Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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 occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.61, per 1000 atoms: 0.48 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 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: 0.36 Conformation dependent library (CDL) restraints added in 209.8 milliseconds Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 716 0.94 - 1.20: 972 1.20 - 1.46: 762 1.46 - 1.72: 690 1.72 - 1.98: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.027 0.208 1.02e-02 9.61e+03 4.16e+02 bond pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 1.237 1.458 -0.221 1.10e-02 8.26e+03 4.03e+02 bond pdb=" CA CYS A 46 " pdb=" C CYS A 46 " ideal model delta sigma weight residual 1.528 1.279 0.250 1.38e-02 5.25e+03 3.27e+02 bond pdb=" C SER A 161 " pdb=" O SER A 161 " ideal model delta sigma weight residual 1.237 1.444 -0.207 1.17e-02 7.31e+03 3.14e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.148 0.173 1.00e-02 1.00e+04 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3450 5.14 - 10.28: 1734 10.28 - 15.42: 524 15.42 - 20.56: 62 20.56 - 25.70: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 135 " pdb=" CB ASN A 135 " pdb=" CG ASN A 135 " ideal model delta sigma weight residual 112.60 128.60 -16.00 1.00e+00 1.00e+00 2.56e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.41 -13.21 9.00e-01 1.23e+00 2.15e+02 angle pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 120.39 106.39 14.00 1.05e+00 9.07e-01 1.78e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.27 108.24 15.03 1.16e+00 7.43e-01 1.68e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 121.32 136.11 -14.79 1.15e+00 7.56e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.98: 934 16.98 - 33.94: 124 33.94 - 50.91: 39 50.91 - 67.88: 10 67.88 - 84.85: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " pdb=" HE1 HIS A 126 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.204: 80 0.204 - 0.406: 74 0.406 - 0.608: 53 0.608 - 0.809: 30 0.809 - 1.011: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" C2 ADTT A 201 " pdb=" C1 ADTT A 201 " pdb=" C3 ADTT A 201 " pdb=" O2 ADTT A 201 " both_signs ideal model delta sigma weight residual False -2.43 -1.42 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA GLU A 116 " pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CB GLU A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.053 2.00e-02 2.50e+03 7.44e-02 1.24e+02 pdb=" CG HIS A 138 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.122 9.50e-02 1.11e+02 8.35e-02 1.21e+02 pdb=" NE ARG A 5 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.070 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.070 2.00e-02 2.50e+03 5.82e-02 1.02e+02 pdb=" CG PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1255 2.35 - 2.91: 8223 2.91 - 3.47: 10470 3.47 - 4.04: 15282 4.04 - 4.60: 21441 Nonbonded interactions: 56671 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.786 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.821 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.862 1.850 x-y,-y,-z-4/3 ... (remaining 56666 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 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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 = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 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 occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 = "shake_2667343_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792063 | | target function (ml) not normalized (work): 232595.585086 | | target function (ml) not normalized (free): 11834.789719 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3035 0.2128 7.009 4.9541| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1814 4.3525 4.341| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1578 4.1331 4.1579| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1429 3.8417 3.8364| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1609 3.8 3.831| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1767 3.4568 3.5187| | 7: 1.97 - 1.87 1.00 2787 165 0.2563 0.1855 3.1194 3.1967| | 8: 1.87 - 1.79 1.00 2789 144 0.2492 0.1815 3.0542 3.0771| | 9: 1.79 - 1.72 1.00 2745 138 0.2431 0.1777 2.9179 2.9212| | 10: 1.72 - 1.66 1.00 2789 158 0.2383 0.1852 2.7985 2.8106| | 11: 1.66 - 1.61 1.00 2740 147 0.2531 0.1860 2.7511 2.7863| | 12: 1.61 - 1.56 1.00 2787 146 0.2560 0.1848 2.6369 2.6134| | 13: 1.56 - 1.52 1.00 2745 130 0.2562 0.1968 2.5932 2.6103| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.2050 2.491 2.5795| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2278 2.4157 2.5554| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2175 2.3877 2.4458| | 17: 1.42 - 1.39 1.00 2785 139 0.2735 0.1961 2.3415 2.283| | 18: 1.39 - 1.36 1.00 2741 179 0.2656 0.2188 2.2766 2.3158| | 19: 1.36 - 1.34 1.00 2807 134 0.2628 0.2523 2.2517 2.3869| | 20: 1.34 - 1.32 1.00 2696 147 0.2721 0.2278 2.2263 2.2223| | 21: 1.32 - 1.30 1.00 2785 112 0.2711 0.2234 2.1774 2.1794| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2504 2.1352 2.191| | 23: 1.27 - 1.26 1.00 2802 156 0.2790 0.2460 2.1162 2.219| | 24: 1.26 - 1.24 1.00 2744 132 0.2763 0.2545 2.0739 2.1926| | 25: 1.24 - 1.22 1.00 2734 148 0.2819 0.2621 2.0448 2.0926| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2246 2.0204 2.0857| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2621 2.0028 1.9903| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2915 1.9918 2.0666| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2760 1.9649 2.0394| | 30: 1.16 - 1.15 1.00 2740 148 0.3023 0.3082 1.928 2.0089| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.58 2941 171 0.87 19.13 0.76 0.23 1512.79| | 2: 3.57 - 2.84 2876 122 0.80 26.41 1.27 0.23 1512.79| | 3: 2.84 - 2.48 2833 165 0.74 32.25 1.24 0.24 1252.77| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 577.97| | 5: 2.25 - 2.09 2756 127 0.77 29.55 1.28 0.25 577.97| | 6: 2.09 - 1.97 2846 113 0.84 22.46 1.29 0.25 312.94| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.29 0.26 86.89| | 8: 1.87 - 1.79 2789 144 0.86 20.51 1.25 0.26 86.89| | 9: 1.79 - 1.72 2745 138 0.89 17.88 1.23 0.26 52.91| | 10: 1.72 - 1.66 2789 158 0.87 19.51 1.22 0.26 46.11| | 11: 1.66 - 1.61 2740 147 0.86 20.82 1.24 0.26 44.55| | 12: 1.61 - 1.56 2787 146 0.89 18.18 1.24 0.25 28.74| | 13: 1.56 - 1.52 2745 130 0.87 19.95 1.23 0.25 28.74| | 14: 1.52 - 1.48 2803 134 0.87 20.53 1.25 0.25 25.88| | 15: 1.48 - 1.45 2738 128 0.87 20.22 1.24 0.25 20.63| | 16: 1.45 - 1.42 2756 161 0.86 21.49 1.23 0.25 20.63| | 17: 1.42 - 1.39 2785 139 0.86 21.07 1.24 0.25 17.63| | 18: 1.39 - 1.36 2741 179 0.86 21.29 1.22 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.86 21.84 1.21 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.87 21.13 1.20 0.24 13.35| | 21: 1.32 - 1.30 2785 112 0.85 22.27 1.19 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.92 1.21 0.24 12.92| | 23: 1.27 - 1.26 2802 156 0.85 22.66 1.21 0.24 11.67| | 24: 1.26 - 1.24 2744 132 0.84 23.53 1.20 0.24 11.67| | 25: 1.24 - 1.22 2734 148 0.83 24.50 1.20 0.24 11.24| | 26: 1.22 - 1.21 2727 135 0.83 24.99 1.20 0.23 10.76| | 27: 1.21 - 1.19 2814 148 0.82 26.16 1.21 0.23 10.76| | 28: 1.19 - 1.18 2671 147 0.81 27.14 1.18 0.22 10.49| | 29: 1.18 - 1.16 2800 134 0.80 27.94 1.16 0.22 10.39| | 30: 1.16 - 1.15 2740 148 0.78 29.69 1.15 0.22 10.39| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.39 max = 1512.79 mean = 218.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.93| |phase err.(test): min = 0.00 max = 89.56 mean = 22.79| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.250 1557 Z= 5.477 Angle : 5.405 17.557 2118 Z= 3.813 Chirality : 0.414 1.011 243 Planarity : 0.030 0.104 284 Dihedral : 13.616 84.852 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % 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: -2.16 (0.48), residues: 224 helix: -2.44 (0.37), residues: 107 sheet: -0.79 (0.94), residues: 28 loop : 0.08 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.022 ARG A 145 TYR 0.086 0.039 TYR A 141 PHE 0.092 0.051 PHE A 162 HIS 0.109 0.043 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792063 | | target function (ml) not normalized (work): 232595.585086 | | target function (ml) not normalized (free): 11834.789719 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2612 0.1943 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2612 0.1943 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1943 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2009 0.2013 0.1959 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1642 0.1760 n_refl.: 87593 ======================== 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 32.574-12.150 98.94 88 5 0.3814 386.380 357.488 0.663 1.002 0.401 11.894-9.307 99.02 97 4 0.1829 613.747 594.993 0.925 1.003 0.375 9.237-7.194 100.00 213 7 0.2141 501.969 491.906 0.957 1.004 0.361 7.162-5.571 100.00 427 22 0.2249 376.700 364.266 0.930 1.004 0.289 5.546-4.326 100.00 867 58 0.1301 517.116 510.431 0.962 1.003 0.219 4.315-3.360 100.00 1859 96 0.1151 491.781 487.995 1.006 1.003 0.209 3.356-2.611 100.00 3867 181 0.1436 323.075 319.434 0.995 1.002 0.119 2.608-2.026 99.99 8198 413 0.1353 214.169 211.849 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1653 104.589 103.942 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.379 45.047 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2559 29.222 26.978 0.978 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1760 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.882360 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2012.849949 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 0.1749 0.1870 0.0121 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1611 0.1750 0.0139 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1458 0.1624 0.0165 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1384 0.1573 0.0189 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1346 0.1541 0.0194 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1347 0.1546 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1290 0.1503 0.0212 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1270 0.1495 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1258 0.1490 0.0233 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1243 0.1472 0.0229 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1244 0.1481 0.0237 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1236 0.1475 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1474 0.0240 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1229 0.1469 0.0240 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1227 0.1470 0.0243 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1225 0.1471 0.0246 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1223 0.1477 0.0255 0.007 1.0 4.2 0.5 0.6 0 12.941 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1469 0.0240 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.69 2.40 3.013 19.068 2012.850 0.017 12.29 14.69 2.40 3.013 19.068 60.385 0.017 12.36 14.67 2.32 2.669 19.067 251.606 0.017 12.74 15.37 2.63 2.847 19.309 1006.425 0.016 12.55 15.50 2.95 3.380 19.662 2012.850 0.016 12.43 15.45 3.02 3.270 19.595 3019.275 0.015 12.35 15.44 3.10 3.392 19.653 4025.700 0.015 12.33 15.49 3.16 3.375 19.630 5032.125 0.015 12.24 15.40 3.17 3.376 19.630 6038.550 0.015 12.24 15.46 3.21 3.341 19.605 7044.975 0.015 12.12 15.33 3.21 3.363 19.609 8051.400 0.015 12.13 15.38 3.25 3.492 19.667 9057.825 0.015 12.11 15.37 3.26 3.370 19.586 10064.250 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: 251.606 Accepted refinement result: 12.36 14.67 2.32 2.669 19.067 251.606 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.09 3.31 0 1785 Protein: 9.08 115.01 17.00 3.32 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.72 26.61 22.06 N/A 0 8 Chain A: 9.08 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1467 r_work=0.1237 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1231 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016972 | | target function (ls_wunit_k1) not normalized (work): 1413.753146 | | target function (ls_wunit_k1) not normalized (free): 111.048419 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1677 0.1688 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1677 0.1688 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1683 0.1692 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1454 n_refl.: 87592 ======================== 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 32.574-12.150 95.83 87 5 0.3648 301.151 281.744 0.637 1.002 0.374 11.894-9.307 99.02 97 4 0.1710 482.428 469.054 0.918 1.003 0.370 9.237-7.194 100.00 213 7 0.1905 394.567 388.610 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1861 296.100 289.991 0.935 1.003 0.253 5.546-4.326 100.00 867 58 0.1015 406.473 403.559 0.963 1.003 0.220 4.315-3.360 100.00 1859 96 0.0873 386.558 385.409 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1172 253.949 252.819 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1019 168.345 167.622 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.211 82.392 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.456 35.960 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2254 22.970 21.454 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1230 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1455 | n_water=258 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1237 r_free=0.1453 | n_water=252 | time (s): 20.750 (total time: 22.690) Filter (q & B) r_work=0.1239 r_free=0.1453 | n_water=249 | time (s): 2.500 (total time: 25.190) Compute maps r_work=0.1239 r_free=0.1453 | n_water=249 | time (s): 1.490 (total time: 26.680) Filter (map) r_work=0.1257 r_free=0.1464 | n_water=227 | time (s): 3.100 (total time: 29.780) Find peaks r_work=0.1257 r_free=0.1464 | n_water=227 | time (s): 0.590 (total time: 30.370) Add new water r_work=0.1401 r_free=0.1634 | n_water=436 | time (s): 3.190 (total time: 33.560) Refine new water occ: r_work=0.1305 r_free=0.1482 adp: r_work=0.1226 r_free=0.1433 occ: r_work=0.1237 r_free=0.1412 adp: r_work=0.1205 r_free=0.1400 occ: r_work=0.1207 r_free=0.1394 adp: r_work=0.1198 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1387 r_work=0.1198 r_free=0.1387 | n_water=436 | time (s): 49.940 (total time: 83.500) Filter (q & B) r_work=0.1202 r_free=0.1393 | n_water=418 | time (s): 2.930 (total time: 86.430) Filter (dist only) r_work=0.1203 r_free=0.1392 | n_water=417 | time (s): 34.230 (total time: 120.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.482692 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1471.326722 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 0.1695 0.1813 0.0118 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1555 0.1688 0.0134 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1417 0.1576 0.0160 0.002 0.4 5.1 0.0 0.0 0 0.500 0.1356 0.1531 0.0175 0.001 0.4 4.8 0.0 0.0 0 0.750 0.1312 0.1498 0.0186 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1324 0.1510 0.0186 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1251 0.1458 0.0207 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1226 0.1448 0.0223 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1218 0.1448 0.0230 0.003 0.6 4.2 0.5 0.0 0 4.000 0.1211 0.1437 0.0226 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1204 0.1427 0.0223 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1202 0.1429 0.0227 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1198 0.1426 0.0228 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1193 0.1421 0.0228 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1189 0.1422 0.0233 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1187 0.1420 0.0232 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1187 0.1422 0.0235 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1185 0.1424 0.0239 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1183 0.1425 0.0242 0.008 0.9 5.1 0.5 0.6 0 14.241 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1420 0.0232 0.007 0.9 5.1 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.20 2.32 3.777 21.776 1471.327 0.016 11.87 14.20 2.32 3.777 21.776 44.140 0.016 11.87 14.20 2.32 3.777 21.776 183.916 0.016 12.02 14.58 2.56 3.639 21.779 735.663 0.015 12.03 14.92 2.89 3.473 21.979 1471.327 0.015 11.98 15.01 3.03 3.506 21.938 2206.990 0.014 11.78 14.82 3.04 3.475 21.999 2942.653 0.014 11.78 14.86 3.09 3.519 22.138 3678.317 0.014 11.68 14.84 3.16 3.516 21.978 4413.980 0.014 11.73 14.93 3.20 3.544 22.148 5149.644 0.014 11.74 15.02 3.28 3.590 22.181 5885.307 0.014 11.74 15.05 3.32 3.605 22.198 6620.970 0.014 11.67 14.99 3.32 3.621 22.228 7356.634 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.140 Accepted refinement result: 11.87 14.20 2.32 3.777 21.776 44.140 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.18 3.31 190 1754 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 40.91 N/A 190 227 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.11 115.04 19.48 N/A 0 1754 Chain S: 15.18 60.00 47.05 N/A 190 0 Histogram: Values Number of atoms 9.11 - 19.70 1261 19.70 - 30.30 245 30.30 - 40.89 160 40.89 - 51.48 138 51.48 - 62.08 117 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1420 r_work=0.1187 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1420 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1186 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014972 | | target function (ls_wunit_k1) not normalized (work): 1247.080590 | | target function (ls_wunit_k1) not normalized (free): 103.792504 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1186 0.1416 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1584 0.1583 0.1637 n_refl.: 87592 remove outliers: r(all,work,free)=0.1584 0.1583 0.1637 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1585 0.1584 0.1637 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1183 0.1408 n_refl.: 87592 remove outliers: r(all,work,free)=0.1193 0.1182 0.1408 n_refl.: 87590 ======================== 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 32.574-12.150 93.75 85 5 0.3419 299.701 276.397 0.584 1.002 0.342 11.894-9.307 99.02 97 4 0.1628 482.428 476.195 0.915 1.003 0.337 9.237-7.194 100.00 213 7 0.1682 394.567 394.187 0.987 1.003 0.300 7.162-5.571 100.00 427 22 0.1569 296.100 291.493 0.937 1.003 0.234 5.546-4.326 100.00 867 58 0.0889 406.473 403.516 0.960 1.003 0.199 4.315-3.360 100.00 1859 96 0.0777 386.558 385.521 1.005 1.002 0.180 3.356-2.611 100.00 3867 181 0.1090 253.949 252.979 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1004 168.345 167.771 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.211 82.413 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.456 35.991 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.970 21.485 0.987 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0102 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1408 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1408 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1408 | n_water=417 | time (s): 1.850 (total time: 1.850) Filter (dist) r_work=0.1182 r_free=0.1406 | n_water=411 | time (s): 34.060 (total time: 35.910) Filter (q & B) r_work=0.1182 r_free=0.1406 | n_water=411 | time (s): 0.920 (total time: 36.830) Compute maps r_work=0.1182 r_free=0.1406 | n_water=411 | time (s): 1.500 (total time: 38.330) Filter (map) r_work=0.1220 r_free=0.1394 | n_water=290 | time (s): 3.010 (total time: 41.340) Find peaks r_work=0.1220 r_free=0.1394 | n_water=290 | time (s): 0.680 (total time: 42.020) Add new water r_work=0.1326 r_free=0.1533 | n_water=467 | time (s): 2.840 (total time: 44.860) Refine new water occ: r_work=0.1241 r_free=0.1455 adp: r_work=0.1243 r_free=0.1455 occ: r_work=0.1220 r_free=0.1434 adp: r_work=0.1221 r_free=0.1433 occ: r_work=0.1204 r_free=0.1414 adp: r_work=0.1201 r_free=0.1408 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1408 r_work=0.1201 r_free=0.1408 | n_water=467 | time (s): 173.490 (total time: 218.350) Filter (q & B) r_work=0.1205 r_free=0.1413 | n_water=428 | time (s): 3.580 (total time: 221.930) Filter (dist only) r_work=0.1205 r_free=0.1413 | n_water=426 | time (s): 38.300 (total time: 260.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.786118 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.254399 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 0.1237 0.1379 0.0142 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1193 0.1351 0.0158 0.003 0.7 4.2 0.5 0.0 0 0.268 0.1174 0.1338 0.0164 0.004 0.8 3.5 0.5 0.0 0 0.536 0.1168 0.1337 0.0170 0.005 0.9 3.2 0.5 0.0 0 0.804 0.1164 0.1336 0.0172 0.006 1.0 3.5 0.5 0.0 0 1.072 0.1161 0.1337 0.0176 0.007 1.0 3.8 0.5 0.0 0 1.340 0.1159 0.1337 0.0178 0.007 1.1 3.8 0.5 0.0 0 1.608 0.1157 0.1337 0.0180 0.008 1.1 4.2 0.5 0.0 0 1.875 0.1167 0.1339 0.0172 0.005 0.9 3.2 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1336 0.0172 0.006 1.0 3.5 0.5 0.0 0 1.072 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 13.36 1.72 3.780 21.225 45.254 3.625 11.64 13.36 1.72 3.780 21.225 1.358 3.625 11.65 13.37 1.71 3.765 21.225 5.657 3.625 11.72 13.48 1.76 3.711 21.212 22.627 3.620 11.71 13.57 1.86 3.736 21.183 45.254 3.619 11.63 13.54 1.91 3.759 21.171 67.882 3.612 11.59 13.52 1.92 3.769 21.164 90.509 3.608 11.55 13.49 1.95 3.782 21.158 113.136 3.605 11.55 13.53 1.98 3.802 21.144 135.763 3.605 11.54 13.54 2.00 3.815 21.133 158.390 3.603 11.51 13.51 2.00 3.823 21.133 181.018 3.602 11.51 13.51 2.00 3.832 21.128 203.645 3.601 11.50 13.49 1.99 3.837 21.125 226.272 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.358 Accepted refinement result: 11.64 13.36 1.72 3.780 21.225 1.358 3.625 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.16 3.31 202 1751 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.51 76.71 35.84 N/A 202 224 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.12 115.05 19.44 N/A 0 1751 Chain S: 15.19 60.01 36.05 N/A 202 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.30 287 30.30 - 40.90 199 40.90 - 51.49 129 51.49 - 62.08 52 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1336 r_work=0.1164 r_free=0.1336 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1336 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1344 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1155 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618484 | | target function (ml) not normalized (work): 301398.044005 | | target function (ml) not normalized (free): 15867.117240 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1155 0.1344 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1509 0.1508 0.1563 n_refl.: 87590 remove outliers: r(all,work,free)=0.1509 0.1508 0.1563 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1507 0.1562 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1152 0.1336 n_refl.: 87590 remove outliers: r(all,work,free)=0.1159 0.1150 0.1336 n_refl.: 87584 ======================== 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 32.574-12.150 92.71 84 5 0.3672 297.059 276.975 0.523 1.000 0.330 11.894-9.307 98.04 96 4 0.2347 482.553 463.399 0.871 1.002 0.313 9.237-7.194 98.18 209 7 0.2260 386.048 386.929 0.953 1.002 0.223 7.162-5.571 100.00 427 22 0.2126 296.100 285.533 0.924 1.002 0.171 5.546-4.326 100.00 867 58 0.1111 406.473 401.949 0.963 1.002 0.148 4.315-3.360 100.00 1859 96 0.0958 386.558 383.663 1.004 1.002 0.133 3.356-2.611 100.00 3867 181 0.1144 253.949 251.998 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0935 168.345 167.532 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.211 82.499 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.456 36.033 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.970 21.504 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1150 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1336 | n_water=426 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1150 r_free=0.1336 | n_water=426 | time (s): 39.870 (total time: 42.380) Filter (q & B) r_work=0.1150 r_free=0.1336 | n_water=426 | time (s): 1.410 (total time: 43.790) Compute maps r_work=0.1150 r_free=0.1336 | n_water=426 | time (s): 1.880 (total time: 45.670) Filter (map) r_work=0.1182 r_free=0.1311 | n_water=314 | time (s): 3.850 (total time: 49.520) Find peaks r_work=0.1182 r_free=0.1311 | n_water=314 | time (s): 0.730 (total time: 50.250) Add new water r_work=0.1254 r_free=0.1400 | n_water=488 | time (s): 3.830 (total time: 54.080) Refine new water occ: r_work=0.1175 r_free=0.1336 adp: r_work=0.1176 r_free=0.1338 occ: r_work=0.1160 r_free=0.1318 adp: r_work=0.1160 r_free=0.1321 occ: r_work=0.1147 r_free=0.1298 adp: r_work=0.1144 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1300 r_work=0.1144 r_free=0.1300 | n_water=488 | time (s): 284.750 (total time: 338.830) Filter (q & B) r_work=0.1151 r_free=0.1302 | n_water=447 | time (s): 4.020 (total time: 342.850) Filter (dist only) r_work=0.1158 r_free=0.1300 | n_water=444 | time (s): 46.890 (total time: 389.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.802900 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.892851 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 0.1216 0.1338 0.0123 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1180 0.1316 0.0136 0.003 0.7 3.5 0.5 0.0 0 0.270 0.1165 0.1303 0.0139 0.005 0.9 5.1 0.5 0.0 0 0.541 0.1159 0.1301 0.0141 0.006 1.0 5.1 0.5 0.0 0 0.811 0.1154 0.1311 0.0157 0.006 1.0 4.2 0.5 0.0 0 1.082 0.1151 0.1305 0.0153 0.007 1.1 4.2 0.5 0.0 0 1.352 0.1149 0.1305 0.0156 0.008 1.1 4.2 0.5 0.0 0 1.623 0.1148 0.1307 0.0160 0.008 1.1 4.2 0.5 0.0 0 1.893 0.1157 0.1305 0.0148 0.006 1.0 4.5 0.5 0.0 0 0.901 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1301 0.0141 0.006 1.0 5.1 0.5 0.0 0 0.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.01 1.41 3.780 21.189 47.893 3.617 11.59 13.01 1.42 3.780 21.189 1.437 3.617 11.60 13.01 1.41 3.765 21.189 5.987 3.617 11.64 13.09 1.44 3.712 21.179 23.946 3.612 11.66 13.20 1.54 3.736 21.153 47.893 3.612 11.59 13.18 1.59 3.758 21.144 71.839 3.606 11.55 13.17 1.61 3.773 21.138 95.786 3.603 11.53 13.15 1.62 3.785 21.134 119.732 3.601 11.51 13.15 1.64 3.800 21.126 143.679 3.599 11.50 13.15 1.65 3.811 21.122 167.625 3.598 11.49 13.13 1.65 3.822 21.118 191.571 3.597 11.48 13.14 1.66 3.830 21.117 215.518 3.596 11.46 13.12 1.66 3.833 21.119 239.464 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.987 Accepted refinement result: 11.60 13.01 1.41 3.765 21.189 5.987 3.617 Individual atomic B min max mean iso aniso Overall: 9.12 114.86 21.10 3.26 224 1747 Protein: 9.12 114.86 17.03 3.27 0 1519 Water: 11.51 76.70 35.00 N/A 224 220 Other: 19.72 26.59 22.09 N/A 0 8 Chain A: 9.12 114.86 19.41 N/A 0 1747 Chain S: 15.16 60.00 34.30 N/A 224 0 Histogram: Values Number of atoms 9.12 - 19.70 1265 19.70 - 30.27 300 30.27 - 40.85 214 40.85 - 51.42 123 51.42 - 61.99 46 61.99 - 72.57 11 72.57 - 83.14 6 83.14 - 93.72 4 93.72 - 104.29 0 104.29 - 114.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1301 r_work=0.1160 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1301 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1295 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1156 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614358 | | target function (ml) not normalized (work): 301032.648496 | | target function (ml) not normalized (free): 15832.405545 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1156 0.1295 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1498 0.1500 0.1482 n_refl.: 87584 remove outliers: r(all,work,free)=0.1498 0.1500 0.1482 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1496 0.1499 0.1481 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1154 0.1293 n_refl.: 87584 remove outliers: r(all,work,free)=0.1159 0.1152 0.1293 n_refl.: 87579 ======================== 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 32.574-12.150 89.58 81 5 0.3846 290.407 257.741 0.463 1.002 0.306 11.894-9.307 96.08 94 4 0.2357 475.798 465.624 0.852 1.003 0.259 9.237-7.194 98.18 209 7 0.2414 386.048 379.912 0.917 1.003 0.195 7.162-5.571 100.00 427 22 0.2180 296.100 286.619 0.907 1.003 0.142 5.546-4.326 100.00 867 58 0.1150 406.473 401.676 0.952 1.003 0.123 4.315-3.360 100.00 1859 96 0.0947 386.558 384.154 0.993 1.003 0.110 3.356-2.611 100.00 3867 181 0.1132 253.949 252.097 0.999 1.002 0.024 2.608-2.026 99.99 8198 413 0.0933 168.345 167.661 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0910 82.211 82.547 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.456 36.064 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.970 21.522 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0217 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1152 r_free=0.1293 After: r_work=0.1153 r_free=0.1293 ================================== NQH flips ================================== r_work=0.1153 r_free=0.1293 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1153 r_free=0.1293 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1153 r_free=0.1293 | n_water=444 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1153 r_free=0.1293 | n_water=444 | time (s): 42.630 (total time: 44.990) Filter (q & B) r_work=0.1154 r_free=0.1292 | n_water=441 | time (s): 3.930 (total time: 48.920) Compute maps r_work=0.1154 r_free=0.1292 | n_water=441 | time (s): 1.890 (total time: 50.810) Filter (map) r_work=0.1182 r_free=0.1307 | n_water=338 | time (s): 4.010 (total time: 54.820) Find peaks r_work=0.1182 r_free=0.1307 | n_water=338 | time (s): 0.730 (total time: 55.550) Add new water r_work=0.1229 r_free=0.1347 | n_water=491 | time (s): 3.810 (total time: 59.360) Refine new water occ: r_work=0.1171 r_free=0.1298 adp: r_work=0.1172 r_free=0.1300 occ: r_work=0.1158 r_free=0.1288 adp: r_work=0.1158 r_free=0.1290 occ: r_work=0.1149 r_free=0.1281 adp: r_work=0.1146 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1283 r_work=0.1146 r_free=0.1283 | n_water=491 | time (s): 286.100 (total time: 345.460) Filter (q & B) r_work=0.1153 r_free=0.1289 | n_water=455 | time (s): 4.020 (total time: 349.480) Filter (dist only) r_work=0.1153 r_free=0.1288 | n_water=452 | time (s): 47.880 (total time: 397.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.764797 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.915430 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 0.1227 0.1337 0.0110 0.004 0.7 8.0 0.0 0.0 0 0.088 0.1184 0.1308 0.0124 0.004 0.8 8.3 0.0 0.0 0 0.265 0.1165 0.1296 0.0131 0.005 0.9 8.0 0.5 0.0 0 0.529 0.1153 0.1288 0.0135 0.006 1.0 8.0 0.5 0.0 0 0.794 0.1152 0.1288 0.0136 0.006 1.0 8.0 0.5 0.0 0 1.059 0.1150 0.1287 0.0137 0.007 1.0 8.0 0.5 0.0 0 1.324 0.1148 0.1286 0.0138 0.008 1.1 8.0 0.5 0.0 0 1.588 0.1146 0.1285 0.0139 0.008 1.1 8.0 0.5 0.0 0 1.853 0.1152 0.1288 0.0136 0.006 1.0 8.0 0.5 0.0 0 0.882 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1285 0.0139 0.008 1.1 8.0 0.5 0.0 0 1.853 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 12.85 1.39 3.758 21.200 51.915 3.606 11.46 12.85 1.39 3.758 21.200 1.557 3.606 11.46 12.85 1.39 3.758 21.200 6.489 3.606 11.47 12.89 1.42 3.699 21.192 25.958 3.599 11.48 13.00 1.52 3.731 21.160 51.915 3.599 11.41 12.97 1.56 3.748 21.154 77.873 3.593 11.39 12.97 1.58 3.764 21.147 103.831 3.591 11.35 12.94 1.59 3.772 21.148 129.789 3.588 11.35 12.97 1.62 3.795 21.133 155.746 3.588 11.34 12.96 1.62 3.806 21.130 181.704 3.586 11.32 12.93 1.61 3.812 21.130 207.662 3.584 11.31 12.92 1.61 3.818 21.131 233.619 3.583 11.30 12.92 1.62 3.825 21.130 259.577 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.489 Accepted refinement result: 11.46 12.85 1.39 3.758 21.200 6.489 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 114.86 21.13 3.26 233 1746 Protein: 9.11 114.86 17.03 3.27 0 1519 Water: 11.50 76.69 34.90 N/A 233 219 Other: 19.71 26.58 22.08 N/A 0 8 Chain A: 9.11 114.86 19.38 N/A 0 1746 Chain S: 15.15 60.00 34.22 N/A 233 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.26 308 30.26 - 40.84 210 40.84 - 51.41 126 51.41 - 61.98 49 61.98 - 72.56 11 72.56 - 83.13 6 83.13 - 93.71 4 93.71 - 104.28 0 104.28 - 114.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1285 r_work=0.1146 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1285 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1282 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1141 r_free= 0.1282 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603510 | | target function (ml) not normalized (work): 300111.129920 | | target function (ml) not normalized (free): 15794.609920 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1358 0.1352 5.6708 5.6053| | 2: 3.57 - 2.84 1.00 2888 124 0.1070 0.1332 5.1553 5.1984| | 3: 2.83 - 2.48 1.00 2820 163 0.1106 0.1212 4.9389 4.9764| | 4: 2.47 - 2.25 1.00 2825 136 0.0906 0.0976 4.6254 4.6526| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0958 4.5677 4.6206| | 6: 2.09 - 1.97 1.00 2846 113 0.0868 0.1016 4.2689 4.3625| | 7: 1.97 - 1.87 1.00 2787 165 0.0895 0.1107 3.9816 4.0788| | 8: 1.87 - 1.79 1.00 2789 144 0.0929 0.1118 3.8962 3.9948| | 9: 1.79 - 1.72 1.00 2745 138 0.0885 0.1206 3.6488 3.8386| | 10: 1.72 - 1.66 1.00 2831 160 0.0937 0.1178 3.5706 3.7075| | 11: 1.66 - 1.61 1.00 2712 147 0.0876 0.1021 3.4965 3.5598| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1105 3.3299 3.4426| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1046 3.3077 3.4081| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1022 3.238 3.3122| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1220 3.1533 3.263| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1237 3.1315 3.2341| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1281 3.1169 3.2213| | 18: 1.39 - 1.36 1.00 2741 179 0.1195 0.1326 3.1023 3.2429| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1556 3.1103 3.2601| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1447 3.1101 3.1451| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1548 3.111 3.116| | 22: 1.29 - 1.27 1.00 2704 152 0.1554 0.1982 3.1195 3.2959| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1779 3.1318 3.1963| | 24: 1.26 - 1.24 1.00 2744 132 0.1701 0.1817 3.1244 3.2198| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2158 3.1412 3.2614| | 26: 1.22 - 1.21 1.00 2727 135 0.1903 0.1770 3.1455 3.2023| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2157 3.1698 3.1605| | 28: 1.19 - 1.18 1.00 2671 147 0.2198 0.2299 3.1649 3.1718| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2396 3.148 3.2311| | 30: 1.16 - 1.15 1.00 2739 148 0.2440 0.2464 3.1415 3.1716| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.57 - 3.58 2921 171 0.95 8.33 1.00 0.98 5578.95| | 2: 3.57 - 2.84 2888 124 0.93 12.36 1.01 0.98 5578.95| | 3: 2.83 - 2.48 2820 163 0.90 16.24 0.99 0.98 4663.50| | 4: 2.47 - 2.25 2825 136 0.92 13.27 1.00 0.99 2302.86| | 5: 2.25 - 2.09 2756 127 0.91 15.40 1.01 0.99 2302.86| | 6: 2.09 - 1.97 2846 113 0.93 12.25 1.02 0.99 1334.73| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.98 509.04| | 8: 1.87 - 1.79 2789 144 0.93 12.55 1.00 0.98 509.04| | 9: 1.79 - 1.72 2745 138 0.94 10.10 0.98 0.98 288.79| | 10: 1.72 - 1.66 2831 160 0.94 11.16 0.98 0.98 244.68| | 11: 1.66 - 1.61 2712 147 0.93 11.75 0.98 0.98 234.29| | 12: 1.61 - 1.56 2773 144 0.96 8.85 0.99 0.98 136.33| | 13: 1.56 - 1.52 2745 130 0.95 10.33 1.02 0.98 136.33| | 14: 1.52 - 1.48 2803 134 0.94 10.68 1.02 0.99 122.43| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.99 96.97| | 16: 1.45 - 1.42 2756 161 0.94 10.99 1.02 0.99 96.97| | 17: 1.42 - 1.39 2785 139 0.95 10.87 1.01 0.99 88.47| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.99 83.54| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.99 83.54| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 79.83| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.97 79.57| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.97 79.99| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.08| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.95 82.08| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.95 84.16| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.94 86.46| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.94 86.46| | 28: 1.19 - 1.18 2671 147 0.88 20.43 1.01 0.94 90.43| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.93 91.92| | 30: 1.16 - 1.15 2739 148 0.86 22.12 0.98 0.93 91.92| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.57 max = 5578.95 mean = 865.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.93 mean = 13.39| |phase err.(test): min = 0.00 max = 89.74 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1141 0.1282 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1467 0.1468 0.1480 n_refl.: 87579 remove outliers: r(all,work,free)=0.1467 0.1468 0.1480 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1466 0.1467 0.1480 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1141 0.1280 n_refl.: 87579 remove outliers: r(all,work,free)=0.1144 0.1137 0.1280 n_refl.: 87571 ======================== 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 32.574-12.150 86.46 78 5 0.3898 290.386 248.778 0.446 1.000 0.310 11.894-9.307 92.16 90 4 0.2204 477.809 451.405 0.863 1.002 0.310 9.237-7.194 97.73 208 7 0.2477 385.568 379.954 0.925 1.003 0.192 7.162-5.571 100.00 427 22 0.2145 296.100 286.610 0.914 1.003 0.160 5.546-4.326 100.00 867 58 0.1140 406.473 401.691 0.963 1.003 0.140 4.315-3.360 100.00 1859 96 0.0930 386.558 384.577 1.003 1.003 0.120 3.356-2.611 100.00 3867 181 0.1116 253.949 252.134 1.010 1.002 0.014 2.608-2.026 99.99 8198 413 0.0916 168.345 167.830 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.211 82.603 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.456 36.085 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.970 21.536 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0154 ================= 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 : 0.2611 0.1943 0.084 5.405 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_weight: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1229 0.1469 0.006 0.858 9.1 119.5 20.1 258 0.133 1_adp: 0.1236 0.1467 0.006 0.858 9.1 119.5 20.1 258 0.133 1_regHadp: 0.1237 0.1471 0.006 0.858 9.1 119.5 20.1 258 0.133 1_occ: 0.1231 0.1462 0.006 0.858 9.1 119.5 20.1 258 0.133 2_bss: 0.1229 0.1454 0.006 0.858 9.1 119.5 20.1 258 0.133 2_settarget: 0.1229 0.1454 0.006 0.858 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1229 0.1454 0.006 0.863 9.1 119.5 20.1 258 0.133 2_nqh: 0.1230 0.1455 0.006 0.863 9.1 119.5 20.1 258 0.136 2_sol: 0.1203 0.1392 0.006 0.863 9.1 115.0 22.2 417 n/a 2_weight: 0.1203 0.1392 0.006 0.863 9.1 115.0 22.2 417 n/a 2_xyzrec: 0.1187 0.1420 0.007 0.879 9.1 115.0 22.2 417 n/a 2_adp: 0.1187 0.1420 0.007 0.879 9.1 115.0 22.2 417 n/a 2_regHadp: 0.1187 0.1420 0.007 0.879 9.1 115.0 22.2 417 n/a 2_occ: 0.1186 0.1416 0.007 0.879 9.1 115.0 22.2 417 n/a 3_bss: 0.1182 0.1408 0.007 0.879 9.1 115.0 22.2 417 n/a 3_settarget: 0.1182 0.1408 0.007 0.879 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1182 0.1408 0.007 0.880 9.1 115.0 22.2 417 n/a 3_nqh: 0.1182 0.1408 0.007 0.880 9.1 115.0 22.2 417 n/a 3_sol: 0.1205 0.1413 0.007 0.880 9.1 115.0 21.2 426 n/a 3_weight: 0.1205 0.1413 0.007 0.880 9.1 115.0 21.2 426 n/a 3_xyzrec: 0.1164 0.1336 0.006 0.967 9.1 115.0 21.2 426 n/a 3_adp: 0.1164 0.1336 0.006 0.967 9.1 115.0 21.2 426 n/a 3_regHadp: 0.1164 0.1336 0.006 0.967 9.1 115.0 21.2 426 n/a 3_occ: 0.1155 0.1344 0.006 0.967 9.1 115.0 21.2 426 n/a 4_bss: 0.1150 0.1336 0.006 0.967 9.1 115.0 21.2 426 n/a 4_settarget: 0.1150 0.1336 0.006 0.967 9.1 115.0 21.2 426 n/a 4_updatecdl: 0.1150 0.1336 0.006 0.968 9.1 115.0 21.2 426 n/a 4_nqh: 0.1150 0.1336 0.006 0.968 9.1 115.0 21.2 426 n/a 4_sol: 0.1158 0.1300 0.006 0.968 9.1 115.0 21.1 444 n/a 4_weight: 0.1158 0.1300 0.006 0.968 9.1 115.0 21.1 444 n/a 4_xyzrec: 0.1159 0.1301 0.006 0.960 9.1 115.0 21.1 444 n/a 4_adp: 0.1160 0.1301 0.006 0.960 9.1 114.9 21.1 444 n/a 4_regHadp: 0.1160 0.1301 0.006 0.960 9.1 114.9 21.1 444 n/a 4_occ: 0.1156 0.1295 0.006 0.960 9.1 114.9 21.1 444 n/a 5_bss: 0.1152 0.1293 0.006 0.960 9.1 114.9 21.1 444 n/a 5_settarget: 0.1152 0.1293 0.006 0.960 9.1 114.9 21.1 444 n/a 5_updatecdl: 0.1152 0.1293 0.006 0.961 9.1 114.9 21.1 444 n/a 5_setrh: 0.1153 0.1293 0.006 0.961 9.1 114.9 21.1 444 n/a 5_nqh: 0.1153 0.1293 0.006 0.961 9.1 114.9 21.1 444 n/a 5_sol: 0.1153 0.1288 0.006 0.961 9.1 114.9 21.1 452 n/a 5_weight: 0.1153 0.1288 0.006 0.961 9.1 114.9 21.1 452 n/a 5_xyzrec: 0.1146 0.1285 0.008 1.102 9.1 114.9 21.1 452 n/a 5_adp: 0.1146 0.1285 0.008 1.102 9.1 114.9 21.1 452 n/a 5_regHadp: 0.1146 0.1285 0.008 1.102 9.1 114.9 21.1 452 n/a 5_occ: 0.1141 0.1282 0.008 1.102 9.1 114.9 21.1 452 n/a end: 0.1137 0.1280 0.008 1.102 9.1 114.8 21.1 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2667343_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2667343_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 13733.0800 Write final files (write_after_run_outputs) : 95.5600 Total : 13831.8100 Total CPU time: 3.85 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:10:10 PST -0800 (1735366210.03 s) Start R-work = 0.1642, R-free = 0.1760 Final R-work = 0.1137, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 14008.51 seconds wall clock time: 254 minutes 17.88 seconds (15257.88 seconds total)