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_8081060.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8081060.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8081060.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" 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 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.24, per 1000 atoms: 0.33 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: 2.762 distance_ideal: 2.720 ideal - model: -0.042 slack: 0.000 delta_slack: -0.042 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: 2.608 distance_ideal: 2.710 ideal - model: 0.102 slack: 0.000 delta_slack: 0.102 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 209.6 milliseconds Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 1.00: 511 1.00 - 1.24: 2705 1.24 - 1.48: 1573 1.48 - 1.73: 1124 1.73 - 1.97: 21 Bond restraints: 5934 Sorted by residual: bond pdb=" CE1 HIS A 96 " pdb=" NE2 HIS A 96 " ideal model delta sigma weight residual 1.321 1.531 -0.210 1.00e-02 1.00e+04 4.40e+02 bond pdb=" C ASP A 68 " pdb=" N VAL A 69 " ideal model delta sigma weight residual 1.330 1.572 -0.242 1.21e-02 6.83e+03 4.00e+02 bond pdb=" N THR B 129 " pdb=" H THR B 129 " ideal model delta sigma weight residual 0.860 1.240 -0.380 2.00e-02 2.50e+03 3.61e+02 bond pdb=" C GLU A 17 " pdb=" O GLU A 17 " ideal model delta sigma weight residual 1.237 1.460 -0.224 1.19e-02 7.06e+03 3.53e+02 bond pdb=" ND2 ASN B 42 " pdb="HD22 ASN B 42 " ideal model delta sigma weight residual 0.860 1.234 -0.374 2.00e-02 2.50e+03 3.49e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 5627 4.08 - 8.16: 3474 8.16 - 12.24: 1352 12.24 - 16.32: 333 16.32 - 20.41: 24 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 83 " pdb=" CZ ARG B 83 " pdb=" NH2 ARG B 83 " ideal model delta sigma weight residual 119.20 134.89 -15.69 9.00e-01 1.23e+00 3.04e+02 angle pdb=" O VAL B 89 " pdb=" C VAL B 89 " pdb=" N GLU B 90 " ideal model delta sigma weight residual 121.94 138.54 -16.60 1.00e+00 1.00e+00 2.76e+02 angle pdb=" O VAL B 32 " pdb=" C VAL B 32 " pdb=" N THR B 33 " ideal model delta sigma weight residual 123.20 139.00 -15.80 1.06e+00 8.90e-01 2.22e+02 angle pdb=" O PHE B 82 " pdb=" C PHE B 82 " pdb=" N ARG B 83 " ideal model delta sigma weight residual 122.07 136.71 -14.64 1.03e+00 9.43e-01 2.02e+02 angle pdb=" CA LEU A 113 " pdb=" C LEU A 113 " pdb=" O LEU A 113 " ideal model delta sigma weight residual 120.24 104.68 15.56 1.11e+00 8.12e-01 1.97e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 1838 17.08 - 34.15: 144 34.15 - 51.23: 44 51.23 - 68.30: 20 68.30 - 85.37: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 234 0.231 - 0.462: 138 0.462 - 0.692: 87 0.692 - 0.922: 28 0.922 - 1.152: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 60 " pdb=" N VAL B 60 " pdb=" C VAL B 60 " pdb=" CB VAL B 60 " both_signs ideal model delta sigma weight residual False 2.44 3.59 -1.15 2.00e-01 2.50e+01 3.32e+01 chirality pdb=" CA THR A 91 " pdb=" N THR A 91 " pdb=" C THR A 91 " pdb=" CB THR A 91 " both_signs ideal model delta sigma weight residual False 2.53 3.56 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CG LEU B 59 " pdb=" CB LEU B 59 " pdb=" CD1 LEU B 59 " pdb=" CD2 LEU B 59 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.160 2.00e-02 2.50e+03 7.41e-02 1.65e+02 pdb=" CG PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.108 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.076 2.00e-02 2.50e+03 6.41e-02 1.64e+02 pdb=" CG TRP A 139 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.077 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.066 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.056 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.073 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.137 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.026 2.00e-02 2.50e+03 6.83e-02 1.40e+02 pdb=" CG PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.100 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " 0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.057 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.126 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 23 1.61 - 2.36: 2359 2.36 - 3.10: 22177 3.10 - 3.85: 33064 3.85 - 4.60: 52736 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110359 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.859 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.968 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.974 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.108 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.164 2.620 ... (remaining 110354 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_8081060_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.1967 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301952 | | target function (ml) not normalized (work): 805811.519499 | | target function (ml) not normalized (free): 16508.988115 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2140 0.2021 6.6639 6.3401| | 2: 2.94 - 2.33 1.00 7339 128 0.1604 0.1545 5.5489 5.5899| | 3: 2.33 - 2.04 0.96 6939 150 0.1638 0.1598 5.1409 5.1374| | 4: 2.04 - 1.85 1.00 7170 155 0.1754 0.1619 4.9674 5.0279| | 5: 1.85 - 1.72 0.99 7113 159 0.1949 0.1607 4.8005 4.7828| | 6: 1.72 - 1.62 0.99 7102 142 0.2002 0.1911 4.668 4.7118| | 7: 1.62 - 1.54 0.99 7104 148 0.2015 0.1809 4.5587 4.5746| | 8: 1.54 - 1.47 0.96 6798 152 0.2035 0.2046 4.4637 4.4832| | 9: 1.47 - 1.41 0.98 6938 155 0.2106 0.2210 4.3952 4.4988| | 10: 1.41 - 1.36 0.99 7022 150 0.2148 0.2139 4.3231 4.3312| | 11: 1.36 - 1.32 0.99 6997 151 0.2117 0.1913 4.2424 4.184| | 12: 1.32 - 1.28 0.98 6976 149 0.2092 0.2107 4.1804 4.2882| | 13: 1.28 - 1.25 0.98 6907 166 0.2019 0.1993 4.1178 4.106| | 14: 1.25 - 1.22 0.98 7015 113 0.2089 0.2279 4.0775 4.2275| | 15: 1.22 - 1.19 0.98 6957 137 0.2097 0.1990 4.0416 4.0164| | 16: 1.19 - 1.17 0.93 6604 132 0.2125 0.2351 4.0149 4.1016| | 17: 1.17 - 1.14 0.98 6941 135 0.2188 0.2029 3.9632 4.0254| | 18: 1.14 - 1.12 0.98 6875 142 0.2173 0.2274 3.9173 3.9196| | 19: 1.12 - 1.10 0.97 6949 106 0.2277 0.2416 3.8724 4.0079| | 20: 1.10 - 1.08 0.97 6884 147 0.2339 0.2059 3.8268 3.7825| | 21: 1.08 - 1.07 0.97 6852 152 0.2471 0.2655 3.8016 3.7835| | 22: 1.07 - 1.05 0.97 6838 135 0.2585 0.2510 3.7574 3.6816| | 23: 1.05 - 1.03 0.97 6829 159 0.2748 0.2549 3.7443 3.7642| | 24: 1.03 - 1.02 0.96 6785 133 0.2902 0.2822 3.7106 3.7914| | 25: 1.02 - 1.01 0.93 6552 130 0.3075 0.3091 3.6747 3.7153| | 26: 1.01 - 0.99 0.96 6767 158 0.3202 0.3214 3.6267 3.6309| | 27: 0.99 - 0.98 0.94 6648 131 0.3459 0.3319 3.6412 3.5819| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 21.10 0.91 0.97 37347.74| | 2: 2.94 - 2.33 7339 128 0.85 21.65 1.08 1.02 15654.36| | 3: 2.33 - 2.04 6939 150 0.93 12.41 1.11 1.05 4052.48| | 4: 2.04 - 1.85 7170 155 0.93 13.22 1.11 1.06 2667.07| | 5: 1.85 - 1.72 7113 159 0.91 15.39 1.12 1.07 1994.29| | 6: 1.72 - 1.62 7102 142 0.90 16.55 1.11 1.07 1579.82| | 7: 1.62 - 1.54 7104 148 0.89 17.49 1.11 1.07 1328.47| | 8: 1.54 - 1.47 6798 152 0.89 18.47 1.10 1.06 1150.78| | 9: 1.47 - 1.41 6938 155 0.88 19.07 1.10 1.06 987.32| | 10: 1.41 - 1.36 7022 150 0.88 19.47 1.09 1.06 828.05| | 11: 1.36 - 1.32 6997 151 0.88 19.16 1.09 1.06 689.44| | 12: 1.32 - 1.28 6976 149 0.88 19.11 1.08 1.06 611.00| | 13: 1.28 - 1.25 6907 166 0.88 18.94 1.07 1.05 564.37| | 14: 1.25 - 1.22 7015 113 0.87 20.09 1.08 1.05 551.27| | 15: 1.22 - 1.19 6957 137 0.87 20.70 1.08 1.04 533.69| | 16: 1.19 - 1.17 6604 132 0.87 21.00 1.07 1.03 510.75| | 17: 1.17 - 1.14 6941 135 0.85 22.01 1.08 1.00 467.15| | 18: 1.14 - 1.12 6875 142 0.86 21.61 1.07 0.98 411.09| | 19: 1.12 - 1.10 6949 106 0.86 21.95 1.07 0.98 368.23| | 20: 1.10 - 1.08 6884 147 0.86 21.82 1.07 0.98 321.06| | 21: 1.08 - 1.07 6852 152 0.85 22.75 1.07 0.97 303.19| | 22: 1.07 - 1.05 6838 135 0.83 24.53 1.06 0.96 298.88| | 23: 1.05 - 1.03 6829 159 0.81 27.05 1.05 0.96 315.85| | 24: 1.03 - 1.02 6785 133 0.78 29.38 1.05 0.96 325.14| | 25: 1.02 - 1.01 6552 130 0.76 31.01 1.03 0.93 313.80| | 26: 1.01 - 0.99 6767 158 0.75 32.47 1.03 0.91 295.40| | 27: 0.99 - 0.98 6648 131 0.75 32.68 1.03 0.90 279.09| |alpha: min = 0.90 max = 1.07 mean = 1.01| |beta: min = 279.09 max = 37347.74 mean = 2901.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.44| |phase err.(test): min = 0.00 max = 89.52 mean = 21.44| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.254 2950 Z= 5.447 Angle : 5.270 16.599 4018 Z= 3.779 Chirality : 0.377 1.152 492 Planarity : 0.032 0.109 512 Dihedral : 12.856 85.373 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.07 % Favored : 97.15 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.84 % Cbeta Deviations : 30.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.38), residues: 386 helix: -2.47 (0.32), residues: 144 sheet: -1.43 (0.50), residues: 82 loop : -0.24 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.014 ARG A 149 TYR 0.096 0.036 TYR B 195 PHE 0.115 0.039 PHE A 164 TRP 0.108 0.037 TRP B 146 HIS 0.091 0.028 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.1967 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301952 | | target function (ml) not normalized (work): 805811.519499 | | target function (ml) not normalized (free): 16508.988115 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2037 0.2039 0.1967 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2037 0.2039 0.1967 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2039 0.1967 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2034 0.2036 0.1966 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1898 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1804 0.1898 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 0.4101 402.814 290.245 0.432 0.913 0.303 13.296-10.522 99.01 99 1 0.2466 528.187 519.427 0.785 0.914 0.258 10.503-8.327 99.45 178 3 0.2524 565.118 555.849 0.962 0.914 0.237 8.318-6.595 100.00 360 8 0.2466 414.736 403.579 0.972 0.914 0.175 6.588-5.215 100.00 711 7 0.2289 381.101 365.687 0.947 0.915 0.160 5.214-4.128 98.38 1367 28 0.1491 557.435 549.977 1.065 0.916 0.070 4.126-3.266 94.74 2603 46 0.1354 508.132 497.756 1.133 0.917 0.014 3.266-2.585 99.86 5447 97 0.1452 342.774 337.363 1.104 0.918 0.000 2.585-2.046 97.45 10613 204 0.1382 258.603 254.287 1.111 0.920 0.000 2.046-1.619 99.39 21536 464 0.1628 153.054 149.858 1.122 0.923 0.000 1.619-1.281 98.00 42464 925 0.1927 82.395 80.470 1.102 0.928 0.000 1.281-0.980 96.53 101826 2056 0.2328 44.203 41.981 1.076 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0565 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1898 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 r_work=0.1805 r_free=0.1900 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.836141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 563.998397 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1501 0.0231 0.038 1.2 11.0 0.0 0.3 0 11.418 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.01 2.31 1.118 13.090 563.998 0.018 12.89 15.60 2.71 1.188 13.305 563.998 0.017 Individual atomic B min max mean iso aniso Overall: 5.27 73.02 14.97 1.39 435 3274 Protein: 5.27 40.66 11.00 1.39 0 2902 Water: 6.31 73.02 29.25 N/A 435 370 Other: 15.89 29.66 22.78 N/A 0 2 Chain A: 5.38 60.21 13.02 N/A 0 1626 Chain B: 5.27 73.02 12.75 N/A 0 1648 Chain S: 12.27 63.71 30.63 N/A 435 0 Histogram: Values Number of atoms 5.27 - 12.05 2178 12.05 - 18.82 634 18.82 - 25.60 326 25.60 - 32.37 259 32.37 - 39.15 149 39.15 - 45.92 103 45.92 - 52.70 36 52.70 - 59.47 19 59.47 - 66.25 4 66.25 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1289 r_free=0.1560 r_work=0.1288 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1288 r_free = 0.1555 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 = 0.1273 r_free = 0.1544 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= 0.1273 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015508 | | target function (ls_wunit_k1) not normalized (work): 2904.690463 | | target function (ls_wunit_k1) not normalized (free): 116.763184 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1278 0.1273 0.1544 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1461 0.1458 0.1620 n_refl.: 191139 remove outliers: r(all,work,free)=0.1461 0.1458 0.1620 n_refl.: 191139 overall B=0.14 to atoms: r(all,work,free)=0.1482 0.1479 0.1630 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1269 0.1263 0.1535 n_refl.: 191139 remove outliers: r(all,work,free)=0.1269 0.1263 0.1534 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 0.3615 402.814 378.486 0.470 1.002 0.281 13.296-10.522 99.01 99 1 0.2115 528.187 522.074 0.715 1.004 0.255 10.503-8.327 99.45 178 3 0.1762 565.118 560.895 0.851 1.004 0.203 8.318-6.595 100.00 360 8 0.1709 414.736 412.076 0.875 1.004 0.155 6.588-5.215 100.00 711 7 0.1541 381.101 373.560 0.851 1.004 0.150 5.214-4.128 98.38 1367 28 0.0907 557.435 554.977 0.937 1.004 0.049 4.126-3.266 94.74 2603 46 0.0834 508.132 504.271 1.001 1.005 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.374 0.983 1.005 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.337 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1074 153.054 151.399 1.012 1.006 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.441 1.005 1.007 0.000 1.281-0.980 96.53 101826 2055 0.1855 44.202 42.158 0.982 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0318 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1263 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 r_work=0.1265 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1265 r_free=0.1536 | n_water=805 | time (s): 2.930 (total time: 2.930) Filter (dist) r_work=0.1269 r_free=0.1540 | n_water=795 | time (s): 102.160 (total time: 105.090) Filter (q & B) r_work=0.1269 r_free=0.1541 | n_water=791 | time (s): 5.540 (total time: 110.630) Compute maps r_work=0.1269 r_free=0.1541 | n_water=791 | time (s): 2.650 (total time: 113.280) Filter (map) r_work=0.1295 r_free=0.1526 | n_water=659 | time (s): 5.350 (total time: 118.630) Find peaks r_work=0.1295 r_free=0.1526 | n_water=659 | time (s): 0.590 (total time: 119.220) Add new water r_work=0.1317 r_free=0.1546 | n_water=963 | time (s): 4.550 (total time: 123.770) Refine new water occ: r_work=0.1273 r_free=0.1508 adp: r_work=0.1261 r_free=0.1503 occ: r_work=0.1263 r_free=0.1504 adp: r_work=0.1257 r_free=0.1502 occ: r_work=0.1258 r_free=0.1501 adp: r_work=0.1255 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1255 r_free=0.1501 r_work=0.1255 r_free=0.1501 | n_water=963 | time (s): 84.000 (total time: 207.770) Filter (q & B) r_work=0.1260 r_free=0.1505 | n_water=890 | time (s): 5.060 (total time: 212.830) Filter (dist only) r_work=0.1260 r_free=0.1503 | n_water=888 | time (s): 119.890 (total time: 332.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.350318 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.801396 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 0.1246 0.1515 0.0270 0.040 1.1 18.4 0.0 0.3 0 11.175 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.46 15.15 2.70 2.033 15.173 592.801 0.014 12.31 15.12 2.81 2.384 15.233 592.801 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.16 16.35 1.20 520 3272 Protein: 5.42 39.97 10.98 1.20 0 2902 Water: 6.55 68.16 33.89 N/A 520 368 Other: 16.29 32.34 24.31 N/A 0 2 Chain A: 5.56 56.80 12.97 N/A 0 1624 Chain B: 5.42 68.16 12.80 N/A 0 1648 Chain S: 9.61 67.73 38.15 N/A 520 0 Histogram: Values Number of atoms 5.42 - 11.70 2063 11.70 - 17.97 709 17.97 - 24.24 266 24.24 - 30.52 219 30.52 - 36.79 166 36.79 - 43.07 161 43.07 - 49.34 101 49.34 - 55.61 51 55.61 - 61.89 41 61.89 - 68.16 15 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1512 r_work=0.1232 r_free=0.1513 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1513 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 = 0.1225 r_free = 0.1510 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013419 | | target function (ls_wunit_k1) not normalized (work): 2513.380225 | | target function (ls_wunit_k1) not normalized (free): 100.503012 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1225 0.1510 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1438 0.1434 0.1615 n_refl.: 191138 remove outliers: r(all,work,free)=0.1438 0.1434 0.1615 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1612 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1516 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1516 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 0.3133 402.814 381.119 0.496 0.962 0.275 13.296-10.522 99.01 99 1 0.1888 528.187 516.618 0.756 0.963 0.212 10.503-8.327 99.45 178 3 0.1427 565.118 566.852 0.921 0.963 0.164 8.318-6.595 100.00 360 8 0.1507 414.736 414.539 0.938 0.963 0.150 6.588-5.215 100.00 711 7 0.1339 381.101 377.063 0.913 0.963 0.150 5.214-4.128 98.38 1367 28 0.0823 557.435 555.993 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0757 508.132 505.445 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0858 342.774 341.343 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.780 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.624 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.351 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.216 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0607 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1516 | n_water=888 | time (s): 3.340 (total time: 3.340) Filter (dist) r_work=0.1233 r_free=0.1516 | n_water=884 | time (s): 114.150 (total time: 117.490) Filter (q & B) r_work=0.1234 r_free=0.1517 | n_water=881 | time (s): 5.680 (total time: 123.170) Compute maps r_work=0.1234 r_free=0.1517 | n_water=881 | time (s): 1.870 (total time: 125.040) Filter (map) r_work=0.1273 r_free=0.1521 | n_water=695 | time (s): 5.240 (total time: 130.280) Find peaks r_work=0.1273 r_free=0.1521 | n_water=695 | time (s): 0.740 (total time: 131.020) Add new water r_work=0.1296 r_free=0.1553 | n_water=1001 | time (s): 4.150 (total time: 135.170) Refine new water occ: r_work=0.1251 r_free=0.1517 adp: r_work=0.1252 r_free=0.1517 occ: r_work=0.1248 r_free=0.1514 adp: r_work=0.1248 r_free=0.1515 occ: r_work=0.1245 r_free=0.1511 adp: r_work=0.1244 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1511 r_work=0.1244 r_free=0.1511 | n_water=1001 | time (s): 313.940 (total time: 449.110) Filter (q & B) r_work=0.1249 r_free=0.1520 | n_water=877 | time (s): 5.290 (total time: 454.400) Filter (dist only) r_work=0.1250 r_free=0.1520 | n_water=876 | time (s): 119.640 (total time: 574.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.707363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.495218 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 0.1241 0.1440 0.0199 0.035 1.1 7.8 0.0 0.0 0 0.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.40 1.99 1.926 14.561 16.495 3.940 12.34 14.02 1.68 2.235 14.463 16.495 3.896 Individual atomic B min max mean iso aniso Overall: 5.53 67.70 15.23 1.05 509 3271 Protein: 5.53 36.33 10.73 1.05 0 2902 Water: 6.72 67.70 30.14 N/A 509 367 Other: 13.95 28.08 21.01 N/A 0 2 Chain A: 5.56 55.81 12.73 N/A 0 1624 Chain B: 5.53 67.70 12.50 N/A 0 1647 Chain S: 12.06 64.09 32.03 N/A 509 0 Histogram: Values Number of atoms 5.53 - 11.75 2132 11.75 - 17.97 690 17.97 - 24.19 297 24.19 - 30.40 230 30.40 - 36.62 186 36.62 - 42.84 133 42.84 - 49.05 74 49.05 - 55.27 23 55.27 - 61.49 12 61.49 - 67.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1402 r_work=0.1235 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1403 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1390 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889745 | | target function (ml) not normalized (work): 728537.519843 | | target function (ml) not normalized (free): 15219.660897 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1390 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1443 0.1443 0.1491 n_refl.: 191138 remove outliers: r(all,work,free)=0.1443 0.1443 0.1491 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1487 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1382 n_refl.: 191138 remove outliers: r(all,work,free)=0.1226 0.1223 0.1382 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3829 398.008 363.926 0.418 0.948 0.241 13.296-10.522 98.02 98 1 0.2291 528.900 506.478 0.705 0.949 0.220 10.503-8.327 98.35 176 3 0.2048 555.265 556.588 0.883 0.949 0.167 8.318-6.595 100.00 360 8 0.2080 414.736 410.178 0.894 0.949 0.128 6.588-5.215 100.00 711 7 0.1813 381.101 371.388 0.885 0.949 0.110 5.214-4.128 98.38 1367 28 0.1177 557.435 552.077 0.970 0.949 0.054 4.126-3.266 94.74 2603 46 0.1099 508.132 501.138 1.032 0.949 0.019 3.266-2.585 99.86 5447 97 0.1091 342.774 339.056 1.019 0.947 0.005 2.585-2.046 97.45 10613 204 0.0970 258.603 255.720 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.394 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1046 82.395 81.495 1.056 0.941 0.000 1.281-0.980 96.53 101826 2055 0.1683 44.202 42.317 1.044 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1039 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1382 | n_water=876 | time (s): 3.310 (total time: 3.310) Filter (dist) r_work=0.1224 r_free=0.1385 | n_water=872 | time (s): 112.630 (total time: 115.940) Filter (q & B) r_work=0.1225 r_free=0.1384 | n_water=858 | time (s): 4.300 (total time: 120.240) Compute maps r_work=0.1225 r_free=0.1384 | n_water=858 | time (s): 2.070 (total time: 122.310) Filter (map) r_work=0.1248 r_free=0.1387 | n_water=723 | time (s): 5.260 (total time: 127.570) Find peaks r_work=0.1248 r_free=0.1387 | n_water=723 | time (s): 0.770 (total time: 128.340) Add new water r_work=0.1261 r_free=0.1397 | n_water=971 | time (s): 5.010 (total time: 133.350) Refine new water occ: r_work=0.1214 r_free=0.1359 adp: r_work=0.1206 r_free=0.1356 occ: r_work=0.1203 r_free=0.1354 adp: r_work=0.1203 r_free=0.1354 occ: r_work=0.1203 r_free=0.1354 adp: r_work=0.1203 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1354 r_work=0.1203 r_free=0.1354 | n_water=971 | time (s): 225.140 (total time: 358.490) Filter (q & B) r_work=0.1209 r_free=0.1366 | n_water=854 | time (s): 5.350 (total time: 363.840) Filter (dist only) r_work=0.1210 r_free=0.1365 | n_water=852 | time (s): 110.380 (total time: 474.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.092202 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1366 0.0157 0.033 1.1 6.0 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.66 1.57 1.824 14.068 15.092 3.873 12.03 13.64 1.60 1.918 14.032 15.092 3.867 Individual atomic B min max mean iso aniso Overall: 5.51 67.28 14.76 0.99 485 3271 Protein: 5.51 33.22 10.65 0.99 0 2902 Water: 5.88 67.28 28.73 N/A 485 367 Other: 13.95 27.40 20.67 N/A 0 2 Chain A: 5.51 54.85 12.60 N/A 0 1624 Chain B: 5.52 67.28 12.41 N/A 0 1647 Chain S: 5.88 61.64 29.94 N/A 485 0 Histogram: Values Number of atoms 5.51 - 11.69 2116 11.69 - 17.87 729 17.87 - 24.04 330 24.04 - 30.22 217 30.22 - 36.40 153 36.40 - 42.57 119 42.57 - 48.75 63 48.75 - 54.93 21 54.93 - 61.10 6 61.10 - 67.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1364 r_work=0.1203 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1364 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865288 | | target function (ml) not normalized (work): 723941.358558 | | target function (ml) not normalized (free): 15146.072083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1435 0.1434 0.1496 n_refl.: 191134 remove outliers: r(all,work,free)=0.1435 0.1434 0.1496 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1427 0.1426 0.1491 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1364 n_refl.: 191134 remove outliers: r(all,work,free)=0.1204 0.1201 0.1364 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3872 360.520 322.878 0.413 0.944 0.251 13.296-10.522 98.02 98 1 0.2405 479.083 459.265 0.703 0.946 0.198 10.503-8.327 98.35 176 3 0.2183 502.965 494.562 0.867 0.946 0.170 8.318-6.595 100.00 360 8 0.2230 375.673 369.095 0.892 0.946 0.123 6.588-5.215 100.00 711 7 0.1946 345.206 335.221 0.885 0.946 0.100 5.214-4.128 98.38 1367 28 0.1232 504.931 499.396 0.974 0.947 0.070 4.126-3.266 94.74 2603 46 0.1122 460.272 453.848 1.037 0.947 0.000 3.266-2.585 99.86 5447 97 0.1090 310.488 307.298 1.023 0.946 0.000 2.585-2.046 97.45 10613 204 0.0939 234.246 231.801 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0915 138.638 137.325 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.635 73.908 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.038 38.370 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1238 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1364 | n_water=852 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1201 r_free=0.1364 | n_water=852 | time (s): 102.520 (total time: 105.220) Filter (q & B) r_work=0.1201 r_free=0.1364 | n_water=841 | time (s): 4.540 (total time: 109.760) Compute maps r_work=0.1201 r_free=0.1364 | n_water=841 | time (s): 1.630 (total time: 111.390) Filter (map) r_work=0.1224 r_free=0.1365 | n_water=715 | time (s): 5.240 (total time: 116.630) Find peaks r_work=0.1224 r_free=0.1365 | n_water=715 | time (s): 0.630 (total time: 117.260) Add new water r_work=0.1237 r_free=0.1392 | n_water=950 | time (s): 4.090 (total time: 121.350) Refine new water occ: r_work=0.1199 r_free=0.1350 adp: r_work=0.1199 r_free=0.1351 occ: r_work=0.1197 r_free=0.1350 adp: r_work=0.1197 r_free=0.1350 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1351 r_work=0.1195 r_free=0.1351 | n_water=950 | time (s): 204.730 (total time: 326.080) Filter (q & B) r_work=0.1199 r_free=0.1353 | n_water=871 | time (s): 5.520 (total time: 331.600) Filter (dist only) r_work=0.1199 r_free=0.1352 | n_water=870 | time (s): 115.100 (total time: 446.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556832 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.259987 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1356 0.0154 0.036 1.1 5.8 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.56 1.54 1.785 14.015 15.260 3.766 12.05 13.60 1.55 1.881 13.974 15.260 3.762 Individual atomic B min max mean iso aniso Overall: 5.55 66.78 14.74 0.95 505 3269 Protein: 5.55 31.47 10.56 0.95 0 2902 Water: 5.87 66.78 28.66 N/A 505 365 Other: 13.87 25.76 19.81 N/A 0 2 Chain A: 5.56 53.70 12.46 N/A 0 1623 Chain B: 5.55 66.78 12.28 N/A 0 1646 Chain S: 5.87 61.68 30.04 N/A 505 0 Histogram: Values Number of atoms 5.55 - 11.67 2132 11.67 - 17.80 735 17.80 - 23.92 306 23.92 - 30.04 221 30.04 - 36.16 173 36.16 - 42.29 118 42.29 - 48.41 62 48.41 - 54.53 20 54.53 - 60.65 5 60.65 - 66.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1360 r_work=0.1205 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1361 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1362 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761604 | | target function (ml) not normalized (work): 704522.129647 | | target function (ml) not normalized (free): 14754.668146 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1432 0.1431 0.1493 n_refl.: 191134 remove outliers: r(all,work,free)=0.1432 0.1431 0.1493 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1424 0.1423 0.1488 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1360 n_refl.: 191134 remove outliers: r(all,work,free)=0.1206 0.1203 0.1360 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3875 361.324 313.721 0.387 0.944 0.217 13.296-10.522 98.02 98 1 0.2472 479.083 458.537 0.702 0.946 0.200 10.503-8.327 98.35 176 3 0.2134 502.965 494.990 0.864 0.946 0.165 8.318-6.595 100.00 360 8 0.2223 375.673 369.650 0.891 0.946 0.113 6.588-5.215 100.00 711 7 0.1950 345.206 334.611 0.888 0.946 0.093 5.214-4.128 98.38 1367 28 0.1230 504.931 499.443 0.977 0.946 0.080 4.126-3.266 94.74 2603 46 0.1150 460.272 453.484 1.039 0.947 0.005 3.266-2.585 99.86 5447 97 0.1113 310.488 307.282 1.024 0.947 0.000 2.585-2.046 97.45 10613 204 0.0953 234.246 231.753 1.035 0.947 0.000 2.046-1.619 99.39 21536 464 0.0913 138.638 137.338 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0977 74.635 73.917 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.038 38.365 1.037 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1328 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1360 | n_water=870 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1203 r_free=0.1360 | n_water=869 | time (s): 125.180 (total time: 128.410) Filter (q & B) r_work=0.1203 r_free=0.1360 | n_water=859 | time (s): 4.430 (total time: 132.840) Compute maps r_work=0.1203 r_free=0.1360 | n_water=859 | time (s): 1.690 (total time: 134.530) Filter (map) r_work=0.1225 r_free=0.1367 | n_water=743 | time (s): 4.150 (total time: 138.680) Find peaks r_work=0.1225 r_free=0.1367 | n_water=743 | time (s): 0.580 (total time: 139.260) Add new water r_work=0.1236 r_free=0.1387 | n_water=947 | time (s): 4.080 (total time: 143.340) Refine new water occ: r_work=0.1200 r_free=0.1354 adp: r_work=0.1200 r_free=0.1355 occ: r_work=0.1198 r_free=0.1352 adp: r_work=0.1198 r_free=0.1353 occ: r_work=0.1197 r_free=0.1350 adp: r_work=0.1196 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1351 r_work=0.1196 r_free=0.1351 | n_water=947 | time (s): 253.250 (total time: 396.590) Filter (q & B) r_work=0.1200 r_free=0.1356 | n_water=882 | time (s): 6.010 (total time: 402.600) Filter (dist only) r_work=0.1201 r_free=0.1356 | n_water=881 | time (s): 115.560 (total time: 518.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.536943 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.144099 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1362 0.0158 0.037 1.1 6.8 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.62 1.58 1.750 13.917 15.144 3.763 12.06 13.64 1.59 1.860 13.876 15.144 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 65.62 14.67 0.90 516 3269 Protein: 5.56 29.08 10.46 0.90 0 2902 Water: 5.86 65.62 28.52 N/A 516 365 Other: 13.83 23.35 18.59 N/A 0 2 Chain A: 5.60 50.86 12.33 N/A 0 1623 Chain B: 5.56 65.62 12.16 N/A 0 1646 Chain S: 5.86 62.00 30.03 N/A 516 0 Histogram: Values Number of atoms 5.56 - 11.57 2110 11.57 - 17.57 775 17.57 - 23.58 283 23.58 - 29.59 223 29.59 - 35.59 174 35.59 - 41.60 127 41.60 - 47.60 60 47.60 - 53.61 25 53.61 - 59.62 5 59.62 - 65.62 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1364 r_work=0.1206 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1365 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1363 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759222 | | target function (ml) not normalized (work): 704072.169438 | | target function (ml) not normalized (free): 14749.849763 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1363 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1412 0.1411 0.1497 n_refl.: 191133 remove outliers: r(all,work,free)=0.1412 0.1411 0.1497 n_refl.: 191133 overall B=-0.22 to atoms: r(all,work,free)=0.1377 0.1376 0.1473 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1362 n_refl.: 191133 remove outliers: r(all,work,free)=0.1206 0.1202 0.1362 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3653 361.020 310.614 0.405 0.947 0.217 13.296-10.522 98.02 98 1 0.2468 479.083 457.501 0.708 0.949 0.163 10.503-8.327 98.35 176 3 0.2223 502.965 495.182 0.883 0.949 0.137 8.318-6.595 100.00 360 8 0.2214 375.673 369.731 0.911 0.949 0.108 6.588-5.215 100.00 711 7 0.1949 345.206 334.944 0.909 0.949 0.090 5.214-4.128 98.38 1367 28 0.1222 504.931 499.812 1.000 0.950 0.090 4.126-3.266 94.74 2603 46 0.1165 460.272 453.317 1.060 0.950 0.000 3.266-2.585 99.86 5447 97 0.1118 310.488 307.345 1.043 0.950 0.000 2.585-2.046 97.45 10613 204 0.0958 234.246 231.775 1.050 0.951 0.000 2.046-1.619 99.39 21536 464 0.0913 138.638 137.369 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0970 74.635 73.932 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.038 38.369 1.019 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0488 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1363 | n_water=881 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1203 r_free=0.1362 | n_water=880 | time (s): 120.650 (total time: 123.350) Filter (q & B) r_work=0.1204 r_free=0.1364 | n_water=870 | time (s): 5.130 (total time: 128.480) Compute maps r_work=0.1204 r_free=0.1364 | n_water=870 | time (s): 2.030 (total time: 130.510) Filter (map) r_work=0.1226 r_free=0.1371 | n_water=751 | time (s): 4.680 (total time: 135.190) Find peaks r_work=0.1226 r_free=0.1371 | n_water=751 | time (s): 0.920 (total time: 136.110) Add new water r_work=0.1236 r_free=0.1390 | n_water=958 | time (s): 4.180 (total time: 140.290) Refine new water occ: r_work=0.1200 r_free=0.1346 adp: r_work=0.1200 r_free=0.1347 occ: r_work=0.1198 r_free=0.1344 adp: r_work=0.1198 r_free=0.1346 occ: r_work=0.1197 r_free=0.1343 adp: r_work=0.1196 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1345 r_work=0.1196 r_free=0.1345 | n_water=958 | time (s): 264.430 (total time: 404.720) Filter (q & B) r_work=0.1200 r_free=0.1352 | n_water=895 | time (s): 4.340 (total time: 409.060) Filter (dist only) r_work=0.1201 r_free=0.1351 | n_water=893 | time (s): 117.900 (total time: 526.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567976 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.239379 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1358 0.0155 0.038 1.1 5.8 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.58 1.55 1.714 13.633 14.239 3.759 12.05 13.60 1.55 1.757 13.613 14.239 3.758 Individual atomic B min max mean iso aniso Overall: 5.40 64.40 14.45 0.88 528 3269 Protein: 5.40 28.17 10.22 0.88 0 2902 Water: 5.74 64.40 28.18 N/A 528 365 Other: 13.64 22.23 17.94 N/A 0 2 Chain A: 5.43 49.96 12.05 N/A 0 1623 Chain B: 5.40 64.40 11.90 N/A 0 1646 Chain S: 5.74 62.06 29.76 N/A 528 0 Histogram: Values Number of atoms 5.40 - 11.30 2093 11.30 - 17.20 795 17.20 - 23.10 284 23.10 - 29.00 224 29.00 - 34.90 169 34.90 - 40.80 123 40.80 - 46.70 71 46.70 - 52.60 28 52.60 - 58.50 6 58.50 - 64.40 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1360 r_work=0.1206 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1359 target_work(ml) = 3.758 | | 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757713 | | target function (ml) not normalized (work): 703785.834888 | | target function (ml) not normalized (free): 14741.571126 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1359 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1373 0.1370 0.1483 n_refl.: 191132 remove outliers: r(all,work,free)=0.1373 0.1370 0.1483 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1373 0.1370 0.1483 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191132 remove outliers: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3605 361.020 330.734 0.444 0.908 0.223 13.296-10.522 98.02 98 1 0.2477 479.083 456.966 0.729 0.910 0.162 10.503-8.327 98.35 176 3 0.2226 502.965 494.558 0.915 0.910 0.133 8.318-6.595 100.00 360 8 0.2221 375.673 369.070 0.942 0.910 0.111 6.588-5.215 100.00 711 7 0.1947 345.206 334.393 0.941 0.910 0.100 5.214-4.128 98.38 1367 28 0.1220 504.931 499.121 1.033 0.911 0.059 4.126-3.266 94.74 2603 46 0.1169 460.272 452.840 1.097 0.912 0.000 3.266-2.585 99.86 5447 97 0.1123 310.488 306.980 1.078 0.912 0.000 2.585-2.046 97.45 10613 204 0.0961 234.246 231.589 1.085 0.914 0.000 2.046-1.619 99.39 21536 464 0.0909 138.638 137.262 1.100 0.916 0.000 1.619-1.281 98.00 42464 925 0.0949 74.635 73.959 1.084 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.038 38.340 1.043 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1259 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1346 | n_water=893 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1193 r_free=0.1346 | n_water=893 | time (s): 112.060 (total time: 115.220) Filter (q & B) r_work=0.1194 r_free=0.1347 | n_water=887 | time (s): 4.700 (total time: 119.920) Compute maps r_work=0.1194 r_free=0.1347 | n_water=887 | time (s): 2.280 (total time: 122.200) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=772 | time (s): 5.050 (total time: 127.250) Find peaks r_work=0.1214 r_free=0.1350 | n_water=772 | time (s): 0.890 (total time: 128.140) Add new water r_work=0.1222 r_free=0.1365 | n_water=971 | time (s): 5.220 (total time: 133.360) Refine new water occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1191 r_free=0.1342 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1341 r_work=0.1188 r_free=0.1341 | n_water=971 | time (s): 176.390 (total time: 309.750) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=903 | time (s): 4.380 (total time: 314.130) Filter (dist only) r_work=0.1192 r_free=0.1344 | n_water=902 | time (s): 117.450 (total time: 431.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594682 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.745862 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1351 0.0157 0.038 1.1 5.1 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.51 1.57 1.671 13.599 14.746 3.756 11.94 13.53 1.59 1.686 13.590 14.746 3.754 Individual atomic B min max mean iso aniso Overall: 5.43 63.43 14.47 0.88 537 3269 Protein: 5.43 28.01 10.23 0.88 0 2902 Water: 5.81 63.43 28.09 N/A 537 365 Other: 13.66 22.05 17.85 N/A 0 2 Chain A: 5.49 49.59 12.03 N/A 0 1623 Chain B: 5.43 63.43 11.88 N/A 0 1646 Chain S: 5.81 62.27 29.78 N/A 537 0 Histogram: Values Number of atoms 5.43 - 11.23 2062 11.23 - 17.03 826 17.03 - 22.83 282 22.83 - 28.63 217 28.63 - 34.43 178 34.43 - 40.23 118 40.23 - 46.03 82 46.03 - 51.83 28 51.83 - 57.63 9 57.63 - 63.43 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1354 r_work=0.1194 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753075 | | target function (ml) not normalized (work): 702917.260005 | | target function (ml) not normalized (free): 14732.284571 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1378 0.1376 0.1483 n_refl.: 191132 remove outliers: r(all,work,free)=0.1378 0.1376 0.1483 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1378 0.1376 0.1483 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1353 n_refl.: 191132 remove outliers: r(all,work,free)=0.1194 0.1191 0.1353 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3611 361.020 330.719 0.436 0.909 0.213 13.296-10.522 98.02 98 1 0.2498 479.083 457.079 0.718 0.911 0.144 10.503-8.327 98.35 176 3 0.2256 502.965 494.201 0.912 0.911 0.113 8.318-6.595 100.00 360 8 0.2216 375.673 369.367 0.936 0.911 0.096 6.588-5.215 100.00 711 7 0.1958 345.206 334.576 0.936 0.912 0.080 5.214-4.128 98.38 1367 28 0.1235 504.931 499.076 1.032 0.913 0.080 4.126-3.266 94.74 2603 46 0.1169 460.272 452.748 1.096 0.914 0.000 3.266-2.585 99.86 5447 97 0.1126 310.488 306.980 1.078 0.914 0.000 2.585-2.046 97.45 10613 204 0.0959 234.246 231.574 1.084 0.916 0.000 2.046-1.619 99.39 21536 464 0.0905 138.638 137.284 1.099 0.919 0.000 1.619-1.281 98.00 42464 925 0.0943 74.635 73.974 1.085 0.923 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.335 1.046 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0936 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=902 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1191 r_free=0.1352 | n_water=901 | time (s): 116.030 (total time: 118.520) Filter (q & B) r_work=0.1192 r_free=0.1353 | n_water=894 | time (s): 4.940 (total time: 123.460) Compute maps r_work=0.1192 r_free=0.1353 | n_water=894 | time (s): 2.450 (total time: 125.910) Filter (map) r_work=0.1212 r_free=0.1354 | n_water=781 | time (s): 5.040 (total time: 130.950) Find peaks r_work=0.1212 r_free=0.1354 | n_water=781 | time (s): 0.750 (total time: 131.700) Add new water r_work=0.1221 r_free=0.1368 | n_water=979 | time (s): 5.140 (total time: 136.840) Refine new water occ: r_work=0.1188 r_free=0.1336 adp: r_work=0.1188 r_free=0.1337 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1336 occ: r_work=0.1185 r_free=0.1335 adp: r_work=0.1184 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1335 r_work=0.1184 r_free=0.1335 | n_water=979 | time (s): 335.410 (total time: 472.250) Filter (q & B) r_work=0.1188 r_free=0.1341 | n_water=915 | time (s): 4.750 (total time: 477.000) Filter (dist only) r_work=0.1188 r_free=0.1341 | n_water=914 | time (s): 118.310 (total time: 595.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.506363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.794992 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 0.1348 0.0155 0.039 1.1 5.6 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.48 1.55 1.669 13.614 13.795 3.754 11.94 13.51 1.57 1.666 13.615 13.795 3.754 Individual atomic B min max mean iso aniso Overall: 5.45 63.27 14.51 0.86 549 3269 Protein: 5.45 27.91 10.25 0.86 0 2902 Water: 5.85 63.27 28.02 N/A 549 365 Other: 13.66 22.09 17.88 N/A 0 2 Chain A: 5.52 49.53 12.02 N/A 0 1623 Chain B: 5.45 63.27 11.89 N/A 0 1646 Chain S: 5.85 62.29 29.71 N/A 549 0 Histogram: Values Number of atoms 5.45 - 11.23 2061 11.23 - 17.01 827 17.01 - 22.79 283 22.79 - 28.57 231 28.57 - 34.36 171 34.36 - 40.14 121 40.14 - 45.92 81 45.92 - 51.70 30 51.70 - 57.48 8 57.48 - 63.27 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1351 r_work=0.1194 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1351 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753639 | | target function (ml) not normalized (work): 703022.793963 | | target function (ml) not normalized (free): 14732.791765 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1351 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1382 0.1381 0.1483 n_refl.: 191132 remove outliers: r(all,work,free)=0.1382 0.1381 0.1483 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1382 0.1381 0.1483 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3647 361.020 329.992 0.397 0.975 0.205 13.296-10.522 98.02 98 1 0.2496 479.083 456.387 0.666 0.977 0.139 10.503-8.327 98.35 176 3 0.2264 502.965 494.358 0.850 0.977 0.110 8.318-6.595 100.00 360 8 0.2210 375.673 369.298 0.873 0.977 0.097 6.588-5.215 100.00 711 7 0.1958 345.206 334.668 0.874 0.978 0.088 5.214-4.128 98.38 1367 28 0.1232 504.931 499.215 0.962 0.979 0.052 4.126-3.266 94.74 2603 46 0.1171 460.272 452.876 1.022 0.980 0.000 3.266-2.585 99.86 5447 97 0.1125 310.488 306.996 1.005 0.981 0.000 2.585-2.046 97.45 10613 204 0.0961 234.246 231.570 1.012 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.638 137.290 1.026 0.987 0.000 1.619-1.281 98.00 42464 925 0.0943 74.635 73.974 1.014 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.038 38.324 0.979 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0595 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1348 After: r_work=0.1193 r_free=0.1349 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1349 | n_water=914 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1193 r_free=0.1349 | n_water=914 | time (s): 119.730 (total time: 122.830) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=905 | time (s): 5.470 (total time: 128.300) Compute maps r_work=0.1193 r_free=0.1348 | n_water=905 | time (s): 2.180 (total time: 130.480) Filter (map) r_work=0.1215 r_free=0.1356 | n_water=786 | time (s): 4.440 (total time: 134.920) Find peaks r_work=0.1215 r_free=0.1356 | n_water=786 | time (s): 0.570 (total time: 135.490) Add new water r_work=0.1223 r_free=0.1366 | n_water=977 | time (s): 4.530 (total time: 140.020) Refine new water occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1343 occ: r_work=0.1188 r_free=0.1344 adp: r_work=0.1188 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1344 r_work=0.1188 r_free=0.1344 | n_water=977 | time (s): 263.170 (total time: 403.190) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=917 | time (s): 4.420 (total time: 407.610) Filter (dist only) r_work=0.1192 r_free=0.1347 | n_water=916 | time (s): 123.910 (total time: 531.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567197 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.908683 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1352 0.0158 0.039 1.2 9.4 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.52 1.58 1.665 13.623 13.909 3.755 11.95 13.54 1.59 1.662 13.624 13.909 3.755 Individual atomic B min max mean iso aniso Overall: 5.47 62.85 14.51 0.86 551 3269 Protein: 5.47 27.81 10.27 0.86 0 2902 Water: 5.91 62.85 27.96 N/A 551 365 Other: 13.69 22.08 17.88 N/A 0 2 Chain A: 5.55 49.40 12.02 N/A 0 1623 Chain B: 5.47 62.85 11.89 N/A 0 1646 Chain S: 5.91 62.33 29.71 N/A 551 0 Histogram: Values Number of atoms 5.47 - 11.21 2051 11.21 - 16.94 838 16.94 - 22.68 281 22.68 - 28.42 228 28.42 - 34.16 171 34.16 - 39.89 124 39.89 - 45.63 84 45.63 - 51.37 30 51.37 - 57.11 8 57.11 - 62.85 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1354 r_work=0.1195 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754318 | | target function (ml) not normalized (work): 703149.991835 | | target function (ml) not normalized (free): 14731.846224 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7400 127 0.1364 0.1456 5.6948 5.7658| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1346 5.0779 5.1752| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1175 4.6537 4.7342| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1061 4.3906 4.5778| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0988 4.1511 4.2528| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1074 3.9478 4.0676| | 7: 1.62 - 1.54 0.99 7104 148 0.0896 0.0965 3.8037 3.9377| | 8: 1.54 - 1.47 0.96 6798 152 0.0894 0.1331 3.7055 3.9223| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1139 3.6238 3.7591| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1207 3.5568 3.6758| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1102 3.4798 3.5765| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1117 3.4544 3.5775| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1249 3.4355 3.5648| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1594 3.4302 3.6799| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1247 3.4487 3.4915| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1561 3.4646 3.6623| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1233 3.4336 3.4477| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1703 3.4378 3.5308| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1764 3.4201 3.5967| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1587 3.4099 3.4364| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2138 3.4189 3.5062| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1953 3.413 3.4154| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2013 3.4334 3.4842| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2258 3.436 3.5119| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2503 3.4491 3.5225| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2868 3.4153 3.4227| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2805 3.4685 3.3962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7400 127 0.93 11.67 1.00 0.96 11187.46| | 2: 2.94 - 2.33 7339 128 0.93 12.74 0.99 0.97 5102.50| | 3: 2.33 - 2.04 6939 150 0.96 7.57 1.01 0.97 1679.44| | 4: 2.04 - 1.85 7170 155 0.96 7.65 1.00 0.97 1006.39| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.97 635.50| | 6: 1.72 - 1.62 7102 142 0.96 8.05 1.00 0.98 444.78| | 7: 1.62 - 1.54 7104 148 0.96 8.24 1.01 0.99 341.18| | 8: 1.54 - 1.47 6798 152 0.96 8.42 1.01 0.99 284.68| | 9: 1.47 - 1.41 6938 155 0.96 8.56 1.00 0.99 234.03| | 10: 1.41 - 1.36 7022 150 0.96 8.90 1.00 0.99 202.65| | 11: 1.36 - 1.32 6997 151 0.96 8.82 0.99 0.97 172.54| | 12: 1.32 - 1.28 6975 149 0.96 8.85 0.98 0.96 158.20| | 13: 1.28 - 1.25 6907 166 0.96 9.47 1.01 0.98 156.76| | 14: 1.25 - 1.22 7015 112 0.95 10.66 1.01 0.98 162.62| | 15: 1.22 - 1.19 6956 137 0.95 11.26 1.01 0.99 167.17| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.98 160.80| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.98 154.69| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.96 148.06| | 19: 1.12 - 1.10 6948 106 0.93 14.17 1.00 0.96 151.64| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.95 150.75| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.94 153.77| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.94 155.08| | 23: 1.05 - 1.03 6827 159 0.87 20.48 0.99 0.93 164.73| | 24: 1.03 - 1.02 6784 133 0.85 23.14 0.99 0.94 178.97| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.97 0.91 182.06| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.69| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.98 0.88 161.41| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.06 max = 11187.46 mean = 923.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.29| |phase err.(test): min = 0.00 max = 89.84 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1193 0.1354 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1493 n_refl.: 191132 remove outliers: r(all,work,free)=0.1391 0.1390 0.1493 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1391 0.1390 0.1493 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191132 remove outliers: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3666 361.020 328.558 0.392 0.975 0.203 13.296-10.522 98.02 98 1 0.2505 479.083 456.251 0.658 0.976 0.138 10.503-8.327 98.35 176 3 0.2236 502.965 494.584 0.843 0.977 0.110 8.318-6.595 100.00 360 8 0.2209 375.673 369.544 0.866 0.977 0.096 6.588-5.215 100.00 711 7 0.1958 345.206 334.625 0.867 0.977 0.083 5.214-4.128 98.38 1367 28 0.1233 504.931 498.963 0.957 0.978 0.080 4.126-3.266 94.74 2603 46 0.1166 460.272 452.941 1.017 0.980 0.000 3.266-2.585 99.86 5447 97 0.1122 310.488 307.042 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0963 234.246 231.562 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0908 138.638 137.285 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0947 74.635 73.973 1.009 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.038 38.322 0.976 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0277 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2039 0.1967 0.082 5.270 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1898 0.082 5.270 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1898 0.082 5.270 5.2 78.0 14.6 805 0.000 1_nqh: 0.1805 0.1900 0.082 5.270 5.2 78.0 14.6 805 0.002 1_weight: 0.1805 0.1900 0.082 5.270 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1270 0.1501 0.038 1.155 5.2 78.0 14.6 805 0.157 1_adp: 0.1289 0.1560 0.038 1.155 5.3 73.0 15.0 805 0.157 1_regHadp: 0.1288 0.1555 0.038 1.155 5.3 73.0 15.0 805 0.157 1_occ: 0.1273 0.1544 0.038 1.155 5.3 73.0 15.0 805 0.157 2_bss: 0.1263 0.1534 0.038 1.155 5.4 73.2 15.1 805 0.157 2_settarget: 0.1263 0.1534 0.038 1.155 5.4 73.2 15.1 805 0.157 2_updatecdl: 0.1263 0.1534 0.038 1.168 5.4 73.2 15.1 805 0.157 2_nqh: 0.1265 0.1536 0.038 1.168 5.4 73.2 15.1 805 0.155 2_sol: 0.1260 0.1503 0.038 1.168 5.4 73.2 16.2 888 n/a 2_weight: 0.1260 0.1503 0.038 1.168 5.4 73.2 16.2 888 n/a 2_xyzrec: 0.1246 0.1515 0.040 1.135 5.4 73.2 16.2 888 n/a 2_adp: 0.1231 0.1512 0.040 1.135 5.4 68.2 16.4 888 n/a 2_regHadp: 0.1232 0.1513 0.040 1.135 5.4 68.2 16.4 888 n/a 2_occ: 0.1225 0.1510 0.040 1.135 5.4 68.2 16.4 888 n/a 3_bss: 0.1232 0.1516 0.040 1.135 5.4 68.1 16.3 888 n/a 3_settarget: 0.1232 0.1516 0.040 1.135 5.4 68.1 16.3 888 n/a 3_updatecdl: 0.1232 0.1516 0.040 1.139 5.4 68.1 16.3 888 n/a 3_nqh: 0.1232 0.1516 0.040 1.139 5.4 68.1 16.3 888 n/a 3_sol: 0.1250 0.1520 0.040 1.139 5.4 68.1 15.4 876 n/a 3_weight: 0.1250 0.1520 0.040 1.139 5.4 68.1 15.4 876 n/a 3_xyzrec: 0.1241 0.1440 0.035 1.104 5.4 68.1 15.4 876 n/a 3_adp: 0.1234 0.1402 0.035 1.104 5.5 67.7 15.2 876 n/a 3_regHadp: 0.1235 0.1403 0.035 1.104 5.5 67.7 15.2 876 n/a 3_occ: 0.1229 0.1390 0.035 1.104 5.5 67.7 15.2 876 n/a 4_bss: 0.1224 0.1382 0.035 1.104 5.5 67.7 15.2 876 n/a 4_settarget: 0.1224 0.1382 0.035 1.104 5.5 67.7 15.2 876 n/a 4_updatecdl: 0.1224 0.1382 0.035 1.104 5.5 67.7 15.2 876 n/a 4_nqh: 0.1224 0.1382 0.035 1.104 5.5 67.7 15.2 876 n/a 4_sol: 0.1210 0.1365 0.035 1.104 5.5 67.7 14.8 852 n/a 4_weight: 0.1210 0.1365 0.035 1.104 5.5 67.7 14.8 852 n/a 4_xyzrec: 0.1208 0.1366 0.033 1.120 5.5 67.7 14.8 852 n/a 4_adp: 0.1203 0.1364 0.033 1.120 5.5 67.3 14.8 852 n/a 4_regHadp: 0.1203 0.1364 0.033 1.120 5.5 67.3 14.8 852 n/a 4_occ: 0.1201 0.1363 0.033 1.120 5.5 67.3 14.8 852 n/a 5_bss: 0.1201 0.1364 0.033 1.120 5.5 67.2 14.7 852 n/a 5_settarget: 0.1201 0.1364 0.033 1.120 5.5 67.2 14.7 852 n/a 5_updatecdl: 0.1201 0.1364 0.033 1.121 5.5 67.2 14.7 852 n/a 5_nqh: 0.1201 0.1364 0.033 1.121 5.5 67.2 14.7 852 n/a 5_sol: 0.1199 0.1352 0.033 1.121 5.5 67.2 14.8 870 n/a 5_weight: 0.1199 0.1352 0.033 1.121 5.5 67.2 14.8 870 n/a 5_xyzrec: 0.1202 0.1356 0.036 1.125 5.5 67.2 14.8 870 n/a 5_adp: 0.1205 0.1360 0.036 1.125 5.6 66.8 14.7 870 n/a 5_regHadp: 0.1205 0.1361 0.036 1.125 5.6 66.8 14.7 870 n/a 5_occ: 0.1204 0.1362 0.036 1.125 5.6 66.8 14.7 870 n/a 6_bss: 0.1203 0.1360 0.036 1.125 5.5 66.7 14.7 870 n/a 6_settarget: 0.1203 0.1360 0.036 1.125 5.5 66.7 14.7 870 n/a 6_updatecdl: 0.1203 0.1360 0.036 1.125 5.5 66.7 14.7 870 n/a 6_nqh: 0.1203 0.1360 0.036 1.125 5.5 66.7 14.7 870 n/a 6_sol: 0.1201 0.1356 0.036 1.125 5.5 66.7 14.7 881 n/a 6_weight: 0.1201 0.1356 0.036 1.125 5.5 66.7 14.7 881 n/a 6_xyzrec: 0.1204 0.1362 0.037 1.125 5.5 66.7 14.7 881 n/a 6_adp: 0.1206 0.1364 0.037 1.125 5.6 65.6 14.7 881 n/a 6_regHadp: 0.1206 0.1365 0.037 1.125 5.6 65.6 14.7 881 n/a 6_occ: 0.1203 0.1363 0.037 1.125 5.6 65.6 14.7 881 n/a 7_bss: 0.1203 0.1363 0.037 1.125 5.3 65.4 14.4 881 n/a 7_settarget: 0.1203 0.1363 0.037 1.125 5.3 65.4 14.4 881 n/a 7_updatecdl: 0.1203 0.1363 0.037 1.125 5.3 65.4 14.4 881 n/a 7_nqh: 0.1203 0.1363 0.037 1.125 5.3 65.4 14.4 881 n/a 7_sol: 0.1201 0.1351 0.037 1.125 5.3 65.4 14.5 893 n/a 7_weight: 0.1201 0.1351 0.037 1.125 5.3 65.4 14.5 893 n/a 7_xyzrec: 0.1203 0.1358 0.038 1.127 5.3 65.4 14.5 893 n/a 7_adp: 0.1206 0.1360 0.038 1.127 5.4 64.4 14.5 893 n/a 7_regHadp: 0.1206 0.1361 0.038 1.127 5.4 64.4 14.5 893 n/a 7_occ: 0.1203 0.1359 0.038 1.127 5.4 64.4 14.5 893 n/a 8_bss: 0.1193 0.1346 0.038 1.127 5.4 64.4 14.5 893 n/a 8_settarget: 0.1193 0.1346 0.038 1.127 5.4 64.4 14.5 893 n/a 8_updatecdl: 0.1193 0.1346 0.038 1.127 5.4 64.4 14.5 893 n/a 8_nqh: 0.1193 0.1346 0.038 1.127 5.4 64.4 14.5 893 n/a 8_sol: 0.1192 0.1344 0.038 1.127 5.4 64.4 14.5 902 n/a 8_weight: 0.1192 0.1344 0.038 1.127 5.4 64.4 14.5 902 n/a 8_xyzrec: 0.1195 0.1351 0.038 1.120 5.4 64.4 14.5 902 n/a 8_adp: 0.1194 0.1354 0.038 1.120 5.4 63.4 14.5 902 n/a 8_regHadp: 0.1194 0.1354 0.038 1.120 5.4 63.4 14.5 902 n/a 8_occ: 0.1192 0.1353 0.038 1.120 5.4 63.4 14.5 902 n/a 9_bss: 0.1191 0.1353 0.038 1.120 5.4 63.4 14.5 902 n/a 9_settarget: 0.1191 0.1353 0.038 1.120 5.4 63.4 14.5 902 n/a 9_updatecdl: 0.1191 0.1353 0.038 1.120 5.4 63.4 14.5 902 n/a 9_nqh: 0.1191 0.1353 0.038 1.120 5.4 63.4 14.5 902 n/a 9_sol: 0.1188 0.1341 0.038 1.120 5.4 63.4 14.5 914 n/a 9_weight: 0.1188 0.1341 0.038 1.120 5.4 63.4 14.5 914 n/a 9_xyzrec: 0.1193 0.1348 0.039 1.116 5.4 63.4 14.5 914 n/a 9_adp: 0.1194 0.1351 0.039 1.116 5.4 63.3 14.5 914 n/a 9_regHadp: 0.1194 0.1351 0.039 1.116 5.4 63.3 14.5 914 n/a 9_occ: 0.1193 0.1351 0.039 1.116 5.4 63.3 14.5 914 n/a 10_bss: 0.1192 0.1348 0.039 1.116 5.4 63.3 14.5 914 n/a 10_settarget: 0.1192 0.1348 0.039 1.116 5.4 63.3 14.5 914 n/a 10_updatecdl: 0.1192 0.1348 0.039 1.116 5.4 63.3 14.5 914 n/a 10_setrh: 0.1193 0.1349 0.039 1.116 5.4 63.3 14.5 914 n/a 10_nqh: 0.1193 0.1349 0.039 1.116 5.4 63.3 14.5 914 n/a 10_sol: 0.1192 0.1347 0.039 1.116 5.4 63.3 14.5 916 n/a 10_weight: 0.1192 0.1347 0.039 1.116 5.4 63.3 14.5 916 n/a 10_xyzrec: 0.1194 0.1352 0.039 1.166 5.4 63.3 14.5 916 n/a 10_adp: 0.1195 0.1354 0.039 1.166 5.5 62.8 14.5 916 n/a 10_regHadp: 0.1195 0.1354 0.039 1.166 5.5 62.8 14.5 916 n/a 10_occ: 0.1193 0.1354 0.039 1.166 5.5 62.8 14.5 916 n/a end: 0.1193 0.1354 0.039 1.166 5.5 62.8 14.5 916 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8081060_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8081060_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.7600 Refinement macro-cycles (run) : 12307.2100 Write final files (write_after_run_outputs) : 138.9600 Total : 12452.9300 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:50 PST -0800 (1736736290.20 s) Start R-work = 0.1804, R-free = 0.1898 Final R-work = 0.1193, R-free = 0.1354 =============================================================================== Job complete usr+sys time: 12704.75 seconds wall clock time: 212 minutes 46.10 seconds (12766.10 seconds total)