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_1498316.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den 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 1 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: 1.83, per 1000 atoms: 0.54 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: 0.30 Conformation dependent library (CDL) restraints added in 108.0 milliseconds Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1164 1.17 - 1.43: 688 1.43 - 1.70: 803 1.70 - 1.96: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.158 0.181 7.50e-03 1.78e+04 5.81e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.292 0.234 1.01e-02 9.80e+03 5.37e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.227 0.230 1.14e-02 7.69e+03 4.08e+02 bond pdb=" CA MET A 133 " pdb=" C MET A 133 " ideal model delta sigma weight residual 1.524 1.752 -0.229 1.29e-02 6.01e+03 3.14e+02 bond pdb=" C PRO A 109 " pdb=" O PRO A 109 " ideal model delta sigma weight residual 1.237 1.006 0.231 1.32e-02 5.74e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 3311 4.92 - 9.84: 1823 9.84 - 14.77: 555 14.77 - 19.69: 80 19.69 - 24.61: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 134.66 -13.43 8.10e-01 1.52e+00 2.75e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 109.32 9.97 6.50e-01 2.37e+00 2.35e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 125.38 -14.76 1.02e+00 9.61e-01 2.09e+02 angle pdb=" O THR A 34 " pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 123.27 140.32 -17.05 1.18e+00 7.18e-01 2.09e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.42 135.34 -14.92 1.06e+00 8.90e-01 1.98e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.32: 955 17.32 - 34.64: 103 34.64 - 51.96: 37 51.96 - 69.28: 13 69.28 - 86.59: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.171: 72 0.171 - 0.341: 69 0.341 - 0.511: 55 0.511 - 0.681: 33 0.681 - 0.851: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 125 " pdb=" CA THR A 125 " pdb=" OG1 THR A 125 " pdb=" CG2 THR A 125 " both_signs ideal model delta sigma weight residual False 2.55 1.70 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.040 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.095 2.00e-02 2.50e+03 7.14e-02 1.15e+02 pdb=" CG HIS A 126 " -0.113 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.048 9.50e-02 1.11e+02 6.84e-02 9.97e+01 pdb=" NE ARG A 48 " 0.104 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.096 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.052 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.056 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.099 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1368 2.36 - 2.92: 8316 2.92 - 3.48: 10404 3.48 - 4.04: 15058 4.04 - 4.60: 21501 Nonbonded interactions: 56647 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.804 1.850 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.808 1.850 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.821 1.850 nonbonded pdb=" O MET A 134 " pdb=" H GLY A 137 " model vdw 1.848 1.850 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.864 1.850 ... (remaining 56642 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_1498316_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= 0.2608 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792382 | | target function (ml) not normalized (work): 232622.140756 | | target function (ml) not normalized (free): 11868.708597 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3021 0.2065 7.0497 4.9419| | 2: 3.57 - 2.84 1.00 2876 122 0.2436 0.1822 4.3523 4.3338| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1637 4.1272 4.1455| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1460 3.8324 3.8359| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1515 3.7982 3.807| | 6: 2.09 - 1.97 1.00 2846 113 0.2566 0.1843 3.4631 3.5367| | 7: 1.97 - 1.87 1.00 2787 165 0.2569 0.1797 3.1239 3.1741| | 8: 1.87 - 1.79 1.00 2789 144 0.2467 0.1940 3.0547 3.1115| | 9: 1.79 - 1.72 1.00 2745 138 0.2339 0.1971 2.8974 2.9742| | 10: 1.72 - 1.66 1.00 2789 158 0.2363 0.1967 2.8118 2.8886| | 11: 1.66 - 1.61 1.00 2740 147 0.2458 0.2166 2.7466 2.8612| | 12: 1.61 - 1.56 1.00 2787 146 0.2540 0.2013 2.6413 2.6683| | 13: 1.56 - 1.52 1.00 2745 130 0.2592 0.2003 2.5756 2.5886| | 14: 1.52 - 1.48 1.00 2803 134 0.2609 0.1896 2.5103 2.5119| | 15: 1.48 - 1.45 1.00 2738 128 0.2591 0.1919 2.4259 2.4502| | 16: 1.45 - 1.42 1.00 2756 161 0.2655 0.2248 2.3875 2.5238| | 17: 1.42 - 1.39 1.00 2785 139 0.2652 0.2237 2.3135 2.378| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.2344 2.2676 2.3717| | 19: 1.36 - 1.34 1.00 2807 134 0.2657 0.2444 2.2565 2.3359| | 20: 1.34 - 1.32 1.00 2696 147 0.2647 0.2176 2.2091 2.2112| | 21: 1.32 - 1.30 1.00 2785 112 0.2685 0.2274 2.1488 2.1704| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2434 2.1447 2.1586| | 23: 1.27 - 1.26 1.00 2802 156 0.2827 0.2559 2.1192 2.206| | 24: 1.26 - 1.24 1.00 2744 132 0.2828 0.2519 2.0905 2.1872| | 25: 1.24 - 1.22 1.00 2734 148 0.2861 0.2741 2.0591 2.1339| | 26: 1.22 - 1.21 1.00 2727 135 0.2920 0.2427 2.0264 2.1405| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2678 2.0138 2.0129| | 28: 1.19 - 1.18 1.00 2671 147 0.2929 0.3088 1.9765 2.0354| | 29: 1.18 - 1.16 1.00 2800 134 0.2955 0.2621 1.9561 2.0116| | 30: 1.16 - 1.15 1.00 2740 148 0.3105 0.2943 1.9368 1.9974| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.85 0.76 0.23 1480.65| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1480.65| | 3: 2.84 - 2.48 2833 165 0.74 32.04 1.24 0.23 1226.74| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 567.80| | 5: 2.25 - 2.09 2756 127 0.77 29.07 1.28 0.25 567.80| | 6: 2.09 - 1.97 2846 113 0.84 22.49 1.30 0.25 309.30| | 7: 1.97 - 1.87 2787 165 0.90 16.41 1.29 0.26 88.82| | 8: 1.87 - 1.79 2789 144 0.86 20.58 1.25 0.26 88.82| | 9: 1.79 - 1.72 2745 138 0.88 18.29 1.22 0.26 55.34| | 10: 1.72 - 1.66 2789 158 0.87 20.13 1.22 0.26 48.63| | 11: 1.66 - 1.61 2740 147 0.86 21.44 1.24 0.26 47.03| | 12: 1.61 - 1.56 2787 146 0.88 18.82 1.24 0.25 30.77| | 13: 1.56 - 1.52 2745 130 0.86 20.89 1.25 0.25 30.77| | 14: 1.52 - 1.48 2803 134 0.86 21.22 1.24 0.25 27.46| | 15: 1.48 - 1.45 2738 128 0.87 20.33 1.23 0.25 21.39| | 16: 1.45 - 1.42 2756 161 0.85 22.21 1.23 0.25 21.39| | 17: 1.42 - 1.39 2785 139 0.86 21.37 1.23 0.25 18.16| | 18: 1.39 - 1.36 2741 179 0.86 21.43 1.24 0.25 16.30| | 19: 1.36 - 1.34 2807 134 0.85 22.34 1.22 0.25 16.30| | 20: 1.34 - 1.32 2696 147 0.87 21.02 1.20 0.25 13.52| | 21: 1.32 - 1.30 2785 112 0.85 22.46 1.21 0.25 13.33| | 22: 1.29 - 1.27 2704 152 0.85 22.96 1.21 0.24 13.04| | 23: 1.27 - 1.26 2802 156 0.85 22.99 1.22 0.24 11.60| | 24: 1.26 - 1.24 2744 132 0.84 23.53 1.20 0.24 11.60| | 25: 1.24 - 1.22 2734 148 0.84 24.27 1.20 0.24 11.08| | 26: 1.22 - 1.21 2727 135 0.83 25.06 1.21 0.23 10.50| | 27: 1.21 - 1.19 2814 148 0.82 25.48 1.20 0.23 10.50| | 28: 1.19 - 1.18 2671 147 0.82 26.10 1.17 0.23 9.77| | 29: 1.18 - 1.16 2800 134 0.82 26.37 1.17 0.22 9.50| | 30: 1.16 - 1.15 2740 148 0.79 28.34 1.16 0.22 9.50| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.50 max = 1480.65 mean = 214.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.94| |phase err.(test): min = 0.00 max = 88.69 mean = 22.72| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.234 1557 Z= 5.492 Angle : 5.277 17.058 2118 Z= 3.714 Chirality : 0.374 0.851 243 Planarity : 0.031 0.102 284 Dihedral : 13.681 86.594 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % 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: -2.38 (0.48), residues: 224 helix: -2.89 (0.33), residues: 103 sheet: -0.37 (0.95), residues: 28 loop : -0.02 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.020 ARG A 98 TYR 0.106 0.042 TYR A 139 PHE 0.076 0.036 PHE A 164 HIS 0.047 0.022 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= 0.2608 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792382 | | target function (ml) not normalized (work): 232622.140756 | | target function (ml) not normalized (free): 11868.708597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1986 0.1962 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2007 0.2011 0.1975 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1636 0.1792 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1792 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 0.3816 386.562 359.643 0.669 1.004 0.407 11.894-9.307 99.02 97 4 0.1812 614.034 593.195 0.929 1.004 0.390 9.237-7.194 100.00 213 7 0.2136 502.204 491.907 0.960 1.004 0.370 7.162-5.571 100.00 427 22 0.2202 376.876 365.483 0.936 1.004 0.288 5.546-4.326 100.00 867 58 0.1305 517.358 511.895 0.963 1.004 0.259 4.315-3.360 100.00 1859 96 0.1137 492.011 488.752 1.001 1.004 0.203 3.356-2.611 100.00 3867 181 0.1433 323.226 319.821 1.000 1.003 0.057 2.608-2.026 99.99 8198 413 0.1359 214.269 212.130 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1639 104.638 104.033 1.011 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2065 46.401 45.096 1.008 0.994 0.000 1.221-1.150 99.97 13689 708 0.2586 29.236 26.960 0.978 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0447 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1792 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1797 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.575969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.813676 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 0.1734 0.1842 0.0109 0.002 0.4 5.1 0.0 0.0 0 0.125 0.1557 0.1689 0.0132 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1472 0.1632 0.0160 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1399 0.1584 0.0184 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1348 0.1540 0.0192 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1360 0.1559 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1293 0.1504 0.0211 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1274 0.1498 0.0224 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1485 0.0227 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1483 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1246 0.1478 0.0232 0.005 0.8 4.2 0.5 0.0 0 6.000 0.1243 0.1479 0.0237 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1238 0.1475 0.0236 0.006 0.8 3.8 0.5 0.0 0 8.000 0.1237 0.1482 0.0244 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1232 0.1475 0.0243 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1231 0.1474 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1230 0.1476 0.0246 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1229 0.1482 0.0253 0.008 1.0 4.2 0.5 0.0 0 13.288 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1474 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.74 2.42 3.013 19.054 2026.814 0.017 12.31 14.73 2.42 2.989 19.054 60.804 0.017 12.41 14.74 2.33 2.604 19.057 253.352 0.017 12.68 15.34 2.66 2.729 19.207 1013.407 0.017 12.56 15.52 2.96 3.358 19.638 2026.814 0.016 12.45 15.53 3.08 3.316 19.613 3040.221 0.015 12.31 15.43 3.12 3.316 19.606 4053.627 0.015 12.31 15.48 3.17 3.393 19.634 5067.034 0.015 12.28 15.51 3.22 3.357 19.610 6080.441 0.015 12.18 15.45 3.26 3.339 19.592 7093.848 0.015 12.17 15.47 3.30 3.450 19.640 8107.255 0.015 12.16 15.45 3.29 3.359 19.579 9120.662 0.015 12.16 15.50 3.33 3.374 19.581 10134.068 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: 60.804 Accepted refinement result: 12.31 14.73 2.42 2.989 19.054 60.804 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.49 20.08 3.86 0 1785 Protein: 9.05 115.94 16.99 3.86 0 1519 Water: 11.55 119.49 38.23 N/A 0 258 Other: 19.26 26.47 21.90 N/A 0 8 Chain A: 9.05 119.49 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1276 20.09 - 31.14 224 31.14 - 42.18 127 42.18 - 53.22 89 53.22 - 64.27 44 64.27 - 75.31 11 75.31 - 86.36 7 86.36 - 97.40 4 97.40 - 108.45 1 108.45 - 119.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1473 r_work=0.1233 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1476 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 = 0.1226 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= 0.1226 r_free= 0.1467 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016970 | | target function (ls_wunit_k1) not normalized (work): 1413.533267 | | target function (ls_wunit_k1) not normalized (free): 110.187669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1226 0.1467 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1703 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1703 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1683 0.1708 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1234 0.1223 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1234 0.1223 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 0.3516 301.272 281.706 0.645 1.003 0.374 11.894-9.307 99.02 97 4 0.1650 482.621 471.315 0.920 1.003 0.370 9.237-7.194 100.00 213 7 0.1918 394.725 388.032 0.960 1.004 0.348 7.162-5.571 100.00 427 22 0.1835 296.219 290.349 0.936 1.004 0.254 5.546-4.326 100.00 867 58 0.1001 406.635 403.759 0.962 1.003 0.230 4.315-3.360 100.00 1859 96 0.0874 386.713 385.692 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1187 254.050 252.812 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.1028 168.412 167.651 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.244 82.415 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1431 36.470 35.984 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2245 22.979 21.468 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0519 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 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** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1221 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1452 | n_water=258 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1231 r_free=0.1451 | n_water=251 | time (s): 21.730 (total time: 23.490) Filter (q & B) r_work=0.1233 r_free=0.1452 | n_water=248 | time (s): 2.820 (total time: 26.310) Compute maps r_work=0.1233 r_free=0.1452 | n_water=248 | time (s): 1.530 (total time: 27.840) Filter (map) r_work=0.1248 r_free=0.1453 | n_water=224 | time (s): 2.870 (total time: 30.710) Find peaks r_work=0.1248 r_free=0.1453 | n_water=224 | time (s): 0.500 (total time: 31.210) Add new water r_work=0.1395 r_free=0.1636 | n_water=432 | time (s): 2.290 (total time: 33.500) Refine new water occ: r_work=0.1302 r_free=0.1483 adp: r_work=0.1219 r_free=0.1439 occ: r_work=0.1232 r_free=0.1419 adp: r_work=0.1198 r_free=0.1410 occ: r_work=0.1201 r_free=0.1398 adp: r_work=0.1191 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1399 r_work=0.1191 r_free=0.1399 | n_water=432 | time (s): 60.070 (total time: 93.570) Filter (q & B) r_work=0.1193 r_free=0.1399 | n_water=418 | time (s): 3.100 (total time: 96.670) Filter (dist only) r_work=0.1193 r_free=0.1397 | n_water=417 | time (s): 35.500 (total time: 132.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.137716 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1876.023523 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 0.1671 0.1786 0.0115 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1565 0.1692 0.0127 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1394 0.1551 0.0157 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1326 0.1500 0.0174 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1319 0.1500 0.0181 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1328 0.1509 0.0181 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1247 0.1443 0.0196 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1220 0.1432 0.0213 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1208 0.1423 0.0215 0.004 0.7 3.8 0.5 0.0 0 4.000 0.1201 0.1422 0.0222 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1194 0.1417 0.0223 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1189 0.1413 0.0224 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1183 0.1409 0.0226 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1181 0.1405 0.0224 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1182 0.1409 0.0227 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1178 0.1406 0.0228 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1178 0.1402 0.0224 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1176 0.1409 0.0232 0.008 0.9 4.8 0.5 0.0 0 13.569 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1178 0.1402 0.0224 0.007 0.9 4.5 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.78 14.02 2.24 4.033 21.789 1876.024 0.016 11.78 14.02 2.23 4.019 21.789 56.281 0.016 11.84 13.99 2.15 3.865 21.787 234.503 0.016 12.02 14.44 2.42 3.640 21.858 938.012 0.015 11.91 14.65 2.74 3.472 22.083 1876.024 0.015 11.86 14.70 2.85 3.520 22.203 2814.035 0.014 11.78 14.70 2.93 3.524 22.177 3752.047 0.014 11.68 14.65 2.97 3.526 22.142 4690.059 0.014 11.67 14.70 3.04 3.550 22.194 5628.071 0.014 11.60 14.64 3.04 3.559 22.091 6566.082 0.014 11.62 14.65 3.03 3.586 22.155 7504.094 0.014 11.58 14.64 3.07 3.597 22.198 8442.106 0.014 11.60 14.74 3.14 3.655 22.281 9380.118 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: 234.503 Accepted refinement result: 11.84 13.99 2.15 3.865 21.787 234.503 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.16 22.17 3.33 193 1751 Protein: 9.11 115.16 17.02 3.33 0 1519 Water: 11.49 76.75 40.94 N/A 193 224 Other: 19.48 26.53 22.01 N/A 0 8 Chain A: 9.11 115.16 19.42 N/A 0 1751 Chain S: 12.33 60.08 47.18 N/A 193 0 Histogram: Values Number of atoms 9.11 - 19.71 1262 19.71 - 30.32 244 30.32 - 40.92 162 40.92 - 51.53 130 51.53 - 62.13 124 62.13 - 72.74 11 72.74 - 83.34 5 83.34 - 93.95 4 93.95 - 104.55 0 104.55 - 115.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1399 r_work=0.1185 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1400 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1400 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1184 r_free= 0.1400 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015043 | | target function (ls_wunit_k1) not normalized (work): 1252.983412 | | target function (ls_wunit_k1) not normalized (free): 100.278306 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1184 0.1400 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1581 0.1579 0.1642 n_refl.: 87592 remove outliers: r(all,work,free)=0.1581 0.1579 0.1642 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1582 0.1581 0.1643 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1182 0.1399 n_refl.: 87592 remove outliers: r(all,work,free)=0.1191 0.1180 0.1399 n_refl.: 87589 ======================== 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 0.3349 297.178 274.078 0.588 1.003 0.342 11.894-9.307 99.02 97 4 0.1619 482.621 474.882 0.919 1.003 0.337 9.237-7.194 100.00 213 7 0.1725 394.725 393.973 0.983 1.003 0.290 7.162-5.571 100.00 427 22 0.1579 296.219 291.622 0.940 1.003 0.240 5.546-4.326 100.00 867 58 0.0886 406.635 403.644 0.961 1.003 0.200 4.315-3.360 100.00 1859 96 0.0788 386.713 385.432 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1079 254.050 253.002 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1013 168.412 167.889 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.244 82.460 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1435 36.470 36.011 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 22.979 21.497 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0120 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1180 r_free=0.1399 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=0.1180 r_free=0.1399 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1399 | n_water=417 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1180 r_free=0.1394 | n_water=413 | time (s): 38.140 (total time: 39.770) Filter (q & B) r_work=0.1180 r_free=0.1394 | n_water=413 | time (s): 0.780 (total time: 40.550) Compute maps r_work=0.1180 r_free=0.1394 | n_water=413 | time (s): 1.300 (total time: 41.850) Filter (map) r_work=0.1217 r_free=0.1387 | n_water=290 | time (s): 2.720 (total time: 44.570) Find peaks r_work=0.1217 r_free=0.1387 | n_water=290 | time (s): 0.480 (total time: 45.050) Add new water r_work=0.1328 r_free=0.1495 | n_water=463 | time (s): 2.840 (total time: 47.890) Refine new water occ: r_work=0.1237 r_free=0.1416 adp: r_work=0.1238 r_free=0.1417 occ: r_work=0.1216 r_free=0.1397 adp: r_work=0.1214 r_free=0.1396 occ: r_work=0.1201 r_free=0.1383 adp: r_work=0.1195 r_free=0.1380 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1380 r_work=0.1195 r_free=0.1380 | n_water=463 | time (s): 171.600 (total time: 219.490) Filter (q & B) r_work=0.1198 r_free=0.1378 | n_water=433 | time (s): 2.920 (total time: 222.410) Filter (dist only) r_work=0.1198 r_free=0.1378 | n_water=432 | time (s): 37.220 (total time: 259.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.753775 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.823894 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 0.1229 0.1355 0.0126 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1187 0.1328 0.0141 0.003 0.7 3.8 0.5 0.0 0 0.263 0.1170 0.1314 0.0145 0.004 0.8 3.5 0.5 0.0 0 0.526 0.1164 0.1312 0.0149 0.005 0.9 3.5 0.5 0.0 0 0.789 0.1159 0.1310 0.0151 0.006 1.0 3.2 0.5 0.0 0 1.052 0.1157 0.1310 0.0153 0.007 1.0 3.2 0.5 0.0 0 1.315 0.1156 0.1309 0.0153 0.007 1.1 3.2 0.5 0.0 0 1.578 0.1152 0.1306 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.841 0.1163 0.1311 0.0148 0.005 0.9 3.5 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1152 0.1306 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.52 13.06 1.54 3.786 21.266 39.824 3.614 11.52 13.06 1.54 3.786 21.266 1.195 3.614 11.52 13.06 1.54 3.786 21.266 4.978 3.614 11.55 13.11 1.56 3.713 21.258 19.912 3.608 11.64 13.28 1.64 3.716 21.231 39.824 3.614 11.54 13.23 1.68 3.745 21.218 59.736 3.606 11.48 13.19 1.71 3.763 21.213 79.648 3.601 11.46 13.20 1.74 3.772 21.205 99.560 3.599 11.42 13.18 1.75 3.783 21.204 119.472 3.597 11.41 13.20 1.79 3.794 21.192 139.384 3.595 11.41 13.22 1.81 3.808 21.185 159.296 3.595 11.39 13.19 1.80 3.816 21.181 179.208 3.593 11.38 13.18 1.80 3.824 21.179 199.119 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.195 Accepted refinement result: 11.52 13.06 1.54 3.786 21.266 1.195 3.614 Individual atomic B min max mean iso aniso Overall: 9.12 115.17 21.25 3.33 212 1747 Protein: 9.12 115.17 17.03 3.33 0 1519 Water: 11.50 76.76 36.07 N/A 212 220 Other: 19.49 26.54 22.02 N/A 0 8 Chain A: 9.12 115.17 19.36 N/A 0 1747 Chain S: 12.33 60.06 36.79 N/A 212 0 Histogram: Values Number of atoms 9.12 - 19.72 1262 19.72 - 30.33 280 30.33 - 40.93 214 40.93 - 51.54 125 51.54 - 62.14 56 62.14 - 72.75 11 72.75 - 83.35 5 83.35 - 93.96 4 93.96 - 104.56 0 104.56 - 115.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1306 r_work=0.1152 r_free=0.1306 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1306 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1300 target_work(ml) = 3.606 | | 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1142 r_free= 0.1300 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.606401 | | target function (ml) not normalized (work): 300387.993655 | | target function (ml) not normalized (free): 15819.934604 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1142 0.1300 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1491 0.1490 0.1540 n_refl.: 87589 remove outliers: r(all,work,free)=0.1491 0.1490 0.1540 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1489 0.1539 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1139 0.1296 n_refl.: 87589 remove outliers: r(all,work,free)=0.1144 0.1136 0.1296 n_refl.: 87581 ======================== 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 90.62 82 5 0.3861 288.365 269.461 0.500 1.001 0.310 11.894-9.307 97.06 95 4 0.2132 475.958 464.553 0.882 1.002 0.297 9.237-7.194 98.18 209 7 0.2266 386.202 387.148 0.965 1.002 0.220 7.162-5.571 100.00 427 22 0.2032 296.219 286.793 0.925 1.002 0.194 5.546-4.326 100.00 867 58 0.1094 406.635 402.014 0.967 1.002 0.180 4.315-3.360 100.00 1859 96 0.0916 386.713 384.116 1.004 1.002 0.170 3.356-2.611 100.00 3867 181 0.1137 254.050 251.798 1.007 1.002 0.100 2.608-2.026 99.99 8198 413 0.0934 168.412 167.619 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.244 82.511 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.470 36.052 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.979 21.520 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1296 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=0.1136 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1296 | n_water=432 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1139 r_free=0.1300 | n_water=429 | time (s): 45.630 (total time: 48.060) Filter (q & B) r_work=0.1139 r_free=0.1299 | n_water=428 | time (s): 3.710 (total time: 51.770) Compute maps r_work=0.1139 r_free=0.1299 | n_water=428 | time (s): 1.830 (total time: 53.600) Filter (map) r_work=0.1158 r_free=0.1291 | n_water=324 | time (s): 3.800 (total time: 57.400) Find peaks r_work=0.1158 r_free=0.1291 | n_water=324 | time (s): 0.690 (total time: 58.090) Add new water r_work=0.1236 r_free=0.1367 | n_water=492 | time (s): 3.720 (total time: 61.810) Refine new water occ: r_work=0.1165 r_free=0.1308 adp: r_work=0.1166 r_free=0.1310 occ: r_work=0.1147 r_free=0.1292 adp: r_work=0.1147 r_free=0.1293 occ: r_work=0.1134 r_free=0.1282 adp: r_work=0.1130 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1279 r_work=0.1130 r_free=0.1279 | n_water=492 | time (s): 257.860 (total time: 319.670) Filter (q & B) r_work=0.1136 r_free=0.1280 | n_water=452 | time (s): 3.830 (total time: 323.500) Filter (dist only) r_work=0.1136 r_free=0.1279 | n_water=451 | time (s): 47.170 (total time: 370.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.818132 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.272614 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 0.1322 0.0119 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1165 0.1293 0.0127 0.003 0.8 2.9 0.5 0.0 0 0.273 0.1151 0.1285 0.0134 0.005 0.9 3.2 0.5 0.0 0 0.545 0.1145 0.1283 0.0138 0.006 1.0 3.2 0.5 0.0 0 0.818 0.1141 0.1282 0.0141 0.007 1.0 3.2 0.5 0.0 0 1.091 0.1136 0.1279 0.0142 0.007 1.1 3.8 0.5 0.0 0 1.364 0.1136 0.1279 0.0143 0.008 1.1 3.2 0.5 0.0 0 1.636 0.1134 0.1279 0.0144 0.009 1.1 3.2 0.5 0.0 0 1.909 0.1143 0.1283 0.0139 0.006 1.0 3.2 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1279 0.0144 0.009 1.1 3.2 0.5 0.0 0 1.909 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.79 1.44 3.786 21.287 38.273 3.601 11.34 12.79 1.44 3.786 21.287 1.148 3.601 11.34 12.79 1.44 3.786 21.287 4.784 3.601 11.38 12.84 1.46 3.713 21.280 19.136 3.598 11.37 12.89 1.52 3.730 21.268 38.273 3.596 11.37 12.94 1.58 3.751 21.245 57.409 3.595 11.35 12.95 1.60 3.760 21.237 76.545 3.592 11.30 12.91 1.61 3.774 21.237 95.682 3.589 11.28 12.91 1.63 3.784 21.233 114.818 3.588 11.26 12.90 1.64 3.792 21.231 133.954 3.585 11.26 12.94 1.68 3.807 21.219 153.090 3.585 11.25 12.93 1.69 3.814 21.219 172.227 3.584 11.25 12.94 1.69 3.826 21.210 191.363 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: 1.148 Accepted refinement result: 11.34 12.79 1.44 3.786 21.287 1.148 3.601 Individual atomic B min max mean iso aniso Overall: 9.11 115.16 21.29 3.33 232 1746 Protein: 9.11 115.16 17.02 3.33 0 1519 Water: 11.49 76.76 35.64 N/A 232 219 Other: 19.48 26.53 22.01 N/A 0 8 Chain A: 9.11 115.16 19.35 N/A 0 1746 Chain S: 12.33 60.05 35.86 N/A 232 0 Histogram: Values Number of atoms 9.11 - 19.72 1264 19.72 - 30.32 290 30.32 - 40.93 219 40.93 - 51.53 133 51.53 - 62.14 50 62.14 - 72.74 11 72.74 - 83.35 5 83.35 - 93.95 4 93.95 - 104.55 0 104.55 - 115.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1279 r_work=0.1134 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1279 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1278 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599173 | | target function (ml) not normalized (work): 299757.143761 | | target function (ml) not normalized (free): 15795.846843 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1129 0.1278 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1476 0.1476 0.1512 n_refl.: 87581 remove outliers: r(all,work,free)=0.1476 0.1476 0.1512 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1475 0.1475 0.1512 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1128 0.1282 n_refl.: 87581 remove outliers: r(all,work,free)=0.1133 0.1125 0.1282 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 88.54 80 5 0.3897 285.779 253.550 0.441 1.001 0.282 11.894-9.307 96.08 94 4 0.2390 475.988 459.520 0.855 1.002 0.270 9.237-7.194 97.27 207 7 0.2289 389.021 379.081 0.937 1.002 0.190 7.162-5.571 100.00 427 22 0.2097 296.219 285.823 0.919 1.003 0.155 5.546-4.326 100.00 867 58 0.1073 406.635 402.427 0.965 1.003 0.150 4.315-3.360 100.00 1859 96 0.0902 386.713 384.781 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1122 254.050 252.280 1.009 1.002 0.038 2.608-2.026 99.99 8198 413 0.0915 168.412 167.907 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.244 82.610 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.470 36.096 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.979 21.536 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0140 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1282 After: r_work=0.1127 r_free=0.1282 ================================== NQH flips ================================== r_work=0.1127 r_free=0.1282 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=0.1127 r_free=0.1282 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1127 r_free=0.1282 | n_water=451 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1127 r_free=0.1283 | n_water=449 | time (s): 49.700 (total time: 52.070) Filter (q & B) r_work=0.1127 r_free=0.1284 | n_water=448 | time (s): 3.850 (total time: 55.920) Compute maps r_work=0.1127 r_free=0.1284 | n_water=448 | time (s): 1.800 (total time: 57.720) Filter (map) r_work=0.1151 r_free=0.1287 | n_water=353 | time (s): 3.940 (total time: 61.660) Find peaks r_work=0.1151 r_free=0.1287 | n_water=353 | time (s): 0.730 (total time: 62.390) Add new water r_work=0.1203 r_free=0.1340 | n_water=494 | time (s): 3.670 (total time: 66.060) Refine new water occ: r_work=0.1144 r_free=0.1289 adp: r_work=0.1145 r_free=0.1290 occ: r_work=0.1132 r_free=0.1279 adp: r_work=0.1131 r_free=0.1280 occ: r_work=0.1123 r_free=0.1271 adp: r_work=0.1120 r_free=0.1271 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1271 r_work=0.1120 r_free=0.1271 | n_water=494 | time (s): 283.600 (total time: 349.660) Filter (q & B) r_work=0.1127 r_free=0.1281 | n_water=458 | time (s): 3.990 (total time: 353.650) Filter (dist only) r_work=0.1127 r_free=0.1279 | n_water=457 | time (s): 47.950 (total time: 401.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.732475 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.538359 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 0.1215 0.1338 0.0123 0.004 0.7 5.4 0.0 0.0 0 0.087 0.1166 0.1306 0.0140 0.004 0.8 5.4 0.0 0.0 0 0.260 0.1149 0.1294 0.0145 0.005 0.9 4.8 0.5 0.0 0 0.520 0.1140 0.1287 0.0147 0.006 1.0 5.1 0.5 0.0 0 0.780 0.1135 0.1283 0.0148 0.006 1.1 5.1 0.5 0.0 0 1.039 0.1132 0.1282 0.0150 0.007 1.1 5.1 0.5 0.0 0 1.299 0.1129 0.1280 0.0151 0.008 1.1 5.1 0.5 0.0 0 1.559 0.1128 0.1279 0.0152 0.009 1.1 4.8 0.5 0.0 0 1.819 0.1139 0.1287 0.0147 0.006 1.0 4.8 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1279 0.0152 0.009 1.1 4.8 0.5 0.0 0 1.819 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.79 1.52 3.786 21.245 37.538 3.600 11.28 12.79 1.52 3.786 21.245 1.126 3.600 11.28 12.79 1.52 3.786 21.245 4.692 3.600 11.31 12.83 1.52 3.713 21.238 18.769 3.596 11.30 12.88 1.59 3.730 21.226 37.538 3.594 11.31 12.98 1.67 3.749 21.202 56.308 3.594 11.25 12.94 1.69 3.766 21.199 75.077 3.590 11.24 12.94 1.70 3.776 21.195 93.846 3.588 11.21 12.91 1.71 3.785 21.195 112.615 3.586 11.20 12.93 1.73 3.794 21.190 131.384 3.585 11.19 12.95 1.75 3.807 21.183 150.153 3.584 11.18 12.94 1.76 3.817 21.178 168.923 3.583 11.17 12.95 1.78 3.826 21.175 187.692 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: 1.126 Accepted refinement result: 11.28 12.79 1.52 3.786 21.245 1.126 3.600 Individual atomic B min max mean iso aniso Overall: 9.11 115.15 21.22 3.33 240 1744 Protein: 9.11 115.15 17.02 3.33 0 1519 Water: 11.49 76.75 35.17 N/A 240 217 Other: 19.48 26.53 22.01 N/A 0 8 Chain A: 9.11 115.15 19.31 N/A 0 1744 Chain S: 12.32 60.05 35.08 N/A 240 0 Histogram: Values Number of atoms 9.11 - 19.71 1265 19.71 - 30.32 303 30.32 - 40.92 213 40.92 - 51.53 132 51.53 - 62.13 49 62.13 - 72.74 11 72.74 - 83.34 5 83.34 - 93.94 4 93.94 - 104.55 0 104.55 - 115.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1128 r_free=0.1279 r_work=0.1128 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1279 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1278 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598674 | | target function (ml) not normalized (work): 299697.545275 | | target function (ml) not normalized (free): 15794.391598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1313 0.1300 5.6253 5.577| | 2: 3.57 - 2.84 1.00 2888 124 0.1061 0.1430 5.1532 5.2545| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1126 4.9382 4.9555| | 4: 2.47 - 2.25 1.00 2825 136 0.0893 0.1002 4.6222 4.6661| | 5: 2.25 - 2.09 1.00 2756 127 0.0870 0.0985 4.5705 4.6295| | 6: 2.09 - 1.97 1.00 2846 113 0.0847 0.0998 4.2604 4.3606| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1120 3.9727 4.0904| | 8: 1.87 - 1.79 1.00 2789 144 0.0901 0.1128 3.8804 3.9967| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1168 3.6384 3.8244| | 10: 1.72 - 1.66 1.00 2831 160 0.0907 0.1175 3.554 3.6888| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.1043 3.4918 3.5679| | 12: 1.61 - 1.56 1.00 2773 144 0.0895 0.1162 3.3225 3.4639| | 13: 1.56 - 1.52 1.00 2745 130 0.0934 0.1025 3.3008 3.3905| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1051 3.2354 3.3173| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1241 3.1468 3.2692| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1246 3.1325 3.248| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1275 3.1138 3.2116| | 18: 1.39 - 1.36 1.00 2741 179 0.1191 0.1297 3.0981 3.2201| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1554 3.1074 3.2655| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1473 3.1102 3.1496| | 21: 1.32 - 1.30 1.00 2785 112 0.1474 0.1504 3.1136 3.1015| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1991 3.1207 3.2936| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1799 3.1313 3.2015| | 24: 1.26 - 1.24 1.00 2744 132 0.1704 0.1860 3.1242 3.2356| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2168 3.1402 3.2599| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1754 3.1471 3.2024| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2175 3.1704 3.1627| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2295 3.1652 3.1711| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2386 3.1471 3.2258| | 30: 1.16 - 1.15 1.00 2739 148 0.2452 0.2448 3.1438 3.166| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.29 1.00 0.97 5626.04| | 2: 3.57 - 2.84 2888 124 0.93 12.34 1.01 0.97 5626.04| | 3: 2.83 - 2.48 2820 163 0.90 16.26 0.99 0.97 4700.89| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.98 2315.22| | 5: 2.25 - 2.09 2756 127 0.91 15.44 1.01 0.98 2315.22| | 6: 2.09 - 1.97 2846 113 0.93 12.28 1.02 0.98 1338.68| | 7: 1.97 - 1.87 2787 165 0.95 9.25 1.02 0.97 505.82| | 8: 1.87 - 1.79 2789 144 0.93 12.55 1.00 0.97 505.82| | 9: 1.79 - 1.72 2745 138 0.94 9.97 0.98 0.97 287.03| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.97 243.21| | 11: 1.66 - 1.61 2712 147 0.94 11.68 0.98 0.97 232.98| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.97 136.55| | 13: 1.56 - 1.52 2745 130 0.95 10.33 1.02 0.97 136.55| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 122.52| | 15: 1.48 - 1.45 2738 128 0.95 9.85 1.02 0.98 96.84| | 16: 1.45 - 1.42 2756 161 0.94 11.03 1.02 0.98 96.84| | 17: 1.42 - 1.39 2785 139 0.95 10.83 1.01 0.98 88.05| | 18: 1.39 - 1.36 2741 179 0.94 11.45 1.01 0.98 82.96| | 19: 1.36 - 1.34 2807 134 0.94 11.79 0.99 0.98 82.96| | 20: 1.34 - 1.32 2696 147 0.94 12.07 0.98 0.96 79.42| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.96 79.18| | 22: 1.29 - 1.27 2704 152 0.93 13.61 0.98 0.96 79.64| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.94 82.03| | 24: 1.26 - 1.24 2744 132 0.92 14.83 0.96 0.94 82.03| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.10| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.39| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.39| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 89.89| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.98 0.92 91.21| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.97 0.92 91.21| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.18 max = 5626.04 mean = 870.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.38| |phase err.(test): min = 0.00 max = 89.23 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1278 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1450 0.1449 0.1497 n_refl.: 87576 remove outliers: r(all,work,free)=0.1450 0.1449 0.1497 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1449 0.1448 0.1497 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1279 n_refl.: 87576 remove outliers: r(all,work,free)=0.1130 0.1122 0.1279 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 0.3805 290.502 248.725 0.432 1.000 0.282 11.894-9.307 93.14 91 4 0.2381 466.997 460.114 0.862 1.001 0.270 9.237-7.194 97.27 207 7 0.2329 389.021 379.767 0.937 1.002 0.190 7.162-5.571 100.00 427 22 0.2087 296.219 286.734 0.917 1.002 0.140 5.546-4.326 100.00 867 58 0.1096 406.635 402.199 0.964 1.002 0.116 4.315-3.360 100.00 1859 96 0.0909 386.713 384.562 1.003 1.002 0.103 3.356-2.611 100.00 3867 181 0.1104 254.050 252.332 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0906 168.412 167.835 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.244 82.586 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.470 36.090 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 22.979 21.540 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0144 ================= 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 : 0.2608 0.1961 0.082 5.277 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1792 0.082 5.277 9.0 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1792 0.082 5.277 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1797 0.082 5.277 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1797 0.082 5.277 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1231 0.1474 0.007 0.907 9.0 119.5 20.1 258 0.136 1_adp: 0.1231 0.1473 0.007 0.907 9.0 119.5 20.1 258 0.136 1_regHadp: 0.1233 0.1476 0.007 0.907 9.0 119.5 20.1 258 0.136 1_occ: 0.1226 0.1467 0.007 0.907 9.0 119.5 20.1 258 0.136 2_bss: 0.1223 0.1454 0.007 0.907 9.1 119.5 20.1 258 0.136 2_settarget: 0.1223 0.1454 0.007 0.907 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1223 0.1454 0.007 0.917 9.1 119.5 20.1 258 0.136 2_nqh: 0.1221 0.1452 0.007 0.917 9.1 119.5 20.1 258 0.136 2_sol: 0.1193 0.1397 0.007 0.917 9.1 116.0 22.2 417 n/a 2_weight: 0.1193 0.1397 0.007 0.917 9.1 116.0 22.2 417 n/a 2_xyzrec: 0.1178 0.1402 0.007 0.903 9.1 116.0 22.2 417 n/a 2_adp: 0.1184 0.1399 0.007 0.903 9.1 115.2 22.2 417 n/a 2_regHadp: 0.1185 0.1400 0.007 0.903 9.1 115.2 22.2 417 n/a 2_occ: 0.1184 0.1400 0.007 0.903 9.1 115.2 22.2 417 n/a 3_bss: 0.1180 0.1399 0.007 0.903 9.1 115.2 22.2 417 n/a 3_settarget: 0.1180 0.1399 0.007 0.903 9.1 115.2 22.2 417 n/a 3_updatecdl: 0.1180 0.1399 0.007 0.905 9.1 115.2 22.2 417 n/a 3_nqh: 0.1180 0.1399 0.007 0.905 9.1 115.2 22.2 417 n/a 3_sol: 0.1198 0.1378 0.007 0.905 9.1 115.2 21.2 432 n/a 3_weight: 0.1198 0.1378 0.007 0.905 9.1 115.2 21.2 432 n/a 3_xyzrec: 0.1152 0.1306 0.008 1.094 9.1 115.2 21.2 432 n/a 3_adp: 0.1152 0.1306 0.008 1.094 9.1 115.2 21.2 432 n/a 3_regHadp: 0.1152 0.1306 0.008 1.094 9.1 115.2 21.2 432 n/a 3_occ: 0.1142 0.1300 0.008 1.094 9.1 115.2 21.2 432 n/a 4_bss: 0.1136 0.1296 0.008 1.094 9.1 115.2 21.2 432 n/a 4_settarget: 0.1136 0.1296 0.008 1.094 9.1 115.2 21.2 432 n/a 4_updatecdl: 0.1136 0.1296 0.008 1.095 9.1 115.2 21.2 432 n/a 4_nqh: 0.1136 0.1296 0.008 1.095 9.1 115.2 21.2 432 n/a 4_sol: 0.1136 0.1279 0.008 1.095 9.1 115.2 21.3 451 n/a 4_weight: 0.1136 0.1279 0.008 1.095 9.1 115.2 21.3 451 n/a 4_xyzrec: 0.1134 0.1279 0.009 1.134 9.1 115.2 21.3 451 n/a 4_adp: 0.1134 0.1279 0.009 1.134 9.1 115.2 21.3 451 n/a 4_regHadp: 0.1134 0.1279 0.009 1.134 9.1 115.2 21.3 451 n/a 4_occ: 0.1129 0.1278 0.009 1.134 9.1 115.2 21.3 451 n/a 5_bss: 0.1125 0.1282 0.009 1.134 9.1 115.2 21.3 451 n/a 5_settarget: 0.1125 0.1282 0.009 1.134 9.1 115.2 21.3 451 n/a 5_updatecdl: 0.1125 0.1282 0.009 1.134 9.1 115.2 21.3 451 n/a 5_setrh: 0.1127 0.1282 0.009 1.134 9.1 115.2 21.3 451 n/a 5_nqh: 0.1127 0.1282 0.009 1.134 9.1 115.2 21.3 451 n/a 5_sol: 0.1127 0.1279 0.009 1.134 9.1 115.2 21.2 457 n/a 5_weight: 0.1127 0.1279 0.009 1.134 9.1 115.2 21.2 457 n/a 5_xyzrec: 0.1128 0.1279 0.009 1.140 9.1 115.2 21.2 457 n/a 5_adp: 0.1128 0.1279 0.009 1.140 9.1 115.2 21.2 457 n/a 5_regHadp: 0.1128 0.1279 0.009 1.140 9.1 115.2 21.2 457 n/a 5_occ: 0.1125 0.1278 0.009 1.140 9.1 115.2 21.2 457 n/a end: 0.1122 0.1279 0.009 1.140 9.1 115.1 21.2 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1498316_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1498316_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4200 Refinement macro-cycles (run) : 13797.0100 Write final files (write_after_run_outputs) : 89.0200 Total : 13889.4500 Total CPU time: 3.87 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:14:22 PST -0800 (1735366462.93 s) Start R-work = 0.1636, R-free = 0.1792 Final R-work = 0.1122, R-free = 0.1279 =============================================================================== Job complete usr+sys time: 14053.77 seconds wall clock time: 258 minutes 16.66 seconds (15496.66 seconds total)