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_3904915.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3904915.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3904915.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.65, per 1000 atoms: 0.25 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: 2.726 distance_ideal: 2.720 ideal - model: -0.006 slack: 0.000 delta_slack: -0.006 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: 2.654 distance_ideal: 2.710 ideal - model: 0.056 slack: 0.000 delta_slack: 0.056 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 128.7 milliseconds Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1089 1.05 - 1.28: 2377 1.28 - 1.51: 1570 1.51 - 1.74: 882 1.74 - 1.97: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" C GLU B 17 " pdb=" O GLU B 17 " ideal model delta sigma weight residual 1.236 1.496 -0.259 1.16e-02 7.43e+03 5.00e+02 bond pdb=" CA VAL B 92 " pdb=" CB VAL B 92 " ideal model delta sigma weight residual 1.538 1.325 0.213 1.06e-02 8.90e+03 4.05e+02 bond pdb=" ND1 HIS B 179 " pdb=" CE1 HIS B 179 " ideal model delta sigma weight residual 1.321 1.122 0.199 1.00e-02 1.00e+04 3.94e+02 bond pdb=" N GLU B 176 " pdb=" H GLU B 176 " ideal model delta sigma weight residual 0.860 1.234 -0.374 2.00e-02 2.50e+03 3.50e+02 bond pdb=" C VAL A 7 " pdb=" O VAL A 7 " ideal model delta sigma weight residual 1.237 1.442 -0.205 1.10e-02 8.26e+03 3.49e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 5232 3.86 - 7.72: 3577 7.72 - 11.58: 1566 11.58 - 15.44: 390 15.44 - 19.30: 45 Bond angle restraints: 10810 Sorted by residual: angle pdb=" C LEU B 113 " pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta sigma weight residual 120.24 130.97 -10.73 6.30e-01 2.52e+00 2.90e+02 angle pdb=" OE1 GLN B 184 " pdb=" CD GLN B 184 " pdb=" NE2 GLN B 184 " ideal model delta sigma weight residual 122.60 106.21 16.39 1.00e+00 1.00e+00 2.69e+02 angle pdb=" CA VAL B 37 " pdb=" C VAL B 37 " pdb=" O VAL B 37 " ideal model delta sigma weight residual 120.14 135.53 -15.39 1.00e+00 1.00e+00 2.37e+02 angle pdb=" CA ASP A 132 " pdb=" CB ASP A 132 " pdb=" CG ASP A 132 " ideal model delta sigma weight residual 112.60 127.46 -14.86 1.00e+00 1.00e+00 2.21e+02 angle pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH1 ARG B 143 " ideal model delta sigma weight residual 121.50 136.27 -14.77 1.00e+00 1.00e+00 2.18e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1830 16.75 - 33.51: 145 33.51 - 50.26: 47 50.26 - 67.01: 22 67.01 - 83.77: 6 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 -144.83 -35.17 0 5.00e+00 4.00e-02 4.95e+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 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -24.69 24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 224 0.257 - 0.514: 167 0.514 - 0.770: 84 0.770 - 1.027: 15 1.027 - 1.284: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 145 " pdb=" N VAL A 145 " pdb=" C VAL A 145 " pdb=" CB VAL A 145 " both_signs ideal model delta sigma weight residual False 2.44 3.73 -1.28 2.00e-01 2.50e+01 4.12e+01 chirality pdb=" CA ILE B 121 " pdb=" N ILE B 121 " pdb=" C ILE B 121 " pdb=" CB ILE B 121 " both_signs ideal model delta sigma weight residual False 2.43 3.47 -1.03 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CA CYS A 106 " pdb=" N CYS A 106 " pdb=" C CYS A 106 " pdb=" CB CYS A 106 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.052 2.00e-02 2.50e+03 5.76e-02 1.33e+02 pdb=" CG TRP A 146 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.093 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.061 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.149 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.074 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.078 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 127 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " 0.123 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " -0.064 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 PHE A 127 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 127 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE A 127 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 127 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.120 2.00e-02 2.50e+03 6.49e-02 1.27e+02 pdb=" CG PHE B 164 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.113 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.076 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.079 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 32 1.63 - 2.37: 2581 2.37 - 3.12: 22377 3.12 - 3.86: 32970 3.86 - 4.60: 52359 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110319 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.889 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.950 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.026 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.033 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.217 2.620 ... (remaining 110314 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_3904915_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= 0.2028 r_free= 0.1987 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296455 | | target function (ml) not normalized (work): 804781.783770 | | target function (ml) not normalized (free): 16534.339292 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2136 0.2009 6.677 6.3155| | 2: 2.94 - 2.33 1.00 7339 128 0.1607 0.1537 5.526 5.5617| | 3: 2.33 - 2.04 0.96 6939 150 0.1642 0.1515 5.1512 5.0495| | 4: 2.04 - 1.85 1.00 7170 155 0.1734 0.1563 4.9558 4.9969| | 5: 1.85 - 1.72 0.99 7113 159 0.1910 0.1912 4.7891 4.9111| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.1926 4.6733 4.7095| | 7: 1.62 - 1.54 0.99 7104 148 0.2003 0.1770 4.5618 4.5955| | 8: 1.54 - 1.47 0.96 6798 152 0.2068 0.2305 4.4739 4.5176| | 9: 1.47 - 1.41 0.98 6938 155 0.2111 0.2166 4.3941 4.4907| | 10: 1.41 - 1.36 0.99 7022 150 0.2107 0.2011 4.2959 4.3031| | 11: 1.36 - 1.32 0.99 6997 151 0.2116 0.2098 4.2291 4.2377| | 12: 1.32 - 1.28 0.98 6976 149 0.2031 0.2028 4.1564 4.2154| | 13: 1.28 - 1.25 0.98 6907 166 0.2028 0.2309 4.117 4.2169| | 14: 1.25 - 1.22 0.98 7015 113 0.2084 0.2496 4.0888 4.2708| | 15: 1.22 - 1.19 0.98 6957 137 0.2099 0.2043 4.0505 4.0458| | 16: 1.19 - 1.17 0.93 6604 132 0.2104 0.2234 4.01 4.064| | 17: 1.17 - 1.14 0.98 6941 135 0.2153 0.1989 3.9476 3.968| | 18: 1.14 - 1.12 0.98 6875 142 0.2218 0.2240 3.9252 3.8846| | 19: 1.12 - 1.10 0.97 6949 106 0.2233 0.2506 3.8679 4.0423| | 20: 1.10 - 1.08 0.97 6884 147 0.2318 0.2262 3.8222 3.8461| | 21: 1.08 - 1.07 0.97 6852 152 0.2416 0.2423 3.7868 3.7584| | 22: 1.07 - 1.05 0.97 6838 135 0.2529 0.2605 3.7446 3.7795| | 23: 1.05 - 1.03 0.97 6829 159 0.2715 0.2647 3.733 3.8258| | 24: 1.03 - 1.02 0.96 6785 133 0.2836 0.2738 3.6903 3.7333| | 25: 1.02 - 1.01 0.93 6552 130 0.3033 0.2851 3.6672 3.7043| | 26: 1.01 - 0.99 0.96 6767 158 0.3201 0.3179 3.6245 3.5843| | 27: 0.99 - 0.98 0.94 6648 131 0.3394 0.3286 3.6327 3.6165| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.55 0.91 0.97 35619.77| | 2: 2.94 - 2.33 7339 128 0.86 20.80 1.08 1.03 14558.77| | 3: 2.33 - 2.04 6939 150 0.94 11.30 1.11 1.06 3548.11| | 4: 2.04 - 1.85 7170 155 0.93 13.12 1.11 1.06 2681.76| | 5: 1.85 - 1.72 7113 159 0.91 16.08 1.12 1.07 2170.10| | 6: 1.72 - 1.62 7102 142 0.89 17.43 1.11 1.07 1759.43| | 7: 1.62 - 1.54 7104 148 0.89 18.02 1.11 1.08 1406.76| | 8: 1.54 - 1.47 6798 152 0.88 18.59 1.11 1.07 1178.11| | 9: 1.47 - 1.41 6938 155 0.88 19.26 1.10 1.06 997.48| | 10: 1.41 - 1.36 7022 150 0.87 19.98 1.10 1.04 842.17| | 11: 1.36 - 1.32 6997 151 0.87 20.15 1.08 1.02 714.00| | 12: 1.32 - 1.28 6976 149 0.87 20.09 1.07 1.02 656.58| | 13: 1.28 - 1.25 6907 166 0.87 20.62 1.07 1.02 628.55| | 14: 1.25 - 1.22 7015 113 0.86 21.69 1.07 1.04 624.01| | 15: 1.22 - 1.19 6957 137 0.86 21.72 1.08 1.04 577.51| | 16: 1.19 - 1.17 6604 132 0.87 20.77 1.07 1.03 512.61| | 17: 1.17 - 1.14 6941 135 0.86 20.94 1.08 1.01 438.36| | 18: 1.14 - 1.12 6875 142 0.86 21.41 1.08 0.97 390.40| | 19: 1.12 - 1.10 6949 106 0.86 22.03 1.07 0.97 366.03| | 20: 1.10 - 1.08 6884 147 0.85 22.59 1.06 0.97 337.38| | 21: 1.08 - 1.07 6852 152 0.85 23.22 1.06 0.99 324.49| | 22: 1.07 - 1.05 6838 135 0.83 24.68 1.05 1.00 318.04| | 23: 1.05 - 1.03 6829 159 0.81 26.91 1.05 1.00 322.37| | 24: 1.03 - 1.02 6785 133 0.79 28.54 1.05 0.98 314.75| | 25: 1.02 - 1.01 6552 130 0.78 29.81 1.03 0.93 296.19| | 26: 1.01 - 0.99 6767 158 0.75 31.85 1.03 0.91 283.89| | 27: 0.99 - 0.98 6648 131 0.75 32.50 1.04 0.92 282.54| |alpha: min = 0.91 max = 1.08 mean = 1.01| |beta: min = 282.54 max = 35619.77 mean = 2798.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.57| |phase err.(test): min = 0.00 max = 89.91 mean = 21.64| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.270 2950 Z= 5.524 Angle : 5.214 18.111 4018 Z= 3.710 Chirality : 0.396 1.284 492 Planarity : 0.033 0.124 512 Dihedral : 12.912 83.768 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 0.32 % Allowed : 5.48 % Favored : 94.19 % Cbeta Deviations : 31.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.21 (0.39), residues: 386 helix: -2.39 (0.34), residues: 144 sheet: -0.85 (0.52), residues: 86 loop : -0.58 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.020 ARG B 49 TYR 0.124 0.041 TYR B 67 PHE 0.118 0.035 PHE A 127 TRP 0.112 0.029 TRP A 146 HIS 0.078 0.027 HIS A 116 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= 0.2028 r_free= 0.1987 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296455 | | target function (ml) not normalized (work): 804781.783770 | | target function (ml) not normalized (free): 16534.339292 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2026 0.2028 0.1987 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2026 0.2028 0.1987 n_refl.: 191155 remove outliers: r(all,work,free)=0.2026 0.2028 0.1987 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2026 0.2028 0.1987 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1799 0.1797 0.1929 n_refl.: 191145 remove outliers: r(all,work,free)=0.1797 0.1794 0.1929 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4117 402.814 286.979 0.425 0.911 0.299 13.296-10.522 98.02 98 1 0.2425 527.329 515.909 0.797 0.912 0.260 10.503-8.327 98.90 177 3 0.2460 564.205 559.148 0.976 0.912 0.240 8.318-6.595 100.00 360 8 0.2529 414.736 404.157 0.976 0.912 0.169 6.588-5.215 100.00 711 7 0.2247 381.101 365.488 0.960 0.912 0.150 5.214-4.128 98.38 1367 28 0.1496 557.435 549.941 1.076 0.912 0.080 4.126-3.266 94.74 2603 46 0.1330 508.132 500.091 1.149 0.913 0.018 3.266-2.585 99.86 5447 97 0.1435 342.774 337.708 1.121 0.912 0.000 2.585-2.046 97.45 10613 204 0.1411 258.603 254.112 1.126 0.911 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 149.807 1.143 0.910 0.000 1.619-1.281 98.00 42464 925 0.1913 82.395 80.210 1.131 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2308 44.203 41.706 1.112 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0008 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1929 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1796 r_free=0.1929 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.763962 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.404489 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 0.1271 0.1506 0.0235 0.038 1.2 10.9 0.0 0.3 0 11.382 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.06 2.35 1.117 13.111 577.404 0.018 12.97 15.70 2.73 1.218 13.297 577.404 0.017 Individual atomic B min max mean iso aniso Overall: 5.12 73.04 14.94 1.39 435 3274 Protein: 5.12 40.38 10.96 1.39 0 2902 Water: 6.33 73.04 29.25 N/A 435 370 Other: 16.00 30.96 23.48 N/A 0 2 Chain A: 5.33 60.29 12.98 N/A 0 1626 Chain B: 5.12 73.04 12.71 N/A 0 1648 Chain S: 11.84 63.58 30.69 N/A 435 0 Histogram: Values Number of atoms 5.12 - 11.91 2161 11.91 - 18.71 650 18.71 - 25.50 310 25.50 - 32.29 270 32.29 - 39.08 151 39.08 - 45.87 105 45.87 - 52.67 37 52.67 - 59.46 20 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1570 r_work=0.1296 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1565 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015520 | | target function (ls_wunit_k1) not normalized (work): 2906.784047 | | target function (ls_wunit_k1) not normalized (free): 117.397656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1556 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1465 0.1462 0.1633 n_refl.: 191137 remove outliers: r(all,work,free)=0.1465 0.1462 0.1633 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1488 0.1485 0.1642 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191137 remove outliers: r(all,work,free)=0.1279 0.1274 0.1545 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3627 402.814 368.407 0.473 0.963 0.281 13.296-10.522 98.02 98 1 0.2010 527.329 519.829 0.744 0.965 0.243 10.503-8.327 98.90 177 3 0.1728 564.205 566.136 0.891 0.965 0.228 8.318-6.595 100.00 360 8 0.1710 414.736 412.242 0.909 0.964 0.155 6.588-5.215 100.00 711 7 0.1535 381.101 374.239 0.890 0.965 0.150 5.214-4.128 98.38 1367 28 0.0903 557.435 554.504 0.976 0.965 0.054 4.126-3.266 94.74 2603 46 0.0828 508.132 504.148 1.044 0.966 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.489 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.348 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.422 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1280 82.395 81.377 1.046 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.221 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0372 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1545 | n_water=805 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1278 r_free=0.1552 | n_water=795 | time (s): 110.140 (total time: 112.610) Filter (q & B) r_work=0.1279 r_free=0.1552 | n_water=790 | time (s): 5.270 (total time: 117.880) Compute maps r_work=0.1279 r_free=0.1552 | n_water=790 | time (s): 1.670 (total time: 119.550) Filter (map) r_work=0.1304 r_free=0.1535 | n_water=654 | time (s): 4.990 (total time: 124.540) Find peaks r_work=0.1304 r_free=0.1535 | n_water=654 | time (s): 0.610 (total time: 125.150) Add new water r_work=0.1328 r_free=0.1565 | n_water=964 | time (s): 4.470 (total time: 129.620) Refine new water occ: r_work=0.1284 r_free=0.1521 adp: r_work=0.1271 r_free=0.1515 occ: r_work=0.1274 r_free=0.1516 adp: r_work=0.1267 r_free=0.1514 occ: r_work=0.1268 r_free=0.1514 adp: r_work=0.1265 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1265 r_free=0.1514 r_work=0.1265 r_free=0.1514 | n_water=964 | time (s): 84.370 (total time: 213.990) Filter (q & B) r_work=0.1269 r_free=0.1514 | n_water=892 | time (s): 5.050 (total time: 219.040) Filter (dist only) r_work=0.1270 r_free=0.1514 | n_water=891 | time (s): 109.590 (total time: 328.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.065457 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.781988 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1255 0.1531 0.0276 0.041 1.1 18.0 0.0 0.0 0 11.533 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.31 2.76 2.030 15.151 594.782 0.014 12.31 15.16 2.85 2.383 15.221 594.782 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.57 16.35 1.20 523 3272 Protein: 5.38 40.71 10.96 1.20 0 2902 Water: 6.60 68.57 33.89 N/A 523 368 Other: 16.38 32.66 24.52 N/A 0 2 Chain A: 5.51 56.50 12.96 N/A 0 1624 Chain B: 5.38 68.21 12.79 N/A 0 1648 Chain S: 12.19 68.57 38.07 N/A 523 0 Histogram: Values Number of atoms 5.38 - 11.70 2061 11.70 - 18.02 720 18.02 - 24.34 267 24.34 - 30.65 205 30.65 - 36.97 170 36.97 - 43.29 169 43.29 - 49.61 102 49.61 - 55.93 55 55.93 - 62.25 35 62.25 - 68.57 11 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1516 r_work=0.1232 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1517 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 = 0.1521 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1521 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013355 | | target function (ls_wunit_k1) not normalized (work): 2501.411400 | | target function (ls_wunit_k1) not normalized (free): 104.125543 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1225 0.1521 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1606 n_refl.: 191136 remove outliers: r(all,work,free)=0.1433 0.1430 0.1606 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1605 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1526 n_refl.: 191136 remove outliers: r(all,work,free)=0.1237 0.1232 0.1526 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3131 402.814 382.109 0.486 0.963 0.270 13.296-10.522 98.02 98 1 0.1913 527.329 520.013 0.760 0.964 0.227 10.503-8.327 98.90 177 3 0.1411 564.205 566.338 0.920 0.964 0.187 8.318-6.595 100.00 360 8 0.1540 414.736 414.855 0.934 0.963 0.144 6.588-5.215 100.00 711 7 0.1356 381.101 377.322 0.912 0.963 0.123 5.214-4.128 98.38 1367 28 0.0823 557.435 556.021 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0761 508.132 505.629 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0858 342.774 341.390 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0904 258.603 256.755 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.628 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.351 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.218 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0479 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1526 | n_water=891 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1233 r_free=0.1527 | n_water=888 | time (s): 113.680 (total time: 116.440) Filter (q & B) r_work=0.1233 r_free=0.1527 | n_water=885 | time (s): 4.620 (total time: 121.060) Compute maps r_work=0.1233 r_free=0.1527 | n_water=885 | time (s): 2.310 (total time: 123.370) Filter (map) r_work=0.1273 r_free=0.1527 | n_water=693 | time (s): 5.220 (total time: 128.590) Find peaks r_work=0.1273 r_free=0.1527 | n_water=693 | time (s): 0.810 (total time: 129.400) Add new water r_work=0.1296 r_free=0.1554 | n_water=1013 | time (s): 5.260 (total time: 134.660) Refine new water occ: r_work=0.1251 r_free=0.1519 adp: r_work=0.1251 r_free=0.1521 occ: r_work=0.1247 r_free=0.1517 adp: r_work=0.1247 r_free=0.1518 occ: r_work=0.1244 r_free=0.1516 adp: r_work=0.1243 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1517 r_work=0.1243 r_free=0.1517 | n_water=1013 | time (s): 297.130 (total time: 431.790) Filter (q & B) r_work=0.1249 r_free=0.1522 | n_water=872 | time (s): 5.180 (total time: 436.970) Filter (dist only) r_work=0.1249 r_free=0.1519 | n_water=870 | time (s): 114.400 (total time: 551.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.725476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.474730 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1439 0.0201 0.035 1.1 7.0 0.0 0.0 0 0.863 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.39 2.01 1.927 14.562 15.475 3.937 12.36 14.00 1.65 2.257 14.458 15.475 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.76 15.23 1.03 503 3271 Protein: 5.53 36.31 10.70 1.03 0 2902 Water: 6.68 67.76 30.34 N/A 503 367 Other: 14.06 28.36 21.21 N/A 0 2 Chain A: 5.56 55.44 12.71 N/A 0 1624 Chain B: 5.53 67.76 12.49 N/A 0 1647 Chain S: 14.71 64.49 32.34 N/A 503 0 Histogram: Values Number of atoms 5.53 - 11.75 2131 11.75 - 17.97 700 17.97 - 24.20 286 24.20 - 30.42 229 30.42 - 36.64 173 36.64 - 42.87 152 42.87 - 49.09 71 49.09 - 55.31 21 55.31 - 61.53 9 61.53 - 67.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1400 r_work=0.1236 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1401 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1389 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892337 | | target function (ml) not normalized (work): 729015.302316 | | target function (ml) not normalized (free): 15222.987425 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1388 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1479 n_refl.: 191136 remove outliers: r(all,work,free)=0.1445 0.1444 0.1479 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1439 0.1476 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1382 n_refl.: 191136 remove outliers: r(all,work,free)=0.1229 0.1226 0.1382 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3686 398.895 359.192 0.419 0.946 0.241 13.296-10.522 98.02 98 1 0.2459 527.329 509.101 0.709 0.948 0.204 10.503-8.327 97.80 175 3 0.1996 554.286 556.797 0.887 0.948 0.166 8.318-6.595 100.00 360 8 0.2105 414.736 410.148 0.896 0.947 0.125 6.588-5.215 100.00 711 7 0.1829 381.101 371.215 0.886 0.947 0.107 5.214-4.128 98.38 1367 28 0.1167 557.435 551.973 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1106 508.132 501.083 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1086 342.774 339.041 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0970 258.603 255.772 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.400 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.484 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.315 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0963 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1382 | n_water=870 | time (s): 2.910 (total time: 2.910) Filter (dist) r_work=0.1227 r_free=0.1383 | n_water=869 | time (s): 111.960 (total time: 114.870) Filter (q & B) r_work=0.1227 r_free=0.1384 | n_water=861 | time (s): 5.150 (total time: 120.020) Compute maps r_work=0.1227 r_free=0.1384 | n_water=861 | time (s): 2.540 (total time: 122.560) Filter (map) r_work=0.1250 r_free=0.1389 | n_water=715 | time (s): 4.270 (total time: 126.830) Find peaks r_work=0.1250 r_free=0.1389 | n_water=715 | time (s): 0.670 (total time: 127.500) Add new water r_work=0.1265 r_free=0.1404 | n_water=964 | time (s): 4.800 (total time: 132.300) Refine new water occ: r_work=0.1225 r_free=0.1370 adp: r_work=0.1226 r_free=0.1370 occ: r_work=0.1223 r_free=0.1369 adp: r_work=0.1223 r_free=0.1369 occ: r_work=0.1220 r_free=0.1368 adp: r_work=0.1220 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1368 r_work=0.1220 r_free=0.1368 | n_water=964 | time (s): 329.510 (total time: 461.810) Filter (q & B) r_work=0.1224 r_free=0.1370 | n_water=883 | time (s): 5.650 (total time: 467.460) Filter (dist only) r_work=0.1225 r_free=0.1369 | n_water=882 | time (s): 113.160 (total time: 580.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.647731 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.864517 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 0.1223 0.1376 0.0153 0.036 1.1 7.8 0.0 0.3 0 0.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 13.76 1.53 1.812 14.220 15.865 3.886 12.16 13.74 1.58 1.899 14.182 15.865 3.877 Individual atomic B min max mean iso aniso Overall: 5.54 67.39 15.05 0.99 515 3271 Protein: 5.54 33.37 10.63 0.99 0 2902 Water: 6.69 67.39 29.58 N/A 515 367 Other: 14.04 27.54 20.79 N/A 0 2 Chain A: 5.56 54.47 12.59 N/A 0 1624 Chain B: 5.54 67.39 12.41 N/A 0 1647 Chain S: 13.02 64.53 31.26 N/A 515 0 Histogram: Values Number of atoms 5.54 - 11.72 2133 11.72 - 17.91 720 17.91 - 24.09 307 24.09 - 30.28 210 30.28 - 36.46 181 36.46 - 42.65 142 42.65 - 48.83 64 48.83 - 55.02 20 55.02 - 61.20 7 61.20 - 67.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1374 r_work=0.1216 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1374 target_work(ml) = 3.877 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1373 target_work(ml) = 3.875 | | 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1214 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.875096 | | target function (ml) not normalized (work): 725770.554354 | | target function (ml) not normalized (free): 15177.291113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1214 0.1373 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1418 0.1417 0.1481 n_refl.: 191132 remove outliers: r(all,work,free)=0.1418 0.1417 0.1481 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1411 0.1410 0.1476 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1213 0.1370 n_refl.: 191132 remove outliers: r(all,work,free)=0.1215 0.1212 0.1370 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3668 356.751 327.987 0.414 0.949 0.237 13.296-10.522 96.04 96 1 0.2355 480.536 454.481 0.696 0.951 0.182 10.503-8.327 97.80 175 3 0.2055 502.017 496.035 0.869 0.951 0.157 8.318-6.595 100.00 360 8 0.2140 375.627 371.039 0.889 0.951 0.118 6.588-5.215 100.00 711 7 0.1894 345.163 335.186 0.884 0.951 0.097 5.214-4.128 98.38 1367 28 0.1208 504.869 499.642 0.969 0.951 0.070 4.126-3.266 94.74 2603 46 0.1128 460.216 453.682 1.031 0.952 0.009 3.266-2.585 99.86 5447 97 0.1109 310.450 307.142 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0954 234.217 231.816 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0942 138.621 137.245 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.1012 74.626 73.891 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1668 40.033 38.369 1.034 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1212 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1212 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1212 r_free=0.1370 | n_water=882 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1213 r_free=0.1370 | n_water=880 | time (s): 115.040 (total time: 117.330) Filter (q & B) r_work=0.1213 r_free=0.1371 | n_water=867 | time (s): 4.660 (total time: 121.990) Compute maps r_work=0.1213 r_free=0.1371 | n_water=867 | time (s): 1.790 (total time: 123.780) Filter (map) r_work=0.1235 r_free=0.1373 | n_water=746 | time (s): 4.930 (total time: 128.710) Find peaks r_work=0.1235 r_free=0.1373 | n_water=746 | time (s): 0.580 (total time: 129.290) Add new water r_work=0.1246 r_free=0.1390 | n_water=964 | time (s): 4.810 (total time: 134.100) Refine new water occ: r_work=0.1200 r_free=0.1356 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1191 r_free=0.1350 occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1191 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1350 r_work=0.1191 r_free=0.1350 | n_water=964 | time (s): 194.450 (total time: 328.550) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=849 | time (s): 5.460 (total time: 334.010) Filter (dist only) r_work=0.1197 r_free=0.1356 | n_water=848 | time (s): 110.010 (total time: 444.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558643 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.967920 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 0.1200 0.1359 0.0160 0.036 1.1 5.1 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.59 1.60 1.782 13.950 14.968 3.765 12.02 13.61 1.59 1.817 13.940 14.968 3.763 Individual atomic B min max mean iso aniso Overall: 5.56 67.16 14.70 0.96 482 3270 Protein: 5.56 32.39 10.59 0.96 0 2902 Water: 6.02 67.16 28.75 N/A 482 366 Other: 13.74 26.75 20.24 N/A 0 2 Chain A: 5.64 53.99 12.51 N/A 0 1623 Chain B: 5.56 67.16 12.35 N/A 0 1647 Chain S: 6.02 64.53 30.09 N/A 482 0 Histogram: Values Number of atoms 5.56 - 11.72 2139 11.72 - 17.88 723 17.88 - 24.04 338 24.04 - 30.20 186 30.20 - 36.36 154 36.36 - 42.52 125 42.52 - 48.68 60 48.68 - 54.84 18 54.84 - 61.00 7 61.00 - 67.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1358 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761795 | | target function (ml) not normalized (work): 704539.124854 | | target function (ml) not normalized (free): 14747.182555 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1358 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1412 0.1410 0.1486 n_refl.: 191129 remove outliers: r(all,work,free)=0.1412 0.1410 0.1486 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1404 0.1403 0.1481 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3680 356.751 325.783 0.408 0.950 0.237 13.296-10.522 96.04 96 1 0.2320 480.536 466.826 0.714 0.952 0.194 10.503-8.327 97.80 175 3 0.2130 502.017 494.677 0.856 0.952 0.173 8.318-6.595 100.00 360 8 0.2239 375.627 369.937 0.883 0.951 0.105 6.588-5.215 100.00 711 7 0.1939 345.163 335.203 0.883 0.952 0.090 5.214-4.128 98.38 1367 28 0.1226 504.869 499.154 0.968 0.952 0.080 4.126-3.266 94.74 2603 46 0.1152 460.216 453.455 1.032 0.952 0.005 3.266-2.585 99.86 5447 97 0.1097 310.450 307.134 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0942 234.217 231.714 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0919 138.621 137.292 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.0979 74.626 73.900 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.033 38.366 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=-0.1254 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1359 | n_water=848 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1199 r_free=0.1359 | n_water=848 | time (s): 100.850 (total time: 103.610) Filter (q & B) r_work=0.1200 r_free=0.1359 | n_water=840 | time (s): 4.420 (total time: 108.030) Compute maps r_work=0.1200 r_free=0.1359 | n_water=840 | time (s): 2.040 (total time: 110.070) Filter (map) r_work=0.1220 r_free=0.1360 | n_water=739 | time (s): 4.840 (total time: 114.910) Find peaks r_work=0.1220 r_free=0.1360 | n_water=739 | time (s): 0.880 (total time: 115.790) Add new water r_work=0.1233 r_free=0.1373 | n_water=958 | time (s): 5.230 (total time: 121.020) Refine new water occ: r_work=0.1196 r_free=0.1343 adp: r_work=0.1196 r_free=0.1342 occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1343 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1344 r_work=0.1192 r_free=0.1344 | n_water=958 | time (s): 247.050 (total time: 368.070) Filter (q & B) r_work=0.1196 r_free=0.1350 | n_water=890 | time (s): 5.910 (total time: 373.980) Filter (dist only) r_work=0.1196 r_free=0.1350 | n_water=889 | time (s): 118.670 (total time: 492.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.588199 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.671003 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 0.1198 0.1357 0.0159 0.037 1.1 5.3 0.0 0.3 0 0.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.57 1.59 1.761 14.025 14.671 3.761 12.02 13.61 1.59 1.895 13.973 14.671 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 66.09 14.81 0.90 523 3270 Protein: 5.58 29.48 10.48 0.90 0 2902 Water: 6.00 66.09 28.91 N/A 523 366 Other: 13.81 23.97 18.89 N/A 0 2 Chain A: 5.65 53.46 12.37 N/A 0 1623 Chain B: 5.58 66.09 12.22 N/A 0 1647 Chain S: 6.00 64.70 30.50 N/A 523 0 Histogram: Values Number of atoms 5.58 - 11.63 2121 11.63 - 17.68 775 17.68 - 23.73 283 23.73 - 29.78 204 29.78 - 35.83 178 35.83 - 41.88 130 41.88 - 47.93 70 47.93 - 53.99 22 53.99 - 60.04 7 60.04 - 66.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758300 | | target function (ml) not normalized (work): 703884.489482 | | target function (ml) not normalized (free): 14740.939048 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1501 n_refl.: 191129 remove outliers: r(all,work,free)=0.1405 0.1403 0.1501 n_refl.: 191129 overall B=-0.22 to atoms: r(all,work,free)=0.1369 0.1367 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3773 356.751 321.482 0.402 0.951 0.219 13.296-10.522 96.04 96 1 0.2383 480.536 463.478 0.722 0.952 0.169 10.503-8.327 97.80 175 3 0.2115 502.017 495.781 0.882 0.953 0.147 8.318-6.595 100.00 360 8 0.2195 375.627 370.481 0.907 0.952 0.100 6.588-5.215 100.00 711 7 0.1916 345.163 335.757 0.907 0.953 0.100 5.214-4.128 98.38 1367 28 0.1226 504.869 499.643 0.992 0.953 0.045 4.126-3.266 94.74 2603 46 0.1158 460.216 453.160 1.057 0.953 0.009 3.266-2.585 99.86 5447 97 0.1113 310.450 307.155 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.217 231.664 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0915 138.621 137.301 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0969 74.626 73.915 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.033 38.365 1.026 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1365 | n_water=889 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1199 r_free=0.1365 | n_water=889 | time (s): 109.620 (total time: 112.790) Filter (q & B) r_work=0.1200 r_free=0.1366 | n_water=880 | time (s): 4.740 (total time: 117.530) Compute maps r_work=0.1200 r_free=0.1366 | n_water=880 | time (s): 2.290 (total time: 119.820) Filter (map) r_work=0.1223 r_free=0.1369 | n_water=755 | time (s): 5.940 (total time: 125.760) Find peaks r_work=0.1223 r_free=0.1369 | n_water=755 | time (s): 0.850 (total time: 126.610) Add new water r_work=0.1233 r_free=0.1383 | n_water=959 | time (s): 4.990 (total time: 131.600) Refine new water occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1198 r_free=0.1346 occ: r_work=0.1196 r_free=0.1347 adp: r_work=0.1196 r_free=0.1347 occ: r_work=0.1194 r_free=0.1347 adp: r_work=0.1194 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1347 r_work=0.1194 r_free=0.1347 | n_water=959 | time (s): 304.490 (total time: 436.090) Filter (q & B) r_work=0.1197 r_free=0.1354 | n_water=893 | time (s): 4.100 (total time: 440.190) Filter (dist only) r_work=0.1198 r_free=0.1354 | n_water=892 | time (s): 115.940 (total time: 556.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.483006 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.370958 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 0.1359 0.0157 0.037 1.1 6.1 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.59 1.57 1.719 13.701 14.371 3.760 12.04 13.63 1.60 1.779 13.677 14.371 3.758 Individual atomic B min max mean iso aniso Overall: 5.41 64.75 14.54 0.88 526 3270 Protein: 5.41 28.29 10.24 0.88 0 2902 Water: 5.82 64.75 28.54 N/A 526 366 Other: 13.66 21.98 17.82 N/A 0 2 Chain A: 5.47 52.65 12.09 N/A 0 1623 Chain B: 5.41 64.64 11.94 N/A 0 1647 Chain S: 5.82 64.75 30.26 N/A 526 0 Histogram: Values Number of atoms 5.41 - 11.35 2103 11.35 - 17.28 789 17.28 - 23.21 282 23.21 - 29.15 202 29.15 - 35.08 176 35.08 - 41.02 124 41.02 - 46.95 81 46.95 - 52.88 30 52.88 - 58.82 5 58.82 - 64.75 4 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1364 r_work=0.1204 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1364 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757906 | | target function (ml) not normalized (work): 703810.727680 | | target function (ml) not normalized (free): 14742.168554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1367 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1484 n_refl.: 191129 remove outliers: r(all,work,free)=0.1377 0.1375 0.1484 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1386 0.1384 0.1490 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3772 356.751 320.782 0.391 0.973 0.213 13.296-10.522 96.04 96 1 0.2403 480.536 463.898 0.709 0.975 0.161 10.503-8.327 97.80 175 3 0.2145 502.017 494.976 0.869 0.975 0.140 8.318-6.595 100.00 360 8 0.2213 375.627 370.236 0.892 0.975 0.105 6.588-5.215 100.00 711 7 0.1912 345.163 335.497 0.893 0.976 0.100 5.214-4.128 98.38 1367 28 0.1230 504.869 498.961 0.979 0.976 0.045 4.126-3.266 94.74 2603 46 0.1174 460.216 452.610 1.043 0.978 0.014 3.266-2.585 99.86 5447 97 0.1118 310.450 306.838 1.025 0.978 0.000 2.585-2.046 97.45 10613 204 0.0957 234.217 231.540 1.033 0.980 0.000 2.046-1.619 99.39 21536 464 0.0912 138.621 137.219 1.049 0.982 0.000 1.619-1.281 98.00 42464 925 0.0950 74.626 73.952 1.038 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.033 38.333 1.004 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1355 | n_water=892 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1193 r_free=0.1355 | n_water=892 | time (s): 111.990 (total time: 115.240) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=878 | time (s): 4.790 (total time: 120.030) Compute maps r_work=0.1194 r_free=0.1356 | n_water=878 | time (s): 1.990 (total time: 122.020) Filter (map) r_work=0.1217 r_free=0.1364 | n_water=762 | time (s): 4.670 (total time: 126.690) Find peaks r_work=0.1217 r_free=0.1364 | n_water=762 | time (s): 0.880 (total time: 127.570) Add new water r_work=0.1227 r_free=0.1378 | n_water=969 | time (s): 4.480 (total time: 132.050) Refine new water occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1342 r_work=0.1188 r_free=0.1342 | n_water=969 | time (s): 228.820 (total time: 360.870) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=902 | time (s): 4.200 (total time: 365.070) Filter (dist only) r_work=0.1192 r_free=0.1348 | n_water=901 | time (s): 115.190 (total time: 480.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.487186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.930095 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 0.1356 0.0160 0.038 1.1 6.0 0.0 0.3 0 0.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.56 1.60 1.674 13.713 14.930 3.757 11.95 13.57 1.62 1.688 13.701 14.930 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 64.91 14.60 0.88 535 3270 Protein: 5.49 28.21 10.31 0.88 0 2902 Water: 5.92 64.91 28.43 N/A 535 366 Other: 13.75 22.14 17.95 N/A 0 2 Chain A: 5.58 52.31 12.12 N/A 0 1623 Chain B: 5.49 63.75 11.99 N/A 0 1647 Chain S: 5.92 64.91 30.20 N/A 535 0 Histogram: Values Number of atoms 5.49 - 11.43 2110 11.43 - 17.38 793 17.38 - 23.32 276 23.32 - 29.26 205 29.26 - 35.20 190 35.20 - 41.14 120 41.14 - 47.09 70 47.09 - 53.03 32 53.03 - 58.97 5 58.97 - 64.91 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1357 r_work=0.1195 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1357 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 = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753583 | | target function (ml) not normalized (work): 703001.053092 | | target function (ml) not normalized (free): 14733.239708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1488 n_refl.: 191129 remove outliers: r(all,work,free)=0.1391 0.1389 0.1488 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1393 0.1391 0.1490 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1357 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1357 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3798 356.751 319.436 0.383 0.973 0.203 13.296-10.522 96.04 96 1 0.2384 480.536 463.703 0.701 0.975 0.147 10.503-8.327 97.80 175 3 0.2166 502.017 494.208 0.864 0.976 0.123 8.318-6.595 100.00 360 8 0.2190 375.627 369.688 0.890 0.975 0.101 6.588-5.215 100.00 711 7 0.1949 345.163 335.325 0.888 0.976 0.080 5.214-4.128 98.38 1367 28 0.1252 504.869 499.007 0.978 0.977 0.035 4.126-3.266 94.74 2603 46 0.1179 460.216 452.511 1.042 0.978 0.009 3.266-2.585 99.86 5447 97 0.1123 310.450 306.815 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0959 234.217 231.518 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.621 137.238 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0943 74.626 73.966 1.041 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.033 38.324 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0210 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1357 | n_water=901 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1192 r_free=0.1356 | n_water=900 | time (s): 127.870 (total time: 130.500) Filter (q & B) r_work=0.1193 r_free=0.1355 | n_water=887 | time (s): 4.770 (total time: 135.270) Compute maps r_work=0.1193 r_free=0.1355 | n_water=887 | time (s): 2.450 (total time: 137.720) Filter (map) r_work=0.1217 r_free=0.1357 | n_water=770 | time (s): 5.730 (total time: 143.450) Find peaks r_work=0.1217 r_free=0.1357 | n_water=770 | time (s): 0.880 (total time: 144.330) Add new water r_work=0.1225 r_free=0.1369 | n_water=969 | time (s): 4.380 (total time: 148.710) Refine new water occ: r_work=0.1190 r_free=0.1339 adp: r_work=0.1190 r_free=0.1339 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1340 r_work=0.1186 r_free=0.1340 | n_water=969 | time (s): 287.040 (total time: 435.750) Filter (q & B) r_work=0.1190 r_free=0.1349 | n_water=903 | time (s): 5.900 (total time: 441.650) Filter (dist only) r_work=0.1191 r_free=0.1349 | n_water=902 | time (s): 114.740 (total time: 556.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531756 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.158093 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 0.1355 0.0162 0.038 1.1 5.6 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.55 1.62 1.679 13.715 14.158 3.754 11.95 13.59 1.64 1.683 13.710 14.158 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 64.97 14.60 0.86 536 3270 Protein: 5.50 28.04 10.33 0.86 0 2902 Water: 5.95 64.97 28.31 N/A 536 366 Other: 13.78 22.09 17.94 N/A 0 2 Chain A: 5.63 52.21 12.12 N/A 0 1623 Chain B: 5.50 63.36 11.99 N/A 0 1647 Chain S: 5.95 64.97 30.11 N/A 536 0 Histogram: Values Number of atoms 5.50 - 11.45 2096 11.45 - 17.40 809 17.40 - 23.34 280 23.34 - 29.29 214 29.29 - 35.24 179 35.24 - 41.18 117 41.18 - 47.13 74 47.13 - 53.08 28 53.08 - 59.03 5 59.03 - 64.97 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1359 r_work=0.1195 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754011 | | target function (ml) not normalized (work): 703081.246939 | | target function (ml) not normalized (free): 14737.816863 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1495 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1401 0.1495 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1402 0.1400 0.1494 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3809 356.751 318.066 0.370 0.994 0.200 13.296-10.522 96.04 96 1 0.2396 480.536 463.877 0.681 0.996 0.141 10.503-8.327 97.80 175 3 0.2191 502.017 494.022 0.844 0.997 0.117 8.318-6.595 100.00 360 8 0.2200 375.627 369.584 0.869 0.997 0.096 6.588-5.215 100.00 711 7 0.1952 345.163 335.345 0.869 0.997 0.077 5.214-4.128 98.38 1367 28 0.1250 504.869 498.934 0.957 0.998 0.035 4.126-3.266 94.74 2603 46 0.1182 460.216 452.509 1.020 0.999 0.009 3.266-2.585 99.86 5447 97 0.1129 310.450 306.811 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.217 231.507 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.621 137.232 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0942 74.626 73.971 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.033 38.318 0.991 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0072 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1360 After: r_work=0.1194 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1364 | n_water=902 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1195 r_free=0.1364 | n_water=901 | time (s): 125.320 (total time: 127.700) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=889 | time (s): 4.890 (total time: 132.590) Compute maps r_work=0.1196 r_free=0.1362 | n_water=889 | time (s): 1.710 (total time: 134.300) Filter (map) r_work=0.1221 r_free=0.1368 | n_water=767 | time (s): 5.360 (total time: 139.660) Find peaks r_work=0.1221 r_free=0.1368 | n_water=767 | time (s): 0.810 (total time: 140.470) Add new water r_work=0.1228 r_free=0.1379 | n_water=969 | time (s): 5.080 (total time: 145.550) Refine new water occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1343 occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 | n_water=969 | time (s): 233.040 (total time: 378.590) Filter (q & B) r_work=0.1194 r_free=0.1354 | n_water=892 | time (s): 5.570 (total time: 384.160) Filter (dist only) r_work=0.1194 r_free=0.1354 | n_water=890 | time (s): 116.410 (total time: 500.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.501183 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.243079 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 0.1198 0.1358 0.0161 0.038 1.2 7.8 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.58 1.61 1.676 13.674 13.243 3.757 12.00 13.61 1.61 1.677 13.671 13.243 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 62.95 14.52 0.85 524 3270 Protein: 5.57 27.80 10.34 0.85 0 2902 Water: 6.01 62.95 28.15 N/A 524 366 Other: 13.80 22.16 17.98 N/A 0 2 Chain A: 5.65 52.07 12.10 N/A 0 1623 Chain B: 5.57 62.95 11.98 N/A 0 1647 Chain S: 6.01 59.69 30.00 N/A 524 0 Histogram: Values Number of atoms 5.57 - 11.31 2059 11.31 - 17.05 829 17.05 - 22.79 280 22.79 - 28.52 199 28.52 - 34.26 186 34.26 - 40.00 115 40.00 - 45.74 80 45.74 - 51.47 34 51.47 - 57.21 8 57.21 - 62.95 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1361 r_work=0.1200 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757436 | | target function (ml) not normalized (work): 703722.684710 | | target function (ml) not normalized (free): 14739.379113 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1372 0.1459 5.6955 5.765| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1352 5.0815 5.175| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1210 4.6632 4.7725| | 4: 2.04 - 1.85 1.00 7170 155 0.0908 0.1047 4.4027 4.5669| | 5: 1.85 - 1.72 0.99 7113 159 0.0941 0.1015 4.1594 4.2579| | 6: 1.72 - 1.62 0.99 7102 142 0.0902 0.1103 3.9523 4.0839| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0973 3.8025 3.9334| | 8: 1.54 - 1.47 0.96 6798 152 0.0898 0.1308 3.7059 3.9037| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1132 3.6277 3.7573| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1197 3.5631 3.6866| | 11: 1.36 - 1.32 0.99 6997 151 0.1001 0.1124 3.4921 3.5944| | 12: 1.32 - 1.28 0.98 6975 149 0.1039 0.1129 3.4645 3.5848| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1243 3.4399 3.5612| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1587 3.4337 3.6799| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1248 3.4497 3.4929| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1543 3.4661 3.6536| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1223 3.4338 3.439| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1714 3.4383 3.5337| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1762 3.4197 3.6006| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1583 3.4107 3.4336| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2131 3.4183 3.5033| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1951 3.4127 3.4149| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2029 3.4335 3.4887| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2257 3.4364 3.514| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2513 3.45 3.5229| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2855 3.4163 3.4241| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2808 3.4692 3.3989| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.65 1.00 0.95 11191.11| | 2: 2.94 - 2.33 7339 128 0.93 12.84 0.99 0.95 5151.48| | 3: 2.33 - 2.04 6939 150 0.96 7.78 1.01 0.95 1733.41| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.95 1022.36| | 5: 1.85 - 1.72 7113 159 0.96 8.20 1.00 0.96 647.20| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.96 449.29| | 7: 1.62 - 1.54 7104 148 0.96 8.20 1.01 0.97 339.66| | 8: 1.54 - 1.47 6798 152 0.96 8.32 1.01 0.97 281.45| | 9: 1.47 - 1.41 6938 155 0.96 8.53 1.00 0.98 233.29| | 10: 1.41 - 1.36 7022 150 0.96 9.04 1.00 0.97 205.72| | 11: 1.36 - 1.32 6997 151 0.96 9.05 0.99 0.96 177.64| | 12: 1.32 - 1.28 6975 149 0.96 9.07 0.98 0.95 162.57| | 13: 1.28 - 1.25 6907 166 0.96 9.55 1.01 0.96 158.75| | 14: 1.25 - 1.22 7015 112 0.95 10.68 1.01 0.96 163.02| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.98 166.07| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 159.77| | 17: 1.17 - 1.14 6940 135 0.94 12.22 1.01 0.96 153.66| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.95 147.86| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.95 151.47| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.94 150.36| | 21: 1.08 - 1.07 6852 152 0.91 16.65 1.00 0.93 153.37| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 155.15| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.92 165.46| | 24: 1.03 - 1.02 6784 133 0.85 23.22 0.99 0.93 179.79| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.90 182.75| | 26: 1.01 - 0.99 6767 158 0.81 26.69 0.98 0.88 177.37| | 27: 0.99 - 0.98 6647 131 0.82 26.45 0.99 0.87 162.41| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.86 max = 11191.11 mean = 929.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.34| |phase err.(test): min = 0.00 max = 88.79 mean = 13.52| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1500 n_refl.: 191129 remove outliers: r(all,work,free)=0.1415 0.1414 0.1500 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1406 0.1404 0.1494 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3727 356.751 319.348 0.371 0.994 0.214 13.296-10.522 96.04 96 1 0.2423 480.536 461.709 0.667 0.996 0.147 10.503-8.327 97.80 175 3 0.2186 502.017 493.716 0.822 0.996 0.120 8.318-6.595 100.00 360 8 0.2190 375.627 369.448 0.851 0.996 0.101 6.588-5.215 100.00 711 7 0.1959 345.163 335.102 0.849 0.997 0.083 5.214-4.128 98.38 1367 28 0.1257 504.869 498.993 0.934 0.998 0.034 4.126-3.266 94.74 2603 46 0.1179 460.216 452.424 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1126 310.450 306.877 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0968 234.217 231.505 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0918 138.621 137.223 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0951 74.626 73.964 0.992 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.033 38.313 0.961 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0119 ================= 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 : 0.2028 0.1987 0.083 5.214 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1929 0.083 5.214 5.2 78.0 14.6 805 0.000 1_settarget: 0.1794 0.1929 0.083 5.214 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1929 0.083 5.214 5.2 78.0 14.6 805 0.002 1_weight: 0.1796 0.1929 0.083 5.214 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1271 0.1506 0.038 1.159 5.2 78.0 14.6 805 0.156 1_adp: 0.1297 0.1570 0.038 1.159 5.1 73.0 14.9 805 0.156 1_regHadp: 0.1296 0.1565 0.038 1.159 5.1 73.0 14.9 805 0.156 1_occ: 0.1282 0.1556 0.038 1.159 5.1 73.0 14.9 805 0.156 2_bss: 0.1274 0.1545 0.038 1.159 5.3 73.2 15.1 805 0.156 2_settarget: 0.1274 0.1545 0.038 1.159 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1274 0.1545 0.038 1.171 5.3 73.2 15.1 805 0.156 2_nqh: 0.1274 0.1545 0.038 1.171 5.3 73.2 15.1 805 0.156 2_sol: 0.1270 0.1514 0.038 1.171 5.3 73.2 16.2 891 n/a 2_weight: 0.1270 0.1514 0.038 1.171 5.3 73.2 16.2 891 n/a 2_xyzrec: 0.1255 0.1531 0.041 1.139 5.3 73.2 16.2 891 n/a 2_adp: 0.1231 0.1516 0.041 1.139 5.4 68.6 16.3 891 n/a 2_regHadp: 0.1232 0.1517 0.041 1.139 5.4 68.6 16.3 891 n/a 2_occ: 0.1225 0.1521 0.041 1.139 5.4 68.6 16.3 891 n/a 3_bss: 0.1232 0.1526 0.041 1.139 5.4 68.6 16.3 891 n/a 3_settarget: 0.1232 0.1526 0.041 1.139 5.4 68.6 16.3 891 n/a 3_updatecdl: 0.1232 0.1526 0.041 1.139 5.4 68.6 16.3 891 n/a 3_nqh: 0.1232 0.1526 0.041 1.139 5.4 68.6 16.3 891 n/a 3_sol: 0.1249 0.1519 0.041 1.139 5.4 68.2 15.4 870 n/a 3_weight: 0.1249 0.1519 0.041 1.139 5.4 68.2 15.4 870 n/a 3_xyzrec: 0.1238 0.1439 0.035 1.102 5.4 68.2 15.4 870 n/a 3_adp: 0.1236 0.1400 0.035 1.102 5.5 67.8 15.2 870 n/a 3_regHadp: 0.1236 0.1401 0.035 1.102 5.5 67.8 15.2 870 n/a 3_occ: 0.1230 0.1389 0.035 1.102 5.5 67.8 15.2 870 n/a 4_bss: 0.1226 0.1382 0.035 1.102 5.5 67.7 15.2 870 n/a 4_settarget: 0.1226 0.1382 0.035 1.102 5.5 67.7 15.2 870 n/a 4_updatecdl: 0.1226 0.1382 0.035 1.106 5.5 67.7 15.2 870 n/a 4_nqh: 0.1226 0.1382 0.035 1.106 5.5 67.7 15.2 870 n/a 4_sol: 0.1225 0.1369 0.035 1.106 5.5 67.7 15.1 882 n/a 4_weight: 0.1225 0.1369 0.035 1.106 5.5 67.7 15.1 882 n/a 4_xyzrec: 0.1223 0.1376 0.036 1.128 5.5 67.7 15.1 882 n/a 4_adp: 0.1216 0.1374 0.036 1.128 5.5 67.4 15.0 882 n/a 4_regHadp: 0.1216 0.1374 0.036 1.128 5.5 67.4 15.0 882 n/a 4_occ: 0.1214 0.1373 0.036 1.128 5.5 67.4 15.0 882 n/a 5_bss: 0.1212 0.1370 0.036 1.128 5.5 67.4 15.0 882 n/a 5_settarget: 0.1212 0.1370 0.036 1.128 5.5 67.4 15.0 882 n/a 5_updatecdl: 0.1212 0.1370 0.036 1.128 5.5 67.4 15.0 882 n/a 5_nqh: 0.1212 0.1370 0.036 1.128 5.5 67.4 15.0 882 n/a 5_sol: 0.1197 0.1356 0.036 1.128 5.5 67.4 14.7 848 n/a 5_weight: 0.1197 0.1356 0.036 1.128 5.5 67.4 14.7 848 n/a 5_xyzrec: 0.1200 0.1359 0.036 1.131 5.5 67.4 14.7 848 n/a 5_adp: 0.1202 0.1361 0.036 1.131 5.6 67.2 14.7 848 n/a 5_regHadp: 0.1202 0.1361 0.036 1.131 5.6 67.2 14.7 848 n/a 5_occ: 0.1201 0.1358 0.036 1.131 5.6 67.2 14.7 848 n/a 6_bss: 0.1199 0.1359 0.036 1.131 5.5 67.1 14.7 848 n/a 6_settarget: 0.1199 0.1359 0.036 1.131 5.5 67.1 14.7 848 n/a 6_updatecdl: 0.1199 0.1359 0.036 1.131 5.5 67.1 14.7 848 n/a 6_nqh: 0.1199 0.1359 0.036 1.131 5.5 67.1 14.7 848 n/a 6_sol: 0.1196 0.1350 0.036 1.131 5.5 67.1 14.9 889 n/a 6_weight: 0.1196 0.1350 0.036 1.131 5.5 67.1 14.9 889 n/a 6_xyzrec: 0.1198 0.1357 0.037 1.127 5.5 67.1 14.9 889 n/a 6_adp: 0.1202 0.1361 0.037 1.127 5.6 66.1 14.8 889 n/a 6_regHadp: 0.1202 0.1361 0.037 1.127 5.6 66.1 14.8 889 n/a 6_occ: 0.1200 0.1366 0.037 1.127 5.6 66.1 14.8 889 n/a 7_bss: 0.1199 0.1365 0.037 1.127 5.4 65.9 14.6 889 n/a 7_settarget: 0.1199 0.1365 0.037 1.127 5.4 65.9 14.6 889 n/a 7_updatecdl: 0.1199 0.1365 0.037 1.126 5.4 65.9 14.6 889 n/a 7_nqh: 0.1199 0.1365 0.037 1.126 5.4 65.9 14.6 889 n/a 7_sol: 0.1198 0.1354 0.037 1.126 5.4 65.9 14.6 892 n/a 7_weight: 0.1198 0.1354 0.037 1.126 5.4 65.9 14.6 892 n/a 7_xyzrec: 0.1202 0.1359 0.037 1.120 5.4 65.9 14.6 892 n/a 7_adp: 0.1204 0.1364 0.037 1.120 5.4 64.8 14.5 892 n/a 7_regHadp: 0.1204 0.1364 0.037 1.120 5.4 64.8 14.5 892 n/a 7_occ: 0.1202 0.1367 0.037 1.120 5.4 64.8 14.5 892 n/a 8_bss: 0.1193 0.1355 0.037 1.120 5.5 64.8 14.6 892 n/a 8_settarget: 0.1193 0.1355 0.037 1.120 5.5 64.8 14.6 892 n/a 8_updatecdl: 0.1193 0.1355 0.037 1.121 5.5 64.8 14.6 892 n/a 8_nqh: 0.1193 0.1355 0.037 1.121 5.5 64.8 14.6 892 n/a 8_sol: 0.1192 0.1348 0.037 1.121 5.5 64.8 14.6 901 n/a 8_weight: 0.1192 0.1348 0.037 1.121 5.5 64.8 14.6 901 n/a 8_xyzrec: 0.1195 0.1356 0.038 1.111 5.5 64.8 14.6 901 n/a 8_adp: 0.1195 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 8_regHadp: 0.1195 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 8_occ: 0.1193 0.1359 0.038 1.111 5.5 64.9 14.6 901 n/a 9_bss: 0.1192 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 9_settarget: 0.1192 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 9_updatecdl: 0.1192 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 9_nqh: 0.1192 0.1357 0.038 1.111 5.5 64.9 14.6 901 n/a 9_sol: 0.1191 0.1349 0.038 1.111 5.5 64.9 14.6 902 n/a 9_weight: 0.1191 0.1349 0.038 1.111 5.5 64.9 14.6 902 n/a 9_xyzrec: 0.1194 0.1355 0.038 1.115 5.5 64.9 14.6 902 n/a 9_adp: 0.1195 0.1359 0.038 1.115 5.5 65.0 14.6 902 n/a 9_regHadp: 0.1195 0.1359 0.038 1.115 5.5 65.0 14.6 902 n/a 9_occ: 0.1194 0.1361 0.038 1.115 5.5 65.0 14.6 902 n/a 10_bss: 0.1193 0.1360 0.038 1.115 5.5 65.0 14.6 902 n/a 10_settarget: 0.1193 0.1360 0.038 1.115 5.5 65.0 14.6 902 n/a 10_updatecdl: 0.1193 0.1360 0.038 1.115 5.5 65.0 14.6 902 n/a 10_setrh: 0.1194 0.1361 0.038 1.115 5.5 65.0 14.6 902 n/a 10_nqh: 0.1195 0.1364 0.038 1.115 5.5 65.0 14.6 902 n/a 10_sol: 0.1194 0.1354 0.038 1.115 5.5 63.4 14.5 890 n/a 10_weight: 0.1194 0.1354 0.038 1.115 5.5 63.4 14.5 890 n/a 10_xyzrec: 0.1198 0.1358 0.038 1.156 5.5 63.4 14.5 890 n/a 10_adp: 0.1200 0.1361 0.038 1.156 5.6 63.0 14.5 890 n/a 10_regHadp: 0.1200 0.1361 0.038 1.156 5.6 63.0 14.5 890 n/a 10_occ: 0.1199 0.1359 0.038 1.156 5.6 63.0 14.5 890 n/a end: 0.1198 0.1359 0.038 1.156 5.5 62.9 14.5 890 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3904915_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3904915_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2200 Refinement macro-cycles (run) : 12415.5100 Write final files (write_after_run_outputs) : 129.2100 Total : 12550.9400 Total CPU time: 3.50 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:46:22 PST -0800 (1736736382.74 s) Start R-work = 0.1794, R-free = 0.1929 Final R-work = 0.1198, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12800.10 seconds wall clock time: 214 minutes 22.46 seconds (12862.46 seconds total)