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_5571520.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" 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_5571520.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5571520.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.00, per 1000 atoms: 0.30 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: 2.754 distance_ideal: 2.720 ideal - model: -0.034 slack: 0.000 delta_slack: -0.034 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: 2.780 distance_ideal: 2.710 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 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: 0.93 Conformation dependent library (CDL) restraints added in 113.2 milliseconds Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 881 1.03 - 1.26: 2432 1.26 - 1.48: 1464 1.48 - 1.71: 1128 1.71 - 1.94: 29 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 1.524 1.274 0.251 1.05e-02 9.07e+03 5.71e+02 bond pdb=" C VAL B 51 " pdb=" O VAL B 51 " ideal model delta sigma weight residual 1.236 1.444 -0.209 9.80e-03 1.04e+04 4.53e+02 bond pdb=" N GLU B 137 " pdb=" H GLU B 137 " ideal model delta sigma weight residual 0.860 1.269 -0.409 2.00e-02 2.50e+03 4.18e+02 bond pdb=" OG SER B 4 " pdb=" HG SER B 4 " ideal model delta sigma weight residual 0.840 1.240 -0.400 2.00e-02 2.50e+03 3.99e+02 bond pdb=" CA VAL B 181 " pdb=" C VAL B 181 " ideal model delta sigma weight residual 1.524 1.759 -0.235 1.22e-02 6.72e+03 3.73e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 5312 3.95 - 7.90: 3614 7.90 - 11.85: 1491 11.85 - 15.79: 348 15.79 - 19.74: 45 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" O ALA B 10 " ideal model delta sigma weight residual 120.71 134.38 -13.67 8.70e-01 1.32e+00 2.47e+02 angle pdb=" OD1 ASN A 193 " pdb=" CG ASN A 193 " pdb=" ND2 ASN A 193 " ideal model delta sigma weight residual 122.60 138.16 -15.56 1.00e+00 1.00e+00 2.42e+02 angle pdb=" CA GLY A 122 " pdb=" C GLY A 122 " pdb=" O GLY A 122 " ideal model delta sigma weight residual 121.90 105.36 16.54 1.08e+00 8.57e-01 2.35e+02 angle pdb=" C VAL B 173 " pdb=" CA VAL B 173 " pdb=" CB VAL B 173 " ideal model delta sigma weight residual 111.05 124.60 -13.55 8.90e-01 1.26e+00 2.32e+02 angle pdb=" OE1 GLN B 94 " pdb=" CD GLN B 94 " pdb=" NE2 GLN B 94 " ideal model delta sigma weight residual 122.60 136.74 -14.14 1.00e+00 1.00e+00 2.00e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.64: 1841 17.64 - 35.27: 143 35.27 - 52.90: 42 52.90 - 70.53: 20 70.53 - 88.16: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA THR A 33 " pdb=" C THR A 33 " pdb=" N THR A 34 " pdb=" CA THR A 34 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.256: 223 0.256 - 0.511: 176 0.511 - 0.765: 61 0.765 - 1.020: 27 1.020 - 1.274: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.32 -1.27 2.00e-01 2.50e+01 4.06e+01 chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 3.60 -1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb=" CG LEU A 54 " pdb=" CB LEU A 54 " pdb=" CD1 LEU A 54 " pdb=" CD2 LEU A 54 " both_signs ideal model delta sigma weight residual False -2.59 -3.66 1.07 2.00e-01 2.50e+01 2.87e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.149 2.00e-02 2.50e+03 7.36e-02 1.63e+02 pdb=" CG PHE B 164 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.046 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 149 " -0.061 9.50e-02 1.11e+02 8.48e-02 1.53e+02 pdb=" NE ARG B 149 " -0.110 2.00e-02 2.50e+03 pdb=" CZ ARG B 149 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 149 " -0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG B 149 " 0.139 2.00e-02 2.50e+03 pdb="HH11 ARG B 149 " 0.126 2.00e-02 2.50e+03 pdb="HH12 ARG B 149 " -0.068 2.00e-02 2.50e+03 pdb="HH21 ARG B 149 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG B 149 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.057 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG PHE A 119 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.057 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.141 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.053 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.002 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 32 1.63 - 2.38: 2638 2.38 - 3.12: 22439 3.12 - 3.86: 32873 3.86 - 4.60: 52460 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110442 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.893 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.910 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.022 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.114 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.268 2.620 ... (remaining 110437 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_5571520_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= 0.2035 r_free= 0.2022 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300650 | | target function (ml) not normalized (work): 805567.641505 | | target function (ml) not normalized (free): 16627.662351 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2138 0.1970 6.6964 6.2941| | 2: 2.94 - 2.33 1.00 7339 128 0.1631 0.1590 5.5334 5.5739| | 3: 2.33 - 2.04 0.96 6939 150 0.1639 0.1604 5.1433 5.1214| | 4: 2.04 - 1.85 1.00 7170 155 0.1756 0.1779 4.9662 5.0977| | 5: 1.85 - 1.72 0.99 7113 159 0.1922 0.1880 4.807 4.871| | 6: 1.72 - 1.62 0.99 7102 142 0.1982 0.1856 4.6696 4.704| | 7: 1.62 - 1.54 0.99 7104 148 0.2044 0.1884 4.5704 4.5894| | 8: 1.54 - 1.47 0.96 6798 152 0.2023 0.2270 4.4758 4.6032| | 9: 1.47 - 1.41 0.98 6938 155 0.2074 0.2369 4.3943 4.5359| | 10: 1.41 - 1.36 0.99 7022 150 0.2110 0.2211 4.3043 4.392| | 11: 1.36 - 1.32 0.99 6997 151 0.2102 0.1950 4.2237 4.1929| | 12: 1.32 - 1.28 0.98 6976 149 0.2075 0.2282 4.1733 4.3947| | 13: 1.28 - 1.25 0.98 6907 166 0.2042 0.1998 4.1369 4.1018| | 14: 1.25 - 1.22 0.98 7015 113 0.2078 0.2536 4.074 4.3417| | 15: 1.22 - 1.19 0.98 6957 137 0.2078 0.2225 4.0411 4.0986| | 16: 1.19 - 1.17 0.93 6604 132 0.2094 0.2129 3.9969 4.0209| | 17: 1.17 - 1.14 0.98 6941 135 0.2162 0.1775 3.9468 3.9312| | 18: 1.14 - 1.12 0.98 6875 142 0.2228 0.2284 3.9207 3.935| | 19: 1.12 - 1.10 0.97 6949 106 0.2291 0.2378 3.8815 3.9908| | 20: 1.10 - 1.08 0.97 6884 147 0.2316 0.2357 3.8267 3.8782| | 21: 1.08 - 1.07 0.97 6852 152 0.2399 0.2704 3.7913 3.8364| | 22: 1.07 - 1.05 0.97 6838 135 0.2537 0.2661 3.7495 3.7955| | 23: 1.05 - 1.03 0.97 6829 159 0.2731 0.2673 3.7326 3.8076| | 24: 1.03 - 1.02 0.96 6785 133 0.2877 0.2706 3.7021 3.787| | 25: 1.02 - 1.01 0.93 6552 130 0.3077 0.2854 3.6752 3.7322| | 26: 1.01 - 0.99 0.96 6767 158 0.3231 0.3272 3.6314 3.6614| | 27: 0.99 - 0.98 0.94 6648 131 0.3399 0.3212 3.6391 3.5927| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.21 0.91 0.97 34331.29| | 2: 2.94 - 2.33 7339 128 0.86 20.83 1.08 1.03 14725.11| | 3: 2.33 - 2.04 6939 150 0.93 12.50 1.11 1.07 4243.74| | 4: 2.04 - 1.85 7170 155 0.92 13.89 1.11 1.07 2923.17| | 5: 1.85 - 1.72 7113 159 0.91 16.13 1.11 1.06 2209.04| | 6: 1.72 - 1.62 7102 142 0.89 17.32 1.12 1.05 1719.57| | 7: 1.62 - 1.54 7104 148 0.88 18.56 1.11 1.05 1422.18| | 8: 1.54 - 1.47 6798 152 0.88 19.46 1.10 1.06 1279.79| | 9: 1.47 - 1.41 6938 155 0.87 20.17 1.10 1.05 1086.59| | 10: 1.41 - 1.36 7022 150 0.86 20.97 1.09 1.04 909.09| | 11: 1.36 - 1.32 6997 151 0.87 20.14 1.08 1.04 725.82| | 12: 1.32 - 1.28 6976 149 0.87 20.08 1.08 1.03 662.41| | 13: 1.28 - 1.25 6907 166 0.87 20.55 1.07 1.04 653.16| | 14: 1.25 - 1.22 7015 113 0.85 22.15 1.08 1.03 634.22| | 15: 1.22 - 1.19 6957 137 0.86 21.71 1.08 1.03 577.15| | 16: 1.19 - 1.17 6604 132 0.87 20.51 1.07 1.02 487.38| | 17: 1.17 - 1.14 6941 135 0.87 20.48 1.08 1.02 419.83| | 18: 1.14 - 1.12 6875 142 0.87 20.90 1.08 1.00 385.77| | 19: 1.12 - 1.10 6949 106 0.85 22.51 1.06 0.99 388.57| | 20: 1.10 - 1.08 6884 147 0.84 24.04 1.06 0.97 379.51| | 21: 1.08 - 1.07 6852 152 0.82 25.30 1.06 0.97 369.60| | 22: 1.07 - 1.05 6838 135 0.81 26.75 1.05 0.96 353.46| | 23: 1.05 - 1.03 6829 159 0.79 28.29 1.06 0.96 343.48| | 24: 1.03 - 1.02 6785 133 0.77 30.14 1.05 0.98 344.13| | 25: 1.02 - 1.01 6552 130 0.76 31.12 1.03 0.95 323.96| | 26: 1.01 - 0.99 6767 158 0.74 32.66 1.03 0.92 299.27| | 27: 0.99 - 0.98 6648 131 0.76 31.80 1.04 0.90 264.19| |alpha: min = 0.90 max = 1.07 mean = 1.01| |beta: min = 264.19 max = 34331.29 mean = 2807.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.11| |phase err.(test): min = 0.00 max = 89.95 mean = 22.26| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.258 2950 Z= 5.482 Angle : 5.250 17.728 4018 Z= 3.774 Chirality : 0.397 1.274 492 Planarity : 0.032 0.093 512 Dihedral : 12.840 88.163 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.97 % Allowed : 2.90 % Favored : 96.13 % Cbeta Deviations : 34.83 % 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: -1.51 (0.38), residues: 386 helix: -1.47 (0.38), residues: 144 sheet: -0.41 (0.59), residues: 66 loop : -0.62 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.015 ARG A 27 TYR 0.141 0.043 TYR B 195 PHE 0.132 0.043 PHE B 164 TRP 0.093 0.031 TRP A 146 HIS 0.090 0.028 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= 0.2035 r_free= 0.2022 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300650 | | target function (ml) not normalized (work): 805567.641505 | | target function (ml) not normalized (free): 16627.662351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2035 0.2022 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2035 0.2022 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2035 0.2022 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2035 0.2036 0.2022 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1802 0.1958 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1958 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4083 402.814 293.358 0.432 0.913 0.294 13.296-10.522 99.01 99 1 0.2482 528.187 519.555 0.783 0.914 0.245 10.503-8.327 98.90 177 3 0.2448 564.205 559.992 0.973 0.914 0.225 8.318-6.595 100.00 360 8 0.2501 414.736 402.522 0.972 0.914 0.174 6.588-5.215 100.00 711 7 0.2305 381.101 365.603 0.958 0.914 0.150 5.214-4.128 98.38 1367 28 0.1494 557.435 548.831 1.077 0.914 0.090 4.126-3.266 94.74 2603 46 0.1333 508.132 499.083 1.144 0.914 0.029 3.266-2.585 99.86 5447 97 0.1437 342.774 337.943 1.118 0.913 0.010 2.585-2.046 97.45 10613 204 0.1406 258.603 254.356 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1627 153.054 149.919 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1916 82.395 80.171 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2318 44.203 41.632 1.111 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0059 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1958 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1958 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.969115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.019501 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 0.1269 0.1500 0.0231 0.039 1.2 10.7 0.0 0.3 0 11.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 15.00 2.31 1.117 13.114 575.020 0.018 12.97 15.70 2.73 1.244 13.321 575.020 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.05 14.98 1.40 435 3274 Protein: 5.18 40.32 10.99 1.40 0 2902 Water: 6.37 73.05 29.34 N/A 435 370 Other: 15.98 30.58 23.28 N/A 0 2 Chain A: 5.34 60.06 13.02 N/A 0 1626 Chain B: 5.18 73.05 12.75 N/A 0 1648 Chain S: 11.61 61.86 30.74 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.96 2169 11.96 - 18.75 636 18.75 - 25.54 316 25.54 - 32.32 266 32.32 - 39.11 154 39.11 - 45.90 104 45.90 - 52.69 39 52.69 - 59.47 20 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1571 r_work=0.1296 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1566 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015511 | | target function (ls_wunit_k1) not normalized (work): 2905.182556 | | target function (ls_wunit_k1) not normalized (free): 115.077788 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1556 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1635 n_refl.: 191138 remove outliers: r(all,work,free)=0.1466 0.1463 0.1635 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1490 0.1487 0.1644 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191138 remove outliers: r(all,work,free)=0.1279 0.1274 0.1545 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3573 402.814 384.501 0.488 0.964 0.269 13.296-10.522 99.01 99 1 0.2090 528.187 522.060 0.736 0.965 0.235 10.503-8.327 98.90 177 3 0.1707 564.205 563.151 0.889 0.965 0.199 8.318-6.595 100.00 360 8 0.1707 414.736 412.917 0.910 0.965 0.160 6.588-5.215 100.00 711 7 0.1523 381.101 373.917 0.888 0.965 0.150 5.214-4.128 98.38 1367 28 0.0901 557.435 554.254 0.977 0.966 0.070 4.126-3.266 94.74 2603 46 0.0831 508.132 504.378 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.325 1.025 0.966 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.379 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.386 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.414 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.174 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0389 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1545 | n_water=805 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1279 r_free=0.1553 | n_water=793 | time (s): 109.370 (total time: 112.070) Filter (q & B) r_work=0.1279 r_free=0.1552 | n_water=790 | time (s): 4.700 (total time: 116.770) Compute maps r_work=0.1279 r_free=0.1552 | n_water=790 | time (s): 1.820 (total time: 118.590) Filter (map) r_work=0.1305 r_free=0.1531 | n_water=651 | time (s): 4.510 (total time: 123.100) Find peaks r_work=0.1305 r_free=0.1531 | n_water=651 | time (s): 0.620 (total time: 123.720) Add new water r_work=0.1329 r_free=0.1561 | n_water=964 | time (s): 4.430 (total time: 128.150) Refine new water occ: r_work=0.1285 r_free=0.1518 adp: r_work=0.1272 r_free=0.1513 occ: r_work=0.1275 r_free=0.1512 adp: r_work=0.1267 r_free=0.1509 occ: r_work=0.1269 r_free=0.1507 adp: r_work=0.1266 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1507 r_work=0.1266 r_free=0.1507 | n_water=964 | time (s): 81.780 (total time: 209.930) Filter (q & B) r_work=0.1270 r_free=0.1509 | n_water=891 | time (s): 4.080 (total time: 214.010) Filter (dist only) r_work=0.1270 r_free=0.1506 | n_water=889 | time (s): 111.870 (total time: 325.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.774707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.700593 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 0.1254 0.1524 0.0270 0.042 1.1 18.7 0.0 0.0 0 11.887 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.24 2.70 2.040 15.223 593.701 0.014 12.33 15.07 2.74 2.357 15.252 593.701 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 68.82 16.37 1.21 521 3272 Protein: 5.43 39.83 11.01 1.21 0 2902 Water: 6.65 68.82 33.81 N/A 521 368 Other: 16.31 33.01 24.66 N/A 0 2 Chain A: 5.55 57.61 12.99 N/A 0 1624 Chain B: 5.43 68.82 12.83 N/A 0 1648 Chain S: 9.35 65.71 38.08 N/A 521 0 Histogram: Values Number of atoms 5.43 - 11.77 2079 11.77 - 18.10 688 18.10 - 24.44 281 24.44 - 30.78 219 30.78 - 37.12 163 37.12 - 43.46 165 43.46 - 49.80 88 49.80 - 56.14 49 56.14 - 62.48 50 62.48 - 68.82 11 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1507 r_work=0.1234 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1508 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1507 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013386 | | target function (ls_wunit_k1) not normalized (work): 2507.103941 | | target function (ls_wunit_k1) not normalized (free): 101.546281 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1507 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1605 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1432 0.1605 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1603 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1516 n_refl.: 191137 remove outliers: r(all,work,free)=0.1240 0.1234 0.1516 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3119 402.814 383.052 0.486 0.964 0.265 13.296-10.522 99.01 99 1 0.1941 528.187 520.099 0.752 0.965 0.224 10.503-8.327 98.90 177 3 0.1364 564.205 568.488 0.918 0.965 0.210 8.318-6.595 100.00 360 8 0.1552 414.736 414.706 0.933 0.965 0.150 6.588-5.215 100.00 711 7 0.1341 381.101 377.172 0.912 0.965 0.150 5.214-4.128 98.38 1367 28 0.0823 557.435 556.362 0.993 0.965 0.090 4.126-3.266 94.74 2603 46 0.0763 508.132 505.443 1.058 0.965 0.014 3.266-2.585 99.86 5447 97 0.0856 342.774 341.374 1.044 0.964 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.726 1.056 0.963 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.610 1.078 0.960 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.351 1.071 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.220 1.057 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0449 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1516 | n_water=889 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1235 r_free=0.1516 | n_water=886 | time (s): 123.090 (total time: 125.830) Filter (q & B) r_work=0.1236 r_free=0.1516 | n_water=883 | time (s): 4.950 (total time: 130.780) Compute maps r_work=0.1236 r_free=0.1516 | n_water=883 | time (s): 2.070 (total time: 132.850) Filter (map) r_work=0.1275 r_free=0.1525 | n_water=688 | time (s): 4.500 (total time: 137.350) Find peaks r_work=0.1275 r_free=0.1525 | n_water=688 | time (s): 0.800 (total time: 138.150) Add new water r_work=0.1299 r_free=0.1556 | n_water=1014 | time (s): 4.610 (total time: 142.760) Refine new water occ: r_work=0.1254 r_free=0.1515 adp: r_work=0.1254 r_free=0.1515 occ: r_work=0.1250 r_free=0.1513 adp: r_work=0.1250 r_free=0.1514 occ: r_work=0.1247 r_free=0.1513 adp: r_work=0.1247 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1513 r_work=0.1247 r_free=0.1513 | n_water=1014 | time (s): 185.190 (total time: 327.950) Filter (q & B) r_work=0.1252 r_free=0.1518 | n_water=871 | time (s): 4.320 (total time: 332.270) Filter (dist only) r_work=0.1253 r_free=0.1517 | n_water=869 | time (s): 126.010 (total time: 458.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.662220 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.221383 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 0.1244 0.1445 0.0201 0.036 1.1 7.0 0.0 0.0 0 0.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.44 14.45 2.01 1.944 14.561 16.221 3.943 12.35 14.02 1.67 2.251 14.463 16.221 3.898 Individual atomic B min max mean iso aniso Overall: 5.51 68.43 15.18 1.07 502 3271 Protein: 5.51 36.40 10.76 1.07 0 2902 Water: 6.70 68.43 29.92 N/A 502 367 Other: 13.98 28.34 21.16 N/A 0 2 Chain A: 5.53 56.75 12.75 N/A 0 1624 Chain B: 5.51 68.43 12.53 N/A 0 1647 Chain S: 13.00 60.94 31.71 N/A 502 0 Histogram: Values Number of atoms 5.51 - 11.81 2145 11.81 - 18.10 678 18.10 - 24.39 297 24.39 - 30.68 244 30.68 - 36.97 171 36.97 - 43.27 146 43.27 - 49.56 59 49.56 - 55.85 24 55.85 - 62.14 8 62.14 - 68.43 1 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1402 r_work=0.1236 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1403 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1393 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.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892034 | | target function (ml) not normalized (work): 728962.404734 | | target function (ml) not normalized (free): 15224.260003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1392 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1493 n_refl.: 191137 remove outliers: r(all,work,free)=0.1445 0.1444 0.1493 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1439 0.1489 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1386 n_refl.: 191137 remove outliers: r(all,work,free)=0.1230 0.1226 0.1386 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3798 398.008 364.590 0.428 0.945 0.251 13.296-10.522 99.01 99 1 0.2514 528.187 506.687 0.709 0.947 0.219 10.503-8.327 97.80 175 3 0.1952 554.286 558.297 0.881 0.947 0.186 8.318-6.595 100.00 360 8 0.2089 414.736 409.416 0.899 0.946 0.140 6.588-5.215 100.00 711 7 0.1843 381.101 370.218 0.887 0.946 0.117 5.214-4.128 98.38 1367 28 0.1176 557.435 551.732 0.971 0.947 0.055 4.126-3.266 94.74 2603 46 0.1105 508.132 500.831 1.034 0.947 0.024 3.266-2.585 99.86 5447 97 0.1085 342.774 339.033 1.021 0.946 0.010 2.585-2.046 97.45 10613 204 0.0968 258.603 255.674 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.404 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.476 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.315 1.039 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0951 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1386 | n_water=869 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1227 r_free=0.1387 | n_water=867 | time (s): 107.430 (total time: 110.750) Filter (q & B) r_work=0.1227 r_free=0.1383 | n_water=855 | time (s): 4.010 (total time: 114.760) Compute maps r_work=0.1227 r_free=0.1383 | n_water=855 | time (s): 2.240 (total time: 117.000) Filter (map) r_work=0.1248 r_free=0.1375 | n_water=720 | time (s): 4.860 (total time: 121.860) Find peaks r_work=0.1248 r_free=0.1375 | n_water=720 | time (s): 0.560 (total time: 122.420) Add new water r_work=0.1262 r_free=0.1384 | n_water=963 | time (s): 4.770 (total time: 127.190) Refine new water occ: r_work=0.1216 r_free=0.1349 adp: r_work=0.1208 r_free=0.1345 occ: r_work=0.1205 r_free=0.1346 adp: r_work=0.1205 r_free=0.1345 occ: r_work=0.1203 r_free=0.1348 adp: r_work=0.1203 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1348 r_work=0.1203 r_free=0.1348 | n_water=963 | time (s): 257.640 (total time: 384.830) Filter (q & B) r_work=0.1208 r_free=0.1355 | n_water=868 | time (s): 4.860 (total time: 389.690) Filter (dist only) r_work=0.1208 r_free=0.1355 | n_water=867 | time (s): 116.010 (total time: 505.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555273 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.499433 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 0.1206 0.1356 0.0150 0.036 1.1 5.6 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.56 1.50 1.842 14.157 16.499 3.874 11.98 13.52 1.54 2.021 14.104 16.499 3.864 Individual atomic B min max mean iso aniso Overall: 5.50 67.80 14.84 1.00 501 3270 Protein: 5.50 32.85 10.64 1.00 0 2902 Water: 5.85 67.80 28.87 N/A 501 366 Other: 13.96 26.86 20.41 N/A 0 2 Chain A: 5.55 55.11 12.58 N/A 0 1624 Chain B: 5.50 67.80 12.38 N/A 0 1646 Chain S: 5.85 59.88 30.23 N/A 501 0 Histogram: Values Number of atoms 5.50 - 11.73 2126 11.73 - 17.96 726 17.96 - 24.19 309 24.19 - 30.42 241 30.42 - 36.65 158 36.65 - 42.88 131 42.88 - 49.11 60 49.11 - 55.34 16 55.34 - 61.57 3 61.57 - 67.80 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1352 r_work=0.1198 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1352 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1351 target_work(ml) = 3.861 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861466 | | target function (ml) not normalized (work): 723225.573660 | | target function (ml) not normalized (free): 15121.791410 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1351 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1422 0.1422 0.1448 n_refl.: 191134 remove outliers: r(all,work,free)=0.1422 0.1422 0.1448 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1415 0.1444 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3532 352.309 308.728 0.406 0.947 0.245 13.296-10.522 97.03 97 1 0.2369 479.680 453.105 0.692 0.948 0.199 10.503-8.327 97.80 175 3 0.2093 501.827 496.536 0.861 0.948 0.177 8.318-6.595 100.00 360 8 0.2191 375.484 369.459 0.889 0.948 0.115 6.588-5.215 100.00 711 7 0.1921 345.032 335.110 0.884 0.948 0.110 5.214-4.128 98.38 1367 28 0.1199 504.678 499.459 0.972 0.948 0.070 4.126-3.266 94.74 2603 46 0.1123 460.041 453.538 1.034 0.949 0.014 3.266-2.585 99.86 5447 97 0.1083 310.333 307.208 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0931 234.128 231.714 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0908 138.569 137.314 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0986 74.597 73.899 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.018 38.367 1.038 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1351 | n_water=867 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1194 r_free=0.1351 | n_water=867 | time (s): 104.820 (total time: 107.540) Filter (q & B) r_work=0.1194 r_free=0.1351 | n_water=858 | time (s): 4.020 (total time: 111.560) Compute maps r_work=0.1194 r_free=0.1351 | n_water=858 | time (s): 1.750 (total time: 113.310) Filter (map) r_work=0.1217 r_free=0.1352 | n_water=729 | time (s): 4.160 (total time: 117.470) Find peaks r_work=0.1217 r_free=0.1352 | n_water=729 | time (s): 0.870 (total time: 118.340) Add new water r_work=0.1229 r_free=0.1366 | n_water=970 | time (s): 4.760 (total time: 123.100) Refine new water occ: r_work=0.1190 r_free=0.1335 adp: r_work=0.1190 r_free=0.1334 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1187 r_free=0.1333 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1185 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1334 r_work=0.1185 r_free=0.1334 | n_water=970 | time (s): 172.830 (total time: 295.930) Filter (q & B) r_work=0.1189 r_free=0.1340 | n_water=889 | time (s): 5.630 (total time: 301.560) Filter (dist only) r_work=0.1190 r_free=0.1340 | n_water=888 | time (s): 122.670 (total time: 424.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524041 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.390048 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1348 0.0156 0.037 1.1 5.8 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.48 1.56 1.788 14.066 15.390 3.761 11.97 13.51 1.55 1.831 14.047 15.390 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 67.51 14.86 0.96 523 3269 Protein: 5.57 31.75 10.59 0.96 0 2902 Water: 5.93 67.51 28.82 N/A 523 365 Other: 13.81 26.03 19.92 N/A 0 2 Chain A: 5.61 54.44 12.49 N/A 0 1623 Chain B: 5.57 67.51 12.31 N/A 0 1646 Chain S: 5.93 59.79 30.26 N/A 523 0 Histogram: Values Number of atoms 5.57 - 11.76 2153 11.76 - 17.96 718 17.96 - 24.15 307 24.15 - 30.34 231 30.34 - 36.54 172 36.54 - 42.73 133 42.73 - 48.93 57 48.93 - 55.12 17 55.12 - 61.31 3 61.31 - 67.51 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758286 | | target function (ml) not normalized (work): 703881.918141 | | target function (ml) not normalized (free): 14735.055622 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1462 n_refl.: 191129 remove outliers: r(all,work,free)=0.1391 0.1390 0.1462 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1384 0.1383 0.1457 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3463 352.309 325.232 0.417 0.954 0.228 13.296-10.522 96.04 96 1 0.2319 480.354 458.533 0.697 0.956 0.190 10.503-8.327 97.80 175 3 0.2076 501.827 495.948 0.854 0.956 0.157 8.318-6.595 100.00 360 8 0.2150 375.484 369.882 0.882 0.956 0.104 6.588-5.215 100.00 711 7 0.1910 345.032 334.953 0.876 0.956 0.083 5.214-4.128 98.38 1367 28 0.1200 504.678 499.255 0.963 0.956 0.045 4.126-3.266 94.74 2603 46 0.1138 460.041 453.318 1.028 0.956 0.014 3.266-2.585 99.86 5447 97 0.1091 310.333 307.210 1.013 0.955 0.000 2.585-2.046 97.45 10613 204 0.0944 234.128 231.709 1.025 0.955 0.000 2.046-1.619 99.39 21536 464 0.0911 138.569 137.283 1.049 0.953 0.000 1.619-1.281 98.00 42464 925 0.0974 74.597 73.890 1.047 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.018 38.355 1.036 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1243 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1352 | n_water=888 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1192 r_free=0.1352 | n_water=887 | time (s): 110.940 (total time: 113.250) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=878 | time (s): 4.010 (total time: 117.260) Compute maps r_work=0.1193 r_free=0.1353 | n_water=878 | time (s): 1.610 (total time: 118.870) Filter (map) r_work=0.1217 r_free=0.1355 | n_water=752 | time (s): 4.570 (total time: 123.440) Find peaks r_work=0.1217 r_free=0.1355 | n_water=752 | time (s): 0.740 (total time: 124.180) Add new water r_work=0.1227 r_free=0.1362 | n_water=975 | time (s): 4.740 (total time: 128.920) Refine new water occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1189 r_free=0.1341 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1340 r_work=0.1188 r_free=0.1340 | n_water=975 | time (s): 280.220 (total time: 409.140) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=894 | time (s): 5.670 (total time: 414.810) Filter (dist only) r_work=0.1192 r_free=0.1344 | n_water=893 | time (s): 114.830 (total time: 529.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599346 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.894252 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1350 0.0156 0.037 1.1 7.0 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.50 1.56 1.763 13.982 14.894 3.759 11.98 13.54 1.56 1.896 13.939 14.894 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 66.35 14.74 0.91 528 3269 Protein: 5.56 29.46 10.49 0.91 0 2902 Water: 5.97 66.35 28.55 N/A 528 365 Other: 13.80 23.45 18.62 N/A 0 2 Chain A: 5.65 52.16 12.35 N/A 0 1623 Chain B: 5.56 66.35 12.19 N/A 0 1646 Chain S: 5.97 59.55 30.03 N/A 528 0 Histogram: Values Number of atoms 5.56 - 11.64 2125 11.64 - 17.72 772 17.72 - 23.80 285 23.80 - 29.88 228 29.88 - 35.95 163 35.95 - 42.03 140 42.03 - 48.11 59 48.11 - 54.19 21 54.19 - 60.27 3 60.27 - 66.35 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1354 r_work=0.1198 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1356 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756018 | | target function (ml) not normalized (work): 703453.296650 | | target function (ml) not normalized (free): 14729.197113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1464 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1389 0.1464 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1383 0.1382 0.1459 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1356 n_refl.: 191128 remove outliers: r(all,work,free)=0.1199 0.1196 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3535 352.309 324.194 0.414 0.954 0.235 13.296-10.522 96.04 96 1 0.2285 480.354 464.137 0.703 0.955 0.175 10.503-8.327 97.80 175 3 0.2101 501.827 495.940 0.850 0.956 0.147 8.318-6.595 100.00 360 8 0.2162 375.484 370.725 0.881 0.955 0.104 6.588-5.215 100.00 711 7 0.1936 345.032 335.343 0.877 0.955 0.083 5.214-4.128 98.38 1367 28 0.1224 504.678 499.306 0.964 0.956 0.034 4.126-3.266 94.74 2603 46 0.1156 460.041 452.990 1.029 0.956 0.010 3.266-2.585 99.86 5447 97 0.1114 310.333 307.064 1.014 0.955 0.010 2.585-2.046 97.45 10613 204 0.0949 234.128 231.660 1.025 0.955 0.000 2.046-1.619 99.39 21536 464 0.0909 138.569 137.272 1.049 0.954 0.000 1.619-1.281 98.00 42464 925 0.0967 74.597 73.892 1.047 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.018 38.352 1.035 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1317 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1356 | n_water=893 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1196 r_free=0.1356 | n_water=893 | time (s): 108.570 (total time: 111.100) Filter (q & B) r_work=0.1197 r_free=0.1357 | n_water=884 | time (s): 5.010 (total time: 116.110) Compute maps r_work=0.1197 r_free=0.1357 | n_water=884 | time (s): 1.860 (total time: 117.970) Filter (map) r_work=0.1221 r_free=0.1363 | n_water=760 | time (s): 4.260 (total time: 122.230) Find peaks r_work=0.1221 r_free=0.1363 | n_water=760 | time (s): 0.580 (total time: 122.810) Add new water r_work=0.1229 r_free=0.1372 | n_water=978 | time (s): 4.130 (total time: 126.940) Refine new water occ: r_work=0.1194 r_free=0.1343 adp: r_work=0.1195 r_free=0.1343 occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1340 adp: r_work=0.1191 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1341 r_work=0.1191 r_free=0.1341 | n_water=978 | time (s): 257.430 (total time: 384.370) Filter (q & B) r_work=0.1195 r_free=0.1344 | n_water=896 | time (s): 4.410 (total time: 388.780) Filter (dist only) r_work=0.1195 r_free=0.1345 | n_water=894 | time (s): 116.600 (total time: 505.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.501610 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.385602 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1347 0.0148 0.038 1.1 5.3 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.47 1.48 1.720 13.849 13.386 3.757 12.02 13.52 1.50 1.741 13.838 13.386 3.758 Individual atomic B min max mean iso aniso Overall: 5.49 65.91 14.68 0.88 529 3269 Protein: 5.49 28.98 10.45 0.88 0 2902 Water: 5.94 65.91 28.42 N/A 529 365 Other: 13.81 23.01 18.41 N/A 0 2 Chain A: 5.63 51.93 12.28 N/A 0 1623 Chain B: 5.49 65.91 12.13 N/A 0 1646 Chain S: 5.94 59.42 29.99 N/A 529 0 Histogram: Values Number of atoms 5.49 - 11.54 2103 11.54 - 17.58 786 17.58 - 23.62 288 23.62 - 29.66 234 29.66 - 35.70 159 35.70 - 41.74 138 41.74 - 47.78 63 47.78 - 53.83 23 53.83 - 59.87 3 59.87 - 65.91 1 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1352 r_work=0.1202 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1352 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1353 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757674 | | target function (ml) not normalized (work): 703763.494167 | | target function (ml) not normalized (free): 14726.430591 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1467 n_refl.: 191128 remove outliers: r(all,work,free)=0.1392 0.1391 0.1467 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1391 0.1389 0.1466 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1343 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1343 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3527 352.309 323.264 0.416 0.973 0.235 13.296-10.522 96.04 96 1 0.2316 480.354 463.847 0.701 0.975 0.167 10.503-8.327 97.80 175 3 0.2122 501.827 493.910 0.852 0.975 0.137 8.318-6.595 100.00 360 8 0.2178 375.484 370.030 0.881 0.975 0.103 6.588-5.215 100.00 711 7 0.1950 345.032 335.055 0.880 0.975 0.083 5.214-4.128 98.38 1367 28 0.1234 504.678 498.675 0.966 0.976 0.034 4.126-3.266 94.74 2603 46 0.1162 460.041 452.404 1.031 0.977 0.005 3.266-2.585 99.86 5447 97 0.1116 310.333 306.842 1.015 0.978 0.000 2.585-2.046 97.45 10613 204 0.0958 234.128 231.500 1.024 0.980 0.000 2.046-1.619 99.39 21536 464 0.0912 138.569 137.159 1.043 0.982 0.000 1.619-1.281 98.00 42464 925 0.0950 74.597 73.932 1.037 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.018 38.316 1.011 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0199 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1343 | n_water=894 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1191 r_free=0.1343 | n_water=894 | time (s): 106.250 (total time: 108.990) Filter (q & B) r_work=0.1192 r_free=0.1343 | n_water=887 | time (s): 4.300 (total time: 113.290) Compute maps r_work=0.1192 r_free=0.1343 | n_water=887 | time (s): 2.120 (total time: 115.410) Filter (map) r_work=0.1217 r_free=0.1352 | n_water=764 | time (s): 4.120 (total time: 119.530) Find peaks r_work=0.1217 r_free=0.1352 | n_water=764 | time (s): 0.650 (total time: 120.180) Add new water r_work=0.1225 r_free=0.1366 | n_water=982 | time (s): 3.910 (total time: 124.090) Refine new water occ: r_work=0.1189 r_free=0.1339 adp: r_work=0.1189 r_free=0.1339 occ: r_work=0.1186 r_free=0.1338 adp: r_work=0.1186 r_free=0.1338 occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1337 r_work=0.1185 r_free=0.1337 | n_water=982 | time (s): 279.680 (total time: 403.770) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=905 | time (s): 4.500 (total time: 408.270) Filter (dist only) r_work=0.1188 r_free=0.1345 | n_water=904 | time (s): 117.080 (total time: 525.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525978 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.925647 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1351 0.0160 0.038 1.1 7.0 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.51 1.60 1.703 13.829 13.926 3.756 11.91 13.52 1.60 1.733 13.818 13.926 3.753 Individual atomic B min max mean iso aniso Overall: 5.61 65.03 14.67 0.87 540 3268 Protein: 5.61 28.43 10.44 0.87 0 2902 Water: 5.96 65.03 28.24 N/A 540 364 Other: 13.87 22.29 18.08 N/A 0 2 Chain A: 5.68 51.49 12.24 N/A 0 1623 Chain B: 5.61 65.03 12.08 N/A 0 1645 Chain S: 5.96 59.13 29.82 N/A 540 0 Histogram: Values Number of atoms 5.61 - 11.55 2103 11.55 - 17.49 793 17.49 - 23.43 286 23.43 - 29.38 228 29.38 - 35.32 160 35.32 - 41.26 142 41.26 - 47.20 68 47.20 - 53.15 24 53.15 - 59.09 2 59.09 - 65.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1352 r_work=0.1192 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752756 | | target function (ml) not normalized (work): 702842.343561 | | target function (ml) not normalized (free): 14720.515286 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1397 0.1396 0.1477 n_refl.: 191128 remove outliers: r(all,work,free)=0.1397 0.1396 0.1477 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1394 0.1393 0.1475 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1349 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1349 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3533 352.309 321.990 0.390 0.974 0.190 13.296-10.522 96.04 96 1 0.2328 480.354 463.963 0.691 0.976 0.140 10.503-8.327 97.80 175 3 0.2133 501.827 493.854 0.850 0.976 0.121 8.318-6.595 100.00 360 8 0.2173 375.484 369.871 0.877 0.976 0.090 6.588-5.215 100.00 711 7 0.1967 345.032 334.980 0.878 0.977 0.077 5.214-4.128 98.38 1367 28 0.1239 504.678 498.639 0.966 0.977 0.034 4.126-3.266 94.74 2603 46 0.1169 460.041 452.167 1.030 0.979 0.005 3.266-2.585 99.86 5447 97 0.1122 310.333 306.816 1.014 0.979 0.000 2.585-2.046 97.45 10613 204 0.0958 234.128 231.512 1.023 0.981 0.000 2.046-1.619 99.39 21536 464 0.0906 138.569 137.202 1.043 0.985 0.000 1.619-1.281 98.00 42464 925 0.0943 74.597 73.943 1.037 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.018 38.309 1.012 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0442 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1349 | n_water=904 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1189 r_free=0.1349 | n_water=904 | time (s): 111.180 (total time: 113.900) Filter (q & B) r_work=0.1190 r_free=0.1351 | n_water=893 | time (s): 4.270 (total time: 118.170) Compute maps r_work=0.1190 r_free=0.1351 | n_water=893 | time (s): 1.600 (total time: 119.770) Filter (map) r_work=0.1215 r_free=0.1359 | n_water=773 | time (s): 4.240 (total time: 124.010) Find peaks r_work=0.1215 r_free=0.1359 | n_water=773 | time (s): 0.710 (total time: 124.720) Add new water r_work=0.1222 r_free=0.1369 | n_water=991 | time (s): 3.920 (total time: 128.640) Refine new water occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1333 r_work=0.1184 r_free=0.1333 | n_water=991 | time (s): 196.180 (total time: 324.820) Filter (q & B) r_work=0.1188 r_free=0.1344 | n_water=903 | time (s): 5.090 (total time: 329.910) Filter (dist only) r_work=0.1189 r_free=0.1344 | n_water=901 | time (s): 121.130 (total time: 451.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.547444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.456442 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1352 0.0159 0.038 1.1 5.6 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.59 1.695 13.788 13.456 3.754 11.94 13.54 1.60 1.716 13.779 13.456 3.754 Individual atomic B min max mean iso aniso Overall: 5.62 64.19 14.62 0.86 537 3268 Protein: 5.62 28.04 10.42 0.86 0 2902 Water: 6.04 64.19 28.14 N/A 537 364 Other: 13.88 22.18 18.03 N/A 0 2 Chain A: 5.71 51.13 12.20 N/A 0 1623 Chain B: 5.62 64.19 12.04 N/A 0 1645 Chain S: 6.04 58.85 29.84 N/A 537 0 Histogram: Values Number of atoms 5.62 - 11.47 2079 11.47 - 17.33 819 17.33 - 23.19 278 23.19 - 29.04 222 29.04 - 34.90 172 34.90 - 40.76 128 40.76 - 46.61 75 46.61 - 52.47 27 52.47 - 58.33 3 58.33 - 64.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1354 r_work=0.1195 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753267 | | target function (ml) not normalized (work): 702938.137504 | | target function (ml) not normalized (free): 14725.617330 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1497 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1404 0.1497 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1401 0.1400 0.1493 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1357 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1357 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3525 352.309 321.971 0.419 0.918 0.200 13.296-10.522 96.04 96 1 0.2341 480.354 463.942 0.735 0.920 0.145 10.503-8.327 97.80 175 3 0.2135 501.827 494.107 0.900 0.920 0.119 8.318-6.595 100.00 360 8 0.2192 375.484 369.693 0.929 0.920 0.088 6.588-5.215 100.00 711 7 0.1990 345.032 334.631 0.929 0.921 0.077 5.214-4.128 98.38 1367 28 0.1246 504.678 498.500 1.025 0.922 0.039 4.126-3.266 94.74 2603 46 0.1179 460.041 452.107 1.093 0.923 0.005 3.266-2.585 99.86 5447 97 0.1131 310.333 306.747 1.076 0.924 0.000 2.585-2.046 97.45 10613 204 0.0960 234.128 231.508 1.086 0.926 0.000 2.046-1.619 99.39 21536 464 0.0909 138.569 137.181 1.106 0.929 0.000 1.619-1.281 98.00 42464 925 0.0941 74.597 73.943 1.100 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.018 38.304 1.073 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0608 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1357 After: r_work=0.1193 r_free=0.1357 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1357 | n_water=901 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1193 r_free=0.1357 | n_water=900 | time (s): 117.110 (total time: 119.700) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=891 | time (s): 4.040 (total time: 123.740) Compute maps r_work=0.1194 r_free=0.1357 | n_water=891 | time (s): 1.800 (total time: 125.540) Filter (map) r_work=0.1217 r_free=0.1358 | n_water=778 | time (s): 4.310 (total time: 129.850) Find peaks r_work=0.1217 r_free=0.1358 | n_water=778 | time (s): 0.640 (total time: 130.490) Add new water r_work=0.1225 r_free=0.1370 | n_water=1000 | time (s): 4.190 (total time: 134.680) Refine new water occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1339 r_work=0.1186 r_free=0.1339 | n_water=1000 | time (s): 294.990 (total time: 429.670) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=918 | time (s): 4.850 (total time: 434.520) Filter (dist only) r_work=0.1190 r_free=0.1345 | n_water=916 | time (s): 124.510 (total time: 559.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.512827 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.557153 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1349 0.0156 0.038 1.2 8.4 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.49 1.56 1.685 13.781 14.557 3.755 11.91 13.50 1.59 1.681 13.784 14.557 3.752 Individual atomic B min max mean iso aniso Overall: 5.62 63.03 14.65 0.87 552 3268 Protein: 5.62 28.30 10.42 0.87 0 2902 Water: 6.08 63.03 28.04 N/A 552 364 Other: 13.92 22.11 18.02 N/A 0 2 Chain A: 5.73 50.65 12.17 N/A 0 1623 Chain B: 5.62 63.03 12.03 N/A 0 1645 Chain S: 6.08 58.51 29.76 N/A 552 0 Histogram: Values Number of atoms 5.62 - 11.36 2052 11.36 - 17.11 837 17.11 - 22.85 285 22.85 - 28.59 222 28.59 - 34.33 176 34.33 - 40.07 130 40.07 - 45.81 77 45.81 - 51.55 34 51.55 - 57.29 4 57.29 - 63.03 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1350 r_work=0.1191 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751661 | | target function (ml) not normalized (work): 702637.402251 | | target function (ml) not normalized (free): 14718.801176 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1360 0.1472 5.6854 5.7576| | 2: 2.94 - 2.33 1.00 7339 128 0.1066 0.1336 5.074 5.1728| | 3: 2.33 - 2.04 0.96 6939 150 0.0900 0.1181 4.6526 4.7551| | 4: 2.04 - 1.85 1.00 7170 155 0.0894 0.1024 4.3849 4.5445| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0997 4.1487 4.2483| | 6: 1.72 - 1.62 0.99 7102 142 0.0892 0.1067 3.9428 4.0687| | 7: 1.62 - 1.54 0.99 7104 148 0.0884 0.0950 3.7927 3.9196| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1303 3.6941 3.8984| | 9: 1.47 - 1.41 0.98 6938 155 0.0919 0.1117 3.6139 3.7452| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1186 3.5514 3.6779| | 11: 1.36 - 1.32 0.99 6997 151 0.0988 0.1120 3.4813 3.5825| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1129 3.4574 3.5823| | 13: 1.28 - 1.25 0.98 6907 166 0.1037 0.1245 3.4347 3.5629| | 14: 1.25 - 1.22 0.98 7015 112 0.1100 0.1570 3.4305 3.674| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1238 3.4477 3.4917| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1543 3.4629 3.6558| | 17: 1.17 - 1.14 0.98 6940 135 0.1295 0.1222 3.4319 3.4412| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1711 3.4374 3.5334| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1763 3.4193 3.5959| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1570 3.4098 3.434| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2141 3.4174 3.5035| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1965 3.4125 3.4183| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4327 3.4872| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2243 3.4355 3.5069| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2532 3.4491 3.5255| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2858 3.4155 3.4234| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2799 3.4689 3.3952| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.55 1.00 0.97 11092.17| | 2: 2.94 - 2.33 7339 128 0.93 12.66 0.99 0.97 5071.49| | 3: 2.33 - 2.04 6939 150 0.96 7.59 1.01 0.96 1678.94| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.97 993.01| | 5: 1.85 - 1.72 7113 159 0.96 8.06 1.00 0.97 632.30| | 6: 1.72 - 1.62 7102 142 0.96 7.98 1.00 0.97 439.20| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.98 331.53| | 8: 1.54 - 1.47 6798 152 0.96 8.17 1.01 0.98 275.01| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 0.99 227.41| | 10: 1.41 - 1.36 7022 150 0.96 8.86 1.00 0.98 200.48| | 11: 1.36 - 1.32 6997 151 0.96 8.89 0.99 0.97 173.50| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.96 160.44| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.97 158.07| | 14: 1.25 - 1.22 7015 112 0.95 10.70 1.01 0.98 163.04| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.99 166.29| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.00 0.97 160.14| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.97 153.85| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.96 147.71| | 19: 1.12 - 1.10 6948 106 0.93 14.15 1.00 0.96 150.99| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.95 150.21| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.94 153.52| | 22: 1.07 - 1.05 6836 135 0.89 18.33 1.00 0.94 155.36| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.93 165.16| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.94 179.25| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.91 182.21| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.90 176.54| | 27: 0.99 - 0.98 6647 131 0.82 26.25 0.99 0.89 160.66| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.71 max = 11092.17 mean = 916.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.26| |phase err.(test): min = 0.00 max = 89.12 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1189 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1491 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1404 0.1491 n_refl.: 191128 overall B=-0.12 to atoms: r(all,work,free)=0.1385 0.1383 0.1476 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1347 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1347 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3514 352.309 321.660 0.400 0.919 0.179 13.296-10.522 96.04 96 1 0.2390 480.354 461.701 0.711 0.920 0.120 10.503-8.327 97.80 175 3 0.2111 501.827 494.638 0.888 0.921 0.106 8.318-6.595 100.00 360 8 0.2152 375.484 370.027 0.915 0.921 0.085 6.588-5.215 100.00 711 7 0.1973 345.032 334.789 0.916 0.921 0.077 5.214-4.128 98.38 1367 28 0.1242 504.678 498.608 1.009 0.922 0.039 4.126-3.266 94.74 2603 46 0.1173 460.041 452.189 1.077 0.924 0.005 3.266-2.585 99.86 5447 97 0.1124 310.333 306.907 1.058 0.925 0.000 2.585-2.046 97.45 10613 204 0.0957 234.128 231.561 1.065 0.927 0.000 2.046-1.619 99.39 21536 464 0.0906 138.569 137.194 1.081 0.931 0.000 1.619-1.281 98.00 42464 925 0.0940 74.597 73.948 1.070 0.938 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.018 38.300 1.035 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0271 ================= 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 : 0.2035 0.2022 0.082 5.250 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1958 0.082 5.250 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1958 0.082 5.250 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1958 0.082 5.250 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1958 0.082 5.250 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1269 0.1500 0.039 1.155 5.2 78.0 14.6 805 0.156 1_adp: 0.1297 0.1571 0.039 1.155 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1296 0.1566 0.039 1.155 5.2 73.0 15.0 805 0.156 1_occ: 0.1282 0.1556 0.039 1.155 5.2 73.0 15.0 805 0.156 2_bss: 0.1274 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.156 2_settarget: 0.1274 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1274 0.1545 0.039 1.173 5.3 73.2 15.1 805 0.156 2_nqh: 0.1274 0.1545 0.039 1.173 5.3 73.2 15.1 805 0.156 2_sol: 0.1270 0.1506 0.039 1.173 5.3 73.2 16.3 889 n/a 2_weight: 0.1270 0.1506 0.039 1.173 5.3 73.2 16.3 889 n/a 2_xyzrec: 0.1254 0.1524 0.042 1.147 5.3 73.2 16.3 889 n/a 2_adp: 0.1233 0.1507 0.042 1.147 5.4 68.8 16.4 889 n/a 2_regHadp: 0.1234 0.1508 0.042 1.147 5.4 68.8 16.4 889 n/a 2_occ: 0.1228 0.1507 0.042 1.147 5.4 68.8 16.4 889 n/a 3_bss: 0.1234 0.1516 0.042 1.147 5.4 68.8 16.3 889 n/a 3_settarget: 0.1234 0.1516 0.042 1.147 5.4 68.8 16.3 889 n/a 3_updatecdl: 0.1234 0.1516 0.042 1.153 5.4 68.8 16.3 889 n/a 3_nqh: 0.1234 0.1516 0.042 1.153 5.4 68.8 16.3 889 n/a 3_sol: 0.1253 0.1517 0.042 1.153 5.4 68.8 15.4 869 n/a 3_weight: 0.1253 0.1517 0.042 1.153 5.4 68.8 15.4 869 n/a 3_xyzrec: 0.1244 0.1445 0.036 1.099 5.4 68.8 15.4 869 n/a 3_adp: 0.1236 0.1402 0.036 1.099 5.5 68.4 15.2 869 n/a 3_regHadp: 0.1236 0.1403 0.036 1.099 5.5 68.4 15.2 869 n/a 3_occ: 0.1231 0.1393 0.036 1.099 5.5 68.4 15.2 869 n/a 4_bss: 0.1226 0.1386 0.036 1.099 5.5 68.4 15.2 869 n/a 4_settarget: 0.1226 0.1386 0.036 1.099 5.5 68.4 15.2 869 n/a 4_updatecdl: 0.1226 0.1386 0.036 1.101 5.5 68.4 15.2 869 n/a 4_nqh: 0.1226 0.1386 0.036 1.101 5.5 68.4 15.2 869 n/a 4_sol: 0.1208 0.1355 0.036 1.101 5.5 68.4 14.9 867 n/a 4_weight: 0.1208 0.1355 0.036 1.101 5.5 68.4 14.9 867 n/a 4_xyzrec: 0.1206 0.1356 0.036 1.113 5.5 68.4 14.9 867 n/a 4_adp: 0.1198 0.1352 0.036 1.113 5.5 67.8 14.8 867 n/a 4_regHadp: 0.1198 0.1352 0.036 1.113 5.5 67.8 14.8 867 n/a 4_occ: 0.1196 0.1351 0.036 1.113 5.5 67.8 14.8 867 n/a 5_bss: 0.1194 0.1351 0.036 1.113 5.5 67.8 14.8 867 n/a 5_settarget: 0.1194 0.1351 0.036 1.113 5.5 67.8 14.8 867 n/a 5_updatecdl: 0.1194 0.1351 0.036 1.113 5.5 67.8 14.8 867 n/a 5_nqh: 0.1194 0.1351 0.036 1.113 5.5 67.8 14.8 867 n/a 5_sol: 0.1190 0.1340 0.036 1.113 5.5 67.8 14.9 888 n/a 5_weight: 0.1190 0.1340 0.036 1.113 5.5 67.8 14.9 888 n/a 5_xyzrec: 0.1192 0.1348 0.037 1.121 5.5 67.8 14.9 888 n/a 5_adp: 0.1197 0.1351 0.037 1.121 5.6 67.5 14.9 888 n/a 5_regHadp: 0.1197 0.1352 0.037 1.121 5.6 67.5 14.9 888 n/a 5_occ: 0.1194 0.1355 0.037 1.121 5.6 67.5 14.9 888 n/a 6_bss: 0.1192 0.1352 0.037 1.121 5.5 67.5 14.8 888 n/a 6_settarget: 0.1192 0.1352 0.037 1.121 5.5 67.5 14.8 888 n/a 6_updatecdl: 0.1192 0.1352 0.037 1.121 5.5 67.5 14.8 888 n/a 6_nqh: 0.1192 0.1352 0.037 1.121 5.5 67.5 14.8 888 n/a 6_sol: 0.1192 0.1344 0.037 1.121 5.5 67.5 14.8 893 n/a 6_weight: 0.1192 0.1344 0.037 1.121 5.5 67.5 14.8 893 n/a 6_xyzrec: 0.1194 0.1350 0.037 1.129 5.5 67.5 14.8 893 n/a 6_adp: 0.1198 0.1354 0.037 1.129 5.6 66.3 14.7 893 n/a 6_regHadp: 0.1198 0.1355 0.037 1.129 5.6 66.3 14.7 893 n/a 6_occ: 0.1197 0.1356 0.037 1.129 5.6 66.3 14.7 893 n/a 7_bss: 0.1196 0.1356 0.037 1.129 5.5 66.3 14.7 893 n/a 7_settarget: 0.1196 0.1356 0.037 1.129 5.5 66.3 14.7 893 n/a 7_updatecdl: 0.1196 0.1356 0.037 1.129 5.5 66.3 14.7 893 n/a 7_nqh: 0.1196 0.1356 0.037 1.129 5.5 66.3 14.7 893 n/a 7_sol: 0.1195 0.1345 0.037 1.129 5.5 66.3 14.7 894 n/a 7_weight: 0.1195 0.1345 0.037 1.129 5.5 66.3 14.7 894 n/a 7_xyzrec: 0.1199 0.1347 0.038 1.119 5.5 66.3 14.7 894 n/a 7_adp: 0.1202 0.1352 0.038 1.119 5.5 65.9 14.7 894 n/a 7_regHadp: 0.1202 0.1352 0.038 1.119 5.5 65.9 14.7 894 n/a 7_occ: 0.1201 0.1353 0.038 1.119 5.5 65.9 14.7 894 n/a 8_bss: 0.1191 0.1343 0.038 1.119 5.5 65.9 14.7 894 n/a 8_settarget: 0.1191 0.1343 0.038 1.119 5.5 65.9 14.7 894 n/a 8_updatecdl: 0.1191 0.1343 0.038 1.119 5.5 65.9 14.7 894 n/a 8_nqh: 0.1191 0.1343 0.038 1.119 5.5 65.9 14.7 894 n/a 8_sol: 0.1188 0.1345 0.038 1.119 5.5 65.9 14.7 904 n/a 8_weight: 0.1188 0.1345 0.038 1.119 5.5 65.9 14.7 904 n/a 8_xyzrec: 0.1192 0.1351 0.038 1.118 5.5 65.9 14.7 904 n/a 8_adp: 0.1191 0.1352 0.038 1.118 5.6 65.0 14.7 904 n/a 8_regHadp: 0.1192 0.1352 0.038 1.118 5.6 65.0 14.7 904 n/a 8_occ: 0.1190 0.1353 0.038 1.118 5.6 65.0 14.7 904 n/a 9_bss: 0.1189 0.1349 0.038 1.118 5.6 65.0 14.6 904 n/a 9_settarget: 0.1189 0.1349 0.038 1.118 5.6 65.0 14.6 904 n/a 9_updatecdl: 0.1189 0.1349 0.038 1.119 5.6 65.0 14.6 904 n/a 9_nqh: 0.1189 0.1349 0.038 1.119 5.6 65.0 14.6 904 n/a 9_sol: 0.1189 0.1344 0.038 1.119 5.6 65.0 14.6 901 n/a 9_weight: 0.1189 0.1344 0.038 1.119 5.6 65.0 14.6 901 n/a 9_xyzrec: 0.1193 0.1352 0.038 1.117 5.6 65.0 14.6 901 n/a 9_adp: 0.1194 0.1354 0.038 1.117 5.6 64.2 14.6 901 n/a 9_regHadp: 0.1195 0.1354 0.038 1.117 5.6 64.2 14.6 901 n/a 9_occ: 0.1193 0.1356 0.038 1.117 5.6 64.2 14.6 901 n/a 10_bss: 0.1192 0.1357 0.038 1.117 5.6 64.2 14.6 901 n/a 10_settarget: 0.1192 0.1357 0.038 1.117 5.6 64.2 14.6 901 n/a 10_updatecdl: 0.1192 0.1357 0.038 1.117 5.6 64.2 14.6 901 n/a 10_setrh: 0.1193 0.1357 0.038 1.117 5.6 64.2 14.6 901 n/a 10_nqh: 0.1193 0.1357 0.038 1.117 5.6 64.2 14.6 901 n/a 10_sol: 0.1190 0.1345 0.038 1.117 5.6 64.2 14.6 916 n/a 10_weight: 0.1190 0.1345 0.038 1.117 5.6 64.2 14.6 916 n/a 10_xyzrec: 0.1193 0.1349 0.038 1.156 5.6 64.2 14.6 916 n/a 10_adp: 0.1191 0.1350 0.038 1.156 5.6 63.0 14.7 916 n/a 10_regHadp: 0.1191 0.1350 0.038 1.156 5.6 63.0 14.7 916 n/a 10_occ: 0.1189 0.1350 0.038 1.156 5.6 63.0 14.7 916 n/a end: 0.1189 0.1347 0.038 1.156 5.5 62.9 14.5 916 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5571520_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5571520_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9800 Refinement macro-cycles (run) : 12082.7000 Write final files (write_after_run_outputs) : 174.9800 Total : 12263.6600 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:34 PST -0800 (1736736094.93 s) Start R-work = 0.1800, R-free = 0.1958 Final R-work = 0.1189, R-free = 0.1347 =============================================================================== Job complete usr+sys time: 12557.30 seconds wall clock time: 210 minutes 17.93 seconds (12617.93 seconds total)