Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7691479.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7691479.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7691479.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" 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 =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.26 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: 2.685 distance_ideal: 2.720 ideal - model: 0.035 slack: 0.000 delta_slack: 0.035 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: 2.737 distance_ideal: 2.710 ideal - model: -0.027 slack: 0.000 delta_slack: -0.027 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 128.7 milliseconds Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 0.98: 404 0.98 - 1.22: 2654 1.22 - 1.45: 1447 1.45 - 1.69: 1378 1.69 - 1.92: 51 Bond restraints: 5934 Sorted by residual: bond pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 1.236 0.987 0.249 1.05e-02 9.07e+03 5.62e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.518 1.729 -0.211 1.02e-02 9.61e+03 4.27e+02 bond pdb=" ND2 ASN B 193 " pdb="HD22 ASN B 193 " ideal model delta sigma weight residual 0.860 1.271 -0.411 2.00e-02 2.50e+03 4.23e+02 bond pdb=" N ALA A 18 " pdb=" CA ALA A 18 " ideal model delta sigma weight residual 1.459 1.223 0.236 1.17e-02 7.31e+03 4.07e+02 bond pdb=" N GLY A 157 " pdb=" H GLY A 157 " ideal model delta sigma weight residual 0.860 1.242 -0.382 2.00e-02 2.50e+03 3.64e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 5757 4.22 - 8.44: 3490 8.44 - 12.66: 1300 12.66 - 16.87: 244 16.87 - 21.09: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CD2 HIS A 96 " pdb=" NE2 HIS A 96 " pdb=" CE1 HIS A 96 " ideal model delta sigma weight residual 109.00 92.95 16.05 1.00e+00 1.00e+00 2.58e+02 angle pdb=" O GLY B 174 " pdb=" C GLY B 174 " pdb=" N ARG B 175 " ideal model delta sigma weight residual 123.48 138.97 -15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" CD2 HIS B 116 " pdb=" NE2 HIS B 116 " pdb=" CE1 HIS B 116 " ideal model delta sigma weight residual 109.00 123.69 -14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" O GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " ideal model delta sigma weight residual 122.77 137.05 -14.28 1.03e+00 9.43e-01 1.92e+02 angle pdb=" CA GLY B 174 " pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 122.37 112.49 9.88 7.30e-01 1.88e+00 1.83e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1833 16.75 - 33.51: 151 33.51 - 50.26: 37 50.26 - 67.01: 25 67.01 - 83.77: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 209 0.210 - 0.419: 141 0.419 - 0.628: 90 0.628 - 0.838: 34 0.838 - 1.047: 18 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA CYS B 47 " pdb=" N CYS B 47 " pdb=" C CYS B 47 " pdb=" CB CYS B 47 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA ALA A 44 " pdb=" N ALA A 44 " pdb=" C ALA A 44 " pdb=" CB ALA A 44 " both_signs ideal model delta sigma weight residual False 2.48 3.51 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA THR B 91 " pdb=" N THR B 91 " pdb=" C THR B 91 " pdb=" CB THR B 91 " both_signs ideal model delta sigma weight residual False 2.53 3.48 -0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.128 2.00e-02 2.50e+03 7.76e-02 1.81e+02 pdb=" CG PHE B 164 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.140 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.069 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.124 2.00e-02 2.50e+03 6.58e-02 1.73e+02 pdb=" CG TRP A 146 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.108 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.077 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.089 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.040 2.00e-02 2.50e+03 7.48e-02 1.68e+02 pdb=" CG PHE A 82 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " 0.088 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.137 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " -0.070 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " -0.071 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 38 1.67 - 2.40: 3120 2.40 - 3.14: 22632 3.14 - 3.87: 32769 3.87 - 4.60: 51748 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110307 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.939 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.018 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.076 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.078 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.153 2.620 ... (remaining 110302 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_7691479_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= 0.2036 r_free= 0.2039 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300029 | | target function (ml) not normalized (work): 805451.363945 | | target function (ml) not normalized (free): 16589.477379 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2067 6.6694 6.3314| | 2: 2.94 - 2.33 1.00 7339 128 0.1610 0.1852 5.5477 5.6387| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1577 5.1476 5.1451| | 4: 2.04 - 1.85 1.00 7170 155 0.1753 0.1581 4.9734 5.0126| | 5: 1.85 - 1.72 0.99 7113 159 0.1924 0.1783 4.798 4.8442| | 6: 1.72 - 1.62 0.99 7102 142 0.2005 0.1984 4.6793 4.7188| | 7: 1.62 - 1.54 0.99 7104 148 0.2024 0.1877 4.5643 4.6311| | 8: 1.54 - 1.47 0.96 6798 152 0.2009 0.2234 4.4733 4.5271| | 9: 1.47 - 1.41 0.98 6938 155 0.2102 0.2171 4.403 4.4593| | 10: 1.41 - 1.36 0.99 7022 150 0.2128 0.2155 4.314 4.3535| | 11: 1.36 - 1.32 0.99 6997 151 0.2090 0.2197 4.2311 4.2921| | 12: 1.32 - 1.28 0.98 6976 149 0.2086 0.2148 4.1735 4.2826| | 13: 1.28 - 1.25 0.98 6907 166 0.2057 0.2166 4.1296 4.1689| | 14: 1.25 - 1.22 0.98 7015 113 0.2078 0.2213 4.0663 4.1812| | 15: 1.22 - 1.19 0.98 6957 137 0.2084 0.2016 4.0383 4.0473| | 16: 1.19 - 1.17 0.93 6604 132 0.2098 0.2179 3.9991 4.1039| | 17: 1.17 - 1.14 0.98 6941 135 0.2170 0.1877 3.9567 3.9982| | 18: 1.14 - 1.12 0.98 6875 142 0.2227 0.2417 3.9214 3.9507| | 19: 1.12 - 1.10 0.97 6949 106 0.2279 0.2610 3.8697 3.9869| | 20: 1.10 - 1.08 0.97 6884 147 0.2316 0.2383 3.8159 3.8773| | 21: 1.08 - 1.07 0.97 6852 152 0.2445 0.2321 3.7925 3.7612| | 22: 1.07 - 1.05 0.97 6838 135 0.2560 0.2609 3.7567 3.7301| | 23: 1.05 - 1.03 0.97 6829 159 0.2710 0.2841 3.7256 3.889| | 24: 1.03 - 1.02 0.96 6785 133 0.2894 0.2816 3.7084 3.763| | 25: 1.02 - 1.01 0.93 6552 130 0.3075 0.2912 3.6757 3.7106| | 26: 1.01 - 0.99 0.96 6767 158 0.3187 0.3176 3.6202 3.5845| | 27: 0.99 - 0.98 0.94 6648 131 0.3423 0.3252 3.6367 3.6169| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.88 0.91 0.97 36921.56| | 2: 2.94 - 2.33 7339 128 0.85 21.50 1.09 1.02 15528.00| | 3: 2.33 - 2.04 6939 150 0.93 12.45 1.11 1.05 4083.21| | 4: 2.04 - 1.85 7170 155 0.92 13.47 1.11 1.05 2732.40| | 5: 1.85 - 1.72 7113 159 0.91 15.90 1.12 1.06 2099.15| | 6: 1.72 - 1.62 7102 142 0.90 17.12 1.12 1.06 1713.23| | 7: 1.62 - 1.54 7104 148 0.88 18.44 1.11 1.06 1421.61| | 8: 1.54 - 1.47 6798 152 0.88 18.82 1.10 1.06 1210.35| | 9: 1.47 - 1.41 6938 155 0.88 19.32 1.10 1.06 1014.39| | 10: 1.41 - 1.36 7022 150 0.87 20.36 1.10 1.06 877.57| | 11: 1.36 - 1.32 6997 151 0.87 20.35 1.08 1.05 761.96| | 12: 1.32 - 1.28 6976 149 0.86 20.76 1.08 1.03 693.29| | 13: 1.28 - 1.25 6907 166 0.87 20.66 1.07 1.03 636.89| | 14: 1.25 - 1.22 7015 113 0.86 21.42 1.08 1.02 592.36| | 15: 1.22 - 1.19 6957 137 0.86 21.06 1.08 1.02 547.03| | 16: 1.19 - 1.17 6604 132 0.87 20.91 1.07 1.02 502.45| | 17: 1.17 - 1.14 6941 135 0.86 21.13 1.08 1.03 448.69| | 18: 1.14 - 1.12 6875 142 0.86 21.28 1.08 1.01 408.01| | 19: 1.12 - 1.10 6949 106 0.86 22.01 1.07 1.01 376.62| | 20: 1.10 - 1.08 6884 147 0.85 22.57 1.06 0.99 347.49| | 21: 1.08 - 1.07 6852 152 0.84 23.57 1.05 0.98 328.55| | 22: 1.07 - 1.05 6838 135 0.82 25.46 1.05 0.97 327.71| | 23: 1.05 - 1.03 6829 159 0.79 28.40 1.06 0.96 342.33| | 24: 1.03 - 1.02 6785 133 0.77 30.14 1.04 0.95 339.09| | 25: 1.02 - 1.01 6552 130 0.76 31.16 1.02 0.92 316.99| | 26: 1.01 - 0.99 6767 158 0.75 32.58 1.02 0.90 292.97| | 27: 0.99 - 0.98 6648 131 0.74 33.54 1.03 0.89 288.96| |alpha: min = 0.89 max = 1.06 mean = 1.01| |beta: min = 288.96 max = 36921.56 mean = 2915.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.96| |phase err.(test): min = 0.00 max = 88.86 mean = 22.01| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.249 2950 Z= 5.484 Angle : 5.169 16.143 4018 Z= 3.660 Chirality : 0.389 1.047 492 Planarity : 0.032 0.140 512 Dihedral : 12.708 83.768 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.37 % Favored : 96.11 % Rotamer: Outliers : 0.32 % Allowed : 4.84 % Favored : 94.84 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.37), residues: 386 helix: -3.13 (0.27), residues: 144 sheet: -0.58 (0.57), residues: 66 loop : -0.61 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.018 ARG A 97 TYR 0.105 0.041 TYR A 67 PHE 0.143 0.038 PHE B 164 TRP 0.108 0.038 TRP B 139 HIS 0.068 0.021 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.2039 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300029 | | target function (ml) not normalized (work): 805451.363945 | | target function (ml) not normalized (free): 16589.477379 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2036 0.2039 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2036 0.2039 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2036 0.2039 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2035 0.2036 0.2039 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1807 0.1804 0.1977 n_refl.: 191145 remove outliers: r(all,work,free)=0.1805 0.1802 0.1977 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4223 400.535 296.012 0.435 0.912 0.299 13.296-10.522 100.00 100 1 0.2553 534.497 520.526 0.785 0.913 0.250 10.503-8.327 99.45 178 3 0.2482 565.118 555.878 0.973 0.913 0.227 8.318-6.595 100.00 360 8 0.2489 414.736 403.041 0.971 0.913 0.175 6.588-5.215 100.00 711 7 0.2280 381.101 365.842 0.958 0.913 0.170 5.214-4.128 98.38 1367 28 0.1513 557.435 549.858 1.075 0.914 0.080 4.126-3.266 94.74 2603 46 0.1329 508.132 499.587 1.150 0.914 0.028 3.266-2.585 99.86 5447 97 0.1435 342.774 337.998 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1400 258.603 254.321 1.126 0.913 0.000 2.046-1.619 99.39 21536 464 0.1627 153.054 149.838 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1923 82.395 80.134 1.127 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2322 44.203 41.665 1.111 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0011 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1802 r_free=0.1977 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1802 r_free=0.1977 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.518449 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.411705 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 0.1270 0.1502 0.0231 0.038 1.2 11.0 0.0 0.0 0 11.259 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.02 2.31 1.117 13.111 578.412 0.018 12.96 15.70 2.74 1.229 13.313 578.412 0.017 Individual atomic B min max mean iso aniso Overall: 5.26 73.04 14.97 1.40 435 3274 Protein: 5.26 40.43 10.97 1.40 0 2902 Water: 6.28 73.04 29.36 N/A 435 370 Other: 16.01 29.63 22.82 N/A 0 2 Chain A: 5.31 59.87 13.01 N/A 0 1626 Chain B: 5.26 73.04 12.74 N/A 0 1648 Chain S: 11.74 62.03 30.70 N/A 435 0 Histogram: Values Number of atoms 5.26 - 12.04 2189 12.04 - 18.82 627 18.82 - 25.60 310 25.60 - 32.37 265 32.37 - 39.15 157 39.15 - 45.93 101 45.93 - 52.71 36 52.71 - 59.49 20 59.49 - 66.27 3 66.27 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1570 r_work=0.1295 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1565 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015649 | | target function (ls_wunit_k1) not normalized (work): 2931.016066 | | target function (ls_wunit_k1) not normalized (free): 117.089292 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1556 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1469 0.1466 0.1633 n_refl.: 191141 remove outliers: r(all,work,free)=0.1469 0.1466 0.1633 n_refl.: 191141 overall B=0.18 to atoms: r(all,work,free)=0.1495 0.1492 0.1644 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1278 0.1273 0.1548 n_refl.: 191141 remove outliers: r(all,work,free)=0.1278 0.1273 0.1547 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3621 402.814 369.900 0.482 0.962 0.285 13.296-10.522 100.00 100 1 0.2095 534.497 527.105 0.744 0.964 0.240 10.503-8.327 99.45 178 3 0.1774 565.118 562.553 0.888 0.964 0.217 8.318-6.595 100.00 360 8 0.1720 414.736 412.498 0.911 0.963 0.155 6.588-5.215 100.00 711 7 0.1544 381.101 373.651 0.889 0.964 0.150 5.214-4.128 98.38 1367 28 0.0904 557.435 554.862 0.977 0.964 0.055 4.126-3.266 94.74 2603 46 0.0835 508.132 504.392 1.046 0.965 0.018 3.266-2.585 99.86 5447 97 0.0923 342.774 340.324 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.379 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1083 153.054 151.381 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.423 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.176 1.025 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0413 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1547 | n_water=805 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1277 r_free=0.1550 | n_water=794 | time (s): 98.400 (total time: 100.650) Filter (q & B) r_work=0.1278 r_free=0.1550 | n_water=791 | time (s): 5.300 (total time: 105.950) Compute maps r_work=0.1278 r_free=0.1550 | n_water=791 | time (s): 2.130 (total time: 108.080) Filter (map) r_work=0.1303 r_free=0.1526 | n_water=651 | time (s): 4.070 (total time: 112.150) Find peaks r_work=0.1303 r_free=0.1526 | n_water=651 | time (s): 0.710 (total time: 112.860) Add new water r_work=0.1326 r_free=0.1558 | n_water=951 | time (s): 4.200 (total time: 117.060) Refine new water occ: r_work=0.1285 r_free=0.1525 adp: r_work=0.1273 r_free=0.1521 occ: r_work=0.1276 r_free=0.1522 adp: r_work=0.1269 r_free=0.1519 occ: r_work=0.1271 r_free=0.1519 adp: r_work=0.1267 r_free=0.1518 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1518 r_work=0.1267 r_free=0.1518 | n_water=951 | time (s): 79.870 (total time: 196.930) Filter (q & B) r_work=0.1271 r_free=0.1519 | n_water=877 | time (s): 4.340 (total time: 201.270) Filter (dist only) r_work=0.1272 r_free=0.1516 | n_water=873 | time (s): 108.960 (total time: 310.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.381918 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.293285 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 0.1256 0.1537 0.0281 0.040 1.1 16.1 0.0 0.0 0 11.691 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.37 2.81 2.038 15.138 594.293 0.015 12.35 15.27 2.92 2.417 15.203 594.293 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 73.21 16.30 1.20 505 3272 Protein: 5.39 40.62 10.97 1.20 0 2902 Water: 6.50 73.21 34.01 N/A 505 368 Other: 16.39 32.94 24.67 N/A 0 2 Chain A: 5.57 55.95 13.00 N/A 0 1624 Chain B: 5.39 68.22 12.81 N/A 0 1648 Chain S: 11.57 73.21 38.31 N/A 505 0 Histogram: Values Number of atoms 5.39 - 12.17 2160 12.17 - 18.96 674 18.96 - 25.74 240 25.74 - 32.52 229 32.52 - 39.30 172 39.30 - 46.08 148 46.08 - 52.86 78 52.86 - 59.65 49 59.65 - 66.43 22 66.43 - 73.21 5 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1527 r_work=0.1236 r_free=0.1528 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1528 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1518 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1518 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013576 | | target function (ls_wunit_k1) not normalized (work): 2542.808044 | | target function (ls_wunit_k1) not normalized (free): 105.368371 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1518 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1443 0.1439 0.1635 n_refl.: 191139 remove outliers: r(all,work,free)=0.1443 0.1439 0.1635 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1440 0.1437 0.1634 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1235 0.1526 n_refl.: 191139 remove outliers: r(all,work,free)=0.1241 0.1235 0.1526 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3256 402.814 376.876 0.495 0.962 0.277 13.296-10.522 100.00 100 1 0.1912 534.497 527.814 0.767 0.963 0.228 10.503-8.327 99.45 178 3 0.1428 565.118 568.397 0.920 0.963 0.200 8.318-6.595 100.00 360 8 0.1586 414.736 414.424 0.934 0.963 0.150 6.588-5.215 100.00 711 7 0.1360 381.101 376.628 0.913 0.963 0.150 5.214-4.128 98.38 1367 28 0.0833 557.435 556.271 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0771 508.132 505.526 1.061 0.963 0.024 3.266-2.585 99.86 5447 97 0.0865 342.774 341.212 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0897 258.603 256.757 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.584 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.350 1.073 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.217 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0461 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1526 | n_water=873 | time (s): 3.480 (total time: 3.480) Filter (dist) r_work=0.1238 r_free=0.1528 | n_water=864 | time (s): 111.110 (total time: 114.590) Filter (q & B) r_work=0.1238 r_free=0.1528 | n_water=862 | time (s): 4.940 (total time: 119.530) Compute maps r_work=0.1238 r_free=0.1528 | n_water=862 | time (s): 2.280 (total time: 121.810) Filter (map) r_work=0.1277 r_free=0.1523 | n_water=679 | time (s): 4.930 (total time: 126.740) Find peaks r_work=0.1277 r_free=0.1523 | n_water=679 | time (s): 0.560 (total time: 127.300) Add new water r_work=0.1304 r_free=0.1565 | n_water=992 | time (s): 3.960 (total time: 131.260) Refine new water occ: r_work=0.1258 r_free=0.1529 adp: r_work=0.1258 r_free=0.1530 occ: r_work=0.1254 r_free=0.1525 adp: r_work=0.1254 r_free=0.1525 occ: r_work=0.1250 r_free=0.1521 adp: r_work=0.1250 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1250 r_free=0.1522 r_work=0.1250 r_free=0.1522 | n_water=992 | time (s): 398.520 (total time: 529.780) Filter (q & B) r_work=0.1254 r_free=0.1526 | n_water=860 | time (s): 5.180 (total time: 534.960) Filter (dist only) r_work=0.1254 r_free=0.1526 | n_water=859 | time (s): 111.230 (total time: 646.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.675734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.083963 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 0.1448 0.0201 0.035 1.1 7.1 0.0 0.0 0 0.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.47 14.48 2.01 1.929 14.554 16.084 3.942 12.39 14.08 1.69 2.184 14.466 16.084 3.900 Individual atomic B min max mean iso aniso Overall: 5.53 67.90 15.24 1.07 493 3270 Protein: 5.53 37.18 10.76 1.07 0 2902 Water: 6.66 67.90 30.37 N/A 493 366 Other: 14.14 29.15 21.64 N/A 0 2 Chain A: 5.53 55.23 12.79 N/A 0 1624 Chain B: 5.54 67.90 12.54 N/A 0 1646 Chain S: 14.80 66.99 32.33 N/A 493 0 Histogram: Values Number of atoms 5.53 - 11.76 2132 11.76 - 18.00 686 18.00 - 24.24 294 24.24 - 30.48 228 30.48 - 36.71 163 36.71 - 42.95 152 42.95 - 49.19 66 49.19 - 55.43 30 55.43 - 61.67 10 61.67 - 67.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1409 r_work=0.1240 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1410 target_work(ml) = 3.900 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1399 target_work(ml) = 3.894 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1234 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.893793 | | target function (ml) not normalized (work): 729299.647470 | | target function (ml) not normalized (free): 15237.654636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1234 0.1398 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1450 0.1449 0.1496 n_refl.: 191139 remove outliers: r(all,work,free)=0.1450 0.1449 0.1496 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1445 0.1444 0.1493 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1230 0.1394 n_refl.: 191139 remove outliers: r(all,work,free)=0.1233 0.1229 0.1394 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3896 398.008 359.923 0.428 0.945 0.251 13.296-10.522 100.00 100 1 0.2547 534.497 511.979 0.716 0.946 0.219 10.503-8.327 98.35 176 3 0.2008 555.265 557.023 0.883 0.946 0.180 8.318-6.595 100.00 360 8 0.2179 414.736 410.750 0.898 0.946 0.131 6.588-5.215 100.00 711 7 0.1872 381.101 370.034 0.885 0.946 0.110 5.214-4.128 98.38 1367 28 0.1179 557.435 551.663 0.973 0.946 0.080 4.126-3.266 94.74 2603 46 0.1107 508.132 501.000 1.034 0.946 0.009 3.266-2.585 99.86 5447 97 0.1096 342.774 338.961 1.021 0.945 0.000 2.585-2.046 97.45 10613 204 0.0964 258.603 255.779 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.392 1.057 0.943 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.486 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.316 1.039 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0909 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1229 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1395 | n_water=859 | time (s): 2.620 (total time: 2.620) Filter (dist) r_work=0.1230 r_free=0.1395 | n_water=858 | time (s): 105.880 (total time: 108.500) Filter (q & B) r_work=0.1230 r_free=0.1392 | n_water=846 | time (s): 4.870 (total time: 113.370) Compute maps r_work=0.1230 r_free=0.1392 | n_water=846 | time (s): 2.430 (total time: 115.800) Filter (map) r_work=0.1254 r_free=0.1402 | n_water=705 | time (s): 5.250 (total time: 121.050) Find peaks r_work=0.1254 r_free=0.1402 | n_water=705 | time (s): 0.720 (total time: 121.770) Add new water r_work=0.1270 r_free=0.1416 | n_water=952 | time (s): 5.400 (total time: 127.170) Refine new water occ: r_work=0.1219 r_free=0.1371 adp: r_work=0.1211 r_free=0.1366 occ: r_work=0.1209 r_free=0.1365 adp: r_work=0.1209 r_free=0.1365 occ: r_work=0.1209 r_free=0.1365 adp: r_work=0.1209 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1365 r_work=0.1209 r_free=0.1365 | n_water=952 | time (s): 213.390 (total time: 340.560) Filter (q & B) r_work=0.1215 r_free=0.1374 | n_water=837 | time (s): 5.270 (total time: 345.830) Filter (dist only) r_work=0.1216 r_free=0.1373 | n_water=835 | time (s): 111.410 (total time: 457.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.620097 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.911993 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 0.1212 0.1375 0.0163 0.035 1.1 6.1 0.0 0.0 0 0.810 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 13.75 1.63 1.838 14.105 15.912 3.877 12.09 13.68 1.59 2.078 14.028 15.912 3.867 Individual atomic B min max mean iso aniso Overall: 5.50 67.05 14.71 0.98 470 3269 Protein: 5.50 32.69 10.59 0.98 0 2902 Water: 5.94 67.05 29.03 N/A 470 365 Other: 13.84 26.66 20.25 N/A 0 2 Chain A: 5.57 54.23 12.55 N/A 0 1623 Chain B: 5.50 67.01 12.35 N/A 0 1646 Chain S: 5.94 67.05 30.45 N/A 470 0 Histogram: Values Number of atoms 5.50 - 11.66 2119 11.66 - 17.81 734 17.81 - 23.97 317 23.97 - 30.12 205 30.12 - 36.27 136 36.27 - 42.43 127 42.43 - 48.58 64 48.58 - 54.74 28 54.74 - 60.89 6 60.89 - 67.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1368 r_work=0.1209 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1369 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1363 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864280 | | target function (ml) not normalized (work): 723760.330792 | | target function (ml) not normalized (free): 15129.935689 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1363 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1440 0.1440 0.1471 n_refl.: 191136 remove outliers: r(all,work,free)=0.1440 0.1440 0.1471 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1432 0.1466 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1205 0.1361 n_refl.: 191136 remove outliers: r(all,work,free)=0.1208 0.1205 0.1361 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3665 360.150 312.288 0.421 0.945 0.257 13.296-10.522 100.00 100 1 0.2607 484.072 463.768 0.705 0.946 0.205 10.503-8.327 98.35 176 3 0.2172 502.881 493.390 0.861 0.947 0.154 8.318-6.595 100.00 360 8 0.2288 375.610 369.853 0.893 0.946 0.125 6.588-5.215 100.00 711 7 0.1944 345.148 335.116 0.883 0.946 0.099 5.214-4.128 98.38 1367 28 0.1222 504.847 499.620 0.974 0.947 0.080 4.126-3.266 94.74 2603 46 0.1142 460.195 453.818 1.036 0.947 0.000 3.266-2.585 99.86 5447 97 0.1098 310.436 307.220 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0950 234.207 231.742 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0920 138.615 137.306 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.0987 74.622 73.926 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.032 38.378 1.040 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1121 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1361 | n_water=835 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1205 r_free=0.1361 | n_water=835 | time (s): 100.220 (total time: 102.730) Filter (q & B) r_work=0.1205 r_free=0.1361 | n_water=829 | time (s): 4.370 (total time: 107.100) Compute maps r_work=0.1205 r_free=0.1361 | n_water=829 | time (s): 1.950 (total time: 109.050) Filter (map) r_work=0.1226 r_free=0.1363 | n_water=715 | time (s): 4.320 (total time: 113.370) Find peaks r_work=0.1226 r_free=0.1363 | n_water=715 | time (s): 0.860 (total time: 114.230) Add new water r_work=0.1239 r_free=0.1381 | n_water=953 | time (s): 5.500 (total time: 119.730) Refine new water occ: r_work=0.1200 r_free=0.1347 adp: r_work=0.1201 r_free=0.1347 occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1198 r_free=0.1347 occ: r_work=0.1196 r_free=0.1346 adp: r_work=0.1196 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1347 r_work=0.1196 r_free=0.1347 | n_water=953 | time (s): 213.520 (total time: 333.250) Filter (q & B) r_work=0.1200 r_free=0.1356 | n_water=870 | time (s): 4.710 (total time: 337.960) Filter (dist only) r_work=0.1201 r_free=0.1355 | n_water=869 | time (s): 114.990 (total time: 452.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.921225 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 0.1204 0.1361 0.0156 0.037 1.1 6.1 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.61 1.56 1.769 14.008 14.921 3.764 12.07 13.68 1.61 1.807 13.986 14.921 3.763 Individual atomic B min max mean iso aniso Overall: 5.56 67.05 14.82 0.94 504 3269 Protein: 5.56 31.27 10.54 0.94 0 2902 Water: 6.04 67.05 29.09 N/A 504 365 Other: 13.77 25.68 19.73 N/A 0 2 Chain A: 5.56 54.06 12.47 N/A 0 1623 Chain B: 5.57 66.66 12.28 N/A 0 1646 Chain S: 6.04 67.05 30.65 N/A 504 0 Histogram: Values Number of atoms 5.56 - 11.71 2148 11.71 - 17.85 726 17.85 - 24.00 292 24.00 - 30.15 221 30.15 - 36.30 161 36.30 - 42.45 124 42.45 - 48.60 64 48.60 - 54.75 30 54.75 - 60.90 5 60.90 - 67.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1368 r_work=0.1207 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1368 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1367 target_work(ml) = 3.762 | | 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1205 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761935 | | target function (ml) not normalized (work): 704587.847036 | | target function (ml) not normalized (free): 14752.291117 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1366 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1472 n_refl.: 191135 remove outliers: r(all,work,free)=0.1425 0.1425 0.1472 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1417 0.1468 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191135 remove outliers: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3746 360.150 327.654 0.424 0.949 0.238 13.296-10.522 99.01 99 1 0.2562 484.768 459.396 0.691 0.950 0.176 10.503-8.327 98.35 176 3 0.2212 502.881 493.062 0.858 0.950 0.150 8.318-6.595 100.00 360 8 0.2248 375.610 369.739 0.889 0.950 0.121 6.588-5.215 100.00 711 7 0.1935 345.148 335.310 0.883 0.950 0.103 5.214-4.128 98.38 1367 28 0.1218 504.847 499.332 0.972 0.950 0.080 4.126-3.266 94.74 2603 46 0.1163 460.195 453.484 1.033 0.950 0.005 3.266-2.585 99.86 5447 97 0.1119 310.436 307.115 1.019 0.949 0.000 2.585-2.046 97.45 10613 204 0.0954 234.207 231.688 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0916 138.615 137.292 1.055 0.947 0.000 1.619-1.281 98.00 42464 925 0.0974 74.622 73.918 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.032 38.371 1.042 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1180 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1362 | n_water=869 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1203 r_free=0.1363 | n_water=868 | time (s): 107.340 (total time: 109.760) Filter (q & B) r_work=0.1204 r_free=0.1363 | n_water=857 | time (s): 4.600 (total time: 114.360) Compute maps r_work=0.1204 r_free=0.1363 | n_water=857 | time (s): 1.840 (total time: 116.200) Filter (map) r_work=0.1227 r_free=0.1367 | n_water=734 | time (s): 4.390 (total time: 120.590) Find peaks r_work=0.1227 r_free=0.1367 | n_water=734 | time (s): 0.870 (total time: 121.460) Add new water r_work=0.1241 r_free=0.1388 | n_water=951 | time (s): 4.390 (total time: 125.850) Refine new water occ: r_work=0.1202 r_free=0.1352 adp: r_work=0.1202 r_free=0.1352 occ: r_work=0.1200 r_free=0.1349 adp: r_work=0.1200 r_free=0.1349 occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1198 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1346 r_work=0.1198 r_free=0.1346 | n_water=951 | time (s): 205.920 (total time: 331.770) Filter (q & B) r_work=0.1202 r_free=0.1354 | n_water=885 | time (s): 4.390 (total time: 336.160) Filter (dist only) r_work=0.1203 r_free=0.1354 | n_water=882 | time (s): 111.140 (total time: 447.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569561 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.627988 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1359 0.0154 0.037 1.1 5.5 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.59 1.54 1.746 13.936 14.628 3.762 12.06 13.60 1.54 1.826 13.900 14.628 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 67.08 14.72 0.90 518 3268 Protein: 5.57 29.44 10.47 0.90 0 2902 Water: 5.96 67.08 28.70 N/A 518 364 Other: 13.85 23.50 18.67 N/A 0 2 Chain A: 5.64 53.63 12.36 N/A 0 1623 Chain B: 5.57 65.63 12.17 N/A 0 1645 Chain S: 5.96 67.08 30.22 N/A 518 0 Histogram: Values Number of atoms 5.57 - 11.72 2150 11.72 - 17.87 753 17.87 - 24.02 289 24.02 - 30.17 219 30.17 - 36.32 166 36.32 - 42.47 117 42.47 - 48.62 60 48.62 - 54.78 26 54.78 - 60.93 4 60.93 - 67.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1360 r_work=0.1207 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1356 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757469 | | target function (ml) not normalized (work): 703747.611433 | | target function (ml) not normalized (free): 14728.981006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1357 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1420 0.1419 0.1473 n_refl.: 191134 remove outliers: r(all,work,free)=0.1420 0.1419 0.1473 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1412 0.1411 0.1468 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1357 n_refl.: 191134 remove outliers: r(all,work,free)=0.1206 0.1203 0.1357 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3823 360.150 325.432 0.413 0.948 0.225 13.296-10.522 98.02 98 1 0.2526 487.077 462.209 0.693 0.950 0.162 10.503-8.327 98.35 176 3 0.2232 502.881 493.237 0.855 0.950 0.138 8.318-6.595 100.00 360 8 0.2212 375.610 371.116 0.887 0.950 0.105 6.588-5.215 100.00 711 7 0.1963 345.148 335.374 0.883 0.950 0.095 5.214-4.128 98.38 1367 28 0.1236 504.847 499.148 0.973 0.950 0.090 4.126-3.266 94.74 2603 46 0.1179 460.195 453.068 1.034 0.950 0.000 3.266-2.585 99.86 5447 97 0.1128 310.436 307.008 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0950 234.207 231.690 1.031 0.949 0.000 2.046-1.619 99.39 21536 464 0.0911 138.615 137.314 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0968 74.622 73.927 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.032 38.372 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1290 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1357 | n_water=882 | time (s): 2.910 (total time: 2.910) Filter (dist) r_work=0.1203 r_free=0.1359 | n_water=880 | time (s): 110.710 (total time: 113.620) Filter (q & B) r_work=0.1203 r_free=0.1358 | n_water=874 | time (s): 4.410 (total time: 118.030) Compute maps r_work=0.1203 r_free=0.1358 | n_water=874 | time (s): 2.580 (total time: 120.610) Filter (map) r_work=0.1225 r_free=0.1363 | n_water=746 | time (s): 4.840 (total time: 125.450) Find peaks r_work=0.1225 r_free=0.1363 | n_water=746 | time (s): 0.670 (total time: 126.120) Add new water r_work=0.1237 r_free=0.1379 | n_water=974 | time (s): 4.800 (total time: 130.920) Refine new water occ: r_work=0.1200 r_free=0.1345 adp: r_work=0.1201 r_free=0.1345 occ: r_work=0.1198 r_free=0.1345 adp: r_work=0.1198 r_free=0.1345 occ: r_work=0.1196 r_free=0.1344 adp: r_work=0.1196 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1344 r_work=0.1196 r_free=0.1344 | n_water=974 | time (s): 249.510 (total time: 380.430) Filter (q & B) r_work=0.1201 r_free=0.1351 | n_water=889 | time (s): 5.450 (total time: 385.880) Filter (dist only) r_work=0.1202 r_free=0.1350 | n_water=887 | time (s): 115.110 (total time: 500.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529266 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.742636 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1357 0.0152 0.038 1.1 7.5 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.57 1.52 1.717 13.836 13.743 3.759 12.09 13.62 1.54 1.770 13.813 13.743 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 67.12 14.65 0.87 523 3268 Protein: 5.59 28.48 10.41 0.87 0 2902 Water: 6.05 67.12 28.50 N/A 523 364 Other: 13.87 22.25 18.06 N/A 0 2 Chain A: 5.62 53.25 12.27 N/A 0 1623 Chain B: 5.59 64.52 12.09 N/A 0 1645 Chain S: 6.05 67.12 30.08 N/A 523 0 Histogram: Values Number of atoms 5.59 - 11.75 2163 11.75 - 17.90 752 17.90 - 24.05 278 24.05 - 30.20 220 30.20 - 36.36 172 36.36 - 42.51 119 42.51 - 48.66 58 48.66 - 54.81 24 54.81 - 60.97 3 60.97 - 67.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1362 r_work=0.1209 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1363 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1207 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757698 | | target function (ml) not normalized (work): 703786.776348 | | target function (ml) not normalized (free): 14734.527514 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1207 0.1360 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1420 0.1419 0.1477 n_refl.: 191133 remove outliers: r(all,work,free)=0.1420 0.1419 0.1477 n_refl.: 191133 overall B=-0.23 to atoms: r(all,work,free)=0.1383 0.1382 0.1455 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1206 0.1358 n_refl.: 191133 remove outliers: r(all,work,free)=0.1209 0.1206 0.1358 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3757 360.960 321.941 0.415 0.948 0.212 13.296-10.522 98.02 98 1 0.2498 487.077 466.017 0.711 0.950 0.147 10.503-8.327 98.35 176 3 0.2263 502.881 493.724 0.874 0.950 0.120 8.318-6.595 100.00 360 8 0.2236 375.610 370.758 0.910 0.950 0.104 6.588-5.215 100.00 711 7 0.1964 345.148 335.239 0.904 0.950 0.085 5.214-4.128 98.38 1367 28 0.1254 504.847 499.117 0.998 0.950 0.080 4.126-3.266 94.74 2603 46 0.1185 460.195 453.092 1.060 0.951 0.005 3.266-2.585 99.86 5447 97 0.1137 310.436 307.043 1.043 0.950 0.000 2.585-2.046 97.45 10613 204 0.0956 234.207 231.647 1.050 0.950 0.000 2.046-1.619 99.39 21536 464 0.0910 138.615 137.332 1.067 0.950 0.000 1.619-1.281 98.00 42464 925 0.0965 74.622 73.933 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.032 38.366 1.026 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0497 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1358 | n_water=887 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1206 r_free=0.1359 | n_water=885 | time (s): 113.420 (total time: 115.920) Filter (q & B) r_work=0.1207 r_free=0.1359 | n_water=873 | time (s): 5.450 (total time: 121.370) Compute maps r_work=0.1207 r_free=0.1359 | n_water=873 | time (s): 2.520 (total time: 123.890) Filter (map) r_work=0.1231 r_free=0.1370 | n_water=747 | time (s): 5.390 (total time: 129.280) Find peaks r_work=0.1231 r_free=0.1370 | n_water=747 | time (s): 0.840 (total time: 130.120) Add new water r_work=0.1242 r_free=0.1391 | n_water=970 | time (s): 5.390 (total time: 135.510) Refine new water occ: r_work=0.1204 r_free=0.1351 adp: r_work=0.1204 r_free=0.1351 occ: r_work=0.1202 r_free=0.1349 adp: r_work=0.1202 r_free=0.1349 occ: r_work=0.1200 r_free=0.1348 adp: r_work=0.1200 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1348 r_work=0.1200 r_free=0.1348 | n_water=970 | time (s): 307.900 (total time: 443.410) Filter (q & B) r_work=0.1205 r_free=0.1349 | n_water=894 | time (s): 5.520 (total time: 448.930) Filter (dist only) r_work=0.1205 r_free=0.1348 | n_water=893 | time (s): 118.110 (total time: 567.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538265 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.852036 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 0.1208 0.1349 0.0142 0.038 1.1 5.6 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.49 1.42 1.695 13.566 13.852 3.759 12.08 13.54 1.46 1.714 13.556 13.852 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 66.96 14.41 0.87 529 3268 Protein: 5.39 27.98 10.20 0.87 0 2902 Water: 5.76 66.96 28.08 N/A 529 364 Other: 13.68 22.06 17.87 N/A 0 2 Chain A: 5.46 52.64 12.01 N/A 0 1623 Chain B: 5.39 63.27 11.85 N/A 0 1645 Chain S: 5.76 66.96 29.71 N/A 529 0 Histogram: Values Number of atoms 5.39 - 11.54 2169 11.54 - 17.70 764 17.70 - 23.86 269 23.86 - 30.02 227 30.02 - 36.17 172 36.17 - 42.33 112 42.33 - 48.49 56 48.49 - 54.64 24 54.64 - 60.80 2 60.80 - 66.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1354 r_work=0.1208 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1354 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1349 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756561 | | target function (ml) not normalized (work): 703570.129611 | | target function (ml) not normalized (free): 14728.846893 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1349 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1376 0.1375 0.1453 n_refl.: 191132 remove outliers: r(all,work,free)=0.1376 0.1375 0.1453 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1376 0.1375 0.1453 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1336 n_refl.: 191132 remove outliers: r(all,work,free)=0.1199 0.1196 0.1336 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 0.3807 360.960 326.850 0.397 0.993 0.199 13.296-10.522 96.04 96 1 0.2357 480.397 457.341 0.687 0.994 0.145 10.503-8.327 98.35 176 3 0.2270 502.881 492.555 0.845 0.995 0.111 8.318-6.595 100.00 360 8 0.2216 375.610 370.635 0.881 0.994 0.095 6.588-5.215 100.00 711 7 0.1972 345.148 334.658 0.874 0.994 0.073 5.214-4.128 98.38 1367 28 0.1268 504.847 498.633 0.967 0.995 0.057 4.126-3.266 94.74 2603 46 0.1188 460.195 452.462 1.029 0.995 0.000 3.266-2.585 99.86 5447 97 0.1134 310.436 306.682 1.013 0.994 0.000 2.585-2.046 97.45 10613 204 0.0959 234.207 231.538 1.022 0.993 0.000 2.046-1.619 99.39 21536 464 0.0906 138.615 137.222 1.039 0.991 0.000 1.619-1.281 98.00 42464 925 0.0945 74.622 73.974 1.032 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.032 38.344 1.004 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.1429 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1336 | n_water=893 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1196 r_free=0.1337 | n_water=892 | time (s): 105.480 (total time: 108.140) Filter (q & B) r_work=0.1196 r_free=0.1336 | n_water=884 | time (s): 4.720 (total time: 112.860) Compute maps r_work=0.1196 r_free=0.1336 | n_water=884 | time (s): 2.250 (total time: 115.110) Filter (map) r_work=0.1220 r_free=0.1359 | n_water=764 | time (s): 4.660 (total time: 119.770) Find peaks r_work=0.1220 r_free=0.1359 | n_water=764 | time (s): 0.760 (total time: 120.530) Add new water r_work=0.1228 r_free=0.1370 | n_water=983 | time (s): 5.000 (total time: 125.530) Refine new water occ: r_work=0.1193 r_free=0.1333 adp: r_work=0.1193 r_free=0.1333 occ: r_work=0.1191 r_free=0.1333 adp: r_work=0.1191 r_free=0.1333 occ: r_work=0.1190 r_free=0.1333 adp: r_work=0.1190 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1333 r_work=0.1190 r_free=0.1333 | n_water=983 | time (s): 244.030 (total time: 369.560) Filter (q & B) r_work=0.1194 r_free=0.1337 | n_water=903 | time (s): 5.780 (total time: 375.340) Filter (dist only) r_work=0.1194 r_free=0.1337 | n_water=902 | time (s): 120.480 (total time: 495.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529016 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.463001 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 0.1340 0.0143 0.038 1.1 7.2 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.40 1.43 1.661 13.564 14.463 3.755 11.96 13.43 1.47 1.662 13.564 14.463 3.752 Individual atomic B min max mean iso aniso Overall: 5.44 67.06 14.45 0.87 538 3268 Protein: 5.44 27.91 10.21 0.87 0 2902 Water: 5.79 67.06 28.08 N/A 538 364 Other: 13.72 22.02 17.87 N/A 0 2 Chain A: 5.51 52.22 12.00 N/A 0 1623 Chain B: 5.44 62.18 11.84 N/A 0 1645 Chain S: 5.79 67.06 29.84 N/A 538 0 Histogram: Values Number of atoms 5.44 - 11.60 2180 11.60 - 17.76 773 17.76 - 23.92 260 23.92 - 30.09 218 30.09 - 36.25 174 36.25 - 42.41 118 42.41 - 48.57 58 48.57 - 54.74 21 54.74 - 60.90 2 60.90 - 67.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1343 r_work=0.1196 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1343 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1344 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752126 | | target function (ml) not normalized (work): 702731.898418 | | target function (ml) not normalized (free): 14722.160062 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1344 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1380 0.1378 0.1472 n_refl.: 191130 remove outliers: r(all,work,free)=0.1380 0.1378 0.1472 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1380 0.1378 0.1472 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1344 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1344 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 0.3775 360.960 325.424 0.392 0.975 0.195 13.296-10.522 96.04 96 1 0.2356 480.397 462.576 0.686 0.977 0.130 10.503-8.327 98.35 176 3 0.2277 502.881 493.200 0.841 0.977 0.099 8.318-6.595 100.00 360 8 0.2217 375.610 370.778 0.875 0.977 0.088 6.588-5.215 100.00 711 7 0.1967 345.148 334.880 0.870 0.978 0.080 5.214-4.128 98.38 1367 28 0.1260 504.847 498.691 0.962 0.978 0.057 4.126-3.266 94.74 2603 46 0.1183 460.195 452.813 1.023 0.980 0.000 3.266-2.585 99.86 5447 97 0.1140 310.436 306.698 1.006 0.980 0.000 2.585-2.046 97.45 10613 204 0.0960 234.207 231.560 1.012 0.982 0.000 2.046-1.619 99.39 21536 464 0.0905 138.615 137.256 1.026 0.986 0.000 1.619-1.281 98.00 42464 925 0.0942 74.622 73.974 1.013 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.032 38.331 0.977 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0789 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1344 After: r_work=0.1196 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1344 | n_water=902 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1196 r_free=0.1344 | n_water=902 | time (s): 112.880 (total time: 115.440) Filter (q & B) r_work=0.1196 r_free=0.1343 | n_water=888 | time (s): 5.470 (total time: 120.910) Compute maps r_work=0.1196 r_free=0.1343 | n_water=888 | time (s): 2.340 (total time: 123.250) Filter (map) r_work=0.1221 r_free=0.1364 | n_water=766 | time (s): 4.850 (total time: 128.100) Find peaks r_work=0.1221 r_free=0.1364 | n_water=766 | time (s): 0.780 (total time: 128.880) Add new water r_work=0.1229 r_free=0.1374 | n_water=983 | time (s): 3.960 (total time: 132.840) Refine new water occ: r_work=0.1194 r_free=0.1338 adp: r_work=0.1194 r_free=0.1337 occ: r_work=0.1192 r_free=0.1337 adp: r_work=0.1192 r_free=0.1337 occ: r_work=0.1191 r_free=0.1338 adp: r_work=0.1191 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1338 r_work=0.1191 r_free=0.1338 | n_water=983 | time (s): 271.350 (total time: 404.190) Filter (q & B) r_work=0.1195 r_free=0.1341 | n_water=901 | time (s): 4.970 (total time: 409.160) Filter (dist only) r_work=0.1195 r_free=0.1341 | n_water=900 | time (s): 119.900 (total time: 529.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557024 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.422535 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 0.1196 0.1342 0.0146 0.038 1.1 7.7 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.42 1.46 1.662 13.555 14.423 3.754 11.96 13.44 1.48 1.654 13.556 14.423 3.752 Individual atomic B min max mean iso aniso Overall: 5.45 67.07 14.42 0.86 536 3268 Protein: 5.45 27.91 10.24 0.86 0 2902 Water: 5.89 67.07 27.92 N/A 536 364 Other: 13.74 22.03 17.89 N/A 0 2 Chain A: 5.52 52.10 12.00 N/A 0 1623 Chain B: 5.45 61.84 11.85 N/A 0 1645 Chain S: 5.89 67.07 29.68 N/A 536 0 Histogram: Values Number of atoms 5.45 - 11.61 2178 11.61 - 17.77 778 17.77 - 23.94 268 23.94 - 30.10 213 30.10 - 36.26 172 36.26 - 42.42 118 42.42 - 48.58 53 48.58 - 54.75 20 54.75 - 60.91 2 60.91 - 67.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1344 r_work=0.1196 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1344 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1344 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752325 | | target function (ml) not normalized (work): 702769.152560 | | target function (ml) not normalized (free): 14716.764965 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1383 0.1429 5.7012 5.7735| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1343 5.081 5.1694| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1168 4.654 4.7369| | 4: 2.04 - 1.85 1.00 7170 155 0.0893 0.1052 4.3857 4.5637| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.0970 4.145 4.2344| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1049 3.9407 4.0573| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0999 3.7951 3.9441| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1323 3.6962 3.9001| | 9: 1.47 - 1.41 0.98 6938 155 0.0919 0.1101 3.6159 3.7348| | 10: 1.41 - 1.36 0.99 7022 150 0.0969 0.1177 3.5488 3.6723| | 11: 1.36 - 1.32 0.99 6997 151 0.0988 0.1120 3.4775 3.5776| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1128 3.4551 3.5776| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1250 3.4348 3.5668| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1597 3.4306 3.6797| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1246 3.4471 3.4928| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1558 3.4639 3.6582| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1231 3.4326 3.4437| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1697 3.4381 3.5279| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1737 3.4179 3.5934| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1571 3.409 3.4319| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2124 3.4177 3.5038| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1960 3.4128 3.4153| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2020 3.4331 3.4847| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2253 3.4353 3.5097| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2516 3.4486 3.5247| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2867 3.4153 3.4228| | 27: 0.99 - 0.98 0.94 6647 131 0.3039 0.2795 3.468 3.3941| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.69 1.00 0.97 11290.92| | 2: 2.94 - 2.33 7339 128 0.93 12.85 0.99 0.97 5148.72| | 3: 2.33 - 2.04 6939 150 0.96 7.58 1.01 0.97 1683.86| | 4: 2.04 - 1.85 7170 155 0.96 7.51 1.00 0.97 981.27| | 5: 1.85 - 1.72 7113 159 0.96 7.95 1.00 0.97 621.55| | 6: 1.72 - 1.62 7102 142 0.96 7.92 1.00 0.98 436.08| | 7: 1.62 - 1.54 7104 148 0.96 8.14 1.01 0.99 335.76| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.99 277.50| | 9: 1.47 - 1.41 6938 155 0.96 8.37 1.00 0.99 227.84| | 10: 1.41 - 1.36 7022 150 0.96 8.77 1.00 0.98 198.83| | 11: 1.36 - 1.32 6997 151 0.96 8.80 0.99 0.97 171.59| | 12: 1.32 - 1.28 6975 149 0.96 8.90 0.98 0.96 158.66| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.98 157.13| | 14: 1.25 - 1.22 7015 112 0.95 10.69 1.02 0.98 162.83| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.99 166.80| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.98 160.44| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.98 153.93| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.96 147.00| | 19: 1.12 - 1.10 6948 106 0.93 14.08 1.00 0.96 150.18| | 20: 1.10 - 1.08 6884 147 0.92 15.15 1.00 0.95 149.36| | 21: 1.08 - 1.07 6852 152 0.91 16.60 1.00 0.94 152.81| | 22: 1.07 - 1.05 6836 135 0.89 18.25 0.99 0.94 154.66| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.93 164.46| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.94 178.71| | 25: 1.02 - 1.01 6552 130 0.83 25.08 0.97 0.91 181.51| | 26: 1.01 - 0.99 6767 158 0.81 26.54 0.98 0.89 175.93| | 27: 0.99 - 0.98 6647 131 0.82 26.16 0.98 0.88 160.28| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 147.00 max = 11290.92 mean = 926.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.23| |phase err.(test): min = 0.00 max = 88.81 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1344 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1388 0.1386 0.1480 n_refl.: 191130 remove outliers: r(all,work,free)=0.1388 0.1386 0.1480 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1388 0.1386 0.1480 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1342 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1342 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 0.3809 360.960 325.639 0.378 0.995 0.191 13.296-10.522 96.04 96 1 0.2376 480.397 462.608 0.663 0.996 0.122 10.503-8.327 98.35 176 3 0.2290 502.881 492.408 0.816 0.997 0.093 8.318-6.595 100.00 360 8 0.2225 375.610 370.798 0.852 0.997 0.088 6.588-5.215 100.00 711 7 0.1973 345.148 334.647 0.847 0.997 0.082 5.214-4.128 98.38 1367 28 0.1267 504.847 498.849 0.936 0.998 0.054 4.126-3.266 94.74 2603 46 0.1184 460.195 452.885 0.997 1.000 0.005 3.266-2.585 99.86 5447 97 0.1138 310.436 306.747 0.980 1.001 0.000 2.585-2.046 97.45 10613 204 0.0961 234.207 231.581 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0904 138.615 137.251 1.000 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.622 73.975 0.988 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.032 38.327 0.954 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0461 ================= 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 : 0.2036 0.2039 0.082 5.169 5.2 78.0 14.6 805 0.000 1_bss: 0.1802 0.1977 0.082 5.169 5.2 78.0 14.6 805 0.000 1_settarget: 0.1802 0.1977 0.082 5.169 5.2 78.0 14.6 805 0.000 1_nqh: 0.1802 0.1977 0.082 5.169 5.2 78.0 14.6 805 0.000 1_weight: 0.1802 0.1977 0.082 5.169 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1502 0.038 1.154 5.2 78.0 14.6 805 0.154 1_adp: 0.1296 0.1570 0.038 1.154 5.3 73.0 15.0 805 0.154 1_regHadp: 0.1295 0.1565 0.038 1.154 5.3 73.0 15.0 805 0.154 1_occ: 0.1281 0.1556 0.038 1.154 5.3 73.0 15.0 805 0.154 2_bss: 0.1273 0.1547 0.038 1.154 5.4 73.2 15.1 805 0.154 2_settarget: 0.1273 0.1547 0.038 1.154 5.4 73.2 15.1 805 0.154 2_updatecdl: 0.1273 0.1547 0.038 1.166 5.4 73.2 15.1 805 0.154 2_nqh: 0.1273 0.1547 0.038 1.166 5.4 73.2 15.1 805 0.154 2_sol: 0.1272 0.1516 0.038 1.166 5.4 73.2 16.2 873 n/a 2_weight: 0.1272 0.1516 0.038 1.166 5.4 73.2 16.2 873 n/a 2_xyzrec: 0.1256 0.1537 0.040 1.131 5.4 73.2 16.2 873 n/a 2_adp: 0.1236 0.1527 0.040 1.131 5.4 73.2 16.3 873 n/a 2_regHadp: 0.1236 0.1528 0.040 1.131 5.4 73.2 16.3 873 n/a 2_occ: 0.1229 0.1518 0.040 1.131 5.4 73.2 16.3 873 n/a 3_bss: 0.1235 0.1526 0.040 1.131 5.4 73.2 16.3 873 n/a 3_settarget: 0.1235 0.1526 0.040 1.131 5.4 73.2 16.3 873 n/a 3_updatecdl: 0.1235 0.1526 0.040 1.137 5.4 73.2 16.3 873 n/a 3_nqh: 0.1235 0.1526 0.040 1.137 5.4 73.2 16.3 873 n/a 3_sol: 0.1254 0.1526 0.040 1.137 5.4 68.2 15.4 859 n/a 3_weight: 0.1254 0.1526 0.040 1.137 5.4 68.2 15.4 859 n/a 3_xyzrec: 0.1247 0.1448 0.035 1.094 5.4 68.2 15.4 859 n/a 3_adp: 0.1239 0.1409 0.035 1.094 5.5 67.9 15.2 859 n/a 3_regHadp: 0.1240 0.1410 0.035 1.094 5.5 67.9 15.2 859 n/a 3_occ: 0.1234 0.1399 0.035 1.094 5.5 67.9 15.2 859 n/a 4_bss: 0.1229 0.1395 0.035 1.094 5.5 67.9 15.2 859 n/a 4_settarget: 0.1229 0.1395 0.035 1.094 5.5 67.9 15.2 859 n/a 4_updatecdl: 0.1229 0.1395 0.035 1.099 5.5 67.9 15.2 859 n/a 4_nqh: 0.1229 0.1395 0.035 1.099 5.5 67.9 15.2 859 n/a 4_sol: 0.1216 0.1373 0.035 1.099 5.5 67.9 14.9 835 n/a 4_weight: 0.1216 0.1373 0.035 1.099 5.5 67.9 14.9 835 n/a 4_xyzrec: 0.1212 0.1375 0.035 1.132 5.5 67.9 14.9 835 n/a 4_adp: 0.1209 0.1368 0.035 1.132 5.5 67.0 14.7 835 n/a 4_regHadp: 0.1209 0.1369 0.035 1.132 5.5 67.0 14.7 835 n/a 4_occ: 0.1206 0.1363 0.035 1.132 5.5 67.0 14.7 835 n/a 5_bss: 0.1205 0.1361 0.035 1.132 5.5 67.0 14.7 835 n/a 5_settarget: 0.1205 0.1361 0.035 1.132 5.5 67.0 14.7 835 n/a 5_updatecdl: 0.1205 0.1361 0.035 1.133 5.5 67.0 14.7 835 n/a 5_nqh: 0.1205 0.1361 0.035 1.133 5.5 67.0 14.7 835 n/a 5_sol: 0.1201 0.1355 0.035 1.133 5.5 67.0 14.9 869 n/a 5_weight: 0.1201 0.1355 0.035 1.133 5.5 67.0 14.9 869 n/a 5_xyzrec: 0.1204 0.1361 0.037 1.130 5.5 67.0 14.9 869 n/a 5_adp: 0.1207 0.1368 0.037 1.130 5.6 67.1 14.8 869 n/a 5_regHadp: 0.1207 0.1368 0.037 1.130 5.6 67.1 14.8 869 n/a 5_occ: 0.1205 0.1367 0.037 1.130 5.6 67.1 14.8 869 n/a 6_bss: 0.1204 0.1362 0.037 1.130 5.5 67.0 14.8 869 n/a 6_settarget: 0.1204 0.1362 0.037 1.130 5.5 67.0 14.8 869 n/a 6_updatecdl: 0.1204 0.1362 0.037 1.130 5.5 67.0 14.8 869 n/a 6_nqh: 0.1204 0.1362 0.037 1.130 5.5 67.0 14.8 869 n/a 6_sol: 0.1203 0.1354 0.037 1.130 5.5 67.0 14.8 882 n/a 6_weight: 0.1203 0.1354 0.037 1.130 5.5 67.0 14.8 882 n/a 6_xyzrec: 0.1205 0.1359 0.037 1.129 5.5 67.0 14.8 882 n/a 6_adp: 0.1206 0.1360 0.037 1.129 5.6 67.1 14.7 882 n/a 6_regHadp: 0.1207 0.1360 0.037 1.129 5.6 67.1 14.7 882 n/a 6_occ: 0.1204 0.1356 0.037 1.129 5.6 67.1 14.7 882 n/a 7_bss: 0.1203 0.1357 0.037 1.129 5.5 67.0 14.7 882 n/a 7_settarget: 0.1203 0.1357 0.037 1.129 5.5 67.0 14.7 882 n/a 7_updatecdl: 0.1203 0.1357 0.037 1.129 5.5 67.0 14.7 882 n/a 7_nqh: 0.1203 0.1357 0.037 1.129 5.5 67.0 14.7 882 n/a 7_sol: 0.1202 0.1350 0.037 1.129 5.5 67.0 14.7 887 n/a 7_weight: 0.1202 0.1350 0.037 1.129 5.5 67.0 14.7 887 n/a 7_xyzrec: 0.1206 0.1357 0.038 1.126 5.5 67.0 14.7 887 n/a 7_adp: 0.1209 0.1362 0.038 1.126 5.6 67.1 14.6 887 n/a 7_regHadp: 0.1209 0.1363 0.038 1.126 5.6 67.1 14.6 887 n/a 7_occ: 0.1207 0.1360 0.038 1.126 5.6 67.1 14.6 887 n/a 8_bss: 0.1206 0.1358 0.038 1.126 5.4 66.9 14.4 887 n/a 8_settarget: 0.1206 0.1358 0.038 1.126 5.4 66.9 14.4 887 n/a 8_updatecdl: 0.1206 0.1358 0.038 1.126 5.4 66.9 14.4 887 n/a 8_nqh: 0.1206 0.1358 0.038 1.126 5.4 66.9 14.4 887 n/a 8_sol: 0.1205 0.1348 0.038 1.126 5.4 66.9 14.4 893 n/a 8_weight: 0.1205 0.1348 0.038 1.126 5.4 66.9 14.4 893 n/a 8_xyzrec: 0.1208 0.1349 0.038 1.125 5.4 66.9 14.4 893 n/a 8_adp: 0.1208 0.1354 0.038 1.125 5.4 67.0 14.4 893 n/a 8_regHadp: 0.1208 0.1354 0.038 1.125 5.4 67.0 14.4 893 n/a 8_occ: 0.1206 0.1349 0.038 1.125 5.4 67.0 14.4 893 n/a 9_bss: 0.1196 0.1336 0.038 1.125 5.4 67.0 14.4 893 n/a 9_settarget: 0.1196 0.1336 0.038 1.125 5.4 67.0 14.4 893 n/a 9_updatecdl: 0.1196 0.1336 0.038 1.125 5.4 67.0 14.4 893 n/a 9_nqh: 0.1196 0.1336 0.038 1.125 5.4 67.0 14.4 893 n/a 9_sol: 0.1194 0.1337 0.038 1.125 5.4 67.0 14.5 902 n/a 9_weight: 0.1194 0.1337 0.038 1.125 5.4 67.0 14.5 902 n/a 9_xyzrec: 0.1197 0.1340 0.038 1.113 5.4 67.0 14.5 902 n/a 9_adp: 0.1196 0.1343 0.038 1.113 5.4 67.1 14.5 902 n/a 9_regHadp: 0.1196 0.1343 0.038 1.113 5.4 67.1 14.5 902 n/a 9_occ: 0.1195 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_bss: 0.1195 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_settarget: 0.1195 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_updatecdl: 0.1195 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_setrh: 0.1196 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_nqh: 0.1196 0.1344 0.038 1.113 5.4 67.1 14.5 902 n/a 10_sol: 0.1195 0.1341 0.038 1.113 5.4 67.1 14.4 900 n/a 10_weight: 0.1195 0.1341 0.038 1.113 5.4 67.1 14.4 900 n/a 10_xyzrec: 0.1196 0.1342 0.038 1.143 5.4 67.1 14.4 900 n/a 10_adp: 0.1196 0.1344 0.038 1.143 5.5 67.1 14.4 900 n/a 10_regHadp: 0.1196 0.1344 0.038 1.143 5.5 67.1 14.4 900 n/a 10_occ: 0.1196 0.1344 0.038 1.143 5.5 67.1 14.4 900 n/a end: 0.1195 0.1342 0.038 1.143 5.5 67.1 14.4 900 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7691479_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7691479_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0900 Refinement macro-cycles (run) : 12219.5300 Write final files (write_after_run_outputs) : 162.6700 Total : 12389.2900 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:41 PST -0800 (1736736221.21 s) Start R-work = 0.1802, R-free = 0.1977 Final R-work = 0.1195, R-free = 0.1342 =============================================================================== Job complete usr+sys time: 12661.39 seconds wall clock time: 212 minutes 3.21 seconds (12723.21 seconds total)