Starting phenix.refine on Fri Jan 3 15:25:45 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, 5SY4.mtz Found model, 5SY4_noAltloc.updated.pdb Found phil, params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "params_restrained.eff" default_phil = "params_restrained.eff" miller_array { file = "5SY4.mtz" } default_miller_array = "5SY4.mtz" model { file = "5SY4_noAltloc.updated.pdb" } default_model = "5SY4_noAltloc.updated.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 nproc = 60 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6310 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2941 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 2941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2941 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Classifications: {'water': 207} Link IDs: {None: 206} Chain: "B" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Classifications: {'water': 219} Link IDs: {None: 218} Residues with excluded nonbonded symmetry interactions: 123 residue: pdb=" N LYS A 31 " occ=0.59 ... (20 atoms not shown) pdb=" HZ3 LYS A 31 " occ=0.59 residue: pdb=" N THR A 33 " occ=0.64 ... (12 atoms not shown) pdb="HG23 THR A 33 " occ=0.64 residue: pdb=" N SER A 36 " occ=0.58 ... (9 atoms not shown) pdb=" HG SER A 36 " occ=0.58 residue: pdb=" N SER A 39 " occ=0.65 ... (9 atoms not shown) pdb=" HG SER A 39 " occ=0.65 residue: pdb=" N ASN A 42 " occ=0.55 ... (12 atoms not shown) pdb="HD22 ASN A 42 " occ=0.55 residue: pdb=" N LEU A 43 " occ=0.54 ... (17 atoms not shown) pdb="HD23 LEU A 43 " occ=0.54 residue: pdb=" N ALA A 44 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 44 " occ=0.50 residue: pdb=" N ILE A 45 " occ=0.50 ... (17 atoms not shown) pdb="HD13 ILE A 45 " occ=0.50 residue: pdb=" N LYS A 52 " occ=0.51 ... (20 atoms not shown) pdb=" HZ3 LYS A 52 " occ=0.51 residue: pdb=" N LEU A 53 " occ=0.67 ... (17 atoms not shown) pdb="HD23 LEU A 53 " occ=0.67 residue: pdb=" N VAL A 60 " occ=0.59 ... (14 atoms not shown) pdb="HG23 VAL A 60 " occ=0.59 residue: pdb=" N GLU A 61 " occ=0.59 ... (13 atoms not shown) pdb=" HG3 GLU A 61 " occ=0.59 ... (remaining 111 not shown) Time building chain proxies: 1.25, per 1000 atoms: 0.20 Number of scatterers: 6310 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 978 8.00 N 488 7.00 C 1850 6.00 H 2980 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.46 Conformation dependent library (CDL) restraints added in 159.7 milliseconds Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 2972 1.05 - 1.27: 481 1.27 - 1.50: 1300 1.50 - 1.72: 1161 1.72 - 1.95: 16 Bond restraints: 5930 Sorted by residual: bond pdb=" C LYS A 52 " pdb=" N LEU A 53 " ideal model delta sigma weight residual 1.329 1.469 -0.140 1.38e-02 5.25e+03 1.03e+02 bond pdb=" C ILE A 76 " pdb=" N LYS A 77 " ideal model delta sigma weight residual 1.335 1.446 -0.111 1.36e-02 5.41e+03 6.68e+01 bond pdb=" CZ ARG A 175 " pdb=" NH1 ARG A 175 " ideal model delta sigma weight residual 1.323 1.417 -0.094 1.40e-02 5.10e+03 4.50e+01 bond pdb=" CD GLU A 90 " pdb=" OE2 GLU A 90 " ideal model delta sigma weight residual 1.249 1.361 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CG MET B 124 " pdb=" SD MET B 124 " ideal model delta sigma weight residual 1.803 1.949 -0.146 2.50e-02 1.60e+03 3.43e+01 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 10544 3.24 - 6.47: 229 6.47 - 9.71: 22 9.71 - 12.95: 4 12.95 - 16.18: 1 Bond angle restraints: 10800 Sorted by residual: angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" C GLU A 196 " ideal model delta sigma weight residual 111.00 127.18 -16.18 2.80e+00 1.28e-01 3.34e+01 angle pdb=" CA ASP A 163 " pdb=" CB ASP A 163 " pdb=" CG ASP A 163 " ideal model delta sigma weight residual 112.60 118.06 -5.46 1.00e+00 1.00e+00 2.98e+01 angle pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " pdb=" CG ASP B 163 " ideal model delta sigma weight residual 112.60 117.82 -5.22 1.00e+00 1.00e+00 2.72e+01 angle pdb=" N GLN B 156 " pdb=" CA GLN B 156 " pdb=" C GLN B 156 " ideal model delta sigma weight residual 113.12 119.02 -5.90 1.25e+00 6.40e-01 2.23e+01 angle pdb=" N GLN A 156 " pdb=" CA GLN A 156 " pdb=" C GLN A 156 " ideal model delta sigma weight residual 113.12 118.96 -5.84 1.25e+00 6.40e-01 2.18e+01 ... (remaining 10795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 1853 17.10 - 34.20: 124 34.20 - 51.30: 49 51.30 - 68.41: 21 68.41 - 85.51: 5 Dihedral angle restraints: 2052 sinusoidal: 1532 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 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -158.72 -21.28 0 5.00e+00 4.00e-02 1.81e+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 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 2049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.268: 474 0.268 - 0.536: 15 0.536 - 0.804: 0 0.804 - 1.072: 0 1.072 - 1.341: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.25 -1.34 2.00e-01 2.50e+01 4.49e+01 chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.31 -1.28 2.00e-01 2.50e+01 4.08e+01 chirality pdb=" CA GLU A 196 " pdb=" N GLU A 196 " pdb=" C GLU A 196 " pdb=" CB GLU A 196 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.071 2.00e-02 2.50e+03 3.26e-02 3.19e+01 pdb=" CG PHE A 164 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.067 2.00e-02 2.50e+03 3.18e-02 3.03e+01 pdb=" CG PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 196 " -0.023 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" CD GLU A 196 " 0.076 2.00e-02 2.50e+03 pdb=" OE1 GLU A 196 " -0.028 2.00e-02 2.50e+03 pdb=" OE2 GLU A 196 " -0.025 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 814 2.24 - 2.83: 14440 2.83 - 3.42: 18928 3.42 - 4.01: 27755 4.01 - 4.60: 40935 Nonbonded interactions: 102872 Sorted by model distance: nonbonded pdb=" OE1 GLN B 94 " pdb="HH11 ARG B 97 " model vdw 1.648 1.850 nonbonded pdb=" O HOH B 344 " pdb=" O HOH B 491 " model vdw 1.652 2.200 nonbonded pdb=" O HOH A 504 " pdb=" O HOH B 412 " model vdw sym.op. 1.688 2.200 -x+1/2,-y+1,z-1/2 nonbonded pdb=" OE1 GLN A 184 " pdb=" O HOH A 388 " model vdw 1.722 2.200 nonbonded pdb=" HE2 HIS A 96 " pdb=" O HOH A 310 " model vdw 1.763 1.850 ... (remaining 102867 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 978 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2980 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 = 6310 n_use_u_iso = 2980 n_use_u_aniso = 3330 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 = 6310 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6310 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2980 aniso = 3330) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1696 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 = 5 max_number_of_iterations = 100 nproc = 60 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "5SY4_noAltloc.updated_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2980 occupancy sum: 2709.95 (% of total atoms 47.15) Rotatable: count: 1010 occupancy sum: 944.71 (% of total atoms 16.44) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.1923 r_free= 0.1772 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.074943 | | target function (ml) not normalized (work): 763289.723827 | | target function (ml) not normalized (free): 15809.214844 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2542 0.2163 6.7387 6.4457| | 2: 2.94 - 2.33 1.00 7339 128 0.1718 0.1788 5.6175 5.6704| | 3: 2.33 - 2.04 0.96 6939 150 0.1733 0.1612 5.1238 5.107| | 4: 2.04 - 1.85 1.00 7170 155 0.1728 0.1476 4.837 4.9407| | 5: 1.85 - 1.72 0.99 7113 159 0.1738 0.1461 4.5564 4.5706| | 6: 1.72 - 1.62 0.99 7102 142 0.1672 0.1491 4.331 4.4067| | 7: 1.62 - 1.54 0.99 7104 148 0.1685 0.1305 4.178 4.1833| | 8: 1.54 - 1.47 0.96 6798 152 0.1626 0.1813 4.076 4.2442| | 9: 1.47 - 1.41 0.98 6938 155 0.1631 0.1650 3.9999 4.116| | 10: 1.41 - 1.36 0.99 7022 150 0.1625 0.1522 3.9177 4.0164| | 11: 1.36 - 1.32 0.99 6997 151 0.1607 0.1543 3.8568 3.9567| | 12: 1.32 - 1.28 0.98 6976 149 0.1582 0.1714 3.8138 4.0086| | 13: 1.28 - 1.25 0.98 6907 166 0.1583 0.1494 3.7727 3.8603| | 14: 1.25 - 1.22 0.98 7015 113 0.1640 0.1796 3.7502 4.0225| | 15: 1.22 - 1.19 0.98 6957 137 0.1652 0.1449 3.7322 3.7472| | 16: 1.19 - 1.17 0.93 6604 132 0.1728 0.1717 3.733 3.8574| | 17: 1.17 - 1.14 0.98 6941 135 0.1761 0.1493 3.6788 3.7193| | 18: 1.14 - 1.12 0.98 6875 142 0.1810 0.1860 3.6596 3.7244| | 19: 1.12 - 1.10 0.97 6949 106 0.1836 0.1858 3.6257 3.7469| | 20: 1.10 - 1.08 0.97 6884 147 0.1894 0.1863 3.5999 3.6434| | 21: 1.08 - 1.07 0.97 6852 152 0.2006 0.2343 3.5868 3.6737| | 22: 1.07 - 1.05 0.97 6838 135 0.2142 0.2093 3.5686 3.5624| | 23: 1.05 - 1.03 0.97 6829 159 0.2313 0.2195 3.5749 3.6562| | 24: 1.03 - 1.02 0.96 6785 133 0.2518 0.2404 3.5742 3.6397| | 25: 1.02 - 1.01 0.93 6552 130 0.2740 0.2576 3.5793 3.6185| | 26: 1.01 - 0.99 0.96 6767 158 0.2885 0.2859 3.5367 3.5563| | 27: 0.99 - 0.98 0.94 6648 131 0.3129 0.2938 3.5786 3.5292| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.82 24.15 0.89 0.96 47293.45| | 2: 2.94 - 2.33 7339 128 0.83 23.81 1.10 1.04 18940.74| | 3: 2.33 - 2.04 6939 150 0.94 11.80 1.13 1.08 3776.41| | 4: 2.04 - 1.85 7170 155 0.94 11.12 1.14 1.09 2057.27| | 5: 1.85 - 1.72 7113 159 0.94 11.39 1.14 1.10 1264.15| | 6: 1.72 - 1.62 7102 142 0.94 11.29 1.14 1.11 877.86| | 7: 1.62 - 1.54 7104 148 0.94 11.39 1.15 1.12 657.92| | 8: 1.54 - 1.47 6798 152 0.94 11.78 1.13 1.12 555.01| | 9: 1.47 - 1.41 6938 155 0.93 12.28 1.13 1.12 480.35| | 10: 1.41 - 1.36 7022 150 0.93 13.15 1.12 1.10 421.39| | 11: 1.36 - 1.32 6997 151 0.93 13.46 1.11 1.09 377.16| | 12: 1.32 - 1.28 6976 149 0.93 13.33 1.10 1.08 344.05| | 13: 1.28 - 1.25 6907 166 0.93 13.71 1.10 1.08 327.11| | 14: 1.25 - 1.22 7015 113 0.92 14.51 1.10 1.07 311.36| | 15: 1.22 - 1.19 6957 137 0.92 14.58 1.10 1.07 299.44| | 16: 1.19 - 1.17 6604 132 0.92 14.58 1.09 1.06 275.37| | 17: 1.17 - 1.14 6941 135 0.92 14.96 1.10 1.06 251.96| | 18: 1.14 - 1.12 6875 142 0.92 15.24 1.10 1.03 231.18| | 19: 1.12 - 1.10 6949 106 0.91 16.34 1.09 1.03 229.28| | 20: 1.10 - 1.08 6884 147 0.90 17.34 1.08 1.01 221.79| | 21: 1.08 - 1.07 6852 152 0.89 18.54 1.08 1.02 221.93| | 22: 1.07 - 1.05 6838 135 0.88 20.04 1.07 1.02 218.43| | 23: 1.05 - 1.03 6829 159 0.86 21.89 1.07 1.01 225.88| | 24: 1.03 - 1.02 6785 133 0.84 24.24 1.07 1.01 236.46| | 25: 1.02 - 1.01 6552 130 0.82 25.99 1.05 0.98 236.47| | 26: 1.01 - 0.99 6767 158 0.80 27.71 1.05 0.96 228.98| | 27: 0.99 - 0.98 6648 131 0.80 27.77 1.06 0.93 211.95| |alpha: min = 0.93 max = 1.12 mean = 1.05| |beta: min = 211.95 max = 47293.45 mean = 3155.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.90| |phase err.(work): min = 0.00 max = 89.99 mean = 16.86| |phase err.(test): min = 0.00 max = 89.05 mean = 16.75| |-----------------------------------------------------------------------------| ----------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 : 0.018 0.146 2950 Z= 1.061 Angle : 1.607 16.181 4018 Z= 0.996 Chirality : 0.160 1.341 492 Planarity : 0.013 0.072 512 Dihedral : 11.816 85.508 1062 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.32 % Allowed : 3.23 % Favored : 96.45 % Cbeta Deviations : 0.84 % 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: 0.69 (0.41), residues: 386 helix: 0.38 (0.38), residues: 146 sheet: -0.23 (0.53), residues: 86 loop : 1.32 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.005 ARG A 83 TYR 0.047 0.016 TYR A 194 PHE 0.067 0.015 PHE A 164 TRP 0.041 0.015 TRP A 146 HIS 0.023 0.006 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.38 109.75 13.10 1.86 0 3330 Protein: 5.38 50.81 10.65 1.86 0 2902 Water: 6.02 109.75 29.77 N/A 0 426 Other: 13.83 22.85 18.34 N/A 0 2 Chain A: 5.49 109.75 13.27 N/A 0 1659 Chain B: 5.38 96.50 12.93 N/A 0 1671 Histogram: Values Number of atoms 5.38 - 15.82 2679 15.82 - 26.26 343 26.26 - 36.69 168 36.69 - 47.13 99 47.13 - 57.56 27 57.56 - 68.00 8 68.00 - 78.44 1 78.44 - 88.87 2 88.87 - 99.31 1 99.31 - 109.75 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.1923 r_free= 0.1772 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.074943 | | target function (ml) not normalized (work): 763289.723827 | | target function (ml) not normalized (free): 15809.214844 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1920 0.1924 0.1773 n_refl.: 191155 re-set all scales: r(all,work,free)=0.1920 0.1924 0.1773 n_refl.: 191155 remove outliers: r(all,work,free)=0.1920 0.1924 0.1773 n_refl.: 191145 overall B=0.04 to atoms: r(all,work,free)=0.1929 0.1934 0.1776 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1550 0.1655 n_refl.: 191145 remove outliers: r(all,work,free)=0.1549 0.1547 0.1655 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 0.4583 398.008 282.571 0.445 0.895 0.299 13.296-10.522 97.03 97 1 0.3234 528.040 485.542 0.842 0.896 0.285 10.503-8.327 100.00 179 3 0.2921 568.071 543.464 1.026 0.897 0.280 8.318-6.595 100.00 359 8 0.2852 411.275 396.005 0.995 0.896 0.272 6.588-5.215 100.00 711 7 0.2696 381.101 362.437 0.983 0.897 0.266 5.214-4.128 98.38 1367 28 0.1834 557.435 545.209 1.092 0.897 0.220 4.126-3.266 94.74 2603 46 0.1618 508.132 497.030 1.156 0.897 0.082 3.266-2.585 99.86 5447 97 0.1567 342.774 336.776 1.127 0.896 0.019 2.585-2.046 97.45 10613 204 0.1363 258.603 254.413 1.138 0.895 0.000 2.046-1.619 99.39 21536 464 0.1273 153.054 151.030 1.161 0.893 0.000 1.619-1.281 98.00 42464 925 0.1251 82.395 81.308 1.149 0.891 0.000 1.281-0.980 96.53 101826 2056 0.1822 44.203 42.126 1.123 0.885 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0586 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1547 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1547 r_free=0.1655 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.242917 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 630.072310 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 0.2054 0.2132 0.0078 0.001 0.4 4.6 0.0 0.0 0 0.125 0.1937 0.2024 0.0087 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1798 0.1897 0.0099 0.002 0.5 3.7 0.0 0.0 0 0.500 0.1724 0.1831 0.0106 0.002 0.5 3.6 0.0 0.0 0 0.750 0.1688 0.1806 0.0118 0.002 0.5 3.6 0.0 0.0 0 1.000 0.1688 0.1806 0.0118 0.002 0.5 3.6 0.0 0.0 0 1.000 0.1636 0.1769 0.0134 0.003 0.6 3.9 0.0 0.3 0 2.000 0.1604 0.1740 0.0136 0.003 0.7 3.2 0.0 0.3 0 3.000 0.1588 0.1726 0.0138 0.004 0.7 3.2 0.0 0.3 0 4.000 0.1581 0.1722 0.0141 0.005 0.7 3.1 0.0 0.3 0 5.000 0.1575 0.1720 0.0145 0.005 0.8 2.7 0.0 0.3 0 6.000 0.1568 0.1714 0.0146 0.006 0.8 2.5 0.0 0.3 0 7.000 0.1568 0.1716 0.0148 0.006 0.8 2.5 0.0 0.3 0 8.000 0.1564 0.1716 0.0152 0.007 0.9 2.4 0.0 0.3 0 9.000 0.1558 0.1711 0.0153 0.007 0.9 2.4 0.0 0.3 0 10.121 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1558 0.1711 0.0153 0.007 0.9 2.4 0.0 0.3 0 10.121 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 15.58 17.11 1.53 1.313 12.094 630.072 0.031 15.58 17.11 1.53 1.311 12.094 18.902 0.031 15.83 17.23 1.40 1.080 12.105 78.759 0.030 15.40 17.52 2.12 1.741 12.184 315.036 0.027 15.02 17.47 2.45 1.825 12.204 630.072 0.026 14.91 17.53 2.62 1.915 12.265 945.108 0.025 14.89 17.72 2.83 2.091 12.391 1260.145 0.025 14.79 17.65 2.85 2.072 12.338 1575.181 0.025 14.74 17.61 2.87 2.115 12.363 1890.217 0.025 14.71 17.62 2.90 2.230 12.435 2205.253 0.025 14.72 17.70 2.98 2.287 12.452 2520.289 0.024 14.69 17.70 3.01 2.300 12.446 2835.325 0.024 14.67 17.71 3.03 2.316 12.443 3150.362 0.024 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 18.902 Accepted refinement result: 15.58 17.11 1.53 1.311 12.094 18.902 0.031 Individual atomic B min max mean iso aniso Overall: 5.42 109.79 13.14 1.86 0 3330 Protein: 5.42 50.85 10.69 1.86 0 2902 Water: 6.06 109.79 29.81 N/A 0 426 Other: 13.87 22.89 18.38 N/A 0 2 Chain A: 5.53 109.79 13.31 N/A 0 1659 Chain B: 5.42 96.54 12.97 N/A 0 1671 Histogram: Values Number of atoms 5.42 - 15.86 2681 15.86 - 26.29 341 26.29 - 36.73 168 36.73 - 47.17 99 47.17 - 57.60 27 57.60 - 68.04 8 68.04 - 78.48 1 78.48 - 88.91 2 88.91 - 99.35 1 99.35 - 109.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1558 r_free=0.1711 r_work=0.1559 r_free=0.1711 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1559 r_free = 0.1711 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1406 r_free = 0.1579 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1406 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.022624 | | target function (ls_wunit_k1) not normalized (work): 4237.351533 | | target function (ls_wunit_k1) not normalized (free): 117.231894 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1410 0.1406 0.1579 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1660 0.1659 0.1701 n_refl.: 191136 remove outliers: r(all,work,free)=0.1660 0.1659 0.1701 n_refl.: 191136 overall B=0.02 to atoms: r(all,work,free)=0.1664 0.1663 0.1704 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1408 0.1404 0.1579 n_refl.: 191136 remove outliers: r(all,work,free)=0.1408 0.1404 0.1578 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3292 398.008 374.687 0.670 0.935 0.323 13.296-10.522 97.03 97 1 0.2273 528.040 514.577 0.884 0.935 0.303 10.503-8.327 100.00 179 3 0.1923 568.071 562.823 0.980 0.935 0.298 8.318-6.595 100.00 359 8 0.2097 411.275 401.582 0.975 0.935 0.282 6.588-5.215 100.00 711 7 0.2039 381.101 368.738 0.947 0.935 0.263 5.214-4.128 98.38 1367 28 0.1328 557.435 551.006 1.041 0.935 0.220 4.126-3.266 94.74 2603 46 0.1230 508.132 501.638 1.105 0.935 0.042 3.266-2.585 99.86 5447 97 0.1244 342.774 339.178 1.085 0.934 0.010 2.585-2.046 97.45 10613 204 0.1173 258.603 255.203 1.093 0.933 0.000 2.046-1.619 99.39 21536 464 0.1176 153.054 151.135 1.114 0.932 0.000 1.619-1.281 98.00 42464 925 0.1268 82.395 81.292 1.104 0.929 0.000 1.281-0.980 96.53 101826 2055 0.1851 44.202 42.093 1.081 0.924 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0345 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1404 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1404 r_free=0.1578 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1404 r_free=0.1578 | n_water=426 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1413 r_free=0.1572 | n_water=399 | time (s): 36.970 (total time: 38.700) Filter (q & B) r_work=0.1414 r_free=0.1572 | n_water=396 | time (s): 2.790 (total time: 41.490) Compute maps r_work=0.1414 r_free=0.1572 | n_water=396 | time (s): 1.230 (total time: 42.720) Filter (map) r_work=0.1419 r_free=0.1578 | n_water=377 | time (s): 2.760 (total time: 45.480) Find peaks r_work=0.1419 r_free=0.1578 | n_water=377 | time (s): 0.500 (total time: 45.980) Add new water r_work=0.1484 r_free=0.1659 | n_water=727 | time (s): 2.880 (total time: 48.860) Refine new water occ: r_work=0.1403 r_free=0.1574 adp: r_work=0.1379 r_free=0.1558 occ: r_work=0.1381 r_free=0.1556 adp: r_work=0.1370 r_free=0.1549 occ: r_work=0.1370 r_free=0.1545 adp: r_work=0.1367 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1367 r_free=0.1542 r_work=0.1367 r_free=0.1542 | n_water=727 | time (s): 51.050 (total time: 99.910) Filter (q & B) r_work=0.1370 r_free=0.1546 | n_water=691 | time (s): 2.910 (total time: 102.820) Filter (dist only) r_work=0.1371 r_free=0.1540 | n_water=687 | time (s): 59.120 (total time: 161.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.203796 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 762.966811 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 0.1940 0.2097 0.0157 0.001 0.4 10.7 0.0 0.3 0 0.125 0.1756 0.1913 0.0157 0.001 0.4 10.5 0.0 0.3 0 0.250 0.1603 0.1772 0.0169 0.001 0.4 10.2 0.0 0.3 0 0.500 0.1544 0.1717 0.0173 0.002 0.5 10.5 0.0 0.3 0 0.750 0.1495 0.1673 0.0178 0.002 0.5 10.5 0.0 0.3 0 1.000 0.1495 0.1673 0.0178 0.002 0.5 10.5 0.0 0.3 0 1.000 0.1416 0.1599 0.0183 0.002 0.6 10.0 0.0 0.3 0 2.000 0.1385 0.1570 0.0185 0.003 0.7 10.2 0.0 0.3 0 3.000 0.1367 0.1553 0.0186 0.004 0.7 10.7 0.0 0.3 0 4.000 0.1355 0.1543 0.0187 0.004 0.7 11.0 0.0 0.3 0 5.000 0.1347 0.1533 0.0186 0.005 0.8 11.2 0.0 0.3 0 6.000 0.1340 0.1524 0.0184 0.005 0.8 11.7 0.0 0.3 0 7.000 0.1336 0.1520 0.0184 0.006 0.8 11.7 0.0 0.3 0 8.000 0.1331 0.1516 0.0185 0.006 0.9 11.7 0.0 0.3 0 9.000 0.1328 0.1511 0.0184 0.006 0.9 12.4 0.0 0.3 0 10.000 0.1325 0.1509 0.0185 0.007 0.9 12.4 0.0 0.3 0 11.102 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1325 0.1509 0.0185 0.007 0.9 12.4 0.0 0.3 0 11.102 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.25 15.09 1.85 2.148 14.278 762.967 0.019 13.25 15.09 1.85 2.148 14.278 22.889 0.019 13.24 15.05 1.81 2.103 14.278 95.371 0.019 13.37 15.81 2.44 2.111 14.403 381.483 0.017 12.95 15.47 2.52 1.992 14.478 762.967 0.016 12.77 15.37 2.60 1.979 14.508 1144.450 0.016 12.71 15.41 2.70 2.047 14.552 1525.934 0.016 12.61 15.32 2.71 2.037 14.536 1907.417 0.016 12.63 15.45 2.82 2.130 14.593 2288.900 0.015 12.54 15.34 2.79 2.105 14.561 2670.384 0.015 12.52 15.31 2.79 2.124 14.568 3051.867 0.015 12.53 15.37 2.84 2.202 14.610 3433.351 0.015 12.52 15.37 2.85 2.209 14.601 3814.834 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 95.371 Accepted refinement result: 13.24 15.05 1.81 2.103 14.278 95.371 0.019 Individual atomic B min max mean iso aniso Overall: 5.47 79.94 15.23 1.68 310 3281 Protein: 5.47 50.83 10.71 1.68 0 2902 Water: 5.99 79.94 34.30 N/A 310 377 Other: 14.00 22.99 18.49 N/A 0 2 Chain A: 5.61 67.88 12.73 N/A 0 1630 Chain B: 5.47 79.94 12.62 N/A 0 1651 Chain S: 14.72 60.01 42.28 N/A 310 0 Histogram: Values Number of atoms 5.47 - 12.92 2407 12.92 - 20.36 477 20.36 - 27.81 212 27.81 - 35.26 151 35.26 - 42.71 140 42.71 - 50.15 89 50.15 - 57.60 63 57.60 - 65.05 50 65.05 - 72.49 1 72.49 - 79.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.1324 r_free=0.1505 r_work=0.1324 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1324 r_free = 0.1505 target_work(ls_wunit_k1) = 0.019 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1321 r_free = 0.1504 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1321 r_free= 0.1504 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.017947 | | target function (ls_wunit_k1) not normalized (work): 3361.415865 | | target function (ls_wunit_k1) not normalized (free): 103.717610 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1325 0.1321 0.1504 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1539 0.1538 0.1601 n_refl.: 191135 remove outliers: r(all,work,free)=0.1539 0.1538 0.1601 n_refl.: 191135 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1537 0.1600 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1324 0.1320 0.1501 n_refl.: 191135 remove outliers: r(all,work,free)=0.1324 0.1320 0.1501 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3058 398.008 382.853 0.647 0.953 0.327 13.296-10.522 97.03 97 1 0.1966 528.040 521.596 0.862 0.954 0.295 10.503-8.327 100.00 179 3 0.1737 568.071 566.679 0.975 0.954 0.283 8.318-6.595 100.00 359 8 0.1808 411.275 406.617 0.965 0.954 0.255 6.588-5.215 100.00 711 7 0.1745 381.101 371.391 0.934 0.954 0.240 5.214-4.128 98.38 1367 28 0.1134 557.435 554.286 1.020 0.954 0.180 4.126-3.266 94.74 2603 46 0.1000 508.132 503.360 1.081 0.954 0.028 3.266-2.585 99.86 5447 97 0.1099 342.774 340.331 1.065 0.952 0.000 2.585-2.046 97.45 10613 204 0.1091 258.603 255.678 1.075 0.952 0.000 2.046-1.619 99.39 21536 464 0.1127 153.054 151.267 1.097 0.949 0.000 1.619-1.281 98.00 42464 925 0.1223 82.395 81.348 1.091 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1821 44.202 42.157 1.074 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0161 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1320 r_free=0.1501 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1320 r_free=0.1501 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1320 r_free=0.1501 | n_water=687 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1343 r_free=0.1509 | n_water=677 | time (s): 60.590 (total time: 62.320) Filter (q & B) r_work=0.1343 r_free=0.1508 | n_water=676 | time (s): 2.850 (total time: 65.170) Compute maps r_work=0.1343 r_free=0.1508 | n_water=676 | time (s): 1.250 (total time: 66.420) Filter (map) r_work=0.1375 r_free=0.1509 | n_water=495 | time (s): 2.840 (total time: 69.260) Find peaks r_work=0.1375 r_free=0.1509 | n_water=495 | time (s): 0.450 (total time: 69.710) Add new water r_work=0.1424 r_free=0.1559 | n_water=795 | time (s): 2.770 (total time: 72.480) Refine new water occ: r_work=0.1363 r_free=0.1505 adp: r_work=0.1363 r_free=0.1506 occ: r_work=0.1358 r_free=0.1502 adp: r_work=0.1357 r_free=0.1502 occ: r_work=0.1353 r_free=0.1502 adp: r_work=0.1352 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1352 r_free=0.1501 r_work=0.1352 r_free=0.1501 | n_water=795 | time (s): 110.010 (total time: 182.490) Filter (q & B) r_work=0.1354 r_free=0.1498 | n_water=757 | time (s): 2.910 (total time: 185.400) Filter (dist only) r_work=0.1354 r_free=0.1498 | n_water=757 | time (s): 62.610 (total time: 248.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.633773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 19.720081 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 0.1405 0.1517 0.0111 0.002 0.6 6.3 0.0 0.0 0 0.082 0.1355 0.1460 0.0106 0.004 0.8 7.0 0.0 0.0 0 0.245 0.1336 0.1445 0.0109 0.005 0.9 8.0 0.0 0.0 0 0.490 0.1328 0.1440 0.0112 0.006 1.0 8.2 0.0 0.0 0 0.735 0.1322 0.1436 0.0114 0.007 1.0 8.2 0.0 0.0 0 0.980 0.1317 0.1435 0.0118 0.007 1.0 8.0 0.0 0.0 0 1.225 0.1315 0.1435 0.0120 0.008 1.1 8.2 0.0 0.0 0 1.470 0.1312 0.1434 0.0123 0.009 1.1 8.3 0.0 0.0 0 1.715 0.1326 0.1440 0.0114 0.006 1.0 8.3 0.0 0.0 0 0.817 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1312 0.1434 0.0123 0.009 1.1 8.3 0.0 0.0 0 1.715 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.12 14.34 1.23 2.072 13.873 19.720 3.919 13.12 14.34 1.23 2.072 13.873 0.592 3.919 13.12 14.34 1.23 2.072 13.873 2.465 3.919 13.04 14.23 1.20 2.029 13.873 9.860 3.908 12.89 14.14 1.24 2.092 13.872 19.720 3.893 12.77 14.09 1.32 2.108 13.878 29.580 3.882 12.69 14.04 1.35 2.094 13.887 39.440 3.877 12.62 14.01 1.39 2.077 13.883 49.300 3.870 12.58 13.99 1.41 2.076 13.899 59.160 3.868 12.55 13.99 1.44 2.067 13.905 69.020 3.866 12.53 13.97 1.44 2.064 13.909 78.880 3.865 12.51 13.97 1.45 2.057 13.912 88.740 3.864 12.49 13.96 1.47 2.051 13.910 98.600 3.862 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 98.600 Accepted refinement result: 12.49 13.96 1.47 2.051 13.910 98.600 3.862 Individual atomic B min max mean iso aniso Overall: 5.38 79.26 14.57 1.61 384 3277 Protein: 5.38 49.23 10.87 1.61 0 2902 Water: 6.71 79.26 28.73 N/A 384 373 Other: 13.78 22.48 18.13 N/A 0 2 Chain A: 5.38 66.75 12.86 N/A 0 1628 Chain B: 5.50 79.26 12.62 N/A 0 1649 Chain S: 13.91 59.94 30.21 N/A 384 0 Histogram: Values Number of atoms 5.38 - 12.76 2322 12.76 - 20.15 581 20.15 - 27.54 329 27.54 - 34.93 208 34.93 - 42.32 133 42.32 - 49.71 54 49.71 - 57.09 21 57.09 - 64.48 11 64.48 - 71.87 1 71.87 - 79.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1249 r_free=0.1396 r_work=0.1249 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1395 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1243 r_free = 0.1399 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1243 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861578 | | target function (ml) not normalized (work): 723250.375870 | | target function (ml) not normalized (free): 15173.898178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1246 0.1243 0.1399 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1481 0.1481 0.1497 n_refl.: 191135 remove outliers: r(all,work,free)=0.1481 0.1481 0.1497 n_refl.: 191135 overall B=-0.01 to atoms: r(all,work,free)=0.1479 0.1479 0.1495 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1236 0.1385 n_refl.: 191135 remove outliers: r(all,work,free)=0.1238 0.1235 0.1385 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3836 393.525 360.242 0.502 0.939 0.285 13.296-10.522 97.03 97 1 0.2427 528.040 512.126 0.783 0.940 0.262 10.503-8.327 98.35 176 3 0.2296 562.248 557.778 0.943 0.940 0.253 8.318-6.595 100.00 359 8 0.2388 411.275 399.684 0.936 0.940 0.240 6.588-5.215 100.00 711 7 0.2200 381.101 367.216 0.913 0.940 0.200 5.214-4.128 98.38 1367 28 0.1426 557.435 550.030 1.013 0.940 0.120 4.126-3.266 94.74 2603 46 0.1252 508.132 499.501 1.080 0.940 0.050 3.266-2.585 99.86 5447 97 0.1206 342.774 338.707 1.064 0.939 0.000 2.585-2.046 97.45 10613 204 0.1023 258.603 255.378 1.077 0.939 0.000 2.046-1.619 99.39 21536 464 0.0928 153.054 151.434 1.104 0.937 0.000 1.619-1.281 98.00 42464 925 0.0962 82.395 81.585 1.099 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1622 44.202 42.376 1.076 0.930 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0285 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1385 | n_water=757 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1235 r_free=0.1387 | n_water=754 | time (s): 96.400 (total time: 98.800) Filter (q & B) r_work=0.1235 r_free=0.1388 | n_water=750 | time (s): 4.980 (total time: 103.780) Compute maps r_work=0.1235 r_free=0.1388 | n_water=750 | time (s): 2.160 (total time: 105.940) Filter (map) r_work=0.1255 r_free=0.1377 | n_water=597 | time (s): 5.630 (total time: 111.570) Find peaks r_work=0.1255 r_free=0.1377 | n_water=597 | time (s): 0.690 (total time: 112.260) Add new water r_work=0.1284 r_free=0.1415 | n_water=855 | time (s): 5.030 (total time: 117.290) Refine new water occ: r_work=0.1236 r_free=0.1364 adp: r_work=0.1236 r_free=0.1365 occ: r_work=0.1232 r_free=0.1365 adp: r_work=0.1232 r_free=0.1364 occ: r_work=0.1229 r_free=0.1365 adp: r_work=0.1228 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1364 r_work=0.1228 r_free=0.1364 | n_water=855 | time (s): 187.600 (total time: 304.890) Filter (q & B) r_work=0.1231 r_free=0.1367 | n_water=797 | time (s): 5.430 (total time: 310.320) Filter (dist only) r_work=0.1231 r_free=0.1367 | n_water=796 | time (s): 102.010 (total time: 412.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533992 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 19.623970 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 0.1316 0.1452 0.0137 0.002 0.6 6.8 0.0 0.0 0 0.077 0.1267 0.1398 0.0131 0.004 0.8 7.1 0.0 0.0 0 0.230 0.1249 0.1385 0.0135 0.005 0.9 8.2 0.0 0.0 0 0.460 0.1242 0.1383 0.0141 0.006 1.0 8.0 0.0 0.0 0 0.690 0.1237 0.1382 0.0146 0.007 1.0 9.7 0.0 0.0 0 0.920 0.1233 0.1379 0.0146 0.007 1.0 9.3 0.0 0.0 0 1.150 0.1230 0.1375 0.0146 0.008 1.1 9.2 0.0 0.0 0 1.381 0.1228 0.1374 0.0146 0.009 1.1 9.3 0.0 0.0 0 1.611 0.1240 0.1382 0.0142 0.006 1.0 8.7 0.0 0.0 0 0.767 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1374 0.0146 0.009 1.1 9.3 0.0 0.0 0 1.611 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 13.74 1.46 2.070 14.101 19.624 3.857 12.28 13.74 1.46 2.070 14.101 0.589 3.857 12.28 13.74 1.46 2.070 14.101 2.453 3.857 12.28 13.74 1.46 2.070 14.101 9.812 3.857 12.28 13.74 1.46 2.070 14.101 19.624 3.857 12.28 13.74 1.46 2.066 14.101 29.436 3.856 12.28 13.74 1.45 2.062 14.102 39.248 3.856 12.30 13.73 1.43 2.054 14.102 49.060 3.856 12.29 13.73 1.44 2.055 14.103 58.872 3.855 12.29 13.73 1.44 2.050 14.097 68.684 3.855 12.30 13.74 1.44 2.061 14.078 78.496 3.854 12.27 13.74 1.46 2.051 14.084 88.308 3.853 12.26 13.73 1.47 2.042 14.089 98.120 3.852 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 98.120 Accepted refinement result: 12.26 13.73 1.47 2.042 14.089 98.120 3.852 Individual atomic B min max mean iso aniso Overall: 5.22 78.07 14.64 1.59 425 3275 Protein: 5.22 45.37 10.91 1.59 0 2902 Water: 6.75 78.07 28.23 N/A 425 371 Other: 13.82 22.36 18.09 N/A 0 2 Chain A: 5.22 64.51 12.82 N/A 0 1626 Chain B: 5.48 78.07 12.58 N/A 0 1649 Chain S: 12.84 59.79 29.59 N/A 425 0 Histogram: Values Number of atoms 5.22 - 12.50 2257 12.50 - 19.79 640 19.79 - 27.08 353 27.08 - 34.36 229 34.36 - 41.65 135 41.65 - 48.93 52 48.93 - 56.22 23 56.22 - 63.50 9 63.50 - 70.79 1 70.79 - 78.07 1 =========================== Idealize ADP of riding H ========================== r_work=0.1226 r_free=0.1373 r_work=0.1226 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1226 r_free = 0.1373 target_work(ml) = 3.852 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1220 r_free = 0.1378 target_work(ml) = 3.851 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1220 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.850970 | | target function (ml) not normalized (work): 721248.143355 | | target function (ml) not normalized (free): 15150.963350 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1220 0.1378 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1461 0.1461 0.1491 n_refl.: 191131 remove outliers: r(all,work,free)=0.1461 0.1461 0.1491 n_refl.: 191131 overall B=-0.01 to atoms: r(all,work,free)=0.1458 0.1458 0.1489 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1218 0.1376 n_refl.: 191131 remove outliers: r(all,work,free)=0.1221 0.1218 0.1376 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3985 393.525 349.127 0.480 0.940 0.282 13.296-10.522 97.03 97 1 0.2401 528.040 515.720 0.765 0.941 0.252 10.503-8.327 98.35 176 3 0.2329 562.248 555.575 0.926 0.941 0.238 8.318-6.595 100.00 359 8 0.2371 411.275 400.069 0.924 0.941 0.184 6.588-5.215 100.00 711 7 0.2146 381.101 367.222 0.907 0.941 0.134 5.214-4.128 98.38 1367 28 0.1424 557.435 550.434 1.009 0.941 0.110 4.126-3.266 94.74 2603 46 0.1222 508.132 500.020 1.078 0.941 0.023 3.266-2.585 99.86 5447 97 0.1204 342.774 338.581 1.062 0.941 0.000 2.585-2.046 97.45 10613 204 0.1003 258.603 255.635 1.076 0.940 0.000 2.046-1.619 99.39 21536 464 0.0897 153.054 151.516 1.103 0.939 0.000 1.619-1.281 98.00 42464 925 0.0937 82.395 81.668 1.099 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1619 44.202 42.389 1.074 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0399 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1218 r_free=0.1376 After: r_work=0.1220 r_free=0.1376 ================================== NQH flips ================================== r_work=0.1220 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1220 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1220 r_free=0.1376 | n_water=796 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1220 r_free=0.1377 | n_water=792 | time (s): 100.910 (total time: 104.150) Filter (q & B) r_work=0.1220 r_free=0.1378 | n_water=786 | time (s): 4.970 (total time: 109.120) Compute maps r_work=0.1220 r_free=0.1378 | n_water=786 | time (s): 2.280 (total time: 111.400) Filter (map) r_work=0.1243 r_free=0.1381 | n_water=636 | time (s): 4.630 (total time: 116.030) Find peaks r_work=0.1243 r_free=0.1381 | n_water=636 | time (s): 0.750 (total time: 116.780) Add new water r_work=0.1264 r_free=0.1415 | n_water=871 | time (s): 5.070 (total time: 121.850) Refine new water occ: r_work=0.1221 r_free=0.1366 adp: r_work=0.1221 r_free=0.1366 occ: r_work=0.1218 r_free=0.1365 adp: r_work=0.1218 r_free=0.1365 occ: r_work=0.1215 r_free=0.1365 adp: r_work=0.1215 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1365 r_work=0.1215 r_free=0.1365 | n_water=871 | time (s): 256.350 (total time: 378.200) Filter (q & B) r_work=0.1219 r_free=0.1371 | n_water=807 | time (s): 4.980 (total time: 383.180) Filter (dist only) r_work=0.1219 r_free=0.1370 | n_water=805 | time (s): 107.980 (total time: 491.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.595872 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 20.006384 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 0.1343 0.1483 0.0141 0.004 0.7 12.6 0.0 0.0 0 0.080 0.1278 0.1422 0.0144 0.005 0.8 13.3 0.0 0.0 0 0.239 0.1253 0.1399 0.0146 0.006 0.9 13.3 0.0 0.0 0 0.479 0.1242 0.1389 0.0147 0.006 1.0 13.1 0.0 0.0 0 0.718 0.1234 0.1382 0.0147 0.006 1.0 13.3 0.0 0.0 0 0.958 0.1228 0.1377 0.0149 0.007 1.1 13.3 0.0 0.0 0 1.197 0.1221 0.1372 0.0151 0.008 1.1 12.9 0.0 0.0 0 1.436 0.1219 0.1371 0.0152 0.009 1.1 12.6 0.0 0.0 0 1.676 0.1240 0.1388 0.0147 0.006 1.0 12.9 0.0 0.0 0 0.798 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1371 0.0152 0.009 1.1 12.6 0.0 0.0 0 1.676 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 13.71 1.52 2.069 14.105 20.006 3.851 12.19 13.71 1.52 2.069 14.105 0.600 3.851 12.19 13.71 1.52 2.069 14.105 2.501 3.851 12.19 13.71 1.52 2.069 14.105 10.003 3.851 12.19 13.71 1.52 2.069 14.105 20.006 3.851 12.19 13.70 1.51 2.067 14.105 30.010 3.851 12.19 13.70 1.51 2.063 14.105 40.013 3.851 12.21 13.71 1.50 2.058 14.106 50.016 3.851 12.21 13.71 1.50 2.058 14.106 60.019 3.850 12.20 13.71 1.51 2.058 14.105 70.022 3.850 12.21 13.73 1.53 2.057 14.101 80.026 3.850 12.20 13.75 1.55 2.054 14.099 90.029 3.850 12.19 13.75 1.56 2.047 14.105 100.032 3.849 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 30.010 Accepted refinement result: 12.19 13.70 1.51 2.067 14.105 30.010 3.851 Individual atomic B min max mean iso aniso Overall: 5.24 78.06 14.61 1.58 435 3274 Protein: 5.24 45.33 10.90 1.58 0 2902 Water: 6.74 78.06 28.01 N/A 435 370 Other: 13.81 22.34 18.08 N/A 0 2 Chain A: 5.24 64.49 12.80 N/A 0 1626 Chain B: 5.48 78.06 12.55 N/A 0 1648 Chain S: 12.83 59.77 29.19 N/A 435 0 Histogram: Values Number of atoms 5.24 - 12.52 2262 12.52 - 19.80 633 19.80 - 27.08 368 27.08 - 34.36 233 34.36 - 41.65 129 41.65 - 48.93 51 48.93 - 56.21 22 56.21 - 63.49 9 63.49 - 70.78 1 70.78 - 78.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1370 r_work=0.1219 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1370 target_work(ml) = 3.851 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1371 target_work(ml) = 3.851 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1217 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.850909 | | target function (ml) not normalized (work): 721236.796344 | | target function (ml) not normalized (free): 15142.847353 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1464 0.1511 5.8598 5.9203| | 2: 2.94 - 2.33 1.00 7339 128 0.1136 0.1365 5.2273 5.3399| | 3: 2.33 - 2.04 0.96 6939 150 0.0928 0.1070 4.7746 4.8234| | 4: 2.04 - 1.85 1.00 7170 155 0.0904 0.1082 4.4991 4.6509| | 5: 1.85 - 1.72 0.99 7113 159 0.0919 0.1059 4.2452 4.3655| | 6: 1.72 - 1.62 0.99 7102 142 0.0867 0.1136 4.0341 4.2148| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0966 3.8851 4.003| | 8: 1.54 - 1.47 0.96 6798 152 0.0878 0.1254 3.7893 3.9607| | 9: 1.47 - 1.41 0.98 6938 155 0.0904 0.1223 3.7159 3.9222| | 10: 1.41 - 1.36 0.99 7022 150 0.0961 0.1250 3.649 3.7903| | 11: 1.36 - 1.32 0.99 6997 151 0.0983 0.1132 3.5725 3.6954| | 12: 1.32 - 1.28 0.98 6975 149 0.1045 0.1133 3.5417 3.6919| | 13: 1.28 - 1.25 0.98 6907 166 0.1062 0.1343 3.5425 3.714| | 14: 1.25 - 1.22 0.98 7015 112 0.1133 0.1567 3.5268 3.7355| | 15: 1.22 - 1.19 0.98 6956 137 0.1179 0.1323 3.5405 3.6222| | 16: 1.19 - 1.17 0.93 6604 132 0.1223 0.1573 3.541 3.7331| | 17: 1.17 - 1.14 0.98 6940 135 0.1277 0.1275 3.5176 3.5753| | 18: 1.14 - 1.12 0.98 6875 142 0.1360 0.1651 3.5228 3.6108| | 19: 1.12 - 1.10 0.97 6948 106 0.1444 0.1781 3.5087 3.7373| | 20: 1.10 - 1.08 0.97 6884 147 0.1555 0.1599 3.4953 3.5552| | 21: 1.08 - 1.07 0.97 6852 152 0.1691 0.2040 3.5031 3.5706| | 22: 1.07 - 1.05 0.97 6836 135 0.1891 0.1937 3.5023 3.5275| | 23: 1.05 - 1.03 0.97 6827 159 0.2104 0.2047 3.5218 3.5895| | 24: 1.03 - 1.02 0.96 6784 133 0.2316 0.2233 3.5248 3.5919| | 25: 1.02 - 1.01 0.93 6552 130 0.2628 0.2541 3.5425 3.627| | 26: 1.01 - 0.99 0.96 6767 158 0.2774 0.2901 3.5102 3.5246| | 27: 0.99 - 0.98 0.94 6647 131 0.3037 0.2769 3.5596 3.4927| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.92 12.71 1.00 1.06 15586.79| | 2: 2.94 - 2.33 7339 128 0.92 13.67 0.99 1.05 6928.70| | 3: 2.33 - 2.04 6939 150 0.96 7.78 1.01 1.05 2105.51| | 4: 2.04 - 1.85 7170 155 0.96 7.73 1.00 1.05 1220.23| | 5: 1.85 - 1.72 7113 159 0.96 8.20 1.00 1.06 790.90| | 6: 1.72 - 1.62 7102 142 0.96 8.16 0.99 1.06 556.82| | 7: 1.62 - 1.54 7104 148 0.96 8.37 1.03 1.08 421.55| | 8: 1.54 - 1.47 6798 152 0.96 8.52 1.02 1.08 351.98| | 9: 1.47 - 1.41 6938 155 0.96 8.77 1.01 1.08 298.97| | 10: 1.41 - 1.36 7022 150 0.96 9.27 0.99 1.06 257.78| | 11: 1.36 - 1.32 6997 151 0.96 9.09 0.98 1.05 220.71| | 12: 1.32 - 1.28 6975 149 0.96 8.95 0.96 1.04 198.26| | 13: 1.28 - 1.25 6907 166 0.95 9.77 1.03 1.06 197.64| | 14: 1.25 - 1.22 7015 112 0.95 10.89 1.04 1.08 201.68| | 15: 1.22 - 1.19 6956 137 0.94 11.35 1.03 1.10 206.63| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.02 1.08 197.00| | 17: 1.17 - 1.14 6940 135 0.94 12.37 1.02 1.07 191.11| | 18: 1.14 - 1.12 6875 142 0.94 12.88 1.01 1.05 182.92| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 1.04 186.57| | 20: 1.10 - 1.08 6884 147 0.92 15.15 0.99 1.03 184.11| | 21: 1.08 - 1.07 6852 152 0.91 16.52 0.98 1.01 186.63| | 22: 1.07 - 1.05 6836 135 0.90 18.15 0.97 1.01 188.88| | 23: 1.05 - 1.03 6827 159 0.88 20.30 0.97 0.99 200.46| | 24: 1.03 - 1.02 6784 133 0.85 22.87 0.96 0.99 216.84| | 25: 1.02 - 1.01 6552 130 0.83 24.89 0.94 0.96 220.25| | 26: 1.01 - 0.99 6767 158 0.82 26.28 0.94 0.94 213.06| | 27: 0.99 - 0.98 6647 131 0.82 25.88 0.94 0.92 194.28| |alpha: min = 0.92 max = 1.10 mean = 1.04| |beta: min = 182.92 max = 15586.79 mean = 1236.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.40| |phase err.(test): min = 0.00 max = 88.27 mean = 13.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1217 0.1371 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1454 0.1454 0.1471 n_refl.: 191131 remove outliers: r(all,work,free)=0.1454 0.1454 0.1471 n_refl.: 191131 overall B=-0.01 to atoms: r(all,work,free)=0.1451 0.1451 0.1469 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1217 0.1370 n_refl.: 191131 remove outliers: r(all,work,free)=0.1219 0.1216 0.1370 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 93.07 91 3 0.4018 393.525 349.154 0.476 0.940 0.281 13.296-10.522 97.03 97 1 0.2386 528.040 514.785 0.755 0.942 0.243 10.503-8.327 98.35 176 3 0.2415 562.248 555.985 0.922 0.942 0.223 8.318-6.595 99.73 358 8 0.2384 408.440 398.050 0.918 0.941 0.160 6.588-5.215 100.00 711 7 0.2193 381.101 366.405 0.905 0.942 0.150 5.214-4.128 98.38 1367 28 0.1412 557.435 550.239 1.007 0.942 0.090 4.126-3.266 94.74 2603 46 0.1213 508.132 499.970 1.077 0.942 0.014 3.266-2.585 99.86 5447 97 0.1186 342.774 338.689 1.063 0.941 0.000 2.585-2.046 97.45 10613 204 0.0998 258.603 255.693 1.077 0.941 0.000 2.046-1.619 99.39 21536 464 0.0900 153.054 151.505 1.102 0.940 0.000 1.619-1.281 98.00 42464 925 0.0936 82.395 81.667 1.098 0.938 0.000 1.281-0.980 96.53 101826 2055 0.1619 44.202 42.391 1.073 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0374 ================= 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 : 0.1923 0.1772 0.018 1.607 5.4 109.7 13.1 426 0.000 1_bss: 0.1547 0.1655 0.018 1.607 5.4 109.8 13.1 426 0.000 1_settarget: 0.1547 0.1655 0.018 1.607 5.4 109.8 13.1 426 0.000 1_nqh: 0.1547 0.1655 0.018 1.607 5.4 109.8 13.1 426 0.000 1_weight: 0.1547 0.1655 0.018 1.607 5.4 109.8 13.1 426 0.000 1_xyzrec: 0.1558 0.1711 0.007 0.907 5.4 109.8 13.1 426 0.084 1_adp: 0.1558 0.1711 0.007 0.907 5.4 109.8 13.1 426 0.084 1_regHadp: 0.1559 0.1711 0.007 0.907 5.4 109.8 13.1 426 0.084 1_occ: 0.1406 0.1579 0.007 0.907 5.4 109.8 13.1 426 0.084 2_bss: 0.1404 0.1578 0.007 0.907 5.4 109.8 13.2 426 0.084 2_settarget: 0.1404 0.1578 0.007 0.907 5.4 109.8 13.2 426 0.084 2_updatecdl: 0.1404 0.1578 0.007 0.915 5.4 109.8 13.2 426 0.084 2_nqh: 0.1404 0.1578 0.007 0.915 5.4 109.8 13.2 426 0.084 2_sol: 0.1371 0.1540 0.007 0.915 5.4 80.0 15.2 687 n/a 2_weight: 0.1371 0.1540 0.007 0.915 5.4 80.0 15.2 687 n/a 2_xyzrec: 0.1325 0.1509 0.007 0.908 5.4 80.0 15.2 687 n/a 2_adp: 0.1324 0.1505 0.007 0.908 5.5 79.9 15.2 687 n/a 2_regHadp: 0.1324 0.1505 0.007 0.908 5.5 79.9 15.2 687 n/a 2_occ: 0.1321 0.1504 0.007 0.908 5.5 79.9 15.2 687 n/a 3_bss: 0.1320 0.1501 0.007 0.908 5.5 79.9 15.2 687 n/a 3_settarget: 0.1320 0.1501 0.007 0.908 5.5 79.9 15.2 687 n/a 3_updatecdl: 0.1320 0.1501 0.007 0.915 5.5 79.9 15.2 687 n/a 3_nqh: 0.1320 0.1501 0.007 0.915 5.5 79.9 15.2 687 n/a 3_sol: 0.1354 0.1498 0.007 0.915 5.5 79.9 14.5 757 n/a 3_weight: 0.1354 0.1498 0.007 0.915 5.5 79.9 14.5 757 n/a 3_xyzrec: 0.1312 0.1434 0.009 1.107 5.5 79.9 14.5 757 n/a 3_adp: 0.1249 0.1396 0.009 1.107 5.4 79.3 14.6 757 n/a 3_regHadp: 0.1249 0.1395 0.009 1.107 5.4 79.3 14.6 757 n/a 3_occ: 0.1243 0.1399 0.009 1.107 5.4 79.3 14.6 757 n/a 4_bss: 0.1235 0.1385 0.009 1.107 5.4 79.2 14.6 757 n/a 4_settarget: 0.1235 0.1385 0.009 1.107 5.4 79.2 14.6 757 n/a 4_updatecdl: 0.1235 0.1385 0.009 1.104 5.4 79.2 14.6 757 n/a 4_nqh: 0.1235 0.1385 0.009 1.104 5.4 79.2 14.6 757 n/a 4_sol: 0.1231 0.1367 0.009 1.104 5.4 79.2 14.7 796 n/a 4_weight: 0.1231 0.1367 0.009 1.104 5.4 79.2 14.7 796 n/a 4_xyzrec: 0.1228 0.1374 0.009 1.107 5.4 79.2 14.7 796 n/a 4_adp: 0.1226 0.1373 0.009 1.107 5.2 78.1 14.6 796 n/a 4_regHadp: 0.1226 0.1373 0.009 1.107 5.2 78.1 14.6 796 n/a 4_occ: 0.1220 0.1378 0.009 1.107 5.2 78.1 14.6 796 n/a 5_bss: 0.1218 0.1376 0.009 1.107 5.2 78.1 14.6 796 n/a 5_settarget: 0.1218 0.1376 0.009 1.107 5.2 78.1 14.6 796 n/a 5_updatecdl: 0.1218 0.1376 0.009 1.107 5.2 78.1 14.6 796 n/a 5_setrh: 0.1220 0.1376 0.009 1.107 5.2 78.1 14.6 796 n/a 5_nqh: 0.1220 0.1376 0.009 1.107 5.2 78.1 14.6 796 n/a 5_sol: 0.1219 0.1370 0.009 1.107 5.2 78.1 14.6 805 n/a 5_weight: 0.1219 0.1370 0.009 1.107 5.2 78.1 14.6 805 n/a 5_xyzrec: 0.1219 0.1371 0.009 1.144 5.2 78.1 14.6 805 n/a 5_adp: 0.1219 0.1370 0.009 1.144 5.2 78.1 14.6 805 n/a 5_regHadp: 0.1219 0.1370 0.009 1.144 5.2 78.1 14.6 805 n/a 5_occ: 0.1217 0.1371 0.009 1.144 5.2 78.1 14.6 805 n/a end: 0.1216 0.1370 0.009 1.144 5.2 78.0 14.6 805 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/00_base/5SY4_noAltloc.updated_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/00_base/5SY4_noAltloc.updated_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0900 Refinement macro-cycles (run) : 3531.7900 Write final files (write_after_run_outputs) : 155.5600 Total : 3691.4400 Total CPU time: 61.94 minutes =========================== phenix.refine: finished =========================== # Date 2025-01-03 Time 16:52:09 PST -0800 (1735951929.51 s) Start R-work = 0.1547, R-free = 0.1655 Final R-work = 0.1216, R-free = 0.1370 =============================================================================== Job complete usr+sys time: 3980.76 seconds wall clock time: 90 minutes 51.74 seconds (5451.74 seconds total)