updatecdl: 0.1193 0.1360 0.038 1.117 5.5 62.9 14.6 904 n/a 10_setrh: 0.1194 0.1361 0.038 1.117 5.5 62.9 14.6 904 n/a 10_nqh: 0.1194 0.1361 0.038 1.117 5.5 62.9 14.6 904 n/a 10_sol: 0.1192 0.1355 0.038 1.117 5.5 62.9 14.6 913 n/a 10_weight: 0.1192 0.1355 0.038 1.117 5.5 62.9 14.6 913 n/a 10_xyzrec: 0.1196 0.1360 0.038 1.154 5.5 62.9 14.6 913 n/a 10_adp: 0.1198 0.1363 0.038 1.154 5.5 62.6 14.6 913 n/a 10_regHadp: 0.1198 0.1363 0.038 1.154 5.5 62.6 14.6 913 n/a 10_occ: 0.1197 0.1363 0.038 1.154 5.5 62.6 14.6 913 n/a end: 0.1196 0.1362 0.038 1.154 5.5 62.6 14.6 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5473392_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5473392_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2200 Refinement macro-cycles (run) : 11888.1700 Write final files (write_after_run_outputs) : 162.7000 Total : 12057.0900 Total CPU time: 3.36 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:12 PST -0800 (1736735892.04 s) Start R-work = 0.1792, R-free = 0.1904 Final R-work = 0.1196, R-free = 0.1362 =============================================================================== Job complete usr+sys time: 12368.59 seconds wall clock time: 207 minutes 9.37 seconds (12429.37 seconds total)