Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9503307.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 { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9503307.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9503307.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.31, per 1000 atoms: 0.35 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: 2.824 distance_ideal: 2.720 ideal - model: -0.104 slack: 0.000 delta_slack: -0.104 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.780 distance_ideal: 2.710 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 163.0 milliseconds Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 904 1.03 - 1.25: 2371 1.25 - 1.48: 1460 1.48 - 1.70: 1176 1.70 - 1.92: 23 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ILE A 134 " pdb=" C ILE A 134 " ideal model delta sigma weight residual 1.525 1.341 0.184 8.10e-03 1.52e+04 5.17e+02 bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.303 0.152 7.00e-03 2.04e+04 4.74e+02 bond pdb=" N ILE B 22 " pdb=" H ILE B 22 " ideal model delta sigma weight residual 0.860 1.271 -0.411 2.00e-02 2.50e+03 4.23e+02 bond pdb=" CE1 HIS A 179 " pdb=" NE2 HIS A 179 " ideal model delta sigma weight residual 1.321 1.518 -0.197 1.00e-02 1.00e+04 3.87e+02 bond pdb=" C PRO B 58 " pdb=" O PRO B 58 " ideal model delta sigma weight residual 1.233 1.451 -0.217 1.12e-02 7.97e+03 3.77e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 6014 4.48 - 8.95: 3553 8.95 - 13.43: 1082 13.43 - 17.90: 152 17.90 - 22.38: 9 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH2 ARG B 143 " ideal model delta sigma weight residual 119.20 102.06 17.14 9.00e-01 1.23e+00 3.63e+02 angle pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " pdb=" NH2 ARG A 49 " ideal model delta sigma weight residual 119.20 105.42 13.78 9.00e-01 1.23e+00 2.35e+02 angle pdb=" CA VAL A 150 " pdb=" C VAL A 150 " pdb=" N LYS A 151 " ideal model delta sigma weight residual 117.97 100.92 17.05 1.14e+00 7.69e-01 2.24e+02 angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 110.53 97.19 13.34 9.40e-01 1.13e+00 2.01e+02 angle pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " pdb=" NH1 ARG A 149 " ideal model delta sigma weight residual 121.50 135.54 -14.04 1.00e+00 1.00e+00 1.97e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 1805 15.68 - 31.36: 164 31.36 - 47.04: 46 47.04 - 62.72: 30 62.72 - 78.40: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -148.97 -31.03 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ILE B 105 " pdb=" C ILE B 105 " pdb=" N CYS B 106 " pdb=" CA CYS B 106 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLY A 75 " pdb=" C GLY A 75 " pdb=" N ILE A 76 " pdb=" CA ILE A 76 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.225: 220 0.225 - 0.446: 167 0.446 - 0.667: 70 0.667 - 0.888: 30 0.888 - 1.110: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA GLU A 180 " pdb=" N GLU A 180 " pdb=" C GLU A 180 " pdb=" CB GLU A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.62 -1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CG LEU A 87 " pdb=" CB LEU A 87 " pdb=" CD1 LEU A 87 " pdb=" CD2 LEU A 87 " both_signs ideal model delta sigma weight residual False -2.59 -3.63 1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA GLU A 17 " pdb=" N GLU A 17 " pdb=" C GLU A 17 " pdb=" CB GLU A 17 " both_signs ideal model delta sigma weight residual False 2.51 3.52 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.171 2.00e-02 2.50e+03 8.67e-02 2.26e+02 pdb=" CG PHE B 164 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.134 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.026 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " 0.060 2.00e-02 2.50e+03 7.81e-02 1.83e+02 pdb=" CG PHE B 82 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " 0.033 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " 0.064 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " 0.141 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.004 2.00e-02 2.50e+03 7.37e-02 1.63e+02 pdb=" CG PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.111 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.142 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.129 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.041 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.65: 34 1.65 - 2.39: 2842 2.39 - 3.13: 22524 3.13 - 3.86: 32754 3.86 - 4.60: 52106 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110260 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.918 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.924 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.939 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.030 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.151 2.620 ... (remaining 110255 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_9503307_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= 0.2037 r_free= 0.2017 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.304253 | | target function (ml) not normalized (work): 806242.509204 | | target function (ml) not normalized (free): 16617.235435 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2146 0.1953 6.6963 6.2934| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1758 5.5357 5.6136| | 3: 2.33 - 2.04 0.96 6939 150 0.1604 0.1554 5.1363 5.1502| | 4: 2.04 - 1.85 1.00 7170 155 0.1775 0.1663 4.9717 5.0757| | 5: 1.85 - 1.72 0.99 7113 159 0.1915 0.1720 4.7867 4.8135| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.1993 4.666 4.7177| | 7: 1.62 - 1.54 0.99 7104 148 0.2009 0.1761 4.5521 4.5758| | 8: 1.54 - 1.47 0.96 6798 152 0.2057 0.2372 4.472 4.5755| | 9: 1.47 - 1.41 0.98 6938 155 0.2103 0.2029 4.4031 4.4006| | 10: 1.41 - 1.36 0.99 7022 150 0.2117 0.2158 4.3081 4.3444| | 11: 1.36 - 1.32 0.99 6997 151 0.2154 0.2240 4.2599 4.2607| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.2049 4.1852 4.2732| | 13: 1.28 - 1.25 0.98 6907 166 0.2041 0.2148 4.1305 4.1785| | 14: 1.25 - 1.22 0.98 7015 113 0.2065 0.2497 4.074 4.355| | 15: 1.22 - 1.19 0.98 6957 137 0.2130 0.2011 4.0733 4.0542| | 16: 1.19 - 1.17 0.93 6604 132 0.2097 0.2324 4.0103 4.1546| | 17: 1.17 - 1.14 0.98 6941 135 0.2172 0.2096 3.9671 4.0543| | 18: 1.14 - 1.12 0.98 6875 142 0.2245 0.2472 3.935 3.9583| | 19: 1.12 - 1.10 0.97 6949 106 0.2275 0.2549 3.8853 4.002| | 20: 1.10 - 1.08 0.97 6884 147 0.2343 0.2182 3.8292 3.8388| | 21: 1.08 - 1.07 0.97 6852 152 0.2450 0.2879 3.7984 3.8608| | 22: 1.07 - 1.05 0.97 6838 135 0.2554 0.2238 3.7467 3.6411| | 23: 1.05 - 1.03 0.97 6829 159 0.2686 0.2661 3.7201 3.824| | 24: 1.03 - 1.02 0.96 6785 133 0.2869 0.2863 3.7002 3.8408| | 25: 1.02 - 1.01 0.93 6552 130 0.3073 0.3107 3.6745 3.7515| | 26: 1.01 - 0.99 0.96 6767 158 0.3223 0.3362 3.6335 3.6514| | 27: 0.99 - 0.98 0.94 6648 131 0.3428 0.3141 3.6506 3.5806| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.22 0.91 0.97 34524.88| | 2: 2.94 - 2.33 7339 128 0.86 21.10 1.08 1.02 14896.03| | 3: 2.33 - 2.04 6939 150 0.93 12.78 1.11 1.06 4277.76| | 4: 2.04 - 1.85 7170 155 0.92 13.69 1.12 1.07 2850.49| | 5: 1.85 - 1.72 7113 159 0.91 15.83 1.11 1.07 2102.83| | 6: 1.72 - 1.62 7102 142 0.90 17.03 1.11 1.06 1683.71| | 7: 1.62 - 1.54 7104 148 0.89 17.73 1.11 1.06 1342.34| | 8: 1.54 - 1.47 6798 152 0.89 18.20 1.10 1.05 1128.71| | 9: 1.47 - 1.41 6938 155 0.88 18.55 1.10 1.05 926.01| | 10: 1.41 - 1.36 7022 150 0.87 19.97 1.09 1.04 842.50| | 11: 1.36 - 1.32 6997 151 0.87 20.67 1.07 1.03 758.85| | 12: 1.32 - 1.28 6976 149 0.86 20.85 1.08 1.02 701.53| | 13: 1.28 - 1.25 6907 166 0.86 21.12 1.07 1.03 670.38| | 14: 1.25 - 1.22 7015 113 0.85 22.24 1.08 1.02 637.90| | 15: 1.22 - 1.19 6957 137 0.85 22.57 1.07 1.04 621.79| | 16: 1.19 - 1.17 6604 132 0.86 22.04 1.07 1.03 556.05| | 17: 1.17 - 1.14 6941 135 0.85 22.38 1.08 1.02 495.89| | 18: 1.14 - 1.12 6875 142 0.85 22.09 1.08 1.00 433.00| | 19: 1.12 - 1.10 6949 106 0.85 22.70 1.07 1.00 403.82| | 20: 1.10 - 1.08 6884 147 0.85 23.00 1.06 0.98 357.64| | 21: 1.08 - 1.07 6852 152 0.84 23.69 1.06 0.97 326.20| | 22: 1.07 - 1.05 6838 135 0.83 24.47 1.06 0.98 302.21| | 23: 1.05 - 1.03 6829 159 0.81 27.01 1.05 0.98 319.85| | 24: 1.03 - 1.02 6785 133 0.78 29.81 1.05 0.97 336.63| | 25: 1.02 - 1.01 6552 130 0.75 31.82 1.03 0.93 330.05| | 26: 1.01 - 0.99 6767 158 0.74 32.99 1.02 0.90 303.82| | 27: 0.99 - 0.98 6648 131 0.75 32.21 1.04 0.89 269.40| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 269.40 max = 34524.88 mean = 2805.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.02| |phase err.(test): min = 0.00 max = 89.97 mean = 21.95| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.243 2950 Z= 5.405 Angle : 5.161 17.597 4018 Z= 3.674 Chirality : 0.364 1.110 492 Planarity : 0.030 0.107 512 Dihedral : 12.725 78.398 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 1.04 % Allowed : 2.59 % Favored : 96.37 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.39), residues: 386 helix: -2.66 (0.28), residues: 144 sheet: -0.37 (0.59), residues: 66 loop : 0.15 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.022 ARG A 27 TYR 0.102 0.035 TYR B 194 PHE 0.138 0.044 PHE B 164 TRP 0.110 0.028 TRP A 146 HIS 0.074 0.035 HIS B 96 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= 0.2037 r_free= 0.2017 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.304253 | | target function (ml) not normalized (work): 806242.509204 | | target function (ml) not normalized (free): 16617.235435 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2037 0.2017 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2037 0.2017 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2038 0.2017 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2037 0.2038 0.2018 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1807 0.1938 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1804 0.1936 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 0.4088 402.814 292.270 0.436 0.912 0.301 13.296-10.522 99.01 99 1 0.2471 528.187 519.359 0.787 0.913 0.251 10.503-8.327 99.45 178 3 0.2514 565.118 554.659 0.974 0.913 0.227 8.318-6.595 100.00 360 8 0.2474 414.736 403.555 0.973 0.913 0.182 6.588-5.215 100.00 711 7 0.2292 381.101 364.809 0.957 0.913 0.150 5.214-4.128 98.38 1367 28 0.1499 557.435 550.004 1.076 0.913 0.090 4.126-3.266 94.74 2603 46 0.1325 508.132 499.591 1.150 0.914 0.028 3.266-2.585 99.86 5447 97 0.1441 342.774 337.563 1.119 0.913 0.010 2.585-2.046 97.45 10613 204 0.1400 258.603 254.337 1.125 0.912 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.924 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1940 82.395 80.223 1.128 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2326 44.202 41.647 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0044 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1936 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1936 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.502026 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.111156 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 0.1268 0.1477 0.0209 0.033 1.2 11.9 0.0 0.3 0 11.251 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 14.77 2.09 1.118 13.113 569.111 0.019 12.93 15.39 2.46 1.210 13.287 569.111 0.018 Individual atomic B min max mean iso aniso Overall: 5.19 73.05 14.92 1.40 435 3274 Protein: 5.19 40.72 10.96 1.40 0 2902 Water: 6.29 73.05 29.18 N/A 435 370 Other: 15.78 29.26 22.52 N/A 0 2 Chain A: 5.31 60.10 12.99 N/A 0 1626 Chain B: 5.19 73.05 12.71 N/A 0 1648 Chain S: 11.53 62.20 30.46 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2178 11.97 - 18.76 635 18.76 - 25.55 318 25.55 - 32.33 251 32.33 - 39.12 165 39.12 - 45.90 101 45.90 - 52.69 39 52.69 - 59.47 17 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1293 r_free=0.1540 r_work=0.1292 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1292 r_free = 0.1535 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1277 r_free = 0.1521 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1277 r_free= 0.1521 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015738 | | target function (ls_wunit_k1) not normalized (work): 2947.591602 | | target function (ls_wunit_k1) not normalized (free): 111.848945 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1282 0.1277 0.1521 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1462 0.1460 0.1592 n_refl.: 191138 remove outliers: r(all,work,free)=0.1462 0.1460 0.1592 n_refl.: 191138 overall B=0.18 to atoms: r(all,work,free)=0.1488 0.1486 0.1604 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1274 0.1270 0.1510 n_refl.: 191138 remove outliers: r(all,work,free)=0.1274 0.1270 0.1510 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 0.3644 402.814 375.148 0.470 0.998 0.287 13.296-10.522 99.01 99 1 0.2102 528.187 518.730 0.710 0.999 0.245 10.503-8.327 99.45 178 3 0.1790 565.118 562.041 0.856 0.999 0.223 8.318-6.595 100.00 360 8 0.1761 414.736 411.994 0.880 0.999 0.160 6.588-5.215 100.00 711 7 0.1587 381.101 372.944 0.856 0.999 0.150 5.214-4.128 98.38 1367 28 0.0933 557.435 553.980 0.944 1.000 0.090 4.126-3.266 94.74 2603 46 0.0859 508.132 504.172 1.009 1.000 0.019 3.266-2.585 99.86 5447 97 0.0930 342.774 340.361 0.990 1.000 0.010 2.585-2.046 97.45 10613 204 0.0942 258.603 256.432 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1068 153.054 151.411 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.418 1.011 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1866 44.202 42.161 0.989 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0409 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1270 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1270 r_free=0.1510 | n_water=805 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1273 r_free=0.1515 | n_water=797 | time (s): 96.560 (total time: 99.020) Filter (q & B) r_work=0.1273 r_free=0.1516 | n_water=793 | time (s): 4.150 (total time: 103.170) Compute maps r_work=0.1273 r_free=0.1516 | n_water=793 | time (s): 1.630 (total time: 104.800) Filter (map) r_work=0.1293 r_free=0.1507 | n_water=667 | time (s): 4.630 (total time: 109.430) Find peaks r_work=0.1293 r_free=0.1507 | n_water=667 | time (s): 0.630 (total time: 110.060) Add new water r_work=0.1318 r_free=0.1536 | n_water=970 | time (s): 5.090 (total time: 115.150) Refine new water occ: r_work=0.1277 r_free=0.1495 adp: r_work=0.1265 r_free=0.1487 occ: r_work=0.1267 r_free=0.1486 adp: r_work=0.1260 r_free=0.1483 occ: r_work=0.1261 r_free=0.1483 adp: r_work=0.1259 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1259 r_free=0.1484 r_work=0.1259 r_free=0.1484 | n_water=970 | time (s): 89.120 (total time: 204.270) Filter (q & B) r_work=0.1262 r_free=0.1487 | n_water=903 | time (s): 5.160 (total time: 209.430) Filter (dist only) r_work=0.1262 r_free=0.1487 | n_water=900 | time (s): 112.220 (total time: 321.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.452086 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.298555 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 0.1247 0.1503 0.0255 0.038 1.1 17.2 0.0 0.3 0 11.726 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.47 15.03 2.55 2.034 15.228 569.299 0.014 12.30 15.03 2.72 2.376 15.270 569.299 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.23 16.42 1.19 531 3273 Protein: 5.40 40.13 10.98 1.19 0 2902 Water: 6.60 68.23 33.94 N/A 531 369 Other: 16.21 33.20 24.71 N/A 0 2 Chain A: 5.61 56.83 13.01 N/A 0 1625 Chain B: 5.40 68.23 12.79 N/A 0 1648 Chain S: 13.03 67.64 38.14 N/A 531 0 Histogram: Values Number of atoms 5.40 - 11.68 2048 11.68 - 17.96 724 17.96 - 24.25 274 24.25 - 30.53 214 30.53 - 36.81 170 36.81 - 43.09 162 43.09 - 49.38 99 49.38 - 55.66 46 55.66 - 61.94 51 61.94 - 68.23 16 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1503 r_work=0.1231 r_free=0.1504 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1504 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1500 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1500 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013310 | | target function (ls_wunit_k1) not normalized (work): 2492.903314 | | target function (ls_wunit_k1) not normalized (free): 100.890728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1500 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1431 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1507 n_refl.: 191138 remove outliers: r(all,work,free)=0.1237 0.1231 0.1507 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 0.3125 402.814 383.150 0.496 0.964 0.271 13.296-10.522 99.01 99 1 0.1878 528.187 520.370 0.758 0.965 0.229 10.503-8.327 99.45 178 3 0.1382 565.118 567.144 0.921 0.964 0.210 8.318-6.595 100.00 360 8 0.1498 414.736 414.002 0.937 0.964 0.160 6.588-5.215 100.00 711 7 0.1347 381.101 376.427 0.910 0.964 0.140 5.214-4.128 98.38 1367 28 0.0827 557.435 556.250 0.995 0.964 0.110 4.126-3.266 94.74 2603 46 0.0754 508.132 505.446 1.058 0.964 0.014 3.266-2.585 99.86 5447 97 0.0854 342.774 341.357 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0893 258.603 256.795 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.629 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.352 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.208 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0470 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1507 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1507 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1507 | n_water=900 | time (s): 3.440 (total time: 3.440) Filter (dist) r_work=0.1233 r_free=0.1509 | n_water=897 | time (s): 122.190 (total time: 125.630) Filter (q & B) r_work=0.1233 r_free=0.1510 | n_water=893 | time (s): 5.690 (total time: 131.320) Compute maps r_work=0.1233 r_free=0.1510 | n_water=893 | time (s): 1.960 (total time: 133.280) Filter (map) r_work=0.1269 r_free=0.1500 | n_water=710 | time (s): 4.710 (total time: 137.990) Find peaks r_work=0.1269 r_free=0.1500 | n_water=710 | time (s): 0.650 (total time: 138.640) Add new water r_work=0.1295 r_free=0.1540 | n_water=1001 | time (s): 4.970 (total time: 143.610) Refine new water occ: r_work=0.1251 r_free=0.1508 adp: r_work=0.1252 r_free=0.1508 occ: r_work=0.1247 r_free=0.1507 adp: r_work=0.1247 r_free=0.1508 occ: r_work=0.1243 r_free=0.1509 adp: r_work=0.1243 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1508 r_work=0.1243 r_free=0.1508 | n_water=1001 | time (s): 292.340 (total time: 435.950) Filter (q & B) r_work=0.1247 r_free=0.1511 | n_water=881 | time (s): 6.110 (total time: 442.060) Filter (dist only) r_work=0.1247 r_free=0.1510 | n_water=880 | time (s): 117.900 (total time: 559.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.677903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.616435 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 0.1239 0.1440 0.0200 0.035 1.1 7.1 0.0 0.0 0 0.839 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.40 2.00 1.928 14.620 15.616 3.942 12.31 13.98 1.67 2.211 14.531 15.616 3.898 Individual atomic B min max mean iso aniso Overall: 5.51 67.86 15.33 1.05 512 3272 Protein: 5.51 36.72 10.75 1.05 0 2902 Water: 6.65 67.86 30.42 N/A 512 368 Other: 14.26 28.74 21.50 N/A 0 2 Chain A: 5.52 56.00 12.78 N/A 0 1625 Chain B: 5.51 67.86 12.52 N/A 0 1647 Chain S: 14.10 61.87 32.45 N/A 512 0 Histogram: Values Number of atoms 5.51 - 11.74 2125 11.74 - 17.98 682 17.98 - 24.21 299 24.21 - 30.45 242 30.45 - 36.68 177 36.68 - 42.92 142 42.92 - 49.15 79 49.15 - 55.39 23 55.39 - 61.62 13 61.62 - 67.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1398 r_work=0.1232 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1399 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1404 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.893062 | | target function (ml) not normalized (work): 729158.828126 | | target function (ml) not normalized (free): 15236.027304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1403 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1505 n_refl.: 191138 remove outliers: r(all,work,free)=0.1438 0.1437 0.1505 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1431 0.1501 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1223 0.1395 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1223 0.1395 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3836 398.008 363.590 0.424 0.948 0.243 13.296-10.522 99.01 99 1 0.2408 528.187 510.335 0.709 0.949 0.219 10.503-8.327 99.45 178 3 0.2028 565.118 561.201 0.886 0.949 0.210 8.318-6.595 100.00 360 8 0.2069 414.736 410.316 0.895 0.948 0.130 6.588-5.215 100.00 711 7 0.1815 381.101 370.477 0.886 0.949 0.130 5.214-4.128 98.38 1367 28 0.1157 557.435 552.438 0.972 0.949 0.100 4.126-3.266 94.74 2603 46 0.1090 508.132 501.077 1.031 0.949 0.005 3.266-2.585 99.86 5447 97 0.1084 342.774 339.231 1.018 0.948 0.000 2.585-2.046 97.45 10613 204 0.0962 258.603 255.785 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.420 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.496 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.323 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0944 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1395 | n_water=880 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1224 r_free=0.1397 | n_water=877 | time (s): 107.640 (total time: 110.210) Filter (q & B) r_work=0.1225 r_free=0.1395 | n_water=864 | time (s): 4.300 (total time: 114.510) Compute maps r_work=0.1225 r_free=0.1395 | n_water=864 | time (s): 1.970 (total time: 116.480) Filter (map) r_work=0.1250 r_free=0.1388 | n_water=718 | time (s): 4.890 (total time: 121.370) Find peaks r_work=0.1250 r_free=0.1388 | n_water=718 | time (s): 0.560 (total time: 121.930) Add new water r_work=0.1267 r_free=0.1407 | n_water=969 | time (s): 4.630 (total time: 126.560) Refine new water occ: r_work=0.1217 r_free=0.1373 adp: r_work=0.1209 r_free=0.1367 occ: r_work=0.1206 r_free=0.1368 adp: r_work=0.1206 r_free=0.1368 occ: r_work=0.1206 r_free=0.1368 adp: r_work=0.1206 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1368 r_work=0.1206 r_free=0.1368 | n_water=969 | time (s): 138.990 (total time: 265.550) Filter (q & B) r_work=0.1212 r_free=0.1374 | n_water=850 | time (s): 5.070 (total time: 270.620) Filter (dist only) r_work=0.1212 r_free=0.1373 | n_water=849 | time (s): 111.810 (total time: 382.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.677887 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.909789 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1373 0.0164 0.035 1.1 5.4 0.0 0.3 0 0.839 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.73 1.64 1.833 14.118 14.910 3.876 12.04 13.70 1.65 1.944 14.075 14.910 3.868 Individual atomic B min max mean iso aniso Overall: 5.51 67.45 14.80 0.99 482 3271 Protein: 5.51 33.62 10.66 0.99 0 2902 Water: 5.92 67.45 28.91 N/A 482 367 Other: 13.99 27.86 20.93 N/A 0 2 Chain A: 5.53 55.07 12.63 N/A 0 1624 Chain B: 5.51 67.45 12.42 N/A 0 1647 Chain S: 5.92 59.40 30.21 N/A 482 0 Histogram: Values Number of atoms 5.51 - 11.71 2125 11.71 - 17.90 711 17.90 - 24.09 351 24.09 - 30.29 211 30.29 - 36.48 137 36.48 - 42.67 124 42.67 - 48.87 62 48.87 - 55.06 20 55.06 - 61.25 11 61.25 - 67.45 1 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1370 r_work=0.1204 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1370 target_work(ml) = 3.869 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1367 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.866432 | | target function (ml) not normalized (work): 724167.252065 | | target function (ml) not normalized (free): 15150.269333 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1431 0.1430 0.1485 n_refl.: 191137 remove outliers: r(all,work,free)=0.1431 0.1430 0.1485 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1424 0.1423 0.1480 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1201 0.1364 n_refl.: 191137 remove outliers: r(all,work,free)=0.1203 0.1200 0.1364 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 92.08 90 3 0.3518 356.057 318.903 0.417 0.947 0.249 13.296-10.522 97.03 97 1 0.2371 478.243 451.971 0.694 0.948 0.199 10.503-8.327 97.80 175 3 0.2165 500.896 497.140 0.878 0.948 0.177 8.318-6.595 100.00 360 8 0.2240 375.624 368.572 0.891 0.948 0.125 6.588-5.215 100.00 711 7 0.1919 345.161 334.680 0.883 0.948 0.104 5.214-4.128 98.38 1367 28 0.1213 504.866 499.848 0.971 0.948 0.061 4.126-3.266 94.74 2603 46 0.1130 460.212 453.559 1.034 0.948 0.017 3.266-2.585 99.86 5447 97 0.1095 310.448 307.263 1.021 0.947 0.003 2.585-2.046 97.45 10613 204 0.0934 234.215 231.808 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0916 138.620 137.334 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0989 74.625 73.917 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1665 40.033 38.366 1.039 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1114 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1364 | n_water=849 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1200 r_free=0.1364 | n_water=849 | time (s): 106.740 (total time: 109.260) Filter (q & B) r_work=0.1200 r_free=0.1364 | n_water=843 | time (s): 4.220 (total time: 113.480) Compute maps r_work=0.1200 r_free=0.1364 | n_water=843 | time (s): 1.680 (total time: 115.160) Filter (map) r_work=0.1223 r_free=0.1369 | n_water=716 | time (s): 4.600 (total time: 119.760) Find peaks r_work=0.1223 r_free=0.1369 | n_water=716 | time (s): 0.710 (total time: 120.470) Add new water r_work=0.1236 r_free=0.1384 | n_water=958 | time (s): 4.860 (total time: 125.330) Refine new water occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1355 occ: r_work=0.1194 r_free=0.1353 adp: r_work=0.1194 r_free=0.1353 occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1351 r_work=0.1192 r_free=0.1351 | n_water=958 | time (s): 161.300 (total time: 286.630) Filter (q & B) r_work=0.1195 r_free=0.1356 | n_water=886 | time (s): 5.330 (total time: 291.960) Filter (dist only) r_work=0.1195 r_free=0.1355 | n_water=885 | time (s): 117.030 (total time: 408.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542012 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.966154 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1360 0.0162 0.036 1.1 7.7 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.60 1.62 1.792 14.119 15.966 3.766 12.01 13.62 1.61 1.900 14.077 15.966 3.760 Individual atomic B min max mean iso aniso Overall: 5.55 66.83 14.89 0.96 519 3270 Protein: 5.55 31.72 10.58 0.96 0 2902 Water: 6.05 66.83 29.04 N/A 519 366 Other: 13.86 26.08 19.97 N/A 0 2 Chain A: 5.56 53.73 12.51 N/A 0 1624 Chain B: 5.55 66.83 12.29 N/A 0 1646 Chain S: 6.05 59.46 30.61 N/A 519 0 Histogram: Values Number of atoms 5.55 - 11.68 2128 11.68 - 17.81 727 17.81 - 23.93 318 23.93 - 30.06 227 30.06 - 36.19 169 36.19 - 42.32 125 42.32 - 48.45 65 48.45 - 54.58 21 54.58 - 60.70 8 60.70 - 66.83 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1362 r_work=0.1201 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1362 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759192 | | target function (ml) not normalized (work): 704055.255311 | | target function (ml) not normalized (free): 14746.372441 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1411 0.1409 0.1494 n_refl.: 191130 remove outliers: r(all,work,free)=0.1411 0.1409 0.1494 n_refl.: 191130 overall B=-0.03 to atoms: r(all,work,free)=0.1403 0.1402 0.1488 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3459 356.830 328.193 0.422 0.951 0.241 13.296-10.522 97.03 97 1 0.2368 478.243 461.045 0.702 0.952 0.189 10.503-8.327 97.80 175 3 0.2147 500.896 495.306 0.866 0.952 0.163 8.318-6.595 100.00 360 8 0.2167 375.624 370.776 0.884 0.952 0.100 6.588-5.215 100.00 711 7 0.1887 345.161 334.663 0.881 0.952 0.084 5.214-4.128 98.38 1367 28 0.1214 504.866 499.352 0.968 0.952 0.070 4.126-3.266 94.74 2603 46 0.1137 460.212 453.378 1.032 0.952 0.021 3.266-2.585 99.86 5447 97 0.1110 310.448 307.181 1.017 0.951 0.010 2.585-2.046 97.45 10613 204 0.0946 234.215 231.713 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0917 138.620 137.285 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.0973 74.625 73.917 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.033 38.371 1.041 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=885 | time (s): 3.310 (total time: 3.310) Filter (dist) r_work=0.1196 r_free=0.1359 | n_water=885 | time (s): 105.870 (total time: 109.180) Filter (q & B) r_work=0.1196 r_free=0.1358 | n_water=876 | time (s): 5.080 (total time: 114.260) Compute maps r_work=0.1196 r_free=0.1358 | n_water=876 | time (s): 2.100 (total time: 116.360) Filter (map) r_work=0.1217 r_free=0.1362 | n_water=756 | time (s): 5.620 (total time: 121.980) Find peaks r_work=0.1217 r_free=0.1362 | n_water=756 | time (s): 0.710 (total time: 122.690) Add new water r_work=0.1229 r_free=0.1379 | n_water=977 | time (s): 3.990 (total time: 126.680) Refine new water occ: r_work=0.1194 r_free=0.1343 adp: r_work=0.1195 r_free=0.1343 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 | n_water=977 | time (s): 234.400 (total time: 361.080) Filter (q & B) r_work=0.1194 r_free=0.1347 | n_water=903 | time (s): 4.570 (total time: 365.650) Filter (dist only) r_work=0.1194 r_free=0.1347 | n_water=902 | time (s): 119.530 (total time: 485.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507953 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.563753 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1354 0.0156 0.037 1.1 5.6 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.56 1.759 14.016 15.564 3.760 11.99 13.57 1.58 1.846 13.980 15.564 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 65.84 14.83 0.92 536 3270 Protein: 5.56 29.75 10.50 0.92 0 2902 Water: 5.91 65.84 28.75 N/A 536 366 Other: 13.84 23.98 18.91 N/A 0 2 Chain A: 5.65 51.38 12.39 N/A 0 1624 Chain B: 5.56 65.84 12.19 N/A 0 1646 Chain S: 5.91 59.62 30.29 N/A 536 0 Histogram: Values Number of atoms 5.56 - 11.59 2110 11.59 - 17.62 763 17.62 - 23.64 308 23.64 - 29.67 222 29.67 - 35.70 180 35.70 - 41.73 125 41.73 - 47.75 61 47.75 - 53.78 28 53.78 - 59.81 8 59.81 - 65.84 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1357 r_work=0.1199 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756366 | | target function (ml) not normalized (work): 703522.365665 | | target function (ml) not normalized (free): 14738.598908 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1480 n_refl.: 191129 remove outliers: r(all,work,free)=0.1393 0.1391 0.1480 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1385 0.1383 0.1475 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1355 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3546 356.830 330.816 0.409 0.954 0.211 13.296-10.522 96.04 96 1 0.2347 480.533 458.205 0.684 0.955 0.152 10.503-8.327 97.80 175 3 0.2205 500.896 495.174 0.864 0.955 0.127 8.318-6.595 100.00 360 8 0.2155 375.624 370.497 0.877 0.955 0.080 6.588-5.215 100.00 711 7 0.1907 345.161 334.933 0.878 0.955 0.080 5.214-4.128 98.38 1367 28 0.1224 504.866 499.515 0.966 0.955 0.070 4.126-3.266 94.74 2603 46 0.1147 460.212 453.267 1.028 0.956 0.005 3.266-2.585 99.86 5447 97 0.1121 310.448 307.080 1.014 0.955 0.000 2.585-2.046 97.45 10613 204 0.0947 234.215 231.714 1.026 0.954 0.000 2.046-1.619 99.39 21536 464 0.0913 138.620 137.306 1.049 0.953 0.000 1.619-1.281 98.00 42464 925 0.0964 74.625 73.929 1.048 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1646 40.033 38.371 1.036 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1355 | n_water=902 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1196 r_free=0.1355 | n_water=902 | time (s): 118.760 (total time: 121.950) Filter (q & B) r_work=0.1196 r_free=0.1353 | n_water=893 | time (s): 4.450 (total time: 126.400) Compute maps r_work=0.1196 r_free=0.1353 | n_water=893 | time (s): 1.700 (total time: 128.100) Filter (map) r_work=0.1216 r_free=0.1355 | n_water=780 | time (s): 4.440 (total time: 132.540) Find peaks r_work=0.1216 r_free=0.1355 | n_water=780 | time (s): 0.610 (total time: 133.150) Add new water r_work=0.1225 r_free=0.1364 | n_water=997 | time (s): 4.640 (total time: 137.790) Refine new water occ: r_work=0.1194 r_free=0.1335 adp: r_work=0.1194 r_free=0.1335 occ: r_work=0.1192 r_free=0.1335 adp: r_work=0.1192 r_free=0.1335 occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1190 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1336 r_work=0.1190 r_free=0.1336 | n_water=997 | time (s): 218.390 (total time: 356.180) Filter (q & B) r_work=0.1194 r_free=0.1344 | n_water=918 | time (s): 5.270 (total time: 361.450) Filter (dist only) r_work=0.1195 r_free=0.1344 | n_water=917 | time (s): 116.260 (total time: 477.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510952 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.097495 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 0.1353 0.0157 0.038 1.1 6.1 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.53 1.57 1.727 13.942 14.097 3.757 12.00 13.57 1.58 1.750 13.929 14.097 3.757 Individual atomic B min max mean iso aniso Overall: 5.54 65.39 14.82 0.89 551 3270 Protein: 5.54 29.19 10.45 0.89 0 2902 Water: 5.99 65.39 28.65 N/A 551 366 Other: 13.80 23.37 18.59 N/A 0 2 Chain A: 5.60 51.10 12.32 N/A 0 1624 Chain B: 5.54 65.39 12.14 N/A 0 1646 Chain S: 5.99 59.61 30.24 N/A 551 0 Histogram: Values Number of atoms 5.54 - 11.52 2104 11.52 - 17.51 777 17.51 - 23.49 299 23.49 - 29.48 228 29.48 - 35.46 182 35.46 - 41.45 131 41.45 - 47.43 63 47.43 - 53.42 27 53.42 - 59.40 8 59.40 - 65.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757041 | | target function (ml) not normalized (work): 703644.903467 | | target function (ml) not normalized (free): 14744.332416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1361 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1389 0.1387 0.1497 n_refl.: 191128 remove outliers: r(all,work,free)=0.1389 0.1387 0.1497 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1388 0.1386 0.1496 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1351 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1351 n_refl.: 191127 ======================== 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 0.3464 356.830 329.945 0.411 0.974 0.215 13.296-10.522 95.05 95 1 0.2280 479.635 453.321 0.689 0.975 0.150 10.503-8.327 97.80 175 3 0.2156 500.896 494.747 0.866 0.976 0.123 8.318-6.595 100.00 360 8 0.2166 375.624 369.188 0.882 0.976 0.101 6.588-5.215 100.00 711 7 0.1915 345.161 334.413 0.880 0.976 0.087 5.214-4.128 98.38 1367 28 0.1234 504.866 498.792 0.969 0.977 0.080 4.126-3.266 94.74 2603 46 0.1160 460.212 452.693 1.029 0.978 0.005 3.266-2.585 99.86 5447 97 0.1127 310.448 306.820 1.013 0.978 0.000 2.585-2.046 97.45 10613 204 0.0952 234.215 231.550 1.024 0.980 0.000 2.046-1.619 99.39 21536 464 0.0911 138.620 137.222 1.042 0.983 0.000 1.619-1.281 98.00 42464 925 0.0946 74.625 73.979 1.037 0.987 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.033 38.342 1.011 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1351 | n_water=917 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1189 r_free=0.1351 | n_water=917 | time (s): 108.140 (total time: 110.700) Filter (q & B) r_work=0.1189 r_free=0.1350 | n_water=907 | time (s): 5.610 (total time: 116.310) Compute maps r_work=0.1189 r_free=0.1350 | n_water=907 | time (s): 2.580 (total time: 118.890) Filter (map) r_work=0.1209 r_free=0.1350 | n_water=787 | time (s): 5.270 (total time: 124.160) Find peaks r_work=0.1209 r_free=0.1350 | n_water=787 | time (s): 0.680 (total time: 124.840) Add new water r_work=0.1218 r_free=0.1360 | n_water=1011 | time (s): 4.420 (total time: 129.260) Refine new water occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1185 r_free=0.1332 occ: r_work=0.1183 r_free=0.1332 adp: r_work=0.1183 r_free=0.1332 occ: r_work=0.1182 r_free=0.1333 adp: r_work=0.1181 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1333 r_work=0.1181 r_free=0.1333 | n_water=1011 | time (s): 175.400 (total time: 304.660) Filter (q & B) r_work=0.1185 r_free=0.1344 | n_water=929 | time (s): 5.450 (total time: 310.110) Filter (dist only) r_work=0.1186 r_free=0.1344 | n_water=926 | time (s): 122.140 (total time: 432.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.571422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.044198 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 0.1188 0.1351 0.0163 0.039 1.1 6.7 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.51 1.63 1.709 13.911 14.044 3.754 11.89 13.53 1.64 1.741 13.894 14.044 3.753 Individual atomic B min max mean iso aniso Overall: 5.60 64.58 14.78 0.87 560 3270 Protein: 5.60 28.50 10.44 0.87 0 2902 Water: 6.00 64.58 28.39 N/A 560 366 Other: 13.84 22.44 18.14 N/A 0 2 Chain A: 5.68 50.98 12.27 N/A 0 1624 Chain B: 5.60 64.58 12.10 N/A 0 1646 Chain S: 6.00 59.61 29.94 N/A 560 0 Histogram: Values Number of atoms 5.60 - 11.50 2088 11.50 - 17.40 800 17.40 - 23.30 292 23.30 - 29.19 233 29.19 - 35.09 183 35.09 - 40.99 126 40.99 - 46.89 72 46.89 - 52.78 26 52.78 - 58.68 8 58.68 - 64.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1353 r_work=0.1189 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1354 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1358 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752514 | | target function (ml) not normalized (work): 702793.392394 | | target function (ml) not normalized (free): 14733.987821 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1188 0.1358 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1392 0.1389 0.1507 n_refl.: 191127 remove outliers: r(all,work,free)=0.1392 0.1389 0.1507 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1388 0.1386 0.1504 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1187 0.1357 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1187 0.1357 n_refl.: 191127 ======================== 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 0.3490 356.830 329.264 0.404 0.975 0.207 13.296-10.522 95.05 95 1 0.2267 479.635 463.624 0.700 0.976 0.142 10.503-8.327 97.80 175 3 0.2165 500.896 494.805 0.863 0.977 0.113 8.318-6.595 100.00 360 8 0.2158 375.624 368.972 0.880 0.977 0.091 6.588-5.215 100.00 711 7 0.1918 345.161 334.373 0.878 0.977 0.077 5.214-4.128 98.38 1367 28 0.1240 504.866 498.874 0.967 0.978 0.070 4.126-3.266 94.74 2603 46 0.1162 460.212 452.535 1.028 0.979 0.000 3.266-2.585 99.86 5447 97 0.1129 310.448 306.723 1.013 0.980 0.000 2.585-2.046 97.45 10613 204 0.0953 234.215 231.497 1.023 0.982 0.000 2.046-1.619 99.39 21536 464 0.0909 138.620 137.236 1.042 0.985 0.000 1.619-1.281 98.00 42464 925 0.0941 74.625 73.978 1.037 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.033 38.328 1.012 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1357 | n_water=926 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1187 r_free=0.1357 | n_water=925 | time (s): 116.750 (total time: 119.350) Filter (q & B) r_work=0.1188 r_free=0.1358 | n_water=920 | time (s): 4.400 (total time: 123.750) Compute maps r_work=0.1188 r_free=0.1358 | n_water=920 | time (s): 1.920 (total time: 125.670) Filter (map) r_work=0.1209 r_free=0.1353 | n_water=797 | time (s): 5.430 (total time: 131.100) Find peaks r_work=0.1209 r_free=0.1353 | n_water=797 | time (s): 0.680 (total time: 131.780) Add new water r_work=0.1217 r_free=0.1362 | n_water=1016 | time (s): 4.130 (total time: 135.910) Refine new water occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1331 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1331 occ: r_work=0.1182 r_free=0.1333 adp: r_work=0.1182 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1333 r_work=0.1182 r_free=0.1333 | n_water=1016 | time (s): 265.470 (total time: 401.380) Filter (q & B) r_work=0.1186 r_free=0.1342 | n_water=931 | time (s): 4.050 (total time: 405.430) Filter (dist only) r_work=0.1187 r_free=0.1342 | n_water=929 | time (s): 122.520 (total time: 527.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.520473 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.061532 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 0.1190 0.1348 0.0158 0.039 1.1 5.1 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.48 1.58 1.698 13.885 15.062 3.754 11.88 13.49 1.61 1.705 13.883 15.062 3.750 Individual atomic B min max mean iso aniso Overall: 5.63 63.60 14.79 0.88 563 3270 Protein: 5.63 28.51 10.44 0.88 0 2902 Water: 6.00 63.60 28.38 N/A 563 366 Other: 13.87 22.19 18.03 N/A 0 2 Chain A: 5.70 50.88 12.24 N/A 0 1624 Chain B: 5.63 63.60 12.08 N/A 0 1646 Chain S: 6.00 59.54 30.07 N/A 563 0 Histogram: Values Number of atoms 5.63 - 11.43 2064 11.43 - 17.22 824 17.22 - 23.02 280 23.02 - 28.82 233 28.82 - 34.61 186 34.61 - 40.41 128 40.41 - 46.21 75 46.21 - 52.01 33 52.01 - 57.80 8 57.80 - 63.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1349 target_work(ml) = 3.750 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1351 target_work(ml) = 3.750 | | 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.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1187 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750092 | | target function (ml) not normalized (work): 702339.692209 | | target function (ml) not normalized (free): 14726.546680 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1187 0.1351 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1508 n_refl.: 191127 remove outliers: r(all,work,free)=0.1395 0.1393 0.1508 n_refl.: 191127 overall B=-0.11 to atoms: r(all,work,free)=0.1377 0.1374 0.1493 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1349 n_refl.: 191127 remove outliers: r(all,work,free)=0.1189 0.1186 0.1349 n_refl.: 191127 ======================== 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 0.3524 356.830 328.709 0.390 0.976 0.196 13.296-10.522 95.05 95 1 0.2280 479.635 462.892 0.688 0.977 0.131 10.503-8.327 97.80 175 3 0.2183 500.896 494.886 0.849 0.977 0.104 8.318-6.595 100.00 360 8 0.2165 375.624 369.248 0.866 0.977 0.087 6.588-5.215 100.00 711 7 0.1919 345.161 334.590 0.864 0.977 0.073 5.214-4.128 98.38 1367 28 0.1237 504.866 499.018 0.951 0.978 0.034 4.126-3.266 94.74 2603 46 0.1174 460.212 452.516 1.013 0.980 0.005 3.266-2.585 99.86 5447 97 0.1126 310.448 306.755 0.997 0.981 0.000 2.585-2.046 97.45 10613 204 0.0954 234.215 231.484 1.005 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.620 137.236 1.020 0.987 0.000 1.619-1.281 98.00 42464 925 0.0935 74.625 73.986 1.011 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1619 40.033 38.323 0.979 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0236 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1349 After: r_work=0.1187 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1187 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1350 | n_water=929 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1187 r_free=0.1350 | n_water=929 | time (s): 128.670 (total time: 131.350) Filter (q & B) r_work=0.1188 r_free=0.1352 | n_water=920 | time (s): 4.550 (total time: 135.900) Compute maps r_work=0.1188 r_free=0.1352 | n_water=920 | time (s): 2.530 (total time: 138.430) Filter (map) r_work=0.1208 r_free=0.1351 | n_water=807 | time (s): 5.510 (total time: 143.940) Find peaks r_work=0.1208 r_free=0.1351 | n_water=807 | time (s): 0.650 (total time: 144.590) Add new water r_work=0.1214 r_free=0.1357 | n_water=1011 | time (s): 4.600 (total time: 149.190) Refine new water occ: r_work=0.1184 r_free=0.1325 adp: r_work=0.1185 r_free=0.1325 occ: r_work=0.1183 r_free=0.1327 adp: r_work=0.1183 r_free=0.1326 occ: r_work=0.1182 r_free=0.1328 adp: r_work=0.1182 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1328 r_work=0.1182 r_free=0.1328 | n_water=1011 | time (s): 256.130 (total time: 405.320) Filter (q & B) r_work=0.1186 r_free=0.1342 | n_water=931 | time (s): 4.460 (total time: 409.780) Filter (dist only) r_work=0.1186 r_free=0.1342 | n_water=929 | time (s): 124.230 (total time: 534.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565533 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.707790 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 0.1187 0.1343 0.0157 0.039 1.1 8.4 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.43 1.57 1.697 13.778 14.708 3.751 11.88 13.45 1.57 1.702 13.776 14.708 3.750 Individual atomic B min max mean iso aniso Overall: 5.54 62.65 14.68 0.87 563 3270 Protein: 5.54 28.19 10.34 0.87 0 2902 Water: 5.99 62.65 28.20 N/A 563 366 Other: 13.85 22.14 17.99 N/A 0 2 Chain A: 5.63 50.68 12.12 N/A 0 1624 Chain B: 5.54 62.65 11.97 N/A 0 1646 Chain S: 5.99 59.39 29.96 N/A 563 0 Histogram: Values Number of atoms 5.54 - 11.25 2044 11.25 - 16.96 837 16.96 - 22.67 283 22.67 - 28.38 222 28.38 - 34.09 194 34.09 - 39.80 123 39.80 - 45.51 82 45.51 - 51.23 34 51.23 - 56.94 11 56.94 - 62.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1345 r_work=0.1188 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1345 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1348 target_work(ml) = 3.750 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1187 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750316 | | target function (ml) not normalized (work): 702381.733470 | | target function (ml) not normalized (free): 14721.811080 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1355 0.1464 5.6786 5.7588| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1298 5.0734 5.162| | 3: 2.33 - 2.04 0.96 6939 150 0.0895 0.1181 4.6522 4.7563| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1063 4.3949 4.5832| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.0996 4.1474 4.2537| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1072 3.9416 4.0691| | 7: 1.62 - 1.54 0.99 7104 148 0.0880 0.0967 3.7917 3.9324| | 8: 1.54 - 1.47 0.96 6798 152 0.0883 0.1304 3.6931 3.905| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1113 3.6136 3.7395| | 10: 1.41 - 1.36 0.99 7022 150 0.0970 0.1178 3.5477 3.6694| | 11: 1.36 - 1.32 0.99 6997 151 0.0986 0.1129 3.4785 3.5835| | 12: 1.32 - 1.28 0.98 6975 149 0.1022 0.1126 3.4515 3.5749| | 13: 1.28 - 1.25 0.98 6907 166 0.1031 0.1221 3.4282 3.5478| | 14: 1.25 - 1.22 0.98 7015 112 0.1097 0.1582 3.4256 3.6734| | 15: 1.22 - 1.19 0.98 6956 137 0.1162 0.1247 3.4444 3.4916| | 16: 1.19 - 1.17 0.93 6604 132 0.1244 0.1556 3.4624 3.6627| | 17: 1.17 - 1.14 0.98 6940 135 0.1295 0.1228 3.4318 3.4435| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1704 3.4364 3.5315| | 19: 1.12 - 1.10 0.97 6948 106 0.1466 0.1748 3.418 3.5959| | 20: 1.10 - 1.08 0.97 6884 147 0.1580 0.1563 3.4087 3.4307| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2136 3.4171 3.5029| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1950 3.4125 3.4139| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2025 3.4323 3.4854| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2246 3.4353 3.5082| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2516 3.4487 3.5254| | 26: 1.01 - 0.99 0.96 6767 158 0.2751 0.2850 3.4153 3.4243| | 27: 0.99 - 0.98 0.94 6647 131 0.3038 0.2812 3.4681 3.3963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7395 127 0.93 11.49 1.00 0.98 10930.98| | 2: 2.94 - 2.33 7339 128 0.93 12.69 0.99 0.98 5067.15| | 3: 2.33 - 2.04 6939 150 0.96 7.74 1.01 0.98 1732.93| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.98 1020.91| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.98 636.34| | 6: 1.72 - 1.62 7102 142 0.96 7.96 1.00 0.99 439.85| | 7: 1.62 - 1.54 7104 148 0.96 8.10 1.01 1.00 334.79| | 8: 1.54 - 1.47 6798 152 0.96 8.20 1.01 1.00 276.69| | 9: 1.47 - 1.41 6938 155 0.96 8.39 1.00 1.00 227.70| | 10: 1.41 - 1.36 7022 150 0.96 8.82 1.00 0.99 199.30| | 11: 1.36 - 1.32 6997 151 0.96 8.84 0.99 0.98 172.33| | 12: 1.32 - 1.28 6975 149 0.96 8.88 0.98 0.97 158.36| | 13: 1.28 - 1.25 6907 166 0.96 9.39 1.01 0.98 155.31| | 14: 1.25 - 1.22 7015 112 0.95 10.56 1.01 0.99 160.28| | 15: 1.22 - 1.19 6956 137 0.95 11.15 1.01 1.00 165.02| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.99 160.08| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.99 154.31| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.97 147.57| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.97 150.61| | 20: 1.10 - 1.08 6884 147 0.92 15.17 1.00 0.96 149.58| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.96 152.87| | 22: 1.07 - 1.05 6836 135 0.89 18.27 1.00 0.95 154.57| | 23: 1.05 - 1.03 6827 159 0.87 20.48 1.00 0.95 164.50| | 24: 1.03 - 1.02 6784 133 0.85 23.14 1.00 0.95 178.81| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.92 181.99| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.99 0.91 176.67| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.90 161.31| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.57 max = 10930.98 mean = 913.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.25| |phase err.(test): min = 0.00 max = 89.19 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1187 0.1348 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1384 0.1382 0.1492 n_refl.: 191127 remove outliers: r(all,work,free)=0.1384 0.1382 0.1492 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1379 0.1377 0.1488 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1348 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 0.1348 n_refl.: 191127 ======================== 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 0.3502 356.830 329.131 0.394 0.975 0.206 13.296-10.522 95.05 95 1 0.2301 479.635 463.584 0.688 0.976 0.136 10.503-8.327 97.80 175 3 0.2180 500.896 495.340 0.850 0.977 0.105 8.318-6.595 100.00 360 8 0.2172 375.624 369.850 0.865 0.977 0.086 6.588-5.215 100.00 711 7 0.1931 345.161 334.254 0.866 0.977 0.077 5.214-4.128 98.38 1367 28 0.1241 504.866 499.056 0.953 0.978 0.046 4.126-3.266 94.74 2603 46 0.1169 460.212 452.513 1.015 0.980 0.000 3.266-2.585 99.86 5447 97 0.1120 310.448 306.860 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0955 234.215 231.508 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0908 138.620 137.256 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0939 74.625 73.983 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1620 40.033 38.323 0.981 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0083 ================= 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 : 0.2037 0.2017 0.081 5.161 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1936 0.081 5.161 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1936 0.081 5.161 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1936 0.081 5.161 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1936 0.081 5.161 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1268 0.1477 0.033 1.168 5.2 78.0 14.6 805 0.140 1_adp: 0.1293 0.1540 0.033 1.168 5.2 73.0 14.9 805 0.140 1_regHadp: 0.1292 0.1535 0.033 1.168 5.2 73.0 14.9 805 0.140 1_occ: 0.1277 0.1521 0.033 1.168 5.2 73.0 14.9 805 0.140 2_bss: 0.1270 0.1510 0.033 1.168 5.4 73.2 15.1 805 0.140 2_settarget: 0.1270 0.1510 0.033 1.168 5.4 73.2 15.1 805 0.140 2_updatecdl: 0.1270 0.1510 0.033 1.179 5.4 73.2 15.1 805 0.140 2_nqh: 0.1270 0.1510 0.033 1.179 5.4 73.2 15.1 805 0.140 2_sol: 0.1262 0.1487 0.033 1.179 5.4 73.2 16.3 900 n/a 2_weight: 0.1262 0.1487 0.033 1.179 5.4 73.2 16.3 900 n/a 2_xyzrec: 0.1247 0.1503 0.038 1.146 5.4 73.2 16.3 900 n/a 2_adp: 0.1231 0.1503 0.038 1.146 5.4 68.2 16.4 900 n/a 2_regHadp: 0.1231 0.1504 0.038 1.146 5.4 68.2 16.4 900 n/a 2_occ: 0.1225 0.1500 0.038 1.146 5.4 68.2 16.4 900 n/a 3_bss: 0.1231 0.1507 0.038 1.146 5.4 68.2 16.4 900 n/a 3_settarget: 0.1231 0.1507 0.038 1.146 5.4 68.2 16.4 900 n/a 3_updatecdl: 0.1231 0.1507 0.038 1.148 5.4 68.2 16.4 900 n/a 3_nqh: 0.1231 0.1507 0.038 1.148 5.4 68.2 16.4 900 n/a 3_sol: 0.1247 0.1510 0.038 1.148 5.4 68.2 15.5 880 n/a 3_weight: 0.1247 0.1510 0.038 1.148 5.4 68.2 15.5 880 n/a 3_xyzrec: 0.1239 0.1440 0.035 1.092 5.4 68.2 15.5 880 n/a 3_adp: 0.1231 0.1398 0.035 1.092 5.5 67.9 15.3 880 n/a 3_regHadp: 0.1232 0.1399 0.035 1.092 5.5 67.9 15.3 880 n/a 3_occ: 0.1227 0.1404 0.035 1.092 5.5 67.9 15.3 880 n/a 4_bss: 0.1223 0.1395 0.035 1.092 5.5 67.8 15.3 880 n/a 4_settarget: 0.1223 0.1395 0.035 1.092 5.5 67.8 15.3 880 n/a 4_updatecdl: 0.1223 0.1395 0.035 1.096 5.5 67.8 15.3 880 n/a 4_nqh: 0.1223 0.1395 0.035 1.096 5.5 67.8 15.3 880 n/a 4_sol: 0.1212 0.1373 0.035 1.096 5.5 67.8 14.9 849 n/a 4_weight: 0.1212 0.1373 0.035 1.096 5.5 67.8 14.9 849 n/a 4_xyzrec: 0.1210 0.1373 0.035 1.128 5.5 67.8 14.9 849 n/a 4_adp: 0.1204 0.1370 0.035 1.128 5.5 67.4 14.8 849 n/a 4_regHadp: 0.1204 0.1370 0.035 1.128 5.5 67.4 14.8 849 n/a 4_occ: 0.1203 0.1367 0.035 1.128 5.5 67.4 14.8 849 n/a 5_bss: 0.1200 0.1364 0.035 1.128 5.5 67.4 14.8 849 n/a 5_settarget: 0.1200 0.1364 0.035 1.128 5.5 67.4 14.8 849 n/a 5_updatecdl: 0.1200 0.1364 0.035 1.128 5.5 67.4 14.8 849 n/a 5_nqh: 0.1200 0.1364 0.035 1.128 5.5 67.4 14.8 849 n/a 5_sol: 0.1195 0.1355 0.035 1.128 5.5 67.4 15.0 885 n/a 5_weight: 0.1195 0.1355 0.035 1.128 5.5 67.4 15.0 885 n/a 5_xyzrec: 0.1199 0.1360 0.036 1.126 5.5 67.4 15.0 885 n/a 5_adp: 0.1201 0.1362 0.036 1.126 5.5 66.8 14.9 885 n/a 5_regHadp: 0.1201 0.1362 0.036 1.126 5.5 66.8 14.9 885 n/a 5_occ: 0.1198 0.1359 0.036 1.126 5.5 66.8 14.9 885 n/a 6_bss: 0.1196 0.1359 0.036 1.126 5.5 66.8 14.9 885 n/a 6_settarget: 0.1196 0.1359 0.036 1.126 5.5 66.8 14.9 885 n/a 6_updatecdl: 0.1196 0.1359 0.036 1.126 5.5 66.8 14.9 885 n/a 6_nqh: 0.1196 0.1359 0.036 1.126 5.5 66.8 14.9 885 n/a 6_sol: 0.1194 0.1347 0.036 1.126 5.5 66.8 14.9 902 n/a 6_weight: 0.1194 0.1347 0.036 1.126 5.5 66.8 14.9 902 n/a 6_xyzrec: 0.1198 0.1354 0.037 1.126 5.5 66.8 14.9 902 n/a 6_adp: 0.1199 0.1357 0.037 1.126 5.6 65.8 14.8 902 n/a 6_regHadp: 0.1199 0.1358 0.037 1.126 5.6 65.8 14.8 902 n/a 6_occ: 0.1197 0.1359 0.037 1.126 5.6 65.8 14.8 902 n/a 7_bss: 0.1196 0.1355 0.037 1.126 5.5 65.8 14.8 902 n/a 7_settarget: 0.1196 0.1355 0.037 1.126 5.5 65.8 14.8 902 n/a 7_updatecdl: 0.1196 0.1355 0.037 1.126 5.5 65.8 14.8 902 n/a 7_nqh: 0.1196 0.1355 0.037 1.126 5.5 65.8 14.8 902 n/a 7_sol: 0.1195 0.1344 0.037 1.126 5.5 65.8 14.8 917 n/a 7_weight: 0.1195 0.1344 0.037 1.126 5.5 65.8 14.8 917 n/a 7_xyzrec: 0.1197 0.1353 0.038 1.119 5.5 65.8 14.8 917 n/a 7_adp: 0.1200 0.1357 0.038 1.119 5.5 65.4 14.8 917 n/a 7_regHadp: 0.1200 0.1358 0.038 1.119 5.5 65.4 14.8 917 n/a 7_occ: 0.1199 0.1361 0.038 1.119 5.5 65.4 14.8 917 n/a 8_bss: 0.1189 0.1351 0.038 1.119 5.5 65.4 14.8 917 n/a 8_settarget: 0.1189 0.1351 0.038 1.119 5.5 65.4 14.8 917 n/a 8_updatecdl: 0.1189 0.1351 0.038 1.119 5.5 65.4 14.8 917 n/a 8_nqh: 0.1189 0.1351 0.038 1.119 5.5 65.4 14.8 917 n/a 8_sol: 0.1186 0.1344 0.038 1.119 5.5 65.4 14.8 926 n/a 8_weight: 0.1186 0.1344 0.038 1.119 5.5 65.4 14.8 926 n/a 8_xyzrec: 0.1188 0.1351 0.039 1.123 5.5 65.4 14.8 926 n/a 8_adp: 0.1189 0.1353 0.039 1.123 5.6 64.6 14.8 926 n/a 8_regHadp: 0.1189 0.1354 0.039 1.123 5.6 64.6 14.8 926 n/a 8_occ: 0.1188 0.1358 0.039 1.123 5.6 64.6 14.8 926 n/a 9_bss: 0.1187 0.1357 0.039 1.123 5.6 64.6 14.8 926 n/a 9_settarget: 0.1187 0.1357 0.039 1.123 5.6 64.6 14.8 926 n/a 9_updatecdl: 0.1187 0.1357 0.039 1.123 5.6 64.6 14.8 926 n/a 9_nqh: 0.1187 0.1357 0.039 1.123 5.6 64.6 14.8 926 n/a 9_sol: 0.1187 0.1342 0.039 1.123 5.6 64.6 14.8 929 n/a 9_weight: 0.1187 0.1342 0.039 1.123 5.6 64.6 14.8 929 n/a 9_xyzrec: 0.1190 0.1348 0.039 1.116 5.6 64.6 14.8 929 n/a 9_adp: 0.1188 0.1349 0.039 1.116 5.6 63.6 14.8 929 n/a 9_regHadp: 0.1188 0.1349 0.039 1.116 5.6 63.6 14.8 929 n/a 9_occ: 0.1187 0.1351 0.039 1.116 5.6 63.6 14.8 929 n/a 10_bss: 0.1186 0.1349 0.039 1.116 5.5 63.5 14.7 929 n/a 10_settarget: 0.1186 0.1349 0.039 1.116 5.5 63.5 14.7 929 n/a 10_updatecdl: 0.1186 0.1349 0.039 1.116 5.5 63.5 14.7 929 n/a 10_setrh: 0.1187 0.1350 0.039 1.116 5.5 63.5 14.7 929 n/a 10_nqh: 0.1187 0.1350 0.039 1.116 5.5 63.5 14.7 929 n/a 10_sol: 0.1186 0.1342 0.039 1.116 5.5 63.5 14.7 929 n/a 10_weight: 0.1186 0.1342 0.039 1.116 5.5 63.5 14.7 929 n/a 10_xyzrec: 0.1187 0.1343 0.039 1.148 5.5 63.5 14.7 929 n/a 10_adp: 0.1188 0.1345 0.039 1.148 5.5 62.6 14.7 929 n/a 10_regHadp: 0.1188 0.1345 0.039 1.148 5.5 62.6 14.7 929 n/a 10_occ: 0.1187 0.1348 0.039 1.148 5.5 62.6 14.7 929 n/a end: 0.1187 0.1348 0.039 1.148 5.5 62.6 14.6 929 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9503307_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9503307_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.5700 Refinement macro-cycles (run) : 12094.4600 Write final files (write_after_run_outputs) : 162.6400 Total : 12263.6700 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:42 PST -0800 (1736736102.95 s) Start R-work = 0.1804, R-free = 0.1936 Final R-work = 0.1187, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12550.59 seconds wall clock time: 210 minutes 13.09 seconds (12613.09 seconds total)