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_3025539.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_3025539.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3025539.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: 1.55, per 1000 atoms: 0.46 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: 0.54 Conformation dependent library (CDL) restraints added in 148.1 milliseconds Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 578 0.92 - 1.18: 1086 1.18 - 1.43: 640 1.43 - 1.68: 822 1.68 - 1.94: 27 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " ideal model delta sigma weight residual 1.522 1.733 -0.211 1.14e-02 7.69e+03 3.42e+02 bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.447 1.643 -0.197 1.12e-02 7.97e+03 3.09e+02 bond pdb=" CA ALYS A 175 " pdb=" C ALYS A 175 " ideal model delta sigma weight residual 1.524 1.744 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta sigma weight residual 1.456 1.685 -0.229 1.33e-02 5.65e+03 2.96e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.524 1.698 -0.173 1.05e-02 9.07e+03 2.72e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3192 4.70 - 9.40: 1847 9.40 - 14.09: 621 14.09 - 18.79: 104 18.79 - 23.48: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.29 -16.69 1.00e+00 1.00e+00 2.79e+02 angle pdb=" O PHE A 162 " pdb=" C PHE A 162 " pdb=" N GLU A 163 " ideal model delta sigma weight residual 122.07 136.88 -14.81 1.03e+00 9.43e-01 2.07e+02 angle pdb=" O ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 122.07 136.31 -14.24 1.03e+00 9.43e-01 1.91e+02 angle pdb=" O AGLU A 96 " pdb=" C AGLU A 96 " pdb=" N AASN A 97 " ideal model delta sigma weight residual 122.07 108.59 13.48 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CD1 TYR A 141 " pdb=" CG TYR A 141 " pdb=" CD2 TYR A 141 " ideal model delta sigma weight residual 118.10 99.46 18.64 1.50e+00 4.44e-01 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.84: 948 17.84 - 35.67: 115 35.67 - 53.50: 36 53.50 - 71.33: 11 71.33 - 89.16: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CD1 PHE A 164 " pdb=" CE1 PHE A 164 " pdb=" CZ PHE A 164 " pdb=" HZ PHE A 164 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+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 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.201: 107 0.201 - 0.401: 66 0.401 - 0.601: 44 0.601 - 0.800: 20 0.800 - 1.000: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.44 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 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 " -0.042 2.00e-02 2.50e+03 7.73e-02 1.79e+02 pdb=" CG PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.111 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.153 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.083 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.032 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.025 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.044 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.114 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.009 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1099 2.33 - 2.90: 8192 2.90 - 3.47: 10526 3.47 - 4.03: 15223 4.03 - 4.60: 21520 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.764 2.100 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.767 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.818 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.824 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.831 1.850 ... (remaining 56555 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_3025539_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= 0.2596 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786432 | | target function (ml) not normalized (work): 232126.519709 | | target function (ml) not normalized (free): 11816.232051 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3013 0.2107 7.0859 4.9444| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1812 4.3423 4.3381| | 3: 2.84 - 2.48 1.00 2833 165 0.2343 0.1607 4.1201 4.1496| | 4: 2.47 - 2.25 1.00 2825 136 0.2313 0.1496 3.829 3.8371| | 5: 2.25 - 2.09 1.00 2756 127 0.2462 0.1593 3.7924 3.8186| | 6: 2.09 - 1.97 1.00 2846 113 0.2562 0.1849 3.4592 3.5417| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1677 3.1336 3.1317| | 8: 1.87 - 1.79 1.00 2789 144 0.2431 0.1927 3.0441 3.1301| | 9: 1.79 - 1.72 1.00 2745 138 0.2401 0.1750 2.8871 2.9039| | 10: 1.72 - 1.66 1.00 2789 158 0.2421 0.1904 2.7945 2.8593| | 11: 1.66 - 1.61 1.00 2740 147 0.2499 0.1773 2.7423 2.7449| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1877 2.6099 2.6109| | 13: 1.56 - 1.52 1.00 2745 130 0.2484 0.1823 2.5502 2.5719| | 14: 1.52 - 1.48 1.00 2803 134 0.2492 0.1856 2.4893 2.513| | 15: 1.48 - 1.45 1.00 2738 128 0.2597 0.2188 2.417 2.5088| | 16: 1.45 - 1.42 1.00 2756 161 0.2636 0.2155 2.3672 2.4595| | 17: 1.42 - 1.39 1.00 2785 139 0.2669 0.1873 2.335 2.3001| | 18: 1.39 - 1.36 1.00 2741 179 0.2692 0.2388 2.2788 2.4164| | 19: 1.36 - 1.34 1.00 2807 134 0.2675 0.2591 2.2482 2.3783| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2250 2.1838 2.2333| | 21: 1.32 - 1.30 1.00 2785 112 0.2738 0.2290 2.1734 2.2003| | 22: 1.29 - 1.27 1.00 2704 152 0.2763 0.2546 2.1351 2.1945| | 23: 1.27 - 1.26 1.00 2802 156 0.2796 0.2144 2.0932 2.1312| | 24: 1.26 - 1.24 1.00 2744 132 0.2809 0.2528 2.0825 2.1777| | 25: 1.24 - 1.22 1.00 2734 148 0.2844 0.2962 2.0424 2.1822| | 26: 1.22 - 1.21 1.00 2727 135 0.2839 0.2422 2.0139 2.1303| | 27: 1.21 - 1.19 1.00 2814 148 0.2954 0.2400 2.0017 1.9519| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2920 1.9863 2.0427| | 29: 1.18 - 1.16 1.00 2800 134 0.2985 0.2592 1.9623 2.0007| | 30: 1.16 - 1.15 1.00 2740 148 0.3046 0.2874 1.9346 1.959| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.73 0.76 0.23 1469.61| | 2: 3.57 - 2.84 2876 122 0.81 25.96 1.27 0.23 1469.61| | 3: 2.84 - 2.48 2833 165 0.74 31.84 1.25 0.24 1218.48| | 4: 2.47 - 2.25 2825 136 0.81 25.46 1.26 0.25 566.77| | 5: 2.25 - 2.09 2756 127 0.77 29.31 1.28 0.25 566.77| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 309.35| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.26 89.80| | 8: 1.87 - 1.79 2789 144 0.86 20.95 1.25 0.26 89.80| | 9: 1.79 - 1.72 2745 138 0.88 18.41 1.23 0.25 54.19| | 10: 1.72 - 1.66 2789 158 0.87 19.91 1.23 0.25 47.06| | 11: 1.66 - 1.61 2740 147 0.86 20.97 1.24 0.25 45.37| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.24 0.25 28.23| | 13: 1.56 - 1.52 2745 130 0.87 19.80 1.23 0.25 28.23| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.56| | 15: 1.48 - 1.45 2738 128 0.87 19.98 1.24 0.25 20.68| | 16: 1.45 - 1.42 2756 161 0.86 21.70 1.24 0.25 20.68| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 17.82| | 18: 1.39 - 1.36 2741 179 0.86 21.68 1.23 0.24 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.35 1.23 0.24 16.17| | 20: 1.34 - 1.32 2696 147 0.86 21.53 1.23 0.24 13.72| | 21: 1.32 - 1.30 2785 112 0.85 22.54 1.20 0.24 13.55| | 22: 1.29 - 1.27 2704 152 0.84 23.28 1.21 0.24 13.22| | 23: 1.27 - 1.26 2802 156 0.85 22.86 1.22 0.24 11.58| | 24: 1.26 - 1.24 2744 132 0.84 23.35 1.21 0.24 11.58| | 25: 1.24 - 1.22 2734 148 0.84 24.28 1.20 0.24 11.01| | 26: 1.22 - 1.21 2727 135 0.83 24.55 1.19 0.23 10.37| | 27: 1.21 - 1.19 2814 148 0.82 25.41 1.21 0.23 10.37| | 28: 1.19 - 1.18 2671 147 0.82 25.83 1.19 0.23 9.59| | 29: 1.18 - 1.16 2800 134 0.82 25.95 1.17 0.23 9.30| | 30: 1.16 - 1.15 2740 148 0.81 27.38 1.16 0.23 9.30| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1469.61 mean = 213.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.76| |phase err.(test): min = 0.00 max = 89.81 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.229 1557 Z= 5.385 Angle : 5.286 18.642 2118 Z= 3.693 Chirality : 0.363 1.000 243 Planarity : 0.034 0.118 284 Dihedral : 13.779 89.165 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.47), residues: 224 helix: -2.53 (0.38), residues: 109 sheet: -1.12 (0.81), residues: 28 loop : -0.37 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.015 ARG A 28 TYR 0.101 0.033 TYR A 141 PHE 0.107 0.047 PHE A 164 HIS 0.062 0.021 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= 0.2596 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.786432 | | target function (ml) not normalized (work): 232126.519709 | | target function (ml) not normalized (free): 11816.232051 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2555 0.2597 0.1935 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2555 0.2597 0.1935 n_refl.: 87602 remove outliers: r(all,work,free)=0.1965 0.1968 0.1935 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1987 0.1992 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1625 0.1619 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1625 0.1618 0.1756 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 0.3804 386.439 357.969 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1806 613.839 595.171 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2174 502.045 490.960 0.961 1.003 0.350 7.162-5.571 100.00 427 22 0.2170 376.757 364.733 0.929 1.003 0.297 5.546-4.326 100.00 867 58 0.1274 517.194 511.679 0.961 1.003 0.234 4.315-3.360 100.00 1859 96 0.1153 491.855 487.792 1.005 1.003 0.219 3.356-2.611 100.00 3867 181 0.1397 323.124 320.253 0.997 1.002 0.129 2.608-2.026 99.99 8198 413 0.1338 214.201 212.143 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1621 104.605 103.943 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2042 46.386 45.134 1.003 0.997 0.000 1.221-1.150 99.97 13689 708 0.2588 29.226 26.953 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0420 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1756 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 173 ASN Total number of N/Q/H flips: 1 r_work=0.1619 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.609844 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2002.636163 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 0.1649 0.1765 0.0115 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1495 0.1633 0.0137 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1379 0.1538 0.0159 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1356 0.1527 0.0171 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1348 0.1533 0.0185 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1358 0.1541 0.0183 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1297 0.1507 0.0210 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1274 0.1492 0.0219 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1245 0.1468 0.0223 0.004 0.7 2.9 0.5 0.0 0 4.000 0.1251 0.1482 0.0231 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1245 0.1477 0.0232 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1237 0.1471 0.0234 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1238 0.1475 0.0236 0.006 0.8 3.8 0.5 0.0 0 8.000 0.1234 0.1469 0.0235 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1230 0.1465 0.0235 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1463 0.0235 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 0.1226 0.1469 0.0243 0.008 1.0 3.5 0.5 0.0 0 13.000 0.1221 0.1459 0.0238 0.008 1.0 3.5 0.5 0.6 0 14.305 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1459 0.0238 0.008 1.0 3.5 0.5 0.6 0 14.305 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.59 2.38 3.013 19.042 2002.636 0.017 12.21 14.59 2.37 2.989 19.042 60.079 0.017 12.28 14.57 2.28 2.669 19.042 250.330 0.017 12.63 15.20 2.58 2.740 19.213 1001.318 0.016 12.45 15.34 2.89 3.191 19.533 2002.636 0.016 12.36 15.39 3.03 3.331 19.632 3003.954 0.015 12.23 15.33 3.10 3.323 19.608 4005.272 0.015 12.25 15.42 3.17 3.368 19.622 5006.590 0.015 12.16 15.40 3.24 3.339 19.608 6007.908 0.015 12.20 15.42 3.22 3.318 19.578 7009.227 0.015 12.10 15.36 3.26 3.403 19.614 8010.545 0.015 12.13 15.41 3.28 3.472 19.646 9011.863 0.015 12.13 15.43 3.30 3.550 19.675 10013.181 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 250.330 Accepted refinement result: 12.28 14.57 2.28 2.669 19.042 250.330 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.07 3.31 0 1785 Protein: 9.05 114.98 16.98 3.32 0 1519 Water: 11.45 119.42 38.21 N/A 0 258 Other: 19.68 26.57 22.03 N/A 0 8 Chain A: 9.05 119.42 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.16 125 42.16 - 53.20 94 53.20 - 64.24 42 64.24 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1457 r_work=0.1230 r_free=0.1459 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1459 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 = 0.1224 r_free = 0.1458 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1224 r_free= 0.1458 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016699 | | target function (ls_wunit_k1) not normalized (work): 1390.996445 | | target function (ls_wunit_k1) not normalized (free): 109.837334 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1224 0.1458 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1694 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1669 0.1694 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1674 0.1675 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1222 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1233 0.1222 0.1454 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3547 301.459 280.670 0.650 1.002 0.380 11.894-9.307 99.02 97 4 0.1629 482.921 470.520 0.923 1.003 0.370 9.237-7.194 100.00 213 7 0.1861 394.970 389.596 0.965 1.003 0.349 7.162-5.571 100.00 427 22 0.1832 296.403 290.375 0.933 1.003 0.263 5.546-4.326 100.00 867 58 0.1003 406.888 403.550 0.962 1.003 0.209 4.315-3.360 100.00 1859 96 0.0865 386.954 385.869 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1170 254.209 253.046 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1019 168.517 167.775 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1104 82.295 82.503 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.493 35.999 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.993 21.477 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0557 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN Total number of N/Q/H flips: 2 r_work=0.1222 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1454 | n_water=258 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1232 r_free=0.1454 | n_water=251 | time (s): 19.390 (total time: 21.200) Filter (q & B) r_work=0.1234 r_free=0.1453 | n_water=248 | time (s): 2.520 (total time: 23.720) Compute maps r_work=0.1234 r_free=0.1453 | n_water=248 | time (s): 1.680 (total time: 25.400) Filter (map) r_work=0.1247 r_free=0.1461 | n_water=227 | time (s): 2.920 (total time: 28.320) Find peaks r_work=0.1247 r_free=0.1461 | n_water=227 | time (s): 0.630 (total time: 28.950) Add new water r_work=0.1390 r_free=0.1625 | n_water=427 | time (s): 2.840 (total time: 31.790) Refine new water occ: r_work=0.1296 r_free=0.1489 adp: r_work=0.1219 r_free=0.1437 occ: r_work=0.1230 r_free=0.1419 adp: r_work=0.1198 r_free=0.1403 occ: r_work=0.1200 r_free=0.1397 adp: r_work=0.1192 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1395 r_work=0.1192 r_free=0.1395 | n_water=427 | time (s): 54.240 (total time: 86.030) Filter (q & B) r_work=0.1196 r_free=0.1397 | n_water=413 | time (s): 2.740 (total time: 88.770) Filter (dist only) r_work=0.1196 r_free=0.1395 | n_water=412 | time (s): 34.160 (total time: 122.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.918614 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.876158 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 0.1703 0.1807 0.0104 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1515 0.1645 0.0130 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1419 0.1570 0.0151 0.002 0.4 5.8 0.0 0.0 0 0.500 0.1347 0.1512 0.0165 0.001 0.5 4.5 0.0 0.0 0 0.750 0.1325 0.1499 0.0175 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1336 0.1512 0.0176 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1249 0.1443 0.0194 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1235 0.1443 0.0207 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1219 0.1427 0.0209 0.004 0.7 4.5 0.5 0.0 0 4.000 0.1207 0.1420 0.0213 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1205 0.1420 0.0215 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1202 0.1422 0.0219 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1198 0.1415 0.0217 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1196 0.1416 0.0221 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1191 0.1411 0.0221 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1189 0.1405 0.0216 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1187 0.1405 0.0218 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1186 0.1410 0.0224 0.008 0.9 5.4 0.5 0.6 0 13.959 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1405 0.0216 0.007 0.9 4.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 14.05 2.16 3.774 21.692 1485.876 0.016 11.89 14.05 2.16 3.774 21.692 44.576 0.016 11.89 14.05 2.16 3.774 21.692 185.735 0.016 12.08 14.45 2.37 3.623 21.698 742.938 0.015 12.09 14.73 2.64 3.554 21.756 1485.876 0.015 11.91 14.65 2.74 3.442 22.060 2228.814 0.015 11.81 14.61 2.80 3.488 21.860 2971.752 0.014 11.79 14.64 2.85 3.483 22.025 3714.690 0.014 11.80 14.72 2.92 3.509 22.092 4457.628 0.014 11.70 14.61 2.91 3.499 21.953 5200.567 0.014 11.70 14.69 2.99 3.548 22.106 5943.505 0.014 11.68 14.67 2.99 3.573 22.130 6686.443 0.014 11.68 14.68 3.00 3.578 22.093 7429.381 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: 185.735 Accepted refinement result: 11.89 14.05 2.16 3.774 21.692 185.735 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.02 22.04 3.31 185 1754 Protein: 9.09 115.02 17.01 3.32 0 1519 Water: 11.49 76.68 40.59 N/A 185 227 Other: 19.72 26.61 22.07 N/A 0 8 Chain A: 9.09 115.02 19.47 N/A 0 1754 Chain S: 17.38 60.00 46.43 N/A 185 0 Histogram: Values Number of atoms 9.09 - 19.68 1259 19.68 - 30.27 244 30.27 - 40.87 164 40.87 - 51.46 136 51.46 - 62.05 113 62.05 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1405 r_work=0.1189 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1405 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 = 0.1188 r_free = 0.1403 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1188 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015111 | | target function (ls_wunit_k1) not normalized (work): 1258.710251 | | target function (ls_wunit_k1) not normalized (free): 99.611830 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1188 0.1403 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1575 0.1575 0.1611 n_refl.: 87592 remove outliers: r(all,work,free)=0.1575 0.1575 0.1611 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1577 0.1577 0.1612 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1185 0.1397 n_refl.: 87592 remove outliers: r(all,work,free)=0.1194 0.1184 0.1397 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 0.3337 297.363 276.117 0.589 1.002 0.350 11.894-9.307 99.02 97 4 0.1651 482.921 473.433 0.913 1.003 0.330 9.237-7.194 100.00 213 7 0.1738 394.970 393.128 0.977 1.003 0.259 7.162-5.571 100.00 427 22 0.1581 296.403 291.963 0.937 1.003 0.224 5.546-4.326 100.00 867 58 0.0890 406.888 403.468 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0789 386.954 385.955 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1072 254.209 253.303 1.011 1.002 0.120 2.608-2.026 99.99 8198 413 0.1015 168.517 168.006 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1097 82.295 82.526 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.493 36.038 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.993 21.513 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=0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1397 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1397 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1397 | n_water=412 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1185 r_free=0.1400 | n_water=408 | time (s): 36.690 (total time: 38.590) Filter (q & B) r_work=0.1185 r_free=0.1400 | n_water=408 | time (s): 1.070 (total time: 39.660) Compute maps r_work=0.1185 r_free=0.1400 | n_water=408 | time (s): 1.810 (total time: 41.470) Filter (map) r_work=0.1227 r_free=0.1379 | n_water=281 | time (s): 3.100 (total time: 44.570) Find peaks r_work=0.1227 r_free=0.1379 | n_water=281 | time (s): 0.600 (total time: 45.170) Add new water r_work=0.1339 r_free=0.1484 | n_water=464 | time (s): 3.240 (total time: 48.410) Refine new water occ: r_work=0.1242 r_free=0.1404 adp: r_work=0.1243 r_free=0.1405 occ: r_work=0.1222 r_free=0.1389 adp: r_work=0.1220 r_free=0.1388 occ: r_work=0.1207 r_free=0.1380 adp: r_work=0.1200 r_free=0.1374 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1374 r_work=0.1200 r_free=0.1374 | n_water=464 | time (s): 190.070 (total time: 238.480) Filter (q & B) r_work=0.1204 r_free=0.1376 | n_water=434 | time (s): 3.070 (total time: 241.550) Filter (dist only) r_work=0.1204 r_free=0.1375 | n_water=433 | time (s): 34.840 (total time: 276.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780633 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.742268 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 0.1234 0.1354 0.0120 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1188 0.1323 0.0135 0.003 0.7 4.2 0.5 0.0 0 0.267 0.1170 0.1313 0.0143 0.004 0.8 3.5 0.5 0.0 0 0.534 0.1162 0.1310 0.0148 0.005 0.9 4.2 0.5 0.0 0 0.801 0.1158 0.1312 0.0154 0.006 1.0 3.8 0.5 0.0 0 1.068 0.1155 0.1310 0.0155 0.007 1.0 3.8 0.5 0.0 0 1.335 0.1152 0.1309 0.0158 0.007 1.1 4.5 0.5 0.0 0 1.603 0.1151 0.1307 0.0156 0.008 1.1 4.5 0.5 0.0 0 1.870 0.1160 0.1307 0.0148 0.006 0.9 3.8 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1307 0.0156 0.008 1.1 4.5 0.5 0.0 0 1.870 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.07 1.56 3.778 21.215 48.742 3.616 11.51 13.07 1.56 3.778 21.215 1.462 3.616 11.52 13.07 1.56 3.759 21.215 6.093 3.615 11.57 13.19 1.62 3.712 21.200 24.371 3.611 11.54 13.27 1.73 3.742 21.172 48.742 3.610 11.48 13.25 1.77 3.761 21.159 73.113 3.604 11.44 13.24 1.79 3.776 21.153 97.485 3.600 11.42 13.24 1.82 3.792 21.143 121.856 3.598 11.40 13.23 1.83 3.806 21.134 146.227 3.596 11.37 13.19 1.83 3.816 21.132 170.598 3.594 11.36 13.21 1.85 3.830 21.129 194.969 3.594 11.36 13.22 1.86 3.841 21.124 219.340 3.593 11.35 13.22 1.87 3.848 21.124 243.711 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.462 Accepted refinement result: 11.51 13.07 1.56 3.778 21.215 1.462 3.616 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.16 3.31 210 1750 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.50 76.69 35.65 N/A 210 223 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.10 115.03 19.42 N/A 0 1750 Chain S: 16.08 60.01 35.65 N/A 210 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 284 30.29 - 40.88 214 40.88 - 51.47 119 51.47 - 62.06 56 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1307 r_work=0.1151 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1307 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1310 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.13 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= 0.1144 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610178 | | target function (ml) not normalized (work): 300702.531345 | | target function (ml) not normalized (free): 15830.230889 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1310 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1483 0.1482 0.1534 n_refl.: 87589 remove outliers: r(all,work,free)=0.1483 0.1482 0.1534 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1482 0.1481 0.1533 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1302 n_refl.: 87589 remove outliers: r(all,work,free)=0.1146 0.1138 0.1302 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3824 294.086 263.420 0.488 1.001 0.302 11.894-9.307 97.06 95 4 0.2297 476.254 466.083 0.879 1.002 0.289 9.237-7.194 98.18 209 7 0.2245 386.443 388.062 0.956 1.002 0.205 7.162-5.571 100.00 427 22 0.2054 296.403 285.442 0.921 1.002 0.184 5.546-4.326 100.00 867 58 0.1086 406.888 402.078 0.965 1.002 0.170 4.315-3.360 100.00 1859 96 0.0928 386.954 384.685 1.006 1.002 0.170 3.356-2.611 100.00 3867 181 0.1132 254.209 252.096 1.008 1.002 0.090 2.608-2.026 99.99 8198 413 0.0931 168.517 167.767 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.295 82.581 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.493 36.076 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.993 21.532 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0108 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1302 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1138 r_free=0.1302 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1302 | n_water=433 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1138 r_free=0.1301 | n_water=431 | time (s): 48.180 (total time: 50.660) Filter (q & B) r_work=0.1139 r_free=0.1304 | n_water=428 | time (s): 4.010 (total time: 54.670) Compute maps r_work=0.1139 r_free=0.1304 | n_water=428 | time (s): 1.940 (total time: 56.610) Filter (map) r_work=0.1162 r_free=0.1302 | n_water=330 | time (s): 4.080 (total time: 60.690) Find peaks r_work=0.1162 r_free=0.1302 | n_water=330 | time (s): 0.730 (total time: 61.420) Add new water r_work=0.1229 r_free=0.1380 | n_water=483 | time (s): 3.990 (total time: 65.410) Refine new water occ: r_work=0.1163 r_free=0.1321 adp: r_work=0.1164 r_free=0.1323 occ: r_work=0.1148 r_free=0.1302 adp: r_work=0.1147 r_free=0.1305 occ: r_work=0.1135 r_free=0.1289 adp: r_work=0.1132 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1290 r_work=0.1132 r_free=0.1290 | n_water=483 | time (s): 234.810 (total time: 300.220) Filter (q & B) r_work=0.1140 r_free=0.1293 | n_water=444 | time (s): 4.100 (total time: 304.320) Filter (dist only) r_work=0.1148 r_free=0.1288 | n_water=441 | time (s): 46.670 (total time: 350.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784558 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.176432 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 0.1214 0.1328 0.0114 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1176 0.1307 0.0131 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1159 0.1300 0.0141 0.005 0.9 4.2 0.5 0.0 0 0.535 0.1153 0.1296 0.0144 0.006 1.0 4.2 0.5 0.0 0 0.803 0.1148 0.1296 0.0147 0.007 1.0 4.2 0.5 0.0 0 1.071 0.1145 0.1295 0.0149 0.007 1.1 3.8 0.5 0.0 0 1.338 0.1143 0.1296 0.0153 0.008 1.1 3.8 0.5 0.0 0 1.606 0.1141 0.1295 0.0154 0.009 1.1 3.8 0.5 0.0 0 1.874 0.1151 0.1298 0.0147 0.006 1.0 4.2 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1295 0.0149 0.007 1.1 3.8 0.5 0.0 0 1.338 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.95 1.49 3.779 21.176 35.176 3.609 11.45 12.95 1.49 3.779 21.176 1.055 3.609 11.45 12.95 1.49 3.779 21.176 4.397 3.609 11.50 12.98 1.49 3.705 21.171 17.588 3.606 11.52 13.07 1.55 3.725 21.156 35.176 3.607 11.52 13.15 1.63 3.738 21.135 52.765 3.606 11.44 13.10 1.66 3.758 21.132 70.353 3.600 11.40 13.09 1.69 3.769 21.128 87.941 3.597 11.39 13.10 1.70 3.775 21.127 105.529 3.596 11.37 13.08 1.71 3.786 21.121 123.118 3.593 11.35 13.07 1.72 3.797 21.118 140.706 3.592 11.35 13.10 1.75 3.810 21.111 158.294 3.593 11.34 13.09 1.75 3.817 21.108 175.882 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: 4.397 Accepted refinement result: 11.45 12.95 1.49 3.779 21.176 4.397 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.09 3.31 221 1747 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.49 76.68 35.09 N/A 221 220 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.10 115.03 19.38 N/A 0 1747 Chain S: 16.08 60.01 34.58 N/A 221 0 Histogram: Values Number of atoms 9.10 - 19.69 1265 19.69 - 30.28 295 30.28 - 40.87 211 40.87 - 51.47 130 51.47 - 62.06 45 62.06 - 72.65 11 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1295 r_work=0.1145 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1295 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1294 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607505 | | target function (ml) not normalized (work): 300451.016400 | | target function (ml) not normalized (free): 15816.771010 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1147 0.1140 0.1294 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1464 0.1463 0.1510 n_refl.: 87581 remove outliers: r(all,work,free)=0.1464 0.1463 0.1510 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1463 0.1462 0.1509 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1139 0.1295 n_refl.: 87581 remove outliers: r(all,work,free)=0.1145 0.1137 0.1295 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3944 288.560 251.176 0.462 1.000 0.314 11.894-9.307 95.10 93 4 0.2247 474.884 460.181 0.864 1.002 0.310 9.237-7.194 98.18 209 7 0.2348 386.443 379.722 0.926 1.002 0.190 7.162-5.571 100.00 427 22 0.2133 296.403 285.608 0.916 1.002 0.160 5.546-4.326 100.00 867 58 0.1122 406.888 401.864 0.964 1.002 0.150 4.315-3.360 100.00 1859 96 0.0920 386.954 384.839 1.006 1.002 0.140 3.356-2.611 100.00 3867 181 0.1125 254.209 252.341 1.010 1.002 0.090 2.608-2.026 99.99 8198 413 0.0920 168.517 167.948 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.295 82.638 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.493 36.104 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.993 21.547 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0109 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1295 After: r_work=0.1138 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1138 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=0.1138 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1295 | n_water=441 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1138 r_free=0.1295 | n_water=441 | time (s): 41.570 (total time: 44.070) Filter (q & B) r_work=0.1138 r_free=0.1296 | n_water=440 | time (s): 4.020 (total time: 48.090) Compute maps r_work=0.1138 r_free=0.1296 | n_water=440 | time (s): 1.910 (total time: 50.000) Filter (map) r_work=0.1161 r_free=0.1295 | n_water=350 | time (s): 3.920 (total time: 53.920) Find peaks r_work=0.1161 r_free=0.1295 | n_water=350 | time (s): 0.720 (total time: 54.640) Add new water r_work=0.1214 r_free=0.1343 | n_water=486 | time (s): 3.780 (total time: 58.420) Refine new water occ: r_work=0.1157 r_free=0.1292 adp: r_work=0.1157 r_free=0.1292 occ: r_work=0.1144 r_free=0.1287 adp: r_work=0.1143 r_free=0.1286 occ: r_work=0.1135 r_free=0.1283 adp: r_work=0.1131 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1281 r_work=0.1131 r_free=0.1281 | n_water=486 | time (s): 221.930 (total time: 280.350) Filter (q & B) r_work=0.1137 r_free=0.1287 | n_water=453 | time (s): 3.820 (total time: 284.170) Filter (dist only) r_work=0.1137 r_free=0.1286 | n_water=452 | time (s): 47.680 (total time: 331.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.834596 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.115872 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1337 0.0125 0.003 0.7 4.8 0.0 0.0 0 0.092 0.1164 0.1302 0.0138 0.004 0.8 3.8 0.5 0.0 0 0.275 0.1148 0.1291 0.0142 0.005 1.0 3.8 0.5 0.0 0 0.550 0.1142 0.1287 0.0145 0.006 1.0 3.8 0.5 0.0 0 0.826 0.1137 0.1286 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.101 0.1137 0.1286 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.376 0.1137 0.1286 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.651 0.1136 0.1285 0.0149 0.008 1.1 3.5 0.5 0.0 0 1.926 0.1140 0.1286 0.0146 0.007 1.0 3.5 0.5 0.0 0 0.917 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1285 0.0149 0.008 1.1 3.5 0.5 0.0 0 1.926 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.85 1.49 3.778 21.207 44.116 3.605 11.36 12.85 1.49 3.778 21.207 1.323 3.605 11.36 12.85 1.49 3.778 21.207 5.514 3.605 11.39 12.92 1.53 3.710 21.200 22.058 3.600 11.45 13.10 1.66 3.731 21.172 44.116 3.603 11.37 13.07 1.70 3.755 21.163 66.174 3.597 11.32 13.04 1.71 3.770 21.159 88.232 3.593 11.29 13.00 1.71 3.778 21.158 110.290 3.590 11.27 12.99 1.73 3.789 21.156 132.348 3.589 11.27 13.02 1.75 3.808 21.145 154.406 3.589 11.25 13.01 1.76 3.816 21.146 176.463 3.588 11.25 13.01 1.76 3.828 21.141 198.521 3.587 11.23 13.00 1.77 3.834 21.142 220.579 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: 1.323 Accepted refinement result: 11.36 12.85 1.49 3.778 21.207 1.323 3.605 Individual atomic B min max mean iso aniso Overall: 9.09 115.02 21.15 3.31 232 1747 Protein: 9.09 115.02 17.02 3.32 0 1519 Water: 11.49 76.68 35.03 N/A 232 220 Other: 19.72 26.61 22.07 N/A 0 8 Chain A: 9.09 115.02 19.38 N/A 0 1747 Chain S: 16.37 60.00 34.48 N/A 232 0 Histogram: Values Number of atoms 9.09 - 19.68 1265 19.68 - 30.28 300 30.28 - 40.87 218 40.87 - 51.46 128 51.46 - 62.06 46 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1285 r_work=0.1136 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1285 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1284 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603912 | | target function (ml) not normalized (work): 300133.799704 | | target function (ml) not normalized (free): 15802.243575 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1314 0.1318 5.6266 5.5736| | 2: 3.57 - 2.84 1.00 2888 124 0.1070 0.1366 5.1562 5.2061| | 3: 2.83 - 2.48 1.00 2820 163 0.1106 0.1280 4.9351 4.9898| | 4: 2.47 - 2.25 1.00 2825 136 0.0902 0.0964 4.6219 4.6454| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0918 4.5672 4.6097| | 6: 2.09 - 1.97 1.00 2846 113 0.0866 0.0989 4.262 4.3559| | 7: 1.97 - 1.87 1.00 2787 165 0.0891 0.1120 3.9829 4.1015| | 8: 1.87 - 1.79 1.00 2789 144 0.0924 0.1125 3.8936 3.9987| | 9: 1.79 - 1.72 1.00 2745 138 0.0884 0.1180 3.6532 3.8157| | 10: 1.72 - 1.66 1.00 2831 160 0.0924 0.1183 3.5701 3.7215| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1038 3.5015 3.5747| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1170 3.3366 3.4754| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1088 3.3137 3.4247| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1041 3.2454 3.3221| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1217 3.1583 3.26| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1255 3.1365 3.246| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1287 3.1209 3.2166| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1320 3.1037 3.2283| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1546 3.1126 3.2615| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1451 3.1137 3.1493| | 21: 1.32 - 1.30 1.00 2785 112 0.1475 0.1538 3.1149 3.1168| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.1978 3.1251 3.2898| | 23: 1.27 - 1.26 1.00 2802 156 0.1650 0.1789 3.1338 3.2012| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1825 3.1274 3.2258| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2136 3.1447 3.256| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1773 3.1474 3.2053| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2164 3.1723 3.1621| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2293 3.1666 3.1733| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2393 3.1483 3.2301| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2456 3.1436 3.168| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 8.30 1.00 0.97 5516.63| | 2: 3.57 - 2.84 2888 124 0.93 12.24 1.01 0.97 5516.63| | 3: 2.83 - 2.48 2820 163 0.90 16.16 0.99 0.97 4613.41| | 4: 2.47 - 2.25 2825 136 0.92 13.21 1.00 0.98 2284.30| | 5: 2.25 - 2.09 2756 127 0.91 15.26 1.01 0.98 2284.30| | 6: 2.09 - 1.97 2846 113 0.93 12.24 1.02 0.98 1328.45| | 7: 1.97 - 1.87 2787 165 0.95 9.30 1.02 0.98 513.24| | 8: 1.87 - 1.79 2789 144 0.93 12.67 0.99 0.98 513.24| | 9: 1.79 - 1.72 2745 138 0.94 10.15 0.98 0.97 292.00| | 10: 1.72 - 1.66 2831 160 0.94 11.18 0.98 0.97 247.69| | 11: 1.66 - 1.61 2712 147 0.93 11.82 0.98 0.97 237.34| | 12: 1.61 - 1.56 2773 144 0.95 8.99 0.99 0.97 139.68| | 13: 1.56 - 1.52 2745 130 0.95 10.52 1.03 0.97 139.68| | 14: 1.52 - 1.48 2803 134 0.94 10.88 1.02 0.98 125.07| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 98.31| | 16: 1.45 - 1.42 2756 161 0.94 11.12 1.02 0.98 98.31| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.98 89.09| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.76| | 19: 1.36 - 1.34 2807 134 0.94 11.84 0.99 0.98 83.76| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.97 79.70| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.96 79.41| | 22: 1.29 - 1.27 2704 152 0.93 13.59 0.98 0.96 79.82| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.94 81.93| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.94 81.93| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.01| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.32| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.32| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 90.13| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 91.56| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 91.56| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.41 max = 5516.63 mean = 858.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.84 mean = 13.40| |phase err.(test): min = 0.00 max = 88.44 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1133 0.1284 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1456 0.1455 0.1511 n_refl.: 87576 remove outliers: r(all,work,free)=0.1456 0.1455 0.1511 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1456 0.1454 0.1511 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1133 0.1287 n_refl.: 87576 remove outliers: r(all,work,free)=0.1140 0.1133 0.1287 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3950 288.560 247.870 0.456 1.000 0.310 11.894-9.307 94.12 92 4 0.2316 468.579 459.479 0.860 1.002 0.249 9.237-7.194 97.73 208 7 0.2284 387.527 380.592 0.933 1.002 0.190 7.162-5.571 100.00 427 22 0.2099 296.403 286.149 0.911 1.002 0.140 5.546-4.326 100.00 867 58 0.1112 406.888 401.928 0.963 1.002 0.130 4.315-3.360 100.00 1859 96 0.0921 386.954 384.877 1.005 1.002 0.130 3.356-2.611 100.00 3867 181 0.1114 254.209 252.323 1.010 1.002 0.070 2.608-2.026 99.99 8198 413 0.0915 168.517 167.868 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.295 82.618 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.493 36.096 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.993 21.541 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0076 ================= 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 : 0.2596 0.1934 0.081 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.000 1_settarget: 0.1618 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.000 1_nqh: 0.1619 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.003 1_weight: 0.1619 0.1756 0.081 5.286 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1221 0.1459 0.008 0.988 9.0 119.5 20.1 258 0.129 1_adp: 0.1228 0.1457 0.008 0.988 9.1 119.4 20.1 258 0.129 1_regHadp: 0.1230 0.1459 0.008 0.988 9.1 119.4 20.1 258 0.129 1_occ: 0.1224 0.1458 0.008 0.988 9.1 119.4 20.1 258 0.129 2_bss: 0.1222 0.1454 0.008 0.988 9.1 119.5 20.1 258 0.129 2_settarget: 0.1222 0.1454 0.008 0.988 9.1 119.5 20.1 258 0.129 2_updatecdl: 0.1222 0.1454 0.008 0.996 9.1 119.5 20.1 258 0.129 2_nqh: 0.1222 0.1454 0.008 0.996 9.1 119.5 20.1 258 0.129 2_sol: 0.1196 0.1395 0.008 0.996 9.1 115.0 22.0 412 n/a 2_weight: 0.1196 0.1395 0.008 0.996 9.1 115.0 22.0 412 n/a 2_xyzrec: 0.1189 0.1405 0.007 0.877 9.1 115.0 22.0 412 n/a 2_adp: 0.1189 0.1405 0.007 0.877 9.1 115.0 22.0 412 n/a 2_regHadp: 0.1189 0.1405 0.007 0.877 9.1 115.0 22.0 412 n/a 2_occ: 0.1188 0.1403 0.007 0.877 9.1 115.0 22.0 412 n/a 3_bss: 0.1184 0.1397 0.007 0.877 9.1 115.0 22.1 412 n/a 3_settarget: 0.1184 0.1397 0.007 0.877 9.1 115.0 22.1 412 n/a 3_updatecdl: 0.1184 0.1397 0.007 0.877 9.1 115.0 22.1 412 n/a 3_nqh: 0.1184 0.1397 0.007 0.877 9.1 115.0 22.1 412 n/a 3_sol: 0.1204 0.1375 0.007 0.877 9.1 115.0 21.2 433 n/a 3_weight: 0.1204 0.1375 0.007 0.877 9.1 115.0 21.2 433 n/a 3_xyzrec: 0.1151 0.1307 0.008 1.095 9.1 115.0 21.2 433 n/a 3_adp: 0.1151 0.1307 0.008 1.095 9.1 115.0 21.2 433 n/a 3_regHadp: 0.1151 0.1307 0.008 1.095 9.1 115.0 21.2 433 n/a 3_occ: 0.1144 0.1310 0.008 1.095 9.1 115.0 21.2 433 n/a 4_bss: 0.1138 0.1302 0.008 1.095 9.1 115.0 21.2 433 n/a 4_settarget: 0.1138 0.1302 0.008 1.095 9.1 115.0 21.2 433 n/a 4_updatecdl: 0.1138 0.1302 0.008 1.097 9.1 115.0 21.2 433 n/a 4_nqh: 0.1138 0.1302 0.008 1.097 9.1 115.0 21.2 433 n/a 4_sol: 0.1148 0.1288 0.008 1.097 9.1 115.0 21.1 441 n/a 4_weight: 0.1148 0.1288 0.008 1.097 9.1 115.0 21.1 441 n/a 4_xyzrec: 0.1145 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 4_adp: 0.1145 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 4_regHadp: 0.1145 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 4_occ: 0.1140 0.1294 0.007 1.058 9.1 115.0 21.1 441 n/a 5_bss: 0.1137 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 5_settarget: 0.1137 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 5_updatecdl: 0.1137 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 5_setrh: 0.1138 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 5_nqh: 0.1138 0.1295 0.007 1.058 9.1 115.0 21.1 441 n/a 5_sol: 0.1137 0.1286 0.007 1.058 9.1 115.0 21.2 452 n/a 5_weight: 0.1137 0.1286 0.007 1.058 9.1 115.0 21.2 452 n/a 5_xyzrec: 0.1136 0.1285 0.008 1.095 9.1 115.0 21.2 452 n/a 5_adp: 0.1136 0.1285 0.008 1.095 9.1 115.0 21.2 452 n/a 5_regHadp: 0.1136 0.1285 0.008 1.095 9.1 115.0 21.2 452 n/a 5_occ: 0.1133 0.1284 0.008 1.095 9.1 115.0 21.2 452 n/a end: 0.1133 0.1287 0.008 1.095 9.1 115.0 21.1 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3025539_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3025539_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9700 Refinement macro-cycles (run) : 14364.1800 Write final files (write_after_run_outputs) : 66.7800 Total : 14433.9300 Total CPU time: 4.02 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:42 PST -0800 (1735366842.95 s) Start R-work = 0.1618, R-free = 0.1756 Final R-work = 0.1133, R-free = 0.1287 =============================================================================== Job complete usr+sys time: 14568.08 seconds wall clock time: 264 minutes 5.37 seconds (15845.37 seconds total)