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_1450452.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1450452.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1450452.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 =============================================================================== 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: 1.63, per 1000 atoms: 0.24 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: 2.819 distance_ideal: 2.720 ideal - model: -0.099 slack: 0.000 delta_slack: -0.099 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: 2.723 distance_ideal: 2.710 ideal - model: -0.013 slack: 0.000 delta_slack: -0.013 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: 0.90 Conformation dependent library (CDL) restraints added in 198.8 milliseconds Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.06: 1055 1.06 - 1.28: 2413 1.28 - 1.51: 1572 1.51 - 1.74: 875 1.74 - 1.96: 19 Bond restraints: 5934 Sorted by residual: bond pdb=" N VAL A 62 " pdb=" CA VAL A 62 " ideal model delta sigma weight residual 1.457 1.651 -0.194 9.30e-03 1.16e+04 4.35e+02 bond pdb=" N ASP A 40 " pdb=" H ASP A 40 " ideal model delta sigma weight residual 0.860 1.264 -0.404 2.00e-02 2.50e+03 4.09e+02 bond pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 1.524 1.733 -0.208 1.05e-02 9.07e+03 3.94e+02 bond pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 1.522 1.294 0.228 1.19e-02 7.06e+03 3.69e+02 bond pdb=" N PRO B 11 " pdb=" CD PRO B 11 " ideal model delta sigma weight residual 1.473 1.738 -0.265 1.40e-02 5.10e+03 3.59e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 5886 4.35 - 8.69: 3525 8.69 - 13.04: 1177 13.04 - 17.38: 203 17.38 - 21.73: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" OD1 ASN A 123 " pdb=" CG ASN A 123 " pdb=" ND2 ASN A 123 " ideal model delta sigma weight residual 122.60 104.33 18.27 1.00e+00 1.00e+00 3.34e+02 angle pdb=" O ARG B 175 " pdb=" C ARG B 175 " pdb=" N GLU B 176 " ideal model delta sigma weight residual 122.03 106.96 15.07 1.04e+00 9.25e-01 2.10e+02 angle pdb=" O LEU A 88 " pdb=" C LEU A 88 " pdb=" N VAL A 89 " ideal model delta sigma weight residual 122.20 139.25 -17.05 1.21e+00 6.83e-01 1.99e+02 angle pdb=" O VAL B 102 " pdb=" C VAL B 102 " pdb=" N ALA B 103 " ideal model delta sigma weight residual 123.20 108.59 14.61 1.06e+00 8.90e-01 1.90e+02 angle pdb=" N VAL B 62 " pdb=" CA VAL B 62 " pdb=" C VAL B 62 " ideal model delta sigma weight residual 113.20 126.37 -13.17 9.60e-01 1.09e+00 1.88e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 1867 17.66 - 35.32: 123 35.32 - 52.98: 41 52.98 - 70.64: 15 70.64 - 88.29: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " pdb=" CA PRO B 11 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 213 0.216 - 0.431: 147 0.431 - 0.647: 80 0.647 - 0.862: 43 0.862 - 1.078: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 3.51 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA ASP B 64 " pdb=" N ASP B 64 " pdb=" C ASP B 64 " pdb=" CB ASP B 64 " both_signs ideal model delta sigma weight residual False 2.51 3.57 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.174 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE B 164 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.039 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.088 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.087 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " -0.083 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR A 67 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " 0.130 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.120 2.00e-02 2.50e+03 6.41e-02 1.23e+02 pdb=" CG PHE A 82 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " 0.043 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " 0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " -0.132 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 31 1.62 - 2.37: 2454 2.37 - 3.11: 22370 3.11 - 3.86: 33014 3.86 - 4.60: 52366 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110235 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.877 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.009 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.028 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.071 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.149 2.620 ... (remaining 110230 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_1450452_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= 0.2031 r_free= 0.1966 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295521 | | target function (ml) not normalized (work): 804606.875858 | | target function (ml) not normalized (free): 16516.094327 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1900 6.7026 6.2974| | 2: 2.94 - 2.33 1.00 7339 128 0.1612 0.1726 5.5302 5.6011| | 3: 2.33 - 2.04 0.96 6939 150 0.1658 0.1563 5.1516 5.109| | 4: 2.04 - 1.85 1.00 7170 155 0.1753 0.1740 4.9566 5.0663| | 5: 1.85 - 1.72 0.99 7113 159 0.1906 0.1691 4.7921 4.821| | 6: 1.72 - 1.62 0.99 7102 142 0.1951 0.1876 4.6552 4.6966| | 7: 1.62 - 1.54 0.99 7104 148 0.2008 0.1829 4.562 4.5708| | 8: 1.54 - 1.47 0.96 6798 152 0.2020 0.2159 4.4673 4.5002| | 9: 1.47 - 1.41 0.98 6938 155 0.2115 0.2074 4.3982 4.3998| | 10: 1.41 - 1.36 0.99 7022 150 0.2137 0.1986 4.3015 4.2641| | 11: 1.36 - 1.32 0.99 6997 151 0.2125 0.2247 4.2273 4.3326| | 12: 1.32 - 1.28 0.98 6976 149 0.2087 0.1813 4.166 4.1474| | 13: 1.28 - 1.25 0.98 6907 166 0.2028 0.2086 4.1072 4.1839| | 14: 1.25 - 1.22 0.98 7015 113 0.2098 0.2152 4.0839 4.1968| | 15: 1.22 - 1.19 0.98 6957 137 0.2084 0.1993 4.0366 4.0259| | 16: 1.19 - 1.17 0.93 6604 132 0.2103 0.2210 3.9931 4.0753| | 17: 1.17 - 1.14 0.98 6941 135 0.2145 0.1984 3.953 4.0423| | 18: 1.14 - 1.12 0.98 6875 142 0.2230 0.2116 3.9244 3.8471| | 19: 1.12 - 1.10 0.97 6949 106 0.2250 0.2359 3.8659 3.9915| | 20: 1.10 - 1.08 0.97 6884 147 0.2272 0.2344 3.8047 3.9042| | 21: 1.08 - 1.07 0.97 6852 152 0.2393 0.2340 3.775 3.739| | 22: 1.07 - 1.05 0.97 6838 135 0.2570 0.2485 3.7563 3.7543| | 23: 1.05 - 1.03 0.97 6829 159 0.2730 0.2669 3.7309 3.7954| | 24: 1.03 - 1.02 0.96 6785 133 0.2839 0.2649 3.6871 3.7418| | 25: 1.02 - 1.01 0.93 6552 130 0.3083 0.3188 3.6751 3.7822| | 26: 1.01 - 0.99 0.96 6767 158 0.3212 0.3262 3.6275 3.6328| | 27: 0.99 - 0.98 0.94 6648 131 0.3393 0.3324 3.6331 3.5939| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.14 0.91 0.97 34278.89| | 2: 2.94 - 2.33 7339 128 0.86 20.91 1.08 1.02 14691.72| | 3: 2.33 - 2.04 6939 150 0.93 12.57 1.11 1.05 4149.80| | 4: 2.04 - 1.85 7170 155 0.92 13.47 1.11 1.07 2784.80| | 5: 1.85 - 1.72 7113 159 0.91 15.46 1.11 1.08 2044.72| | 6: 1.72 - 1.62 7102 142 0.90 16.37 1.11 1.08 1604.44| | 7: 1.62 - 1.54 7104 148 0.90 17.27 1.11 1.07 1307.76| | 8: 1.54 - 1.47 6798 152 0.89 17.59 1.10 1.08 1087.32| | 9: 1.47 - 1.41 6938 155 0.89 17.96 1.10 1.06 887.41| | 10: 1.41 - 1.36 7022 150 0.89 18.57 1.10 1.06 756.06| | 11: 1.36 - 1.32 6997 151 0.88 19.23 1.08 1.04 676.63| | 12: 1.32 - 1.28 6976 149 0.88 19.57 1.09 1.03 631.04| | 13: 1.28 - 1.25 6907 166 0.87 19.92 1.08 1.03 597.95| | 14: 1.25 - 1.22 7015 113 0.86 20.81 1.08 1.03 578.65| | 15: 1.22 - 1.19 6957 137 0.86 21.21 1.08 1.03 555.85| | 16: 1.19 - 1.17 6604 132 0.87 20.92 1.08 1.02 497.15| | 17: 1.17 - 1.14 6941 135 0.87 20.64 1.08 1.02 432.56| | 18: 1.14 - 1.12 6875 142 0.87 20.17 1.08 1.00 368.94| | 19: 1.12 - 1.10 6949 106 0.86 21.16 1.07 1.00 356.01| | 20: 1.10 - 1.08 6884 147 0.86 21.91 1.06 0.98 330.93| | 21: 1.08 - 1.07 6852 152 0.85 22.87 1.06 0.99 318.90| | 22: 1.07 - 1.05 6838 135 0.83 24.49 1.05 0.98 306.14| | 23: 1.05 - 1.03 6829 159 0.81 26.84 1.05 0.98 316.53| | 24: 1.03 - 1.02 6785 133 0.78 29.46 1.05 0.97 328.95| | 25: 1.02 - 1.01 6552 130 0.76 31.25 1.03 0.93 320.16| | 26: 1.01 - 0.99 6767 158 0.74 32.92 1.02 0.91 301.12| | 27: 0.99 - 0.98 6648 131 0.75 32.67 1.04 0.89 277.01| |alpha: min = 0.89 max = 1.08 mean = 1.02| |beta: min = 277.01 max = 34278.89 mean = 2744.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.26| |phase err.(test): min = 0.00 max = 87.48 mean = 21.27| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.265 2950 Z= 5.489 Angle : 5.249 18.935 4018 Z= 3.730 Chirality : 0.384 1.078 492 Planarity : 0.032 0.191 512 Dihedral : 12.547 88.294 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.85 % Favored : 96.63 % Rotamer: Outliers : 0.97 % Allowed : 3.55 % Favored : 95.48 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.40), residues: 386 helix: -2.82 (0.30), residues: 146 sheet: -1.45 (0.54), residues: 86 loop : -0.11 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.119 0.024 ARG A 149 TYR 0.091 0.037 TYR B 194 PHE 0.116 0.034 PHE B 164 TRP 0.098 0.037 TRP A 139 HIS 0.075 0.033 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= 0.2031 r_free= 0.1966 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295521 | | target function (ml) not normalized (work): 804606.875858 | | target function (ml) not normalized (free): 16516.094327 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2031 0.1966 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2031 0.1966 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2031 0.1966 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2029 0.2031 0.1966 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1796 0.1899 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1794 0.1899 n_refl.: 191141 ======================== 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 96.04 94 3 0.4274 400.535 295.065 0.434 0.913 0.303 13.296-10.522 100.00 100 1 0.2533 534.497 522.626 0.788 0.913 0.253 10.503-8.327 99.45 178 3 0.2573 565.118 555.642 0.971 0.914 0.227 8.318-6.595 100.00 360 8 0.2510 414.736 404.183 0.967 0.913 0.155 6.588-5.215 100.00 711 7 0.2258 381.101 364.980 0.955 0.913 0.124 5.214-4.128 98.38 1367 28 0.1480 557.435 550.198 1.074 0.914 0.100 4.126-3.266 94.74 2603 46 0.1350 508.132 499.418 1.142 0.914 0.014 3.266-2.585 99.86 5447 97 0.1441 342.774 337.923 1.117 0.913 0.000 2.585-2.046 97.45 10613 204 0.1407 258.603 254.342 1.126 0.913 0.000 2.046-1.619 99.39 21536 464 0.1602 153.054 149.856 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1913 82.395 80.233 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2308 44.203 41.713 1.112 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0006 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1899 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 123 ASN Total number of N/Q/H flips: 2 r_work=0.1800 r_free=0.1911 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.265767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.531613 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 0.1273 0.1507 0.0233 0.039 1.1 10.9 0.0 0.0 0 11.133 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.07 2.33 1.117 13.110 571.532 0.019 12.92 15.61 2.69 1.206 13.318 571.532 0.017 Individual atomic B min max mean iso aniso Overall: 5.26 73.04 14.97 1.40 435 3274 Protein: 5.26 40.53 11.00 1.40 0 2902 Water: 6.39 73.04 29.28 N/A 435 370 Other: 15.96 29.95 22.96 N/A 0 2 Chain A: 5.42 60.04 13.02 N/A 0 1626 Chain B: 5.26 73.04 12.76 N/A 0 1648 Chain S: 12.19 61.69 30.66 N/A 435 0 Histogram: Values Number of atoms 5.26 - 12.03 2175 12.03 - 18.81 632 18.81 - 25.59 319 25.59 - 32.37 269 32.37 - 39.15 154 39.15 - 45.93 100 45.93 - 52.71 36 52.71 - 59.49 18 59.49 - 66.26 5 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1293 r_free=0.1562 r_work=0.1292 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1292 r_free = 0.1557 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 = 0.1277 r_free = 0.1548 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1277 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015644 | | target function (ls_wunit_k1) not normalized (work): 2930.076024 | | target function (ls_wunit_k1) not normalized (free): 117.134385 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1283 0.1277 0.1548 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1626 n_refl.: 191141 remove outliers: r(all,work,free)=0.1471 0.1468 0.1626 n_refl.: 191141 overall B=0.15 to atoms: r(all,work,free)=0.1494 0.1491 0.1636 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1275 0.1270 0.1535 n_refl.: 191141 remove outliers: r(all,work,free)=0.1275 0.1270 0.1534 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3582 402.814 377.584 0.461 1.002 0.270 13.296-10.522 100.00 100 1 0.2129 534.497 526.904 0.713 1.003 0.235 10.503-8.327 99.45 178 3 0.1775 565.118 564.441 0.854 1.003 0.230 8.318-6.595 100.00 360 8 0.1713 414.736 412.603 0.872 1.003 0.145 6.588-5.215 100.00 711 7 0.1546 381.101 373.346 0.852 1.003 0.140 5.214-4.128 98.38 1367 28 0.0905 557.435 554.121 0.939 1.003 0.080 4.126-3.266 94.74 2603 46 0.0840 508.132 504.191 1.002 1.004 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.355 0.985 1.004 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.393 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1083 153.054 151.414 1.014 1.004 0.000 1.619-1.281 98.00 42464 925 0.1265 82.395 81.439 1.008 1.005 0.000 1.281-0.980 96.53 101826 2055 0.1864 44.202 42.171 0.984 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0346 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1270 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1270 r_free=0.1534 | n_water=805 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1275 r_free=0.1541 | n_water=793 | time (s): 102.990 (total time: 106.050) Filter (q & B) r_work=0.1275 r_free=0.1540 | n_water=790 | time (s): 5.210 (total time: 111.260) Compute maps r_work=0.1275 r_free=0.1540 | n_water=790 | time (s): 1.790 (total time: 113.050) Filter (map) r_work=0.1299 r_free=0.1524 | n_water=655 | time (s): 4.970 (total time: 118.020) Find peaks r_work=0.1299 r_free=0.1524 | n_water=655 | time (s): 0.580 (total time: 118.600) Add new water r_work=0.1322 r_free=0.1549 | n_water=954 | time (s): 4.670 (total time: 123.270) Refine new water occ: r_work=0.1280 r_free=0.1517 adp: r_work=0.1268 r_free=0.1510 occ: r_work=0.1270 r_free=0.1510 adp: r_work=0.1264 r_free=0.1507 occ: r_work=0.1265 r_free=0.1508 adp: r_work=0.1262 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1262 r_free=0.1507 r_work=0.1262 r_free=0.1507 | n_water=954 | time (s): 82.020 (total time: 205.290) Filter (q & B) r_work=0.1266 r_free=0.1508 | n_water=886 | time (s): 4.390 (total time: 209.680) Filter (dist only) r_work=0.1266 r_free=0.1508 | n_water=885 | time (s): 110.930 (total time: 320.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.031663 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.121877 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 0.1249 0.1518 0.0269 0.040 1.1 16.3 0.0 0.0 0 11.516 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.49 15.18 2.69 2.040 15.122 577.122 0.015 12.36 15.14 2.78 2.398 15.163 577.122 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 68.19 16.21 1.19 517 3272 Protein: 5.45 40.04 10.99 1.19 0 2902 Water: 6.55 68.19 33.34 N/A 517 368 Other: 16.26 32.40 24.33 N/A 0 2 Chain A: 5.59 56.20 12.98 N/A 0 1624 Chain B: 5.45 68.19 12.80 N/A 0 1648 Chain S: 12.46 65.98 37.26 N/A 517 0 Histogram: Values Number of atoms 5.45 - 11.73 2064 11.73 - 18.00 712 18.00 - 24.27 256 24.27 - 30.55 221 30.55 - 36.82 181 36.82 - 43.10 161 43.10 - 49.37 106 49.37 - 55.65 50 55.65 - 61.92 31 61.92 - 68.19 7 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1514 r_work=0.1236 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1515 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 = 0.1229 r_free = 0.1508 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013584 | | target function (ls_wunit_k1) not normalized (work): 2544.195723 | | target function (ls_wunit_k1) not normalized (free): 101.977279 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1509 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1442 0.1439 0.1614 n_refl.: 191139 remove outliers: r(all,work,free)=0.1442 0.1439 0.1614 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1439 0.1436 0.1611 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1236 0.1519 n_refl.: 191139 remove outliers: r(all,work,free)=0.1242 0.1236 0.1519 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3324 402.814 376.023 0.491 0.962 0.273 13.296-10.522 100.00 100 1 0.1921 534.497 530.506 0.779 0.963 0.260 10.503-8.327 99.45 178 3 0.1424 565.118 566.837 0.916 0.963 0.181 8.318-6.595 100.00 360 8 0.1577 414.736 414.602 0.935 0.963 0.145 6.588-5.215 100.00 711 7 0.1379 381.101 376.226 0.910 0.963 0.127 5.214-4.128 98.38 1367 28 0.0827 557.435 556.118 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0764 508.132 505.461 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0860 342.774 341.265 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0902 258.603 256.751 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.619 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.349 1.075 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.212 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0584 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1519 | n_water=885 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1237 r_free=0.1519 | n_water=883 | time (s): 114.010 (total time: 116.620) Filter (q & B) r_work=0.1237 r_free=0.1520 | n_water=878 | time (s): 4.970 (total time: 121.590) Compute maps r_work=0.1237 r_free=0.1520 | n_water=878 | time (s): 2.560 (total time: 124.150) Filter (map) r_work=0.1272 r_free=0.1522 | n_water=703 | time (s): 5.630 (total time: 129.780) Find peaks r_work=0.1272 r_free=0.1522 | n_water=703 | time (s): 0.560 (total time: 130.340) Add new water r_work=0.1294 r_free=0.1567 | n_water=999 | time (s): 4.450 (total time: 134.790) Refine new water occ: r_work=0.1254 r_free=0.1531 adp: r_work=0.1255 r_free=0.1531 occ: r_work=0.1251 r_free=0.1528 adp: r_work=0.1251 r_free=0.1528 occ: r_work=0.1248 r_free=0.1526 adp: r_work=0.1248 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1526 r_work=0.1248 r_free=0.1526 | n_water=999 | time (s): 272.620 (total time: 407.410) Filter (q & B) r_work=0.1251 r_free=0.1534 | n_water=877 | time (s): 4.920 (total time: 412.330) Filter (dist only) r_work=0.1251 r_free=0.1534 | n_water=876 | time (s): 105.340 (total time: 517.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.682345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.998056 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 0.1242 0.1461 0.0218 0.035 1.1 8.0 0.0 0.0 0 0.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.42 14.61 2.18 1.926 14.561 16.998 3.942 12.33 14.20 1.87 2.217 14.467 16.998 3.898 Individual atomic B min max mean iso aniso Overall: 5.54 67.79 15.23 1.06 508 3272 Protein: 5.54 36.46 10.74 1.06 0 2902 Water: 6.67 67.79 30.09 N/A 508 368 Other: 14.14 28.06 21.10 N/A 0 2 Chain A: 5.55 55.28 12.74 N/A 0 1624 Chain B: 5.54 67.79 12.54 N/A 0 1648 Chain S: 15.01 61.60 31.91 N/A 508 0 Histogram: Values Number of atoms 5.54 - 11.77 2132 11.77 - 17.99 688 17.99 - 24.22 289 24.22 - 30.44 244 30.44 - 36.67 191 36.67 - 42.89 133 42.89 - 49.11 67 49.11 - 55.34 26 55.34 - 61.56 8 61.56 - 67.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1420 r_work=0.1234 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1420 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1405 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891589 | | target function (ml) not normalized (work): 728886.895434 | | target function (ml) not normalized (free): 15226.704949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1228 0.1405 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1504 n_refl.: 191139 remove outliers: r(all,work,free)=0.1445 0.1444 0.1504 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1437 0.1500 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1395 n_refl.: 191139 remove outliers: r(all,work,free)=0.1227 0.1224 0.1395 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3778 398.008 361.229 0.428 0.946 0.251 13.296-10.522 99.01 99 1 0.2515 528.187 512.387 0.714 0.947 0.219 10.503-8.327 98.35 176 3 0.1948 555.265 558.509 0.888 0.947 0.177 8.318-6.595 100.00 360 8 0.2074 414.736 410.562 0.896 0.947 0.124 6.588-5.215 100.00 711 7 0.1845 381.101 370.594 0.886 0.947 0.103 5.214-4.128 98.38 1367 28 0.1182 557.435 552.027 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1102 508.132 500.928 1.034 0.947 0.019 3.266-2.585 99.86 5447 97 0.1090 342.774 339.063 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0962 258.603 255.779 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0968 153.054 151.408 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.480 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.314 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1018 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1395 | n_water=876 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1224 r_free=0.1395 | n_water=874 | time (s): 108.740 (total time: 111.940) Filter (q & B) r_work=0.1225 r_free=0.1390 | n_water=857 | time (s): 4.970 (total time: 116.910) Compute maps r_work=0.1225 r_free=0.1390 | n_water=857 | time (s): 2.320 (total time: 119.230) Filter (map) r_work=0.1250 r_free=0.1387 | n_water=711 | time (s): 5.740 (total time: 124.970) Find peaks r_work=0.1250 r_free=0.1387 | n_water=711 | time (s): 0.760 (total time: 125.730) Add new water r_work=0.1267 r_free=0.1405 | n_water=960 | time (s): 4.890 (total time: 130.620) Refine new water occ: r_work=0.1217 r_free=0.1369 adp: r_work=0.1209 r_free=0.1364 occ: r_work=0.1207 r_free=0.1365 adp: r_work=0.1207 r_free=0.1365 occ: r_work=0.1207 r_free=0.1365 adp: r_work=0.1207 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1365 r_work=0.1207 r_free=0.1365 | n_water=960 | time (s): 147.190 (total time: 277.810) Filter (q & B) r_work=0.1211 r_free=0.1372 | n_water=841 | time (s): 5.260 (total time: 283.070) Filter (dist only) r_work=0.1211 r_free=0.1372 | n_water=840 | time (s): 108.090 (total time: 391.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541998 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.288273 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 0.1210 0.1371 0.0162 0.033 1.1 5.8 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.71 1.62 1.831 14.065 15.288 3.875 12.06 13.71 1.65 1.904 14.036 15.288 3.868 Individual atomic B min max mean iso aniso Overall: 5.53 67.46 14.75 1.00 472 3272 Protein: 5.53 33.65 10.68 1.00 0 2902 Water: 5.87 67.46 28.80 N/A 472 368 Other: 14.00 27.50 20.75 N/A 0 2 Chain A: 5.53 54.54 12.63 N/A 0 1624 Chain B: 5.54 67.46 12.47 N/A 0 1648 Chain S: 5.87 61.58 29.98 N/A 472 0 Histogram: Values Number of atoms 5.53 - 11.72 2122 11.72 - 17.92 718 17.92 - 24.11 338 24.11 - 30.30 213 30.30 - 36.50 142 36.50 - 42.69 121 42.69 - 48.88 62 48.88 - 55.07 22 55.07 - 61.27 4 61.27 - 67.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1371 r_work=0.1206 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1371 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1371 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.866620 | | target function (ml) not normalized (work): 724194.651976 | | target function (ml) not normalized (free): 15148.926673 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1371 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1494 n_refl.: 191135 remove outliers: r(all,work,free)=0.1438 0.1437 0.1494 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1430 0.1429 0.1489 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191135 remove outliers: r(all,work,free)=0.1205 0.1202 0.1367 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3818 360.530 323.461 0.416 0.945 0.251 13.296-10.522 98.02 98 1 0.2468 480.696 455.974 0.701 0.946 0.201 10.503-8.327 98.35 176 3 0.2110 502.979 495.273 0.864 0.947 0.177 8.315-6.595 100.00 359 8 0.2226 374.737 370.073 0.888 0.946 0.120 6.588-5.215 100.00 711 7 0.1935 345.215 335.092 0.886 0.946 0.120 5.214-4.128 98.38 1367 28 0.1218 504.945 499.499 0.974 0.947 0.070 4.126-3.266 94.74 2603 46 0.1134 460.285 453.413 1.036 0.947 0.005 3.266-2.585 99.86 5447 97 0.1096 310.497 307.305 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0939 234.252 231.817 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0916 138.642 137.340 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.0991 74.637 73.908 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.039 38.370 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1223 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1367 | n_water=840 | time (s): 3.110 (total time: 3.110) Filter (dist) r_work=0.1202 r_free=0.1367 | n_water=839 | time (s): 102.410 (total time: 105.520) Filter (q & B) r_work=0.1202 r_free=0.1367 | n_water=833 | time (s): 4.870 (total time: 110.390) Compute maps r_work=0.1202 r_free=0.1367 | n_water=833 | time (s): 1.580 (total time: 111.970) Filter (map) r_work=0.1226 r_free=0.1373 | n_water=716 | time (s): 4.270 (total time: 116.240) Find peaks r_work=0.1226 r_free=0.1373 | n_water=716 | time (s): 0.640 (total time: 116.880) Add new water r_work=0.1238 r_free=0.1391 | n_water=943 | time (s): 4.140 (total time: 121.020) Refine new water occ: r_work=0.1199 r_free=0.1356 adp: r_work=0.1200 r_free=0.1356 occ: r_work=0.1197 r_free=0.1354 adp: r_work=0.1197 r_free=0.1354 occ: r_work=0.1195 r_free=0.1353 adp: r_work=0.1195 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 | n_water=943 | time (s): 216.450 (total time: 337.470) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=881 | time (s): 5.090 (total time: 342.560) Filter (dist only) r_work=0.1198 r_free=0.1356 | n_water=880 | time (s): 114.750 (total time: 457.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.584777 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.209240 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 0.1362 0.0161 0.034 1.1 7.5 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.62 1.61 1.796 14.116 15.209 3.766 12.04 13.66 1.62 1.923 14.069 15.209 3.762 Individual atomic B min max mean iso aniso Overall: 5.55 66.89 14.87 0.95 512 3272 Protein: 5.55 31.42 10.57 0.95 0 2902 Water: 6.02 66.89 29.04 N/A 512 368 Other: 13.87 25.53 19.70 N/A 0 2 Chain A: 5.55 53.21 12.49 N/A 0 1624 Chain B: 5.55 66.89 12.34 N/A 0 1648 Chain S: 6.02 61.57 30.57 N/A 512 0 Histogram: Values Number of atoms 5.55 - 11.69 2132 11.69 - 17.82 736 17.82 - 23.95 302 23.95 - 30.09 223 30.09 - 36.22 172 36.22 - 42.35 125 42.35 - 48.49 66 48.49 - 54.62 20 54.62 - 60.75 6 60.75 - 66.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1366 r_work=0.1204 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.761 | | 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761454 | | target function (ml) not normalized (work): 704490.233322 | | target function (ml) not normalized (free): 14744.111129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1366 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1498 n_refl.: 191133 remove outliers: r(all,work,free)=0.1430 0.1429 0.1498 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1422 0.1420 0.1492 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1200 0.1364 n_refl.: 191133 remove outliers: r(all,work,free)=0.1203 0.1200 0.1364 n_refl.: 191131 ======================== 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 0.3819 361.334 315.546 0.392 0.947 0.225 13.296-10.522 97.03 97 1 0.2489 481.371 455.773 0.696 0.948 0.183 10.503-8.327 98.35 176 3 0.2149 502.979 495.206 0.863 0.949 0.163 8.315-6.595 100.00 359 8 0.2163 374.737 369.839 0.886 0.948 0.115 6.588-5.215 100.00 711 7 0.1913 345.215 335.334 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1223 504.945 499.493 0.974 0.949 0.080 4.126-3.266 94.74 2603 46 0.1150 460.285 453.298 1.035 0.949 0.000 3.266-2.585 99.86 5447 97 0.1105 310.497 307.266 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0950 234.252 231.763 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.642 137.340 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0977 74.637 73.924 1.056 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.039 38.374 1.044 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1364 | n_water=880 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1200 r_free=0.1365 | n_water=879 | time (s): 112.870 (total time: 115.960) Filter (q & B) r_work=0.1201 r_free=0.1366 | n_water=870 | time (s): 4.350 (total time: 120.310) Compute maps r_work=0.1201 r_free=0.1366 | n_water=870 | time (s): 2.030 (total time: 122.340) Filter (map) r_work=0.1223 r_free=0.1359 | n_water=751 | time (s): 4.100 (total time: 126.440) Find peaks r_work=0.1223 r_free=0.1359 | n_water=751 | time (s): 0.860 (total time: 127.300) Add new water r_work=0.1233 r_free=0.1376 | n_water=944 | time (s): 4.210 (total time: 131.510) Refine new water occ: r_work=0.1199 r_free=0.1351 adp: r_work=0.1199 r_free=0.1351 occ: r_work=0.1197 r_free=0.1349 adp: r_work=0.1197 r_free=0.1350 occ: r_work=0.1195 r_free=0.1349 adp: r_work=0.1195 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 | n_water=944 | time (s): 269.920 (total time: 401.430) Filter (q & B) r_work=0.1198 r_free=0.1358 | n_water=887 | time (s): 4.590 (total time: 406.020) Filter (dist only) r_work=0.1198 r_free=0.1357 | n_water=886 | time (s): 111.690 (total time: 517.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.827809 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 0.0159 0.035 1.1 6.6 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.59 1.59 1.753 13.979 14.828 3.761 12.02 13.61 1.59 1.863 13.941 14.828 3.758 Individual atomic B min max mean iso aniso Overall: 5.56 65.74 14.77 0.90 519 3271 Protein: 5.56 29.08 10.48 0.90 0 2902 Water: 5.94 65.74 28.82 N/A 519 367 Other: 13.90 22.97 18.43 N/A 0 2 Chain A: 5.62 51.81 12.36 N/A 0 1624 Chain B: 5.56 65.74 12.21 N/A 0 1647 Chain S: 5.94 61.63 30.45 N/A 519 0 Histogram: Values Number of atoms 5.56 - 11.58 2108 11.58 - 17.60 771 17.60 - 23.62 281 23.62 - 29.63 231 29.63 - 35.65 172 35.65 - 41.67 123 41.67 - 47.69 70 47.69 - 53.70 27 53.70 - 59.72 5 59.72 - 65.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757679 | | target function (ml) not normalized (work): 703775.786455 | | target function (ml) not normalized (free): 14731.336053 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1498 n_refl.: 191131 remove outliers: r(all,work,free)=0.1411 0.1410 0.1498 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1374 0.1372 0.1472 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191131 ======================== 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 0.3876 361.334 319.503 0.399 0.950 0.209 13.296-10.522 97.03 97 1 0.2426 481.371 461.085 0.714 0.951 0.168 10.503-8.327 98.35 176 3 0.2194 502.979 495.274 0.883 0.952 0.147 8.315-6.595 100.00 359 8 0.2164 374.737 369.335 0.905 0.951 0.110 6.588-5.215 100.00 711 7 0.1938 345.215 335.260 0.904 0.951 0.090 5.214-4.128 98.38 1367 28 0.1224 504.945 499.477 0.994 0.952 0.034 4.126-3.266 94.74 2603 46 0.1157 460.285 453.461 1.058 0.952 0.000 3.266-2.585 99.86 5447 97 0.1110 310.497 307.283 1.040 0.951 0.000 2.585-2.046 97.45 10613 204 0.0953 234.252 231.739 1.049 0.951 0.000 2.046-1.619 99.39 21536 464 0.0913 138.642 137.320 1.067 0.950 0.000 1.619-1.281 98.00 42464 925 0.0968 74.637 73.928 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.039 38.368 1.026 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0500 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1362 | n_water=886 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1199 r_free=0.1362 | n_water=886 | time (s): 110.010 (total time: 112.330) Filter (q & B) r_work=0.1200 r_free=0.1360 | n_water=878 | time (s): 4.050 (total time: 116.380) Compute maps r_work=0.1200 r_free=0.1360 | n_water=878 | time (s): 1.740 (total time: 118.120) Filter (map) r_work=0.1221 r_free=0.1365 | n_water=775 | time (s): 4.850 (total time: 122.970) Find peaks r_work=0.1221 r_free=0.1365 | n_water=775 | time (s): 0.630 (total time: 123.600) Add new water r_work=0.1229 r_free=0.1378 | n_water=966 | time (s): 4.390 (total time: 127.990) Refine new water occ: r_work=0.1198 r_free=0.1357 adp: r_work=0.1199 r_free=0.1358 occ: r_work=0.1197 r_free=0.1357 adp: r_work=0.1197 r_free=0.1357 occ: r_work=0.1197 r_free=0.1357 adp: r_work=0.1197 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1357 | n_water=966 | time (s): 189.680 (total time: 317.670) Filter (q & B) r_work=0.1200 r_free=0.1363 | n_water=885 | time (s): 4.310 (total time: 321.980) Filter (dist only) r_work=0.1201 r_free=0.1362 | n_water=883 | time (s): 108.100 (total time: 430.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539390 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.919252 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1369 0.0164 0.036 1.1 6.1 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.69 1.64 1.717 13.578 13.919 3.760 12.09 13.72 1.63 1.768 13.559 13.919 3.760 Individual atomic B min max mean iso aniso Overall: 5.37 64.48 14.35 0.87 516 3271 Protein: 5.37 28.02 10.23 0.87 0 2902 Water: 5.74 64.48 27.86 N/A 516 367 Other: 13.68 21.96 17.82 N/A 0 2 Chain A: 5.45 51.17 12.07 N/A 0 1624 Chain B: 5.37 64.48 11.94 N/A 0 1647 Chain S: 5.74 61.32 29.18 N/A 516 0 Histogram: Values Number of atoms 5.37 - 11.28 2077 11.28 - 17.19 806 17.19 - 23.11 302 23.11 - 29.02 226 29.02 - 34.93 162 34.93 - 40.84 102 40.84 - 46.75 78 46.75 - 52.66 27 52.66 - 58.57 4 58.57 - 64.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1372 r_work=0.1209 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1373 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1375 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1208 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759542 | | target function (ml) not normalized (work): 704124.714202 | | target function (ml) not normalized (free): 14746.873041 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1208 0.1375 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1488 n_refl.: 191131 remove outliers: r(all,work,free)=0.1389 0.1388 0.1488 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1398 0.1396 0.1493 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191131 ======================== 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 0.3934 361.334 317.845 0.370 0.995 0.195 13.296-10.522 97.03 97 1 0.2456 481.371 460.575 0.677 0.997 0.151 10.503-8.327 98.35 176 3 0.2296 502.979 492.673 0.842 0.998 0.130 8.315-6.595 100.00 359 8 0.2199 374.737 368.226 0.868 0.998 0.099 6.588-5.215 100.00 711 7 0.2007 345.215 333.868 0.867 0.998 0.083 5.214-4.128 98.38 1367 28 0.1267 504.945 498.544 0.959 0.999 0.070 4.126-3.266 94.74 2603 46 0.1178 460.285 452.798 1.020 1.000 0.000 3.266-2.585 99.86 5447 97 0.1130 310.497 306.906 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.252 231.582 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0910 138.642 137.264 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0951 74.637 73.969 1.015 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.039 38.342 0.982 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0565 ============================ 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=883 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1199 r_free=0.1365 | n_water=883 | time (s): 116.160 (total time: 118.870) Filter (q & B) r_work=0.1199 r_free=0.1365 | n_water=874 | time (s): 5.340 (total time: 124.210) Compute maps r_work=0.1199 r_free=0.1365 | n_water=874 | time (s): 2.350 (total time: 126.560) Filter (map) r_work=0.1220 r_free=0.1363 | n_water=768 | time (s): 4.220 (total time: 130.780) Find peaks r_work=0.1220 r_free=0.1363 | n_water=768 | time (s): 0.640 (total time: 131.420) Add new water r_work=0.1229 r_free=0.1378 | n_water=956 | time (s): 3.930 (total time: 135.350) Refine new water occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1355 occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1354 occ: r_work=0.1193 r_free=0.1354 adp: r_work=0.1193 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1354 r_work=0.1193 r_free=0.1354 | n_water=956 | time (s): 213.750 (total time: 349.100) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=895 | time (s): 4.360 (total time: 353.460) Filter (dist only) r_work=0.1196 r_free=0.1360 | n_water=894 | time (s): 115.000 (total time: 468.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537644 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.190061 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 0.1367 0.0167 0.036 1.1 7.8 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.67 1.67 1.670 13.654 14.190 3.758 11.99 13.68 1.69 1.690 13.641 14.190 3.755 Individual atomic B min max mean iso aniso Overall: 5.49 63.56 14.51 0.87 527 3271 Protein: 5.49 27.86 10.30 0.87 0 2902 Water: 5.91 63.56 28.18 N/A 527 367 Other: 13.75 22.03 17.89 N/A 0 2 Chain A: 5.56 50.78 12.10 N/A 0 1624 Chain B: 5.49 63.56 11.98 N/A 0 1647 Chain S: 5.91 61.32 29.85 N/A 527 0 Histogram: Values Number of atoms 5.49 - 11.30 2065 11.30 - 17.11 818 17.11 - 22.92 278 22.92 - 28.72 221 28.72 - 34.53 180 34.53 - 40.34 110 40.34 - 46.14 85 46.14 - 51.95 32 51.95 - 57.76 6 57.76 - 63.56 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1368 r_work=0.1199 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1368 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1369 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755072 | | target function (ml) not normalized (work): 703287.432798 | | target function (ml) not normalized (free): 14736.001784 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191131 remove outliers: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1402 0.1400 0.1497 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191131 ======================== 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 0.3950 361.334 317.902 0.368 0.995 0.193 13.296-10.522 97.03 97 1 0.2482 481.371 460.923 0.672 0.997 0.146 10.503-8.327 98.35 176 3 0.2265 502.979 493.084 0.842 0.997 0.123 8.315-6.595 100.00 359 8 0.2164 374.737 368.806 0.866 0.997 0.091 6.588-5.215 100.00 711 7 0.1983 345.215 333.897 0.865 0.998 0.073 5.214-4.128 98.38 1367 28 0.1261 504.945 498.694 0.959 0.999 0.060 4.126-3.266 94.74 2603 46 0.1178 460.285 452.611 1.020 1.000 0.000 3.266-2.585 99.86 5447 97 0.1135 310.497 306.871 1.002 1.001 0.000 2.585-2.046 97.45 10613 204 0.0966 234.252 231.579 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0907 138.642 137.277 1.027 1.005 0.000 1.619-1.281 98.00 42464 925 0.0944 74.637 73.983 1.018 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.039 38.327 0.988 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1367 | n_water=894 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1196 r_free=0.1367 | n_water=894 | time (s): 117.980 (total time: 121.050) Filter (q & B) r_work=0.1197 r_free=0.1366 | n_water=879 | time (s): 5.470 (total time: 126.520) Compute maps r_work=0.1197 r_free=0.1366 | n_water=879 | time (s): 2.470 (total time: 128.990) Filter (map) r_work=0.1220 r_free=0.1364 | n_water=761 | time (s): 5.150 (total time: 134.140) Find peaks r_work=0.1220 r_free=0.1364 | n_water=761 | time (s): 0.550 (total time: 134.690) Add new water r_work=0.1228 r_free=0.1376 | n_water=954 | time (s): 4.220 (total time: 138.910) Refine new water occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1351 occ: r_work=0.1192 r_free=0.1349 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=954 | time (s): 198.030 (total time: 336.940) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=896 | time (s): 5.400 (total time: 342.340) Filter (dist only) r_work=0.1195 r_free=0.1356 | n_water=894 | time (s): 109.840 (total time: 452.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.489692 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 0.1367 0.0169 0.037 1.1 6.0 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.67 1.69 1.674 13.665 13.490 3.756 12.00 13.70 1.70 1.669 13.665 13.490 3.756 Individual atomic B min max mean iso aniso Overall: 5.53 63.42 14.53 0.85 527 3271 Protein: 5.53 27.80 10.33 0.85 0 2902 Water: 5.98 63.42 28.18 N/A 527 367 Other: 13.79 22.04 17.91 N/A 0 2 Chain A: 5.60 50.72 12.11 N/A 0 1624 Chain B: 5.53 63.42 11.99 N/A 0 1647 Chain S: 5.98 61.33 29.93 N/A 527 0 Histogram: Values Number of atoms 5.53 - 11.32 2065 11.32 - 17.11 820 17.11 - 22.90 277 22.90 - 28.69 224 28.69 - 34.47 176 34.47 - 40.26 115 40.26 - 46.05 80 46.05 - 51.84 32 51.84 - 57.63 6 57.63 - 63.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1371 r_work=0.1200 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1371 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1372 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755533 | | target function (ml) not normalized (work): 703373.799513 | | target function (ml) not normalized (free): 14740.533282 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1372 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1410 0.1408 0.1512 n_refl.: 191131 remove outliers: r(all,work,free)=0.1410 0.1408 0.1512 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1409 0.1408 0.1511 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1369 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1369 n_refl.: 191131 ======================== 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 0.3966 361.334 315.876 0.372 0.975 0.189 13.296-10.522 97.03 97 1 0.2463 481.371 461.083 0.684 0.977 0.139 10.503-8.327 98.35 176 3 0.2256 502.979 493.220 0.859 0.978 0.117 8.315-6.595 100.00 359 8 0.2175 374.737 368.983 0.882 0.978 0.090 6.588-5.215 100.00 711 7 0.1974 345.215 334.569 0.883 0.978 0.073 5.214-4.128 98.38 1367 28 0.1257 504.945 498.704 0.977 0.979 0.029 4.126-3.266 94.74 2603 46 0.1180 460.285 452.498 1.041 0.980 0.000 3.266-2.585 99.86 5447 97 0.1142 310.497 306.896 1.023 0.981 0.000 2.585-2.046 97.45 10613 204 0.0969 234.252 231.551 1.032 0.983 0.000 2.046-1.619 99.39 21536 464 0.0911 138.642 137.270 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.637 73.985 1.040 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.039 38.316 1.011 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0116 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1198 r_free=0.1369 After: r_work=0.1198 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1198 r_free=0.1370 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=0.1199 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1373 | n_water=894 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1199 r_free=0.1373 | n_water=894 | time (s): 113.860 (total time: 116.520) Filter (q & B) r_work=0.1199 r_free=0.1373 | n_water=886 | time (s): 4.700 (total time: 121.220) Compute maps r_work=0.1199 r_free=0.1373 | n_water=886 | time (s): 2.200 (total time: 123.420) Filter (map) r_work=0.1221 r_free=0.1373 | n_water=770 | time (s): 4.940 (total time: 128.360) Find peaks r_work=0.1221 r_free=0.1373 | n_water=770 | time (s): 0.860 (total time: 129.220) Add new water r_work=0.1228 r_free=0.1385 | n_water=965 | time (s): 5.150 (total time: 134.370) Refine new water occ: r_work=0.1197 r_free=0.1364 adp: r_work=0.1197 r_free=0.1365 occ: r_work=0.1195 r_free=0.1363 adp: r_work=0.1195 r_free=0.1364 occ: r_work=0.1194 r_free=0.1362 adp: r_work=0.1193 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1364 r_work=0.1193 r_free=0.1364 | n_water=965 | time (s): 232.040 (total time: 366.410) Filter (q & B) r_work=0.1197 r_free=0.1369 | n_water=899 | time (s): 4.180 (total time: 370.590) Filter (dist only) r_work=0.1197 r_free=0.1369 | n_water=896 | time (s): 115.680 (total time: 486.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.517737 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.905334 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1374 0.0174 0.037 1.2 8.9 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.74 1.74 1.672 13.667 13.905 3.759 12.01 13.75 1.75 1.672 13.665 13.905 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 62.64 14.52 0.85 529 3271 Protein: 5.57 27.70 10.34 0.85 0 2902 Water: 6.01 62.64 28.05 N/A 529 367 Other: 13.85 21.98 17.92 N/A 0 2 Chain A: 5.64 50.38 12.10 N/A 0 1624 Chain B: 5.57 62.64 11.99 N/A 0 1647 Chain S: 6.01 61.26 29.84 N/A 529 0 Histogram: Values Number of atoms 5.57 - 11.28 2048 11.28 - 16.98 835 16.98 - 22.69 271 22.69 - 28.40 225 28.40 - 34.10 180 34.10 - 39.81 115 39.81 - 45.52 84 45.52 - 51.22 30 51.22 - 56.93 9 56.93 - 62.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1375 r_work=0.1201 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1375 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1375 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757397 | | target function (ml) not normalized (work): 703722.897767 | | target function (ml) not normalized (free): 14742.543787 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1380 0.1533 5.7043 5.795| | 2: 2.94 - 2.33 1.00 7339 128 0.1084 0.1368 5.0963 5.1966| | 3: 2.33 - 2.04 0.96 6939 150 0.0912 0.1212 4.6676 4.7636| | 4: 2.04 - 1.85 1.00 7170 155 0.0907 0.1063 4.4004 4.5721| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.1008 4.1543 4.2487| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1089 3.9479 4.0786| | 7: 1.62 - 1.54 0.99 7104 148 0.0890 0.0973 3.8003 3.9321| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1312 3.7029 3.9001| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1141 3.6248 3.7565| | 10: 1.41 - 1.36 0.99 7022 150 0.0978 0.1200 3.5589 3.6792| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1117 3.4866 3.5763| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1123 3.4604 3.583| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1261 3.4399 3.5727| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1598 3.4351 3.6885| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1241 3.4503 3.4929| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1549 3.4656 3.6504| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1236 3.4338 3.4458| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1708 3.4385 3.5364| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1768 3.4211 3.6041| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1584 3.4104 3.4332| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2152 3.4181 3.5086| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1954 3.4131 3.4153| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2021 3.4336 3.4872| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2274 3.4362 3.5156| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2519 3.4499 3.5213| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2855 3.416 3.4245| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2794 3.4695 3.3953| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7399 127 0.93 12.12 1.00 0.95 11803.48| | 2: 2.94 - 2.33 7339 128 0.92 13.18 0.99 0.95 5382.61| | 3: 2.33 - 2.04 6939 150 0.96 7.85 1.01 0.95 1759.74| | 4: 2.04 - 1.85 7170 155 0.96 7.79 1.00 0.95 1027.17| | 5: 1.85 - 1.72 7113 159 0.96 8.14 1.00 0.96 641.95| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.96 442.88| | 7: 1.62 - 1.54 7104 148 0.96 8.11 1.01 0.97 336.72| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.01 0.97 279.35| | 9: 1.47 - 1.41 6938 155 0.96 8.48 1.00 0.98 231.70| | 10: 1.41 - 1.36 7022 150 0.96 8.91 1.00 0.97 202.77| | 11: 1.36 - 1.32 6997 151 0.96 8.91 0.99 0.96 174.25| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 160.88| | 13: 1.28 - 1.25 6907 166 0.96 9.57 1.01 0.96 159.24| | 14: 1.25 - 1.22 7015 112 0.95 10.77 1.01 0.97 164.81| | 15: 1.22 - 1.19 6956 137 0.95 11.30 1.01 0.98 167.89| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.01 0.96 160.69| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.96 154.41| | 18: 1.14 - 1.12 6875 142 0.94 12.78 1.01 0.95 148.41| | 19: 1.12 - 1.10 6948 106 0.93 14.23 1.00 0.95 152.40| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.94 151.19| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.93 154.03| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.33| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.24| | 24: 1.03 - 1.02 6784 133 0.85 23.21 0.99 0.93 179.68| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.40| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.89 176.61| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.99 0.87 160.64| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.41 max = 11803.48 mean = 963.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.35| |phase err.(test): min = 0.00 max = 89.72 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1375 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1419 0.1417 0.1519 n_refl.: 191131 remove outliers: r(all,work,free)=0.1419 0.1417 0.1519 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1409 0.1407 0.1512 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1373 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1373 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3901 361.334 317.957 0.365 0.974 0.190 13.296-10.522 97.03 97 1 0.2477 481.371 459.513 0.664 0.976 0.131 10.503-8.327 98.35 176 3 0.2250 502.979 492.899 0.837 0.977 0.105 8.315-6.595 100.00 359 8 0.2162 374.737 368.627 0.863 0.977 0.091 6.588-5.215 100.00 711 7 0.1977 345.215 334.449 0.862 0.977 0.080 5.214-4.128 98.38 1367 28 0.1258 504.945 498.653 0.953 0.978 0.034 4.126-3.266 94.74 2603 46 0.1182 460.285 452.400 1.017 0.980 0.000 3.266-2.585 99.86 5447 97 0.1133 310.497 306.997 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0971 234.252 231.551 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0915 138.642 137.252 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0947 74.637 73.979 1.011 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.039 38.314 0.979 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0130 ================= 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 : 0.2031 0.1966 0.081 5.249 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1899 0.081 5.249 5.2 78.0 14.6 805 0.000 1_settarget: 0.1794 0.1899 0.081 5.249 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1911 0.081 5.249 5.2 78.0 14.6 805 0.003 1_weight: 0.1800 0.1911 0.081 5.249 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1273 0.1507 0.039 1.150 5.2 78.0 14.6 805 0.160 1_adp: 0.1293 0.1562 0.039 1.150 5.3 73.0 15.0 805 0.160 1_regHadp: 0.1292 0.1557 0.039 1.150 5.3 73.0 15.0 805 0.160 1_occ: 0.1277 0.1548 0.039 1.150 5.3 73.0 15.0 805 0.160 2_bss: 0.1270 0.1534 0.039 1.150 5.4 73.2 15.1 805 0.160 2_settarget: 0.1270 0.1534 0.039 1.150 5.4 73.2 15.1 805 0.160 2_updatecdl: 0.1270 0.1534 0.039 1.162 5.4 73.2 15.1 805 0.160 2_nqh: 0.1270 0.1534 0.039 1.162 5.4 73.2 15.1 805 0.160 2_sol: 0.1266 0.1508 0.039 1.162 5.4 73.2 16.1 885 n/a 2_weight: 0.1266 0.1508 0.039 1.162 5.4 73.2 16.1 885 n/a 2_xyzrec: 0.1249 0.1518 0.040 1.130 5.4 73.2 16.1 885 n/a 2_adp: 0.1236 0.1514 0.040 1.130 5.5 68.2 16.2 885 n/a 2_regHadp: 0.1236 0.1515 0.040 1.130 5.5 68.2 16.2 885 n/a 2_occ: 0.1229 0.1508 0.040 1.130 5.5 68.2 16.2 885 n/a 3_bss: 0.1236 0.1519 0.040 1.130 5.4 68.2 16.2 885 n/a 3_settarget: 0.1236 0.1519 0.040 1.130 5.4 68.2 16.2 885 n/a 3_updatecdl: 0.1236 0.1519 0.040 1.133 5.4 68.2 16.2 885 n/a 3_nqh: 0.1236 0.1519 0.040 1.133 5.4 68.2 16.2 885 n/a 3_sol: 0.1251 0.1534 0.040 1.133 5.4 68.2 15.4 876 n/a 3_weight: 0.1251 0.1534 0.040 1.133 5.4 68.2 15.4 876 n/a 3_xyzrec: 0.1242 0.1461 0.035 1.098 5.4 68.2 15.4 876 n/a 3_adp: 0.1233 0.1420 0.035 1.098 5.5 67.8 15.2 876 n/a 3_regHadp: 0.1234 0.1420 0.035 1.098 5.5 67.8 15.2 876 n/a 3_occ: 0.1228 0.1405 0.035 1.098 5.5 67.8 15.2 876 n/a 4_bss: 0.1224 0.1395 0.035 1.098 5.5 67.8 15.2 876 n/a 4_settarget: 0.1224 0.1395 0.035 1.098 5.5 67.8 15.2 876 n/a 4_updatecdl: 0.1224 0.1395 0.035 1.103 5.5 67.8 15.2 876 n/a 4_nqh: 0.1224 0.1395 0.035 1.103 5.5 67.8 15.2 876 n/a 4_sol: 0.1211 0.1372 0.035 1.103 5.5 67.8 14.8 840 n/a 4_weight: 0.1211 0.1372 0.035 1.103 5.5 67.8 14.8 840 n/a 4_xyzrec: 0.1210 0.1371 0.033 1.107 5.5 67.8 14.8 840 n/a 4_adp: 0.1206 0.1371 0.033 1.107 5.5 67.5 14.7 840 n/a 4_regHadp: 0.1206 0.1371 0.033 1.107 5.5 67.5 14.7 840 n/a 4_occ: 0.1204 0.1371 0.033 1.107 5.5 67.5 14.7 840 n/a 5_bss: 0.1202 0.1367 0.033 1.107 5.5 67.4 14.7 840 n/a 5_settarget: 0.1202 0.1367 0.033 1.107 5.5 67.4 14.7 840 n/a 5_updatecdl: 0.1202 0.1367 0.033 1.107 5.5 67.4 14.7 840 n/a 5_nqh: 0.1202 0.1367 0.033 1.107 5.5 67.4 14.7 840 n/a 5_sol: 0.1198 0.1356 0.033 1.107 5.5 67.4 15.0 880 n/a 5_weight: 0.1198 0.1356 0.033 1.107 5.5 67.4 15.0 880 n/a 5_xyzrec: 0.1200 0.1362 0.034 1.128 5.5 67.4 15.0 880 n/a 5_adp: 0.1204 0.1366 0.034 1.128 5.6 66.9 14.9 880 n/a 5_regHadp: 0.1204 0.1366 0.034 1.128 5.6 66.9 14.9 880 n/a 5_occ: 0.1202 0.1366 0.034 1.128 5.6 66.9 14.9 880 n/a 6_bss: 0.1200 0.1364 0.034 1.128 5.5 66.8 14.8 880 n/a 6_settarget: 0.1200 0.1364 0.034 1.128 5.5 66.8 14.8 880 n/a 6_updatecdl: 0.1200 0.1364 0.034 1.128 5.5 66.8 14.8 880 n/a 6_nqh: 0.1200 0.1364 0.034 1.128 5.5 66.8 14.8 880 n/a 6_sol: 0.1198 0.1357 0.034 1.128 5.5 66.8 14.8 886 n/a 6_weight: 0.1198 0.1357 0.034 1.128 5.5 66.8 14.8 886 n/a 6_xyzrec: 0.1200 0.1359 0.035 1.135 5.5 66.8 14.8 886 n/a 6_adp: 0.1202 0.1361 0.035 1.135 5.6 65.7 14.8 886 n/a 6_regHadp: 0.1202 0.1362 0.035 1.135 5.6 65.7 14.8 886 n/a 6_occ: 0.1200 0.1365 0.035 1.135 5.6 65.7 14.8 886 n/a 7_bss: 0.1199 0.1362 0.035 1.135 5.3 65.5 14.5 886 n/a 7_settarget: 0.1199 0.1362 0.035 1.135 5.3 65.5 14.5 886 n/a 7_updatecdl: 0.1199 0.1362 0.035 1.135 5.3 65.5 14.5 886 n/a 7_nqh: 0.1199 0.1362 0.035 1.135 5.3 65.5 14.5 886 n/a 7_sol: 0.1201 0.1362 0.035 1.135 5.3 65.5 14.4 883 n/a 7_weight: 0.1201 0.1362 0.035 1.135 5.3 65.5 14.4 883 n/a 7_xyzrec: 0.1205 0.1369 0.036 1.117 5.3 65.5 14.4 883 n/a 7_adp: 0.1209 0.1372 0.036 1.117 5.4 64.5 14.3 883 n/a 7_regHadp: 0.1209 0.1373 0.036 1.117 5.4 64.5 14.3 883 n/a 7_occ: 0.1208 0.1375 0.036 1.117 5.4 64.5 14.3 883 n/a 8_bss: 0.1199 0.1365 0.036 1.117 5.4 64.5 14.4 883 n/a 8_settarget: 0.1199 0.1365 0.036 1.117 5.4 64.5 14.4 883 n/a 8_updatecdl: 0.1199 0.1365 0.036 1.117 5.4 64.5 14.4 883 n/a 8_nqh: 0.1199 0.1365 0.036 1.117 5.4 64.5 14.4 883 n/a 8_sol: 0.1196 0.1360 0.036 1.117 5.4 64.5 14.5 894 n/a 8_weight: 0.1196 0.1360 0.036 1.117 5.4 64.5 14.5 894 n/a 8_xyzrec: 0.1200 0.1367 0.036 1.117 5.4 64.5 14.5 894 n/a 8_adp: 0.1199 0.1368 0.036 1.117 5.5 63.6 14.5 894 n/a 8_regHadp: 0.1199 0.1368 0.036 1.117 5.5 63.6 14.5 894 n/a 8_occ: 0.1197 0.1369 0.036 1.117 5.5 63.6 14.5 894 n/a 9_bss: 0.1196 0.1367 0.036 1.117 5.5 63.6 14.5 894 n/a 9_settarget: 0.1196 0.1367 0.036 1.117 5.5 63.6 14.5 894 n/a 9_updatecdl: 0.1196 0.1367 0.036 1.117 5.5 63.6 14.5 894 n/a 9_nqh: 0.1196 0.1367 0.036 1.117 5.5 63.6 14.5 894 n/a 9_sol: 0.1195 0.1356 0.036 1.117 5.5 63.6 14.5 894 n/a 9_weight: 0.1195 0.1356 0.036 1.117 5.5 63.6 14.5 894 n/a 9_xyzrec: 0.1198 0.1367 0.037 1.116 5.5 63.6 14.5 894 n/a 9_adp: 0.1200 0.1371 0.037 1.116 5.5 63.4 14.5 894 n/a 9_regHadp: 0.1200 0.1371 0.037 1.116 5.5 63.4 14.5 894 n/a 9_occ: 0.1199 0.1372 0.037 1.116 5.5 63.4 14.5 894 n/a 10_bss: 0.1198 0.1369 0.037 1.116 5.5 63.4 14.5 894 n/a 10_settarget: 0.1198 0.1369 0.037 1.116 5.5 63.4 14.5 894 n/a 10_updatecdl: 0.1198 0.1369 0.037 1.116 5.5 63.4 14.5 894 n/a 10_setrh: 0.1198 0.1370 0.037 1.116 5.5 63.4 14.5 894 n/a 10_nqh: 0.1199 0.1373 0.037 1.116 5.5 63.4 14.5 894 n/a 10_sol: 0.1197 0.1369 0.037 1.116 5.5 63.4 14.5 896 n/a 10_weight: 0.1197 0.1369 0.037 1.116 5.5 63.4 14.5 896 n/a 10_xyzrec: 0.1201 0.1374 0.037 1.164 5.5 63.4 14.5 896 n/a 10_adp: 0.1201 0.1375 0.037 1.164 5.6 62.6 14.5 896 n/a 10_regHadp: 0.1201 0.1375 0.037 1.164 5.6 62.6 14.5 896 n/a 10_occ: 0.1200 0.1375 0.037 1.164 5.6 62.6 14.5 896 n/a end: 0.1199 0.1373 0.037 1.164 5.5 62.6 14.5 896 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1450452_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1450452_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9900 Refinement macro-cycles (run) : 11772.3400 Write final files (write_after_run_outputs) : 176.3000 Total : 11954.6300 Total CPU time: 3.33 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:31 PST -0800 (1736735791.84 s) Start R-work = 0.1794, R-free = 0.1899 Final R-work = 0.1199, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 12295.95 seconds wall clock time: 205 minutes 59.19 seconds (12359.19 seconds total)