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_2951004.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2951004.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2951004.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.95, per 1000 atoms: 0.29 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: 2.657 distance_ideal: 2.720 ideal - model: 0.063 slack: 0.000 delta_slack: 0.063 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: 2.781 distance_ideal: 2.710 ideal - model: -0.071 slack: 0.000 delta_slack: -0.071 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: 0.84 Conformation dependent library (CDL) restraints added in 121.8 milliseconds Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.04: 958 1.04 - 1.28: 2460 1.28 - 1.52: 1626 1.52 - 1.75: 877 1.75 - 1.99: 13 Bond restraints: 5934 Sorted by residual: bond pdb=" C ALA B 10 " pdb=" O ALA B 10 " ideal model delta sigma weight residual 1.236 1.066 0.170 8.90e-03 1.26e+04 3.66e+02 bond pdb=" C THR B 125 " pdb=" N GLY B 126 " ideal model delta sigma weight residual 1.327 1.150 0.177 9.60e-03 1.09e+04 3.42e+02 bond pdb=" CA VAL A 89 " pdb=" HA VAL A 89 " ideal model delta sigma weight residual 0.970 1.339 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" N LEU B 171 " pdb=" H LEU B 171 " ideal model delta sigma weight residual 0.860 1.226 -0.366 2.00e-02 2.50e+03 3.35e+02 bond pdb=" C ASN A 123 " pdb=" O ASN A 123 " ideal model delta sigma weight residual 1.234 1.455 -0.220 1.22e-02 6.72e+03 3.26e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 5771 4.33 - 8.66: 3599 8.66 - 13.00: 1220 13.00 - 17.33: 203 17.33 - 21.66: 17 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" O VAL B 114 " ideal model delta sigma weight residual 118.69 130.62 -11.93 6.70e-01 2.23e+00 3.17e+02 angle pdb=" O VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 120.42 110.23 10.19 6.40e-01 2.44e+00 2.53e+02 angle pdb=" CA ASP B 170 " pdb=" CB ASP B 170 " pdb=" CG ASP B 170 " ideal model delta sigma weight residual 112.60 127.79 -15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" O VAL B 19 " pdb=" C VAL B 19 " pdb=" N THR B 20 " ideal model delta sigma weight residual 121.83 137.08 -15.25 1.03e+00 9.43e-01 2.19e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.71 130.85 -9.14 6.40e-01 2.44e+00 2.04e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.97: 1829 15.97 - 31.94: 139 31.94 - 47.91: 50 47.91 - 63.88: 27 63.88 - 79.85: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual 180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA THR B 33 " pdb=" C THR B 33 " pdb=" N THR B 34 " pdb=" CA THR B 34 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.250: 236 0.250 - 0.498: 166 0.498 - 0.746: 68 0.746 - 0.994: 17 0.994 - 1.242: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.85e+01 chirality pdb=" CA ALA B 110 " pdb=" N ALA B 110 " pdb=" C ALA B 110 " pdb=" CB ALA B 110 " both_signs ideal model delta sigma weight residual False 2.48 3.65 -1.17 2.00e-01 2.50e+01 3.40e+01 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 -1.45 -1.14 2.00e-01 2.50e+01 3.25e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " -0.080 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE B 95 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.093 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " -0.109 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " -0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " 0.133 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.074 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " -0.026 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " 0.071 2.00e-02 2.50e+03 7.41e-02 1.65e+02 pdb=" CG PHE B 119 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.138 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " 0.063 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " 0.059 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " 0.113 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.144 2.00e-02 2.50e+03 7.09e-02 1.51e+02 pdb=" CG PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.129 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 28 1.63 - 2.37: 2564 2.37 - 3.11: 22346 3.11 - 3.86: 32972 3.86 - 4.60: 52266 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110176 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.885 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.926 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.059 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.070 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.166 2.620 ... (remaining 110171 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_2951004_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295602 | | target function (ml) not normalized (work): 804622.107423 | | target function (ml) not normalized (free): 16532.926015 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1918 6.6848 6.3071| | 2: 2.94 - 2.33 1.00 7339 128 0.1610 0.1517 5.5312 5.5377| | 3: 2.33 - 2.04 0.96 6939 150 0.1652 0.1519 5.1496 5.102| | 4: 2.04 - 1.85 1.00 7170 155 0.1746 0.1629 4.9596 5.0917| | 5: 1.85 - 1.72 0.99 7113 159 0.1920 0.1858 4.8003 4.889| | 6: 1.72 - 1.62 0.99 7102 142 0.1960 0.1967 4.6547 4.6918| | 7: 1.62 - 1.54 0.99 7104 148 0.1985 0.1669 4.543 4.5229| | 8: 1.54 - 1.47 0.96 6798 152 0.2035 0.2047 4.4631 4.5059| | 9: 1.47 - 1.41 0.98 6938 155 0.2116 0.2127 4.3903 4.428| | 10: 1.41 - 1.36 0.99 7022 150 0.2103 0.2074 4.3037 4.3066| | 11: 1.36 - 1.32 0.99 6997 151 0.2093 0.2116 4.2183 4.268| | 12: 1.32 - 1.28 0.98 6976 149 0.2033 0.2126 4.161 4.2874| | 13: 1.28 - 1.25 0.98 6907 166 0.2032 0.2268 4.1259 4.2307| | 14: 1.25 - 1.22 0.98 7015 113 0.2088 0.2330 4.0808 4.2238| | 15: 1.22 - 1.19 0.98 6957 137 0.2128 0.2044 4.0468 4.0325| | 16: 1.19 - 1.17 0.93 6604 132 0.2138 0.1943 3.9988 3.9935| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.1883 3.9558 4.0075| | 18: 1.14 - 1.12 0.98 6875 142 0.2186 0.2240 3.9085 3.9064| | 19: 1.12 - 1.10 0.97 6949 106 0.2265 0.2582 3.8631 4.0462| | 20: 1.10 - 1.08 0.97 6884 147 0.2312 0.2155 3.8164 3.8072| | 21: 1.08 - 1.07 0.97 6852 152 0.2455 0.2577 3.791 3.798| | 22: 1.07 - 1.05 0.97 6838 135 0.2583 0.2580 3.7599 3.7416| | 23: 1.05 - 1.03 0.97 6829 159 0.2712 0.2581 3.7272 3.7655| | 24: 1.03 - 1.02 0.96 6785 133 0.2872 0.2692 3.7009 3.7605| | 25: 1.02 - 1.01 0.93 6552 130 0.3067 0.3053 3.6792 3.7216| | 26: 1.01 - 0.99 0.96 6767 158 0.3147 0.3085 3.6147 3.6013| | 27: 0.99 - 0.98 0.94 6648 131 0.3414 0.3380 3.6404 3.6454| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.46 0.91 0.97 35115.72| | 2: 2.94 - 2.33 7339 128 0.86 20.91 1.08 1.02 14678.45| | 3: 2.33 - 2.04 6939 150 0.93 12.01 1.11 1.05 3921.79| | 4: 2.04 - 1.85 7170 155 0.92 13.79 1.11 1.06 2895.49| | 5: 1.85 - 1.72 7113 159 0.90 16.40 1.12 1.06 2222.43| | 6: 1.72 - 1.62 7102 142 0.90 17.02 1.11 1.06 1670.13| | 7: 1.62 - 1.54 7104 148 0.90 17.05 1.10 1.05 1231.51| | 8: 1.54 - 1.47 6798 152 0.89 17.46 1.11 1.05 1035.52| | 9: 1.47 - 1.41 6938 155 0.89 18.33 1.11 1.05 899.54| | 10: 1.41 - 1.36 7022 150 0.88 19.46 1.09 1.05 814.28| | 11: 1.36 - 1.32 6997 151 0.87 19.73 1.08 1.04 709.86| | 12: 1.32 - 1.28 6976 149 0.87 20.12 1.08 1.04 670.51| | 13: 1.28 - 1.25 6907 166 0.86 20.87 1.07 1.03 652.18| | 14: 1.25 - 1.22 7015 113 0.85 21.79 1.08 1.03 623.13| | 15: 1.22 - 1.19 6957 137 0.86 21.36 1.08 1.03 556.37| | 16: 1.19 - 1.17 6604 132 0.87 20.08 1.08 1.03 468.95| | 17: 1.17 - 1.14 6941 135 0.87 20.38 1.08 1.03 426.33| | 18: 1.14 - 1.12 6875 142 0.87 20.68 1.08 1.01 388.99| | 19: 1.12 - 1.10 6949 106 0.86 22.03 1.08 1.00 374.38| | 20: 1.10 - 1.08 6884 147 0.85 22.20 1.06 0.99 334.36| | 21: 1.08 - 1.07 6852 152 0.84 23.33 1.06 0.99 325.00| | 22: 1.07 - 1.05 6838 135 0.83 24.89 1.05 0.98 313.71| | 23: 1.05 - 1.03 6829 159 0.80 27.31 1.05 0.97 322.97| | 24: 1.03 - 1.02 6785 133 0.78 29.02 1.04 0.98 323.47| | 25: 1.02 - 1.01 6552 130 0.77 30.51 1.03 0.95 315.14| | 26: 1.01 - 0.99 6767 158 0.74 32.67 1.03 0.92 303.13| | 27: 0.99 - 0.98 6648 131 0.73 33.99 1.03 0.87 295.45| |alpha: min = 0.87 max = 1.06 mean = 1.01| |beta: min = 295.45 max = 35115.72 mean = 2788.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.54| |phase err.(test): min = 0.00 max = 89.87 mean = 21.62| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.263 2950 Z= 5.533 Angle : 5.170 18.975 4018 Z= 3.686 Chirality : 0.383 1.242 492 Planarity : 0.033 0.194 512 Dihedral : 12.731 79.850 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.37 % Rotamer: Outliers : 0.65 % Allowed : 5.16 % Favored : 94.19 % Cbeta Deviations : 30.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.38), residues: 386 helix: -2.26 (0.32), residues: 148 sheet: -0.97 (0.52), residues: 86 loop : -0.60 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.021 ARG A 175 TYR 0.115 0.037 TYR A 192 PHE 0.120 0.043 PHE B 95 TRP 0.103 0.038 TRP A 146 HIS 0.072 0.025 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295602 | | target function (ml) not normalized (work): 804622.107423 | | target function (ml) not normalized (free): 16532.926015 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2031 0.1953 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2031 0.1953 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2031 0.1953 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2030 0.2032 0.1954 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1796 0.1881 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1794 0.1879 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 0.4075 402.814 293.072 0.424 0.932 0.301 13.296-10.522 99.01 99 1 0.2474 528.187 520.544 0.770 0.933 0.251 10.503-8.327 99.45 178 3 0.2493 565.118 556.249 0.949 0.933 0.227 8.318-6.595 100.00 360 8 0.2466 414.736 403.516 0.943 0.933 0.160 6.588-5.215 100.00 711 7 0.2263 381.101 366.340 0.933 0.933 0.150 5.214-4.128 98.38 1367 28 0.1483 557.435 549.330 1.052 0.932 0.090 4.126-3.266 94.74 2603 46 0.1336 508.132 499.196 1.121 0.931 0.014 3.266-2.585 99.86 5447 97 0.1444 342.774 337.609 1.098 0.929 0.000 2.585-2.046 97.45 10613 204 0.1409 258.603 254.045 1.105 0.925 0.000 2.046-1.619 99.39 21536 464 0.1609 153.054 149.840 1.130 0.920 0.000 1.619-1.281 98.00 42464 925 0.1905 82.395 80.218 1.124 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2313 44.202 41.687 1.125 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0130 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1879 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1800 r_free=0.1880 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.813624 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.394000 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1499 0.0226 0.039 1.2 10.4 0.0 0.3 0 11.407 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 14.99 2.26 1.118 13.119 570.394 0.019 12.99 15.68 2.69 1.268 13.403 570.394 0.017 Individual atomic B min max mean iso aniso Overall: 5.28 73.05 15.12 1.41 435 3274 Protein: 5.28 40.51 11.04 1.41 0 2902 Water: 6.38 73.05 29.83 N/A 435 370 Other: 15.97 30.43 23.20 N/A 0 2 Chain A: 5.29 60.01 13.11 N/A 0 1626 Chain B: 5.28 73.05 12.84 N/A 0 1648 Chain S: 11.36 64.61 31.30 N/A 435 0 Histogram: Values Number of atoms 5.28 - 12.06 2186 12.06 - 18.84 620 18.84 - 25.61 303 25.61 - 32.39 260 32.39 - 39.17 158 39.17 - 45.94 116 45.94 - 52.72 41 52.72 - 59.50 17 59.50 - 66.27 7 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1568 r_work=0.1299 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1562 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 = 0.1283 r_free = 0.1550 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= 0.1283 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015628 | | target function (ls_wunit_k1) not normalized (work): 2927.097186 | | target function (ls_wunit_k1) not normalized (free): 116.124053 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1283 0.1550 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1471 0.1469 0.1627 n_refl.: 191138 remove outliers: r(all,work,free)=0.1471 0.1469 0.1627 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1494 0.1491 0.1638 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1543 n_refl.: 191138 remove outliers: r(all,work,free)=0.1283 0.1278 0.1543 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 0.3597 402.814 380.720 0.468 1.002 0.275 13.296-10.522 99.01 99 1 0.2085 528.187 521.863 0.711 1.004 0.245 10.503-8.327 99.45 178 3 0.1765 565.118 561.298 0.853 1.004 0.198 8.318-6.595 100.00 360 8 0.1705 414.736 412.496 0.873 1.004 0.155 6.588-5.215 100.00 711 7 0.1540 381.101 373.181 0.851 1.004 0.150 5.214-4.128 98.38 1367 28 0.0903 557.435 555.136 0.938 1.005 0.054 4.126-3.266 94.74 2603 46 0.0835 508.132 504.076 1.002 1.005 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.287 0.985 1.005 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.318 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1094 153.054 151.369 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.412 1.005 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.168 0.983 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0351 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1543 | n_water=805 | time (s): 2.910 (total time: 2.910) Filter (dist) r_work=0.1282 r_free=0.1544 | n_water=793 | time (s): 103.330 (total time: 106.240) Filter (q & B) r_work=0.1283 r_free=0.1544 | n_water=788 | time (s): 5.080 (total time: 111.320) Compute maps r_work=0.1283 r_free=0.1544 | n_water=788 | time (s): 1.740 (total time: 113.060) Filter (map) r_work=0.1308 r_free=0.1534 | n_water=654 | time (s): 5.410 (total time: 118.470) Find peaks r_work=0.1308 r_free=0.1534 | n_water=654 | time (s): 0.610 (total time: 119.080) Add new water r_work=0.1329 r_free=0.1562 | n_water=951 | time (s): 4.080 (total time: 123.160) Refine new water occ: r_work=0.1288 r_free=0.1503 adp: r_work=0.1276 r_free=0.1502 occ: r_work=0.1277 r_free=0.1497 adp: r_work=0.1271 r_free=0.1499 occ: r_work=0.1272 r_free=0.1496 adp: r_work=0.1270 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1270 r_free=0.1499 r_work=0.1270 r_free=0.1499 | n_water=951 | time (s): 95.170 (total time: 218.330) Filter (q & B) r_work=0.1273 r_free=0.1500 | n_water=885 | time (s): 4.770 (total time: 223.100) Filter (dist only) r_work=0.1274 r_free=0.1500 | n_water=884 | time (s): 113.660 (total time: 336.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.418391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.288377 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 0.1257 0.1521 0.0264 0.041 1.1 17.5 0.0 0.3 0 11.709 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.21 2.64 2.055 15.295 596.288 0.015 12.36 15.11 2.75 2.439 15.326 596.288 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 68.25 16.46 1.21 517 3271 Protein: 5.41 40.32 11.01 1.21 0 2902 Water: 6.58 68.25 34.35 N/A 517 367 Other: 16.37 33.18 24.78 N/A 0 2 Chain A: 5.57 56.80 13.03 N/A 0 1624 Chain B: 5.41 68.25 12.85 N/A 0 1647 Chain S: 13.20 66.53 38.75 N/A 517 0 Histogram: Values Number of atoms 5.41 - 11.69 2062 11.69 - 17.98 705 17.98 - 24.26 258 24.26 - 30.54 209 30.54 - 36.83 179 36.83 - 43.11 149 43.11 - 49.40 111 49.40 - 55.68 56 55.68 - 61.97 46 61.97 - 68.25 13 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1511 r_work=0.1236 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1502 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013510 | | target function (ls_wunit_k1) not normalized (work): 2530.429369 | | target function (ls_wunit_k1) not normalized (free): 99.176163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1502 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1436 0.1433 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1509 n_refl.: 191138 remove outliers: r(all,work,free)=0.1241 0.1236 0.1509 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 0.3258 402.814 377.502 0.494 0.963 0.271 13.296-10.522 99.01 99 1 0.1854 528.187 518.544 0.753 0.964 0.212 10.503-8.327 99.45 178 3 0.1395 565.118 568.085 0.922 0.964 0.164 8.318-6.595 100.00 360 8 0.1530 414.736 414.546 0.934 0.963 0.150 6.588-5.215 100.00 711 7 0.1345 381.101 376.786 0.911 0.963 0.150 5.214-4.128 98.38 1367 28 0.0835 557.435 556.395 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0770 508.132 505.626 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0853 342.774 341.363 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.723 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.628 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1262 82.395 81.346 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.212 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0545 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1510 | n_water=884 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1238 r_free=0.1511 | n_water=880 | time (s): 125.690 (total time: 128.970) Filter (q & B) r_work=0.1239 r_free=0.1513 | n_water=874 | time (s): 5.540 (total time: 134.510) Compute maps r_work=0.1239 r_free=0.1513 | n_water=874 | time (s): 2.070 (total time: 136.580) Filter (map) r_work=0.1273 r_free=0.1525 | n_water=699 | time (s): 5.100 (total time: 141.680) Find peaks r_work=0.1273 r_free=0.1525 | n_water=699 | time (s): 0.610 (total time: 142.290) Add new water r_work=0.1295 r_free=0.1553 | n_water=1004 | time (s): 4.610 (total time: 146.900) Refine new water occ: r_work=0.1254 r_free=0.1518 adp: r_work=0.1254 r_free=0.1518 occ: r_work=0.1251 r_free=0.1514 adp: r_work=0.1250 r_free=0.1514 occ: r_work=0.1248 r_free=0.1510 adp: r_work=0.1247 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1510 r_work=0.1247 r_free=0.1510 | n_water=1004 | time (s): 315.150 (total time: 462.050) Filter (q & B) r_work=0.1251 r_free=0.1511 | n_water=875 | time (s): 5.250 (total time: 467.300) Filter (dist only) r_work=0.1252 r_free=0.1512 | n_water=874 | time (s): 110.920 (total time: 578.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.716655 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.630365 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1241 0.1431 0.0190 0.035 1.1 9.0 0.0 0.0 0 0.858 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.31 1.90 1.939 14.664 16.630 3.942 12.32 13.89 1.57 2.203 14.575 16.630 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 67.93 15.40 1.08 508 3270 Protein: 5.54 37.08 10.78 1.08 0 2902 Water: 6.65 67.93 30.69 N/A 508 366 Other: 14.05 29.18 21.61 N/A 0 2 Chain A: 5.57 56.04 12.82 N/A 0 1624 Chain B: 5.54 67.93 12.58 N/A 0 1646 Chain S: 14.33 60.71 32.76 N/A 508 0 Histogram: Values Number of atoms 5.54 - 11.78 2132 11.78 - 18.02 674 18.02 - 24.25 289 24.25 - 30.49 249 30.49 - 36.73 179 36.73 - 42.97 133 42.97 - 49.21 78 49.21 - 55.45 30 55.45 - 61.69 13 61.69 - 67.93 1 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1389 r_work=0.1232 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1389 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1384 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891413 | | target function (ml) not normalized (work): 728849.992209 | | target function (ml) not normalized (free): 15223.189815 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1384 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1436 0.1437 0.1457 n_refl.: 191138 remove outliers: r(all,work,free)=0.1436 0.1437 0.1457 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1430 0.1430 0.1453 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1380 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 93.07 91 3 0.3791 398.895 354.610 0.409 0.947 0.234 13.296-10.522 99.01 99 1 0.2433 528.187 507.300 0.709 0.949 0.209 10.503-8.327 98.35 176 3 0.1994 555.265 557.001 0.887 0.949 0.167 8.318-6.595 100.00 360 8 0.2012 414.736 410.801 0.896 0.948 0.128 6.588-5.215 100.00 711 7 0.1810 381.101 370.959 0.883 0.948 0.110 5.214-4.128 98.38 1367 28 0.1146 557.435 552.241 0.972 0.949 0.080 4.126-3.266 94.74 2603 46 0.1089 508.132 501.807 1.031 0.949 0.014 3.266-2.585 99.86 5447 97 0.1075 342.774 339.280 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0964 258.603 255.748 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.418 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1056 82.395 81.474 1.051 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.315 1.037 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1022 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1380 | n_water=874 | time (s): 2.750 (total time: 2.750) Filter (dist) r_work=0.1224 r_free=0.1380 | n_water=870 | time (s): 120.720 (total time: 123.470) Filter (q & B) r_work=0.1224 r_free=0.1381 | n_water=859 | time (s): 4.340 (total time: 127.810) Compute maps r_work=0.1224 r_free=0.1381 | n_water=859 | time (s): 1.940 (total time: 129.750) Filter (map) r_work=0.1244 r_free=0.1380 | n_water=722 | time (s): 5.320 (total time: 135.070) Find peaks r_work=0.1244 r_free=0.1380 | n_water=722 | time (s): 0.910 (total time: 135.980) Add new water r_work=0.1259 r_free=0.1395 | n_water=952 | time (s): 4.930 (total time: 140.910) Refine new water occ: r_work=0.1214 r_free=0.1366 adp: r_work=0.1206 r_free=0.1365 occ: r_work=0.1203 r_free=0.1366 adp: r_work=0.1203 r_free=0.1365 occ: r_work=0.1201 r_free=0.1367 adp: r_work=0.1201 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1366 r_work=0.1201 r_free=0.1366 | n_water=952 | time (s): 230.170 (total time: 371.080) Filter (q & B) r_work=0.1205 r_free=0.1366 | n_water=865 | time (s): 5.490 (total time: 376.570) Filter (dist only) r_work=0.1206 r_free=0.1364 | n_water=863 | time (s): 111.080 (total time: 487.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568580 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.627212 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1361 0.0156 0.035 1.1 7.5 0.0 0.0 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.61 1.56 1.849 14.274 15.627 3.874 12.00 13.58 1.58 1.979 14.229 15.627 3.866 Individual atomic B min max mean iso aniso Overall: 5.49 67.48 15.04 1.01 497 3270 Protein: 5.49 33.72 10.69 1.01 0 2902 Water: 5.87 67.48 29.67 N/A 497 366 Other: 13.93 27.90 20.91 N/A 0 2 Chain A: 5.57 54.87 12.67 N/A 0 1624 Chain B: 5.49 67.48 12.47 N/A 0 1646 Chain S: 5.87 60.71 31.31 N/A 497 0 Histogram: Values Number of atoms 5.49 - 11.69 2113 11.69 - 17.89 723 17.89 - 24.09 288 24.09 - 30.29 251 30.29 - 36.49 168 36.49 - 42.68 121 42.68 - 48.88 68 48.88 - 55.08 26 55.08 - 61.28 8 61.28 - 67.48 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1358 r_work=0.1200 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1356 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864088 | | target function (ml) not normalized (work): 723716.560429 | | target function (ml) not normalized (free): 15128.792090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1356 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1455 n_refl.: 191134 remove outliers: r(all,work,free)=0.1406 0.1405 0.1455 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1399 0.1398 0.1451 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191134 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3728 357.169 323.547 0.407 0.952 0.233 13.296-10.522 98.02 98 1 0.2440 479.004 453.694 0.693 0.953 0.188 10.503-8.327 98.35 176 3 0.2150 502.882 497.152 0.864 0.954 0.142 8.318-6.595 100.00 360 8 0.2122 375.611 370.804 0.888 0.953 0.115 6.588-5.215 100.00 711 7 0.1880 345.148 335.511 0.880 0.953 0.110 5.214-4.128 98.38 1367 28 0.1196 504.847 499.901 0.967 0.953 0.070 4.126-3.266 94.74 2603 46 0.1110 460.196 453.961 1.026 0.953 0.000 3.266-2.585 99.86 5447 97 0.1082 310.437 307.163 1.015 0.952 0.000 2.585-2.046 97.45 10613 204 0.0933 234.207 231.756 1.028 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.615 137.314 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0989 74.622 73.906 1.051 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.032 38.364 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1351 | n_water=863 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1195 r_free=0.1350 | n_water=861 | time (s): 107.290 (total time: 110.300) Filter (q & B) r_work=0.1196 r_free=0.1352 | n_water=850 | time (s): 5.070 (total time: 115.370) Compute maps r_work=0.1196 r_free=0.1352 | n_water=850 | time (s): 1.980 (total time: 117.350) Filter (map) r_work=0.1214 r_free=0.1346 | n_water=749 | time (s): 5.370 (total time: 122.720) Find peaks r_work=0.1214 r_free=0.1346 | n_water=749 | time (s): 0.800 (total time: 123.520) Add new water r_work=0.1225 r_free=0.1357 | n_water=966 | time (s): 4.000 (total time: 127.520) Refine new water occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1189 r_free=0.1336 adp: r_work=0.1189 r_free=0.1337 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1186 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1338 r_work=0.1186 r_free=0.1338 | n_water=966 | time (s): 253.880 (total time: 381.400) Filter (q & B) r_work=0.1191 r_free=0.1342 | n_water=889 | time (s): 4.600 (total time: 386.000) Filter (dist only) r_work=0.1191 r_free=0.1341 | n_water=888 | time (s): 112.970 (total time: 498.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.641544 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.531572 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 0.1347 0.0155 0.035 1.1 6.5 0.0 0.3 0 0.821 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.47 1.55 1.801 14.240 15.532 3.763 11.97 13.53 1.56 1.883 14.207 15.532 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 67.06 15.10 0.97 523 3269 Protein: 5.56 32.12 10.61 0.97 0 2902 Water: 6.08 67.06 29.78 N/A 523 365 Other: 13.82 26.55 20.19 N/A 0 2 Chain A: 5.56 53.88 12.55 N/A 0 1623 Chain B: 5.59 67.06 12.37 N/A 0 1646 Chain S: 6.08 60.68 31.66 N/A 523 0 Histogram: Values Number of atoms 5.56 - 11.71 2135 11.71 - 17.86 718 17.86 - 24.01 282 24.01 - 30.16 236 30.16 - 36.31 177 36.31 - 42.46 134 42.46 - 48.61 73 48.61 - 54.76 29 54.76 - 60.91 7 60.91 - 67.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1353 r_work=0.1197 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.759 | | 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759136 | | target function (ml) not normalized (work): 704052.341247 | | target function (ml) not normalized (free): 14732.967948 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1399 0.1397 0.1479 n_refl.: 191132 remove outliers: r(all,work,free)=0.1399 0.1397 0.1479 n_refl.: 191132 overall B=-0.22 to atoms: r(all,work,free)=0.1361 0.1360 0.1453 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191132 remove outliers: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3662 357.169 322.594 0.414 0.953 0.233 13.296-10.522 98.02 98 1 0.2390 479.004 461.543 0.716 0.955 0.185 10.503-8.327 98.35 176 3 0.2128 502.882 497.850 0.886 0.955 0.160 8.318-6.595 100.00 360 8 0.2095 375.611 371.646 0.909 0.954 0.100 6.588-5.215 100.00 711 7 0.1841 345.148 336.179 0.904 0.955 0.100 5.214-4.128 98.38 1367 28 0.1192 504.847 500.165 0.992 0.955 0.070 4.126-3.266 94.74 2603 46 0.1105 460.196 454.287 1.051 0.955 0.000 3.266-2.585 99.86 5447 97 0.1101 310.437 307.237 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0949 234.207 231.668 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0918 138.615 137.291 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0980 74.622 73.895 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.032 38.355 1.027 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1349 | n_water=888 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1194 r_free=0.1349 | n_water=888 | time (s): 109.910 (total time: 112.520) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=882 | time (s): 4.120 (total time: 116.640) Compute maps r_work=0.1194 r_free=0.1350 | n_water=882 | time (s): 2.210 (total time: 118.850) Filter (map) r_work=0.1214 r_free=0.1347 | n_water=782 | time (s): 5.600 (total time: 124.450) Find peaks r_work=0.1214 r_free=0.1347 | n_water=782 | time (s): 0.710 (total time: 125.160) Add new water r_work=0.1223 r_free=0.1360 | n_water=986 | time (s): 4.880 (total time: 130.040) 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=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1343 adp: r_work=0.1187 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1342 r_work=0.1187 r_free=0.1342 | n_water=986 | time (s): 209.270 (total time: 339.310) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=903 | time (s): 5.020 (total time: 344.330) Filter (dist only) r_work=0.1192 r_free=0.1348 | n_water=902 | time (s): 112.380 (total time: 456.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.320926 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 0.1197 0.1357 0.0160 0.037 1.1 7.0 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.60 1.767 13.963 15.321 3.762 11.99 13.62 1.63 1.889 13.918 15.321 3.759 Individual atomic B min max mean iso aniso Overall: 5.39 65.85 14.83 0.92 537 3269 Protein: 5.39 29.63 10.32 0.92 0 2902 Water: 5.85 65.85 29.32 N/A 537 365 Other: 13.67 23.69 18.68 N/A 0 2 Chain A: 5.44 51.98 12.22 N/A 0 1623 Chain B: 5.39 65.85 12.05 N/A 0 1646 Chain S: 5.85 60.54 31.22 N/A 537 0 Histogram: Values Number of atoms 5.39 - 11.44 2116 11.44 - 17.48 763 17.48 - 23.53 272 23.53 - 29.58 221 29.58 - 35.62 186 35.62 - 41.67 125 41.67 - 47.71 83 47.71 - 53.76 30 53.76 - 59.81 6 59.81 - 65.85 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1362 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1363 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758344 | | target function (ml) not normalized (work): 703904.070683 | | target function (ml) not normalized (free): 14742.871160 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1469 n_refl.: 191132 remove outliers: r(all,work,free)=0.1371 0.1369 0.1469 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1379 0.1378 0.1475 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1355 n_refl.: 191132 remove outliers: r(all,work,free)=0.1191 0.1188 0.1355 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3667 357.169 320.633 0.402 0.974 0.225 13.296-10.522 98.02 98 1 0.2386 479.004 460.654 0.701 0.976 0.168 10.503-8.327 98.35 176 3 0.2132 502.882 497.581 0.875 0.976 0.140 8.318-6.595 100.00 360 8 0.2095 375.611 371.283 0.896 0.976 0.105 6.588-5.215 100.00 711 7 0.1864 345.148 335.850 0.891 0.976 0.090 5.214-4.128 98.38 1367 28 0.1203 504.847 499.514 0.982 0.977 0.090 4.126-3.266 94.74 2603 46 0.1125 460.196 453.410 1.039 0.978 0.000 3.266-2.585 99.86 5447 97 0.1119 310.437 306.892 1.024 0.978 0.000 2.585-2.046 97.45 10613 204 0.0956 234.207 231.525 1.033 0.979 0.000 2.046-1.619 99.39 21536 464 0.0912 138.615 137.219 1.050 0.981 0.000 1.619-1.281 98.00 42464 925 0.0957 74.622 73.935 1.040 0.985 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.032 38.333 1.007 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0590 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1355 | n_water=902 | time (s): 3.370 (total time: 3.370) Filter (dist) r_work=0.1188 r_free=0.1355 | n_water=901 | time (s): 114.300 (total time: 117.670) Filter (q & B) r_work=0.1189 r_free=0.1355 | n_water=892 | time (s): 4.190 (total time: 121.860) Compute maps r_work=0.1189 r_free=0.1355 | n_water=892 | time (s): 1.910 (total time: 123.770) Filter (map) r_work=0.1208 r_free=0.1350 | n_water=785 | time (s): 4.430 (total time: 128.200) Find peaks r_work=0.1208 r_free=0.1350 | n_water=785 | time (s): 0.650 (total time: 128.850) Add new water r_work=0.1217 r_free=0.1361 | n_water=973 | time (s): 4.170 (total time: 133.020) Refine new water occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1186 r_free=0.1341 occ: r_work=0.1184 r_free=0.1339 adp: r_work=0.1184 r_free=0.1340 occ: r_work=0.1182 r_free=0.1340 adp: r_work=0.1182 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1340 r_work=0.1182 r_free=0.1340 | n_water=973 | time (s): 281.570 (total time: 414.590) Filter (q & B) r_work=0.1186 r_free=0.1346 | n_water=908 | time (s): 5.380 (total time: 419.970) Filter (dist only) r_work=0.1187 r_free=0.1346 | n_water=906 | time (s): 114.480 (total time: 534.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607792 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.253512 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 0.1189 0.1347 0.0158 0.037 1.1 6.1 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.47 1.58 1.705 13.923 14.254 3.756 11.91 13.51 1.60 1.760 13.901 14.254 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 65.02 14.86 0.89 541 3269 Protein: 5.50 28.73 10.36 0.89 0 2902 Water: 5.91 65.02 29.26 N/A 541 365 Other: 13.79 22.45 18.12 N/A 0 2 Chain A: 5.56 51.69 12.22 N/A 0 1623 Chain B: 5.50 65.02 12.07 N/A 0 1646 Chain S: 5.91 60.75 31.27 N/A 541 0 Histogram: Values Number of atoms 5.50 - 11.45 2100 11.45 - 17.40 781 17.40 - 23.35 269 23.35 - 29.31 219 29.31 - 35.26 183 35.26 - 41.21 127 41.21 - 47.16 86 47.16 - 53.11 36 53.11 - 59.06 5 59.06 - 65.02 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1351 r_work=0.1191 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1351 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1350 target_work(ml) = 3.754 | | 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.=191132 (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): 3.754317 | | target function (ml) not normalized (work): 703149.715619 | | target function (ml) not normalized (free): 14724.661655 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1350 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1385 0.1384 0.1479 n_refl.: 191132 remove outliers: r(all,work,free)=0.1385 0.1384 0.1479 n_refl.: 191132 overall B=0.01 to atoms: r(all,work,free)=0.1387 0.1386 0.1480 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1347 n_refl.: 191132 remove outliers: r(all,work,free)=0.1190 0.1187 0.1347 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3709 352.547 319.358 0.383 0.976 0.201 13.296-10.522 98.02 98 1 0.2408 479.004 460.735 0.685 0.977 0.141 10.503-8.327 98.35 176 3 0.2167 502.882 496.994 0.872 0.978 0.113 8.318-6.595 100.00 360 8 0.2120 375.611 371.104 0.888 0.978 0.088 6.588-5.215 100.00 711 7 0.1881 345.148 335.869 0.886 0.978 0.073 5.214-4.128 98.38 1367 28 0.1216 504.847 499.541 0.978 0.979 0.070 4.126-3.266 94.74 2603 46 0.1126 460.196 453.250 1.037 0.980 0.000 3.266-2.585 99.86 5447 97 0.1123 310.437 306.821 1.022 0.980 0.000 2.585-2.046 97.45 10613 204 0.0961 234.207 231.500 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0909 138.615 137.237 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0950 74.622 73.948 1.041 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.032 38.317 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1347 | n_water=906 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1188 r_free=0.1346 | n_water=905 | time (s): 115.210 (total time: 118.130) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=895 | time (s): 5.460 (total time: 123.590) Compute maps r_work=0.1188 r_free=0.1345 | n_water=895 | time (s): 2.320 (total time: 125.910) Filter (map) r_work=0.1208 r_free=0.1341 | n_water=789 | time (s): 4.140 (total time: 130.050) Find peaks r_work=0.1208 r_free=0.1341 | n_water=789 | time (s): 0.590 (total time: 130.640) Add new water r_work=0.1216 r_free=0.1351 | n_water=987 | time (s): 4.570 (total time: 135.210) Refine new water occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1337 occ: r_work=0.1184 r_free=0.1336 adp: r_work=0.1183 r_free=0.1336 occ: r_work=0.1182 r_free=0.1335 adp: r_work=0.1182 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1335 r_work=0.1182 r_free=0.1335 | n_water=987 | time (s): 311.550 (total time: 446.760) Filter (q & B) r_work=0.1185 r_free=0.1340 | n_water=919 | time (s): 5.150 (total time: 451.910) Filter (dist only) r_work=0.1186 r_free=0.1340 | n_water=917 | time (s): 117.920 (total time: 569.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560126 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.262364 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 0.1189 0.1346 0.0157 0.038 1.1 7.0 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.46 1.57 1.694 13.919 14.262 3.755 11.90 13.49 1.59 1.719 13.906 14.262 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 64.10 14.88 0.88 552 3269 Protein: 5.54 28.37 10.38 0.88 0 2902 Water: 5.98 64.10 29.14 N/A 552 365 Other: 13.84 22.34 18.09 N/A 0 2 Chain A: 5.60 51.38 12.21 N/A 0 1623 Chain B: 5.54 64.10 12.06 N/A 0 1646 Chain S: 5.98 60.96 31.18 N/A 552 0 Histogram: Values Number of atoms 5.54 - 11.39 2075 11.39 - 17.25 808 17.25 - 23.10 263 23.10 - 28.96 217 28.96 - 34.82 193 34.82 - 40.67 126 40.67 - 46.53 90 46.53 - 52.38 38 52.38 - 58.24 7 58.24 - 64.10 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1349 r_work=0.1190 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1349 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1349 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753157 | | target function (ml) not normalized (work): 702928.740656 | | target function (ml) not normalized (free): 14727.094759 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1349 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1393 0.1392 0.1478 n_refl.: 191131 remove outliers: r(all,work,free)=0.1393 0.1392 0.1478 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1393 0.1391 0.1478 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1347 n_refl.: 191131 remove outliers: r(all,work,free)=0.1190 0.1187 0.1347 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3780 352.547 315.068 0.364 0.977 0.181 13.296-10.522 98.02 98 1 0.2463 479.004 460.582 0.680 0.978 0.135 10.503-8.327 98.35 176 3 0.2152 502.882 496.549 0.869 0.979 0.113 8.318-6.595 100.00 360 8 0.2107 375.611 370.611 0.887 0.978 0.090 6.588-5.215 100.00 711 7 0.1865 345.148 336.184 0.886 0.979 0.080 5.214-4.128 98.38 1367 28 0.1220 504.847 499.376 0.978 0.980 0.080 4.126-3.266 94.74 2603 46 0.1136 460.196 453.066 1.036 0.981 0.000 3.266-2.585 99.86 5447 97 0.1127 310.437 306.798 1.021 0.982 0.000 2.585-2.046 97.45 10613 204 0.0962 234.207 231.519 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.615 137.240 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.622 73.959 1.041 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.314 1.013 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0097 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1347 | n_water=917 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1187 r_free=0.1347 | n_water=916 | time (s): 129.990 (total time: 132.950) Filter (q & B) r_work=0.1188 r_free=0.1347 | n_water=908 | time (s): 4.300 (total time: 137.250) Compute maps r_work=0.1188 r_free=0.1347 | n_water=908 | time (s): 2.140 (total time: 139.390) Filter (map) r_work=0.1210 r_free=0.1344 | n_water=794 | time (s): 4.560 (total time: 143.950) Find peaks r_work=0.1210 r_free=0.1344 | n_water=794 | time (s): 0.920 (total time: 144.870) Add new water r_work=0.1218 r_free=0.1354 | n_water=981 | time (s): 4.320 (total time: 149.190) Refine new water occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1187 r_free=0.1332 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1331 occ: r_work=0.1183 r_free=0.1333 adp: r_work=0.1183 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1332 r_work=0.1183 r_free=0.1332 | n_water=981 | time (s): 230.350 (total time: 379.540) Filter (q & B) r_work=0.1186 r_free=0.1341 | n_water=922 | time (s): 4.550 (total time: 384.090) Filter (dist only) r_work=0.1186 r_free=0.1341 | n_water=920 | time (s): 122.200 (total time: 506.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.144052 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1349 0.0158 0.039 1.1 7.0 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.49 1.58 1.689 13.893 14.144 3.755 11.92 13.52 1.60 1.700 13.884 14.144 3.754 Individual atomic B min max mean iso aniso Overall: 5.59 63.32 14.85 0.87 555 3269 Protein: 5.59 28.16 10.38 0.87 0 2902 Water: 5.96 63.32 28.94 N/A 555 365 Other: 13.84 22.31 18.08 N/A 0 2 Chain A: 5.67 51.11 12.18 N/A 0 1623 Chain B: 5.59 63.32 12.04 N/A 0 1646 Chain S: 5.96 61.07 31.01 N/A 555 0 Histogram: Values Number of atoms 5.59 - 11.36 2067 11.36 - 17.13 816 17.13 - 22.91 265 22.91 - 28.68 214 28.68 - 34.45 201 34.45 - 40.22 117 40.22 - 46.00 91 46.00 - 51.77 39 51.77 - 57.54 9 57.54 - 63.32 5 =========================== Idealize ADP of riding H ========================== r_work=0.1192 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) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1351 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753449 | | target function (ml) not normalized (work): 702983.424961 | | target function (ml) not normalized (free): 14731.145710 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1486 n_refl.: 191131 remove outliers: r(all,work,free)=0.1404 0.1403 0.1486 n_refl.: 191131 overall B=-0.07 to atoms: r(all,work,free)=0.1393 0.1392 0.1478 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1343 n_refl.: 191131 remove outliers: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3917 352.547 316.854 0.301 0.995 0.080 13.296-10.522 97.03 97 1 0.2397 481.278 456.961 0.634 0.996 0.087 10.503-8.327 98.35 176 3 0.2184 502.882 496.229 0.833 0.996 0.090 8.318-6.595 100.00 360 8 0.2099 375.611 371.085 0.849 0.996 0.080 6.588-5.215 100.00 711 7 0.1895 345.148 335.822 0.849 0.997 0.080 5.214-4.128 98.38 1367 28 0.1231 504.847 499.385 0.937 0.998 0.070 4.126-3.266 94.74 2603 46 0.1147 460.196 452.958 0.994 0.999 0.000 3.266-2.585 99.86 5447 97 0.1132 310.437 306.751 0.979 1.000 0.000 2.585-2.046 97.45 10613 204 0.0963 234.207 231.516 0.987 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.615 137.267 1.002 1.006 0.000 1.619-1.281 98.00 42464 925 0.0943 74.622 73.971 0.993 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.315 0.962 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0146 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1343 After: r_work=0.1190 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1344 | n_water=920 | time (s): 3.080 (total time: 3.080) Filter (dist) r_work=0.1191 r_free=0.1343 | n_water=918 | time (s): 128.380 (total time: 131.460) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=901 | time (s): 4.670 (total time: 136.130) Compute maps r_work=0.1192 r_free=0.1344 | n_water=901 | time (s): 2.210 (total time: 138.340) Filter (map) r_work=0.1214 r_free=0.1347 | n_water=790 | time (s): 4.540 (total time: 142.880) Find peaks r_work=0.1214 r_free=0.1347 | n_water=790 | time (s): 0.890 (total time: 143.770) Add new water r_work=0.1221 r_free=0.1354 | n_water=986 | time (s): 5.080 (total time: 148.850) Refine new water occ: r_work=0.1190 r_free=0.1328 adp: r_work=0.1190 r_free=0.1328 occ: r_work=0.1188 r_free=0.1327 adp: r_work=0.1188 r_free=0.1327 occ: r_work=0.1187 r_free=0.1327 adp: r_work=0.1186 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1327 r_work=0.1186 r_free=0.1327 | n_water=986 | time (s): 240.450 (total time: 389.300) Filter (q & B) r_work=0.1189 r_free=0.1335 | n_water=916 | time (s): 4.390 (total time: 393.690) Filter (dist only) r_work=0.1190 r_free=0.1335 | n_water=914 | time (s): 119.320 (total time: 513.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525993 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.922475 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1340 0.0149 0.039 1.1 8.0 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.40 1.49 1.683 13.793 13.922 3.755 11.92 13.42 1.50 1.676 13.794 13.922 3.754 Individual atomic B min max mean iso aniso Overall: 5.53 63.00 14.74 0.86 549 3269 Protein: 5.53 28.06 10.34 0.86 0 2902 Water: 6.00 63.00 28.71 N/A 549 365 Other: 13.83 22.25 18.04 N/A 0 2 Chain A: 5.62 50.95 12.11 N/A 0 1623 Chain B: 5.53 63.00 11.98 N/A 0 1646 Chain S: 6.00 61.01 30.81 N/A 549 0 Histogram: Values Number of atoms 5.53 - 11.27 2056 11.27 - 17.02 827 17.02 - 22.77 268 22.77 - 28.52 218 28.52 - 34.26 187 34.26 - 40.01 114 40.01 - 45.76 94 45.76 - 51.50 39 51.50 - 57.25 11 57.25 - 63.00 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1342 r_work=0.1192 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1342 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1341 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753933 | | target function (ml) not normalized (work): 703070.425050 | | target function (ml) not normalized (free): 14726.575502 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1341 0.1350 5.6777 5.7343| | 2: 2.94 - 2.33 1.00 7339 128 0.1080 0.1403 5.0743 5.2022| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1179 4.6623 4.7454| | 4: 2.04 - 1.85 1.00 7170 155 0.0904 0.1052 4.3957 4.5622| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.1006 4.1503 4.2552| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1085 3.9473 4.0799| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0971 3.8014 3.9449| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1302 3.6986 3.8972| | 9: 1.47 - 1.41 0.98 6938 155 0.0924 0.1106 3.6193 3.7421| | 10: 1.41 - 1.36 0.99 7022 150 0.0978 0.1193 3.5565 3.6774| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1150 3.4877 3.5986| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1134 3.4623 3.5818| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1230 3.437 3.5565| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1585 3.4313 3.681| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1237 3.4466 3.4889| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1539 3.4639 3.6525| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1230 3.4328 3.439| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1706 3.4374 3.5331| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1754 3.419 3.5973| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1577 3.4097 3.4303| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2142 3.4184 3.5057| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1944 3.4128 3.4112| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2021 3.4333 3.4848| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2264 3.4357 3.5125| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2510 3.4495 3.5229| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2862 3.4162 3.4233| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2807 3.4686 3.396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7398 127 0.93 11.11 1.00 0.98 10546.78| | 2: 2.94 - 2.33 7339 128 0.93 12.53 0.99 0.98 4944.59| | 3: 2.33 - 2.04 6939 150 0.96 7.73 1.01 0.98 1733.72| | 4: 2.04 - 1.85 7170 155 0.96 7.67 1.00 0.98 1009.59| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.98 637.86| | 6: 1.72 - 1.62 7102 142 0.96 8.08 1.00 0.99 447.60| | 7: 1.62 - 1.54 7104 148 0.96 8.23 1.01 1.00 340.85| | 8: 1.54 - 1.47 6798 152 0.96 8.26 1.01 1.00 279.27| | 9: 1.47 - 1.41 6938 155 0.96 8.44 1.00 1.00 229.79| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 0.99 202.45| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.98 176.02| | 12: 1.32 - 1.28 6975 149 0.96 9.02 0.98 0.97 161.89| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.99 157.95| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.99 161.98| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 1.00 165.24| | 16: 1.19 - 1.17 6604 132 0.95 11.37 1.01 0.98 159.06| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.99 152.98| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.97 147.05| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.97 150.81| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.96 149.91| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.96 152.96| | 22: 1.07 - 1.05 6836 135 0.89 18.25 1.00 0.95 154.46| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.94 164.57| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.95 178.92| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.92 182.02| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.91 176.71| | 27: 0.99 - 0.98 6647 131 0.82 26.36 0.99 0.90 161.72| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.05 max = 10546.78 mean = 894.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.26| |phase err.(test): min = 0.00 max = 89.79 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1191 0.1341 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1482 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1400 0.1482 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1394 0.1478 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1339 n_refl.: 191130 remove outliers: r(all,work,free)=0.1193 0.1190 0.1339 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3891 352.547 316.447 0.321 0.915 0.070 13.296-10.522 97.03 97 1 0.2411 481.278 460.598 0.695 0.916 0.090 10.503-8.327 98.35 176 3 0.2185 502.882 496.279 0.905 0.916 0.093 8.318-6.595 100.00 360 8 0.2104 375.611 370.781 0.927 0.916 0.088 6.588-5.215 100.00 711 7 0.1890 345.148 336.108 0.925 0.917 0.083 5.214-4.128 98.38 1367 28 0.1228 504.847 499.456 1.018 0.918 0.052 4.126-3.266 94.74 2603 46 0.1147 460.196 453.042 1.082 0.919 0.000 3.266-2.585 99.86 5447 97 0.1124 310.437 306.941 1.066 0.920 0.000 2.585-2.046 97.45 10613 204 0.0968 234.207 231.528 1.073 0.922 0.000 2.046-1.619 99.39 21536 464 0.0911 138.615 137.260 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0946 74.622 73.967 1.080 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.304 1.046 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0081 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2031 0.1953 0.083 5.170 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1879 0.083 5.170 5.2 78.1 14.6 805 0.000 1_settarget: 0.1794 0.1879 0.083 5.170 5.2 78.1 14.6 805 0.000 1_nqh: 0.1800 0.1880 0.083 5.170 5.2 78.1 14.6 805 0.002 1_weight: 0.1800 0.1880 0.083 5.170 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1272 0.1499 0.039 1.174 5.2 78.1 14.6 805 0.156 1_adp: 0.1299 0.1568 0.039 1.174 5.3 73.1 15.1 805 0.156 1_regHadp: 0.1299 0.1562 0.039 1.174 5.3 73.1 15.1 805 0.156 1_occ: 0.1283 0.1550 0.039 1.174 5.3 73.1 15.1 805 0.156 2_bss: 0.1278 0.1543 0.039 1.174 5.4 73.2 15.3 805 0.156 2_settarget: 0.1278 0.1543 0.039 1.174 5.4 73.2 15.3 805 0.156 2_updatecdl: 0.1278 0.1543 0.039 1.182 5.4 73.2 15.3 805 0.156 2_nqh: 0.1278 0.1543 0.039 1.182 5.4 73.2 15.3 805 0.156 2_sol: 0.1274 0.1500 0.039 1.182 5.4 73.2 16.4 884 n/a 2_weight: 0.1274 0.1500 0.039 1.182 5.4 73.2 16.4 884 n/a 2_xyzrec: 0.1257 0.1521 0.041 1.129 5.4 73.2 16.4 884 n/a 2_adp: 0.1236 0.1511 0.041 1.129 5.4 68.3 16.5 884 n/a 2_regHadp: 0.1236 0.1512 0.041 1.129 5.4 68.3 16.5 884 n/a 2_occ: 0.1229 0.1502 0.041 1.129 5.4 68.3 16.5 884 n/a 3_bss: 0.1236 0.1510 0.041 1.129 5.4 68.2 16.4 884 n/a 3_settarget: 0.1236 0.1510 0.041 1.129 5.4 68.2 16.4 884 n/a 3_updatecdl: 0.1236 0.1510 0.041 1.131 5.4 68.2 16.4 884 n/a 3_nqh: 0.1236 0.1510 0.041 1.131 5.4 68.2 16.4 884 n/a 3_sol: 0.1252 0.1512 0.041 1.131 5.4 68.2 15.6 874 n/a 3_weight: 0.1252 0.1512 0.041 1.131 5.4 68.2 15.6 874 n/a 3_xyzrec: 0.1241 0.1431 0.035 1.098 5.4 68.2 15.6 874 n/a 3_adp: 0.1232 0.1389 0.035 1.098 5.5 67.9 15.4 874 n/a 3_regHadp: 0.1232 0.1389 0.035 1.098 5.5 67.9 15.4 874 n/a 3_occ: 0.1226 0.1384 0.035 1.098 5.5 67.9 15.4 874 n/a 4_bss: 0.1222 0.1380 0.035 1.098 5.5 67.9 15.4 874 n/a 4_settarget: 0.1222 0.1380 0.035 1.098 5.5 67.9 15.4 874 n/a 4_updatecdl: 0.1222 0.1380 0.035 1.103 5.5 67.9 15.4 874 n/a 4_nqh: 0.1222 0.1380 0.035 1.103 5.5 67.9 15.4 874 n/a 4_sol: 0.1206 0.1364 0.035 1.103 5.5 67.9 15.1 863 n/a 4_weight: 0.1206 0.1364 0.035 1.103 5.5 67.9 15.1 863 n/a 4_xyzrec: 0.1205 0.1361 0.035 1.121 5.5 67.9 15.1 863 n/a 4_adp: 0.1200 0.1358 0.035 1.121 5.5 67.5 15.0 863 n/a 4_regHadp: 0.1200 0.1359 0.035 1.121 5.5 67.5 15.0 863 n/a 4_occ: 0.1198 0.1356 0.035 1.121 5.5 67.5 15.0 863 n/a 5_bss: 0.1195 0.1351 0.035 1.121 5.5 67.4 15.0 863 n/a 5_settarget: 0.1195 0.1351 0.035 1.121 5.5 67.4 15.0 863 n/a 5_updatecdl: 0.1195 0.1351 0.035 1.121 5.5 67.4 15.0 863 n/a 5_nqh: 0.1195 0.1351 0.035 1.121 5.5 67.4 15.0 863 n/a 5_sol: 0.1191 0.1341 0.035 1.121 5.5 67.4 15.2 888 n/a 5_weight: 0.1191 0.1341 0.035 1.121 5.5 67.4 15.2 888 n/a 5_xyzrec: 0.1192 0.1347 0.035 1.139 5.5 67.4 15.2 888 n/a 5_adp: 0.1197 0.1353 0.035 1.139 5.6 67.1 15.1 888 n/a 5_regHadp: 0.1197 0.1353 0.035 1.139 5.6 67.1 15.1 888 n/a 5_occ: 0.1195 0.1350 0.035 1.139 5.6 67.1 15.1 888 n/a 6_bss: 0.1194 0.1349 0.035 1.139 5.3 66.8 14.9 888 n/a 6_settarget: 0.1194 0.1349 0.035 1.139 5.3 66.8 14.9 888 n/a 6_updatecdl: 0.1194 0.1349 0.035 1.139 5.3 66.8 14.9 888 n/a 6_nqh: 0.1194 0.1349 0.035 1.139 5.3 66.8 14.9 888 n/a 6_sol: 0.1192 0.1348 0.035 1.139 5.3 66.8 14.9 902 n/a 6_weight: 0.1192 0.1348 0.035 1.139 5.3 66.8 14.9 902 n/a 6_xyzrec: 0.1197 0.1357 0.037 1.126 5.3 66.8 14.9 902 n/a 6_adp: 0.1199 0.1362 0.037 1.126 5.4 65.9 14.8 902 n/a 6_regHadp: 0.1199 0.1362 0.037 1.126 5.4 65.9 14.8 902 n/a 6_occ: 0.1197 0.1363 0.037 1.126 5.4 65.9 14.8 902 n/a 7_bss: 0.1188 0.1355 0.037 1.126 5.5 65.9 14.9 902 n/a 7_settarget: 0.1188 0.1355 0.037 1.126 5.5 65.9 14.9 902 n/a 7_updatecdl: 0.1188 0.1355 0.037 1.126 5.5 65.9 14.9 902 n/a 7_nqh: 0.1188 0.1355 0.037 1.126 5.5 65.9 14.9 902 n/a 7_sol: 0.1187 0.1346 0.037 1.126 5.5 65.9 14.9 906 n/a 7_weight: 0.1187 0.1346 0.037 1.126 5.5 65.9 14.9 906 n/a 7_xyzrec: 0.1189 0.1347 0.037 1.129 5.5 65.9 14.9 906 n/a 7_adp: 0.1191 0.1351 0.037 1.129 5.5 65.0 14.9 906 n/a 7_regHadp: 0.1191 0.1351 0.037 1.129 5.5 65.0 14.9 906 n/a 7_occ: 0.1189 0.1350 0.037 1.129 5.5 65.0 14.9 906 n/a 8_bss: 0.1187 0.1347 0.037 1.129 5.5 65.0 14.9 906 n/a 8_settarget: 0.1187 0.1347 0.037 1.129 5.5 65.0 14.9 906 n/a 8_updatecdl: 0.1187 0.1347 0.037 1.129 5.5 65.0 14.9 906 n/a 8_nqh: 0.1187 0.1347 0.037 1.129 5.5 65.0 14.9 906 n/a 8_sol: 0.1186 0.1340 0.037 1.129 5.5 65.0 14.9 917 n/a 8_weight: 0.1186 0.1340 0.037 1.129 5.5 65.0 14.9 917 n/a 8_xyzrec: 0.1189 0.1346 0.038 1.116 5.5 65.0 14.9 917 n/a 8_adp: 0.1190 0.1349 0.038 1.116 5.5 64.1 14.9 917 n/a 8_regHadp: 0.1190 0.1349 0.038 1.116 5.5 64.1 14.9 917 n/a 8_occ: 0.1188 0.1349 0.038 1.116 5.5 64.1 14.9 917 n/a 9_bss: 0.1187 0.1347 0.038 1.116 5.5 64.1 14.9 917 n/a 9_settarget: 0.1187 0.1347 0.038 1.116 5.5 64.1 14.9 917 n/a 9_updatecdl: 0.1187 0.1347 0.038 1.117 5.5 64.1 14.9 917 n/a 9_nqh: 0.1187 0.1347 0.038 1.117 5.5 64.1 14.9 917 n/a 9_sol: 0.1186 0.1341 0.038 1.117 5.5 64.1 14.9 920 n/a 9_weight: 0.1186 0.1341 0.038 1.117 5.5 64.1 14.9 920 n/a 9_xyzrec: 0.1191 0.1349 0.039 1.113 5.5 64.1 14.9 920 n/a 9_adp: 0.1192 0.1352 0.039 1.113 5.6 63.3 14.9 920 n/a 9_regHadp: 0.1192 0.1352 0.039 1.113 5.6 63.3 14.9 920 n/a 9_occ: 0.1190 0.1351 0.039 1.113 5.6 63.3 14.9 920 n/a 10_bss: 0.1190 0.1343 0.039 1.113 5.5 63.3 14.8 920 n/a 10_settarget: 0.1190 0.1343 0.039 1.113 5.5 63.3 14.8 920 n/a 10_updatecdl: 0.1190 0.1343 0.039 1.113 5.5 63.3 14.8 920 n/a 10_setrh: 0.1190 0.1344 0.039 1.113 5.5 63.3 14.8 920 n/a 10_nqh: 0.1190 0.1344 0.039 1.113 5.5 63.3 14.8 920 n/a 10_sol: 0.1190 0.1335 0.039 1.113 5.5 63.3 14.7 914 n/a 10_weight: 0.1190 0.1335 0.039 1.113 5.5 63.3 14.7 914 n/a 10_xyzrec: 0.1191 0.1340 0.039 1.148 5.5 63.3 14.7 914 n/a 10_adp: 0.1192 0.1342 0.039 1.148 5.5 63.0 14.7 914 n/a 10_regHadp: 0.1192 0.1342 0.039 1.148 5.5 63.0 14.7 914 n/a 10_occ: 0.1191 0.1341 0.039 1.148 5.5 63.0 14.7 914 n/a end: 0.1190 0.1339 0.039 1.148 5.5 63.0 14.7 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2951004_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2951004_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.6000 Refinement macro-cycles (run) : 12289.2400 Write final files (write_after_run_outputs) : 158.9900 Total : 12455.8300 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:50 PST -0800 (1736736290.40 s) Start R-work = 0.1794, R-free = 0.1879 Final R-work = 0.1190, R-free = 0.1339 =============================================================================== Job complete usr+sys time: 12729.57 seconds wall clock time: 213 minutes 13.12 seconds (12793.12 seconds total)