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_4813131.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_4813131.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.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 =============================================================================== 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: 1.37, per 1000 atoms: 0.41 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 103.7 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 406 0.89 - 1.15: 1203 1.15 - 1.41: 628 1.41 - 1.67: 881 1.67 - 1.93: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 11 " pdb=" N LYS A 12 " ideal model delta sigma weight residual 1.332 1.626 -0.295 1.35e-02 5.49e+03 4.76e+02 bond pdb=" CA ALA A 104 " pdb=" C ALA A 104 " ideal model delta sigma weight residual 1.520 1.294 0.227 1.22e-02 6.72e+03 3.46e+02 bond pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 1.456 1.214 0.242 1.32e-02 5.74e+03 3.36e+02 bond pdb=" N GLU A 163 " pdb=" CA GLU A 163 " ideal model delta sigma weight residual 1.459 1.671 -0.212 1.19e-02 7.06e+03 3.18e+02 bond pdb=" C ARG A 145 " pdb=" O ARG A 145 " ideal model delta sigma weight residual 1.237 1.441 -0.205 1.16e-02 7.43e+03 3.11e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3333 4.94 - 9.87: 1811 9.87 - 14.81: 548 14.81 - 19.74: 79 19.74 - 24.68: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA BLYS A 175 " pdb=" C BLYS A 175 " pdb=" O BLYS A 175 " ideal model delta sigma weight residual 120.55 136.26 -15.71 1.06e+00 8.90e-01 2.20e+02 angle pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " pdb=" O ATYR A 67 " ideal model delta sigma weight residual 120.71 135.51 -14.80 1.06e+00 8.90e-01 1.95e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 106.38 15.77 1.14e+00 7.69e-01 1.91e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.76 107.13 13.63 1.03e+00 9.43e-01 1.75e+02 angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.07 109.11 12.96 1.03e+00 9.43e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 938 17.33 - 34.66: 115 34.66 - 51.98: 40 51.98 - 69.31: 16 69.31 - 86.64: 2 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 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+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 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.215: 103 0.215 - 0.427: 77 0.427 - 0.640: 41 0.640 - 0.852: 19 0.852 - 1.065: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 51 " pdb=" N VAL A 51 " pdb=" C VAL A 51 " pdb=" CB VAL A 51 " both_signs ideal model delta sigma weight residual False 2.44 3.51 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CG LEU A 187 " pdb=" CB LEU A 187 " pdb=" CD1 LEU A 187 " pdb=" CD2 LEU A 187 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.105 9.50e-02 1.11e+02 8.77e-02 1.47e+02 pdb=" NE ARG A 27 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " -0.131 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.069 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.073 2.00e-02 2.50e+03 6.18e-02 1.15e+02 pdb=" CG PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.042 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 869 2.29 - 2.87: 7884 2.87 - 3.44: 10567 3.44 - 4.02: 15298 4.02 - 4.60: 22023 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.710 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.805 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.870 2.100 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.895 1.850 ... (remaining 56636 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_4813131_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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785229 | | target function (ml) not normalized (work): 232026.292978 | | target function (ml) not normalized (free): 11790.774630 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2105 7.0314 4.9449| | 2: 3.57 - 2.84 1.00 2876 122 0.2442 0.1826 4.3529 4.3434| | 3: 2.84 - 2.48 1.00 2833 165 0.2345 0.1737 4.131 4.1624| | 4: 2.47 - 2.25 1.00 2825 136 0.2305 0.1516 3.8313 3.8385| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1592 3.7983 3.812| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1622 3.4568 3.5318| | 7: 1.97 - 1.87 1.00 2787 165 0.2510 0.1761 3.1262 3.1778| | 8: 1.87 - 1.79 1.00 2789 144 0.2447 0.1980 3.0443 3.1744| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.1764 2.8805 2.873| | 10: 1.72 - 1.66 1.00 2789 158 0.2305 0.1847 2.7867 2.8348| | 11: 1.66 - 1.61 1.00 2740 147 0.2456 0.1833 2.7261 2.7774| | 12: 1.61 - 1.56 1.00 2787 146 0.2517 0.2161 2.6274 2.7102| | 13: 1.56 - 1.52 1.00 2745 130 0.2567 0.1914 2.5625 2.6066| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1815 2.5112 2.4832| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2195 2.4295 2.5005| | 16: 1.45 - 1.42 1.00 2756 161 0.2587 0.2175 2.3656 2.4316| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.2203 2.3358 2.4169| | 18: 1.39 - 1.36 1.00 2741 179 0.2653 0.2109 2.2658 2.3145| | 19: 1.36 - 1.34 1.00 2807 134 0.2658 0.2180 2.2415 2.2595| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2252 2.2042 2.1934| | 21: 1.32 - 1.30 1.00 2785 112 0.2767 0.2286 2.1699 2.1835| | 22: 1.29 - 1.27 1.00 2704 152 0.2713 0.2619 2.1235 2.2224| | 23: 1.27 - 1.26 1.00 2802 156 0.2811 0.2311 2.1032 2.1478| | 24: 1.26 - 1.24 1.00 2744 132 0.2787 0.2272 2.0746 2.0893| | 25: 1.24 - 1.22 1.00 2734 148 0.2821 0.2554 2.0443 2.094| | 26: 1.22 - 1.21 1.00 2727 135 0.2828 0.2175 2.0115 2.0508| | 27: 1.21 - 1.19 1.00 2814 148 0.2899 0.2731 1.9923 2.0343| | 28: 1.19 - 1.18 1.00 2671 147 0.2941 0.2819 1.9743 1.9624| | 29: 1.18 - 1.16 1.00 2800 134 0.2976 0.2895 1.9617 2.0665| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2724 1.9371 1.9489| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.99 0.76 0.23 1490.98| | 2: 3.57 - 2.84 2876 122 0.80 26.23 1.27 0.23 1490.98| | 3: 2.84 - 2.48 2833 165 0.74 31.99 1.24 0.23 1235.68| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.25 0.25 573.11| | 5: 2.25 - 2.09 2756 127 0.77 29.30 1.28 0.25 573.11| | 6: 2.09 - 1.97 2846 113 0.83 22.62 1.29 0.25 312.28| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.25 89.82| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.25 89.82| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.23 0.25 53.83| | 10: 1.72 - 1.66 2789 158 0.87 19.64 1.21 0.25 46.63| | 11: 1.66 - 1.61 2740 147 0.86 21.22 1.24 0.25 45.04| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.23 0.25 28.99| | 13: 1.56 - 1.52 2745 130 0.87 20.12 1.25 0.25 28.99| | 14: 1.52 - 1.48 2803 134 0.87 20.50 1.24 0.25 25.85| | 15: 1.48 - 1.45 2738 128 0.87 19.91 1.23 0.25 20.10| | 16: 1.45 - 1.42 2756 161 0.86 21.18 1.23 0.25 20.10| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.23 0.25 17.23| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.22 0.25 15.57| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.21 0.25 15.57| | 20: 1.34 - 1.32 2696 147 0.87 20.59 1.20 0.24 12.69| | 21: 1.32 - 1.30 2785 112 0.86 21.99 1.20 0.24 12.48| | 22: 1.29 - 1.27 2704 152 0.86 22.14 1.21 0.24 12.23| | 23: 1.27 - 1.26 2802 156 0.86 22.03 1.21 0.24 10.91| | 24: 1.26 - 1.24 2744 132 0.85 22.58 1.20 0.24 10.91| | 25: 1.24 - 1.22 2734 148 0.85 23.47 1.20 0.23 10.41| | 26: 1.22 - 1.21 2727 135 0.84 23.90 1.19 0.23 9.85| | 27: 1.21 - 1.19 2814 148 0.83 24.54 1.20 0.23 9.85| | 28: 1.19 - 1.18 2671 147 0.82 25.55 1.17 0.23 9.40| | 29: 1.18 - 1.16 2800 134 0.82 25.92 1.16 0.23 9.23| | 30: 1.16 - 1.15 2740 148 0.80 27.41 1.14 0.23 9.23| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.23 max = 1490.98 mean = 215.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.50| |phase err.(test): min = 0.00 max = 89.84 mean = 22.35| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.295 1557 Z= 5.317 Angle : 5.198 18.421 2118 Z= 3.650 Chirality : 0.370 1.065 243 Planarity : 0.032 0.132 284 Dihedral : 14.016 86.638 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.65 % 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 (0.47), residues: 224 helix: -1.87 (0.39), residues: 109 sheet: -1.46 (0.77), residues: 38 loop : -0.76 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.125 0.030 ARG A 28 TYR 0.076 0.029 TYR A 139 PHE 0.121 0.037 PHE A 164 HIS 0.088 0.036 HIS A 115 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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785229 | | target function (ml) not normalized (work): 232026.292978 | | target function (ml) not normalized (free): 11790.774630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1971 0.1946 n_refl.: 87594 overall B=0.24 to atoms: r(all,work,free)=0.1997 0.2001 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1761 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 386.100 356.779 0.717 0.931 0.402 11.894-9.307 99.02 97 4 0.1847 613.301 595.548 1.001 0.932 0.380 9.237-7.194 100.00 213 7 0.2164 501.605 490.120 1.031 0.932 0.344 7.162-5.571 100.00 427 22 0.2181 376.427 364.331 0.999 0.932 0.329 5.546-4.326 100.00 867 58 0.1284 516.741 511.288 1.033 0.932 0.218 4.315-3.360 100.00 1859 96 0.1147 491.424 487.517 1.079 0.932 0.189 3.356-2.611 100.00 3867 181 0.1445 322.840 319.707 1.074 0.931 0.043 2.608-2.026 99.99 8198 413 0.1336 214.014 212.001 1.082 0.930 0.000 2.025-1.573 100.00 17313 902 0.1616 104.513 103.823 1.086 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2058 46.345 45.040 1.079 0.927 0.000 1.221-1.150 99.97 13689 708 0.2572 29.201 26.911 1.046 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0542 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1761 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.280717 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.693997 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 0.1712 0.1828 0.0116 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1585 0.1719 0.0134 0.002 0.4 4.2 0.0 0.0 0 0.250 0.1449 0.1607 0.0157 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1383 0.1566 0.0183 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1350 0.1540 0.0190 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1362 0.1558 0.0196 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1297 0.1511 0.0214 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1273 0.1497 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1253 0.1484 0.0231 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1481 0.0233 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1244 0.1479 0.0235 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1235 0.1471 0.0236 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1232 0.1472 0.0240 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1472 0.0241 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1230 0.1473 0.0242 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1471 0.0242 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1225 0.1473 0.0248 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1222 0.1473 0.0251 0.008 1.0 4.2 0.5 0.6 0 13.640 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1471 0.0236 0.005 0.8 3.5 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.71 2.36 3.013 19.095 2029.694 0.018 12.35 14.70 2.35 2.988 19.095 60.891 0.018 12.41 14.67 2.26 2.669 19.093 253.712 0.018 12.75 15.37 2.61 2.905 19.371 1014.847 0.017 12.56 15.46 2.91 3.057 19.486 2029.694 0.016 12.54 15.56 3.02 3.383 19.692 3044.541 0.016 12.35 15.41 3.05 3.337 19.660 4059.388 0.015 12.33 15.40 3.07 3.251 19.584 5074.235 0.015 12.27 15.40 3.13 3.368 19.659 6089.082 0.015 12.31 15.57 3.26 3.561 19.755 7103.929 0.015 12.28 15.56 3.28 3.443 19.679 8118.776 0.015 12.28 15.61 3.32 3.547 19.721 9133.623 0.015 12.27 15.62 3.35 3.452 19.658 10148.470 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: 253.712 Accepted refinement result: 12.41 14.67 2.26 2.669 19.093 253.712 0.018 Individual atomic B min max mean iso aniso Overall: 9.09 119.47 20.12 3.31 0 1785 Protein: 9.09 115.04 17.03 3.32 0 1519 Water: 11.49 119.47 38.26 N/A 0 258 Other: 19.76 26.65 22.09 N/A 0 8 Chain A: 9.09 119.47 20.12 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.17 227 31.17 - 42.21 125 42.21 - 53.25 94 53.25 - 64.28 42 64.28 - 75.32 11 75.32 - 86.36 7 86.36 - 97.40 4 97.40 - 108.44 1 108.44 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1467 r_work=0.1242 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1469 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1238 r_free = 0.1466 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1238 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.017196 | | target function (ls_wunit_k1) not normalized (work): 1432.346316 | | target function (ls_wunit_k1) not normalized (free): 109.869448 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1249 0.1238 0.1466 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1689 0.1691 0.1697 n_refl.: 87593 remove outliers: r(all,work,free)=0.1689 0.1691 0.1697 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1693 0.1695 0.1700 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1248 0.1237 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1247 0.1236 0.1458 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 0.3572 297.249 281.751 0.644 1.002 0.380 11.894-9.307 99.02 97 4 0.1683 481.675 468.904 0.921 1.003 0.371 9.237-7.194 100.00 213 7 0.1912 393.951 388.619 0.962 1.003 0.319 7.162-5.571 100.00 427 22 0.1872 295.638 289.277 0.933 1.003 0.259 5.546-4.326 100.00 867 58 0.1029 405.838 402.279 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0878 385.955 384.808 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1182 253.552 252.405 1.011 1.002 0.100 2.608-2.026 99.99 8198 413 0.1027 168.082 167.327 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1118 82.083 82.261 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1461 36.399 35.894 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2263 22.934 21.415 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1458 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1238 r_free=0.1460 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1460 | n_water=258 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1245 r_free=0.1457 | n_water=251 | time (s): 20.320 (total time: 21.990) Filter (q & B) r_work=0.1247 r_free=0.1457 | n_water=248 | time (s): 2.750 (total time: 24.740) Compute maps r_work=0.1247 r_free=0.1457 | n_water=248 | time (s): 1.590 (total time: 26.330) Filter (map) r_work=0.1265 r_free=0.1459 | n_water=229 | time (s): 3.320 (total time: 29.650) Find peaks r_work=0.1265 r_free=0.1459 | n_water=229 | time (s): 0.450 (total time: 30.100) Add new water r_work=0.1409 r_free=0.1640 | n_water=439 | time (s): 2.620 (total time: 32.720) Refine new water occ: r_work=0.1316 r_free=0.1490 adp: r_work=0.1235 r_free=0.1440 occ: r_work=0.1248 r_free=0.1424 adp: r_work=0.1214 r_free=0.1412 occ: r_work=0.1216 r_free=0.1400 adp: r_work=0.1208 r_free=0.1403 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1403 r_work=0.1208 r_free=0.1403 | n_water=439 | time (s): 54.430 (total time: 87.150) Filter (q & B) r_work=0.1212 r_free=0.1406 | n_water=422 | time (s): 2.760 (total time: 89.910) Filter (dist only) r_work=0.1212 r_free=0.1403 | n_water=421 | time (s): 35.210 (total time: 125.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.519358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1471.592254 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 0.1571 0.1706 0.0135 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1521 0.1663 0.0142 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1415 0.1579 0.0164 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1363 0.1542 0.0179 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1312 0.1504 0.0191 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1326 0.1517 0.0191 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1253 0.1464 0.0211 0.002 0.5 5.1 0.5 0.0 0 2.000 0.1223 0.1443 0.0219 0.003 0.6 6.1 0.5 0.0 0 3.000 0.1212 0.1432 0.0220 0.003 0.7 6.4 0.5 0.0 0 4.000 0.1208 0.1435 0.0227 0.004 0.7 6.4 0.5 0.0 0 5.000 0.1201 0.1426 0.0225 0.004 0.7 6.4 0.5 0.0 0 6.000 0.1197 0.1424 0.0227 0.005 0.8 6.7 0.5 0.0 0 7.000 0.1196 0.1424 0.0228 0.005 0.8 5.8 0.5 0.0 0 8.000 0.1192 0.1416 0.0224 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1190 0.1416 0.0226 0.006 0.8 6.1 0.5 0.0 0 10.000 0.1190 0.1423 0.0233 0.007 0.9 7.0 0.5 0.0 0 11.000 0.1186 0.1421 0.0235 0.007 0.9 7.7 0.5 0.0 0 12.000 0.1186 0.1423 0.0237 0.007 0.9 8.0 0.5 0.0 0 13.000 0.1184 0.1424 0.0240 0.008 0.9 7.0 0.5 0.0 0 14.260 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1416 0.0224 0.006 0.8 6.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 14.16 2.24 3.779 21.809 1471.592 0.016 11.92 14.16 2.24 3.779 21.809 44.148 0.016 11.92 14.16 2.24 3.779 21.809 183.949 0.016 12.11 14.63 2.52 3.627 21.822 735.796 0.015 12.09 15.02 2.93 3.475 22.140 1471.592 0.015 11.97 15.06 3.09 3.525 21.958 2207.388 0.014 11.84 14.95 3.11 3.523 21.965 2943.185 0.014 11.78 14.84 3.07 3.493 22.147 3678.981 0.014 11.77 14.90 3.13 3.522 22.203 4414.777 0.014 11.74 14.95 3.21 3.552 22.244 5150.573 0.014 11.74 15.00 3.26 3.575 22.268 5886.369 0.014 11.70 15.00 3.30 3.559 22.149 6622.165 0.014 11.70 15.03 3.32 3.582 22.200 7357.961 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.148 Accepted refinement result: 11.92 14.16 2.24 3.779 21.809 44.148 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.06 22.22 3.31 192 1756 Protein: 9.12 115.06 17.05 3.32 0 1519 Water: 11.51 76.72 40.85 N/A 192 229 Other: 19.79 26.67 22.12 N/A 0 8 Chain A: 9.12 115.06 19.54 N/A 0 1756 Chain S: 13.60 60.00 46.73 N/A 192 0 Histogram: Values Number of atoms 9.12 - 19.71 1260 19.71 - 30.31 243 30.31 - 40.90 170 40.90 - 51.50 130 51.50 - 62.09 122 62.09 - 72.68 12 72.68 - 83.28 5 83.28 - 93.87 4 93.87 - 104.47 0 104.47 - 115.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1416 r_work=0.1192 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1416 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1412 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= 0.1189 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015049 | | target function (ls_wunit_k1) not normalized (work): 1253.542104 | | target function (ls_wunit_k1) not normalized (free): 98.166163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1412 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1584 0.1582 0.1655 n_refl.: 87591 remove outliers: r(all,work,free)=0.1584 0.1582 0.1655 n_refl.: 87591 overall B=0.00 to atoms: r(all,work,free)=0.1584 0.1582 0.1655 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1187 0.1411 n_refl.: 87591 remove outliers: r(all,work,free)=0.1197 0.1186 0.1411 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 0.3231 296.595 275.175 0.582 1.002 0.350 11.894-9.307 99.02 97 4 0.1691 481.675 474.156 0.912 1.003 0.333 9.237-7.194 100.00 213 7 0.1728 393.951 393.595 0.982 1.003 0.290 7.162-5.571 100.00 427 22 0.1625 295.638 290.903 0.937 1.003 0.230 5.546-4.326 100.00 867 58 0.0881 405.838 402.749 0.960 1.003 0.204 4.315-3.360 100.00 1859 96 0.0793 385.955 385.062 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1090 253.552 252.635 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1002 168.082 167.570 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.083 82.310 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.399 35.945 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.934 21.456 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0015 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1411 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1411 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1411 | n_water=421 | time (s): 1.610 (total time: 1.610) Filter (dist) r_work=0.1187 r_free=0.1415 | n_water=419 | time (s): 38.450 (total time: 40.060) Filter (q & B) r_work=0.1187 r_free=0.1415 | n_water=419 | time (s): 0.900 (total time: 40.960) Compute maps r_work=0.1187 r_free=0.1415 | n_water=419 | time (s): 1.130 (total time: 42.090) Filter (map) r_work=0.1226 r_free=0.1388 | n_water=285 | time (s): 2.600 (total time: 44.690) Find peaks r_work=0.1226 r_free=0.1388 | n_water=285 | time (s): 0.450 (total time: 45.140) Add new water r_work=0.1341 r_free=0.1500 | n_water=475 | time (s): 2.500 (total time: 47.640) Refine new water occ: r_work=0.1247 r_free=0.1418 adp: r_work=0.1248 r_free=0.1420 occ: r_work=0.1225 r_free=0.1396 adp: r_work=0.1224 r_free=0.1398 occ: r_work=0.1208 r_free=0.1387 adp: r_work=0.1203 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1385 r_work=0.1203 r_free=0.1385 | n_water=475 | time (s): 176.280 (total time: 223.920) Filter (q & B) r_work=0.1210 r_free=0.1387 | n_water=440 | time (s): 2.820 (total time: 226.740) Filter (dist only) r_work=0.1210 r_free=0.1386 | n_water=439 | time (s): 38.190 (total time: 264.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.731176 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.052172 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1356 0.0119 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1195 0.1326 0.0131 0.003 0.7 3.8 0.5 0.0 0 0.260 0.1176 0.1311 0.0135 0.004 0.8 4.2 0.5 0.0 0 0.519 0.1167 0.1307 0.0141 0.005 0.9 4.5 0.5 0.0 0 0.779 0.1163 0.1305 0.0142 0.006 1.0 4.5 0.5 0.0 0 1.039 0.1162 0.1308 0.0146 0.007 1.0 4.5 0.5 0.0 0 1.298 0.1159 0.1304 0.0145 0.007 1.0 4.8 0.5 0.0 0 1.558 0.1158 0.1307 0.0150 0.008 1.1 5.1 0.5 0.0 0 1.818 0.1166 0.1307 0.0141 0.005 0.9 4.5 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1304 0.0145 0.007 1.0 4.8 0.5 0.0 0 1.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.04 1.45 3.782 21.269 47.052 3.617 11.59 13.04 1.45 3.782 21.269 1.412 3.617 11.59 13.05 1.45 3.766 21.269 5.882 3.616 11.65 13.14 1.50 3.717 21.252 23.526 3.612 11.60 13.17 1.57 3.747 21.227 47.052 3.609 11.56 13.18 1.63 3.767 21.210 70.578 3.604 11.53 13.18 1.66 3.780 21.205 94.104 3.601 11.49 13.15 1.67 3.793 21.197 117.630 3.597 11.47 13.17 1.70 3.811 21.187 141.157 3.596 11.46 13.17 1.71 3.823 21.181 164.683 3.595 11.45 13.16 1.71 3.833 21.174 188.209 3.594 11.46 13.19 1.73 3.844 21.169 211.735 3.594 11.41 13.13 1.72 3.843 21.176 235.261 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.412 Accepted refinement result: 11.59 13.04 1.45 3.782 21.269 1.412 3.617 Individual atomic B min max mean iso aniso Overall: 9.12 115.06 21.23 3.31 213 1753 Protein: 9.12 115.06 17.05 3.32 0 1519 Water: 11.51 76.72 35.67 N/A 213 226 Other: 19.79 26.67 22.12 N/A 0 8 Chain A: 9.12 115.06 19.49 N/A 0 1753 Chain S: 13.60 60.00 35.55 N/A 213 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.31 287 30.31 - 40.90 212 40.90 - 51.50 125 51.50 - 62.09 56 62.09 - 72.69 12 72.69 - 83.28 5 83.28 - 93.87 4 93.87 - 104.47 0 104.47 - 115.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1304 r_work=0.1159 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1304 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1305 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.12 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= 0.1151 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610721 | | target function (ml) not normalized (work): 300747.796165 | | target function (ml) not normalized (free): 15826.913464 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1151 0.1305 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1497 0.1498 0.1521 n_refl.: 87589 remove outliers: r(all,work,free)=0.1497 0.1498 0.1521 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1496 0.1496 0.1520 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1146 0.1302 n_refl.: 87589 remove outliers: r(all,work,free)=0.1152 0.1144 0.1302 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 0.3832 298.801 265.511 0.496 1.000 0.318 11.894-9.307 97.06 95 4 0.2314 481.898 463.008 0.864 1.001 0.253 9.237-7.194 98.64 210 7 0.2352 386.450 387.233 0.943 1.002 0.200 7.162-5.571 100.00 427 22 0.2125 295.638 284.950 0.910 1.002 0.170 5.546-4.326 100.00 867 58 0.1094 405.838 401.680 0.953 1.002 0.150 4.315-3.360 100.00 1859 96 0.0943 385.955 383.462 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1134 253.552 251.847 0.998 1.002 0.090 2.608-2.026 99.99 8198 413 0.0930 168.082 167.396 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0898 82.083 82.397 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.399 35.994 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.934 21.482 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=-0.0213 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1302 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=0.1144 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1302 | n_water=439 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1144 r_free=0.1303 | n_water=438 | time (s): 44.730 (total time: 47.170) Filter (q & B) r_work=0.1144 r_free=0.1303 | n_water=437 | time (s): 3.910 (total time: 51.080) Compute maps r_work=0.1144 r_free=0.1303 | n_water=437 | time (s): 1.870 (total time: 52.950) Filter (map) r_work=0.1171 r_free=0.1271 | n_water=333 | time (s): 3.880 (total time: 56.830) Find peaks r_work=0.1171 r_free=0.1271 | n_water=333 | time (s): 0.660 (total time: 57.490) Add new water r_work=0.1239 r_free=0.1333 | n_water=499 | time (s): 3.840 (total time: 61.330) Refine new water occ: r_work=0.1164 r_free=0.1286 adp: r_work=0.1165 r_free=0.1287 occ: r_work=0.1149 r_free=0.1280 adp: r_work=0.1148 r_free=0.1279 occ: r_work=0.1137 r_free=0.1280 adp: r_work=0.1133 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1276 r_work=0.1133 r_free=0.1276 | n_water=499 | time (s): 321.410 (total time: 382.740) Filter (q & B) r_work=0.1140 r_free=0.1286 | n_water=462 | time (s): 3.950 (total time: 386.690) Filter (dist only) r_work=0.1147 r_free=0.1282 | n_water=460 | time (s): 47.910 (total time: 434.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.759641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.814978 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1326 0.0118 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1170 0.1298 0.0129 0.003 0.7 3.8 0.5 0.0 0 0.264 0.1155 0.1288 0.0132 0.005 0.9 4.5 0.5 0.0 0 0.528 0.1149 0.1285 0.0135 0.006 1.0 5.1 0.5 0.0 0 0.792 0.1145 0.1284 0.0139 0.006 1.0 4.5 0.5 0.0 0 1.056 0.1142 0.1284 0.0142 0.007 1.0 4.5 0.5 0.0 0 1.320 0.1141 0.1282 0.0141 0.008 1.1 4.8 0.5 0.0 0 1.584 0.1138 0.1281 0.0143 0.009 1.1 4.5 0.5 0.0 0 1.848 0.1147 0.1285 0.0138 0.006 1.0 4.8 0.5 0.0 0 0.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1281 0.0143 0.009 1.1 4.5 0.5 0.0 0 1.848 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 12.81 1.43 3.782 21.317 42.815 3.603 11.38 12.81 1.43 3.782 21.317 1.284 3.603 11.38 12.81 1.43 3.782 21.317 5.352 3.603 11.41 12.87 1.46 3.717 21.309 21.407 3.598 11.43 12.96 1.53 3.742 21.284 42.815 3.599 11.41 13.00 1.59 3.754 21.266 64.222 3.596 11.33 12.93 1.59 3.774 21.263 85.630 3.590 11.32 12.91 1.60 3.781 21.262 107.037 3.588 11.28 12.89 1.61 3.791 21.258 128.445 3.585 11.28 12.91 1.64 3.805 21.252 149.852 3.585 11.27 12.93 1.66 3.818 21.241 171.260 3.584 11.26 12.92 1.66 3.826 21.240 192.667 3.583 11.25 12.91 1.67 3.832 21.239 214.075 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.284 Accepted refinement result: 11.38 12.81 1.43 3.782 21.317 1.284 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.32 3.31 236 1751 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.50 76.71 35.44 N/A 236 224 Other: 19.78 26.67 22.11 N/A 0 8 Chain A: 9.11 115.05 19.48 N/A 0 1751 Chain S: 13.59 59.99 35.02 N/A 236 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.30 295 30.30 - 40.89 218 40.89 - 51.49 138 51.49 - 62.08 49 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.87 4 93.87 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1138 r_free=0.1281 r_work=0.1138 r_free=0.1281 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1281 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1282 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 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= 0.1131 r_free= 0.1282 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600324 | | target function (ml) not normalized (work): 299860.163289 | | target function (ml) not normalized (free): 15795.694918 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1282 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1447 0.1444 0.1519 n_refl.: 87583 remove outliers: r(all,work,free)=0.1447 0.1444 0.1519 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1446 0.1443 0.1519 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1130 0.1289 n_refl.: 87583 remove outliers: r(all,work,free)=0.1136 0.1128 0.1289 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4085 288.686 262.170 0.468 0.999 0.308 11.894-9.307 96.08 94 4 0.2430 475.055 465.218 0.864 1.001 0.223 9.237-7.194 98.18 209 7 0.2337 385.445 382.486 0.930 1.002 0.150 7.162-5.571 100.00 427 22 0.2100 295.638 285.809 0.915 1.002 0.133 5.546-4.326 100.00 867 58 0.1111 405.838 401.029 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0911 385.955 383.746 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1105 253.552 251.593 1.009 1.002 0.070 2.608-2.026 99.99 8198 413 0.0911 168.082 167.382 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.083 82.388 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.399 35.983 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2168 22.934 21.467 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=-0.0147 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1128 r_free=0.1289 After: r_work=0.1130 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1130 r_free=0.1289 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=0.1130 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1130 r_free=0.1289 | n_water=460 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1130 r_free=0.1288 | n_water=458 | time (s): 50.660 (total time: 53.060) Filter (q & B) r_work=0.1130 r_free=0.1286 | n_water=457 | time (s): 3.900 (total time: 56.960) Compute maps r_work=0.1130 r_free=0.1286 | n_water=457 | time (s): 1.840 (total time: 58.800) Filter (map) r_work=0.1159 r_free=0.1294 | n_water=361 | time (s): 3.860 (total time: 62.660) Find peaks r_work=0.1159 r_free=0.1294 | n_water=361 | time (s): 0.710 (total time: 63.370) Add new water r_work=0.1205 r_free=0.1336 | n_water=515 | time (s): 3.990 (total time: 67.360) Refine new water occ: r_work=0.1149 r_free=0.1292 adp: r_work=0.1149 r_free=0.1294 occ: r_work=0.1138 r_free=0.1282 adp: r_work=0.1137 r_free=0.1282 occ: r_work=0.1130 r_free=0.1276 adp: r_work=0.1127 r_free=0.1274 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1274 r_work=0.1127 r_free=0.1274 | n_water=515 | time (s): 224.880 (total time: 292.240) Filter (q & B) r_work=0.1135 r_free=0.1284 | n_water=466 | time (s): 4.070 (total time: 296.310) Filter (dist only) r_work=0.1135 r_free=0.1283 | n_water=465 | time (s): 48.890 (total time: 345.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.824274 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.277506 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 0.1219 0.1339 0.0120 0.004 0.7 5.8 0.0 0.0 0 0.091 0.1175 0.1308 0.0133 0.004 0.8 5.8 0.0 0.0 0 0.274 0.1154 0.1295 0.0140 0.005 0.9 5.1 0.5 0.0 0 0.547 0.1146 0.1289 0.0143 0.006 1.0 5.1 0.5 0.0 0 0.821 0.1142 0.1287 0.0145 0.006 1.1 4.8 0.5 0.0 0 1.095 0.1138 0.1284 0.0146 0.007 1.1 4.8 0.5 0.0 0 1.368 0.1136 0.1283 0.0147 0.008 1.1 4.5 0.5 0.0 0 1.642 0.1135 0.1283 0.0148 0.009 1.1 4.5 0.5 0.0 0 1.915 0.1144 0.1288 0.0144 0.006 1.0 5.1 0.5 0.0 0 0.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1283 0.0148 0.009 1.1 4.5 0.5 0.0 0 1.915 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.83 1.48 3.781 21.328 39.278 3.602 11.35 12.83 1.48 3.781 21.328 1.178 3.602 11.35 12.83 1.48 3.781 21.328 4.910 3.602 11.38 12.88 1.50 3.714 21.320 19.639 3.597 11.45 13.07 1.62 3.735 21.291 39.278 3.602 11.39 13.05 1.66 3.754 21.278 58.916 3.596 11.34 13.01 1.68 3.770 21.274 78.555 3.592 11.30 12.98 1.68 3.780 21.272 98.194 3.588 11.28 12.97 1.69 3.791 21.269 117.833 3.587 11.28 13.00 1.72 3.806 21.261 137.471 3.587 11.26 12.99 1.73 3.814 21.256 157.110 3.585 11.25 12.98 1.73 3.823 21.255 176.749 3.584 11.23 12.96 1.73 3.828 21.254 196.388 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: 1.178 Accepted refinement result: 11.35 12.83 1.48 3.781 21.328 1.178 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.35 3.31 243 1749 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.50 76.71 35.41 N/A 243 222 Other: 19.77 26.66 22.10 N/A 0 8 Chain A: 9.11 115.05 19.43 N/A 0 1749 Chain S: 13.59 59.99 35.12 N/A 243 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 305 30.29 - 40.89 208 40.89 - 51.48 144 51.48 - 62.08 48 62.08 - 72.67 12 72.67 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1283 r_work=0.1135 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1283 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1281 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600765 | | target function (ml) not normalized (work): 299882.519173 | | target function (ml) not normalized (free): 15796.113939 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1323 0.1303 5.639 5.5959| | 2: 3.57 - 2.84 1.00 2888 124 0.1073 0.1365 5.157 5.2058| | 3: 2.83 - 2.48 1.00 2820 163 0.1101 0.1252 4.938 4.9839| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.0980 4.6212 4.6455| | 5: 2.25 - 2.09 1.00 2756 127 0.0856 0.0970 4.5671 4.6236| | 6: 2.09 - 1.97 1.00 2846 113 0.0862 0.0968 4.2647 4.353| | 7: 1.97 - 1.87 1.00 2787 165 0.0887 0.1122 3.9808 4.0878| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1107 3.8849 3.9809| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1209 3.6427 3.8371| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1164 3.5616 3.7047| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.1026 3.4912 3.5651| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1140 3.3252 3.4501| | 13: 1.56 - 1.52 1.00 2745 130 0.0938 0.1034 3.3001 3.3992| | 14: 1.52 - 1.48 1.00 2803 134 0.0975 0.1058 3.2359 3.3224| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1224 3.1497 3.2608| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1251 3.1331 3.2319| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1319 3.1171 3.2387| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1336 3.1043 3.2389| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1561 3.1115 3.2674| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1459 3.1119 3.1514| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1526 3.1128 3.1143| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1982 3.1218 3.2959| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1806 3.1322 3.2019| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1818 3.1242 3.2199| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2145 3.1414 3.2504| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1777 3.1458 3.2011| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2168 3.1697 3.1624| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2296 3.1647 3.1726| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2394 3.1466 3.2303| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2459 3.1417 3.1684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.46 1.00 0.97 5599.26| | 2: 3.57 - 2.84 2888 124 0.93 12.35 1.01 0.97 5599.26| | 3: 2.83 - 2.48 2820 163 0.90 16.28 0.99 0.97 4679.55| | 4: 2.47 - 2.25 2825 136 0.92 13.32 1.00 0.98 2307.91| | 5: 2.25 - 2.09 2756 127 0.90 15.45 1.01 0.98 2307.91| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.98 1336.04| | 7: 1.97 - 1.87 2787 165 0.95 9.27 1.02 0.97 507.17| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.97 507.17| | 9: 1.79 - 1.72 2745 138 0.94 10.05 0.98 0.97 287.64| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.97 243.68| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.97 233.41| | 12: 1.61 - 1.56 2773 144 0.96 8.87 0.99 0.97 136.50| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.02 0.97 136.50| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 122.71| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.98 97.45| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.45| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.03| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 84.15| | 19: 1.36 - 1.34 2807 134 0.94 11.91 0.99 0.98 84.15| | 20: 1.34 - 1.32 2696 147 0.94 12.17 0.98 0.96 80.19| | 21: 1.32 - 1.30 2785 112 0.94 13.17 0.98 0.96 79.91| | 22: 1.29 - 1.27 2704 152 0.93 13.70 0.98 0.96 80.30| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.27| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.96 0.94 82.27| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.23| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.02 0.93 86.40| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 86.40| | 28: 1.19 - 1.18 2671 147 0.88 20.49 1.01 0.92 90.29| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 91.75| | 30: 1.16 - 1.15 2739 148 0.86 22.15 0.98 0.92 91.75| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.91 max = 5599.26 mean = 867.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.44| |phase err.(test): min = 0.00 max = 87.78 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1281 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1446 0.1443 0.1519 n_refl.: 87579 remove outliers: r(all,work,free)=0.1446 0.1443 0.1519 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1445 0.1442 0.1518 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1131 0.1282 n_refl.: 87579 remove outliers: r(all,work,free)=0.1137 0.1129 0.1282 n_refl.: 87574 ======================== 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 0.4030 287.815 246.114 0.438 0.999 0.298 11.894-9.307 93.14 91 4 0.2244 481.522 461.179 0.861 1.001 0.225 9.237-7.194 98.18 209 7 0.2326 385.445 381.735 0.924 1.001 0.167 7.162-5.571 100.00 427 22 0.2076 295.638 285.714 0.913 1.002 0.118 5.546-4.326 100.00 867 58 0.1117 405.838 401.329 0.963 1.002 0.106 4.315-3.360 100.00 1859 96 0.0922 385.955 384.039 1.003 1.002 0.097 3.356-2.611 100.00 3867 181 0.1114 253.552 251.765 1.011 1.001 0.060 2.608-2.026 99.99 8198 413 0.0905 168.082 167.481 1.027 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.083 82.433 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.399 36.009 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2168 22.934 21.488 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=-0.0170 ================= 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 : 0.2598 0.1946 0.080 5.198 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1235 0.1471 0.005 0.790 9.1 119.5 20.1 258 0.127 1_adp: 0.1241 0.1467 0.005 0.790 9.1 119.5 20.1 258 0.127 1_regHadp: 0.1242 0.1469 0.005 0.790 9.1 119.5 20.1 258 0.127 1_occ: 0.1238 0.1466 0.005 0.790 9.1 119.5 20.1 258 0.127 2_bss: 0.1236 0.1458 0.005 0.790 9.1 119.5 20.1 258 0.127 2_settarget: 0.1236 0.1458 0.005 0.790 9.1 119.5 20.1 258 0.127 2_updatecdl: 0.1236 0.1458 0.005 0.807 9.1 119.5 20.1 258 0.127 2_nqh: 0.1238 0.1460 0.005 0.807 9.1 119.5 20.1 258 0.133 2_sol: 0.1212 0.1403 0.005 0.807 9.1 115.1 22.2 421 n/a 2_weight: 0.1212 0.1403 0.005 0.807 9.1 115.1 22.2 421 n/a 2_xyzrec: 0.1192 0.1416 0.006 0.817 9.1 115.1 22.2 421 n/a 2_adp: 0.1192 0.1416 0.006 0.817 9.1 115.1 22.2 421 n/a 2_regHadp: 0.1192 0.1416 0.006 0.817 9.1 115.1 22.2 421 n/a 2_occ: 0.1189 0.1412 0.006 0.817 9.1 115.1 22.2 421 n/a 3_bss: 0.1186 0.1411 0.006 0.817 9.1 115.1 22.2 421 n/a 3_settarget: 0.1186 0.1411 0.006 0.817 9.1 115.1 22.2 421 n/a 3_updatecdl: 0.1186 0.1411 0.006 0.820 9.1 115.1 22.2 421 n/a 3_nqh: 0.1186 0.1411 0.006 0.820 9.1 115.1 22.2 421 n/a 3_sol: 0.1210 0.1386 0.006 0.820 9.1 115.1 21.2 439 n/a 3_weight: 0.1210 0.1386 0.006 0.820 9.1 115.1 21.2 439 n/a 3_xyzrec: 0.1159 0.1304 0.007 1.047 9.1 115.1 21.2 439 n/a 3_adp: 0.1159 0.1304 0.007 1.047 9.1 115.1 21.2 439 n/a 3_regHadp: 0.1159 0.1304 0.007 1.047 9.1 115.1 21.2 439 n/a 3_occ: 0.1151 0.1305 0.007 1.047 9.1 115.1 21.2 439 n/a 4_bss: 0.1144 0.1302 0.007 1.047 9.1 115.1 21.2 439 n/a 4_settarget: 0.1144 0.1302 0.007 1.047 9.1 115.1 21.2 439 n/a 4_updatecdl: 0.1144 0.1302 0.007 1.048 9.1 115.1 21.2 439 n/a 4_nqh: 0.1144 0.1302 0.007 1.048 9.1 115.1 21.2 439 n/a 4_sol: 0.1147 0.1282 0.007 1.048 9.1 115.1 21.3 460 n/a 4_weight: 0.1147 0.1282 0.007 1.048 9.1 115.1 21.3 460 n/a 4_xyzrec: 0.1138 0.1281 0.009 1.120 9.1 115.1 21.3 460 n/a 4_adp: 0.1138 0.1281 0.009 1.120 9.1 115.1 21.3 460 n/a 4_regHadp: 0.1138 0.1281 0.009 1.120 9.1 115.1 21.3 460 n/a 4_occ: 0.1131 0.1282 0.009 1.120 9.1 115.1 21.3 460 n/a 5_bss: 0.1128 0.1289 0.009 1.120 9.1 115.0 21.3 460 n/a 5_settarget: 0.1128 0.1289 0.009 1.120 9.1 115.0 21.3 460 n/a 5_updatecdl: 0.1128 0.1289 0.009 1.121 9.1 115.0 21.3 460 n/a 5_setrh: 0.1130 0.1289 0.009 1.121 9.1 115.0 21.3 460 n/a 5_nqh: 0.1130 0.1289 0.009 1.121 9.1 115.0 21.3 460 n/a 5_sol: 0.1135 0.1283 0.009 1.121 9.1 115.0 21.3 465 n/a 5_weight: 0.1135 0.1283 0.009 1.121 9.1 115.0 21.3 465 n/a 5_xyzrec: 0.1135 0.1283 0.009 1.130 9.1 115.0 21.3 465 n/a 5_adp: 0.1135 0.1283 0.009 1.130 9.1 115.0 21.3 465 n/a 5_regHadp: 0.1135 0.1283 0.009 1.130 9.1 115.0 21.3 465 n/a 5_occ: 0.1132 0.1281 0.009 1.130 9.1 115.0 21.3 465 n/a end: 0.1129 0.1282 0.009 1.130 9.1 115.0 21.3 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4813131_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4813131_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0600 Refinement macro-cycles (run) : 13572.3000 Write final files (write_after_run_outputs) : 94.2600 Total : 13669.6200 Total CPU time: 3.80 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:03 PST -0800 (1735366263.71 s) Start R-work = 0.1626, R-free = 0.1761 Final R-work = 0.1129, R-free = 0.1282 =============================================================================== Job complete usr+sys time: 13853.92 seconds wall clock time: 255 minutes 23.56 seconds (15323.56 seconds total)