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_7657487.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" 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_7657487.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7657487.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } 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: 2.39, per 1000 atoms: 0.36 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.755 distance_ideal: 2.720 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 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: 2.689 distance_ideal: 2.710 ideal - model: 0.021 slack: 0.000 delta_slack: 0.021 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: 0.80 Conformation dependent library (CDL) restraints added in 159.9 milliseconds Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.05: 1073 1.05 - 1.30: 2459 1.30 - 1.54: 1693 1.54 - 1.78: 700 1.78 - 2.03: 9 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ILE B 134 " pdb=" C ILE B 134 " ideal model delta sigma weight residual 1.525 1.329 0.196 8.40e-03 1.42e+04 5.43e+02 bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.453 1.636 -0.183 9.20e-03 1.18e+04 3.95e+02 bond pdb=" C VAL B 19 " pdb=" O VAL B 19 " ideal model delta sigma weight residual 1.237 1.447 -0.211 1.12e-02 7.97e+03 3.54e+02 bond pdb=" CG HIS B 179 " pdb=" CD2 HIS B 179 " ideal model delta sigma weight residual 1.354 1.151 0.203 1.10e-02 8.26e+03 3.39e+02 bond pdb=" N LYS B 133 " pdb=" H LYS B 133 " ideal model delta sigma weight residual 0.860 1.227 -0.367 2.00e-02 2.50e+03 3.36e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 5617 4.16 - 8.31: 3557 8.31 - 12.47: 1326 12.47 - 16.63: 281 16.63 - 20.79: 29 Bond angle restraints: 10810 Sorted by residual: angle pdb=" OD1 ASN A 123 " pdb=" CG ASN A 123 " pdb=" ND2 ASN A 123 " ideal model delta sigma weight residual 122.60 142.84 -20.24 1.00e+00 1.00e+00 4.09e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.65 107.81 13.84 7.30e-01 1.88e+00 3.59e+02 angle pdb=" O VAL A 144 " pdb=" C VAL A 144 " pdb=" N VAL A 145 " ideal model delta sigma weight residual 123.09 141.32 -18.23 1.16e+00 7.43e-01 2.47e+02 angle pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 120.83 111.59 9.24 6.10e-01 2.69e+00 2.30e+02 angle pdb=" O VAL B 181 " pdb=" C VAL B 181 " pdb=" N ALA B 182 " ideal model delta sigma weight residual 121.94 107.29 14.65 1.00e+00 1.00e+00 2.15e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.25: 1844 17.25 - 34.49: 140 34.49 - 51.74: 47 51.74 - 68.98: 14 68.98 - 86.23: 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 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 202 0.216 - 0.432: 164 0.432 - 0.649: 89 0.649 - 0.865: 32 0.865 - 1.081: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 1.35 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CB THR B 33 " pdb=" CA THR B 33 " pdb=" OG1 THR B 33 " pdb=" CG2 THR B 33 " both_signs ideal model delta sigma weight residual False 2.55 1.50 1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" CG LEU A 6 " pdb=" CB LEU A 6 " pdb=" CD1 LEU A 6 " pdb=" CD2 LEU A 6 " both_signs ideal model delta sigma weight residual False -2.59 -3.58 0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.084 2.00e-02 2.50e+03 6.98e-02 1.95e+02 pdb=" CG TRP A 146 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.110 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.079 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.105 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.051 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.055 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.084 2.00e-02 2.50e+03 7.76e-02 1.81e+02 pdb=" CG TYR B 67 " 0.152 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " -0.107 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.092 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.095 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.066 2.00e-02 2.50e+03 6.96e-02 1.45e+02 pdb=" CG TYR A 192 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.123 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " -0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.132 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.63: 28 1.63 - 2.37: 2530 2.37 - 3.11: 22405 3.11 - 3.86: 32903 3.86 - 4.60: 52332 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110198 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.882 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.926 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.961 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.009 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.166 2.620 ... (remaining 110193 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_7657487_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= 0.2029 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298896 | | target function (ml) not normalized (work): 805239.100191 | | target function (ml) not normalized (free): 16594.860155 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.1956 6.681 6.3064| | 2: 2.94 - 2.33 1.00 7339 128 0.1619 0.1564 5.5455 5.5924| | 3: 2.33 - 2.04 0.96 6939 150 0.1620 0.1619 5.1421 5.2033| | 4: 2.04 - 1.85 1.00 7170 155 0.1732 0.1770 4.96 5.1131| | 5: 1.85 - 1.72 0.99 7113 159 0.1913 0.1800 4.7956 4.8569| | 6: 1.72 - 1.62 0.99 7102 142 0.1998 0.1844 4.6662 4.6889| | 7: 1.62 - 1.54 0.99 7104 148 0.2054 0.1659 4.5751 4.5131| | 8: 1.54 - 1.47 0.96 6798 152 0.2026 0.2211 4.4637 4.487| | 9: 1.47 - 1.41 0.98 6938 155 0.2073 0.2317 4.3886 4.5216| | 10: 1.41 - 1.36 0.99 7022 150 0.2132 0.1924 4.3102 4.2721| | 11: 1.36 - 1.32 0.99 6997 151 0.2069 0.2332 4.2235 4.3461| | 12: 1.32 - 1.28 0.98 6976 149 0.2049 0.2236 4.1727 4.3262| | 13: 1.28 - 1.25 0.98 6907 166 0.2037 0.2087 4.1301 4.1665| | 14: 1.25 - 1.22 0.98 7015 113 0.2065 0.2351 4.0763 4.2709| | 15: 1.22 - 1.19 0.98 6957 137 0.2088 0.2070 4.0519 4.105| | 16: 1.19 - 1.17 0.93 6604 132 0.2109 0.2329 4.0051 4.1399| | 17: 1.17 - 1.14 0.98 6941 135 0.2181 0.1964 3.9603 3.9991| | 18: 1.14 - 1.12 0.98 6875 142 0.2195 0.2322 3.9076 3.8956| | 19: 1.12 - 1.10 0.97 6949 106 0.2271 0.2279 3.8742 3.8985| | 20: 1.10 - 1.08 0.97 6884 147 0.2342 0.2211 3.8322 3.8633| | 21: 1.08 - 1.07 0.97 6852 152 0.2426 0.2704 3.7828 3.8315| | 22: 1.07 - 1.05 0.97 6838 135 0.2562 0.2675 3.7557 3.7726| | 23: 1.05 - 1.03 0.97 6829 159 0.2719 0.2465 3.7289 3.7526| | 24: 1.03 - 1.02 0.96 6785 133 0.2828 0.2774 3.6948 3.7097| | 25: 1.02 - 1.01 0.93 6552 130 0.3076 0.2566 3.6757 3.6482| | 26: 1.01 - 0.99 0.96 6767 158 0.3190 0.3501 3.6214 3.7112| | 27: 0.99 - 0.98 0.94 6648 131 0.3405 0.3156 3.6351 3.6248| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.56 0.91 0.97 35957.08| | 2: 2.94 - 2.33 7339 128 0.85 21.45 1.08 1.02 15363.72| | 3: 2.33 - 2.04 6939 150 0.93 13.08 1.11 1.05 4366.63| | 4: 2.04 - 1.85 7170 155 0.92 14.33 1.11 1.05 3024.34| | 5: 1.85 - 1.72 7113 159 0.90 16.46 1.12 1.05 2211.58| | 6: 1.72 - 1.62 7102 142 0.90 16.86 1.12 1.06 1630.39| | 7: 1.62 - 1.54 7104 148 0.89 17.30 1.11 1.06 1280.32| | 8: 1.54 - 1.47 6798 152 0.89 18.06 1.10 1.06 1097.73| | 9: 1.47 - 1.41 6938 155 0.88 19.21 1.10 1.04 983.74| | 10: 1.41 - 1.36 7022 150 0.86 20.88 1.09 1.03 893.85| | 11: 1.36 - 1.32 6997 151 0.86 20.92 1.08 1.04 797.05| | 12: 1.32 - 1.28 6976 149 0.86 20.86 1.07 1.04 713.15| | 13: 1.28 - 1.25 6907 166 0.87 20.54 1.07 1.05 640.88| | 14: 1.25 - 1.22 7015 113 0.86 21.76 1.08 1.03 623.96| | 15: 1.22 - 1.19 6957 137 0.85 22.05 1.07 1.03 594.06| | 16: 1.19 - 1.17 6604 132 0.86 21.75 1.07 1.01 536.38| | 17: 1.17 - 1.14 6941 135 0.86 21.44 1.08 1.02 453.78| | 18: 1.14 - 1.12 6875 142 0.86 21.14 1.08 1.00 399.99| | 19: 1.12 - 1.10 6949 106 0.86 21.82 1.07 1.01 377.01| | 20: 1.10 - 1.08 6884 147 0.85 22.71 1.06 0.99 352.33| | 21: 1.08 - 1.07 6852 152 0.84 23.68 1.06 0.99 334.65| | 22: 1.07 - 1.05 6838 135 0.83 24.75 1.05 0.99 314.17| | 23: 1.05 - 1.03 6829 159 0.82 25.57 1.06 0.99 295.68| | 24: 1.03 - 1.02 6785 133 0.81 26.76 1.05 1.00 288.34| | 25: 1.02 - 1.01 6552 130 0.79 28.67 1.03 0.96 279.10| | 26: 1.01 - 0.99 6767 158 0.75 31.80 1.03 0.93 287.53| | 27: 0.99 - 0.98 6648 131 0.73 33.57 1.04 0.90 292.41| |alpha: min = 0.90 max = 1.06 mean = 1.01| |beta: min = 279.10 max = 35957.08 mean = 2884.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.70| |phase err.(test): min = 0.00 max = 88.81 mean = 21.86| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.240 2950 Z= 5.586 Angle : 5.261 20.236 4018 Z= 3.753 Chirality : 0.371 1.081 492 Planarity : 0.032 0.162 512 Dihedral : 12.846 86.229 1062 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.18 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 28.37 % 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: -2.22 (0.38), residues: 386 helix: -2.40 (0.33), residues: 140 sheet: -1.21 (0.48), residues: 86 loop : -0.41 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.021 ARG B 149 TYR 0.127 0.043 TYR B 67 PHE 0.111 0.037 PHE B 164 TRP 0.125 0.041 TRP B 146 HIS 0.066 0.023 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298896 | | target function (ml) not normalized (work): 805239.100191 | | target function (ml) not normalized (free): 16594.860155 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2027 0.2029 0.1995 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2027 0.2029 0.1995 n_refl.: 191155 remove outliers: r(all,work,free)=0.2027 0.2029 0.1995 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2027 0.2028 0.1995 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1799 0.1797 0.1936 n_refl.: 191145 remove outliers: r(all,work,free)=0.1797 0.1795 0.1936 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4127 402.814 291.011 0.438 0.910 0.303 13.296-10.522 99.01 99 1 0.2498 528.187 518.445 0.788 0.911 0.255 10.503-8.327 99.45 178 3 0.2532 565.118 556.391 0.974 0.911 0.230 8.318-6.595 100.00 360 8 0.2464 414.736 403.861 0.971 0.911 0.160 6.588-5.215 100.00 711 7 0.2246 381.101 366.055 0.961 0.911 0.150 5.214-4.128 98.38 1367 28 0.1472 557.435 549.422 1.080 0.911 0.090 4.126-3.266 94.74 2603 46 0.1354 508.132 498.990 1.152 0.912 0.033 3.266-2.585 99.86 5447 97 0.1445 342.774 337.256 1.121 0.911 0.010 2.585-2.046 97.45 10613 204 0.1392 258.603 253.997 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 149.645 1.146 0.909 0.000 1.619-1.281 98.00 42464 925 0.1916 82.395 80.216 1.130 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2313 44.203 41.693 1.114 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0053 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1795 r_free=0.1936 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1799 r_free=0.1940 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.622359 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 572.779251 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1497 0.0227 0.038 1.2 11.4 0.0 0.3 0 11.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.97 2.27 1.117 13.109 572.779 0.018 12.98 15.67 2.69 1.229 13.311 572.779 0.017 Individual atomic B min max mean iso aniso Overall: 5.21 73.04 14.96 1.39 435 3274 Protein: 5.21 40.31 10.98 1.39 0 2902 Water: 6.30 73.04 29.32 N/A 435 370 Other: 15.96 30.23 23.10 N/A 0 2 Chain A: 5.36 59.98 13.01 N/A 0 1626 Chain B: 5.21 73.04 12.74 N/A 0 1648 Chain S: 11.34 61.19 30.71 N/A 435 0 Histogram: Values Number of atoms 5.21 - 12.00 2176 12.00 - 18.78 635 18.78 - 25.56 311 25.56 - 32.34 266 32.34 - 39.13 152 39.13 - 45.91 108 45.91 - 52.69 39 52.69 - 59.48 17 59.48 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1567 r_work=0.1297 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1562 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1550 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015642 | | target function (ls_wunit_k1) not normalized (work): 2929.767692 | | target function (ls_wunit_k1) not normalized (free): 117.406811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1282 0.1550 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1466 0.1464 0.1627 n_refl.: 191139 remove outliers: r(all,work,free)=0.1466 0.1464 0.1627 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1490 0.1487 0.1636 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1541 n_refl.: 191139 remove outliers: r(all,work,free)=0.1280 0.1275 0.1540 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3598 402.814 376.978 0.470 1.001 0.285 13.296-10.522 99.01 99 1 0.2074 528.187 520.361 0.707 1.003 0.238 10.503-8.327 99.45 178 3 0.1782 565.118 562.438 0.853 1.003 0.213 8.318-6.595 100.00 360 8 0.1736 414.736 410.666 0.873 1.002 0.157 6.588-5.215 100.00 711 7 0.1559 381.101 374.256 0.855 1.003 0.130 5.214-4.128 98.38 1367 28 0.0907 557.435 555.023 0.941 1.003 0.059 4.126-3.266 94.74 2603 46 0.0833 508.132 504.109 1.006 1.004 0.024 3.266-2.585 99.86 5447 97 0.0924 342.774 340.293 0.986 1.003 0.005 2.585-2.046 97.45 10613 204 0.0949 258.603 256.337 0.998 1.004 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.385 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.419 1.006 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.165 0.984 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0380 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1540 | n_water=805 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1279 r_free=0.1545 | n_water=794 | time (s): 106.610 (total time: 109.150) Filter (q & B) r_work=0.1280 r_free=0.1546 | n_water=789 | time (s): 4.110 (total time: 113.260) Compute maps r_work=0.1280 r_free=0.1546 | n_water=789 | time (s): 1.800 (total time: 115.060) Filter (map) r_work=0.1305 r_free=0.1527 | n_water=658 | time (s): 5.450 (total time: 120.510) Find peaks r_work=0.1305 r_free=0.1527 | n_water=658 | time (s): 0.820 (total time: 121.330) Add new water r_work=0.1327 r_free=0.1562 | n_water=952 | time (s): 5.400 (total time: 126.730) Refine new water occ: r_work=0.1285 r_free=0.1509 adp: r_work=0.1272 r_free=0.1506 occ: r_work=0.1274 r_free=0.1502 adp: r_work=0.1268 r_free=0.1503 occ: r_work=0.1269 r_free=0.1499 adp: r_work=0.1267 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1501 r_work=0.1267 r_free=0.1501 | n_water=952 | time (s): 99.590 (total time: 226.320) Filter (q & B) r_work=0.1271 r_free=0.1508 | n_water=884 | time (s): 4.120 (total time: 230.440) Filter (dist only) r_work=0.1271 r_free=0.1507 | n_water=883 | time (s): 114.080 (total time: 344.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.038372 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.262682 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1523 0.0267 0.040 1.1 16.8 0.0 0.3 0 11.519 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.23 2.67 2.036 15.165 590.263 0.015 12.34 15.11 2.76 2.390 15.222 590.263 0.014 Individual atomic B min max mean iso aniso Overall: 5.36 68.48 16.33 1.20 515 3272 Protein: 5.36 39.94 10.98 1.20 0 2902 Water: 6.51 68.48 33.90 N/A 515 368 Other: 16.13 33.25 24.69 N/A 0 2 Chain A: 5.51 56.34 12.98 N/A 0 1624 Chain B: 5.36 68.32 12.80 N/A 0 1648 Chain S: 13.43 68.48 38.19 N/A 515 0 Histogram: Values Number of atoms 5.36 - 11.67 2063 11.67 - 17.98 704 17.98 - 24.29 272 24.29 - 30.61 215 30.61 - 36.92 169 36.92 - 43.23 157 43.23 - 49.54 105 49.54 - 55.86 46 55.86 - 62.17 42 62.17 - 68.48 14 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1511 r_work=0.1235 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 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 = 0.1228 r_free = 0.1511 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013479 | | target function (ls_wunit_k1) not normalized (work): 2524.547565 | | target function (ls_wunit_k1) not normalized (free): 104.533123 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1228 0.1511 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1608 n_refl.: 191138 remove outliers: r(all,work,free)=0.1436 0.1433 0.1608 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1606 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1235 0.1518 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1235 0.1518 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3130 402.814 380.161 0.497 0.963 0.275 13.296-10.522 99.01 99 1 0.1904 528.187 522.233 0.756 0.964 0.223 10.503-8.327 99.45 178 3 0.1405 565.118 566.994 0.921 0.963 0.169 8.318-6.595 100.00 360 8 0.1514 414.736 414.893 0.935 0.963 0.140 6.588-5.215 100.00 711 7 0.1342 381.101 376.573 0.913 0.963 0.130 5.214-4.128 98.38 1367 28 0.0829 557.435 556.360 0.995 0.963 0.070 4.126-3.266 94.74 2603 46 0.0763 508.132 505.562 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0864 342.774 341.324 1.046 0.962 0.005 2.585-2.046 97.45 10613 204 0.0903 258.603 256.665 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.612 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.351 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.214 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0469 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1517 | n_water=883 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1237 r_free=0.1522 | n_water=876 | time (s): 118.750 (total time: 121.470) Filter (q & B) r_work=0.1238 r_free=0.1523 | n_water=871 | time (s): 4.210 (total time: 125.680) Compute maps r_work=0.1238 r_free=0.1523 | n_water=871 | time (s): 2.530 (total time: 128.210) Filter (map) r_work=0.1278 r_free=0.1525 | n_water=682 | time (s): 5.160 (total time: 133.370) Find peaks r_work=0.1278 r_free=0.1525 | n_water=682 | time (s): 0.630 (total time: 134.000) Add new water r_work=0.1299 r_free=0.1553 | n_water=1002 | time (s): 4.470 (total time: 138.470) Refine new water occ: r_work=0.1253 r_free=0.1512 adp: r_work=0.1254 r_free=0.1513 occ: r_work=0.1249 r_free=0.1509 adp: r_work=0.1249 r_free=0.1510 occ: r_work=0.1246 r_free=0.1507 adp: r_work=0.1245 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1508 r_work=0.1245 r_free=0.1508 | n_water=1002 | time (s): 231.850 (total time: 370.320) Filter (q & B) r_work=0.1250 r_free=0.1515 | n_water=881 | time (s): 6.110 (total time: 376.430) Filter (dist only) r_work=0.1250 r_free=0.1515 | n_water=880 | time (s): 123.250 (total time: 499.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.747357 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.821822 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 0.1240 0.1440 0.0200 0.035 1.1 8.2 0.0 0.0 0 0.874 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.40 2.00 1.931 14.572 15.822 3.941 12.34 14.01 1.67 2.197 14.484 15.822 3.898 Individual atomic B min max mean iso aniso Overall: 5.51 68.00 15.26 1.06 515 3269 Protein: 5.51 36.63 10.76 1.06 0 2902 Water: 6.68 68.00 30.08 N/A 515 365 Other: 13.97 29.31 21.64 N/A 0 2 Chain A: 5.51 55.64 12.75 N/A 0 1623 Chain B: 5.56 68.00 12.52 N/A 0 1646 Chain S: 14.78 66.33 31.91 N/A 515 0 Histogram: Values Number of atoms 5.51 - 11.76 2131 11.76 - 18.01 684 18.01 - 24.26 310 24.26 - 30.51 249 30.51 - 36.76 164 36.76 - 43.01 135 43.01 - 49.26 75 49.26 - 55.51 22 55.51 - 61.75 11 61.75 - 68.00 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1402 r_work=0.1235 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1403 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1387 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892315 | | target function (ml) not normalized (work): 729018.868320 | | target function (ml) not normalized (free): 15230.697238 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1229 0.1387 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1505 n_refl.: 191138 remove outliers: r(all,work,free)=0.1443 0.1442 0.1505 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1501 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1381 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1381 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 94.06 92 3 0.3827 398.008 361.737 0.426 0.947 0.257 13.296-10.522 99.01 99 1 0.2500 528.187 507.360 0.699 0.948 0.200 10.503-8.327 98.90 177 3 0.2043 557.261 557.907 0.884 0.948 0.172 8.318-6.595 100.00 360 8 0.2084 414.736 411.380 0.893 0.947 0.105 6.588-5.215 100.00 711 7 0.1842 381.101 370.701 0.884 0.948 0.100 5.214-4.128 98.38 1367 28 0.1167 557.435 552.428 0.972 0.948 0.090 4.126-3.266 94.74 2603 46 0.1088 508.132 501.158 1.034 0.948 0.014 3.266-2.585 99.86 5447 97 0.1094 342.774 339.074 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0964 258.603 255.685 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.427 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.478 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.317 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0993 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1381 | n_water=880 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1225 r_free=0.1381 | n_water=880 | time (s): 114.740 (total time: 117.970) Filter (q & B) r_work=0.1226 r_free=0.1378 | n_water=867 | time (s): 4.770 (total time: 122.740) Compute maps r_work=0.1226 r_free=0.1378 | n_water=867 | time (s): 1.850 (total time: 124.590) Filter (map) r_work=0.1250 r_free=0.1385 | n_water=724 | time (s): 4.220 (total time: 128.810) Find peaks r_work=0.1250 r_free=0.1385 | n_water=724 | time (s): 0.530 (total time: 129.340) Add new water r_work=0.1266 r_free=0.1404 | n_water=954 | time (s): 3.930 (total time: 133.270) Refine new water occ: r_work=0.1218 r_free=0.1369 adp: r_work=0.1210 r_free=0.1366 occ: r_work=0.1208 r_free=0.1366 adp: r_work=0.1208 r_free=0.1365 occ: r_work=0.1206 r_free=0.1366 adp: r_work=0.1205 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1365 r_work=0.1205 r_free=0.1365 | n_water=954 | time (s): 285.780 (total time: 419.050) Filter (q & B) r_work=0.1209 r_free=0.1367 | n_water=875 | time (s): 5.280 (total time: 424.330) Filter (dist only) r_work=0.1209 r_free=0.1367 | n_water=874 | time (s): 114.160 (total time: 538.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.547271 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.550579 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1367 0.0159 0.035 1.1 6.3 0.0 0.0 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.67 1.59 1.837 14.239 15.551 3.875 12.02 13.61 1.59 2.015 14.177 15.551 3.866 Individual atomic B min max mean iso aniso Overall: 5.49 67.38 14.98 0.99 509 3269 Protein: 5.49 32.90 10.63 0.99 0 2902 Water: 5.95 67.38 29.39 N/A 509 365 Other: 13.93 27.54 20.74 N/A 0 2 Chain A: 5.54 54.16 12.57 N/A 0 1623 Chain B: 5.49 67.38 12.38 N/A 0 1646 Chain S: 5.95 66.25 31.05 N/A 509 0 Histogram: Values Number of atoms 5.49 - 11.68 2119 11.68 - 17.87 729 17.87 - 24.06 307 24.06 - 30.25 237 30.25 - 36.44 159 36.44 - 42.62 129 42.62 - 48.81 67 48.81 - 55.00 19 55.00 - 61.19 9 61.19 - 67.38 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863582 | | target function (ml) not normalized (work): 723629.498290 | | target function (ml) not normalized (free): 15127.369269 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1422 0.1421 0.1480 n_refl.: 191136 remove outliers: r(all,work,free)=0.1422 0.1421 0.1480 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1414 0.1475 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1355 n_refl.: 191136 remove outliers: r(all,work,free)=0.1199 0.1196 0.1355 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 92.08 90 3 0.3644 361.131 310.568 0.401 0.946 0.235 13.296-10.522 96.04 96 1 0.2406 480.742 447.172 0.697 0.948 0.205 10.503-8.327 98.35 176 3 0.2093 503.119 499.545 0.869 0.948 0.164 8.318-6.595 100.00 360 8 0.2170 375.788 370.220 0.890 0.948 0.109 6.588-5.215 100.00 711 7 0.1893 345.312 335.343 0.883 0.948 0.085 5.214-4.128 98.38 1367 28 0.1193 505.086 500.049 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1111 460.413 453.968 1.034 0.948 0.000 3.266-2.585 99.86 5447 97 0.1094 310.584 307.440 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.318 231.907 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.681 137.431 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0987 74.658 73.970 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.051 38.397 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1355 | n_water=874 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1197 r_free=0.1356 | n_water=873 | time (s): 106.590 (total time: 109.820) Filter (q & B) r_work=0.1197 r_free=0.1357 | n_water=864 | time (s): 4.760 (total time: 114.580) Compute maps r_work=0.1197 r_free=0.1357 | n_water=864 | time (s): 1.940 (total time: 116.520) Filter (map) r_work=0.1219 r_free=0.1354 | n_water=738 | time (s): 5.570 (total time: 122.090) Find peaks r_work=0.1219 r_free=0.1354 | n_water=738 | time (s): 0.890 (total time: 122.980) Add new water r_work=0.1230 r_free=0.1368 | n_water=959 | time (s): 5.100 (total time: 128.080) Refine new water occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1190 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 | n_water=959 | time (s): 290.560 (total time: 418.640) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=891 | time (s): 3.950 (total time: 422.590) Filter (dist only) r_work=0.1194 r_free=0.1350 | n_water=890 | time (s): 108.600 (total time: 531.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.466091 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.081018 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1358 0.0161 0.035 1.1 7.5 0.0 0.3 0 0.733 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.58 1.61 1.782 14.111 15.081 3.765 12.00 13.65 1.65 1.823 14.092 15.081 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.14 14.96 0.96 525 3269 Protein: 5.57 31.78 10.58 0.96 0 2902 Water: 5.93 67.14 29.22 N/A 525 365 Other: 13.79 26.80 20.29 N/A 0 2 Chain A: 5.57 53.54 12.49 N/A 0 1623 Chain B: 5.58 67.14 12.31 N/A 0 1646 Chain S: 5.93 66.19 30.87 N/A 525 0 Histogram: Values Number of atoms 5.57 - 11.73 2142 11.73 - 17.89 717 17.89 - 24.04 313 24.04 - 30.20 228 30.20 - 36.35 164 36.35 - 42.51 132 42.51 - 48.67 67 48.67 - 54.82 20 54.82 - 60.98 7 60.98 - 67.14 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1365 r_work=0.1200 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1365 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1374 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761660 | | target function (ml) not normalized (work): 704517.507380 | | target function (ml) not normalized (free): 14753.700330 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1374 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1483 n_refl.: 191130 remove outliers: r(all,work,free)=0.1393 0.1391 0.1483 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1386 0.1384 0.1478 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1372 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1372 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 92.08 90 3 0.3647 361.131 333.115 0.413 0.954 0.217 13.296-10.522 96.04 96 1 0.2381 480.742 461.504 0.702 0.955 0.173 10.503-8.327 98.35 176 3 0.2149 503.119 496.533 0.856 0.956 0.150 8.318-6.595 100.00 360 8 0.2128 375.788 370.845 0.880 0.955 0.085 6.588-5.215 100.00 711 7 0.1900 345.312 335.980 0.877 0.955 0.080 5.214-4.128 98.38 1367 28 0.1218 505.086 499.905 0.967 0.956 0.080 4.126-3.266 94.74 2603 46 0.1136 460.413 453.580 1.028 0.956 0.000 3.266-2.585 99.86 5447 97 0.1108 310.584 307.333 1.013 0.955 0.000 2.585-2.046 97.45 10613 204 0.0944 234.318 231.809 1.026 0.954 0.000 2.046-1.619 99.39 21536 464 0.0913 138.681 137.370 1.049 0.953 0.000 1.619-1.281 98.00 42464 925 0.0977 74.658 73.940 1.047 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.051 38.384 1.036 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1234 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1372 | n_water=890 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1197 r_free=0.1371 | n_water=889 | time (s): 111.870 (total time: 114.930) Filter (q & B) r_work=0.1198 r_free=0.1370 | n_water=875 | time (s): 4.650 (total time: 119.580) Compute maps r_work=0.1198 r_free=0.1370 | n_water=875 | time (s): 2.510 (total time: 122.090) Filter (map) r_work=0.1215 r_free=0.1358 | n_water=767 | time (s): 5.040 (total time: 127.130) Find peaks r_work=0.1215 r_free=0.1358 | n_water=767 | time (s): 0.610 (total time: 127.740) Add new water r_work=0.1225 r_free=0.1363 | n_water=985 | time (s): 3.820 (total time: 131.560) Refine new water occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1344 r_work=0.1189 r_free=0.1344 | n_water=985 | time (s): 345.830 (total time: 477.390) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=915 | time (s): 5.780 (total time: 483.170) Filter (dist only) r_work=0.1194 r_free=0.1350 | n_water=913 | time (s): 120.450 (total time: 603.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.585278 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.480394 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 0.1355 0.0160 0.034 1.1 7.2 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.60 1.759 14.083 14.480 3.760 12.00 13.62 1.62 1.909 14.034 14.480 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 66.00 14.91 0.90 548 3269 Protein: 5.59 28.99 10.47 0.90 0 2902 Water: 6.03 66.00 29.04 N/A 548 365 Other: 13.84 23.63 18.74 N/A 0 2 Chain A: 5.61 52.22 12.34 N/A 0 1623 Chain B: 5.59 65.94 12.18 N/A 0 1646 Chain S: 6.03 66.00 30.75 N/A 548 0 Histogram: Values Number of atoms 5.59 - 11.63 2125 11.63 - 17.67 764 17.67 - 23.71 285 23.71 - 29.75 220 29.75 - 35.79 181 35.79 - 41.83 140 41.83 - 47.88 68 47.88 - 53.92 22 53.92 - 59.96 7 59.96 - 66.00 5 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1362 r_work=0.1200 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758405 | | target function (ml) not normalized (work): 703907.909173 | | target function (ml) not normalized (free): 14742.974061 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1489 n_refl.: 191130 remove outliers: r(all,work,free)=0.1391 0.1389 0.1489 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1383 0.1381 0.1483 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 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 92.08 90 3 0.3772 361.131 329.419 0.379 0.954 0.168 13.296-10.522 96.04 96 1 0.2368 480.742 461.838 0.697 0.956 0.150 10.503-8.327 98.35 176 3 0.2154 503.119 496.867 0.855 0.956 0.137 8.318-6.595 100.00 360 8 0.2098 375.788 370.972 0.878 0.956 0.080 6.588-5.215 100.00 711 7 0.1911 345.312 336.138 0.877 0.956 0.075 5.214-4.128 98.38 1367 28 0.1224 505.086 500.161 0.966 0.956 0.039 4.126-3.266 94.74 2603 46 0.1137 460.413 453.571 1.028 0.956 0.005 3.266-2.585 99.86 5447 97 0.1117 310.584 307.384 1.014 0.956 0.000 2.585-2.046 97.45 10613 204 0.0951 234.318 231.802 1.026 0.955 0.000 2.046-1.619 99.39 21536 464 0.0909 138.681 137.398 1.049 0.955 0.000 1.619-1.281 98.00 42464 925 0.0971 74.658 73.950 1.046 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.051 38.385 1.034 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1382 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1362 | n_water=913 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1197 r_free=0.1361 | n_water=912 | time (s): 119.930 (total time: 122.730) Filter (q & B) r_work=0.1198 r_free=0.1361 | n_water=896 | time (s): 4.740 (total time: 127.470) Compute maps r_work=0.1198 r_free=0.1361 | n_water=896 | time (s): 1.790 (total time: 129.260) Filter (map) r_work=0.1221 r_free=0.1352 | n_water=783 | time (s): 4.260 (total time: 133.520) Find peaks r_work=0.1221 r_free=0.1352 | n_water=783 | time (s): 0.560 (total time: 134.080) Add new water r_work=0.1228 r_free=0.1357 | n_water=986 | time (s): 4.010 (total time: 138.090) Refine new water occ: r_work=0.1196 r_free=0.1341 adp: r_work=0.1196 r_free=0.1341 occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1343 r_work=0.1192 r_free=0.1343 | n_water=986 | time (s): 174.810 (total time: 312.900) Filter (q & B) r_work=0.1196 r_free=0.1352 | n_water=918 | time (s): 5.380 (total time: 318.280) Filter (dist only) r_work=0.1196 r_free=0.1351 | n_water=917 | time (s): 113.790 (total time: 432.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522991 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.117700 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0158 0.036 1.1 7.8 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.58 1.713 13.945 15.118 3.759 11.98 13.59 1.61 1.747 13.930 15.118 3.756 Individual atomic B min max mean iso aniso Overall: 5.58 65.93 14.86 0.89 553 3268 Protein: 5.58 28.64 10.42 0.89 0 2902 Water: 6.06 65.93 28.90 N/A 553 364 Other: 13.88 22.27 18.07 N/A 0 2 Chain A: 5.64 51.73 12.26 N/A 0 1623 Chain B: 5.58 64.74 12.09 N/A 0 1645 Chain S: 6.06 65.93 30.74 N/A 553 0 Histogram: Values Number of atoms 5.58 - 11.61 2125 11.61 - 17.65 771 17.65 - 23.68 284 23.68 - 29.72 219 29.72 - 35.75 183 35.75 - 41.79 136 41.79 - 47.82 71 47.82 - 53.86 21 53.86 - 59.89 6 59.89 - 65.93 5 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1359 r_work=0.1199 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755288 | | target function (ml) not normalized (work): 703324.178957 | | target function (ml) not normalized (free): 14734.553638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1500 n_refl.: 191130 remove outliers: r(all,work,free)=0.1390 0.1388 0.1500 n_refl.: 191130 overall B=-0.01 to atoms: r(all,work,free)=0.1389 0.1387 0.1499 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1350 n_refl.: 191130 remove outliers: r(all,work,free)=0.1189 0.1186 0.1350 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3683 361.131 330.030 0.424 0.917 0.195 13.296-10.522 96.04 96 1 0.2321 480.742 462.949 0.736 0.918 0.141 10.503-8.327 98.35 176 3 0.2173 503.119 495.336 0.906 0.919 0.110 8.315-6.595 100.00 359 8 0.2055 374.841 370.410 0.934 0.919 0.090 6.588-5.215 100.00 711 7 0.1922 345.312 335.626 0.931 0.919 0.073 5.214-4.128 98.38 1367 28 0.1242 505.086 499.253 1.028 0.920 0.039 4.126-3.266 94.74 2603 46 0.1144 460.413 452.934 1.093 0.921 0.005 3.266-2.585 99.86 5447 97 0.1119 310.584 307.042 1.076 0.922 0.000 2.585-2.046 97.45 10613 204 0.0955 234.318 231.643 1.087 0.923 0.000 2.046-1.619 99.39 21536 464 0.0903 138.681 137.290 1.107 0.926 0.000 1.619-1.281 98.00 42464 925 0.0942 74.658 74.001 1.100 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.051 38.352 1.071 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0234 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1350 | n_water=917 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1186 r_free=0.1350 | n_water=916 | time (s): 111.350 (total time: 113.580) Filter (q & B) r_work=0.1186 r_free=0.1350 | n_water=907 | time (s): 5.310 (total time: 118.890) Compute maps r_work=0.1186 r_free=0.1350 | n_water=907 | time (s): 1.820 (total time: 120.710) Filter (map) r_work=0.1209 r_free=0.1352 | n_water=791 | time (s): 4.440 (total time: 125.150) Find peaks r_work=0.1209 r_free=0.1352 | n_water=791 | time (s): 0.770 (total time: 125.920) Add new water r_work=0.1216 r_free=0.1361 | n_water=992 | time (s): 4.190 (total time: 130.110) Refine new water occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1333 occ: r_work=0.1182 r_free=0.1332 adp: r_work=0.1182 r_free=0.1333 occ: r_work=0.1181 r_free=0.1333 adp: r_work=0.1181 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1334 r_work=0.1181 r_free=0.1334 | n_water=992 | time (s): 227.320 (total time: 357.430) Filter (q & B) r_work=0.1184 r_free=0.1341 | n_water=923 | time (s): 5.600 (total time: 363.030) Filter (dist only) r_work=0.1185 r_free=0.1340 | n_water=921 | time (s): 128.910 (total time: 491.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.576466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.191168 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 0.1188 0.1347 0.0160 0.038 1.1 6.1 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.47 1.60 1.701 13.896 14.191 3.753 11.89 13.51 1.62 1.704 13.892 14.191 3.753 Individual atomic B min max mean iso aniso Overall: 5.60 64.46 14.82 0.87 557 3268 Protein: 5.60 28.40 10.43 0.87 0 2902 Water: 6.07 64.46 28.63 N/A 557 364 Other: 13.88 22.24 18.06 N/A 0 2 Chain A: 5.66 51.62 12.24 N/A 0 1623 Chain B: 5.60 64.46 12.08 N/A 0 1645 Chain S: 6.07 63.43 30.41 N/A 557 0 Histogram: Values Number of atoms 5.60 - 11.49 2087 11.49 - 17.37 798 17.37 - 23.26 288 23.26 - 29.15 223 29.15 - 35.03 182 35.03 - 40.92 131 40.92 - 46.80 78 46.80 - 52.69 26 52.69 - 58.58 7 58.58 - 64.46 5 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1351 r_work=0.1189 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1351 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1355 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752636 | | target function (ml) not normalized (work): 702823.709441 | | target function (ml) not normalized (free): 14727.142915 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1510 n_refl.: 191129 remove outliers: r(all,work,free)=0.1398 0.1396 0.1510 n_refl.: 191129 overall B=-0.02 to atoms: r(all,work,free)=0.1395 0.1393 0.1507 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1190 0.1187 0.1351 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3742 356.548 326.978 0.359 0.994 0.148 13.296-10.522 96.04 96 1 0.2376 480.742 461.670 0.671 0.996 0.124 10.503-8.327 98.35 176 3 0.2227 503.119 493.857 0.835 0.996 0.103 8.315-6.595 100.00 359 8 0.2073 374.841 369.878 0.859 0.996 0.083 6.588-5.215 100.00 711 7 0.1923 345.312 335.633 0.858 0.997 0.070 5.214-4.128 98.38 1367 28 0.1238 505.086 499.276 0.948 0.997 0.029 4.126-3.266 94.74 2603 46 0.1152 460.413 452.929 1.009 0.999 0.000 3.266-2.585 99.86 5447 97 0.1126 310.584 307.054 0.994 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.318 231.632 1.003 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.681 137.312 1.022 1.005 0.000 1.619-1.281 98.00 42464 925 0.0940 74.658 74.009 1.016 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.051 38.343 0.991 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0481 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1351 | n_water=921 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1187 r_free=0.1351 | n_water=918 | time (s): 114.350 (total time: 117.080) Filter (q & B) r_work=0.1187 r_free=0.1352 | n_water=906 | time (s): 4.620 (total time: 121.700) Compute maps r_work=0.1187 r_free=0.1352 | n_water=906 | time (s): 1.710 (total time: 123.410) Filter (map) r_work=0.1209 r_free=0.1352 | n_water=795 | time (s): 5.170 (total time: 128.580) Find peaks r_work=0.1209 r_free=0.1352 | n_water=795 | time (s): 0.630 (total time: 129.210) Add new water r_work=0.1215 r_free=0.1359 | n_water=990 | time (s): 4.130 (total time: 133.340) Refine new water occ: r_work=0.1186 r_free=0.1329 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1184 r_free=0.1328 adp: r_work=0.1184 r_free=0.1329 occ: r_work=0.1182 r_free=0.1328 adp: r_work=0.1182 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1329 r_work=0.1182 r_free=0.1329 | n_water=990 | time (s): 300.110 (total time: 433.450) Filter (q & B) r_work=0.1186 r_free=0.1343 | n_water=915 | time (s): 4.590 (total time: 438.040) Filter (dist only) r_work=0.1186 r_free=0.1342 | n_water=914 | time (s): 114.110 (total time: 552.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.157338 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 0.1190 0.1348 0.0157 0.038 1.1 6.3 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.48 1.57 1.695 13.862 14.157 3.754 11.91 13.51 1.60 1.708 13.856 14.157 3.753 Individual atomic B min max mean iso aniso Overall: 5.64 63.58 14.76 0.86 550 3268 Protein: 5.64 27.97 10.42 0.86 0 2902 Water: 6.05 63.58 28.54 N/A 550 364 Other: 13.89 22.17 18.03 N/A 0 2 Chain A: 5.70 51.31 12.20 N/A 0 1623 Chain B: 5.64 63.58 12.05 N/A 0 1645 Chain S: 6.05 63.18 30.44 N/A 550 0 Histogram: Values Number of atoms 5.64 - 11.43 2074 11.43 - 17.23 817 17.23 - 23.02 274 23.02 - 28.81 218 28.81 - 34.61 182 34.61 - 40.40 126 40.40 - 46.19 82 46.19 - 51.99 32 51.99 - 57.78 8 57.78 - 63.58 5 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1351 r_work=0.1191 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1351 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752737 | | target function (ml) not normalized (work): 702838.828199 | | target function (ml) not normalized (free): 14729.731151 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1509 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1404 0.1509 n_refl.: 191128 overall B=-0.11 to atoms: r(all,work,free)=0.1388 0.1386 0.1494 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1353 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1353 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3667 356.548 324.032 0.371 0.975 0.171 13.296-10.522 96.04 96 1 0.2406 480.742 461.826 0.672 0.977 0.123 10.503-8.327 98.35 176 3 0.2245 503.119 494.439 0.837 0.978 0.097 8.315-6.595 100.00 359 8 0.2057 374.841 370.012 0.862 0.978 0.078 6.588-5.215 100.00 711 7 0.1942 345.312 335.770 0.860 0.978 0.063 5.214-4.128 98.38 1367 28 0.1253 505.086 498.934 0.951 0.979 0.029 4.126-3.266 94.74 2603 46 0.1159 460.413 452.880 1.013 0.981 0.000 3.266-2.585 99.86 5447 97 0.1132 310.584 307.012 0.996 0.982 0.000 2.585-2.046 97.45 10613 204 0.0959 234.318 231.623 1.004 0.984 0.000 2.046-1.619 99.39 21536 464 0.0906 138.681 137.333 1.020 0.988 0.000 1.619-1.281 98.00 42464 925 0.0939 74.658 74.010 1.010 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.051 38.333 0.978 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0232 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1353 After: r_work=0.1190 r_free=0.1353 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1353 | n_water=914 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1190 r_free=0.1352 | n_water=913 | time (s): 118.050 (total time: 120.460) Filter (q & B) r_work=0.1191 r_free=0.1354 | n_water=902 | time (s): 5.120 (total time: 125.580) Compute maps r_work=0.1191 r_free=0.1354 | n_water=902 | time (s): 2.260 (total time: 127.840) Filter (map) r_work=0.1212 r_free=0.1358 | n_water=798 | time (s): 4.780 (total time: 132.620) Find peaks r_work=0.1212 r_free=0.1358 | n_water=798 | time (s): 0.750 (total time: 133.370) Add new water r_work=0.1218 r_free=0.1370 | n_water=1003 | time (s): 4.430 (total time: 137.800) Refine new water occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1334 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=1003 | time (s): 208.460 (total time: 346.260) Filter (q & B) r_work=0.1188 r_free=0.1343 | n_water=923 | time (s): 4.580 (total time: 350.840) Filter (dist only) r_work=0.1188 r_free=0.1343 | n_water=921 | time (s): 123.540 (total time: 474.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.490848 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.685219 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 0.1348 0.0156 0.038 1.2 10.4 0.0 0.3 0 0.745 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.48 1.56 1.687 13.760 13.685 3.756 11.94 13.51 1.57 1.692 13.755 13.685 3.756 Individual atomic B min max mean iso aniso Overall: 5.55 62.87 14.67 0.85 558 3267 Protein: 5.55 27.74 10.33 0.85 0 2902 Water: 5.99 62.87 28.33 N/A 558 363 Other: 13.83 22.09 17.96 N/A 0 2 Chain A: 5.65 50.97 12.08 N/A 0 1623 Chain B: 5.55 62.66 11.91 N/A 0 1644 Chain S: 5.99 62.87 30.29 N/A 558 0 Histogram: Values Number of atoms 5.55 - 11.28 2055 11.28 - 17.01 837 17.01 - 22.75 274 22.75 - 28.48 217 28.48 - 34.21 182 34.21 - 39.94 135 39.94 - 45.67 80 45.67 - 51.41 29 51.41 - 57.14 10 57.14 - 62.87 6 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1351 r_work=0.1194 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755661 | | target function (ml) not normalized (work): 703386.431458 | | target function (ml) not normalized (free): 14734.013925 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1353 0.1468 5.6849 5.7602| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1327 5.0806 5.1864| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1198 4.6607 4.7575| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1049 4.3939 4.579| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0985 4.1528 4.2459| | 6: 1.72 - 1.62 0.99 7102 142 0.0897 0.1077 3.948 4.0815| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0962 3.8006 3.935| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1313 3.7024 3.8993| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1128 3.6227 3.7506| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1186 3.5568 3.6729| | 11: 1.36 - 1.32 0.99 6997 151 0.0996 0.1120 3.4895 3.591| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1128 3.4614 3.5839| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1249 3.438 3.5666| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1562 3.4341 3.6704| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1245 3.4504 3.4937| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1538 3.4669 3.6601| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1222 3.4342 3.4391| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1702 3.4392 3.5296| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1769 3.4211 3.6022| | 20: 1.10 - 1.08 0.97 6884 147 0.1588 0.1573 3.4122 3.4323| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2142 3.4197 3.5078| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1957 3.4145 3.4162| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2021 3.4342 3.4859| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2261 3.437 3.5137| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2528 3.4505 3.5278| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2858 3.4163 3.4221| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2804 3.4696 3.3966| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 11.59 1.00 0.98 11152.29| | 2: 2.94 - 2.33 7339 128 0.93 12.75 0.99 0.98 5133.46| | 3: 2.33 - 2.04 6939 150 0.96 7.71 1.01 0.98 1721.62| | 4: 2.04 - 1.85 7170 155 0.96 7.68 1.00 0.98 1015.80| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.98 637.12| | 6: 1.72 - 1.62 7102 142 0.96 8.04 1.00 0.99 444.84| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 1.00 336.67| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 1.00 278.56| | 9: 1.47 - 1.41 6938 155 0.96 8.45 1.00 1.00 230.48| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 1.00 203.15| | 11: 1.36 - 1.32 6997 151 0.96 8.98 0.99 0.98 175.86| | 12: 1.32 - 1.28 6975 149 0.96 9.03 0.98 0.97 161.79| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.99 158.40| | 14: 1.25 - 1.22 7015 112 0.95 10.70 1.01 0.99 163.20| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 1.00 166.66| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.99 160.50| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.99 153.97| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.97 147.52| | 19: 1.12 - 1.10 6948 106 0.93 14.15 1.00 0.97 151.28| | 20: 1.10 - 1.08 6884 147 0.92 15.25 1.00 0.96 150.47| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.96 153.74| | 22: 1.07 - 1.05 6836 135 0.89 18.32 1.00 0.95 155.15| | 23: 1.05 - 1.03 6827 159 0.87 20.54 1.00 0.95 165.32| | 24: 1.03 - 1.02 6784 133 0.85 23.23 1.00 0.95 179.87| | 25: 1.02 - 1.01 6552 130 0.83 25.23 0.98 0.92 183.05| | 26: 1.01 - 0.99 6767 158 0.81 26.68 0.99 0.91 177.32| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.90 161.35| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.52 max = 11152.29 mean = 925.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.30| |phase err.(test): min = 0.00 max = 89.31 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1494 n_refl.: 191128 remove outliers: r(all,work,free)=0.1397 0.1395 0.1494 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1391 0.1389 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3657 356.548 324.099 0.362 0.976 0.155 13.296-10.522 96.04 96 1 0.2444 480.742 460.138 0.667 0.978 0.114 10.503-8.327 98.35 176 3 0.2206 503.119 495.619 0.836 0.978 0.090 8.315-6.595 100.00 359 8 0.2056 374.841 370.312 0.863 0.978 0.077 6.588-5.215 100.00 711 7 0.1938 345.312 335.384 0.861 0.979 0.073 5.214-4.128 98.38 1367 28 0.1250 505.086 499.079 0.952 0.980 0.034 4.126-3.266 94.74 2603 46 0.1153 460.413 452.991 1.015 0.981 0.000 3.266-2.585 99.86 5447 97 0.1126 310.584 307.186 0.998 0.983 0.000 2.585-2.046 97.45 10613 204 0.0964 234.318 231.653 1.004 0.985 0.000 2.046-1.619 99.39 21536 464 0.0911 138.681 137.343 1.020 0.990 0.000 1.619-1.281 98.00 42464 925 0.0948 74.658 74.005 1.009 0.996 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.051 38.330 0.978 1.009 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0088 ================= 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 : 0.2029 0.1995 0.083 5.261 5.2 78.0 14.6 805 0.000 1_bss: 0.1795 0.1936 0.083 5.261 5.2 78.0 14.6 805 0.000 1_settarget: 0.1795 0.1936 0.083 5.261 5.2 78.0 14.6 805 0.000 1_nqh: 0.1799 0.1940 0.083 5.261 5.2 78.0 14.6 805 0.002 1_weight: 0.1799 0.1940 0.083 5.261 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1270 0.1497 0.038 1.175 5.2 78.0 14.6 805 0.154 1_adp: 0.1298 0.1567 0.038 1.175 5.2 73.0 15.0 805 0.154 1_regHadp: 0.1297 0.1562 0.038 1.175 5.2 73.0 15.0 805 0.154 1_occ: 0.1282 0.1550 0.038 1.175 5.2 73.0 15.0 805 0.154 2_bss: 0.1275 0.1540 0.038 1.175 5.4 73.2 15.1 805 0.154 2_settarget: 0.1275 0.1540 0.038 1.175 5.4 73.2 15.1 805 0.154 2_updatecdl: 0.1275 0.1540 0.038 1.186 5.4 73.2 15.1 805 0.154 2_nqh: 0.1275 0.1540 0.038 1.186 5.4 73.2 15.1 805 0.154 2_sol: 0.1271 0.1507 0.038 1.186 5.4 73.2 16.2 883 n/a 2_weight: 0.1271 0.1507 0.038 1.186 5.4 73.2 16.2 883 n/a 2_xyzrec: 0.1257 0.1523 0.040 1.135 5.4 73.2 16.2 883 n/a 2_adp: 0.1234 0.1511 0.040 1.135 5.4 68.5 16.3 883 n/a 2_regHadp: 0.1235 0.1512 0.040 1.135 5.4 68.5 16.3 883 n/a 2_occ: 0.1228 0.1511 0.040 1.135 5.4 68.5 16.3 883 n/a 3_bss: 0.1235 0.1517 0.040 1.135 5.3 68.5 16.3 883 n/a 3_settarget: 0.1235 0.1517 0.040 1.135 5.3 68.5 16.3 883 n/a 3_updatecdl: 0.1235 0.1517 0.040 1.138 5.3 68.5 16.3 883 n/a 3_nqh: 0.1235 0.1517 0.040 1.138 5.3 68.5 16.3 883 n/a 3_sol: 0.1250 0.1515 0.040 1.138 5.3 68.3 15.4 880 n/a 3_weight: 0.1250 0.1515 0.040 1.138 5.3 68.3 15.4 880 n/a 3_xyzrec: 0.1240 0.1440 0.035 1.101 5.3 68.3 15.4 880 n/a 3_adp: 0.1235 0.1402 0.035 1.101 5.5 68.0 15.3 880 n/a 3_regHadp: 0.1235 0.1403 0.035 1.101 5.5 68.0 15.3 880 n/a 3_occ: 0.1230 0.1387 0.035 1.101 5.5 68.0 15.3 880 n/a 4_bss: 0.1225 0.1381 0.035 1.101 5.5 68.0 15.2 880 n/a 4_settarget: 0.1225 0.1381 0.035 1.101 5.5 68.0 15.2 880 n/a 4_updatecdl: 0.1225 0.1381 0.035 1.106 5.5 68.0 15.2 880 n/a 4_nqh: 0.1225 0.1381 0.035 1.106 5.5 68.0 15.2 880 n/a 4_sol: 0.1209 0.1367 0.035 1.106 5.5 68.0 15.1 874 n/a 4_weight: 0.1209 0.1367 0.035 1.106 5.5 68.0 15.1 874 n/a 4_xyzrec: 0.1208 0.1367 0.035 1.121 5.5 68.0 15.1 874 n/a 4_adp: 0.1202 0.1361 0.035 1.121 5.5 67.4 15.0 874 n/a 4_regHadp: 0.1202 0.1361 0.035 1.121 5.5 67.4 15.0 874 n/a 4_occ: 0.1199 0.1357 0.035 1.121 5.5 67.4 15.0 874 n/a 5_bss: 0.1196 0.1355 0.035 1.121 5.5 67.3 14.9 874 n/a 5_settarget: 0.1196 0.1355 0.035 1.121 5.5 67.3 14.9 874 n/a 5_updatecdl: 0.1196 0.1355 0.035 1.121 5.5 67.3 14.9 874 n/a 5_nqh: 0.1196 0.1355 0.035 1.121 5.5 67.3 14.9 874 n/a 5_sol: 0.1194 0.1350 0.035 1.121 5.5 67.3 15.0 890 n/a 5_weight: 0.1194 0.1350 0.035 1.121 5.5 67.3 15.0 890 n/a 5_xyzrec: 0.1197 0.1358 0.035 1.110 5.5 67.3 15.0 890 n/a 5_adp: 0.1200 0.1365 0.035 1.110 5.6 67.1 15.0 890 n/a 5_regHadp: 0.1200 0.1365 0.035 1.110 5.6 67.1 15.0 890 n/a 5_occ: 0.1198 0.1374 0.035 1.110 5.6 67.1 15.0 890 n/a 6_bss: 0.1197 0.1372 0.035 1.110 5.5 67.1 14.9 890 n/a 6_settarget: 0.1197 0.1372 0.035 1.110 5.5 67.1 14.9 890 n/a 6_updatecdl: 0.1197 0.1372 0.035 1.110 5.5 67.1 14.9 890 n/a 6_nqh: 0.1197 0.1372 0.035 1.110 5.5 67.1 14.9 890 n/a 6_sol: 0.1194 0.1350 0.035 1.110 5.5 67.1 15.0 913 n/a 6_weight: 0.1194 0.1350 0.035 1.110 5.5 67.1 15.0 913 n/a 6_xyzrec: 0.1196 0.1355 0.034 1.122 5.5 67.1 15.0 913 n/a 6_adp: 0.1200 0.1362 0.034 1.122 5.6 66.0 14.9 913 n/a 6_regHadp: 0.1200 0.1363 0.034 1.122 5.6 66.0 14.9 913 n/a 6_occ: 0.1197 0.1367 0.034 1.122 5.6 66.0 14.9 913 n/a 7_bss: 0.1197 0.1362 0.034 1.122 5.5 66.0 14.9 913 n/a 7_settarget: 0.1197 0.1362 0.034 1.122 5.5 66.0 14.9 913 n/a 7_updatecdl: 0.1197 0.1362 0.034 1.123 5.5 66.0 14.9 913 n/a 7_nqh: 0.1197 0.1362 0.034 1.123 5.5 66.0 14.9 913 n/a 7_sol: 0.1196 0.1351 0.034 1.123 5.5 66.0 14.9 917 n/a 7_weight: 0.1196 0.1351 0.034 1.123 5.5 66.0 14.9 917 n/a 7_xyzrec: 0.1199 0.1357 0.036 1.113 5.5 66.0 14.9 917 n/a 7_adp: 0.1198 0.1359 0.036 1.113 5.6 65.9 14.9 917 n/a 7_regHadp: 0.1199 0.1359 0.036 1.113 5.6 65.9 14.9 917 n/a 7_occ: 0.1196 0.1361 0.036 1.113 5.6 65.9 14.9 917 n/a 8_bss: 0.1186 0.1350 0.036 1.113 5.6 65.9 14.9 917 n/a 8_settarget: 0.1186 0.1350 0.036 1.113 5.6 65.9 14.9 917 n/a 8_updatecdl: 0.1186 0.1350 0.036 1.113 5.6 65.9 14.9 917 n/a 8_nqh: 0.1186 0.1350 0.036 1.113 5.6 65.9 14.9 917 n/a 8_sol: 0.1185 0.1340 0.036 1.113 5.6 64.7 14.8 921 n/a 8_weight: 0.1185 0.1340 0.036 1.113 5.6 64.7 14.8 921 n/a 8_xyzrec: 0.1188 0.1347 0.038 1.114 5.6 64.7 14.8 921 n/a 8_adp: 0.1189 0.1351 0.038 1.114 5.6 64.5 14.8 921 n/a 8_regHadp: 0.1189 0.1351 0.038 1.114 5.6 64.5 14.8 921 n/a 8_occ: 0.1188 0.1355 0.038 1.114 5.6 64.5 14.8 921 n/a 9_bss: 0.1187 0.1351 0.038 1.114 5.6 64.4 14.8 921 n/a 9_settarget: 0.1187 0.1351 0.038 1.114 5.6 64.4 14.8 921 n/a 9_updatecdl: 0.1187 0.1351 0.038 1.114 5.6 64.4 14.8 921 n/a 9_nqh: 0.1187 0.1351 0.038 1.114 5.6 64.4 14.8 921 n/a 9_sol: 0.1186 0.1342 0.038 1.114 5.6 64.4 14.8 914 n/a 9_weight: 0.1186 0.1342 0.038 1.114 5.6 64.4 14.8 914 n/a 9_xyzrec: 0.1190 0.1348 0.038 1.112 5.6 64.4 14.8 914 n/a 9_adp: 0.1191 0.1351 0.038 1.112 5.6 63.6 14.8 914 n/a 9_regHadp: 0.1191 0.1351 0.038 1.112 5.6 63.6 14.8 914 n/a 9_occ: 0.1190 0.1353 0.038 1.112 5.6 63.6 14.8 914 n/a 10_bss: 0.1189 0.1353 0.038 1.112 5.5 63.5 14.7 914 n/a 10_settarget: 0.1189 0.1353 0.038 1.112 5.5 63.5 14.7 914 n/a 10_updatecdl: 0.1189 0.1353 0.038 1.113 5.5 63.5 14.7 914 n/a 10_setrh: 0.1190 0.1353 0.038 1.113 5.5 63.5 14.7 914 n/a 10_nqh: 0.1190 0.1353 0.038 1.113 5.5 63.5 14.7 914 n/a 10_sol: 0.1188 0.1343 0.038 1.113 5.5 63.5 14.7 921 n/a 10_weight: 0.1188 0.1343 0.038 1.113 5.5 63.5 14.7 921 n/a 10_xyzrec: 0.1192 0.1348 0.038 1.154 5.5 63.5 14.7 921 n/a 10_adp: 0.1194 0.1351 0.038 1.154 5.6 62.9 14.7 921 n/a 10_regHadp: 0.1194 0.1351 0.038 1.154 5.6 62.9 14.7 921 n/a 10_occ: 0.1192 0.1353 0.038 1.154 5.6 62.9 14.7 921 n/a end: 0.1192 0.1350 0.038 1.154 5.5 62.8 14.6 921 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7657487_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7657487_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3200 Refinement macro-cycles (run) : 12131.2200 Write final files (write_after_run_outputs) : 168.6000 Total : 12307.1400 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:19 PST -0800 (1736736139.91 s) Start R-work = 0.1795, R-free = 0.1936 Final R-work = 0.1192, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12595.08 seconds wall clock time: 210 minutes 56.28 seconds (12656.28 seconds total)