Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.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_4426565.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 3 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: 1.58, per 1000 atoms: 0.47 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: 0.31 Conformation dependent library (CDL) restraints added in 114.1 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: 0.60 - 0.86: 293 0.86 - 1.12: 1283 1.12 - 1.38: 539 1.38 - 1.64: 957 1.64 - 1.90: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 1.331 1.591 -0.260 1.34e-02 5.57e+03 3.77e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.334 1.104 0.230 1.25e-02 6.40e+03 3.38e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.130 0.196 1.10e-02 8.26e+03 3.16e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.183 0.195 1.10e-02 8.26e+03 3.15e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.034 0.202 1.15e-02 7.56e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 2974 4.40 - 8.80: 1886 8.80 - 13.20: 737 13.20 - 17.60: 160 17.60 - 22.00: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.02 14.18 9.00e-01 1.23e+00 2.48e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 137.48 -15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" O SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " ideal model delta sigma weight residual 122.96 105.96 17.00 1.13e+00 7.83e-01 2.26e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.07 106.73 15.34 1.03e+00 9.43e-01 2.22e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 135.38 -16.06 1.12e+00 7.97e-01 2.06e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.43: 947 17.43 - 34.84: 110 34.84 - 52.25: 36 52.25 - 69.65: 16 69.65 - 87.06: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.193: 92 0.193 - 0.385: 70 0.385 - 0.577: 51 0.577 - 0.769: 23 0.769 - 0.961: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 2 " pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CB ALA A 2 " both_signs ideal model delta sigma weight residual False 2.48 3.40 -0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.053 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.117 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.108 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.029 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.142 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.98e-02 1.10e+02 pdb=" CG HIS A 126 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.044 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.121 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1105 2.33 - 2.90: 8231 2.90 - 3.47: 10484 3.47 - 4.03: 15091 4.03 - 4.60: 21643 Nonbonded interactions: 56554 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.767 2.100 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.802 2.270 -y,x-y-1,z+1/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.828 2.100 ... (remaining 56549 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_4426565_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792806 | | target function (ml) not normalized (work): 232657.475660 | | target function (ml) not normalized (free): 11842.586551 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3043 0.2101 6.9975 4.9503| | 2: 3.57 - 2.84 1.00 2876 122 0.2430 0.1876 4.3575 4.352| | 3: 2.84 - 2.48 1.00 2833 165 0.2379 0.1741 4.138 4.1772| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1333 3.8441 3.8206| | 5: 2.25 - 2.09 1.00 2756 127 0.2447 0.1621 3.8105 3.8272| | 6: 2.09 - 1.97 1.00 2846 113 0.2507 0.1800 3.4887 3.5444| | 7: 1.97 - 1.87 1.00 2787 165 0.2549 0.1829 3.1513 3.271| | 8: 1.87 - 1.79 1.00 2789 144 0.2464 0.1929 3.0805 3.1881| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.1844 2.9085 2.9308| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2172 2.8183 2.9595| | 11: 1.66 - 1.61 1.00 2740 147 0.2489 0.1648 2.778 2.7036| | 12: 1.61 - 1.56 1.00 2787 146 0.2533 0.2003 2.6336 2.6385| | 13: 1.56 - 1.52 1.00 2745 130 0.2641 0.1965 2.5734 2.6186| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.1910 2.5249 2.5572| | 15: 1.48 - 1.45 1.00 2738 128 0.2614 0.2158 2.4336 2.5122| | 16: 1.45 - 1.42 1.00 2756 161 0.2665 0.2262 2.3937 2.4986| | 17: 1.42 - 1.39 1.00 2785 139 0.2608 0.2004 2.3064 2.367| | 18: 1.39 - 1.36 1.00 2741 179 0.2653 0.2220 2.2712 2.3358| | 19: 1.36 - 1.34 1.00 2807 134 0.2649 0.2542 2.2556 2.3704| | 20: 1.34 - 1.32 1.00 2696 147 0.2615 0.2004 2.1949 2.158| | 21: 1.32 - 1.30 1.00 2785 112 0.2749 0.2418 2.1464 2.2028| | 22: 1.29 - 1.27 1.00 2704 152 0.2750 0.2447 2.1239 2.1595| | 23: 1.27 - 1.26 1.00 2802 156 0.2780 0.2136 2.1027 2.0747| | 24: 1.26 - 1.24 1.00 2744 132 0.2722 0.2424 2.0583 2.1034| | 25: 1.24 - 1.22 1.00 2734 148 0.2829 0.2366 2.0452 2.0582| | 26: 1.22 - 1.21 1.00 2727 135 0.2913 0.2350 2.0189 2.0789| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2507 2.0061 1.9711| | 28: 1.19 - 1.18 1.00 2671 147 0.2967 0.2710 1.9853 2.023| | 29: 1.18 - 1.16 1.00 2800 134 0.2912 0.2855 1.9565 2.0719| | 30: 1.16 - 1.15 1.00 2740 148 0.3052 0.2972 1.9271 2.0208| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.10 0.76 0.23 1518.32| | 2: 3.57 - 2.84 2876 122 0.80 26.40 1.27 0.23 1518.32| | 3: 2.84 - 2.48 2833 165 0.74 32.38 1.25 0.23 1260.10| | 4: 2.47 - 2.25 2825 136 0.81 26.07 1.26 0.25 589.98| | 5: 2.25 - 2.09 2756 127 0.77 29.66 1.28 0.25 589.98| | 6: 2.09 - 1.97 2846 113 0.83 23.20 1.28 0.25 324.13| | 7: 1.97 - 1.87 2787 165 0.90 17.09 1.28 0.26 97.40| | 8: 1.87 - 1.79 2789 144 0.85 21.88 1.25 0.26 97.40| | 9: 1.79 - 1.72 2745 138 0.88 18.86 1.23 0.25 57.98| | 10: 1.72 - 1.66 2789 158 0.86 20.41 1.22 0.25 50.09| | 11: 1.66 - 1.61 2740 147 0.85 21.67 1.23 0.25 48.23| | 12: 1.61 - 1.56 2787 146 0.89 18.39 1.24 0.25 29.31| | 13: 1.56 - 1.52 2745 130 0.86 20.61 1.25 0.25 29.31| | 14: 1.52 - 1.48 2803 134 0.86 20.82 1.24 0.25 26.38| | 15: 1.48 - 1.45 2738 128 0.87 20.42 1.23 0.25 21.01| | 16: 1.45 - 1.42 2756 161 0.85 21.80 1.23 0.25 21.01| | 17: 1.42 - 1.39 2785 139 0.86 20.87 1.23 0.25 17.72| | 18: 1.39 - 1.36 2741 179 0.86 21.15 1.23 0.25 15.81| | 19: 1.36 - 1.34 2807 134 0.86 21.70 1.22 0.25 15.81| | 20: 1.34 - 1.32 2696 147 0.87 20.44 1.19 0.25 12.81| | 21: 1.32 - 1.30 2785 112 0.86 22.00 1.21 0.25 12.60| | 22: 1.29 - 1.27 2704 152 0.86 22.10 1.22 0.25 12.25| | 23: 1.27 - 1.26 2802 156 0.86 21.40 1.21 0.24 10.47| | 24: 1.26 - 1.24 2744 132 0.86 21.99 1.19 0.24 10.47| | 25: 1.24 - 1.22 2734 148 0.85 22.97 1.21 0.24 10.13| | 26: 1.22 - 1.21 2727 135 0.84 23.97 1.20 0.23 9.76| | 27: 1.21 - 1.19 2814 148 0.83 24.62 1.20 0.23 9.76| | 28: 1.19 - 1.18 2671 147 0.82 26.16 1.18 0.23 9.81| | 29: 1.18 - 1.16 2800 134 0.81 26.95 1.16 0.22 9.83| | 30: 1.16 - 1.15 2740 148 0.79 28.61 1.16 0.22 9.83| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.76 max = 1518.32 mean = 220.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.79| |phase err.(test): min = 0.00 max = 89.87 mean = 22.64| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.260 1557 Z= 5.645 Angle : 5.327 18.348 2118 Z= 3.706 Chirality : 0.379 0.961 243 Planarity : 0.029 0.128 284 Dihedral : 13.731 87.063 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 25.41 % 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: -2.74 (0.46), residues: 224 helix: -2.53 (0.34), residues: 109 sheet: -0.74 (0.77), residues: 40 loop : -0.85 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.025 ARG A 28 TYR 0.079 0.025 TYR A 139 PHE 0.093 0.035 PHE A 119 HIS 0.067 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792806 | | target function (ml) not normalized (work): 232657.475660 | | target function (ml) not normalized (free): 11842.586551 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2608 0.1953 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2608 0.1953 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1953 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2006 0.2010 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1642 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 0.3904 386.357 358.262 0.677 1.003 0.407 11.894-9.307 99.02 97 4 0.1864 613.709 596.170 0.932 1.004 0.390 9.237-7.194 100.00 213 7 0.2126 501.938 491.493 0.963 1.004 0.354 7.162-5.571 100.00 427 22 0.2210 376.677 362.536 0.933 1.004 0.320 5.546-4.326 100.00 867 58 0.1282 517.084 511.874 0.959 1.004 0.209 4.315-3.360 100.00 1859 96 0.1155 491.751 487.557 1.008 1.003 0.179 3.356-2.611 100.00 3867 181 0.1439 323.055 319.714 0.998 1.002 0.089 2.608-2.026 99.99 8198 413 0.1347 214.156 212.070 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1666 104.583 103.827 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2067 46.376 45.073 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2583 29.220 26.951 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1644 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.823706 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.195538 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 0.1659 0.1777 0.0117 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1561 0.1698 0.0137 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1443 0.1606 0.0164 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1395 0.1575 0.0180 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1355 0.1553 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1351 0.1549 0.0197 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1290 0.1504 0.0214 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1264 0.1486 0.0222 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1258 0.1487 0.0228 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1247 0.1478 0.0232 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1239 0.1468 0.0229 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1236 0.1469 0.0233 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1233 0.1465 0.0232 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1231 0.1465 0.0234 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1229 0.1466 0.0237 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1227 0.1465 0.0238 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1226 0.1462 0.0236 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1225 0.1468 0.0243 0.008 1.0 4.2 0.5 0.0 0 13.412 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1462 0.0236 0.007 0.9 3.8 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.62 2.36 3.013 19.051 2011.196 0.017 12.26 14.62 2.36 3.013 19.051 60.336 0.017 12.31 14.61 2.29 2.695 19.048 251.399 0.017 12.72 15.38 2.66 2.911 19.319 1005.598 0.016 12.49 15.42 2.93 3.222 19.558 2011.196 0.016 12.39 15.38 3.00 3.259 19.592 3016.793 0.015 12.28 15.37 3.09 3.293 19.602 4022.391 0.015 12.32 15.54 3.22 3.411 19.648 5027.989 0.015 12.21 15.40 3.19 3.307 19.595 6033.587 0.015 12.13 15.33 3.21 3.337 19.615 7039.184 0.015 12.14 15.38 3.25 3.252 19.545 8044.782 0.015 12.18 15.54 3.35 3.511 19.676 9050.380 0.015 12.17 15.52 3.35 3.519 19.674 10055.978 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 251.399 Accepted refinement result: 12.31 14.61 2.29 2.695 19.048 251.399 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.45 20.07 3.36 0 1785 Protein: 9.06 115.24 16.98 3.37 0 1519 Water: 11.46 119.45 38.22 N/A 0 258 Other: 19.66 26.59 22.02 N/A 0 8 Chain A: 9.06 119.45 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1273 20.10 - 31.14 227 31.14 - 42.18 124 42.18 - 53.21 95 53.21 - 64.25 41 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1461 r_work=0.1233 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 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 = 0.1226 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016808 | | target function (ls_wunit_k1) not normalized (work): 1400.032354 | | target function (ls_wunit_k1) not normalized (free): 108.994730 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1226 0.1457 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1691 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1669 0.1691 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1675 0.1676 0.1696 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1449 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1449 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3509 301.926 282.422 0.653 1.003 0.380 11.894-9.307 99.02 97 4 0.1661 483.669 472.069 0.924 1.003 0.380 9.237-7.194 100.00 213 7 0.1905 395.582 389.355 0.964 1.003 0.349 7.162-5.571 100.00 427 22 0.1825 296.862 291.146 0.937 1.003 0.300 5.546-4.326 100.00 867 58 0.0998 407.518 404.609 0.962 1.003 0.199 4.315-3.360 100.00 1859 96 0.0862 387.553 386.480 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1171 254.602 253.462 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1023 168.778 168.068 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.422 82.613 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.549 36.056 1.018 0.996 0.000 1.221-1.150 99.97 13689 708 0.2249 23.029 21.510 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0604 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1449 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** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1224 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1450 | n_water=258 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1233 r_free=0.1450 | n_water=252 | time (s): 21.500 (total time: 23.440) Filter (q & B) r_work=0.1235 r_free=0.1450 | n_water=249 | time (s): 2.600 (total time: 26.040) Compute maps r_work=0.1235 r_free=0.1450 | n_water=249 | time (s): 1.170 (total time: 27.210) Filter (map) r_work=0.1254 r_free=0.1452 | n_water=226 | time (s): 3.050 (total time: 30.260) Find peaks r_work=0.1254 r_free=0.1452 | n_water=226 | time (s): 0.680 (total time: 30.940) Add new water r_work=0.1400 r_free=0.1639 | n_water=430 | time (s): 2.990 (total time: 33.930) Refine new water occ: r_work=0.1308 r_free=0.1503 adp: r_work=0.1224 r_free=0.1443 occ: r_work=0.1237 r_free=0.1430 adp: r_work=0.1202 r_free=0.1413 occ: r_work=0.1205 r_free=0.1393 adp: r_work=0.1196 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1393 r_work=0.1196 r_free=0.1393 | n_water=430 | time (s): 62.900 (total time: 96.830) Filter (q & B) r_work=0.1200 r_free=0.1395 | n_water=413 | time (s): 3.100 (total time: 99.930) Filter (dist only) r_work=0.1200 r_free=0.1395 | n_water=412 | time (s): 33.890 (total time: 133.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.385956 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1505.635160 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 0.1655 0.1767 0.0113 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1460 0.1608 0.0148 0.001 0.5 8.3 0.0 0.0 0 0.250 0.1432 0.1582 0.0149 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1352 0.1521 0.0169 0.002 0.5 6.4 0.0 0.0 0 0.750 0.1312 0.1491 0.0180 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1325 0.1504 0.0179 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1265 0.1470 0.0205 0.002 0.5 6.1 0.5 0.0 0 2.000 0.1236 0.1455 0.0220 0.003 0.6 6.1 0.5 0.0 0 3.000 0.1222 0.1444 0.0222 0.003 0.7 5.8 0.5 0.0 0 4.000 0.1213 0.1433 0.0220 0.004 0.7 6.7 0.5 0.0 0 5.000 0.1210 0.1436 0.0226 0.004 0.7 6.1 0.5 0.0 0 6.000 0.1202 0.1428 0.0226 0.005 0.8 6.7 0.5 0.0 0 7.000 0.1196 0.1420 0.0224 0.005 0.8 7.0 0.5 0.0 0 8.000 0.1193 0.1425 0.0232 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1191 0.1426 0.0235 0.006 0.9 6.1 0.5 0.0 0 10.000 0.1188 0.1422 0.0234 0.007 0.9 6.7 0.5 0.0 0 11.000 0.1189 0.1427 0.0238 0.007 0.9 6.4 0.5 0.0 0 12.000 0.1186 0.1427 0.0241 0.007 0.9 7.0 0.5 0.0 0 13.000 0.1184 0.1422 0.0238 0.008 0.9 6.7 0.5 0.0 0 14.193 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1420 0.0224 0.005 0.8 7.0 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.20 2.24 3.798 21.791 1505.635 0.016 11.96 14.20 2.24 3.798 21.791 45.169 0.016 11.96 14.20 2.24 3.798 21.791 188.204 0.016 12.17 14.68 2.50 3.619 21.807 752.818 0.016 12.15 14.99 2.84 3.447 22.082 1505.635 0.015 12.06 15.01 2.95 3.479 22.223 2258.453 0.015 11.97 14.94 2.97 3.501 22.182 3011.270 0.014 11.84 14.90 3.06 3.482 22.054 3764.088 0.014 11.84 14.93 3.09 3.513 22.150 4516.905 0.014 11.82 14.95 3.13 3.550 22.218 5269.723 0.014 11.80 14.98 3.18 3.565 22.188 6022.541 0.014 11.80 15.02 3.22 3.588 22.206 6775.358 0.014 11.76 15.01 3.25 3.603 22.199 7528.176 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: 188.204 Accepted refinement result: 11.96 14.20 2.24 3.798 21.791 188.204 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.28 22.22 3.36 186 1753 Protein: 9.10 115.28 17.02 3.37 0 1519 Water: 11.50 76.71 41.38 N/A 186 226 Other: 19.70 26.63 22.06 N/A 0 8 Chain A: 9.10 115.28 19.47 N/A 0 1753 Chain S: 14.70 60.00 48.12 N/A 186 0 Histogram: Values Number of atoms 9.10 - 19.72 1261 19.72 - 30.33 241 30.33 - 40.95 161 40.95 - 51.57 129 51.57 - 62.19 124 62.19 - 72.81 12 72.81 - 83.42 5 83.42 - 94.04 4 94.04 - 104.66 0 104.66 - 115.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1420 r_work=0.1196 r_free=0.1420 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1420 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1419 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1193 r_free= 0.1419 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015180 | | target function (ls_wunit_k1) not normalized (work): 1264.422119 | | target function (ls_wunit_k1) not normalized (free): 101.065539 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1193 0.1419 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1591 0.1589 0.1659 n_refl.: 87592 remove outliers: r(all,work,free)=0.1591 0.1589 0.1659 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1593 0.1591 0.1660 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1190 0.1410 n_refl.: 87592 remove outliers: r(all,work,free)=0.1199 0.1189 0.1410 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 0.3184 297.266 278.307 0.602 1.002 0.350 11.894-9.307 99.02 97 4 0.1583 483.669 479.337 0.924 1.003 0.337 9.237-7.194 100.00 213 7 0.1710 395.582 393.985 0.982 1.003 0.282 7.162-5.571 100.00 427 22 0.1582 296.862 292.530 0.938 1.003 0.246 5.546-4.326 100.00 867 58 0.0898 407.518 404.471 0.959 1.003 0.199 4.315-3.360 100.00 1859 96 0.0803 387.553 386.494 1.004 1.002 0.180 3.356-2.611 100.00 3867 181 0.1088 254.602 253.723 1.011 1.002 0.053 2.608-2.026 99.99 8198 413 0.1013 168.778 168.186 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.422 82.630 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.549 36.082 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.029 21.537 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1410 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1410 | n_water=412 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1189 r_free=0.1410 | n_water=409 | time (s): 36.790 (total time: 38.480) Filter (q & B) r_work=0.1189 r_free=0.1410 | n_water=409 | time (s): 1.070 (total time: 39.550) Compute maps r_work=0.1189 r_free=0.1410 | n_water=409 | time (s): 1.650 (total time: 41.200) Filter (map) r_work=0.1224 r_free=0.1397 | n_water=283 | time (s): 3.400 (total time: 44.600) Find peaks r_work=0.1224 r_free=0.1397 | n_water=283 | time (s): 0.700 (total time: 45.300) Add new water r_work=0.1343 r_free=0.1532 | n_water=473 | time (s): 3.070 (total time: 48.370) Refine new water occ: r_work=0.1253 r_free=0.1455 adp: r_work=0.1254 r_free=0.1456 occ: r_work=0.1230 r_free=0.1433 adp: r_work=0.1229 r_free=0.1433 occ: r_work=0.1213 r_free=0.1414 adp: r_work=0.1207 r_free=0.1411 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1411 r_work=0.1207 r_free=0.1411 | n_water=473 | time (s): 205.710 (total time: 254.080) Filter (q & B) r_work=0.1211 r_free=0.1409 | n_water=442 | time (s): 3.070 (total time: 257.150) Filter (dist only) r_work=0.1211 r_free=0.1405 | n_water=441 | time (s): 36.770 (total time: 293.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705323 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.822638 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 0.1239 0.1381 0.0142 0.002 0.6 5.1 0.5 0.0 0 0.085 0.1191 0.1342 0.0151 0.003 0.7 3.8 0.5 0.0 0 0.256 0.1176 0.1331 0.0155 0.004 0.8 3.2 0.5 0.0 0 0.512 0.1168 0.1326 0.0159 0.005 0.9 3.5 0.5 0.0 0 0.767 0.1161 0.1323 0.0162 0.006 1.0 3.2 0.5 0.0 0 1.023 0.1158 0.1323 0.0165 0.006 1.0 3.8 0.5 0.0 0 1.279 0.1156 0.1323 0.0167 0.007 1.0 3.8 0.5 0.0 0 1.535 0.1154 0.1323 0.0169 0.008 1.1 3.8 0.5 0.0 0 1.791 0.1165 0.1325 0.0160 0.005 0.9 3.5 0.5 0.0 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1323 0.0165 0.006 1.0 3.8 0.5 0.0 0 1.279 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.23 1.65 3.801 21.304 41.823 3.623 11.58 13.23 1.65 3.801 21.304 1.255 3.623 11.59 13.23 1.65 3.789 21.304 5.228 3.623 11.66 13.36 1.69 3.722 21.291 20.911 3.620 11.69 13.45 1.76 3.738 21.268 41.823 3.620 11.63 13.43 1.80 3.758 21.253 62.734 3.615 11.57 13.40 1.83 3.775 21.246 83.645 3.610 11.54 13.37 1.84 3.787 21.244 104.557 3.608 11.51 13.36 1.85 3.795 21.240 125.468 3.605 11.49 13.37 1.88 3.807 21.230 146.379 3.604 11.51 13.40 1.89 3.822 21.214 167.291 3.604 11.50 13.39 1.89 3.830 21.212 188.202 3.603 11.48 13.37 1.89 3.837 21.209 209.113 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.255 Accepted refinement result: 11.58 13.23 1.65 3.801 21.304 1.255 3.623 Individual atomic B min max mean iso aniso Overall: 9.11 115.29 21.31 3.36 217 1751 Protein: 9.11 115.29 17.03 3.37 0 1519 Water: 11.52 76.73 36.03 N/A 217 224 Other: 19.71 26.64 22.08 N/A 0 8 Chain A: 9.11 115.29 19.44 N/A 0 1751 Chain S: 14.71 60.01 36.37 N/A 217 0 Histogram: Values Number of atoms 9.11 - 19.73 1264 19.73 - 30.35 288 30.35 - 40.97 203 40.97 - 51.58 135 51.58 - 62.20 55 62.20 - 72.82 12 72.82 - 83.44 5 83.44 - 94.06 4 94.06 - 104.67 0 104.67 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1323 r_work=0.1158 r_free=0.1323 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1323 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1322 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.19 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= 0.1322 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616943 | | target function (ml) not normalized (work): 301266.005578 | | target function (ml) not normalized (free): 15864.621319 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1322 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1490 0.1488 0.1551 n_refl.: 87589 remove outliers: r(all,work,free)=0.1490 0.1488 0.1551 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1489 0.1487 0.1550 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1145 0.1317 n_refl.: 87589 remove outliers: r(all,work,free)=0.1151 0.1142 0.1317 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 0.3850 294.550 272.231 0.489 1.001 0.320 11.894-9.307 98.04 96 4 0.2331 483.794 465.197 0.869 1.002 0.320 9.237-7.194 98.18 209 7 0.2300 387.041 387.187 0.954 1.002 0.204 7.162-5.571 100.00 427 22 0.2121 296.862 284.766 0.918 1.003 0.170 5.546-4.326 100.00 867 58 0.1117 407.518 402.670 0.962 1.002 0.160 4.315-3.360 100.00 1859 96 0.0936 387.553 384.966 1.006 1.002 0.160 3.356-2.611 100.00 3867 181 0.1130 254.602 252.442 1.008 1.002 0.080 2.608-2.026 99.99 8198 413 0.0931 168.778 167.998 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.422 82.701 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.549 36.133 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.029 21.565 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=-0.0105 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1317 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=0.1142 r_free=0.1317 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1317 | n_water=441 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1145 r_free=0.1318 | n_water=438 | time (s): 49.490 (total time: 51.800) Filter (q & B) r_work=0.1146 r_free=0.1320 | n_water=436 | time (s): 4.110 (total time: 55.910) Compute maps r_work=0.1146 r_free=0.1320 | n_water=436 | time (s): 1.930 (total time: 57.840) Filter (map) r_work=0.1165 r_free=0.1310 | n_water=325 | time (s): 3.960 (total time: 61.800) Find peaks r_work=0.1165 r_free=0.1310 | n_water=325 | time (s): 0.760 (total time: 62.560) Add new water r_work=0.1233 r_free=0.1397 | n_water=477 | time (s): 3.680 (total time: 66.240) Refine new water occ: r_work=0.1169 r_free=0.1336 adp: r_work=0.1170 r_free=0.1339 occ: r_work=0.1154 r_free=0.1321 adp: r_work=0.1154 r_free=0.1323 occ: r_work=0.1141 r_free=0.1309 adp: r_work=0.1139 r_free=0.1310 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1310 r_work=0.1139 r_free=0.1310 | n_water=477 | time (s): 284.980 (total time: 351.220) Filter (q & B) r_work=0.1144 r_free=0.1322 | n_water=441 | time (s): 4.050 (total time: 355.270) Filter (dist only) r_work=0.1144 r_free=0.1320 | n_water=439 | time (s): 45.710 (total time: 400.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.818347 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.120372 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 0.1207 0.1363 0.0156 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1169 0.1333 0.0164 0.003 0.8 3.2 0.5 0.0 0 0.273 0.1155 0.1327 0.0172 0.005 0.9 3.5 0.5 0.0 0 0.546 0.1149 0.1325 0.0176 0.006 1.0 3.5 0.5 0.0 0 0.818 0.1145 0.1323 0.0178 0.007 1.0 3.5 0.5 0.0 0 1.091 0.1142 0.1320 0.0178 0.007 1.1 3.5 0.5 0.0 0 1.364 0.1141 0.1322 0.0181 0.008 1.1 3.2 0.5 0.0 0 1.637 0.1139 0.1320 0.0181 0.008 1.1 3.5 0.5 0.0 0 1.909 0.1147 0.1324 0.0176 0.006 1.0 3.5 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1320 0.0181 0.008 1.1 3.5 0.5 0.0 0 1.909 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 13.20 1.81 3.802 21.174 49.120 3.610 11.39 13.20 1.81 3.802 21.174 1.474 3.610 11.39 13.20 1.80 3.791 21.174 6.140 3.609 11.47 13.32 1.85 3.731 21.157 24.560 3.608 11.40 13.32 1.91 3.755 21.147 49.120 3.603 11.43 13.39 1.96 3.778 21.120 73.681 3.602 11.38 13.36 1.98 3.792 21.114 98.241 3.598 11.34 13.32 1.98 3.800 21.114 122.801 3.595 11.34 13.36 2.02 3.819 21.101 147.361 3.594 11.32 13.35 2.03 3.831 21.090 171.921 3.592 11.33 13.37 2.05 3.845 21.085 196.481 3.593 11.31 13.36 2.05 3.853 21.083 221.042 3.592 11.30 13.35 2.05 3.861 21.083 245.602 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: 1.474 Accepted refinement result: 11.39 13.20 1.81 3.802 21.174 1.474 3.610 Individual atomic B min max mean iso aniso Overall: 9.11 115.29 21.08 3.36 216 1750 Protein: 9.11 115.29 17.03 3.37 0 1519 Water: 11.51 76.72 35.06 N/A 216 223 Other: 19.71 26.64 22.07 N/A 0 8 Chain A: 9.11 115.29 19.44 N/A 0 1750 Chain S: 14.71 60.01 34.35 N/A 216 0 Histogram: Values Number of atoms 9.11 - 19.73 1265 19.73 - 30.34 292 30.34 - 40.96 220 40.96 - 51.58 123 51.58 - 62.20 43 62.20 - 72.82 12 72.82 - 83.43 5 83.43 - 94.05 4 94.05 - 104.67 0 104.67 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1320 r_work=0.1139 r_free=0.1320 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1320 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1316 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.21 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= 0.1135 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607501 | | target function (ml) not normalized (work): 300457.927923 | | target function (ml) not normalized (free): 15845.423533 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1135 0.1316 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1479 0.1477 0.1549 n_refl.: 87583 remove outliers: r(all,work,free)=0.1479 0.1477 0.1549 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1478 0.1476 0.1549 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1134 0.1316 n_refl.: 87583 remove outliers: r(all,work,free)=0.1142 0.1133 0.1316 n_refl.: 87580 ======================== 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 0.4092 288.991 262.474 0.466 1.001 0.312 11.894-9.307 96.08 94 4 0.2530 477.022 464.602 0.854 1.002 0.306 9.237-7.194 98.18 209 7 0.2383 387.041 379.310 0.925 1.002 0.180 7.162-5.571 100.00 427 22 0.2219 296.862 284.056 0.908 1.002 0.150 5.546-4.326 100.00 867 58 0.1145 407.518 402.361 0.963 1.002 0.123 4.315-3.360 100.00 1859 96 0.0916 387.553 385.320 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1115 254.602 252.561 1.010 1.002 0.034 2.608-2.026 99.99 8198 413 0.0909 168.778 168.090 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0875 82.422 82.740 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.549 36.147 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.029 21.564 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=-0.0094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1316 After: r_work=0.1134 r_free=0.1316 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1316 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=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1316 | n_water=439 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1134 r_free=0.1316 | n_water=439 | time (s): 44.680 (total time: 47.190) Filter (q & B) r_work=0.1134 r_free=0.1316 | n_water=439 | time (s): 1.410 (total time: 48.600) Compute maps r_work=0.1134 r_free=0.1316 | n_water=439 | time (s): 1.930 (total time: 50.530) Filter (map) r_work=0.1154 r_free=0.1314 | n_water=350 | time (s): 3.930 (total time: 54.460) Find peaks r_work=0.1154 r_free=0.1314 | n_water=350 | time (s): 0.710 (total time: 55.170) Add new water r_work=0.1202 r_free=0.1367 | n_water=490 | time (s): 3.810 (total time: 58.980) Refine new water occ: r_work=0.1148 r_free=0.1317 adp: r_work=0.1148 r_free=0.1319 occ: r_work=0.1138 r_free=0.1307 adp: r_work=0.1137 r_free=0.1309 occ: r_work=0.1130 r_free=0.1301 adp: r_work=0.1127 r_free=0.1301 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1301 r_work=0.1127 r_free=0.1301 | n_water=490 | time (s): 228.400 (total time: 287.380) Filter (q & B) r_work=0.1133 r_free=0.1299 | n_water=457 | time (s): 4.050 (total time: 291.430) Filter (dist only) r_work=0.1133 r_free=0.1299 | n_water=455 | time (s): 48.600 (total time: 340.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.741339 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.242193 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 0.1342 0.0137 0.004 0.7 5.1 0.0 0.0 0 0.087 0.1165 0.1317 0.0152 0.004 0.8 4.5 0.0 0.0 0 0.261 0.1150 0.1308 0.0158 0.005 0.9 4.2 0.5 0.0 0 0.522 0.1143 0.1304 0.0161 0.006 1.0 4.2 0.5 0.0 0 0.784 0.1138 0.1301 0.0163 0.007 1.1 4.2 0.5 0.0 0 1.045 0.1136 0.1299 0.0164 0.008 1.1 4.2 0.5 0.0 0 1.306 0.1134 0.1299 0.0165 0.008 1.1 4.2 0.5 0.0 0 1.567 0.1133 0.1299 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.828 0.1141 0.1303 0.0161 0.006 1.0 4.2 0.5 0.0 0 0.871 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1299 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.99 1.66 3.802 21.209 43.242 3.605 11.33 12.99 1.66 3.802 21.209 1.297 3.605 11.34 12.99 1.65 3.792 21.209 5.405 3.605 11.39 13.07 1.68 3.728 21.197 21.621 3.603 11.38 13.12 1.75 3.751 21.182 43.242 3.602 11.33 13.12 1.79 3.771 21.168 64.863 3.598 11.31 13.12 1.80 3.787 21.156 86.484 3.595 11.29 13.09 1.80 3.795 21.153 108.105 3.592 11.25 13.07 1.81 3.800 21.155 129.727 3.589 11.25 13.10 1.85 3.816 21.144 151.348 3.589 11.25 13.13 1.88 3.832 21.132 172.969 3.588 11.24 13.12 1.88 3.841 21.129 194.590 3.587 11.22 13.10 1.88 3.845 21.131 216.211 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.297 Accepted refinement result: 11.33 12.99 1.66 3.802 21.209 1.297 3.605 Individual atomic B min max mean iso aniso Overall: 9.11 115.28 21.14 3.36 233 1749 Protein: 9.11 115.28 17.03 3.37 0 1519 Water: 11.51 76.72 34.87 N/A 233 222 Other: 19.71 26.63 22.07 N/A 0 8 Chain A: 9.11 115.28 19.42 N/A 0 1749 Chain S: 14.70 60.01 34.10 N/A 233 0 Histogram: Values Number of atoms 9.11 - 19.72 1265 19.72 - 30.34 301 30.34 - 40.96 225 40.96 - 51.58 122 51.58 - 62.19 46 62.19 - 72.81 12 72.81 - 83.43 5 83.43 - 94.05 4 94.05 - 104.67 0 104.67 - 115.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1299 r_work=0.1133 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1299 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1298 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1298 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604251 | | target function (ml) not normalized (work): 300176.467359 | | target function (ml) not normalized (free): 15822.371207 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1361 0.1427 5.6672 5.6631| | 2: 3.57 - 2.84 1.00 2888 124 0.1068 0.1412 5.1843 5.2456| | 3: 2.83 - 2.48 1.00 2820 163 0.1094 0.1147 4.9694 4.9908| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0983 4.6499 4.6781| | 5: 2.25 - 2.09 1.00 2756 127 0.0856 0.0971 4.6003 4.6461| | 6: 2.09 - 1.97 1.00 2846 113 0.0848 0.1015 4.2737 4.3692| | 7: 1.97 - 1.87 1.00 2787 165 0.0866 0.1114 3.9631 4.08| | 8: 1.87 - 1.79 1.00 2789 144 0.0903 0.1073 3.8765 3.9793| | 9: 1.79 - 1.72 1.00 2745 138 0.0858 0.1139 3.6285 3.8125| | 10: 1.72 - 1.66 1.00 2831 160 0.0896 0.1186 3.5481 3.7079| | 11: 1.66 - 1.61 1.00 2712 147 0.0854 0.0970 3.4836 3.5346| | 12: 1.61 - 1.56 1.00 2773 144 0.0888 0.1179 3.3158 3.4665| | 13: 1.56 - 1.52 1.00 2745 130 0.0935 0.1029 3.2959 3.3852| | 14: 1.52 - 1.48 1.00 2803 134 0.0975 0.1040 3.234 3.3149| | 15: 1.48 - 1.45 1.00 2738 128 0.0994 0.1230 3.1472 3.2606| | 16: 1.45 - 1.42 1.00 2756 161 0.1049 0.1263 3.1321 3.2545| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1306 3.1168 3.2366| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1333 3.1015 3.2482| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1580 3.1121 3.2792| | 20: 1.34 - 1.32 1.00 2696 147 0.1362 0.1467 3.1115 3.1525| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1501 3.1151 3.1005| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1987 3.1242 3.295| | 23: 1.27 - 1.26 1.00 2802 156 0.1642 0.1793 3.1329 3.2013| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1845 3.128 3.2345| | 25: 1.24 - 1.22 1.00 2733 148 0.1882 0.2143 3.1434 3.2599| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1762 3.1491 3.2026| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2162 3.1717 3.1628| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2293 3.1682 3.1736| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2381 3.1489 3.2305| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2452 3.1452 3.1698| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2922 171 0.95 9.10 1.00 0.97 6258.48| | 2: 3.57 - 2.84 2888 124 0.92 13.15 1.01 0.97 6258.48| | 3: 2.83 - 2.48 2820 163 0.89 17.18 0.99 0.97 5214.04| | 4: 2.47 - 2.25 2825 136 0.91 13.97 1.00 0.98 2520.78| | 5: 2.25 - 2.09 2756 127 0.90 16.20 1.01 0.98 2520.78| | 6: 2.09 - 1.97 2846 113 0.92 12.54 1.02 0.98 1429.70| | 7: 1.97 - 1.87 2787 165 0.95 9.17 1.02 0.98 499.15| | 8: 1.87 - 1.79 2789 144 0.93 12.38 1.00 0.98 499.15| | 9: 1.79 - 1.72 2745 138 0.95 9.87 0.98 0.98 282.48| | 10: 1.72 - 1.66 2831 160 0.94 10.89 0.98 0.98 239.09| | 11: 1.66 - 1.61 2712 147 0.94 11.51 0.98 0.98 229.09| | 12: 1.61 - 1.56 2773 144 0.96 8.78 0.99 0.98 134.75| | 13: 1.56 - 1.52 2745 130 0.95 10.23 1.03 0.98 134.75| | 14: 1.52 - 1.48 2803 134 0.94 10.59 1.02 0.98 121.38| | 15: 1.48 - 1.45 2738 128 0.95 9.79 1.02 0.99 96.90| | 16: 1.45 - 1.42 2756 161 0.94 10.96 1.02 0.99 96.90| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.99 88.87| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.99 84.23| | 19: 1.36 - 1.34 2807 134 0.94 11.88 1.00 0.99 84.23| | 20: 1.34 - 1.32 2696 147 0.94 12.14 0.98 0.97 80.43| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 80.16| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.57| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 82.62| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.95 82.62| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.53| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.66| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.66| | 28: 1.19 - 1.18 2671 147 0.88 20.40 1.01 0.93 90.37| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.76| | 30: 1.16 - 1.15 2739 148 0.86 22.04 0.98 0.93 91.76| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.16 max = 6258.48 mean = 948.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.50| |phase err.(test): min = 0.00 max = 90.00 mean = 13.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1298 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1465 0.1462 0.1530 n_refl.: 87580 remove outliers: r(all,work,free)=0.1465 0.1462 0.1530 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1464 0.1462 0.1529 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1132 0.1299 n_refl.: 87580 remove outliers: r(all,work,free)=0.1138 0.1130 0.1299 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 88.54 80 5 0.4154 286.399 248.079 0.411 0.999 0.270 11.894-9.307 95.10 93 4 0.2564 473.273 461.299 0.852 1.001 0.257 9.237-7.194 98.18 209 7 0.2382 387.041 379.146 0.927 1.002 0.170 7.162-5.571 100.00 427 22 0.2221 296.862 284.305 0.908 1.002 0.150 5.546-4.326 100.00 867 58 0.1132 407.518 402.395 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0930 387.553 385.393 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1104 254.602 252.826 1.011 1.002 0.019 2.608-2.026 99.99 8198 413 0.0902 168.778 168.145 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0872 82.422 82.770 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.549 36.156 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 23.029 21.569 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0107 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1953 0.083 5.327 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1761 0.083 5.327 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1761 0.083 5.327 9.0 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1768 0.083 5.327 9.0 119.5 20.1 258 0.006 1_weight: 0.1644 0.1768 0.083 5.327 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1226 0.1462 0.007 0.926 9.0 119.5 20.1 258 0.140 1_adp: 0.1231 0.1461 0.007 0.926 9.1 119.4 20.1 258 0.140 1_regHadp: 0.1233 0.1464 0.007 0.926 9.1 119.4 20.1 258 0.140 1_occ: 0.1226 0.1457 0.007 0.926 9.1 119.4 20.1 258 0.140 2_bss: 0.1224 0.1449 0.007 0.926 9.1 119.5 20.1 258 0.140 2_settarget: 0.1224 0.1449 0.007 0.926 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1224 0.1449 0.007 0.940 9.1 119.5 20.1 258 0.140 2_nqh: 0.1224 0.1450 0.007 0.940 9.1 119.5 20.1 258 0.138 2_sol: 0.1200 0.1395 0.007 0.940 9.1 115.3 22.2 412 n/a 2_weight: 0.1200 0.1395 0.007 0.940 9.1 115.3 22.2 412 n/a 2_xyzrec: 0.1196 0.1420 0.005 0.803 9.1 115.3 22.2 412 n/a 2_adp: 0.1196 0.1420 0.005 0.803 9.1 115.3 22.2 412 n/a 2_regHadp: 0.1196 0.1420 0.005 0.803 9.1 115.3 22.2 412 n/a 2_occ: 0.1193 0.1419 0.005 0.803 9.1 115.3 22.2 412 n/a 3_bss: 0.1189 0.1410 0.005 0.803 9.1 115.3 22.2 412 n/a 3_settarget: 0.1189 0.1410 0.005 0.803 9.1 115.3 22.2 412 n/a 3_updatecdl: 0.1189 0.1410 0.005 0.805 9.1 115.3 22.2 412 n/a 3_nqh: 0.1189 0.1410 0.005 0.805 9.1 115.3 22.2 412 n/a 3_sol: 0.1211 0.1405 0.005 0.805 9.1 115.3 21.3 441 n/a 3_weight: 0.1211 0.1405 0.005 0.805 9.1 115.3 21.3 441 n/a 3_xyzrec: 0.1158 0.1323 0.006 1.005 9.1 115.3 21.3 441 n/a 3_adp: 0.1158 0.1323 0.006 1.005 9.1 115.3 21.3 441 n/a 3_regHadp: 0.1158 0.1323 0.006 1.005 9.1 115.3 21.3 441 n/a 3_occ: 0.1151 0.1322 0.006 1.005 9.1 115.3 21.3 441 n/a 4_bss: 0.1142 0.1317 0.006 1.005 9.1 115.3 21.3 441 n/a 4_settarget: 0.1142 0.1317 0.006 1.005 9.1 115.3 21.3 441 n/a 4_updatecdl: 0.1142 0.1317 0.006 1.008 9.1 115.3 21.3 441 n/a 4_nqh: 0.1142 0.1317 0.006 1.008 9.1 115.3 21.3 441 n/a 4_sol: 0.1144 0.1320 0.006 1.008 9.1 115.3 21.1 439 n/a 4_weight: 0.1144 0.1320 0.006 1.008 9.1 115.3 21.1 439 n/a 4_xyzrec: 0.1139 0.1320 0.008 1.127 9.1 115.3 21.1 439 n/a 4_adp: 0.1139 0.1320 0.008 1.127 9.1 115.3 21.1 439 n/a 4_regHadp: 0.1139 0.1320 0.008 1.127 9.1 115.3 21.1 439 n/a 4_occ: 0.1135 0.1316 0.008 1.127 9.1 115.3 21.1 439 n/a 5_bss: 0.1133 0.1316 0.008 1.127 9.1 115.3 21.1 439 n/a 5_settarget: 0.1133 0.1316 0.008 1.127 9.1 115.3 21.1 439 n/a 5_updatecdl: 0.1133 0.1316 0.008 1.128 9.1 115.3 21.1 439 n/a 5_setrh: 0.1134 0.1316 0.008 1.128 9.1 115.3 21.1 439 n/a 5_nqh: 0.1134 0.1316 0.008 1.128 9.1 115.3 21.1 439 n/a 5_sol: 0.1133 0.1299 0.008 1.128 9.1 115.3 21.1 455 n/a 5_weight: 0.1133 0.1299 0.008 1.128 9.1 115.3 21.1 455 n/a 5_xyzrec: 0.1133 0.1299 0.008 1.134 9.1 115.3 21.1 455 n/a 5_adp: 0.1133 0.1299 0.008 1.134 9.1 115.3 21.1 455 n/a 5_regHadp: 0.1133 0.1299 0.008 1.134 9.1 115.3 21.1 455 n/a 5_occ: 0.1131 0.1298 0.008 1.134 9.1 115.3 21.1 455 n/a end: 0.1130 0.1299 0.008 1.134 9.1 115.3 21.1 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4426565_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4426565_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1400 Refinement macro-cycles (run) : 14348.6200 Write final files (write_after_run_outputs) : 70.8900 Total : 14423.6500 Total CPU time: 4.01 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:37 PST -0800 (1735366837.35 s) Start R-work = 0.1642, R-free = 0.1761 Final R-work = 0.1130, R-free = 0.1299 =============================================================================== Job complete usr+sys time: 14568.04 seconds wall clock time: 264 minutes 11.32 seconds (15851.32 seconds total)