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_3975290.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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 =============================================================================== 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: 1.52, per 1000 atoms: 0.45 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: 0.55 Conformation dependent library (CDL) restraints added in 176.8 milliseconds Time building geometry restraints manager: 0.75 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: 703 0.94 - 1.20: 1000 1.20 - 1.46: 743 1.46 - 1.73: 696 1.73 - 1.99: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.700 -0.241 1.23e-02 6.61e+03 3.83e+02 bond pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " ideal model delta sigma weight residual 1.524 1.753 -0.229 1.26e-02 6.30e+03 3.30e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.669 -0.213 1.18e-02 7.18e+03 3.26e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.458 1.224 0.233 1.30e-02 5.92e+03 3.22e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.437 -0.201 1.13e-02 7.83e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3221 4.84 - 9.68: 1828 9.68 - 14.52: 613 14.52 - 19.36: 100 19.36 - 24.20: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 123.27 144.05 -20.78 1.16e+00 7.43e-01 3.21e+02 angle pdb=" O GLU A 59 " pdb=" C GLU A 59 " pdb=" N ASP A 60 " ideal model delta sigma weight residual 122.12 140.18 -18.06 1.06e+00 8.90e-01 2.90e+02 angle pdb=" C GLY A 40 " pdb=" N ALYS A 41 " pdb=" CA ALYS A 41 " ideal model delta sigma weight residual 120.31 140.41 -20.10 1.52e+00 4.33e-01 1.75e+02 angle pdb=" O GLY A 75 " pdb=" C GLY A 75 " pdb=" N AASN A 76 " ideal model delta sigma weight residual 122.70 105.88 16.82 1.30e+00 5.92e-01 1.67e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 109.05 12.72 1.00e+00 1.00e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.69: 916 15.69 - 31.36: 125 31.36 - 47.03: 44 47.03 - 62.70: 22 62.70 - 78.37: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.240: 116 0.240 - 0.479: 67 0.479 - 0.718: 46 0.718 - 0.956: 13 0.956 - 1.195: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA LYS A 89 " pdb=" N LYS A 89 " pdb=" C LYS A 89 " pdb=" CB LYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.026 9.50e-02 1.11e+02 6.31e-02 8.80e+01 pdb=" NE ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.132 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.043 2.00e-02 2.50e+03 5.24e-02 8.23e+01 pdb=" CG BTYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.148 9.50e-02 1.11e+02 7.69e-02 8.11e+01 pdb=" NE ARG A 156 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1049 2.32 - 2.89: 8078 2.89 - 3.46: 10513 3.46 - 4.03: 15254 4.03 - 4.60: 21801 Nonbonded interactions: 56695 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.750 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.762 1.850 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.782 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.784 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.819 1.850 ... (remaining 56690 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_3975290_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= 0.2612 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796841 | | target function (ml) not normalized (work): 232993.643161 | | target function (ml) not normalized (free): 11855.759271 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2089 7.0516 4.9487| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1690 4.3494 4.3288| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1771 4.1248 4.1603| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1588 3.8387 3.8502| | 5: 2.25 - 2.09 1.00 2756 127 0.2487 0.1671 3.8016 3.8205| | 6: 2.09 - 1.97 1.00 2846 113 0.2575 0.1853 3.4647 3.5759| | 7: 1.97 - 1.87 1.00 2787 165 0.2534 0.1870 3.1494 3.2297| | 8: 1.87 - 1.79 1.00 2789 144 0.2454 0.1960 3.0807 3.1719| | 9: 1.79 - 1.72 1.00 2745 138 0.2391 0.2044 2.9173 3.0304| | 10: 1.72 - 1.66 1.00 2789 158 0.2422 0.1995 2.8084 2.8686| | 11: 1.66 - 1.61 1.00 2740 147 0.2447 0.1744 2.7588 2.7573| | 12: 1.61 - 1.56 1.00 2787 146 0.2536 0.1985 2.6388 2.6115| | 13: 1.56 - 1.52 1.00 2745 130 0.2601 0.1859 2.5819 2.5964| | 14: 1.52 - 1.48 1.00 2803 134 0.2603 0.2099 2.5093 2.5952| | 15: 1.48 - 1.45 1.00 2738 128 0.2624 0.2330 2.4329 2.5618| | 16: 1.45 - 1.42 1.00 2756 161 0.2709 0.2178 2.3913 2.4203| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2199 2.3271 2.3459| | 18: 1.39 - 1.36 1.00 2741 179 0.2644 0.2217 2.2859 2.3566| | 19: 1.36 - 1.34 1.00 2807 134 0.2682 0.2251 2.2578 2.287| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2148 2.2008 2.1682| | 21: 1.32 - 1.30 1.00 2785 112 0.2737 0.2163 2.1842 2.1136| | 22: 1.29 - 1.27 1.00 2704 152 0.2771 0.2498 2.1415 2.1915| | 23: 1.27 - 1.26 1.00 2802 156 0.2804 0.2548 2.0991 2.1847| | 24: 1.26 - 1.24 1.00 2744 132 0.2832 0.2545 2.0948 2.1452| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2240 2.0489 2.0368| | 26: 1.22 - 1.21 1.00 2727 135 0.2889 0.2615 2.0185 2.1772| | 27: 1.21 - 1.19 1.00 2814 148 0.3011 0.2633 2.0245 2.037| | 28: 1.19 - 1.18 1.00 2671 147 0.2967 0.2888 1.9857 2.0129| | 29: 1.18 - 1.16 1.00 2800 134 0.2947 0.2992 1.9516 2.096| | 30: 1.16 - 1.15 1.00 2740 148 0.3066 0.2820 1.9305 1.9662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1470.08| | 2: 3.57 - 2.84 2876 122 0.80 26.06 1.27 0.23 1470.08| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.24 0.23 1221.56| | 4: 2.47 - 2.25 2825 136 0.81 25.75 1.26 0.25 576.63| | 5: 2.25 - 2.09 2756 127 0.77 29.55 1.29 0.25 576.63| | 6: 2.09 - 1.97 2846 113 0.83 23.40 1.30 0.25 319.63| | 7: 1.97 - 1.87 2787 165 0.89 17.64 1.28 0.25 100.44| | 8: 1.87 - 1.79 2789 144 0.85 22.19 1.25 0.25 100.44| | 9: 1.79 - 1.72 2745 138 0.87 19.31 1.23 0.25 59.42| | 10: 1.72 - 1.66 2789 158 0.86 20.89 1.23 0.25 51.21| | 11: 1.66 - 1.61 2740 147 0.85 21.95 1.23 0.25 49.27| | 12: 1.61 - 1.56 2787 146 0.88 18.48 1.24 0.25 29.67| | 13: 1.56 - 1.52 2745 130 0.87 20.44 1.24 0.25 29.67| | 14: 1.52 - 1.48 2803 134 0.86 20.74 1.25 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.16 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.85 21.74 1.25 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.23 0.25 17.56| | 18: 1.39 - 1.36 2741 179 0.87 20.95 1.22 0.25 15.64| | 19: 1.36 - 1.34 2807 134 0.86 21.96 1.22 0.25 15.64| | 20: 1.34 - 1.32 2696 147 0.87 20.96 1.21 0.24 13.01| | 21: 1.32 - 1.30 2785 112 0.86 21.67 1.20 0.24 12.83| | 22: 1.29 - 1.27 2704 152 0.85 22.41 1.21 0.24 12.58| | 23: 1.27 - 1.26 2802 156 0.85 22.54 1.22 0.24 11.29| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.20 0.24 11.29| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.90| | 26: 1.22 - 1.21 2727 135 0.83 24.82 1.21 0.23 10.47| | 27: 1.21 - 1.19 2814 148 0.82 25.67 1.20 0.23 10.47| | 28: 1.19 - 1.18 2671 147 0.81 26.45 1.17 0.23 10.07| | 29: 1.18 - 1.16 2800 134 0.81 27.18 1.16 0.22 9.92| | 30: 1.16 - 1.15 2740 148 0.79 28.83 1.15 0.22 9.92| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.92 max = 1470.08 mean = 215.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.01| |phase err.(test): min = 0.00 max = 89.25 mean = 22.99| |-----------------------------------------------------------------------------| ----------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= 5.583 Angle : 5.396 20.784 2118 Z= 3.828 Chirality : 0.384 1.195 243 Planarity : 0.030 0.116 284 Dihedral : 13.889 78.366 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -2.76 (0.44), residues: 224 helix: -2.90 (0.32), residues: 102 sheet: -2.04 (0.75), residues: 30 loop : -0.04 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.016 ARG A 145 TYR 0.082 0.035 TYR A 139 PHE 0.087 0.030 PHE A 164 HIS 0.050 0.028 HIS A 126 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= 0.2612 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796841 | | target function (ml) not normalized (work): 232993.643161 | | target function (ml) not normalized (free): 11855.759271 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2612 0.1977 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2612 0.1977 n_refl.: 87602 remove outliers: r(all,work,free)=0.1986 0.1989 0.1977 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2009 0.2012 0.1992 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1642 0.1801 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1642 0.1801 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 0.3811 386.680 357.572 0.667 1.001 0.401 11.894-9.307 99.02 97 4 0.1797 614.222 596.480 0.926 1.003 0.380 9.237-7.194 100.00 213 7 0.2155 502.358 492.007 0.957 1.003 0.359 7.162-5.571 100.00 427 22 0.2220 376.992 364.207 0.931 1.003 0.340 5.546-4.326 100.00 867 58 0.1244 517.516 512.512 0.961 1.003 0.209 4.315-3.360 100.00 1859 96 0.1155 492.162 488.770 1.001 1.003 0.153 3.356-2.611 100.00 3867 181 0.1435 323.325 319.600 0.997 1.002 0.119 2.608-2.026 99.99 8198 413 0.1364 214.335 212.023 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1647 104.670 103.967 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2080 46.415 45.114 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2597 29.245 26.928 0.974 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1801 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1801 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.006950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.879593 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 0.1616 0.1734 0.0118 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1536 0.1673 0.0137 0.001 0.5 3.8 0.0 0.0 0 0.250 0.1449 0.1607 0.0158 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1380 0.1560 0.0180 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1544 0.0191 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1353 0.1550 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1295 0.1513 0.0218 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1256 0.1481 0.0224 0.003 0.7 3.2 0.5 0.0 0 3.000 0.1252 0.1482 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1486 0.0239 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1484 0.0241 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1237 0.1477 0.0241 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1233 0.1474 0.0241 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1475 0.0244 0.006 0.9 2.9 0.5 0.0 0 9.000 0.1229 0.1472 0.0243 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1226 0.1470 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1225 0.1472 0.0246 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1222 0.1470 0.0248 0.008 1.0 3.2 0.5 0.6 0 13.503 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1470 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.70 2.44 3.013 19.050 2007.880 0.017 12.26 14.70 2.44 2.994 19.050 60.236 0.017 12.33 14.67 2.35 2.676 19.050 250.985 0.017 12.63 15.25 2.62 2.681 19.176 1003.940 0.017 12.54 15.46 2.92 3.258 19.605 2007.880 0.016 12.40 15.46 3.06 3.298 19.656 3011.819 0.015 12.34 15.46 3.12 3.365 19.656 4015.759 0.015 12.30 15.45 3.16 3.376 19.649 5019.699 0.015 12.17 15.34 3.16 3.292 19.604 6023.639 0.015 12.16 15.38 3.22 3.366 19.640 7027.579 0.015 12.15 15.41 3.25 3.315 19.600 8031.518 0.015 12.15 15.42 3.27 3.345 19.597 9035.458 0.015 12.16 15.53 3.37 3.406 19.627 10039.398 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: 250.985 Accepted refinement result: 12.33 14.67 2.35 2.676 19.050 250.985 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.33 0 1785 Protein: 9.07 115.06 16.99 3.33 0 1519 Water: 11.49 119.44 38.22 N/A 0 258 Other: 19.68 26.59 22.04 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1273 20.11 - 31.15 226 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1467 r_work=0.1234 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 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 = 0.1228 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1228 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016906 | | target function (ls_wunit_k1) not normalized (work): 1408.184827 | | target function (ls_wunit_k1) not normalized (free): 108.564827 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1467 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1673 0.1674 0.1695 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1679 0.1680 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1226 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1237 0.1225 0.1457 n_refl.: 87591 ======================== 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 94.79 86 5 0.3398 303.485 278.432 0.640 1.002 0.370 11.894-9.307 99.02 97 4 0.1617 482.954 471.337 0.925 1.003 0.366 9.237-7.194 100.00 213 7 0.1877 394.997 390.070 0.965 1.003 0.324 7.162-5.571 100.00 427 22 0.1820 296.423 290.598 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1004 406.916 404.037 0.966 1.003 0.230 4.315-3.360 100.00 1859 96 0.0877 386.980 385.806 1.007 1.002 0.170 3.356-2.611 100.00 3867 181 0.1171 254.226 253.116 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1022 168.529 167.831 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1110 82.301 82.501 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.495 36.006 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.995 21.478 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0506 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1457 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=0.1227 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1459 | n_water=258 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1236 r_free=0.1455 | n_water=250 | time (s): 21.780 (total time: 23.620) Filter (q & B) r_work=0.1238 r_free=0.1455 | n_water=247 | time (s): 2.340 (total time: 25.960) Compute maps r_work=0.1238 r_free=0.1455 | n_water=247 | time (s): 1.420 (total time: 27.380) Filter (map) r_work=0.1252 r_free=0.1455 | n_water=228 | time (s): 2.270 (total time: 29.650) Find peaks r_work=0.1252 r_free=0.1455 | n_water=228 | time (s): 0.540 (total time: 30.190) Add new water r_work=0.1395 r_free=0.1636 | n_water=432 | time (s): 3.180 (total time: 33.370) Refine new water occ: r_work=0.1304 r_free=0.1495 adp: r_work=0.1223 r_free=0.1439 occ: r_work=0.1235 r_free=0.1425 adp: r_work=0.1201 r_free=0.1408 occ: r_work=0.1205 r_free=0.1403 adp: r_work=0.1195 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1399 r_work=0.1195 r_free=0.1399 | n_water=432 | time (s): 92.080 (total time: 125.450) Filter (q & B) r_work=0.1198 r_free=0.1401 | n_water=418 | time (s): 3.090 (total time: 128.540) Filter (dist only) r_work=0.1198 r_free=0.1401 | n_water=417 | time (s): 34.150 (total time: 162.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.180747 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1495.665641 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 0.1639 0.1755 0.0116 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1476 0.1618 0.0143 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1405 0.1564 0.0160 0.002 0.4 5.8 0.0 0.0 0 0.500 0.1345 0.1522 0.0177 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1314 0.1501 0.0187 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1307 0.1496 0.0189 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1253 0.1462 0.0208 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1226 0.1446 0.0220 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1214 0.1433 0.0219 0.004 0.7 4.2 0.5 0.0 0 4.000 0.1204 0.1428 0.0223 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1198 0.1426 0.0228 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1195 0.1425 0.0231 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1192 0.1424 0.0232 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1187 0.1420 0.0232 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1184 0.1418 0.0234 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1183 0.1420 0.0236 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1182 0.1416 0.0235 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1180 0.1417 0.0237 0.008 0.9 5.1 0.5 0.6 0 13.000 0.1180 0.1416 0.0236 0.008 1.0 4.8 0.5 0.6 0 14.090 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1180 0.1416 0.0236 0.008 1.0 4.8 0.5 0.6 0 14.090 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 14.16 2.36 3.781 21.746 1495.666 0.015 11.80 14.16 2.36 3.781 21.746 44.870 0.015 11.80 14.16 2.36 3.781 21.746 186.958 0.015 12.02 14.66 2.65 3.609 21.765 747.833 0.015 11.99 14.96 2.96 3.542 21.826 1495.666 0.014 11.91 15.08 3.18 3.487 21.930 2243.498 0.014 11.78 14.99 3.21 3.484 21.946 2991.331 0.014 11.75 14.89 3.15 3.510 22.137 3739.164 0.014 11.67 14.81 3.14 3.509 22.084 4486.997 0.014 11.60 14.86 3.27 3.518 22.136 5234.830 0.013 11.65 14.97 3.32 3.557 22.159 5982.663 0.013 11.60 14.92 3.33 3.565 22.171 6730.495 0.013 11.55 14.85 3.31 3.563 22.134 7478.328 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 186.958 Accepted refinement result: 11.80 14.16 2.36 3.781 21.746 186.958 0.015 Individual atomic B min max mean iso aniso Overall: 9.11 115.09 22.14 3.33 189 1755 Protein: 9.11 115.09 17.02 3.33 0 1519 Water: 11.52 76.69 40.78 N/A 189 228 Other: 19.71 26.62 22.07 N/A 0 8 Chain A: 9.11 115.09 19.49 N/A 0 1755 Chain S: 12.88 60.00 46.71 N/A 189 0 Histogram: Values Number of atoms 9.11 - 19.71 1260 19.71 - 30.30 242 30.30 - 40.90 169 40.90 - 51.50 135 51.50 - 62.10 115 62.10 - 72.70 12 72.70 - 83.30 5 83.30 - 93.89 4 93.89 - 104.49 0 104.49 - 115.09 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1416 r_work=0.1180 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1177 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014602 | | target function (ls_wunit_k1) not normalized (work): 1216.267154 | | target function (ls_wunit_k1) not normalized (free): 105.100912 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1177 0.1416 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1526 0.1522 0.1639 n_refl.: 87591 remove outliers: r(all,work,free)=0.1526 0.1522 0.1639 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1528 0.1523 0.1641 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1174 0.1413 n_refl.: 87591 remove outliers: r(all,work,free)=0.1185 0.1174 0.1413 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 0.3307 300.028 281.953 0.605 1.002 0.349 11.894-9.307 99.02 97 4 0.1590 482.954 475.127 0.925 1.003 0.349 9.237-7.194 100.00 213 7 0.1673 394.997 394.386 0.987 1.003 0.270 7.162-5.571 100.00 427 22 0.1563 296.423 291.755 0.942 1.003 0.230 5.546-4.326 100.00 867 58 0.0833 406.916 403.499 0.962 1.003 0.220 4.315-3.360 100.00 1859 96 0.0771 386.980 386.187 1.004 1.002 0.190 3.356-2.611 100.00 3867 181 0.1073 254.226 253.453 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1006 168.529 167.993 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1093 82.301 82.484 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1436 36.495 36.024 1.025 0.996 0.000 1.221-1.150 99.97 13689 708 0.2246 22.995 21.497 0.989 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0178 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1174 r_free=0.1413 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=0.1174 r_free=0.1413 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1413 | n_water=417 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1173 r_free=0.1410 | n_water=415 | time (s): 38.540 (total time: 40.100) Filter (q & B) r_work=0.1173 r_free=0.1410 | n_water=415 | time (s): 1.300 (total time: 41.400) Compute maps r_work=0.1173 r_free=0.1410 | n_water=415 | time (s): 1.640 (total time: 43.040) Filter (map) r_work=0.1215 r_free=0.1389 | n_water=289 | time (s): 3.620 (total time: 46.660) Find peaks r_work=0.1215 r_free=0.1389 | n_water=289 | time (s): 0.550 (total time: 47.210) Add new water r_work=0.1342 r_free=0.1528 | n_water=484 | time (s): 2.390 (total time: 49.600) Refine new water occ: r_work=0.1245 r_free=0.1450 adp: r_work=0.1247 r_free=0.1451 occ: r_work=0.1220 r_free=0.1424 adp: r_work=0.1220 r_free=0.1424 occ: r_work=0.1201 r_free=0.1401 adp: r_work=0.1196 r_free=0.1397 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1397 r_work=0.1196 r_free=0.1397 | n_water=484 | time (s): 210.050 (total time: 259.650) Filter (q & B) r_work=0.1201 r_free=0.1400 | n_water=454 | time (s): 2.510 (total time: 262.160) Filter (dist only) r_work=0.1201 r_free=0.1399 | n_water=452 | time (s): 39.700 (total time: 301.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.738548 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.842172 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 0.1232 0.1374 0.0142 0.002 0.6 5.1 0.5 0.0 0 0.087 0.1191 0.1344 0.0154 0.003 0.7 3.5 0.5 0.0 0 0.261 0.1172 0.1332 0.0160 0.004 0.8 3.5 0.5 0.0 0 0.522 0.1167 0.1330 0.0164 0.005 0.9 3.8 0.5 0.0 0 0.782 0.1161 0.1329 0.0168 0.006 1.0 3.8 0.5 0.0 0 1.043 0.1159 0.1328 0.0169 0.007 1.0 3.2 0.5 0.6 0 1.304 0.1157 0.1329 0.0172 0.007 1.1 3.8 0.5 0.6 0 1.565 0.1156 0.1329 0.0173 0.008 1.1 3.8 0.5 0.6 0 1.825 0.1162 0.1327 0.0165 0.005 0.9 3.8 0.5 0.0 0 0.869 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1327 0.0165 0.005 0.9 3.8 0.5 0.0 0 0.869 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.27 1.65 3.784 21.306 48.842 3.625 11.62 13.27 1.65 3.784 21.306 1.465 3.625 11.63 13.27 1.64 3.769 21.306 6.105 3.625 11.70 13.36 1.66 3.715 21.291 24.421 3.621 11.71 13.45 1.73 3.728 21.262 48.842 3.620 11.61 13.39 1.78 3.759 21.255 73.263 3.613 11.59 13.41 1.83 3.769 21.242 97.684 3.610 11.56 13.41 1.85 3.783 21.234 122.105 3.608 11.54 13.41 1.87 3.800 21.232 146.527 3.607 11.51 13.36 1.85 3.807 21.223 170.948 3.603 11.49 13.33 1.84 3.816 21.220 195.369 3.602 11.49 13.37 1.88 3.825 21.224 219.790 3.603 11.48 13.36 1.87 3.836 21.215 244.211 3.602 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.105 Accepted refinement result: 11.63 13.27 1.64 3.769 21.306 6.105 3.625 Individual atomic B min max mean iso aniso Overall: 9.13 114.93 21.32 3.28 228 1751 Protein: 9.13 114.93 17.03 3.28 0 1519 Water: 11.54 76.70 35.72 N/A 228 224 Other: 19.67 26.57 22.07 N/A 0 8 Chain A: 9.13 114.93 19.44 N/A 0 1751 Chain S: 12.87 60.01 35.79 N/A 228 0 Histogram: Values Number of atoms 9.13 - 19.71 1267 19.71 - 30.29 287 30.29 - 40.87 211 40.87 - 51.45 141 51.45 - 62.03 50 62.03 - 72.61 11 72.61 - 83.19 6 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1327 r_work=0.1163 r_free=0.1327 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1327 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1326 target_work(ml) = 3.620 | | 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= 0.1154 r_free= 0.1326 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619624 | | target function (ml) not normalized (work): 301492.975316 | | target function (ml) not normalized (free): 15867.081924 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1326 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1488 0.1486 0.1542 n_refl.: 87590 remove outliers: r(all,work,free)=0.1488 0.1486 0.1542 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1486 0.1485 0.1541 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1148 0.1324 n_refl.: 87590 remove outliers: r(all,work,free)=0.1154 0.1145 0.1324 n_refl.: 87583 ======================== 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 91.67 83 5 0.4093 291.932 264.599 0.484 1.000 0.320 11.894-9.307 97.06 95 4 0.2303 483.178 462.385 0.873 1.002 0.283 9.237-7.194 98.64 210 7 0.2242 388.499 387.664 0.951 1.002 0.195 7.162-5.571 100.00 427 22 0.2085 296.423 286.491 0.914 1.002 0.174 5.546-4.326 100.00 867 58 0.1113 406.916 402.058 0.955 1.002 0.160 4.315-3.360 100.00 1859 96 0.0934 386.980 384.721 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1109 254.226 252.152 0.997 1.002 0.080 2.608-2.026 99.99 8198 413 0.0939 168.529 167.733 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0912 82.301 82.597 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1264 36.495 36.088 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.995 21.538 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0201 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1324 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=0.1145 r_free=0.1324 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1324 | n_water=452 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1145 r_free=0.1324 | n_water=451 | time (s): 50.530 (total time: 52.980) Filter (q & B) r_work=0.1145 r_free=0.1325 | n_water=450 | time (s): 3.980 (total time: 56.960) Compute maps r_work=0.1145 r_free=0.1325 | n_water=450 | time (s): 1.900 (total time: 58.860) Filter (map) r_work=0.1168 r_free=0.1307 | n_water=335 | time (s): 3.960 (total time: 62.820) Find peaks r_work=0.1168 r_free=0.1307 | n_water=335 | time (s): 0.700 (total time: 63.520) Add new water r_work=0.1230 r_free=0.1376 | n_water=496 | time (s): 3.830 (total time: 67.350) Refine new water occ: r_work=0.1161 r_free=0.1310 adp: r_work=0.1161 r_free=0.1312 occ: r_work=0.1147 r_free=0.1295 adp: r_work=0.1146 r_free=0.1295 occ: r_work=0.1136 r_free=0.1289 adp: r_work=0.1133 r_free=0.1287 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1287 r_work=0.1133 r_free=0.1287 | n_water=496 | time (s): 251.460 (total time: 318.810) Filter (q & B) r_work=0.1140 r_free=0.1297 | n_water=460 | time (s): 3.940 (total time: 322.750) Filter (dist only) r_work=0.1146 r_free=0.1296 | n_water=458 | time (s): 48.350 (total time: 371.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.778597 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.587017 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 0.1202 0.1338 0.0136 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1161 0.1306 0.0145 0.003 0.8 4.2 0.5 0.0 0 0.267 0.1150 0.1299 0.0149 0.005 0.9 4.2 0.5 0.0 0 0.534 0.1145 0.1304 0.0159 0.006 0.9 3.8 0.5 0.0 0 0.800 0.1141 0.1303 0.0162 0.007 1.0 3.8 0.5 0.0 0 1.067 0.1138 0.1302 0.0164 0.007 1.1 3.8 0.5 0.0 0 1.334 0.1136 0.1303 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.601 0.1135 0.1299 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.868 0.1143 0.1305 0.0161 0.006 1.0 3.8 0.5 0.0 0 0.889 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1299 0.0164 0.008 1.1 3.8 0.5 0.0 0 1.868 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.99 1.64 3.763 21.250 43.587 3.604 11.35 12.99 1.64 3.763 21.250 1.308 3.604 11.35 12.99 1.64 3.763 21.250 5.448 3.604 11.39 13.06 1.68 3.701 21.240 21.794 3.601 11.42 13.20 1.78 3.727 21.212 43.587 3.601 11.37 13.18 1.81 3.747 21.200 65.381 3.597 11.30 13.13 1.83 3.764 21.198 87.174 3.592 11.29 13.14 1.85 3.773 21.197 108.968 3.590 11.28 13.16 1.88 3.792 21.185 130.761 3.589 11.26 13.15 1.89 3.804 21.181 152.555 3.588 11.25 13.13 1.88 3.813 21.175 174.348 3.586 11.23 13.12 1.88 3.822 21.174 196.142 3.585 11.22 13.11 1.89 3.828 21.174 217.935 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.308 Accepted refinement result: 11.35 12.99 1.64 3.763 21.250 1.308 3.604 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.22 3.28 236 1749 Protein: 9.12 114.92 17.02 3.28 0 1519 Water: 11.53 76.69 35.14 N/A 236 222 Other: 19.66 26.56 22.06 N/A 0 8 Chain A: 9.12 114.92 19.42 N/A 0 1749 Chain S: 12.87 60.00 34.59 N/A 236 0 Histogram: Values Number of atoms 9.12 - 19.70 1267 19.70 - 30.28 295 30.28 - 40.86 218 40.86 - 51.44 135 51.44 - 62.02 47 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1299 r_work=0.1135 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1299 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1291 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1291 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600881 | | target function (ml) not normalized (work): 299906.611907 | | target function (ml) not normalized (free): 15798.571192 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1291 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1463 0.1462 0.1504 n_refl.: 87583 remove outliers: r(all,work,free)=0.1463 0.1462 0.1504 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1461 0.1461 0.1503 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1127 0.1294 n_refl.: 87583 remove outliers: r(all,work,free)=0.1133 0.1125 0.1294 n_refl.: 87578 ======================== 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 88.54 80 5 0.4032 285.976 248.983 0.445 0.999 0.320 11.894-9.307 96.08 94 4 0.2350 476.317 469.298 0.879 1.002 0.243 9.237-7.194 98.18 209 7 0.2311 386.469 382.750 0.935 1.002 0.170 7.162-5.571 100.00 427 22 0.2045 296.423 287.935 0.917 1.003 0.160 5.546-4.326 100.00 867 58 0.1118 406.916 401.912 0.967 1.003 0.150 4.315-3.360 100.00 1859 96 0.0903 386.980 384.668 1.002 1.003 0.120 3.356-2.611 100.00 3867 181 0.1105 254.226 252.267 1.009 1.002 0.070 2.608-2.026 99.99 8198 413 0.0911 168.529 167.809 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.301 82.613 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.495 36.090 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.995 21.539 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1294 After: r_work=0.1126 r_free=0.1294 ================================== NQH flips ================================== r_work=0.1126 r_free=0.1294 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=0.1126 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1126 r_free=0.1294 | n_water=458 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1126 r_free=0.1294 | n_water=458 | time (s): 44.390 (total time: 46.930) Filter (q & B) r_work=0.1127 r_free=0.1292 | n_water=456 | time (s): 4.070 (total time: 51.000) Compute maps r_work=0.1127 r_free=0.1292 | n_water=456 | time (s): 1.940 (total time: 52.940) Filter (map) r_work=0.1152 r_free=0.1284 | n_water=368 | time (s): 4.070 (total time: 57.010) Find peaks r_work=0.1152 r_free=0.1284 | n_water=368 | time (s): 0.710 (total time: 57.720) Add new water r_work=0.1197 r_free=0.1341 | n_water=492 | time (s): 3.780 (total time: 61.500) Refine new water occ: r_work=0.1145 r_free=0.1287 adp: r_work=0.1145 r_free=0.1289 occ: r_work=0.1134 r_free=0.1277 adp: r_work=0.1134 r_free=0.1278 occ: r_work=0.1126 r_free=0.1270 adp: r_work=0.1124 r_free=0.1269 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1269 r_work=0.1124 r_free=0.1269 | n_water=492 | time (s): 281.030 (total time: 342.530) Filter (q & B) r_work=0.1129 r_free=0.1278 | n_water=464 | time (s): 3.870 (total time: 346.400) Filter (dist only) r_work=0.1129 r_free=0.1278 | n_water=463 | time (s): 48.740 (total time: 395.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.753235 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.483853 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1336 0.0124 0.004 0.7 5.8 0.0 0.0 0 0.088 0.1164 0.1302 0.0139 0.004 0.8 5.4 0.0 0.0 0 0.263 0.1149 0.1293 0.0143 0.005 0.9 5.1 0.5 0.0 0 0.526 0.1141 0.1286 0.0145 0.006 1.0 5.1 0.5 0.0 0 0.789 0.1135 0.1282 0.0147 0.007 1.1 4.8 0.5 0.0 0 1.052 0.1132 0.1279 0.0147 0.008 1.1 4.5 0.5 0.0 0 1.315 0.1130 0.1278 0.0148 0.008 1.1 4.5 0.5 0.0 0 1.578 0.1129 0.1278 0.0149 0.008 1.1 4.5 0.5 0.0 0 1.841 0.1138 0.1284 0.0146 0.006 1.0 4.8 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1129 0.1278 0.0149 0.008 1.1 4.5 0.5 0.0 0 1.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 12.78 1.49 3.763 21.242 43.484 3.601 11.29 12.78 1.49 3.763 21.242 1.305 3.601 11.29 12.78 1.49 3.763 21.242 5.435 3.601 11.32 12.83 1.51 3.700 21.234 21.742 3.597 11.31 12.92 1.61 3.723 21.219 43.484 3.595 11.31 12.99 1.68 3.748 21.195 65.226 3.595 11.24 12.94 1.70 3.762 21.194 86.968 3.589 11.23 12.95 1.72 3.773 21.193 108.710 3.588 11.22 12.97 1.75 3.791 21.183 130.452 3.586 11.21 12.98 1.77 3.803 21.178 152.193 3.585 11.19 12.96 1.77 3.814 21.174 173.935 3.583 11.17 12.94 1.77 3.820 21.174 195.677 3.582 11.16 12.94 1.77 3.827 21.174 217.419 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.435 Accepted refinement result: 11.29 12.78 1.49 3.763 21.242 5.435 3.601 Individual atomic B min max mean iso aniso Overall: 9.12 114.91 21.22 3.28 242 1748 Protein: 9.12 114.91 17.02 3.28 0 1519 Water: 11.52 76.69 34.98 N/A 242 221 Other: 19.66 26.56 22.06 N/A 0 8 Chain A: 9.12 114.91 19.40 N/A 0 1748 Chain S: 12.86 60.00 34.36 N/A 242 0 Histogram: Values Number of atoms 9.12 - 19.70 1267 19.70 - 30.28 304 30.28 - 40.86 213 40.86 - 51.44 138 51.44 - 62.02 45 62.02 - 72.60 11 72.60 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1129 r_free=0.1278 r_work=0.1129 r_free=0.1278 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1129 r_free = 0.1278 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1273 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1273 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598748 | | target function (ml) not normalized (work): 299710.911253 | | target function (ml) not normalized (free): 15785.681909 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1301 0.1318 5.6107 5.6066| | 2: 3.57 - 2.84 1.00 2888 124 0.1061 0.1364 5.1602 5.2048| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1224 4.9432 4.9766| | 4: 2.47 - 2.25 1.00 2825 136 0.0898 0.0954 4.6288 4.6564| | 5: 2.25 - 2.09 1.00 2756 127 0.0868 0.0938 4.5757 4.623| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.0983 4.2661 4.3616| | 7: 1.97 - 1.87 1.00 2787 165 0.0876 0.1116 3.9691 4.0865| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1082 3.8819 3.9823| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1153 3.6343 3.8044| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1168 3.5554 3.7008| | 11: 1.66 - 1.61 1.00 2712 147 0.0870 0.1005 3.4862 3.5521| | 12: 1.61 - 1.56 1.00 2773 144 0.0905 0.1148 3.3245 3.4595| | 13: 1.56 - 1.52 1.00 2745 130 0.0938 0.1026 3.2992 3.3809| | 14: 1.52 - 1.48 1.00 2803 134 0.0973 0.1055 3.2334 3.3224| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1209 3.1482 3.2517| | 16: 1.45 - 1.42 1.00 2756 161 0.1046 0.1226 3.1284 3.2263| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1308 3.1143 3.2286| | 18: 1.39 - 1.36 1.00 2741 179 0.1191 0.1312 3.0999 3.2344| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1536 3.1081 3.2546| | 20: 1.34 - 1.32 1.00 2696 147 0.1362 0.1458 3.1081 3.1478| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1510 3.1113 3.1056| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1989 3.121 3.2992| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1782 3.1313 3.2028| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1830 3.1259 3.2258| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2147 3.1405 3.2619| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1750 3.1481 3.1968| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2177 3.17 3.1643| | 28: 1.19 - 1.18 1.00 2671 147 0.2198 0.2298 3.1652 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2373 3.1472 3.226| | 30: 1.16 - 1.15 1.00 2739 148 0.2442 0.2445 3.1428 3.1685| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.58 1.00 0.97 5752.15| | 2: 3.57 - 2.84 2888 124 0.93 12.58 1.01 0.97 5752.15| | 3: 2.83 - 2.48 2820 163 0.89 16.49 0.99 0.97 4801.31| | 4: 2.47 - 2.25 2825 136 0.92 13.40 1.00 0.98 2349.38| | 5: 2.25 - 2.09 2756 127 0.90 15.57 1.01 0.98 2349.38| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.98 1349.58| | 7: 1.97 - 1.87 2787 165 0.95 9.11 1.02 0.98 496.89| | 8: 1.87 - 1.79 2789 144 0.93 12.40 1.00 0.98 496.89| | 9: 1.79 - 1.72 2745 138 0.95 9.83 0.98 0.97 280.79| | 10: 1.72 - 1.66 2831 160 0.94 10.93 0.98 0.97 237.51| | 11: 1.66 - 1.61 2712 147 0.94 11.52 0.98 0.97 227.66| | 12: 1.61 - 1.56 2773 144 0.96 8.75 0.99 0.97 134.75| | 13: 1.56 - 1.52 2745 130 0.95 10.22 1.02 0.97 134.75| | 14: 1.52 - 1.48 2803 134 0.94 10.63 1.02 0.98 121.09| | 15: 1.48 - 1.45 2738 128 0.95 9.79 1.02 0.98 96.07| | 16: 1.45 - 1.42 2756 161 0.94 10.93 1.02 0.98 96.07| | 17: 1.42 - 1.39 2785 139 0.95 10.81 1.01 0.98 87.79| | 18: 1.39 - 1.36 2741 179 0.94 11.44 1.01 0.98 83.00| | 19: 1.36 - 1.34 2807 134 0.94 11.74 1.00 0.98 83.00| | 20: 1.34 - 1.32 2696 147 0.94 12.03 0.98 0.97 79.36| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.96 79.11| | 22: 1.29 - 1.27 2704 152 0.93 13.57 0.98 0.96 79.56| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.94 81.88| | 24: 1.26 - 1.24 2744 132 0.93 14.81 0.96 0.94 81.88| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 83.91| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.16| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 86.16| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.93 89.84| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.93 91.22| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 91.22| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.11 max = 5752.15 mean = 883.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.35| |phase err.(test): min = 0.00 max = 87.96 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1273 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1484 n_refl.: 87578 remove outliers: r(all,work,free)=0.1446 0.1445 0.1484 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1445 0.1444 0.1484 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1125 0.1271 n_refl.: 87578 remove outliers: r(all,work,free)=0.1131 0.1124 0.1271 n_refl.: 87576 ======================== 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 87.50 79 5 0.4084 281.023 246.619 0.443 1.000 0.308 11.894-9.307 95.10 93 4 0.2327 480.227 464.807 0.870 1.002 0.228 9.237-7.194 98.18 209 7 0.2325 386.469 380.107 0.929 1.002 0.162 7.162-5.571 100.00 427 22 0.2010 296.423 288.090 0.915 1.003 0.150 5.546-4.326 100.00 867 58 0.1098 406.916 402.016 0.966 1.003 0.140 4.315-3.360 100.00 1859 96 0.0912 386.980 384.798 1.003 1.003 0.130 3.356-2.611 100.00 3867 181 0.1101 254.226 252.372 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0909 168.529 167.914 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.301 82.634 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.495 36.102 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.995 21.549 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0135 ================= 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 : 0.2612 0.1977 0.084 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_weight: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1226 0.1470 0.007 0.906 9.0 119.5 20.1 258 0.131 1_adp: 0.1233 0.1467 0.007 0.906 9.1 119.4 20.1 258 0.131 1_regHadp: 0.1234 0.1471 0.007 0.906 9.1 119.4 20.1 258 0.131 1_occ: 0.1228 0.1467 0.007 0.906 9.1 119.4 20.1 258 0.131 2_bss: 0.1225 0.1457 0.007 0.906 9.1 119.5 20.1 258 0.131 2_settarget: 0.1225 0.1457 0.007 0.906 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1225 0.1457 0.007 0.914 9.1 119.5 20.1 258 0.131 2_nqh: 0.1227 0.1459 0.007 0.914 9.1 119.5 20.1 258 0.134 2_sol: 0.1198 0.1401 0.007 0.914 9.1 115.1 22.1 417 n/a 2_weight: 0.1198 0.1401 0.007 0.914 9.1 115.1 22.1 417 n/a 2_xyzrec: 0.1180 0.1416 0.008 0.955 9.1 115.1 22.1 417 n/a 2_adp: 0.1180 0.1416 0.008 0.955 9.1 115.1 22.1 417 n/a 2_regHadp: 0.1180 0.1416 0.008 0.955 9.1 115.1 22.1 417 n/a 2_occ: 0.1177 0.1416 0.008 0.955 9.1 115.1 22.1 417 n/a 3_bss: 0.1174 0.1413 0.008 0.955 9.1 115.1 22.1 417 n/a 3_settarget: 0.1174 0.1413 0.008 0.955 9.1 115.1 22.1 417 n/a 3_updatecdl: 0.1174 0.1413 0.008 0.957 9.1 115.1 22.1 417 n/a 3_nqh: 0.1174 0.1413 0.008 0.957 9.1 115.1 22.1 417 n/a 3_sol: 0.1201 0.1399 0.008 0.957 9.1 115.1 21.3 452 n/a 3_weight: 0.1201 0.1399 0.008 0.957 9.1 115.1 21.3 452 n/a 3_xyzrec: 0.1162 0.1327 0.005 0.936 9.1 115.1 21.3 452 n/a 3_adp: 0.1163 0.1327 0.005 0.936 9.1 114.9 21.3 452 n/a 3_regHadp: 0.1163 0.1327 0.005 0.936 9.1 114.9 21.3 452 n/a 3_occ: 0.1154 0.1326 0.005 0.936 9.1 114.9 21.3 452 n/a 4_bss: 0.1145 0.1324 0.005 0.936 9.1 114.9 21.3 452 n/a 4_settarget: 0.1145 0.1324 0.005 0.936 9.1 114.9 21.3 452 n/a 4_updatecdl: 0.1145 0.1324 0.005 0.935 9.1 114.9 21.3 452 n/a 4_nqh: 0.1145 0.1324 0.005 0.935 9.1 114.9 21.3 452 n/a 4_sol: 0.1146 0.1296 0.005 0.935 9.1 114.9 21.2 458 n/a 4_weight: 0.1146 0.1296 0.005 0.935 9.1 114.9 21.2 458 n/a 4_xyzrec: 0.1135 0.1299 0.008 1.129 9.1 114.9 21.2 458 n/a 4_adp: 0.1135 0.1299 0.008 1.129 9.1 114.9 21.2 458 n/a 4_regHadp: 0.1135 0.1299 0.008 1.129 9.1 114.9 21.2 458 n/a 4_occ: 0.1128 0.1291 0.008 1.129 9.1 114.9 21.2 458 n/a 5_bss: 0.1125 0.1294 0.008 1.129 9.1 114.9 21.2 458 n/a 5_settarget: 0.1125 0.1294 0.008 1.129 9.1 114.9 21.2 458 n/a 5_updatecdl: 0.1125 0.1294 0.008 1.131 9.1 114.9 21.2 458 n/a 5_setrh: 0.1126 0.1294 0.008 1.131 9.1 114.9 21.2 458 n/a 5_nqh: 0.1126 0.1294 0.008 1.131 9.1 114.9 21.2 458 n/a 5_sol: 0.1129 0.1278 0.008 1.131 9.1 114.9 21.2 463 n/a 5_weight: 0.1129 0.1278 0.008 1.131 9.1 114.9 21.2 463 n/a 5_xyzrec: 0.1129 0.1278 0.008 1.140 9.1 114.9 21.2 463 n/a 5_adp: 0.1129 0.1278 0.008 1.140 9.1 114.9 21.2 463 n/a 5_regHadp: 0.1129 0.1278 0.008 1.140 9.1 114.9 21.2 463 n/a 5_occ: 0.1125 0.1273 0.008 1.140 9.1 114.9 21.2 463 n/a end: 0.1124 0.1271 0.008 1.140 9.1 114.9 21.2 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3975290_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3975290_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1900 Refinement macro-cycles (run) : 13962.1800 Write final files (write_after_run_outputs) : 95.3400 Total : 14061.7100 Total CPU time: 3.91 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:13:51 PST -0800 (1735366431.21 s) Start R-work = 0.1642, R-free = 0.1801 Final R-work = 0.1124, R-free = 0.1271 =============================================================================== Job complete usr+sys time: 14234.30 seconds wall clock time: 257 minutes 52.38 seconds (15472.38 seconds total)