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_2348261.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.47, per 1000 atoms: 0.43 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: 0.55 Conformation dependent library (CDL) restraints added in 206.3 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 609 0.93 - 1.19: 1053 1.19 - 1.45: 737 1.45 - 1.72: 738 1.72 - 1.98: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALYS A 175 " pdb=" CA ALYS A 175 " ideal model delta sigma weight residual 1.459 1.219 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.19e-02 7.06e+03 3.67e+02 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.695 -0.236 1.27e-02 6.20e+03 3.46e+02 bond pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 1.237 1.440 -0.203 1.19e-02 7.06e+03 2.91e+02 bond pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 1.524 1.305 0.218 1.30e-02 5.92e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3308 4.89 - 9.78: 1855 9.78 - 14.67: 527 14.67 - 19.56: 82 19.56 - 24.45: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.50 132.51 -18.01 1.16e+00 7.43e-01 2.41e+02 angle pdb=" O AASN A 76 " pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.12 105.97 16.15 1.06e+00 8.90e-01 2.32e+02 angle pdb=" O PRO A 54 " pdb=" C PRO A 54 " pdb=" N ASP A 55 " ideal model delta sigma weight residual 123.00 105.52 17.48 1.22e+00 6.72e-01 2.05e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 109.37 13.23 1.00e+00 1.00e+00 1.75e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.24: 927 16.24 - 32.48: 119 32.48 - 48.72: 43 48.72 - 64.95: 18 64.95 - 81.19: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+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 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+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 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 104 0.207 - 0.414: 74 0.414 - 0.620: 38 0.620 - 0.827: 23 0.827 - 1.034: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.49 -1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.058 9.50e-02 1.11e+02 7.06e-02 1.04e+02 pdb=" NE ARG A 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.107 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.053 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.115 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.014 2.00e-02 2.50e+03 5.76e-02 9.94e+01 pdb=" CG TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.091 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 664 2.26 - 2.84: 7701 2.84 - 3.43: 10651 3.43 - 4.01: 15373 4.01 - 4.60: 22153 Nonbonded interactions: 56542 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.670 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.756 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.809 1.850 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.845 2.270 -y,x-y-1,z+1/3 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.847 1.850 ... (remaining 56537 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_2348261_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= 0.2611 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.800356 | | target function (ml) not normalized (work): 233286.478146 | | target function (ml) not normalized (free): 11851.840274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3040 0.2038 7.0933 4.9424| | 2: 3.57 - 2.84 1.00 2876 122 0.2422 0.1719 4.3459 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2390 0.1630 4.123 4.1593| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1532 3.83 3.8326| | 5: 2.25 - 2.09 1.00 2756 127 0.2443 0.1518 3.7948 3.8165| | 6: 2.09 - 1.97 1.00 2846 113 0.2563 0.1847 3.4719 3.6129| | 7: 1.97 - 1.87 1.00 2787 165 0.2539 0.1773 3.1457 3.1964| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1798 3.076 3.1244| | 9: 1.79 - 1.72 1.00 2745 138 0.2406 0.1943 2.906 2.9608| | 10: 1.72 - 1.66 1.00 2789 158 0.2428 0.2164 2.8104 2.9544| | 11: 1.66 - 1.61 1.00 2740 147 0.2536 0.2003 2.7685 2.818| | 12: 1.61 - 1.56 1.00 2787 146 0.2519 0.1922 2.6538 2.6543| | 13: 1.56 - 1.52 1.00 2745 130 0.2567 0.1986 2.5933 2.6528| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.2107 2.5212 2.5854| | 15: 1.48 - 1.45 1.00 2738 128 0.2565 0.2050 2.4364 2.474| | 16: 1.45 - 1.42 1.00 2756 161 0.2625 0.2037 2.3839 2.4323| | 17: 1.42 - 1.39 1.00 2785 139 0.2657 0.2299 2.3394 2.4508| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2270 2.2919 2.363| | 19: 1.36 - 1.34 1.00 2807 134 0.2603 0.2178 2.2606 2.2397| | 20: 1.34 - 1.32 1.00 2696 147 0.2716 0.2078 2.2065 2.1603| | 21: 1.32 - 1.30 1.00 2785 112 0.2689 0.2319 2.1732 2.196| | 22: 1.29 - 1.27 1.00 2704 152 0.2812 0.2596 2.167 2.1942| | 23: 1.27 - 1.26 1.00 2802 156 0.2819 0.2426 2.1136 2.1663| | 24: 1.26 - 1.24 1.00 2744 132 0.2812 0.2676 2.09 2.2197| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2237 2.0495 1.9864| | 26: 1.22 - 1.21 1.00 2727 135 0.2907 0.2065 2.0122 2.0294| | 27: 1.21 - 1.19 1.00 2814 148 0.3007 0.2744 2.0185 2.0119| | 28: 1.19 - 1.18 1.00 2671 147 0.2978 0.2777 1.9922 1.9958| | 29: 1.18 - 1.16 1.00 2800 134 0.2921 0.2802 1.9533 2.0707| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.3048 1.9324 1.9926| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.77 0.76 0.23 1460.83| | 2: 3.57 - 2.84 2876 122 0.81 25.82 1.27 0.23 1460.83| | 3: 2.84 - 2.48 2833 165 0.74 32.03 1.25 0.24 1212.28| | 4: 2.47 - 2.25 2825 136 0.81 25.38 1.26 0.25 567.26| | 5: 2.25 - 2.09 2756 127 0.77 29.13 1.28 0.25 567.26| | 6: 2.09 - 1.97 2846 113 0.83 22.81 1.29 0.25 312.52| | 7: 1.97 - 1.87 2787 165 0.90 17.04 1.28 0.26 95.27| | 8: 1.87 - 1.79 2789 144 0.85 21.46 1.24 0.26 95.27| | 9: 1.79 - 1.72 2745 138 0.88 19.01 1.23 0.25 58.36| | 10: 1.72 - 1.66 2789 158 0.86 21.16 1.23 0.25 50.97| | 11: 1.66 - 1.61 2740 147 0.85 22.10 1.24 0.25 49.22| | 12: 1.61 - 1.56 2787 146 0.88 19.18 1.23 0.25 31.39| | 13: 1.56 - 1.52 2745 130 0.86 21.45 1.24 0.25 31.39| | 14: 1.52 - 1.48 2803 134 0.86 21.46 1.24 0.25 27.86| | 15: 1.48 - 1.45 2738 128 0.86 20.69 1.23 0.25 21.39| | 16: 1.45 - 1.42 2756 161 0.85 22.16 1.24 0.25 21.39| | 17: 1.42 - 1.39 2785 139 0.86 21.18 1.22 0.25 18.10| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.22 0.25 16.20| | 19: 1.36 - 1.34 2807 134 0.85 22.06 1.20 0.25 16.20| | 20: 1.34 - 1.32 2696 147 0.86 21.15 1.21 0.24 12.89| | 21: 1.32 - 1.30 2785 112 0.86 21.67 1.20 0.24 12.66| | 22: 1.29 - 1.27 2704 152 0.85 22.36 1.21 0.24 12.38| | 23: 1.27 - 1.26 2802 156 0.86 21.87 1.22 0.24 10.96| | 24: 1.26 - 1.24 2744 132 0.85 22.38 1.21 0.24 10.96| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.21 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.84 24.09 1.21 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.68 1.20 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.82 25.70 1.18 0.23 9.60| | 29: 1.18 - 1.16 2800 134 0.82 26.30 1.15 0.22 9.49| | 30: 1.16 - 1.15 2740 148 0.80 27.94 1.15 0.22 9.49| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.49 max = 1460.83 mean = 213.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.89| |phase err.(test): min = 0.00 max = 89.40 mean = 22.66| |-----------------------------------------------------------------------------| ----------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 0.258 1557 Z= 5.390 Angle : 5.224 18.008 2118 Z= 3.706 Chirality : 0.371 1.034 243 Planarity : 0.032 0.089 284 Dihedral : 13.767 81.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 29.19 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.25 (0.49), residues: 224 helix: -2.33 (0.41), residues: 102 sheet: -1.05 (0.91), residues: 28 loop : -0.30 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.028 ARG A 27 TYR 0.107 0.036 TYR A 141 PHE 0.121 0.037 PHE A 164 HIS 0.065 0.033 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= 0.2611 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.800356 | | target function (ml) not normalized (work): 233286.478146 | | target function (ml) not normalized (free): 11851.840274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2611 0.1934 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2611 0.1934 n_refl.: 87602 remove outliers: r(all,work,free)=0.1984 0.1989 0.1934 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2009 0.2015 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1653 0.1647 0.1766 n_refl.: 87594 remove outliers: r(all,work,free)=0.1652 0.1646 0.1766 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 97.87 87 5 0.3776 389.396 355.160 0.671 1.004 0.411 11.894-9.307 99.02 97 4 0.1913 613.345 590.540 0.924 1.004 0.376 9.237-7.194 100.00 213 7 0.2121 501.641 490.186 0.953 1.004 0.356 7.162-5.571 100.00 427 22 0.2200 376.454 364.667 0.932 1.004 0.310 5.546-4.326 100.00 867 58 0.1303 516.778 511.207 0.963 1.004 0.233 4.315-3.360 100.00 1859 96 0.1144 491.459 487.162 1.005 1.003 0.217 3.356-2.611 100.00 3867 181 0.1436 322.863 319.756 0.997 1.002 0.033 2.608-2.026 99.99 8198 413 0.1338 214.029 211.903 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1666 104.521 103.844 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2099 46.349 45.044 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2604 29.203 26.946 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0496 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1766 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1651 r_free=0.1769 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.838730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.147206 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 0.1752 0.1871 0.0119 0.002 0.4 5.4 0.0 0.0 0 0.125 0.1574 0.1715 0.0140 0.002 0.4 4.8 0.0 0.0 0 0.250 0.1446 0.1614 0.0167 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1395 0.1588 0.0193 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1351 0.1555 0.0204 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1362 0.1571 0.0209 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1304 0.1527 0.0223 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1276 0.1503 0.0227 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1262 0.1492 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1251 0.1482 0.0231 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1248 0.1480 0.0233 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1241 0.1474 0.0233 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1239 0.1476 0.0237 0.005 0.8 2.9 0.5 0.0 0 8.000 0.1233 0.1471 0.0238 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1232 0.1470 0.0238 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1473 0.0245 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1228 0.1476 0.0248 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1225 0.1480 0.0255 0.008 1.0 3.8 0.5 0.0 0 13.419 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1470 0.0238 0.006 0.9 3.8 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.70 2.38 3.013 19.074 1992.147 0.017 12.32 14.69 2.38 2.992 19.074 59.764 0.017 12.38 14.65 2.27 2.668 19.073 249.018 0.017 12.69 15.29 2.61 2.735 19.231 996.074 0.017 12.55 15.47 2.92 3.213 19.569 1992.147 0.016 12.46 15.45 3.00 3.112 19.514 2988.221 0.015 12.41 15.51 3.09 3.394 19.669 3984.294 0.015 12.31 15.44 3.13 3.330 19.626 4980.368 0.015 12.27 15.42 3.15 3.320 19.614 5976.442 0.015 12.21 15.39 3.18 3.333 19.615 6972.515 0.015 12.20 15.41 3.21 3.376 19.630 7968.589 0.015 12.17 15.42 3.25 3.429 19.646 8964.662 0.015 12.18 15.46 3.28 3.471 19.657 9960.736 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: 249.018 Accepted refinement result: 12.38 14.65 2.27 2.668 19.073 249.018 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.46 20.10 3.31 0 1785 Protein: 9.07 115.01 17.01 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.74 26.61 22.07 N/A 0 8 Chain A: 9.07 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1465 r_work=0.1239 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1469 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 = 0.1232 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016923 | | target function (ls_wunit_k1) not normalized (work): 1409.610965 | | target function (ls_wunit_k1) not normalized (free): 109.335522 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1460 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1689 n_refl.: 87592 remove outliers: r(all,work,free)=0.1673 0.1674 0.1689 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1679 0.1680 0.1693 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1229 0.1450 n_refl.: 87592 remove outliers: r(all,work,free)=0.1239 0.1229 0.1450 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 0.3476 306.312 285.378 0.674 1.002 0.393 11.894-9.307 99.02 97 4 0.1648 482.478 470.819 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.1914 394.608 388.102 0.964 1.003 0.340 7.162-5.571 100.00 427 22 0.1812 296.131 290.680 0.939 1.003 0.300 5.546-4.326 100.00 867 58 0.0998 406.515 403.650 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0874 386.599 385.468 1.008 1.002 0.190 3.356-2.611 100.00 3867 181 0.1180 253.975 252.794 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1021 168.362 167.649 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.219 82.405 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.459 35.964 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.972 21.454 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0462 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1450 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 80 GLN B A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1227 r_free=0.1449 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1449 | n_water=258 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1235 r_free=0.1448 | n_water=253 | time (s): 21.870 (total time: 23.500) Filter (q & B) r_work=0.1237 r_free=0.1448 | n_water=250 | time (s): 2.360 (total time: 25.860) Compute maps r_work=0.1237 r_free=0.1448 | n_water=250 | time (s): 1.260 (total time: 27.120) Filter (map) r_work=0.1254 r_free=0.1452 | n_water=225 | time (s): 3.160 (total time: 30.280) Find peaks r_work=0.1254 r_free=0.1452 | n_water=225 | time (s): 0.550 (total time: 30.830) Add new water r_work=0.1411 r_free=0.1647 | n_water=434 | time (s): 2.360 (total time: 33.190) Refine new water occ: r_work=0.1321 r_free=0.1501 adp: r_work=0.1232 r_free=0.1440 occ: r_work=0.1246 r_free=0.1430 adp: r_work=0.1209 r_free=0.1412 occ: r_work=0.1211 r_free=0.1399 adp: r_work=0.1201 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1399 r_work=0.1201 r_free=0.1399 | n_water=434 | time (s): 59.000 (total time: 92.190) Filter (q & B) r_work=0.1203 r_free=0.1402 | n_water=421 | time (s): 3.240 (total time: 95.430) Filter (dist only) r_work=0.1203 r_free=0.1400 | n_water=420 | time (s): 37.010 (total time: 132.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.943016 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1488.391877 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 0.1647 0.1761 0.0114 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1546 0.1675 0.0128 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1391 0.1547 0.0157 0.002 0.4 5.8 0.0 0.0 0 0.500 0.1356 0.1524 0.0169 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1316 0.1498 0.0182 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1325 0.1508 0.0182 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1259 0.1463 0.0203 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1230 0.1448 0.0219 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1219 0.1441 0.0222 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1213 0.1438 0.0225 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1206 0.1438 0.0231 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1196 0.1426 0.0230 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1198 0.1432 0.0234 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1192 0.1436 0.0244 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1190 0.1432 0.0242 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1186 0.1431 0.0245 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1183 0.1432 0.0249 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1184 0.1438 0.0253 0.008 0.9 5.8 0.5 0.0 0 13.472 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1426 0.0230 0.005 0.8 4.2 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.26 2.30 3.777 21.862 1488.392 0.016 11.96 14.26 2.30 3.777 21.862 44.652 0.016 11.96 14.26 2.30 3.777 21.862 186.049 0.016 12.09 14.58 2.49 3.642 21.857 744.196 0.015 12.17 15.05 2.87 3.462 22.172 1488.392 0.015 12.02 14.99 2.97 3.466 22.061 2232.588 0.014 11.91 14.96 3.04 3.505 22.014 2976.784 0.014 11.79 14.87 3.08 3.565 21.952 3720.980 0.014 11.77 14.89 3.13 3.527 22.026 4465.176 0.014 11.78 14.86 3.08 3.517 22.161 5209.372 0.014 11.74 14.94 3.20 3.545 22.227 5953.568 0.014 11.75 14.91 3.17 3.561 22.211 6697.763 0.014 11.71 14.91 3.20 3.573 22.210 7441.959 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: 186.049 Accepted refinement result: 11.96 14.26 2.30 3.777 21.862 186.049 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 22.33 3.31 195 1752 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 41.46 N/A 195 225 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.10 115.04 19.46 N/A 0 1752 Chain S: 15.93 60.00 48.06 N/A 195 0 Histogram: Values Number of atoms 9.10 - 19.70 1259 19.70 - 30.29 244 30.29 - 40.88 162 40.88 - 51.48 125 51.48 - 62.07 134 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1426 r_work=0.1196 r_free=0.1426 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1426 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1423 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= 0.1197 r_free= 0.1423 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015281 | | target function (ls_wunit_k1) not normalized (work): 1272.812438 | | target function (ls_wunit_k1) not normalized (free): 104.787168 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1197 0.1423 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1596 0.1595 0.1646 n_refl.: 87592 remove outliers: r(all,work,free)=0.1596 0.1595 0.1646 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1597 0.1596 0.1647 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1195 0.1415 n_refl.: 87592 remove outliers: r(all,work,free)=0.1204 0.1193 0.1415 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 0.3241 302.345 275.516 0.607 1.003 0.350 11.894-9.307 99.02 97 4 0.1603 482.478 478.250 0.926 1.003 0.333 9.237-7.194 100.00 213 7 0.1771 394.608 392.909 0.982 1.003 0.280 7.162-5.571 100.00 427 22 0.1637 296.131 291.650 0.936 1.003 0.270 5.546-4.326 100.00 867 58 0.0902 406.515 403.639 0.961 1.003 0.200 4.315-3.360 100.00 1859 96 0.0791 386.599 385.648 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1095 253.975 252.958 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1020 168.362 167.747 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.219 82.411 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.459 35.989 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.972 21.488 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=0.0082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1415 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=0.1193 r_free=0.1415 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1415 | n_water=420 | time (s): 1.490 (total time: 1.490) Filter (dist) r_work=0.1193 r_free=0.1414 | n_water=416 | time (s): 36.410 (total time: 37.900) Filter (q & B) r_work=0.1193 r_free=0.1414 | n_water=416 | time (s): 1.030 (total time: 38.930) Compute maps r_work=0.1193 r_free=0.1414 | n_water=416 | time (s): 1.660 (total time: 40.590) Filter (map) r_work=0.1236 r_free=0.1396 | n_water=285 | time (s): 3.280 (total time: 43.870) Find peaks r_work=0.1236 r_free=0.1396 | n_water=285 | time (s): 0.520 (total time: 44.390) Add new water r_work=0.1358 r_free=0.1535 | n_water=469 | time (s): 2.500 (total time: 46.890) Refine new water occ: r_work=0.1262 r_free=0.1444 adp: r_work=0.1263 r_free=0.1446 occ: r_work=0.1240 r_free=0.1419 adp: r_work=0.1239 r_free=0.1422 occ: r_work=0.1222 r_free=0.1395 adp: r_work=0.1216 r_free=0.1396 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1396 r_work=0.1216 r_free=0.1396 | n_water=469 | time (s): 141.070 (total time: 187.960) Filter (q & B) r_work=0.1221 r_free=0.1406 | n_water=441 | time (s): 3.490 (total time: 191.450) Filter (dist only) r_work=0.1221 r_free=0.1404 | n_water=440 | time (s): 38.110 (total time: 229.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.750660 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.072217 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 0.1235 0.1370 0.0134 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1196 0.1342 0.0147 0.003 0.7 4.2 0.5 0.0 0 0.263 0.1179 0.1332 0.0153 0.004 0.8 3.5 0.5 0.0 0 0.525 0.1171 0.1328 0.0157 0.005 0.9 3.8 0.5 0.0 0 0.788 0.1168 0.1327 0.0159 0.006 1.0 3.8 0.5 0.0 0 1.050 0.1164 0.1327 0.0163 0.007 1.0 3.8 0.5 0.0 0 1.313 0.1162 0.1328 0.0166 0.007 1.1 3.8 0.5 0.0 0 1.576 0.1160 0.1326 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.838 0.1169 0.1329 0.0160 0.005 0.9 3.8 0.5 0.0 0 0.875 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1326 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.26 1.66 3.779 21.283 44.072 3.619 11.60 13.26 1.66 3.779 21.283 1.322 3.619 11.60 13.26 1.66 3.777 21.283 5.509 3.619 11.67 13.36 1.69 3.711 21.269 22.036 3.614 11.70 13.46 1.76 3.730 21.239 44.072 3.615 11.61 13.41 1.80 3.756 21.230 66.108 3.608 11.56 13.38 1.82 3.767 21.224 88.144 3.604 11.53 13.38 1.84 3.779 21.216 110.181 3.601 11.50 13.36 1.85 3.790 21.212 132.217 3.598 11.53 13.41 1.88 3.808 21.192 154.253 3.599 11.48 13.36 1.88 3.814 21.197 176.289 3.596 11.48 13.37 1.89 3.827 21.189 198.325 3.596 11.47 13.36 1.89 3.832 21.192 220.361 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.322 Accepted refinement result: 11.60 13.26 1.66 3.779 21.283 1.322 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.27 3.31 218 1749 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.52 76.71 35.83 N/A 218 222 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.11 115.04 19.42 N/A 0 1749 Chain S: 15.73 60.00 36.07 N/A 218 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 286 30.29 - 40.89 209 40.89 - 51.48 129 51.48 - 62.07 56 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1326 r_work=0.1160 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1326 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1313 target_work(ml) = 3.612 | | 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= 0.1147 r_free= 0.1313 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612046 | | target function (ml) not normalized (work): 300858.179518 | | target function (ml) not normalized (free): 15851.912741 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1147 0.1313 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1492 0.1493 0.1514 n_refl.: 87589 remove outliers: r(all,work,free)=0.1492 0.1493 0.1514 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1491 0.1491 0.1513 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1142 0.1309 n_refl.: 87589 remove outliers: r(all,work,free)=0.1147 0.1139 0.1309 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 0.3948 294.224 271.895 0.490 1.000 0.298 11.894-9.307 97.06 95 4 0.2304 482.702 461.841 0.871 1.001 0.282 9.237-7.194 98.18 209 7 0.2265 386.088 385.690 0.943 1.002 0.214 7.162-5.571 100.00 427 22 0.2083 296.131 284.444 0.913 1.002 0.186 5.546-4.326 100.00 867 58 0.1124 406.515 401.440 0.952 1.002 0.150 4.315-3.360 100.00 1859 96 0.0922 386.599 383.875 0.995 1.002 0.140 3.356-2.611 100.00 3867 181 0.1133 253.975 252.034 0.999 1.002 0.080 2.608-2.026 99.99 8198 413 0.0926 168.362 167.610 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.219 82.519 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.459 36.049 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 22.972 21.518 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1309 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=0.1139 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1309 | n_water=440 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1141 r_free=0.1308 | n_water=438 | time (s): 48.440 (total time: 50.850) Filter (q & B) r_work=0.1141 r_free=0.1311 | n_water=436 | time (s): 3.760 (total time: 54.610) Compute maps r_work=0.1141 r_free=0.1311 | n_water=436 | time (s): 1.860 (total time: 56.470) Filter (map) r_work=0.1163 r_free=0.1318 | n_water=324 | time (s): 3.880 (total time: 60.350) Find peaks r_work=0.1163 r_free=0.1318 | n_water=324 | time (s): 0.690 (total time: 61.040) Add new water r_work=0.1232 r_free=0.1399 | n_water=487 | time (s): 3.730 (total time: 64.770) Refine new water occ: r_work=0.1166 r_free=0.1326 adp: r_work=0.1167 r_free=0.1329 occ: r_work=0.1151 r_free=0.1308 adp: r_work=0.1151 r_free=0.1309 occ: r_work=0.1140 r_free=0.1298 adp: r_work=0.1136 r_free=0.1296 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1296 r_work=0.1136 r_free=0.1296 | n_water=487 | time (s): 271.330 (total time: 336.100) Filter (q & B) r_work=0.1142 r_free=0.1309 | n_water=452 | time (s): 3.660 (total time: 339.760) Filter (dist only) r_work=0.1143 r_free=0.1308 | n_water=450 | time (s): 46.910 (total time: 386.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784448 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.747795 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 0.1206 0.1344 0.0138 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1171 0.1324 0.0153 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1156 0.1316 0.0160 0.005 0.9 3.8 0.5 0.0 0 0.535 0.1150 0.1315 0.0165 0.005 0.9 3.8 0.5 0.0 0 0.803 0.1146 0.1313 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.071 0.1143 0.1310 0.0167 0.007 1.1 3.8 0.5 0.0 0 1.338 0.1141 0.1311 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.606 0.1139 0.1308 0.0169 0.009 1.1 4.2 0.5 0.0 0 1.874 0.1148 0.1312 0.0164 0.006 1.0 3.8 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1308 0.0169 0.009 1.1 4.2 0.5 0.0 0 1.874 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 13.08 1.69 3.780 21.235 34.748 3.607 11.39 13.08 1.69 3.780 21.235 1.042 3.607 11.39 13.08 1.69 3.780 21.235 4.343 3.607 11.44 13.13 1.69 3.709 21.228 17.374 3.603 11.48 13.23 1.75 3.731 21.207 34.748 3.603 11.44 13.24 1.80 3.750 21.191 52.122 3.600 11.41 13.25 1.85 3.765 21.184 69.496 3.597 11.37 13.22 1.85 3.775 21.180 86.869 3.593 11.36 13.21 1.85 3.783 21.172 104.243 3.592 11.33 13.18 1.85 3.791 21.174 121.617 3.590 11.32 13.19 1.87 3.802 21.168 138.991 3.589 11.31 13.18 1.88 3.810 21.166 156.365 3.588 11.31 13.20 1.89 3.822 21.157 173.739 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.042 Accepted refinement result: 11.39 13.08 1.69 3.780 21.235 1.042 3.607 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.18 3.31 229 1748 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 35.17 N/A 229 221 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.10 115.04 19.41 N/A 0 1748 Chain S: 15.72 60.00 34.73 N/A 229 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 295 30.29 - 40.88 222 40.88 - 51.47 123 51.47 - 62.07 50 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1308 r_work=0.1139 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1308 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1305 target_work(ml) = 3.604 | | 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.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1305 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604276 | | target function (ml) not normalized (work): 300182.139912 | | target function (ml) not normalized (free): 15822.052212 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1136 0.1305 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1474 0.1474 0.1506 n_refl.: 87581 remove outliers: r(all,work,free)=0.1474 0.1474 0.1506 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1473 0.1472 0.1505 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1305 n_refl.: 87581 remove outliers: r(all,work,free)=0.1141 0.1133 0.1305 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4002 293.064 256.182 0.438 0.999 0.286 11.894-9.307 96.08 94 4 0.2584 475.848 464.432 0.855 1.001 0.224 9.237-7.194 98.18 209 7 0.2433 386.088 377.040 0.912 1.002 0.175 7.162-5.571 100.00 427 22 0.2213 296.131 284.026 0.906 1.002 0.154 5.546-4.326 100.00 867 58 0.1148 406.515 402.040 0.953 1.002 0.123 4.315-3.360 100.00 1859 96 0.0915 386.599 384.259 0.994 1.002 0.107 3.356-2.611 100.00 3867 181 0.1104 253.975 252.009 1.001 1.002 0.070 2.608-2.026 99.99 8198 413 0.0911 168.362 167.706 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.219 82.561 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.459 36.066 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 22.972 21.521 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1305 After: r_work=0.1135 r_free=0.1305 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1305 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=0.1135 r_free=0.1305 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1305 | n_water=450 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1135 r_free=0.1305 | n_water=450 | time (s): 43.600 (total time: 45.910) Filter (q & B) r_work=0.1135 r_free=0.1305 | n_water=450 | time (s): 1.350 (total time: 47.260) Compute maps r_work=0.1135 r_free=0.1305 | n_water=450 | time (s): 1.840 (total time: 49.100) Filter (map) r_work=0.1163 r_free=0.1318 | n_water=340 | time (s): 3.710 (total time: 52.810) Find peaks r_work=0.1163 r_free=0.1318 | n_water=340 | time (s): 0.670 (total time: 53.480) Add new water r_work=0.1207 r_free=0.1365 | n_water=480 | time (s): 3.520 (total time: 57.000) Refine new water occ: r_work=0.1155 r_free=0.1304 adp: r_work=0.1155 r_free=0.1308 occ: r_work=0.1144 r_free=0.1290 adp: r_work=0.1142 r_free=0.1294 occ: r_work=0.1135 r_free=0.1281 adp: r_work=0.1132 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1283 r_work=0.1132 r_free=0.1283 | n_water=480 | time (s): 186.350 (total time: 243.350) Filter (q & B) r_work=0.1138 r_free=0.1293 | n_water=443 | time (s): 3.720 (total time: 247.070) Filter (dist only) r_work=0.1138 r_free=0.1292 | n_water=442 | time (s): 45.880 (total time: 292.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.692385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.748106 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 0.1238 0.1356 0.0118 0.003 0.7 7.4 0.5 0.0 0 0.085 0.1184 0.1319 0.0135 0.004 0.8 6.4 0.0 0.0 0 0.254 0.1161 0.1306 0.0145 0.005 0.9 5.8 0.5 0.0 0 0.508 0.1154 0.1303 0.0149 0.006 1.0 5.8 0.5 0.0 0 0.762 0.1148 0.1298 0.0150 0.006 1.0 5.4 0.5 0.0 0 1.015 0.1143 0.1294 0.0151 0.007 1.1 5.8 0.5 0.0 0 1.269 0.1140 0.1292 0.0152 0.008 1.1 5.4 0.5 0.0 0 1.523 0.1138 0.1291 0.0153 0.008 1.1 5.4 0.5 0.0 0 1.777 0.1150 0.1300 0.0149 0.006 1.0 5.4 0.5 0.0 0 0.846 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1291 0.0153 0.008 1.1 5.4 0.5 0.0 0 1.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 12.91 1.53 3.779 21.139 43.748 3.603 11.38 12.91 1.53 3.779 21.139 1.312 3.603 11.38 12.92 1.53 3.772 21.139 5.469 3.603 11.40 12.95 1.55 3.716 21.130 21.874 3.597 11.42 13.05 1.63 3.741 21.106 43.748 3.598 11.40 13.10 1.70 3.761 21.088 65.622 3.595 11.36 13.08 1.72 3.775 21.084 87.496 3.591 11.32 13.05 1.73 3.786 21.082 109.370 3.588 11.31 13.04 1.74 3.799 21.074 131.244 3.586 11.29 13.03 1.75 3.810 21.070 153.118 3.584 11.28 13.03 1.75 3.823 21.062 174.992 3.583 11.27 13.02 1.75 3.832 21.060 196.866 3.582 11.25 13.02 1.77 3.835 21.062 218.741 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.312 Accepted refinement result: 11.38 12.91 1.53 3.779 21.139 1.312 3.603 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.02 3.31 223 1746 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.50 76.69 34.70 N/A 223 219 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.09 115.03 19.36 N/A 0 1746 Chain S: 15.92 59.99 33.95 N/A 223 0 Histogram: Values Number of atoms 9.09 - 19.69 1264 19.69 - 30.28 301 30.28 - 40.87 217 40.87 - 51.47 118 51.47 - 62.06 46 62.06 - 72.65 12 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=0.1138 r_free=0.1291 r_work=0.1138 r_free=0.1291 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1291 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1288 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601357 | | target function (ml) not normalized (work): 299928.199677 | | target function (ml) not normalized (free): 15787.022327 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1366 0.1321 5.6887 5.5903| | 2: 3.57 - 2.84 1.00 2888 124 0.1056 0.1452 5.1585 5.2415| | 3: 2.83 - 2.48 1.00 2820 163 0.1100 0.1220 4.9429 4.9739| | 4: 2.47 - 2.25 1.00 2825 136 0.0898 0.1009 4.6231 4.6598| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0966 4.5706 4.6205| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.0961 4.2575 4.3459| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1105 3.9703 4.0695| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1096 3.878 3.9816| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1140 3.6375 3.8058| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1186 3.5556 3.7052| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1033 3.4861 3.5619| | 12: 1.61 - 1.56 1.00 2773 144 0.0900 0.1125 3.321 3.4367| | 13: 1.56 - 1.52 1.00 2745 130 0.0938 0.1027 3.3001 3.3895| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1053 3.2347 3.3227| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1204 3.1485 3.2618| | 16: 1.45 - 1.42 1.00 2756 161 0.1046 0.1226 3.1297 3.2323| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1304 3.1158 3.2281| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1318 3.1024 3.2361| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1570 3.111 3.2743| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1464 3.1109 3.1526| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1502 3.1128 3.1002| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.2000 3.1237 3.2952| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1800 3.1313 3.2014| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1845 3.1266 3.2316| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2157 3.1425 3.2579| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1761 3.1482 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2168 3.1703 3.1633| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2298 3.1658 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2267 0.2372 3.1471 3.2257| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2440 3.1426 3.165| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.46 1.00 0.98 5675.06| | 2: 3.57 - 2.84 2888 124 0.93 12.44 1.01 0.98 5675.06| | 3: 2.83 - 2.48 2820 163 0.90 16.34 0.99 0.98 4738.72| | 4: 2.47 - 2.25 2825 136 0.92 13.32 1.00 0.99 2324.19| | 5: 2.25 - 2.09 2756 127 0.90 15.47 1.01 0.99 2324.19| | 6: 2.09 - 1.97 2846 113 0.93 12.18 1.02 0.99 1338.04| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.98 496.98| | 8: 1.87 - 1.79 2789 144 0.93 12.47 1.00 0.98 496.98| | 9: 1.79 - 1.72 2745 138 0.95 9.87 0.98 0.98 281.97| | 10: 1.72 - 1.66 2831 160 0.94 10.89 0.98 0.98 238.91| | 11: 1.66 - 1.61 2712 147 0.94 11.56 0.98 0.98 228.88| | 12: 1.61 - 1.56 2773 144 0.96 8.70 0.99 0.98 134.30| | 13: 1.56 - 1.52 2745 130 0.95 10.24 1.03 0.98 134.30| | 14: 1.52 - 1.48 2803 134 0.94 10.61 1.02 0.99 120.84| | 15: 1.48 - 1.45 2738 128 0.95 9.80 1.02 0.99 96.18| | 16: 1.45 - 1.42 2756 161 0.94 10.97 1.02 0.99 96.18| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.99 88.06| | 18: 1.39 - 1.36 2741 179 0.94 11.48 1.01 0.99 83.37| | 19: 1.36 - 1.34 2807 134 0.94 11.83 0.99 0.99 83.37| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 79.86| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.97 79.61| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.97 80.06| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.95 82.31| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.95 82.31| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.95 84.20| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.94 86.30| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 86.30| | 28: 1.19 - 1.18 2671 147 0.88 20.40 1.01 0.93 89.73| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 91.03| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.97 0.93 91.03| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.61 max = 5675.06 mean = 874.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.36| |phase err.(test): min = 0.00 max = 89.11 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1136 0.1288 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1462 0.1462 0.1494 n_refl.: 87578 remove outliers: r(all,work,free)=0.1462 0.1462 0.1494 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1462 0.1462 0.1494 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1136 0.1287 n_refl.: 87578 remove outliers: r(all,work,free)=0.1141 0.1134 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 88.54 80 5 0.4021 293.064 252.933 0.449 1.000 0.314 11.894-9.307 94.12 92 4 0.2381 479.780 461.191 0.850 1.002 0.310 9.237-7.194 97.27 207 7 0.2452 386.694 376.565 0.914 1.003 0.160 7.162-5.571 100.00 427 22 0.2241 296.131 283.285 0.907 1.003 0.150 5.546-4.326 100.00 867 58 0.1124 406.515 401.942 0.961 1.003 0.115 4.315-3.360 100.00 1859 96 0.0926 386.599 384.610 1.004 1.003 0.110 3.356-2.611 100.00 3867 181 0.1106 253.975 252.310 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0907 168.362 167.820 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.219 82.592 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.459 36.073 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2171 22.972 21.518 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0078 ================= 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 : 0.2611 0.1933 0.081 5.224 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1766 0.081 5.224 9.1 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1766 0.081 5.224 9.1 119.5 20.1 258 0.000 1_nqh: 0.1651 0.1769 0.081 5.224 9.1 119.5 20.1 258 0.006 1_weight: 0.1651 0.1769 0.081 5.224 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1232 0.1470 0.006 0.883 9.1 119.5 20.1 258 0.137 1_adp: 0.1238 0.1465 0.006 0.883 9.1 119.5 20.1 258 0.137 1_regHadp: 0.1239 0.1469 0.006 0.883 9.1 119.5 20.1 258 0.137 1_occ: 0.1232 0.1460 0.006 0.883 9.1 119.5 20.1 258 0.137 2_bss: 0.1229 0.1450 0.006 0.883 9.1 119.5 20.1 258 0.137 2_settarget: 0.1229 0.1450 0.006 0.883 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1229 0.1450 0.006 0.893 9.1 119.5 20.1 258 0.137 2_nqh: 0.1227 0.1449 0.006 0.893 9.1 119.5 20.1 258 0.135 2_sol: 0.1203 0.1400 0.006 0.893 9.1 115.0 22.3 420 n/a 2_weight: 0.1203 0.1400 0.006 0.893 9.1 115.0 22.3 420 n/a 2_xyzrec: 0.1196 0.1426 0.005 0.775 9.1 115.0 22.3 420 n/a 2_adp: 0.1196 0.1426 0.005 0.775 9.1 115.0 22.3 420 n/a 2_regHadp: 0.1196 0.1426 0.005 0.775 9.1 115.0 22.3 420 n/a 2_occ: 0.1197 0.1423 0.005 0.775 9.1 115.0 22.3 420 n/a 3_bss: 0.1193 0.1415 0.005 0.775 9.1 115.0 22.3 420 n/a 3_settarget: 0.1193 0.1415 0.005 0.775 9.1 115.0 22.3 420 n/a 3_updatecdl: 0.1193 0.1415 0.005 0.776 9.1 115.0 22.3 420 n/a 3_nqh: 0.1193 0.1415 0.005 0.776 9.1 115.0 22.3 420 n/a 3_sol: 0.1221 0.1404 0.005 0.776 9.1 115.0 21.3 440 n/a 3_weight: 0.1221 0.1404 0.005 0.776 9.1 115.0 21.3 440 n/a 3_xyzrec: 0.1160 0.1326 0.008 1.087 9.1 115.0 21.3 440 n/a 3_adp: 0.1160 0.1326 0.008 1.087 9.1 115.0 21.3 440 n/a 3_regHadp: 0.1160 0.1326 0.008 1.087 9.1 115.0 21.3 440 n/a 3_occ: 0.1147 0.1313 0.008 1.087 9.1 115.0 21.3 440 n/a 4_bss: 0.1139 0.1309 0.008 1.087 9.1 115.0 21.3 440 n/a 4_settarget: 0.1139 0.1309 0.008 1.087 9.1 115.0 21.3 440 n/a 4_updatecdl: 0.1139 0.1309 0.008 1.091 9.1 115.0 21.3 440 n/a 4_nqh: 0.1139 0.1309 0.008 1.091 9.1 115.0 21.3 440 n/a 4_sol: 0.1143 0.1308 0.008 1.091 9.1 115.0 21.2 450 n/a 4_weight: 0.1143 0.1308 0.008 1.091 9.1 115.0 21.2 450 n/a 4_xyzrec: 0.1139 0.1308 0.009 1.126 9.1 115.0 21.2 450 n/a 4_adp: 0.1139 0.1308 0.009 1.126 9.1 115.0 21.2 450 n/a 4_regHadp: 0.1139 0.1308 0.009 1.126 9.1 115.0 21.2 450 n/a 4_occ: 0.1136 0.1305 0.009 1.126 9.1 115.0 21.2 450 n/a 5_bss: 0.1133 0.1305 0.009 1.126 9.1 115.0 21.2 450 n/a 5_settarget: 0.1133 0.1305 0.009 1.126 9.1 115.0 21.2 450 n/a 5_updatecdl: 0.1133 0.1305 0.009 1.125 9.1 115.0 21.2 450 n/a 5_setrh: 0.1135 0.1305 0.009 1.125 9.1 115.0 21.2 450 n/a 5_nqh: 0.1135 0.1305 0.009 1.125 9.1 115.0 21.2 450 n/a 5_sol: 0.1138 0.1292 0.009 1.125 9.1 115.0 21.0 442 n/a 5_weight: 0.1138 0.1292 0.009 1.125 9.1 115.0 21.0 442 n/a 5_xyzrec: 0.1138 0.1291 0.008 1.132 9.1 115.0 21.0 442 n/a 5_adp: 0.1138 0.1291 0.008 1.132 9.1 115.0 21.0 442 n/a 5_regHadp: 0.1138 0.1291 0.008 1.132 9.1 115.0 21.0 442 n/a 5_occ: 0.1136 0.1288 0.008 1.132 9.1 115.0 21.0 442 n/a end: 0.1134 0.1287 0.008 1.132 9.1 115.0 21.0 442 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2348261_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2348261_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.6800 Refinement macro-cycles (run) : 13223.6500 Write final files (write_after_run_outputs) : 91.5600 Total : 13317.8900 Total CPU time: 3.71 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:02:34 PST -0800 (1735365754.88 s) Start R-work = 0.1646, R-free = 0.1766 Final R-work = 0.1134, R-free = 0.1287 =============================================================================== Job complete usr+sys time: 13495.32 seconds wall clock time: 247 minutes 0.19 seconds (14820.19 seconds total)