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_6113322.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_6113322.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.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: 1.49, per 1000 atoms: 0.44 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 106.3 milliseconds Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.96: 898 0.96 - 1.24: 861 1.24 - 1.52: 928 1.52 - 1.79: 458 1.79 - 2.07: 8 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.237 1.020 0.217 1.09e-02 8.42e+03 3.96e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.233 0.226 1.23e-02 6.61e+03 3.37e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.27e-02 6.20e+03 3.36e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.050 0.187 1.13e-02 7.83e+03 2.73e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.728 -0.190 1.19e-02 7.06e+03 2.54e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3219 4.69 - 9.39: 1812 9.39 - 14.08: 621 14.08 - 18.77: 114 18.77 - 23.46: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 120.57 103.80 16.77 1.07e+00 8.73e-01 2.46e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 108.26 14.34 1.00e+00 1.00e+00 2.06e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.65 -12.45 9.00e-01 1.23e+00 1.91e+02 angle pdb=" CA ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 116.51 101.93 14.58 1.07e+00 8.73e-01 1.86e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 106.64 14.21 1.06e+00 8.90e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 914 15.39 - 30.78: 129 30.78 - 46.17: 45 46.17 - 61.56: 17 61.56 - 76.95: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual 180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " ideal model delta harmonic sigma weight residual 0.00 20.30 -20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 99 0.214 - 0.428: 78 0.428 - 0.642: 38 0.642 - 0.856: 20 0.856 - 1.070: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.63 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.63 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 9.57e-02 2.75e+02 pdb=" CG PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.126 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.173 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.160 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" CG PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.159 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.108 9.50e-02 1.11e+02 8.40e-02 1.31e+02 pdb=" NE ARG A 48 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.114 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.120 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 811 2.28 - 2.86: 7922 2.86 - 3.44: 10498 3.44 - 4.02: 15339 4.02 - 4.60: 22072 Nonbonded interactions: 56642 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.705 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.829 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.843 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.845 1.850 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.846 1.850 ... (remaining 56637 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_6113322_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= 0.2601 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784618 | | target function (ml) not normalized (work): 231975.423290 | | target function (ml) not normalized (free): 11783.235251 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2133 7.0292 4.9492| | 2: 3.57 - 2.84 1.00 2876 122 0.2455 0.1798 4.3553 4.3373| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1612 4.1314 4.1425| | 4: 2.47 - 2.25 1.00 2825 136 0.2308 0.1430 3.8326 3.8319| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1482 3.8028 3.8321| | 6: 2.09 - 1.97 1.00 2846 113 0.2517 0.1682 3.4563 3.587| | 7: 1.97 - 1.87 1.00 2787 165 0.2568 0.1965 3.1406 3.236| | 8: 1.87 - 1.79 1.00 2789 144 0.2442 0.1862 3.0601 3.148| | 9: 1.79 - 1.72 1.00 2745 138 0.2433 0.1996 2.8877 2.9522| | 10: 1.72 - 1.66 1.00 2789 158 0.2388 0.1860 2.7943 2.8408| | 11: 1.66 - 1.61 1.00 2740 147 0.2520 0.1616 2.7352 2.6754| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.2092 2.6543 2.7| | 13: 1.56 - 1.52 1.00 2745 130 0.2544 0.1934 2.5579 2.6257| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2016 2.4934 2.5645| | 15: 1.48 - 1.45 1.00 2738 128 0.2584 0.1756 2.4098 2.3288| | 16: 1.45 - 1.42 1.00 2756 161 0.2631 0.1981 2.3699 2.3892| | 17: 1.42 - 1.39 1.00 2785 139 0.2650 0.2057 2.3236 2.3755| | 18: 1.39 - 1.36 1.00 2741 179 0.2636 0.2292 2.253 2.3469| | 19: 1.36 - 1.34 1.00 2807 134 0.2651 0.2239 2.2418 2.2276| | 20: 1.34 - 1.32 1.00 2696 147 0.2630 0.2326 2.19 2.2238| | 21: 1.32 - 1.30 1.00 2785 112 0.2762 0.2074 2.1675 2.1446| | 22: 1.29 - 1.27 1.00 2704 152 0.2743 0.2501 2.1303 2.227| | 23: 1.27 - 1.26 1.00 2802 156 0.2700 0.2502 2.0817 2.1986| | 24: 1.26 - 1.24 1.00 2744 132 0.2749 0.2280 2.068 2.089| | 25: 1.24 - 1.22 1.00 2734 148 0.2800 0.2530 2.0428 2.0515| | 26: 1.22 - 1.21 1.00 2727 135 0.2837 0.2205 2.0085 2.0764| | 27: 1.21 - 1.19 1.00 2814 148 0.2958 0.2618 2.003 2.0258| | 28: 1.19 - 1.18 1.00 2671 147 0.2957 0.2782 1.982 2.0061| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2655 1.9507 1.9918| | 30: 1.16 - 1.15 1.00 2740 148 0.3069 0.2799 1.9292 1.9848| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.95 0.76 0.23 1497.13| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.28 0.23 1497.13| | 3: 2.84 - 2.48 2833 165 0.74 32.11 1.24 0.23 1241.81| | 4: 2.47 - 2.25 2825 136 0.81 25.71 1.25 0.25 579.20| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.27 0.25 579.20| | 6: 2.09 - 1.97 2846 113 0.83 22.92 1.29 0.25 317.36| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 94.04| | 8: 1.87 - 1.79 2789 144 0.86 21.32 1.24 0.26 94.04| | 9: 1.79 - 1.72 2745 138 0.88 18.73 1.24 0.25 56.04| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.22 0.25 48.43| | 11: 1.66 - 1.61 2740 147 0.85 21.63 1.25 0.25 46.65| | 12: 1.61 - 1.56 2787 146 0.89 18.30 1.23 0.25 28.61| | 13: 1.56 - 1.52 2745 130 0.87 20.07 1.24 0.25 28.61| | 14: 1.52 - 1.48 2803 134 0.87 20.34 1.24 0.25 25.37| | 15: 1.48 - 1.45 2738 128 0.87 19.73 1.23 0.25 19.43| | 16: 1.45 - 1.42 2756 161 0.86 21.09 1.23 0.25 19.43| | 17: 1.42 - 1.39 2785 139 0.87 20.12 1.23 0.25 16.69| | 18: 1.39 - 1.36 2741 179 0.87 20.59 1.23 0.25 15.10| | 19: 1.36 - 1.34 2807 134 0.86 21.41 1.21 0.25 15.10| | 20: 1.34 - 1.32 2696 147 0.88 20.13 1.20 0.25 12.42| | 21: 1.32 - 1.30 2785 112 0.86 21.31 1.21 0.25 12.23| | 22: 1.29 - 1.27 2704 152 0.86 21.95 1.21 0.24 11.98| | 23: 1.27 - 1.26 2802 156 0.86 21.63 1.21 0.24 10.73| | 24: 1.26 - 1.24 2744 132 0.86 22.25 1.20 0.24 10.73| | 25: 1.24 - 1.22 2734 148 0.85 23.15 1.19 0.24 10.27| | 26: 1.22 - 1.21 2727 135 0.84 23.73 1.19 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.83 24.72 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 25.42 1.18 0.23 9.42| | 29: 1.18 - 1.16 2800 134 0.82 26.09 1.17 0.23 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.16 0.23 9.30| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1497.13 mean = 217.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.47| |phase err.(test): min = 0.00 max = 89.66 mean = 22.37| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.276 1557 Z= 5.511 Angle : 5.139 16.891 2118 Z= 3.679 Chirality : 0.395 1.070 243 Planarity : 0.032 0.119 284 Dihedral : 13.647 76.946 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 25.95 % 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: -2.37 (0.49), residues: 224 helix: -2.22 (0.41), residues: 109 sheet: -0.66 (0.85), residues: 38 loop : -0.61 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.026 ARG A 98 TYR 0.083 0.041 TYR A 139 PHE 0.190 0.055 PHE A 164 HIS 0.069 0.042 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= 0.2601 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784618 | | target function (ml) not normalized (work): 231975.423290 | | target function (ml) not normalized (free): 11783.235251 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2602 0.1925 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2602 0.1925 n_refl.: 87602 remove outliers: r(all,work,free)=0.1969 0.1973 0.1925 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1996 0.2001 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1735 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1626 0.1735 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 0.3875 386.308 353.769 0.665 1.002 0.401 11.894-9.307 99.02 97 4 0.1814 613.631 594.186 0.924 1.003 0.375 9.237-7.194 100.00 213 7 0.2111 501.875 491.466 0.952 1.003 0.349 7.162-5.571 100.00 427 22 0.2187 376.629 364.364 0.930 1.003 0.330 5.546-4.326 100.00 867 58 0.1273 517.019 511.077 0.962 1.002 0.224 4.315-3.360 100.00 1859 96 0.1165 491.689 487.543 1.007 1.002 0.199 3.356-2.611 100.00 3867 181 0.1428 323.014 319.646 1.000 1.001 0.043 2.608-2.026 99.99 8198 413 0.1349 214.129 211.933 1.004 0.999 0.000 2.025-1.573 100.00 17313 902 0.1621 104.569 103.719 1.016 0.996 0.000 1.573-1.221 100.00 36679 1900 0.2046 46.370 45.116 1.008 0.991 0.000 1.221-1.150 99.97 13689 708 0.2571 29.217 26.979 0.987 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1735 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1627 r_free=0.1737 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.368677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1982.955643 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 0.1772 0.1882 0.0110 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1617 0.1746 0.0129 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1450 0.1616 0.0165 0.001 0.4 3.5 0.0 0.0 0 0.500 0.1412 0.1599 0.0187 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1353 0.1553 0.0199 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1361 0.1559 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1298 0.1516 0.0218 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1267 0.1492 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1483 0.0229 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1246 0.1477 0.0231 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1241 0.1473 0.0232 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1238 0.1474 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1231 0.1468 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1226 0.1464 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1226 0.1465 0.0239 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1224 0.1472 0.0248 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1224 0.1471 0.0247 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1222 0.1472 0.0250 0.008 1.0 3.8 0.5 0.6 0 13.184 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1464 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.64 2.38 3.013 19.078 1982.956 0.017 12.26 14.64 2.37 2.989 19.077 59.489 0.017 12.33 14.60 2.27 2.666 19.076 247.869 0.017 12.71 15.33 2.62 2.838 19.307 991.478 0.016 12.51 15.40 2.89 3.124 19.530 1982.956 0.016 12.48 15.55 3.07 3.446 19.727 2974.433 0.015 12.32 15.41 3.09 3.306 19.632 3965.911 0.015 12.27 15.40 3.13 3.345 19.638 4957.389 0.015 12.24 15.43 3.19 3.429 19.679 5948.867 0.015 12.20 15.34 3.14 3.245 19.571 6940.345 0.015 12.21 15.46 3.25 3.394 19.633 7931.823 0.015 12.15 15.39 3.24 3.369 19.608 8923.300 0.015 12.15 15.43 3.28 3.436 19.638 9914.778 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: 247.869 Accepted refinement result: 12.33 14.60 2.27 2.666 19.076 247.869 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.47 20.10 3.31 0 1785 Protein: 9.08 115.00 17.01 3.31 0 1519 Water: 11.48 119.47 38.24 N/A 0 258 Other: 19.73 26.63 22.07 N/A 0 8 Chain A: 9.08 119.47 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1460 r_work=0.1235 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1458 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= 0.1228 r_free= 0.1458 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016866 | | target function (ls_wunit_k1) not normalized (work): 1404.914421 | | target function (ls_wunit_k1) not normalized (free): 108.368708 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1458 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1678 0.1680 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1678 0.1680 0.1694 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1684 0.1685 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1453 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 96.88 88 5 0.3544 303.685 280.224 0.663 1.002 0.390 11.894-9.307 99.02 97 4 0.1628 482.389 470.006 0.924 1.003 0.362 9.237-7.194 100.00 213 7 0.1864 394.535 389.622 0.964 1.003 0.327 7.162-5.571 100.00 427 22 0.1816 296.076 290.613 0.936 1.003 0.268 5.546-4.326 100.00 867 58 0.1012 406.440 403.463 0.962 1.003 0.209 4.315-3.360 100.00 1859 96 0.0876 386.527 385.318 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1178 253.928 252.753 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1026 168.331 167.620 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.204 82.393 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.453 35.951 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2255 22.968 21.444 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1453 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 144 ASN Total number of N/Q/H flips: 2 r_work=0.1230 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1453 | n_water=258 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1240 r_free=0.1452 | n_water=251 | time (s): 22.430 (total time: 24.010) Filter (q & B) r_work=0.1242 r_free=0.1451 | n_water=248 | time (s): 2.320 (total time: 26.330) Compute maps r_work=0.1242 r_free=0.1451 | n_water=248 | time (s): 1.220 (total time: 27.550) Filter (map) r_work=0.1259 r_free=0.1457 | n_water=223 | time (s): 2.350 (total time: 29.900) Find peaks r_work=0.1259 r_free=0.1457 | n_water=223 | time (s): 0.530 (total time: 30.430) Add new water r_work=0.1412 r_free=0.1625 | n_water=427 | time (s): 2.640 (total time: 33.070) Refine new water occ: r_work=0.1315 r_free=0.1495 adp: r_work=0.1233 r_free=0.1435 occ: r_work=0.1244 r_free=0.1429 adp: r_work=0.1211 r_free=0.1413 occ: r_work=0.1213 r_free=0.1405 adp: r_work=0.1204 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1402 r_work=0.1204 r_free=0.1402 | n_water=427 | time (s): 59.420 (total time: 92.490) Filter (q & B) r_work=0.1205 r_free=0.1402 | n_water=420 | time (s): 2.890 (total time: 95.380) Filter (dist only) r_work=0.1206 r_free=0.1401 | n_water=419 | time (s): 37.110 (total time: 132.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.757518 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.739839 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 0.1663 0.1765 0.0103 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1524 0.1646 0.0122 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1406 0.1552 0.0146 0.002 0.4 6.7 0.0 0.0 0 0.500 0.1360 0.1520 0.0160 0.002 0.4 5.4 0.0 0.0 0 0.750 0.1310 0.1474 0.0164 0.002 0.5 6.4 0.0 0.0 0 1.000 0.1306 0.1471 0.0164 0.002 0.5 6.7 0.0 0.0 0 1.000 0.1249 0.1434 0.0184 0.002 0.6 5.8 0.5 0.0 0 2.000 0.1222 0.1423 0.0201 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1215 0.1425 0.0209 0.003 0.6 4.8 0.5 0.0 0 4.000 0.1209 0.1428 0.0219 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1205 0.1421 0.0216 0.004 0.7 5.8 0.5 0.0 0 6.000 0.1202 0.1427 0.0225 0.005 0.8 5.8 0.5 0.0 0 7.000 0.1199 0.1424 0.0225 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1198 0.1428 0.0230 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1197 0.1423 0.0226 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1194 0.1422 0.0228 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1193 0.1419 0.0225 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1191 0.1428 0.0237 0.008 1.0 5.4 0.5 0.0 0 13.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1419 0.0225 0.007 0.9 4.8 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 14.19 2.25 3.775 21.766 1498.740 0.016 11.93 14.19 2.25 3.775 21.766 44.962 0.016 11.93 14.19 2.25 3.775 21.766 187.342 0.016 12.07 14.54 2.47 3.640 21.767 749.370 0.015 12.10 14.96 2.86 3.451 22.066 1498.740 0.015 11.90 14.77 2.86 3.459 22.163 2248.110 0.015 11.83 14.83 3.00 3.494 21.958 2997.480 0.014 11.78 14.84 3.06 3.521 21.948 3746.850 0.014 11.74 14.76 3.02 3.505 22.074 4496.220 0.014 11.72 14.79 3.06 3.502 22.111 5245.589 0.014 11.78 15.04 3.26 3.565 22.235 5994.959 0.014 11.70 14.89 3.19 3.545 22.161 6744.329 0.014 11.70 14.90 3.20 3.564 22.199 7493.699 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: 44.962 Accepted refinement result: 11.93 14.19 2.25 3.775 21.766 44.962 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 22.15 3.31 196 1750 Protein: 9.11 115.02 17.04 3.31 0 1519 Water: 11.51 76.70 40.68 N/A 196 223 Other: 19.76 26.66 22.10 N/A 0 8 Chain A: 9.11 115.02 19.42 N/A 0 1750 Chain S: 14.38 60.00 46.52 N/A 196 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 247 30.29 - 40.89 171 40.89 - 51.48 125 51.48 - 62.07 121 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1419 r_work=0.1193 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1419 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 = 0.1195 r_free = 0.1418 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1195 r_free= 0.1418 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015208 | | target function (ls_wunit_k1) not normalized (work): 1266.772470 | | target function (ls_wunit_k1) not normalized (free): 103.183055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1195 0.1418 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1592 0.1590 0.1656 n_refl.: 87593 remove outliers: r(all,work,free)=0.1592 0.1590 0.1656 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1593 0.1591 0.1657 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1191 0.1409 n_refl.: 87593 remove outliers: r(all,work,free)=0.1200 0.1190 0.1409 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3353 299.724 276.482 0.615 1.002 0.370 11.894-9.307 99.02 97 4 0.1560 482.389 475.407 0.919 1.003 0.304 9.237-7.194 100.00 213 7 0.1682 394.535 395.672 0.984 1.003 0.270 7.162-5.571 100.00 427 22 0.1580 296.076 291.916 0.938 1.003 0.230 5.546-4.326 100.00 867 58 0.0873 406.440 403.462 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0796 386.527 385.386 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1096 253.928 252.948 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1026 168.331 167.762 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.204 82.400 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.453 35.975 1.026 0.996 0.000 1.221-1.150 99.97 13689 708 0.2251 22.968 21.469 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0096 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1409 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=0.1190 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1409 | n_water=419 | time (s): 2.050 (total time: 2.050) Filter (dist) r_work=0.1189 r_free=0.1408 | n_water=414 | time (s): 36.200 (total time: 38.250) Filter (q & B) r_work=0.1189 r_free=0.1408 | n_water=414 | time (s): 0.790 (total time: 39.040) Compute maps r_work=0.1189 r_free=0.1408 | n_water=414 | time (s): 1.350 (total time: 40.390) Filter (map) r_work=0.1230 r_free=0.1407 | n_water=278 | time (s): 3.110 (total time: 43.500) Find peaks r_work=0.1230 r_free=0.1407 | n_water=278 | time (s): 0.510 (total time: 44.010) Add new water r_work=0.1352 r_free=0.1552 | n_water=460 | time (s): 2.960 (total time: 46.970) Refine new water occ: r_work=0.1258 r_free=0.1460 adp: r_work=0.1260 r_free=0.1463 occ: r_work=0.1237 r_free=0.1429 adp: r_work=0.1237 r_free=0.1433 occ: r_work=0.1220 r_free=0.1399 adp: r_work=0.1215 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1402 r_work=0.1215 r_free=0.1402 | n_water=460 | time (s): 192.740 (total time: 239.710) Filter (q & B) r_work=0.1220 r_free=0.1405 | n_water=434 | time (s): 2.830 (total time: 242.540) Filter (dist only) r_work=0.1220 r_free=0.1403 | n_water=433 | time (s): 35.320 (total time: 277.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.788175 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.613183 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 0.1250 0.1379 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1206 0.1345 0.0139 0.003 0.7 3.2 0.5 0.0 0 0.268 0.1189 0.1328 0.0139 0.004 0.8 3.5 0.5 0.0 0 0.536 0.1180 0.1323 0.0142 0.005 0.9 3.5 0.5 0.0 0 0.805 0.1177 0.1321 0.0144 0.006 1.0 3.2 0.5 0.0 0 1.073 0.1174 0.1321 0.0147 0.007 1.0 3.2 0.5 0.0 0 1.341 0.1171 0.1317 0.0146 0.007 1.1 3.5 0.5 0.0 0 1.609 0.1169 0.1316 0.0147 0.008 1.1 3.8 0.5 0.0 0 1.878 0.1179 0.1322 0.0143 0.005 0.9 3.2 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1316 0.0147 0.008 1.1 3.8 0.5 0.0 0 1.878 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 13.16 1.47 3.778 21.186 44.613 3.622 11.69 13.16 1.47 3.778 21.186 1.338 3.622 11.70 13.17 1.47 3.763 21.186 5.577 3.622 11.77 13.27 1.50 3.711 21.170 22.307 3.618 11.73 13.33 1.59 3.738 21.145 44.613 3.615 11.69 13.34 1.65 3.756 21.128 66.920 3.610 11.64 13.31 1.67 3.771 21.124 89.226 3.606 11.63 13.33 1.70 3.783 21.114 111.533 3.605 11.59 13.31 1.72 3.795 21.110 133.840 3.602 11.57 13.29 1.72 3.804 21.106 156.146 3.600 11.57 13.29 1.72 3.819 21.089 178.453 3.600 11.56 13.29 1.73 3.829 21.088 200.759 3.599 11.54 13.28 1.73 3.833 21.088 223.066 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.338 Accepted refinement result: 11.69 13.16 1.47 3.778 21.186 1.338 3.622 Individual atomic B min max mean iso aniso Overall: 9.12 115.03 21.09 3.31 214 1746 Protein: 9.12 115.03 17.04 3.31 0 1519 Water: 11.52 76.70 35.25 N/A 214 219 Other: 19.77 26.66 22.11 N/A 0 8 Chain A: 9.12 115.03 19.35 N/A 0 1746 Chain S: 14.39 60.01 35.29 N/A 214 0 Histogram: Values Number of atoms 9.12 - 19.71 1264 19.71 - 30.30 296 30.30 - 40.89 205 40.89 - 51.48 122 51.48 - 62.07 50 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1169 r_free=0.1316 r_work=0.1169 r_free=0.1316 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1169 r_free = 0.1316 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1160 r_free = 0.1307 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1160 r_free= 0.1307 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614711 | | target function (ml) not normalized (work): 301083.734661 | | target function (ml) not normalized (free): 15845.340606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1160 0.1307 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1505 0.1505 0.1537 n_refl.: 87590 remove outliers: r(all,work,free)=0.1505 0.1505 0.1537 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1505 0.1504 0.1537 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1154 0.1295 n_refl.: 87590 remove outliers: r(all,work,free)=0.1159 0.1152 0.1295 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3917 297.035 275.796 0.490 0.999 0.303 11.894-9.307 98.04 96 4 0.2518 475.671 465.460 0.863 1.001 0.283 9.237-7.194 98.18 209 7 0.2405 386.017 385.471 0.944 1.001 0.180 7.162-5.571 100.00 427 22 0.2223 296.076 285.817 0.920 1.001 0.160 5.546-4.326 100.00 867 58 0.1120 406.440 401.426 0.962 1.001 0.160 4.315-3.360 100.00 1859 96 0.0949 386.527 383.861 1.005 1.001 0.160 3.356-2.611 100.00 3867 181 0.1153 253.928 251.795 1.008 1.001 0.038 2.608-2.026 99.99 8198 413 0.0931 168.331 167.495 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.204 82.479 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.453 36.013 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 22.968 21.415 0.981 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0064 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1295 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=0.1152 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1295 | n_water=433 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1152 r_free=0.1294 | n_water=431 | time (s): 45.500 (total time: 48.110) Filter (q & B) r_work=0.1153 r_free=0.1293 | n_water=428 | time (s): 4.090 (total time: 52.200) Compute maps r_work=0.1153 r_free=0.1293 | n_water=428 | time (s): 1.900 (total time: 54.100) Filter (map) r_work=0.1175 r_free=0.1303 | n_water=319 | time (s): 3.930 (total time: 58.030) Find peaks r_work=0.1175 r_free=0.1303 | n_water=319 | time (s): 0.720 (total time: 58.750) Add new water r_work=0.1240 r_free=0.1366 | n_water=484 | time (s): 3.660 (total time: 62.410) Refine new water occ: r_work=0.1169 r_free=0.1304 adp: r_work=0.1169 r_free=0.1305 occ: r_work=0.1154 r_free=0.1296 adp: r_work=0.1153 r_free=0.1295 occ: r_work=0.1143 r_free=0.1291 adp: r_work=0.1139 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1288 r_work=0.1139 r_free=0.1288 | n_water=484 | time (s): 246.080 (total time: 308.490) Filter (q & B) r_work=0.1147 r_free=0.1297 | n_water=445 | time (s): 4.110 (total time: 312.600) Filter (dist only) r_work=0.1147 r_free=0.1297 | n_water=444 | time (s): 45.890 (total time: 358.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.825241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.478606 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 0.1205 0.1330 0.0125 0.002 0.6 3.8 0.5 0.0 0 0.091 0.1172 0.1311 0.0139 0.003 0.8 2.9 0.5 0.0 0 0.274 0.1157 0.1303 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.548 0.1152 0.1302 0.0150 0.006 0.9 3.2 0.5 0.0 0 0.821 0.1148 0.1303 0.0155 0.007 1.0 2.9 0.5 0.0 0 1.095 0.1146 0.1302 0.0156 0.007 1.1 2.9 0.5 0.0 0 1.369 0.1144 0.1302 0.0158 0.008 1.1 2.9 0.5 0.0 0 1.643 0.1143 0.1296 0.0154 0.009 1.1 3.2 0.5 0.0 0 1.917 0.1150 0.1302 0.0152 0.006 1.0 3.2 0.5 0.0 0 0.913 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1296 0.0154 0.009 1.1 3.2 0.5 0.0 0 1.917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.96 1.54 3.778 21.165 37.479 3.607 11.43 12.96 1.54 3.778 21.165 1.124 3.607 11.43 12.96 1.54 3.778 21.165 4.685 3.607 11.46 12.99 1.53 3.711 21.158 18.739 3.602 11.56 13.16 1.60 3.723 21.128 37.479 3.606 11.48 13.14 1.66 3.746 21.115 56.218 3.601 11.40 13.08 1.69 3.766 21.115 74.957 3.595 11.40 13.10 1.70 3.777 21.107 93.697 3.593 11.34 13.04 1.69 3.782 21.110 112.436 3.589 11.36 13.09 1.73 3.797 21.099 131.175 3.590 11.33 13.06 1.73 3.804 21.097 149.914 3.588 11.34 13.08 1.74 3.820 21.084 168.654 3.588 11.32 13.07 1.75 3.827 21.084 187.393 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.124 Accepted refinement result: 11.43 12.96 1.54 3.778 21.165 1.124 3.607 Individual atomic B min max mean iso aniso Overall: 9.12 115.03 21.05 3.31 226 1745 Protein: 9.12 115.03 17.04 3.31 0 1519 Water: 11.52 76.70 34.74 N/A 226 218 Other: 19.76 26.66 22.11 N/A 0 8 Chain A: 9.12 115.03 19.32 N/A 0 1745 Chain S: 14.38 60.00 34.37 N/A 226 0 Histogram: Values Number of atoms 9.12 - 19.71 1265 19.71 - 30.30 303 30.30 - 40.89 215 40.89 - 51.48 120 51.48 - 62.07 45 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1296 r_work=0.1143 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1296 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1294 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1137 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604236 | | target function (ml) not normalized (work): 300189.593131 | | target function (ml) not normalized (free): 15808.346074 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1137 0.1294 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1482 0.1481 0.1531 n_refl.: 87584 remove outliers: r(all,work,free)=0.1482 0.1481 0.1531 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1481 0.1479 0.1530 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1136 0.1295 n_refl.: 87584 remove outliers: r(all,work,free)=0.1141 0.1133 0.1295 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4074 293.762 252.849 0.461 1.000 0.320 11.894-9.307 94.12 92 4 0.2267 483.019 457.707 0.827 1.001 0.320 9.237-7.194 98.18 209 7 0.2438 386.017 378.095 0.912 1.002 0.144 7.162-5.571 100.00 427 22 0.2202 296.076 285.344 0.904 1.002 0.130 5.546-4.326 100.00 867 58 0.1136 406.440 402.081 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0924 386.527 384.833 0.994 1.002 0.107 3.356-2.611 100.00 3867 181 0.1111 253.928 252.262 1.001 1.001 0.024 2.608-2.026 99.99 8198 413 0.0908 168.331 167.731 1.016 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.204 82.564 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.453 36.069 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.968 21.523 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1295 After: r_work=0.1134 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1295 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=0.1134 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1295 | n_water=444 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1134 r_free=0.1295 | n_water=444 | time (s): 43.940 (total time: 46.420) Filter (q & B) r_work=0.1134 r_free=0.1295 | n_water=444 | time (s): 1.420 (total time: 47.840) Compute maps r_work=0.1134 r_free=0.1295 | n_water=444 | time (s): 1.920 (total time: 49.760) Filter (map) r_work=0.1171 r_free=0.1322 | n_water=353 | time (s): 4.160 (total time: 53.920) Find peaks r_work=0.1171 r_free=0.1322 | n_water=353 | time (s): 0.680 (total time: 54.600) Add new water r_work=0.1212 r_free=0.1371 | n_water=484 | time (s): 3.810 (total time: 58.410) Refine new water occ: r_work=0.1150 r_free=0.1314 adp: r_work=0.1150 r_free=0.1314 occ: r_work=0.1141 r_free=0.1304 adp: r_work=0.1140 r_free=0.1304 occ: r_work=0.1133 r_free=0.1295 adp: r_work=0.1131 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1295 r_work=0.1131 r_free=0.1295 | n_water=484 | time (s): 275.420 (total time: 333.830) Filter (q & B) r_work=0.1139 r_free=0.1306 | n_water=446 | time (s): 3.910 (total time: 337.740) Filter (dist only) r_work=0.1139 r_free=0.1304 | n_water=445 | time (s): 46.410 (total time: 384.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.815815 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.285598 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1360 0.0128 0.004 0.7 6.1 0.0 0.0 0 0.091 0.1177 0.1325 0.0148 0.004 0.8 5.4 0.0 0.0 0 0.272 0.1160 0.1315 0.0155 0.005 0.9 5.1 0.5 0.0 0 0.545 0.1153 0.1310 0.0157 0.006 1.0 4.8 0.5 0.0 0 0.817 0.1148 0.1307 0.0160 0.006 1.1 4.8 0.5 0.0 0 1.089 0.1144 0.1305 0.0161 0.007 1.1 4.8 0.5 0.0 0 1.362 0.1142 0.1303 0.0162 0.008 1.1 4.8 0.5 0.0 0 1.634 0.1140 0.1303 0.0163 0.009 1.1 4.8 0.5 0.0 0 1.907 0.1152 0.1309 0.0158 0.006 1.0 4.8 0.5 0.0 0 0.908 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1140 0.1303 0.0163 0.009 1.1 4.8 0.5 0.0 0 1.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.40 13.03 1.63 3.778 21.138 46.286 3.608 11.40 13.03 1.63 3.778 21.138 1.389 3.608 11.41 13.03 1.62 3.763 21.138 5.786 3.608 11.47 13.12 1.65 3.714 21.122 23.143 3.605 11.43 13.14 1.71 3.741 21.105 46.286 3.602 11.42 13.18 1.76 3.762 21.085 69.428 3.599 11.36 13.15 1.78 3.776 21.085 92.571 3.595 11.33 13.11 1.79 3.783 21.085 115.714 3.591 11.31 13.10 1.79 3.793 21.081 138.857 3.590 11.34 13.15 1.82 3.819 21.061 162.000 3.591 11.32 13.14 1.82 3.827 21.060 185.142 3.589 11.30 13.11 1.81 3.834 21.058 208.285 3.587 11.30 13.12 1.82 3.841 21.058 231.428 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.389 Accepted refinement result: 11.40 13.03 1.63 3.778 21.138 1.389 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.01 3.31 228 1744 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 11.51 76.69 34.56 N/A 228 217 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.02 19.32 N/A 0 1744 Chain S: 14.38 60.00 33.94 N/A 228 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 308 30.29 - 40.88 213 40.88 - 51.47 120 51.47 - 62.06 44 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1140 r_free=0.1303 r_work=0.1140 r_free=0.1303 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1140 r_free = 0.1303 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1302 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1302 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607728 | | target function (ml) not normalized (work): 300458.843112 | | target function (ml) not normalized (free): 15827.042379 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1369 0.1372 5.6712 5.655| | 2: 3.57 - 2.84 1.00 2888 124 0.1081 0.1430 5.1871 5.2546| | 3: 2.83 - 2.48 1.00 2820 163 0.1097 0.1231 4.9679 5.0058| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.0999 4.6502 4.6809| | 5: 2.25 - 2.09 1.00 2756 127 0.0856 0.0987 4.6009 4.6559| | 6: 2.09 - 1.97 1.00 2846 113 0.0844 0.1033 4.2771 4.3962| | 7: 1.97 - 1.87 1.00 2787 165 0.0879 0.1098 3.9799 4.0791| | 8: 1.87 - 1.79 1.00 2789 144 0.0916 0.1116 3.8913 4.0004| | 9: 1.79 - 1.72 1.00 2745 138 0.0876 0.1152 3.6476 3.8138| | 10: 1.72 - 1.66 1.00 2831 160 0.0929 0.1191 3.5689 3.7166| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1051 3.4992 3.5789| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1148 3.3273 3.4618| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1041 3.3072 3.3951| | 14: 1.52 - 1.48 1.00 2803 134 0.0986 0.1073 3.24 3.326| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1205 3.1528 3.2587| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1239 3.1336 3.2398| | 17: 1.42 - 1.39 1.00 2785 139 0.1136 0.1292 3.1157 3.2276| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1326 3.1029 3.2318| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1563 3.1084 3.264| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1436 3.1081 3.1438| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1508 3.1116 3.1031| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1975 3.1208 3.2883| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1805 3.1324 3.2| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1834 3.1268 3.2234| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2132 3.141 3.2584| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1769 3.1475 3.1971| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2159 3.1705 3.1607| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2296 3.1657 3.1695| | 29: 1.18 - 1.16 1.00 2800 134 0.2270 0.2377 3.1476 3.2279| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2448 3.1422 3.1665| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 9.03 1.00 0.97 6242.27| | 2: 3.57 - 2.84 2888 124 0.92 13.28 1.01 0.97 6242.27| | 3: 2.83 - 2.48 2820 163 0.89 17.24 0.99 0.98 5205.40| | 4: 2.47 - 2.25 2825 136 0.91 14.06 1.00 0.99 2531.65| | 5: 2.25 - 2.09 2756 127 0.90 16.29 1.01 0.99 2531.65| | 6: 2.09 - 1.97 2846 113 0.92 12.70 1.02 0.98 1444.84| | 7: 1.97 - 1.87 2787 165 0.95 9.38 1.02 0.98 517.94| | 8: 1.87 - 1.79 2789 144 0.92 12.76 0.99 0.98 517.94| | 9: 1.79 - 1.72 2745 138 0.94 10.15 0.98 0.98 292.36| | 10: 1.72 - 1.66 2831 160 0.94 11.20 0.98 0.98 247.18| | 11: 1.66 - 1.61 2712 147 0.93 11.79 0.98 0.98 236.73| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.98 138.18| | 13: 1.56 - 1.52 2745 130 0.95 10.45 1.03 0.98 138.18| | 14: 1.52 - 1.48 2803 134 0.94 10.77 1.02 0.99 123.78| | 15: 1.48 - 1.45 2738 128 0.95 9.89 1.02 0.99 97.40| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.99 97.40| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.99 88.50| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.99 83.36| | 19: 1.36 - 1.34 2807 134 0.94 11.81 0.99 0.99 83.36| | 20: 1.34 - 1.32 2696 147 0.94 12.04 0.98 0.97 79.22| | 21: 1.32 - 1.30 2785 112 0.94 13.02 0.98 0.97 78.93| | 22: 1.29 - 1.27 2704 152 0.93 13.58 0.98 0.97 79.36| | 23: 1.27 - 1.26 2802 156 0.92 14.78 0.97 0.95 81.53| | 24: 1.26 - 1.24 2744 132 0.93 14.79 0.96 0.95 81.53| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.95 83.54| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.02 0.94 85.77| | 27: 1.21 - 1.19 2814 148 0.89 18.70 1.02 0.94 85.77| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 89.49| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.99 0.93 90.89| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 90.89| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 78.93 max = 6242.27 mean = 949.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.56| |phase err.(test): min = 0.00 max = 89.38 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1302 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1467 0.1466 0.1518 n_refl.: 87578 remove outliers: r(all,work,free)=0.1467 0.1466 0.1518 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1466 0.1465 0.1517 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1302 n_refl.: 87578 remove outliers: r(all,work,free)=0.1146 0.1138 0.1302 n_refl.: 87577 ======================== 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 0.4125 293.762 249.503 0.449 1.001 0.314 11.894-9.307 93.14 91 4 0.2401 483.127 462.406 0.849 1.002 0.222 9.237-7.194 98.18 209 7 0.2464 386.017 378.984 0.916 1.002 0.140 7.162-5.571 100.00 427 22 0.2223 296.076 285.675 0.910 1.002 0.120 5.546-4.326 100.00 867 58 0.1156 406.440 401.579 0.962 1.002 0.110 4.315-3.360 100.00 1859 96 0.0930 386.527 384.572 1.005 1.002 0.110 3.356-2.611 100.00 3867 181 0.1118 253.928 252.140 1.012 1.001 0.014 2.608-2.026 99.99 8198 413 0.0900 168.331 167.712 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.204 82.553 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.453 36.062 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.968 21.517 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0175 ================= 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 : 0.2601 0.1924 0.084 5.139 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1735 0.084 5.139 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1735 0.084 5.139 9.1 119.5 20.1 258 0.000 1_nqh: 0.1627 0.1737 0.084 5.139 9.1 119.5 20.1 258 0.003 1_weight: 0.1627 0.1737 0.084 5.139 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1226 0.1464 0.006 0.854 9.1 119.5 20.1 258 0.136 1_adp: 0.1233 0.1460 0.006 0.854 9.1 119.5 20.1 258 0.136 1_regHadp: 0.1235 0.1464 0.006 0.854 9.1 119.5 20.1 258 0.136 1_occ: 0.1228 0.1458 0.006 0.854 9.1 119.5 20.1 258 0.136 2_bss: 0.1229 0.1453 0.006 0.854 9.1 119.5 20.1 258 0.136 2_settarget: 0.1229 0.1453 0.006 0.854 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1229 0.1453 0.006 0.861 9.1 119.5 20.1 258 0.136 2_nqh: 0.1230 0.1453 0.006 0.861 9.1 119.5 20.1 258 0.136 2_sol: 0.1206 0.1401 0.006 0.861 9.1 115.0 22.2 419 n/a 2_weight: 0.1206 0.1401 0.006 0.861 9.1 115.0 22.2 419 n/a 2_xyzrec: 0.1193 0.1419 0.007 0.903 9.1 115.0 22.2 419 n/a 2_adp: 0.1193 0.1419 0.007 0.903 9.1 115.0 22.2 419 n/a 2_regHadp: 0.1193 0.1419 0.007 0.903 9.1 115.0 22.2 419 n/a 2_occ: 0.1195 0.1418 0.007 0.903 9.1 115.0 22.2 419 n/a 3_bss: 0.1190 0.1409 0.007 0.903 9.1 115.0 22.2 419 n/a 3_settarget: 0.1190 0.1409 0.007 0.903 9.1 115.0 22.2 419 n/a 3_updatecdl: 0.1190 0.1409 0.007 0.905 9.1 115.0 22.2 419 n/a 3_nqh: 0.1190 0.1409 0.007 0.905 9.1 115.0 22.2 419 n/a 3_sol: 0.1220 0.1403 0.007 0.905 9.1 115.0 21.1 433 n/a 3_weight: 0.1220 0.1403 0.007 0.905 9.1 115.0 21.1 433 n/a 3_xyzrec: 0.1169 0.1316 0.008 1.086 9.1 115.0 21.1 433 n/a 3_adp: 0.1169 0.1316 0.008 1.086 9.1 115.0 21.1 433 n/a 3_regHadp: 0.1169 0.1316 0.008 1.086 9.1 115.0 21.1 433 n/a 3_occ: 0.1160 0.1307 0.008 1.086 9.1 115.0 21.1 433 n/a 4_bss: 0.1152 0.1295 0.008 1.086 9.1 115.0 21.1 433 n/a 4_settarget: 0.1152 0.1295 0.008 1.086 9.1 115.0 21.1 433 n/a 4_updatecdl: 0.1152 0.1295 0.008 1.089 9.1 115.0 21.1 433 n/a 4_nqh: 0.1152 0.1295 0.008 1.089 9.1 115.0 21.1 433 n/a 4_sol: 0.1147 0.1297 0.008 1.089 9.1 115.0 21.0 444 n/a 4_weight: 0.1147 0.1297 0.008 1.089 9.1 115.0 21.0 444 n/a 4_xyzrec: 0.1143 0.1296 0.009 1.134 9.1 115.0 21.0 444 n/a 4_adp: 0.1143 0.1296 0.009 1.134 9.1 115.0 21.0 444 n/a 4_regHadp: 0.1143 0.1296 0.009 1.134 9.1 115.0 21.0 444 n/a 4_occ: 0.1137 0.1294 0.009 1.134 9.1 115.0 21.0 444 n/a 5_bss: 0.1133 0.1295 0.009 1.134 9.1 115.0 21.0 444 n/a 5_settarget: 0.1133 0.1295 0.009 1.134 9.1 115.0 21.0 444 n/a 5_updatecdl: 0.1133 0.1295 0.009 1.133 9.1 115.0 21.0 444 n/a 5_setrh: 0.1134 0.1295 0.009 1.133 9.1 115.0 21.0 444 n/a 5_nqh: 0.1134 0.1295 0.009 1.133 9.1 115.0 21.0 444 n/a 5_sol: 0.1139 0.1304 0.009 1.133 9.1 115.0 21.0 445 n/a 5_weight: 0.1139 0.1304 0.009 1.133 9.1 115.0 21.0 445 n/a 5_xyzrec: 0.1140 0.1303 0.009 1.146 9.1 115.0 21.0 445 n/a 5_adp: 0.1140 0.1303 0.009 1.146 9.1 115.0 21.0 445 n/a 5_regHadp: 0.1140 0.1303 0.009 1.146 9.1 115.0 21.0 445 n/a 5_occ: 0.1138 0.1302 0.009 1.146 9.1 115.0 21.0 445 n/a end: 0.1138 0.1302 0.009 1.146 9.1 115.0 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6113322_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6113322_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5900 Refinement macro-cycles (run) : 13933.8300 Write final files (write_after_run_outputs) : 92.9200 Total : 14030.3400 Total CPU time: 3.90 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:15:18 PST -0800 (1735366518.04 s) Start R-work = 0.1626, R-free = 0.1735 Final R-work = 0.1138, R-free = 0.1302 =============================================================================== Job complete usr+sys time: 14192.51 seconds wall clock time: 259 minutes 9.44 seconds (15549.44 seconds total)