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_4437829.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4437829.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4437829.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" 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" } 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: 2.15, per 1000 atoms: 0.32 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: 2.772 distance_ideal: 2.720 ideal - model: -0.052 slack: 0.000 delta_slack: -0.052 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: 2.700 distance_ideal: 2.710 ideal - model: 0.010 slack: 0.000 delta_slack: 0.010 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 116.6 milliseconds Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 639 1.02 - 1.25: 2599 1.25 - 1.48: 1539 1.48 - 1.71: 1126 1.71 - 1.94: 31 Bond restraints: 5934 Sorted by residual: bond pdb=" C LYS B 31 " pdb=" O LYS B 31 " ideal model delta sigma weight residual 1.235 1.473 -0.238 1.21e-02 6.83e+03 3.86e+02 bond pdb=" N ILE A 191 " pdb=" H ILE A 191 " ideal model delta sigma weight residual 0.860 1.253 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" CG GLU A 196 " pdb=" HG3 GLU A 196 " ideal model delta sigma weight residual 0.970 1.352 -0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" N GLY B 50 " pdb=" H GLY B 50 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" N LYS A 77 " pdb=" H LYS A 77 " ideal model delta sigma weight residual 0.860 1.230 -0.370 2.00e-02 2.50e+03 3.42e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 5672 4.20 - 8.40: 3481 8.40 - 12.60: 1373 12.60 - 16.81: 266 16.81 - 21.01: 18 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CD2 TRP A 146 " pdb=" CE2 TRP A 146 " pdb=" CZ2 TRP A 146 " ideal model delta sigma weight residual 122.40 138.85 -16.45 1.00e+00 1.00e+00 2.71e+02 angle pdb=" CA VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " ideal model delta sigma weight residual 117.37 127.99 -10.62 7.40e-01 1.83e+00 2.06e+02 angle pdb=" O VAL B 150 " pdb=" C VAL B 150 " pdb=" N LYS B 151 " ideal model delta sigma weight residual 122.16 134.53 -12.37 9.10e-01 1.21e+00 1.85e+02 angle pdb=" CA VAL A 89 " pdb=" C VAL A 89 " pdb=" O VAL A 89 " ideal model delta sigma weight residual 121.17 107.06 14.11 1.06e+00 8.90e-01 1.77e+02 angle pdb=" CA GLN A 94 " pdb=" C GLN A 94 " pdb=" N PHE A 95 " ideal model delta sigma weight residual 117.39 133.70 -16.31 1.24e+00 6.50e-01 1.73e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 1826 16.93 - 33.87: 154 33.87 - 50.80: 42 50.80 - 67.73: 23 67.73 - 84.67: 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 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB TRP A 146 " pdb=" CG TRP A 146 " pdb=" CD1 TRP A 146 " pdb=" HD1 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 22.34 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.231: 215 0.231 - 0.460: 160 0.460 - 0.689: 85 0.689 - 0.918: 26 0.918 - 1.147: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.44 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" CA LYS A 142 " pdb=" N LYS A 142 " pdb=" C LYS A 142 " pdb=" CB LYS A 142 " both_signs ideal model delta sigma weight residual False 2.51 3.57 -1.06 2.00e-01 2.50e+01 2.81e+01 chirality pdb=" CB ILE A 134 " pdb=" CA ILE A 134 " pdb=" CG1 ILE A 134 " pdb=" CG2 ILE A 134 " both_signs ideal model delta sigma weight residual False 2.64 3.64 -0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.151 2.00e-02 2.50e+03 8.00e-02 1.92e+02 pdb=" CG PHE A 164 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.124 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.046 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.131 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.112 2.00e-02 2.50e+03 6.60e-02 1.74e+02 pdb=" CG TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.096 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.090 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.119 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.043 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.074 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.072 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.073 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.024 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" CG PHE A 82 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " 0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.053 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.135 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " -0.119 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.63: 28 1.63 - 2.37: 2508 2.37 - 3.11: 22374 3.11 - 3.86: 32963 3.86 - 4.60: 52384 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110257 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.881 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.968 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.049 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.112 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.184 2.620 ... (remaining 110252 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_4437829_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= 0.2036 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301552 | | target function (ml) not normalized (work): 805736.580353 | | target function (ml) not normalized (free): 16572.935944 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2130 0.1997 6.6838 6.3111| | 2: 2.94 - 2.33 1.00 7339 128 0.1627 0.1588 5.54 5.5636| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1663 5.1495 5.198| | 4: 2.04 - 1.85 1.00 7170 155 0.1769 0.1608 4.9725 5.0407| | 5: 1.85 - 1.72 0.99 7113 159 0.1917 0.1703 4.7893 4.8174| | 6: 1.72 - 1.62 0.99 7102 142 0.1972 0.2009 4.6639 4.7805| | 7: 1.62 - 1.54 0.99 7104 148 0.2003 0.1776 4.5547 4.5929| | 8: 1.54 - 1.47 0.96 6798 152 0.2041 0.2058 4.4734 4.5116| | 9: 1.47 - 1.41 0.98 6938 155 0.2111 0.2230 4.4045 4.4893| | 10: 1.41 - 1.36 0.99 7022 150 0.2120 0.2393 4.3175 4.4266| | 11: 1.36 - 1.32 0.99 6997 151 0.2129 0.2160 4.2486 4.291| | 12: 1.32 - 1.28 0.98 6976 149 0.2089 0.2001 4.1825 4.2508| | 13: 1.28 - 1.25 0.98 6907 166 0.2038 0.2283 4.1189 4.26| | 14: 1.25 - 1.22 0.98 7015 113 0.2093 0.2272 4.0795 4.1514| | 15: 1.22 - 1.19 0.98 6957 137 0.2124 0.1772 4.048 3.9713| | 16: 1.19 - 1.17 0.93 6604 132 0.2108 0.2408 3.9991 4.1808| | 17: 1.17 - 1.14 0.98 6941 135 0.2162 0.1882 3.9468 3.951| | 18: 1.14 - 1.12 0.98 6875 142 0.2225 0.2263 3.9293 3.9143| | 19: 1.12 - 1.10 0.97 6949 106 0.2285 0.2259 3.878 3.958| | 20: 1.10 - 1.08 0.97 6884 147 0.2311 0.2267 3.8213 3.9144| | 21: 1.08 - 1.07 0.97 6852 152 0.2421 0.2545 3.7845 3.7857| | 22: 1.07 - 1.05 0.97 6838 135 0.2561 0.2491 3.7511 3.7889| | 23: 1.05 - 1.03 0.97 6829 159 0.2731 0.2427 3.7277 3.7391| | 24: 1.03 - 1.02 0.96 6785 133 0.2879 0.2666 3.7067 3.7067| | 25: 1.02 - 1.01 0.93 6552 130 0.3064 0.2774 3.6788 3.691| | 26: 1.01 - 0.99 0.96 6767 158 0.3231 0.3082 3.6399 3.5946| | 27: 0.99 - 0.98 0.94 6648 131 0.3375 0.3196 3.6387 3.574| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.50 0.91 0.97 35451.71| | 2: 2.94 - 2.33 7339 128 0.85 21.29 1.09 1.02 15182.83| | 3: 2.33 - 2.04 6939 150 0.93 12.83 1.11 1.05 4263.82| | 4: 2.04 - 1.85 7170 155 0.92 13.68 1.12 1.05 2834.01| | 5: 1.85 - 1.72 7113 159 0.90 16.14 1.12 1.06 2154.17| | 6: 1.72 - 1.62 7102 142 0.90 17.21 1.11 1.06 1703.84| | 7: 1.62 - 1.54 7104 148 0.89 17.97 1.10 1.05 1385.26| | 8: 1.54 - 1.47 6798 152 0.88 18.75 1.10 1.04 1190.95| | 9: 1.47 - 1.41 6938 155 0.87 20.13 1.10 1.04 1068.26| | 10: 1.41 - 1.36 7022 150 0.86 21.13 1.09 1.03 940.51| | 11: 1.36 - 1.32 6997 151 0.86 21.38 1.08 1.02 826.61| | 12: 1.32 - 1.28 6976 149 0.86 21.29 1.08 1.02 715.15| | 13: 1.28 - 1.25 6907 166 0.86 20.73 1.08 1.04 643.16| | 14: 1.25 - 1.22 7015 113 0.86 20.86 1.08 1.04 576.11| | 15: 1.22 - 1.19 6957 137 0.87 20.20 1.08 1.05 515.03| | 16: 1.19 - 1.17 6604 132 0.88 19.92 1.07 1.03 470.50| | 17: 1.17 - 1.14 6941 135 0.87 20.47 1.08 1.02 423.27| | 18: 1.14 - 1.12 6875 142 0.86 21.04 1.09 0.99 391.83| | 19: 1.12 - 1.10 6949 106 0.85 22.29 1.08 0.98 372.29| | 20: 1.10 - 1.08 6884 147 0.84 23.14 1.06 0.98 359.48| | 21: 1.08 - 1.07 6852 152 0.84 24.07 1.06 0.99 342.62| | 22: 1.07 - 1.05 6838 135 0.83 24.99 1.05 0.98 316.73| | 23: 1.05 - 1.03 6829 159 0.82 25.69 1.06 1.00 298.35| | 24: 1.03 - 1.02 6785 133 0.81 26.75 1.05 1.01 288.15| | 25: 1.02 - 1.01 6552 130 0.80 27.96 1.03 0.98 274.99| | 26: 1.01 - 0.99 6767 158 0.78 29.96 1.02 0.93 264.44| | 27: 0.99 - 0.98 6648 131 0.76 31.51 1.03 0.88 256.47| |alpha: min = 0.88 max = 1.06 mean = 1.01| |beta: min = 256.47 max = 35451.71 mean = 2850.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.49| |phase err.(test): min = 0.00 max = 89.44 mean = 21.42| |-----------------------------------------------------------------------------| ----------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 0.273 2950 Z= 5.585 Angle : 5.221 16.451 4018 Z= 3.732 Chirality : 0.384 1.147 492 Planarity : 0.033 0.184 512 Dihedral : 12.841 84.668 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.97 % Allowed : 5.16 % Favored : 93.87 % Cbeta Deviations : 29.49 % 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: -2.25 (0.40), residues: 386 helix: -2.94 (0.31), residues: 146 sheet: -0.64 (0.54), residues: 82 loop : -0.16 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.117 0.021 ARG B 149 TYR 0.116 0.037 TYR B 195 PHE 0.122 0.038 PHE A 164 TRP 0.107 0.044 TRP A 146 HIS 0.107 0.036 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= 0.2036 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301552 | | target function (ml) not normalized (work): 805736.580353 | | target function (ml) not normalized (free): 16572.935944 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.1984 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.1984 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.1984 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2034 0.2036 0.1984 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1803 0.1801 0.1925 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1799 0.1925 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 0.4063 402.814 293.047 0.434 0.912 0.301 13.296-10.522 99.01 99 1 0.2457 528.187 521.590 0.789 0.913 0.253 10.503-8.327 99.45 178 3 0.2530 565.118 557.057 0.977 0.913 0.230 8.318-6.595 100.00 360 8 0.2465 414.736 403.576 0.979 0.913 0.180 6.588-5.215 100.00 711 7 0.2246 381.101 365.791 0.960 0.913 0.170 5.214-4.128 98.38 1367 28 0.1500 557.435 549.790 1.073 0.913 0.080 4.126-3.266 94.74 2603 46 0.1350 508.132 498.698 1.144 0.914 0.014 3.266-2.585 99.86 5447 97 0.1429 342.774 337.738 1.121 0.913 0.000 2.585-2.046 97.45 10613 204 0.1406 258.603 254.194 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1613 153.054 149.922 1.145 0.911 0.000 1.619-1.281 98.00 42464 925 0.1923 82.395 80.256 1.128 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2318 44.203 41.688 1.113 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0062 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1799 r_free=0.1925 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1800 r_free=0.1928 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.772899 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.876571 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1498 0.0226 0.038 1.1 11.0 0.0 0.3 0 10.886 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 14.98 2.26 1.118 13.108 573.877 0.018 13.01 15.72 2.70 1.254 13.329 573.877 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.04 15.00 1.40 435 3274 Protein: 5.18 40.31 11.01 1.40 0 2902 Water: 6.38 73.04 29.36 N/A 435 370 Other: 16.02 30.61 23.32 N/A 0 2 Chain A: 5.35 59.82 13.04 N/A 0 1626 Chain B: 5.18 73.04 12.77 N/A 0 1648 Chain S: 11.67 64.29 30.75 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.97 2160 11.97 - 18.75 643 18.75 - 25.54 319 25.54 - 32.32 265 32.32 - 39.11 157 39.11 - 45.90 101 45.90 - 52.68 39 52.68 - 59.47 21 59.47 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1572 r_work=0.1301 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1301 r_free = 0.1568 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 = 0.1286 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 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= 0.1286 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015640 | | target function (ls_wunit_k1) not normalized (work): 2929.268369 | | target function (ls_wunit_k1) not normalized (free): 116.233835 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1286 0.1557 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1634 n_refl.: 191139 remove outliers: r(all,work,free)=0.1471 0.1468 0.1634 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1494 0.1492 0.1644 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1547 n_refl.: 191139 remove outliers: r(all,work,free)=0.1283 0.1278 0.1546 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 0.3606 402.814 377.793 0.489 0.963 0.283 13.296-10.522 99.01 99 1 0.2061 528.187 517.871 0.732 0.965 0.236 10.503-8.327 99.45 178 3 0.1771 565.118 562.190 0.888 0.964 0.213 8.318-6.595 100.00 360 8 0.1712 414.736 411.851 0.912 0.964 0.160 6.588-5.215 100.00 711 7 0.1536 381.101 373.585 0.889 0.965 0.160 5.214-4.128 98.38 1367 28 0.0905 557.435 554.985 0.975 0.965 0.049 4.126-3.266 94.74 2603 46 0.0835 508.132 504.318 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0923 342.774 340.349 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.402 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.377 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1285 82.395 81.396 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.151 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1546 | n_water=805 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1282 r_free=0.1550 | n_water=795 | time (s): 105.070 (total time: 108.140) Filter (q & B) r_work=0.1283 r_free=0.1551 | n_water=789 | time (s): 4.100 (total time: 112.240) Compute maps r_work=0.1283 r_free=0.1551 | n_water=789 | time (s): 1.810 (total time: 114.050) Filter (map) r_work=0.1308 r_free=0.1536 | n_water=654 | time (s): 4.130 (total time: 118.180) Find peaks r_work=0.1308 r_free=0.1536 | n_water=654 | time (s): 0.620 (total time: 118.800) Add new water r_work=0.1330 r_free=0.1564 | n_water=951 | time (s): 4.560 (total time: 123.360) Refine new water occ: r_work=0.1289 r_free=0.1521 adp: r_work=0.1276 r_free=0.1517 occ: r_work=0.1279 r_free=0.1516 adp: r_work=0.1272 r_free=0.1514 occ: r_work=0.1273 r_free=0.1514 adp: r_work=0.1271 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1514 r_work=0.1271 r_free=0.1514 | n_water=951 | time (s): 95.060 (total time: 218.420) Filter (q & B) r_work=0.1274 r_free=0.1520 | n_water=885 | time (s): 4.370 (total time: 222.790) Filter (dist only) r_work=0.1275 r_free=0.1520 | n_water=884 | time (s): 112.170 (total time: 334.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.116457 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 597.064190 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 0.1259 0.1541 0.0282 0.041 1.1 16.8 0.0 0.3 0 11.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.59 15.41 2.82 2.043 15.200 597.064 0.015 12.34 15.22 2.88 2.405 15.239 597.064 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.75 16.33 1.21 516 3272 Protein: 5.42 40.19 10.99 1.21 0 2902 Water: 6.63 68.75 33.84 N/A 516 368 Other: 16.26 32.76 24.51 N/A 0 2 Chain A: 5.57 56.01 12.99 N/A 0 1624 Chain B: 5.42 68.53 12.81 N/A 0 1648 Chain S: 13.37 68.75 38.07 N/A 516 0 Histogram: Values Number of atoms 5.42 - 11.76 2073 11.76 - 18.09 699 18.09 - 24.42 263 24.42 - 30.75 219 30.75 - 37.09 176 37.09 - 43.42 162 43.42 - 49.75 96 49.75 - 56.09 53 56.09 - 62.42 31 62.42 - 68.75 16 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1522 r_work=0.1234 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1523 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1522 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1522 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013489 | | target function (ls_wunit_k1) not normalized (work): 2526.524349 | | target function (ls_wunit_k1) not normalized (free): 103.293328 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1227 0.1522 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1612 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1431 0.1612 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1611 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1531 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1234 0.1531 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3222 402.814 379.512 0.492 0.963 0.271 13.296-10.522 99.01 99 1 0.1914 528.187 520.001 0.756 0.964 0.223 10.503-8.327 99.45 178 3 0.1411 565.118 568.214 0.922 0.964 0.188 8.318-6.595 100.00 360 8 0.1576 414.736 412.763 0.936 0.963 0.153 6.588-5.215 100.00 711 7 0.1388 381.101 376.312 0.910 0.963 0.130 5.214-4.128 98.38 1367 28 0.0829 557.435 556.084 0.993 0.963 0.060 4.126-3.266 94.74 2603 46 0.0761 508.132 505.496 1.058 0.963 0.005 3.266-2.585 99.86 5447 97 0.0860 342.774 341.364 1.045 0.962 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.776 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.613 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.345 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.216 1.057 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1531 | n_water=884 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1235 r_free=0.1529 | n_water=880 | time (s): 113.670 (total time: 116.360) Filter (q & B) r_work=0.1236 r_free=0.1529 | n_water=876 | time (s): 5.640 (total time: 122.000) Compute maps r_work=0.1236 r_free=0.1529 | n_water=876 | time (s): 2.020 (total time: 124.020) Filter (map) r_work=0.1278 r_free=0.1528 | n_water=684 | time (s): 5.630 (total time: 129.650) Find peaks r_work=0.1278 r_free=0.1528 | n_water=684 | time (s): 0.920 (total time: 130.570) Add new water r_work=0.1300 r_free=0.1566 | n_water=1024 | time (s): 4.390 (total time: 134.960) Refine new water occ: r_work=0.1253 r_free=0.1522 adp: r_work=0.1253 r_free=0.1523 occ: r_work=0.1249 r_free=0.1520 adp: r_work=0.1249 r_free=0.1521 occ: r_work=0.1246 r_free=0.1518 adp: r_work=0.1245 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1520 r_work=0.1245 r_free=0.1520 | n_water=1024 | time (s): 314.130 (total time: 449.090) Filter (q & B) r_work=0.1250 r_free=0.1519 | n_water=880 | time (s): 4.240 (total time: 453.330) Filter (dist only) r_work=0.1251 r_free=0.1519 | n_water=878 | time (s): 110.830 (total time: 564.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.719533 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.169188 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1439 0.0200 0.035 1.1 7.5 0.0 0.0 0 0.860 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.39 2.00 1.935 14.591 17.169 3.939 12.33 13.99 1.66 2.258 14.488 17.169 3.895 Individual atomic B min max mean iso aniso Overall: 5.51 68.01 15.25 1.07 511 3271 Protein: 5.51 36.37 10.73 1.07 0 2902 Water: 6.70 68.01 30.16 N/A 511 367 Other: 13.90 28.26 21.08 N/A 0 2 Chain A: 5.56 54.98 12.75 N/A 0 1624 Chain B: 5.51 68.01 12.51 N/A 0 1647 Chain S: 13.17 63.10 32.03 N/A 511 0 Histogram: Values Number of atoms 5.51 - 11.76 2138 11.76 - 18.01 681 18.01 - 24.26 299 24.26 - 30.51 247 30.51 - 36.76 168 36.76 - 43.01 141 43.01 - 49.26 68 49.26 - 55.51 26 55.51 - 61.76 12 61.76 - 68.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1399 r_work=0.1233 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1400 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1387 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889089 | | target function (ml) not normalized (work): 728414.754764 | | target function (ml) not normalized (free): 15214.492941 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1387 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1441 0.1440 0.1491 n_refl.: 191138 remove outliers: r(all,work,free)=0.1441 0.1440 0.1491 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1435 0.1434 0.1487 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1381 n_refl.: 191138 remove outliers: r(all,work,free)=0.1226 0.1223 0.1381 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3702 398.008 363.016 0.437 0.946 0.260 13.296-10.522 99.01 99 1 0.2352 528.187 508.543 0.706 0.947 0.209 10.503-8.327 98.35 176 3 0.1948 555.265 558.550 0.890 0.948 0.190 8.318-6.595 100.00 360 8 0.2071 414.736 411.251 0.899 0.947 0.130 6.588-5.215 100.00 711 7 0.1856 381.101 369.976 0.885 0.947 0.120 5.214-4.128 98.38 1367 28 0.1189 557.435 551.822 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1097 508.132 501.038 1.033 0.948 0.015 3.266-2.585 99.86 5447 97 0.1090 342.774 339.050 1.020 0.947 0.005 2.585-2.046 97.45 10613 204 0.0964 258.603 255.799 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.401 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.486 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1684 44.202 42.319 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=-0.1012 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1381 | n_water=878 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1223 r_free=0.1382 | n_water=877 | time (s): 106.610 (total time: 109.200) Filter (q & B) r_work=0.1224 r_free=0.1382 | n_water=867 | time (s): 4.440 (total time: 113.640) Compute maps r_work=0.1224 r_free=0.1382 | n_water=867 | time (s): 2.010 (total time: 115.650) Filter (map) r_work=0.1248 r_free=0.1389 | n_water=716 | time (s): 5.550 (total time: 121.200) Find peaks r_work=0.1248 r_free=0.1389 | n_water=716 | time (s): 0.890 (total time: 122.090) Add new water r_work=0.1262 r_free=0.1402 | n_water=950 | time (s): 5.480 (total time: 127.570) Refine new water occ: r_work=0.1214 r_free=0.1362 adp: r_work=0.1207 r_free=0.1357 occ: r_work=0.1204 r_free=0.1356 adp: r_work=0.1204 r_free=0.1356 occ: r_work=0.1202 r_free=0.1356 adp: r_work=0.1202 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1356 r_work=0.1202 r_free=0.1356 | n_water=950 | time (s): 282.090 (total time: 409.660) Filter (q & B) r_work=0.1207 r_free=0.1357 | n_water=854 | time (s): 5.060 (total time: 414.720) Filter (dist only) r_work=0.1207 r_free=0.1356 | n_water=853 | time (s): 107.730 (total time: 522.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.072501 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1360 0.0154 0.036 1.1 5.8 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.60 1.54 1.832 14.151 15.073 3.871 12.00 13.59 1.59 1.910 14.119 15.073 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.62 14.90 1.00 486 3271 Protein: 5.51 33.42 10.67 1.00 0 2902 Water: 5.92 67.62 29.27 N/A 486 367 Other: 13.94 27.52 20.73 N/A 0 2 Chain A: 5.56 54.05 12.63 N/A 0 1624 Chain B: 5.51 67.62 12.44 N/A 0 1647 Chain S: 5.92 60.67 30.81 N/A 486 0 Histogram: Values Number of atoms 5.51 - 11.72 2119 11.72 - 17.93 732 17.93 - 24.14 295 24.14 - 30.35 228 30.35 - 36.56 162 36.56 - 42.77 131 42.77 - 48.99 60 48.99 - 55.20 21 55.20 - 61.41 8 61.41 - 67.62 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1359 r_work=0.1200 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863752 | | target function (ml) not normalized (work): 723657.474440 | | target function (ml) not normalized (free): 15131.466089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1427 0.1426 0.1471 n_refl.: 191135 remove outliers: r(all,work,free)=0.1427 0.1426 0.1471 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1419 0.1467 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1357 n_refl.: 191135 remove outliers: r(all,work,free)=0.1199 0.1196 0.1357 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 0.3496 361.041 311.242 0.412 0.946 0.239 13.296-10.522 97.03 97 1 0.2421 479.949 450.831 0.702 0.947 0.210 10.503-8.327 97.80 175 3 0.1997 502.107 499.687 0.871 0.948 0.210 8.318-6.595 100.00 360 8 0.2197 375.694 371.079 0.896 0.947 0.130 6.588-5.215 100.00 711 7 0.1903 345.226 335.099 0.885 0.947 0.100 5.214-4.128 98.38 1367 28 0.1193 504.960 499.813 0.976 0.948 0.090 4.126-3.266 94.74 2603 46 0.1123 460.298 453.807 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1086 310.506 307.462 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0934 234.259 231.898 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.646 137.387 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0989 74.639 73.933 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.041 38.384 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1225 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1357 | n_water=853 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1196 r_free=0.1357 | n_water=852 | time (s): 105.250 (total time: 107.970) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=845 | time (s): 4.160 (total time: 112.130) Compute maps r_work=0.1196 r_free=0.1356 | n_water=845 | time (s): 2.210 (total time: 114.340) Filter (map) r_work=0.1216 r_free=0.1358 | n_water=734 | time (s): 4.260 (total time: 118.600) Find peaks r_work=0.1216 r_free=0.1358 | n_water=734 | time (s): 0.560 (total time: 119.160) Add new water r_work=0.1229 r_free=0.1367 | n_water=959 | time (s): 4.160 (total time: 123.320) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1191 r_free=0.1345 occ: r_work=0.1190 r_free=0.1347 adp: r_work=0.1189 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1346 r_work=0.1189 r_free=0.1346 | n_water=959 | time (s): 227.560 (total time: 350.880) Filter (q & B) r_work=0.1193 r_free=0.1346 | n_water=886 | time (s): 4.990 (total time: 355.870) Filter (dist only) r_work=0.1193 r_free=0.1345 | n_water=885 | time (s): 112.080 (total time: 467.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533708 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.418167 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 0.0159 0.037 1.1 8.5 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 1.794 14.144 14.418 3.765 12.01 13.60 1.58 1.880 14.110 14.418 3.763 Individual atomic B min max mean iso aniso Overall: 5.58 67.23 14.95 0.95 519 3270 Protein: 5.58 31.89 10.59 0.95 0 2902 Water: 6.19 67.23 29.24 N/A 519 366 Other: 13.82 26.25 20.03 N/A 0 2 Chain A: 5.58 53.13 12.51 N/A 0 1623 Chain B: 5.58 67.23 12.33 N/A 0 1647 Chain S: 6.19 60.65 30.89 N/A 519 0 Histogram: Values Number of atoms 5.58 - 11.74 2153 11.74 - 17.91 721 17.91 - 24.07 288 24.07 - 30.24 230 30.24 - 36.40 168 36.40 - 42.57 138 42.57 - 48.74 62 48.74 - 54.90 20 54.90 - 61.07 8 61.07 - 67.23 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762347 | | target function (ml) not normalized (work): 704646.130716 | | target function (ml) not normalized (free): 14754.425153 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1400 0.1399 0.1478 n_refl.: 191130 remove outliers: r(all,work,free)=0.1400 0.1399 0.1478 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1393 0.1391 0.1473 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1364 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 0.3557 361.041 332.511 0.428 0.953 0.229 13.296-10.522 96.04 96 1 0.2376 480.622 457.004 0.701 0.954 0.200 10.503-8.327 97.80 175 3 0.2036 502.107 498.839 0.863 0.954 0.200 8.318-6.595 100.00 360 8 0.2141 375.694 371.680 0.886 0.954 0.100 6.588-5.215 100.00 711 7 0.1904 345.226 334.754 0.880 0.954 0.090 5.214-4.128 98.38 1367 28 0.1196 504.960 500.281 0.971 0.954 0.080 4.126-3.266 94.74 2603 46 0.1125 460.298 453.576 1.028 0.955 0.000 3.266-2.585 99.86 5447 97 0.1102 310.506 307.243 1.015 0.954 0.000 2.585-2.046 97.45 10613 204 0.0948 234.259 231.772 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0920 138.646 137.328 1.051 0.953 0.000 1.619-1.281 98.00 42464 925 0.0982 74.639 73.925 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.041 38.381 1.037 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1364 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1364 | n_water=885 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1197 r_free=0.1364 | n_water=885 | time (s): 104.670 (total time: 107.070) Filter (q & B) r_work=0.1197 r_free=0.1364 | n_water=874 | time (s): 5.550 (total time: 112.620) Compute maps r_work=0.1197 r_free=0.1364 | n_water=874 | time (s): 2.010 (total time: 114.630) Filter (map) r_work=0.1218 r_free=0.1370 | n_water=753 | time (s): 4.360 (total time: 118.990) Find peaks r_work=0.1218 r_free=0.1370 | n_water=753 | time (s): 0.690 (total time: 119.680) Add new water r_work=0.1230 r_free=0.1376 | n_water=963 | time (s): 4.290 (total time: 123.970) Refine new water occ: r_work=0.1195 r_free=0.1349 adp: r_work=0.1196 r_free=0.1349 occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1349 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1192 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1348 r_work=0.1192 r_free=0.1348 | n_water=963 | time (s): 224.030 (total time: 348.000) Filter (q & B) r_work=0.1195 r_free=0.1357 | n_water=902 | time (s): 4.870 (total time: 352.870) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=901 | time (s): 112.530 (total time: 465.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.610411 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.996046 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1369 0.0170 0.038 1.1 6.3 0.0 0.3 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.69 1.70 1.757 13.988 14.996 3.763 12.00 13.71 1.71 1.881 13.953 14.996 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 66.23 14.77 0.90 535 3270 Protein: 5.59 29.43 10.49 0.90 0 2902 Water: 6.01 66.23 28.56 N/A 535 366 Other: 13.80 23.60 18.70 N/A 0 2 Chain A: 5.62 50.53 12.37 N/A 0 1623 Chain B: 5.59 66.23 12.21 N/A 0 1647 Chain S: 6.01 60.85 29.94 N/A 535 0 Histogram: Values Number of atoms 5.59 - 11.66 2137 11.66 - 17.72 762 17.72 - 23.79 279 23.79 - 29.85 239 29.85 - 35.91 177 35.91 - 41.98 118 41.98 - 48.04 60 48.04 - 54.11 24 54.11 - 60.17 6 60.17 - 66.23 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1371 r_work=0.1200 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1371 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1374 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758702 | | target function (ml) not normalized (work): 703959.732895 | | target function (ml) not normalized (free): 14755.322739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1375 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1396 0.1394 0.1500 n_refl.: 191129 remove outliers: r(all,work,free)=0.1396 0.1394 0.1500 n_refl.: 191129 overall B=-0.23 to atoms: r(all,work,free)=0.1361 0.1359 0.1477 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1375 n_refl.: 191129 remove outliers: r(all,work,free)=0.1201 0.1198 0.1375 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 0.3621 361.041 333.090 0.437 0.953 0.233 13.296-10.522 96.04 96 1 0.2414 480.622 461.616 0.715 0.954 0.172 10.503-8.327 97.80 175 3 0.2160 502.107 495.517 0.882 0.955 0.143 8.318-6.595 100.00 360 8 0.2150 375.694 371.589 0.907 0.954 0.101 6.588-5.215 100.00 711 7 0.1939 345.226 335.217 0.901 0.954 0.083 5.214-4.128 98.38 1367 28 0.1216 504.960 499.977 0.996 0.955 0.080 4.126-3.266 94.74 2603 46 0.1147 460.298 453.208 1.053 0.955 0.000 3.266-2.585 99.86 5447 97 0.1116 310.506 307.208 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0953 234.259 231.754 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0913 138.646 137.331 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0970 74.639 73.933 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1647 40.041 38.378 1.021 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1375 | n_water=901 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1198 r_free=0.1375 | n_water=900 | time (s): 113.000 (total time: 115.500) Filter (q & B) r_work=0.1199 r_free=0.1376 | n_water=891 | time (s): 5.160 (total time: 120.660) Compute maps r_work=0.1199 r_free=0.1376 | n_water=891 | time (s): 2.220 (total time: 122.880) Filter (map) r_work=0.1218 r_free=0.1378 | n_water=773 | time (s): 5.140 (total time: 128.020) Find peaks r_work=0.1218 r_free=0.1378 | n_water=773 | time (s): 0.600 (total time: 128.620) Add new water r_work=0.1228 r_free=0.1382 | n_water=981 | time (s): 3.860 (total time: 132.480) Refine new water occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1355 occ: r_work=0.1194 r_free=0.1355 adp: r_work=0.1194 r_free=0.1355 occ: r_work=0.1193 r_free=0.1354 adp: r_work=0.1192 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1354 r_work=0.1192 r_free=0.1354 | n_water=981 | time (s): 275.420 (total time: 407.900) Filter (q & B) r_work=0.1197 r_free=0.1365 | n_water=911 | time (s): 4.590 (total time: 412.490) Filter (dist only) r_work=0.1198 r_free=0.1365 | n_water=909 | time (s): 114.840 (total time: 527.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.554623 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1369 0.0169 0.038 1.1 6.0 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.69 1.69 1.720 13.702 14.555 3.760 12.00 13.69 1.69 1.764 13.690 14.555 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 65.04 14.56 0.88 543 3270 Protein: 5.39 28.48 10.24 0.88 0 2902 Water: 5.81 65.04 28.36 N/A 543 366 Other: 13.68 22.25 17.96 N/A 0 2 Chain A: 5.44 49.66 12.08 N/A 0 1623 Chain B: 5.39 65.04 11.94 N/A 0 1647 Chain S: 5.81 60.82 29.92 N/A 543 0 Histogram: Values Number of atoms 5.39 - 11.36 2110 11.36 - 17.32 780 17.32 - 23.29 275 23.29 - 29.25 240 29.25 - 35.22 190 35.22 - 41.18 116 41.18 - 47.15 66 47.15 - 53.11 25 53.11 - 59.08 7 59.08 - 65.04 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1370 r_work=0.1200 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1370 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1372 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757034 | | target function (ml) not normalized (work): 703647.410830 | | target function (ml) not normalized (free): 14740.219575 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1372 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1368 0.1366 0.1479 n_refl.: 191129 remove outliers: r(all,work,free)=0.1368 0.1366 0.1479 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1375 0.1373 0.1484 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1360 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1190 0.1360 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3673 361.041 330.101 0.415 0.974 0.213 13.296-10.522 96.04 96 1 0.2435 480.622 460.415 0.701 0.976 0.156 10.503-8.327 97.80 175 3 0.2155 502.107 494.004 0.868 0.976 0.130 8.318-6.595 100.00 360 8 0.2147 375.694 371.204 0.893 0.976 0.098 6.588-5.215 100.00 711 7 0.1928 345.226 334.756 0.889 0.977 0.080 5.214-4.128 98.38 1367 28 0.1227 504.960 499.406 0.982 0.977 0.070 4.126-3.266 94.74 2603 46 0.1162 460.298 452.534 1.041 0.978 0.000 3.266-2.585 99.86 5447 97 0.1115 310.506 306.932 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0959 234.259 231.647 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0908 138.646 137.258 1.048 0.984 0.000 1.619-1.281 98.00 42464 925 0.0950 74.639 73.971 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.041 38.350 1.001 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0601 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1360 | n_water=909 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1190 r_free=0.1360 | n_water=909 | time (s): 112.170 (total time: 115.360) Filter (q & B) r_work=0.1191 r_free=0.1360 | n_water=904 | time (s): 4.830 (total time: 120.190) Compute maps r_work=0.1191 r_free=0.1360 | n_water=904 | time (s): 2.540 (total time: 122.730) Filter (map) r_work=0.1209 r_free=0.1360 | n_water=792 | time (s): 5.070 (total time: 127.800) Find peaks r_work=0.1209 r_free=0.1360 | n_water=792 | time (s): 0.610 (total time: 128.410) Add new water r_work=0.1217 r_free=0.1368 | n_water=987 | time (s): 5.330 (total time: 133.740) Refine new water occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1337 occ: r_work=0.1185 r_free=0.1335 adp: r_work=0.1185 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1335 r_work=0.1185 r_free=0.1335 | n_water=987 | time (s): 270.550 (total time: 404.290) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=918 | time (s): 5.740 (total time: 410.030) Filter (dist only) r_work=0.1189 r_free=0.1350 | n_water=916 | time (s): 116.640 (total time: 526.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529945 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.336288 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1355 0.0163 0.038 1.1 5.6 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.55 1.63 1.677 13.736 14.336 3.756 11.92 13.57 1.65 1.700 13.729 14.336 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 64.17 14.64 0.87 551 3269 Protein: 5.49 28.16 10.31 0.87 0 2902 Water: 5.91 64.17 28.38 N/A 551 365 Other: 13.74 22.08 17.91 N/A 0 2 Chain A: 5.55 49.39 12.12 N/A 0 1623 Chain B: 5.49 64.17 11.97 N/A 0 1646 Chain S: 5.91 61.10 30.07 N/A 551 0 Histogram: Values Number of atoms 5.49 - 11.36 2077 11.36 - 17.23 810 17.23 - 23.09 281 23.09 - 28.96 226 28.96 - 34.83 189 34.83 - 40.70 121 40.70 - 46.57 73 46.57 - 52.43 32 52.43 - 58.30 7 58.30 - 64.17 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1357 r_work=0.1193 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753460 | | target function (ml) not normalized (work): 702977.951507 | | target function (ml) not normalized (free): 14726.784505 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1356 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1383 0.1381 0.1483 n_refl.: 191129 remove outliers: r(all,work,free)=0.1383 0.1381 0.1483 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1385 0.1383 0.1485 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3724 361.041 329.091 0.430 0.913 0.201 13.296-10.522 96.04 96 1 0.2416 480.622 460.531 0.745 0.914 0.153 10.503-8.327 97.80 175 3 0.2149 502.107 494.823 0.921 0.915 0.130 8.318-6.595 100.00 360 8 0.2164 375.694 371.046 0.952 0.915 0.101 6.588-5.215 100.00 711 7 0.1938 345.226 334.919 0.948 0.915 0.083 5.214-4.128 98.38 1367 28 0.1227 504.960 499.815 1.045 0.916 0.034 4.126-3.266 94.74 2603 46 0.1162 460.298 452.590 1.110 0.917 0.000 3.266-2.585 99.86 5447 97 0.1121 310.506 306.904 1.093 0.918 0.000 2.585-2.046 97.45 10613 204 0.0961 234.259 231.648 1.101 0.920 0.000 2.046-1.619 99.39 21536 464 0.0909 138.646 137.265 1.119 0.923 0.000 1.619-1.281 98.00 42464 925 0.0945 74.639 73.984 1.108 0.928 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.041 38.334 1.074 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0216 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1355 | n_water=916 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1191 r_free=0.1355 | n_water=916 | time (s): 108.340 (total time: 110.880) Filter (q & B) r_work=0.1191 r_free=0.1355 | n_water=908 | time (s): 4.640 (total time: 115.520) Compute maps r_work=0.1191 r_free=0.1355 | n_water=908 | time (s): 1.850 (total time: 117.370) Filter (map) r_work=0.1211 r_free=0.1358 | n_water=796 | time (s): 4.870 (total time: 122.240) Find peaks r_work=0.1211 r_free=0.1358 | n_water=796 | time (s): 0.560 (total time: 122.800) Add new water r_work=0.1218 r_free=0.1365 | n_water=986 | time (s): 5.010 (total time: 127.810) Refine new water occ: r_work=0.1189 r_free=0.1346 adp: r_work=0.1189 r_free=0.1346 occ: r_work=0.1188 r_free=0.1346 adp: r_work=0.1187 r_free=0.1346 occ: r_work=0.1186 r_free=0.1346 adp: r_work=0.1186 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1346 r_work=0.1186 r_free=0.1346 | n_water=986 | time (s): 226.520 (total time: 354.330) Filter (q & B) r_work=0.1190 r_free=0.1356 | n_water=919 | time (s): 5.520 (total time: 359.850) Filter (dist only) r_work=0.1190 r_free=0.1356 | n_water=917 | time (s): 120.780 (total time: 480.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570632 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.443177 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1358 0.0165 0.039 1.1 6.1 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.65 1.678 13.741 14.443 3.755 11.93 13.59 1.66 1.691 13.739 14.443 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 63.13 14.65 0.87 552 3269 Protein: 5.55 27.99 10.33 0.87 0 2902 Water: 6.00 63.13 28.30 N/A 552 365 Other: 13.78 22.13 17.96 N/A 0 2 Chain A: 5.60 49.10 12.11 N/A 0 1623 Chain B: 5.55 63.13 11.97 N/A 0 1646 Chain S: 6.00 61.27 30.08 N/A 552 0 Histogram: Values Number of atoms 5.55 - 11.30 2059 11.30 - 17.06 828 17.06 - 22.82 279 22.82 - 28.58 216 28.58 - 34.34 188 34.34 - 40.10 127 40.10 - 45.86 78 45.86 - 51.61 32 51.61 - 57.37 7 57.37 - 63.13 7 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1359 r_work=0.1193 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1359 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1359 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752949 | | target function (ml) not normalized (work): 702882.301501 | | target function (ml) not normalized (free): 14728.943973 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1495 n_refl.: 191129 remove outliers: r(all,work,free)=0.1393 0.1391 0.1495 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1392 0.1391 0.1495 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1362 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1362 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 0.3692 361.041 330.111 0.412 0.974 0.217 13.296-10.522 96.04 96 1 0.2415 480.622 461.129 0.695 0.976 0.152 10.503-8.327 97.80 175 3 0.2176 502.107 494.944 0.861 0.976 0.118 8.318-6.595 100.00 360 8 0.2176 375.694 370.930 0.889 0.976 0.096 6.588-5.215 100.00 711 7 0.1951 345.226 334.955 0.886 0.977 0.080 5.214-4.128 98.38 1367 28 0.1243 504.960 499.323 0.981 0.978 0.080 4.126-3.266 94.74 2603 46 0.1164 460.298 452.622 1.041 0.979 0.000 3.266-2.585 99.86 5447 97 0.1124 310.506 306.904 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0964 234.259 231.619 1.032 0.982 0.000 2.046-1.619 99.39 21536 464 0.0908 138.646 137.264 1.049 0.986 0.000 1.619-1.281 98.00 42464 925 0.0942 74.639 73.988 1.040 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.041 38.326 1.009 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0084 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1362 After: r_work=0.1192 r_free=0.1362 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1362 | n_water=917 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1192 r_free=0.1362 | n_water=917 | time (s): 112.050 (total time: 115.060) Filter (q & B) r_work=0.1192 r_free=0.1361 | n_water=904 | time (s): 5.400 (total time: 120.460) Compute maps r_work=0.1192 r_free=0.1361 | n_water=904 | time (s): 1.680 (total time: 122.140) Filter (map) r_work=0.1213 r_free=0.1364 | n_water=790 | time (s): 5.010 (total time: 127.150) Find peaks r_work=0.1213 r_free=0.1364 | n_water=790 | time (s): 0.610 (total time: 127.760) Add new water r_work=0.1221 r_free=0.1372 | n_water=985 | time (s): 4.430 (total time: 132.190) Refine new water occ: r_work=0.1189 r_free=0.1350 adp: r_work=0.1190 r_free=0.1349 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1350 occ: r_work=0.1187 r_free=0.1350 adp: r_work=0.1187 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1350 r_work=0.1187 r_free=0.1350 | n_water=985 | time (s): 213.720 (total time: 345.910) Filter (q & B) r_work=0.1190 r_free=0.1359 | n_water=919 | time (s): 4.760 (total time: 350.670) Filter (dist only) r_work=0.1191 r_free=0.1359 | n_water=917 | time (s): 118.460 (total time: 469.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526334 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.506510 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 0.1191 0.1359 0.0168 0.039 1.1 6.8 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.59 1.68 1.676 13.722 14.507 3.754 11.91 13.61 1.70 1.669 13.723 14.507 3.752 Individual atomic B min max mean iso aniso Overall: 5.54 62.72 14.61 0.87 552 3269 Protein: 5.54 28.01 10.35 0.87 0 2902 Water: 6.02 62.72 28.10 N/A 552 365 Other: 13.81 22.13 17.97 N/A 0 2 Chain A: 5.64 48.98 12.11 N/A 0 1623 Chain B: 5.54 62.72 11.97 N/A 0 1646 Chain S: 6.02 61.32 29.88 N/A 552 0 Histogram: Values Number of atoms 5.54 - 11.26 2047 11.26 - 16.98 832 16.98 - 22.69 290 22.69 - 28.41 220 28.41 - 34.13 189 34.13 - 39.85 120 39.85 - 45.57 75 45.57 - 51.28 33 51.28 - 57.00 8 57.00 - 62.72 7 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1361 r_work=0.1191 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1361 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1363 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752118 | | target function (ml) not normalized (work): 702726.675930 | | target function (ml) not normalized (free): 14721.211802 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1361 0.1520 5.6904 5.7698| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1348 5.0795 5.18| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1198 4.6561 4.763| | 4: 2.04 - 1.85 1.00 7170 155 0.0893 0.1022 4.3878 4.5428| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.1008 4.1526 4.2561| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1078 3.9429 4.0712| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0985 3.7959 3.9369| | 8: 1.54 - 1.47 0.96 6798 152 0.0884 0.1313 3.6934 3.8897| | 9: 1.47 - 1.41 0.98 6938 155 0.0919 0.1100 3.6142 3.7408| | 10: 1.41 - 1.36 0.99 7022 150 0.0970 0.1186 3.5502 3.6783| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1116 3.479 3.5734| | 12: 1.32 - 1.28 0.98 6975 149 0.1026 0.1136 3.4536 3.5849| | 13: 1.28 - 1.25 0.98 6907 166 0.1035 0.1221 3.4312 3.5446| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1599 3.4284 3.6828| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1250 3.4466 3.4986| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1565 3.4638 3.6636| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1235 3.4338 3.445| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1693 3.4383 3.5326| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1729 3.4181 3.5911| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1571 3.4089 3.4292| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2115 3.4175 3.4999| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1953 3.4128 3.4148| | 23: 1.05 - 1.03 0.97 6827 159 0.2115 0.2025 3.4327 3.4841| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2249 3.4355 3.5078| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2513 3.4487 3.5258| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2861 3.4159 3.4247| | 27: 0.99 - 0.98 0.94 6647 131 0.3037 0.2795 3.4684 3.3939| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.80 1.00 0.95 11322.00| | 2: 2.94 - 2.33 7339 128 0.93 12.88 0.99 0.95 5176.08| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.95 1709.64| | 4: 2.04 - 1.85 7170 155 0.96 7.58 1.00 0.95 997.14| | 5: 1.85 - 1.72 7113 159 0.96 8.12 1.00 0.96 637.51| | 6: 1.72 - 1.62 7102 142 0.96 8.00 1.00 0.96 442.55| | 7: 1.62 - 1.54 7104 148 0.96 8.11 1.01 0.97 336.01| | 8: 1.54 - 1.47 6798 152 0.96 8.21 1.01 0.97 276.54| | 9: 1.47 - 1.41 6938 155 0.96 8.37 1.00 0.98 227.85| | 10: 1.41 - 1.36 7022 150 0.96 8.82 1.00 0.97 199.74| | 11: 1.36 - 1.32 6997 151 0.96 8.84 0.99 0.96 172.25| | 12: 1.32 - 1.28 6975 149 0.96 8.88 0.98 0.95 158.62| | 13: 1.28 - 1.25 6907 166 0.96 9.43 1.01 0.96 156.03| | 14: 1.25 - 1.22 7015 112 0.95 10.61 1.01 0.96 161.45| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 166.21| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.96 160.60| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.96 154.49| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.25| | 19: 1.12 - 1.10 6948 106 0.93 14.08 1.00 0.95 150.07| | 20: 1.10 - 1.08 6884 147 0.92 15.12 1.00 0.94 148.90| | 21: 1.08 - 1.07 6852 152 0.91 16.55 1.00 0.93 152.06| | 22: 1.07 - 1.05 6836 135 0.89 18.21 0.99 0.93 154.01| | 23: 1.05 - 1.03 6827 159 0.87 20.43 0.99 0.92 164.18| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.93 178.73| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.98 0.90 181.85| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.88 176.14| | 27: 0.99 - 0.98 6647 131 0.82 26.18 0.99 0.87 160.24| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.25 max = 11322.00 mean = 931.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.25| |phase err.(test): min = 0.00 max = 88.32 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1363 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1399 0.1398 0.1501 n_refl.: 191129 remove outliers: r(all,work,free)=0.1399 0.1398 0.1501 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1391 0.1390 0.1496 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1359 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 0.3677 361.041 328.879 0.397 0.974 0.212 13.296-10.522 96.04 96 1 0.2422 480.622 461.133 0.674 0.976 0.145 10.503-8.327 97.80 175 3 0.2167 502.107 494.223 0.839 0.976 0.098 8.318-6.595 100.00 360 8 0.2160 375.694 371.172 0.866 0.976 0.080 6.588-5.215 100.00 711 7 0.1963 345.226 334.835 0.865 0.977 0.080 5.214-4.128 98.38 1367 28 0.1249 504.960 499.420 0.955 0.978 0.034 4.126-3.266 94.74 2603 46 0.1164 460.298 452.581 1.016 0.979 0.000 3.266-2.585 99.86 5447 97 0.1121 310.506 306.919 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0963 234.259 231.637 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.646 137.266 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0939 74.639 73.990 1.010 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.041 38.322 0.977 1.009 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0118 ================= 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 : 0.2036 0.1984 0.083 5.221 5.2 78.0 14.6 805 0.000 1_bss: 0.1799 0.1925 0.083 5.221 5.2 78.0 14.6 805 0.000 1_settarget: 0.1799 0.1925 0.083 5.221 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1928 0.083 5.221 5.2 78.0 14.6 805 0.002 1_weight: 0.1800 0.1928 0.083 5.221 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1498 0.038 1.149 5.2 78.0 14.6 805 0.156 1_adp: 0.1301 0.1572 0.038 1.149 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1301 0.1568 0.038 1.149 5.2 73.0 15.0 805 0.156 1_occ: 0.1286 0.1557 0.038 1.149 5.2 73.0 15.0 805 0.156 2_bss: 0.1278 0.1546 0.038 1.149 5.3 73.2 15.2 805 0.156 2_settarget: 0.1278 0.1546 0.038 1.149 5.3 73.2 15.2 805 0.156 2_updatecdl: 0.1278 0.1546 0.038 1.154 5.3 73.2 15.2 805 0.156 2_nqh: 0.1278 0.1546 0.038 1.154 5.3 73.2 15.2 805 0.156 2_sol: 0.1275 0.1520 0.038 1.154 5.3 73.2 16.3 884 n/a 2_weight: 0.1275 0.1520 0.038 1.154 5.3 73.2 16.3 884 n/a 2_xyzrec: 0.1259 0.1541 0.041 1.124 5.3 73.2 16.3 884 n/a 2_adp: 0.1234 0.1522 0.041 1.124 5.4 68.8 16.3 884 n/a 2_regHadp: 0.1234 0.1523 0.041 1.124 5.4 68.8 16.3 884 n/a 2_occ: 0.1227 0.1522 0.041 1.124 5.4 68.8 16.3 884 n/a 3_bss: 0.1235 0.1531 0.041 1.124 5.4 68.7 16.3 884 n/a 3_settarget: 0.1235 0.1531 0.041 1.124 5.4 68.7 16.3 884 n/a 3_updatecdl: 0.1235 0.1531 0.041 1.123 5.4 68.7 16.3 884 n/a 3_nqh: 0.1235 0.1531 0.041 1.123 5.4 68.7 16.3 884 n/a 3_sol: 0.1251 0.1519 0.041 1.123 5.4 68.5 15.4 878 n/a 3_weight: 0.1251 0.1519 0.041 1.123 5.4 68.5 15.4 878 n/a 3_xyzrec: 0.1238 0.1439 0.035 1.106 5.4 68.5 15.4 878 n/a 3_adp: 0.1233 0.1399 0.035 1.106 5.5 68.0 15.2 878 n/a 3_regHadp: 0.1233 0.1400 0.035 1.106 5.5 68.0 15.2 878 n/a 3_occ: 0.1228 0.1387 0.035 1.106 5.5 68.0 15.2 878 n/a 4_bss: 0.1223 0.1381 0.035 1.106 5.5 68.0 15.2 878 n/a 4_settarget: 0.1223 0.1381 0.035 1.106 5.5 68.0 15.2 878 n/a 4_updatecdl: 0.1223 0.1381 0.035 1.106 5.5 68.0 15.2 878 n/a 4_nqh: 0.1223 0.1381 0.035 1.106 5.5 68.0 15.2 878 n/a 4_sol: 0.1207 0.1356 0.035 1.106 5.5 68.0 15.0 853 n/a 4_weight: 0.1207 0.1356 0.035 1.106 5.5 68.0 15.0 853 n/a 4_xyzrec: 0.1205 0.1360 0.036 1.118 5.5 68.0 15.0 853 n/a 4_adp: 0.1200 0.1359 0.036 1.118 5.5 67.6 14.9 853 n/a 4_regHadp: 0.1200 0.1360 0.036 1.118 5.5 67.6 14.9 853 n/a 4_occ: 0.1199 0.1358 0.036 1.118 5.5 67.6 14.9 853 n/a 5_bss: 0.1196 0.1357 0.036 1.118 5.5 67.6 14.9 853 n/a 5_settarget: 0.1196 0.1357 0.036 1.118 5.5 67.6 14.9 853 n/a 5_updatecdl: 0.1196 0.1357 0.036 1.118 5.5 67.6 14.9 853 n/a 5_nqh: 0.1196 0.1357 0.036 1.118 5.5 67.6 14.9 853 n/a 5_sol: 0.1193 0.1345 0.036 1.118 5.5 67.6 15.0 885 n/a 5_weight: 0.1193 0.1345 0.036 1.118 5.5 67.6 15.0 885 n/a 5_xyzrec: 0.1196 0.1355 0.037 1.118 5.5 67.6 15.0 885 n/a 5_adp: 0.1201 0.1360 0.037 1.118 5.6 67.2 14.9 885 n/a 5_regHadp: 0.1201 0.1360 0.037 1.118 5.6 67.2 14.9 885 n/a 5_occ: 0.1199 0.1366 0.037 1.118 5.6 67.2 14.9 885 n/a 6_bss: 0.1197 0.1364 0.037 1.118 5.5 67.2 14.9 885 n/a 6_settarget: 0.1197 0.1364 0.037 1.118 5.5 67.2 14.9 885 n/a 6_updatecdl: 0.1197 0.1364 0.037 1.118 5.5 67.2 14.9 885 n/a 6_nqh: 0.1197 0.1364 0.037 1.118 5.5 67.2 14.9 885 n/a 6_sol: 0.1196 0.1356 0.037 1.118 5.5 67.2 14.8 901 n/a 6_weight: 0.1196 0.1356 0.037 1.118 5.5 67.2 14.8 901 n/a 6_xyzrec: 0.1199 0.1369 0.038 1.130 5.5 67.2 14.8 901 n/a 6_adp: 0.1200 0.1371 0.038 1.130 5.6 66.2 14.8 901 n/a 6_regHadp: 0.1200 0.1371 0.038 1.130 5.6 66.2 14.8 901 n/a 6_occ: 0.1199 0.1374 0.038 1.130 5.6 66.2 14.8 901 n/a 7_bss: 0.1198 0.1375 0.038 1.130 5.4 66.0 14.5 901 n/a 7_settarget: 0.1198 0.1375 0.038 1.130 5.4 66.0 14.5 901 n/a 7_updatecdl: 0.1198 0.1375 0.038 1.130 5.4 66.0 14.5 901 n/a 7_nqh: 0.1198 0.1375 0.038 1.130 5.4 66.0 14.5 901 n/a 7_sol: 0.1198 0.1365 0.038 1.130 5.4 66.0 14.6 909 n/a 7_weight: 0.1198 0.1365 0.038 1.130 5.4 66.0 14.6 909 n/a 7_xyzrec: 0.1199 0.1369 0.038 1.143 5.4 66.0 14.6 909 n/a 7_adp: 0.1200 0.1370 0.038 1.143 5.4 65.0 14.6 909 n/a 7_regHadp: 0.1200 0.1370 0.038 1.143 5.4 65.0 14.6 909 n/a 7_occ: 0.1199 0.1372 0.038 1.143 5.4 65.0 14.6 909 n/a 8_bss: 0.1190 0.1360 0.038 1.143 5.5 65.1 14.6 909 n/a 8_settarget: 0.1190 0.1360 0.038 1.143 5.5 65.1 14.6 909 n/a 8_updatecdl: 0.1190 0.1360 0.038 1.142 5.5 65.1 14.6 909 n/a 8_nqh: 0.1190 0.1360 0.038 1.142 5.5 65.1 14.6 909 n/a 8_sol: 0.1189 0.1350 0.038 1.142 5.5 65.1 14.7 916 n/a 8_weight: 0.1189 0.1350 0.038 1.142 5.5 65.1 14.7 916 n/a 8_xyzrec: 0.1192 0.1355 0.038 1.123 5.5 65.1 14.7 916 n/a 8_adp: 0.1193 0.1357 0.038 1.123 5.5 64.2 14.6 916 n/a 8_regHadp: 0.1193 0.1357 0.038 1.123 5.5 64.2 14.6 916 n/a 8_occ: 0.1191 0.1356 0.038 1.123 5.5 64.2 14.6 916 n/a 9_bss: 0.1190 0.1353 0.038 1.123 5.5 64.2 14.7 916 n/a 9_settarget: 0.1190 0.1353 0.038 1.123 5.5 64.2 14.7 916 n/a 9_updatecdl: 0.1190 0.1353 0.038 1.124 5.5 64.2 14.7 916 n/a 9_nqh: 0.1191 0.1355 0.038 1.124 5.5 64.2 14.7 916 n/a 9_sol: 0.1190 0.1356 0.038 1.124 5.5 64.2 14.6 917 n/a 9_weight: 0.1190 0.1356 0.038 1.124 5.5 64.2 14.6 917 n/a 9_xyzrec: 0.1193 0.1358 0.039 1.126 5.5 64.2 14.6 917 n/a 9_adp: 0.1193 0.1359 0.039 1.126 5.5 63.1 14.6 917 n/a 9_regHadp: 0.1193 0.1359 0.039 1.126 5.5 63.1 14.6 917 n/a 9_occ: 0.1192 0.1359 0.039 1.126 5.5 63.1 14.6 917 n/a 10_bss: 0.1191 0.1362 0.039 1.126 5.5 63.1 14.6 917 n/a 10_settarget: 0.1191 0.1362 0.039 1.126 5.5 63.1 14.6 917 n/a 10_updatecdl: 0.1191 0.1362 0.039 1.126 5.5 63.1 14.6 917 n/a 10_setrh: 0.1192 0.1362 0.039 1.126 5.5 63.1 14.6 917 n/a 10_nqh: 0.1192 0.1362 0.039 1.126 5.5 63.1 14.6 917 n/a 10_sol: 0.1191 0.1359 0.039 1.126 5.5 63.1 14.6 917 n/a 10_weight: 0.1191 0.1359 0.039 1.126 5.5 63.1 14.6 917 n/a 10_xyzrec: 0.1191 0.1359 0.039 1.129 5.5 63.1 14.6 917 n/a 10_adp: 0.1191 0.1361 0.039 1.129 5.5 62.7 14.6 917 n/a 10_regHadp: 0.1191 0.1361 0.039 1.129 5.5 62.7 14.6 917 n/a 10_occ: 0.1191 0.1363 0.039 1.129 5.5 62.7 14.6 917 n/a end: 0.1190 0.1359 0.039 1.129 5.5 62.7 14.6 917 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4437829_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4437829_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3600 Refinement macro-cycles (run) : 12106.3500 Write final files (write_after_run_outputs) : 159.3600 Total : 12273.0700 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:46 PST -0800 (1736736106.88 s) Start R-work = 0.1799, R-free = 0.1925 Final R-work = 0.1190, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12549.03 seconds wall clock time: 210 minutes 10.15 seconds (12610.15 seconds total)