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_5352376.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_5352376.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.41, per 1000 atoms: 0.42 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: 0.46 Conformation dependent library (CDL) restraints added in 214.6 milliseconds Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 575 0.92 - 1.18: 1088 1.18 - 1.45: 716 1.45 - 1.71: 753 1.71 - 1.97: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.411 0.128 5.40e-03 3.43e+04 5.60e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.778 -0.255 1.24e-02 6.50e+03 4.23e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.683 -0.220 1.08e-02 8.57e+03 4.16e+02 bond pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 1.236 1.469 -0.233 1.16e-02 7.43e+03 4.04e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.237 1.033 0.204 1.10e-02 8.26e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2950 4.24 - 8.47: 1875 8.47 - 12.71: 757 12.71 - 16.94: 167 16.94 - 21.18: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 137.17 -15.08 1.04e+00 9.25e-01 2.10e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.15 138.02 -15.87 1.14e+00 7.69e-01 1.94e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 129.31 -8.89 6.40e-01 2.44e+00 1.93e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 122.99 108.81 14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" O BLYS A 132 " pdb=" C BLYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.15 136.49 -14.34 1.14e+00 7.69e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 949 18.33 - 36.66: 117 36.66 - 54.98: 36 54.98 - 73.31: 8 73.31 - 91.64: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 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 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+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 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.197: 107 0.197 - 0.392: 61 0.392 - 0.587: 46 0.587 - 0.782: 20 0.782 - 0.977: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.78 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.072 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.040 2.00e-02 2.50e+03 5.68e-02 9.67e+01 pdb=" CG TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.046 2.00e-02 2.50e+03 5.34e-02 8.55e+01 pdb=" CG ATYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.057 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.075 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.084 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1151 2.33 - 2.90: 8199 2.90 - 3.47: 10484 3.47 - 4.03: 15169 4.03 - 4.60: 21583 Nonbonded interactions: 56586 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.799 2.100 nonbonded pdb=" HB3 LYS A 188 " pdb=" HE2 LYS A 188 " model vdw 1.808 2.440 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.821 2.100 ... (remaining 56581 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_5352376_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= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794328 | | target function (ml) not normalized (work): 232784.303686 | | target function (ml) not normalized (free): 11790.999980 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3019 0.2115 7.0268 4.9462| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1840 4.3523 4.354| | 3: 2.84 - 2.48 1.00 2833 165 0.2355 0.1677 4.1354 4.16| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1540 3.8436 3.8339| | 5: 2.25 - 2.09 1.00 2756 127 0.2540 0.1690 3.8091 3.8245| | 6: 2.09 - 1.97 1.00 2846 113 0.2567 0.1736 3.4844 3.5406| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1874 3.1432 3.2349| | 8: 1.87 - 1.79 1.00 2789 144 0.2460 0.1806 3.0719 3.0883| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1782 2.9013 2.9017| | 10: 1.72 - 1.66 1.00 2789 158 0.2373 0.1902 2.7962 2.844| | 11: 1.66 - 1.61 1.00 2740 147 0.2555 0.1786 2.7534 2.711| | 12: 1.61 - 1.56 1.00 2787 146 0.2510 0.2045 2.6112 2.6798| | 13: 1.56 - 1.52 1.00 2745 130 0.2564 0.2010 2.5779 2.6338| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.1964 2.504 2.5197| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.2219 2.4267 2.547| | 16: 1.45 - 1.42 1.00 2756 161 0.2610 0.1923 2.3974 2.3719| | 17: 1.42 - 1.39 1.00 2785 139 0.2758 0.2156 2.3391 2.3893| | 18: 1.39 - 1.36 1.00 2741 179 0.2742 0.2151 2.2712 2.2997| | 19: 1.36 - 1.34 1.00 2807 134 0.2647 0.2317 2.2359 2.2668| | 20: 1.34 - 1.32 1.00 2696 147 0.2710 0.2383 2.2054 2.2921| | 21: 1.32 - 1.30 1.00 2785 112 0.2711 0.2233 2.1803 2.1545| | 22: 1.29 - 1.27 1.00 2704 152 0.2794 0.2419 2.1545 2.1745| | 23: 1.27 - 1.26 1.00 2802 156 0.2807 0.2679 2.1115 2.2203| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2564 2.0764 2.1275| | 25: 1.24 - 1.22 1.00 2734 148 0.2834 0.2479 2.0463 2.0708| | 26: 1.22 - 1.21 1.00 2727 135 0.2831 0.2249 2.0121 2.0639| | 27: 1.21 - 1.19 1.00 2814 148 0.3045 0.2621 2.0215 1.9841| | 28: 1.19 - 1.18 1.00 2671 147 0.3015 0.2896 1.9984 1.9764| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2811 1.9605 2.0634| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2711 1.9287 1.9271| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1506.69| | 2: 3.57 - 2.84 2876 122 0.80 26.25 1.27 0.23 1506.69| | 3: 2.84 - 2.48 2833 165 0.74 32.19 1.24 0.24 1249.31| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.25 0.25 581.36| | 5: 2.25 - 2.09 2756 127 0.77 29.58 1.29 0.25 581.36| | 6: 2.09 - 1.97 2846 113 0.83 22.93 1.29 0.25 317.44| | 7: 1.97 - 1.87 2787 165 0.90 16.62 1.28 0.26 92.35| | 8: 1.87 - 1.79 2789 144 0.86 21.25 1.25 0.26 92.35| | 9: 1.79 - 1.72 2745 138 0.88 18.10 1.23 0.26 54.08| | 10: 1.72 - 1.66 2789 158 0.87 19.68 1.22 0.26 46.42| | 11: 1.66 - 1.61 2740 147 0.86 21.00 1.24 0.25 44.81| | 12: 1.61 - 1.56 2787 146 0.89 17.90 1.24 0.25 28.50| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.50| | 14: 1.52 - 1.48 2803 134 0.87 20.24 1.23 0.25 25.63| | 15: 1.48 - 1.45 2738 128 0.87 20.02 1.23 0.25 20.36| | 16: 1.45 - 1.42 2756 161 0.86 21.14 1.23 0.25 20.36| | 17: 1.42 - 1.39 2785 139 0.86 20.91 1.25 0.25 17.50| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.24 0.25 15.85| | 19: 1.36 - 1.34 2807 134 0.85 21.99 1.22 0.25 15.85| | 20: 1.34 - 1.32 2696 147 0.87 21.05 1.21 0.25 13.27| | 21: 1.32 - 1.30 2785 112 0.86 21.92 1.19 0.25 13.09| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.24 12.78| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.22 0.24 11.20| | 24: 1.26 - 1.24 2744 132 0.85 22.81 1.20 0.24 11.20| | 25: 1.24 - 1.22 2734 148 0.84 23.72 1.20 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 23.82 1.19 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.83 24.85 1.19 0.23 9.13| | 29: 1.18 - 1.16 2800 134 0.83 25.16 1.16 0.23 8.84| | 30: 1.16 - 1.15 2740 148 0.81 26.54 1.16 0.23 8.84| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.84 max = 1506.69 mean = 218.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.52| |phase err.(test): min = 0.00 max = 89.38 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 : 0.082 0.255 1557 Z= 5.584 Angle : 5.278 20.057 2118 Z= 3.756 Chirality : 0.368 0.977 243 Planarity : 0.030 0.080 284 Dihedral : 13.689 91.641 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.97 % Favored : 93.79 % Cbeta Deviations : 27.03 % 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: -2.80 (0.44), residues: 224 helix: -2.46 (0.36), residues: 108 sheet: -1.01 (0.72), residues: 38 loop : -0.95 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 27 TYR 0.085 0.033 TYR A 139 PHE 0.108 0.042 PHE A 119 HIS 0.053 0.025 HIS A 126 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= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794328 | | target function (ml) not normalized (work): 232784.303686 | | target function (ml) not normalized (free): 11790.999980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2611 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2611 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1990 0.1994 0.1961 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2013 0.2018 0.1974 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1656 0.1650 0.1780 n_refl.: 87594 remove outliers: r(all,work,free)=0.1656 0.1649 0.1780 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 0.3829 386.618 358.733 0.669 1.003 0.407 11.894-9.307 99.02 97 4 0.1775 614.124 594.023 0.927 1.004 0.390 9.237-7.194 100.00 213 7 0.2114 502.278 494.448 0.961 1.004 0.344 7.162-5.571 100.00 427 22 0.2172 376.932 364.723 0.934 1.004 0.293 5.546-4.326 100.00 867 58 0.1286 517.434 511.358 0.959 1.004 0.223 4.315-3.360 100.00 1859 96 0.1155 492.084 488.068 1.003 1.004 0.189 3.356-2.611 100.00 3867 181 0.1451 323.273 320.175 0.997 1.003 0.043 2.608-2.026 99.99 8198 413 0.1379 214.301 212.017 1.008 1.002 0.000 2.025-1.573 100.00 17313 902 0.1656 104.653 103.911 1.011 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.408 45.072 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2602 29.240 26.974 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=0.0441 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1649 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1651 r_free=0.1783 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.232968 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2003.047069 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 0.1631 0.1737 0.0106 0.002 0.5 5.1 0.0 0.0 0 0.125 0.1539 0.1664 0.0125 0.002 0.5 4.8 0.0 0.0 0 0.250 0.1419 0.1571 0.0152 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1398 0.1567 0.0169 0.002 0.5 4.5 0.0 0.0 0 0.750 0.1351 0.1532 0.0182 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1327 0.1511 0.0184 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1290 0.1501 0.0211 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1276 0.1497 0.0221 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1262 0.1493 0.0231 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1252 0.1484 0.0232 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1251 0.1489 0.0237 0.005 0.8 4.5 0.5 0.0 0 6.000 0.1242 0.1482 0.0240 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1236 0.1475 0.0238 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1235 0.1474 0.0239 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1231 0.1472 0.0241 0.006 0.9 3.8 0.5 0.6 0 10.000 0.1228 0.1470 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1224 0.1467 0.0243 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1221 0.1468 0.0247 0.008 1.0 4.2 0.5 0.6 0 13.616 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1467 0.0243 0.007 0.9 4.2 0.5 0.6 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.67 2.43 3.013 19.051 2003.047 0.017 12.24 14.66 2.43 2.986 19.051 60.091 0.017 12.30 14.64 2.34 2.669 19.050 250.381 0.017 12.63 15.26 2.64 2.739 19.222 1001.524 0.016 12.55 15.51 2.97 3.243 19.581 2003.047 0.016 12.32 15.31 2.98 3.106 19.508 3004.571 0.015 12.34 15.49 3.15 3.455 19.692 4006.094 0.015 12.26 15.43 3.16 3.394 19.649 5007.618 0.015 12.21 15.51 3.30 3.456 19.690 6009.141 0.015 12.14 15.40 3.26 3.403 19.648 7010.665 0.015 12.15 15.42 3.27 3.316 19.587 8012.188 0.015 12.14 15.48 3.34 3.456 19.656 9013.712 0.015 12.14 15.50 3.37 3.542 19.689 10015.235 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: 250.381 Accepted refinement result: 12.30 14.64 2.34 2.669 19.050 250.381 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.08 3.31 0 1785 Protein: 9.06 114.99 16.99 3.32 0 1519 Water: 11.46 119.43 38.22 N/A 0 258 Other: 19.71 26.58 22.05 N/A 0 8 Chain A: 9.06 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1464 r_work=0.1232 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1467 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 = 0.1225 r_free = 0.1461 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1225 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016727 | | target function (ls_wunit_k1) not normalized (work): 1393.272353 | | target function (ls_wunit_k1) not normalized (free): 110.290780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1225 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1696 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1677 0.1678 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1457 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3518 304.100 283.488 0.669 1.003 0.396 11.894-9.307 99.02 97 4 0.1634 483.048 470.362 0.925 1.003 0.368 9.237-7.194 100.00 213 7 0.1875 395.074 389.515 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1807 296.481 290.710 0.937 1.003 0.259 5.546-4.326 100.00 867 58 0.0994 406.995 404.076 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0870 387.056 386.093 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1174 254.275 253.099 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1022 168.561 167.829 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1107 82.317 82.508 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.503 36.008 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.999 21.480 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=0.0539 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1457 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 A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.1225 r_free=0.1458 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1458 | n_water=258 | time (s): 1.530 (total time: 1.530) Filter (dist) r_work=0.1235 r_free=0.1459 | n_water=251 | time (s): 22.120 (total time: 23.650) Filter (q & B) r_work=0.1237 r_free=0.1460 | n_water=248 | time (s): 2.630 (total time: 26.280) Compute maps r_work=0.1237 r_free=0.1460 | n_water=248 | time (s): 1.450 (total time: 27.730) Filter (map) r_work=0.1253 r_free=0.1465 | n_water=225 | time (s): 3.330 (total time: 31.060) Find peaks r_work=0.1253 r_free=0.1465 | n_water=225 | time (s): 0.530 (total time: 31.590) Add new water r_work=0.1397 r_free=0.1626 | n_water=426 | time (s): 2.270 (total time: 33.860) Refine new water occ: r_work=0.1310 r_free=0.1496 adp: r_work=0.1228 r_free=0.1436 occ: r_work=0.1239 r_free=0.1425 adp: r_work=0.1207 r_free=0.1409 occ: r_work=0.1209 r_free=0.1400 adp: r_work=0.1200 r_free=0.1398 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1398 r_work=0.1200 r_free=0.1398 | n_water=426 | time (s): 57.780 (total time: 91.640) Filter (q & B) r_work=0.1203 r_free=0.1400 | n_water=413 | time (s): 3.580 (total time: 95.220) Filter (dist only) r_work=0.1203 r_free=0.1400 | n_water=412 | time (s): 35.560 (total time: 130.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.821536 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1474.848376 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 0.1682 0.1784 0.0102 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1569 0.1685 0.0117 0.001 0.4 8.3 0.0 0.0 0 0.250 0.1424 0.1563 0.0139 0.002 0.4 6.4 0.0 0.0 0 0.500 0.1353 0.1511 0.0157 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1324 0.1491 0.0167 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1332 0.1498 0.0166 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1252 0.1444 0.0192 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1234 0.1440 0.0206 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1219 0.1427 0.0208 0.004 0.7 4.2 0.5 0.0 0 4.000 0.1214 0.1425 0.0211 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1207 0.1414 0.0207 0.005 0.7 5.1 0.5 0.0 0 6.000 0.1205 0.1417 0.0212 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1201 0.1414 0.0214 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1197 0.1412 0.0215 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1195 0.1413 0.0218 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1195 0.1418 0.0223 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1193 0.1421 0.0227 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1190 0.1418 0.0228 0.008 0.9 5.1 0.5 0.6 0 13.911 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1412 0.0215 0.006 0.8 5.4 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 14.12 2.15 3.775 21.766 1474.848 0.016 11.97 14.12 2.15 3.775 21.766 44.245 0.016 11.97 14.12 2.15 3.775 21.766 184.356 0.016 12.16 14.54 2.38 3.613 21.782 737.424 0.015 12.13 14.84 2.70 3.502 21.898 1474.848 0.015 12.01 14.81 2.80 3.466 22.208 2212.273 0.015 11.88 14.76 2.88 3.483 21.965 2949.697 0.014 11.81 14.70 2.89 3.477 22.108 3687.121 0.014 11.78 14.68 2.90 3.505 22.091 4424.545 0.014 11.76 14.72 2.96 3.523 22.117 5161.969 0.014 11.75 14.77 3.03 3.548 22.193 5899.394 0.014 11.74 14.84 3.10 3.570 22.233 6636.818 0.014 11.77 14.90 3.14 3.603 22.240 7374.242 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: 184.356 Accepted refinement result: 11.97 14.12 2.15 3.775 21.766 184.356 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 22.17 3.31 187 1752 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.49 76.68 41.17 N/A 187 225 Other: 19.75 26.62 22.08 N/A 0 8 Chain A: 9.10 115.03 19.43 N/A 0 1752 Chain S: 14.28 60.00 47.85 N/A 187 0 Histogram: Values Number of atoms 9.10 - 19.69 1260 19.69 - 30.28 241 30.28 - 40.88 160 40.88 - 51.47 132 51.47 - 62.06 123 62.06 - 72.66 12 72.66 - 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=0.1197 r_free=0.1412 r_work=0.1197 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1412 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 = 0.1201 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015395 | | target function (ls_wunit_k1) not normalized (work): 1282.385008 | | target function (ls_wunit_k1) not normalized (free): 102.590602 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1201 0.1412 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1600 0.1599 0.1647 n_refl.: 87593 remove outliers: r(all,work,free)=0.1600 0.1599 0.1647 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1602 0.1601 0.1649 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1198 0.1407 n_refl.: 87593 remove outliers: r(all,work,free)=0.1207 0.1197 0.1407 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3469 300.086 278.695 0.602 1.003 0.360 11.894-9.307 99.02 97 4 0.1629 483.048 476.495 0.920 1.003 0.360 9.237-7.194 100.00 213 7 0.1747 395.074 393.562 0.974 1.003 0.300 7.162-5.571 100.00 427 22 0.1614 296.481 291.438 0.937 1.003 0.240 5.546-4.326 100.00 867 58 0.0892 406.995 404.113 0.957 1.003 0.210 4.315-3.360 100.00 1859 96 0.0806 387.056 386.160 1.006 1.003 0.210 3.356-2.611 100.00 3867 181 0.1112 254.275 253.157 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1016 168.561 167.975 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.317 82.517 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.503 36.028 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.999 21.508 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=0.0201 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1407 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1407 | n_water=412 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1197 r_free=0.1407 | n_water=406 | time (s): 34.150 (total time: 36.140) Filter (q & B) r_work=0.1197 r_free=0.1407 | n_water=406 | time (s): 1.250 (total time: 37.390) Compute maps r_work=0.1197 r_free=0.1407 | n_water=406 | time (s): 1.770 (total time: 39.160) Filter (map) r_work=0.1241 r_free=0.1410 | n_water=278 | time (s): 2.780 (total time: 41.940) Find peaks r_work=0.1241 r_free=0.1410 | n_water=278 | time (s): 0.450 (total time: 42.390) Add new water r_work=0.1369 r_free=0.1555 | n_water=458 | time (s): 2.790 (total time: 45.180) Refine new water occ: r_work=0.1269 r_free=0.1459 adp: r_work=0.1270 r_free=0.1462 occ: r_work=0.1246 r_free=0.1429 adp: r_work=0.1245 r_free=0.1431 occ: r_work=0.1228 r_free=0.1408 adp: r_work=0.1222 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1406 r_work=0.1222 r_free=0.1406 | n_water=458 | time (s): 226.020 (total time: 271.200) Filter (q & B) r_work=0.1227 r_free=0.1417 | n_water=425 | time (s): 2.630 (total time: 273.830) Filter (dist only) r_work=0.1227 r_free=0.1414 | n_water=424 | time (s): 37.390 (total time: 311.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.687775 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.266322 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 0.1256 0.1391 0.0135 0.002 0.6 3.8 0.5 0.0 0 0.084 0.1212 0.1361 0.0149 0.003 0.7 3.5 0.5 0.0 0 0.253 0.1190 0.1344 0.0154 0.004 0.8 3.5 0.5 0.0 0 0.506 0.1184 0.1339 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.759 0.1180 0.1335 0.0155 0.006 1.0 3.2 0.5 0.0 0 1.013 0.1177 0.1334 0.0158 0.006 1.0 3.2 0.5 0.0 0 1.266 0.1174 0.1335 0.0161 0.007 1.0 3.8 0.5 0.0 0 1.519 0.1172 0.1334 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.772 0.1183 0.1337 0.0154 0.005 0.9 3.2 0.5 0.0 0 0.844 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1172 0.1334 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 13.34 1.62 3.778 21.208 49.266 3.626 11.72 13.34 1.62 3.778 21.208 1.478 3.626 11.73 13.34 1.61 3.768 21.208 6.158 3.625 11.77 13.44 1.68 3.712 21.191 24.633 3.620 11.76 13.51 1.75 3.735 21.159 49.266 3.618 11.70 13.50 1.80 3.759 21.148 73.899 3.614 11.65 13.46 1.82 3.776 21.141 98.533 3.609 11.63 13.46 1.84 3.789 21.130 123.166 3.607 11.61 13.47 1.86 3.807 21.119 147.799 3.606 11.60 13.46 1.87 3.819 21.114 172.432 3.604 11.57 13.42 1.85 3.826 21.111 197.065 3.602 11.58 13.45 1.87 3.840 21.102 221.698 3.602 11.56 13.42 1.86 3.844 21.104 246.332 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.478 Accepted refinement result: 11.72 13.34 1.62 3.778 21.208 1.478 3.626 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.14 3.31 205 1746 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.51 76.70 35.83 N/A 205 219 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.11 115.04 19.37 N/A 0 1746 Chain S: 14.30 60.01 36.23 N/A 205 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.30 286 30.30 - 40.89 197 40.89 - 51.48 131 51.48 - 62.07 52 62.07 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1172 r_free=0.1334 r_work=0.1172 r_free=0.1334 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1172 r_free = 0.1334 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1161 r_free = 0.1336 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1161 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618291 | | target function (ml) not normalized (work): 301381.902169 | | target function (ml) not normalized (free): 15864.451800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1161 0.1336 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1504 0.1504 0.1537 n_refl.: 87590 remove outliers: r(all,work,free)=0.1504 0.1504 0.1537 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1502 0.1536 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1156 0.1322 n_refl.: 87590 remove outliers: r(all,work,free)=0.1161 0.1152 0.1322 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3831 299.653 265.633 0.500 0.999 0.320 11.894-9.307 96.08 94 4 0.2217 476.410 461.741 0.875 1.001 0.290 9.237-7.194 97.73 208 7 0.2297 387.629 384.869 0.955 1.001 0.210 7.162-5.571 100.00 427 22 0.2150 296.481 285.340 0.916 1.002 0.194 5.546-4.326 100.00 867 58 0.1110 406.995 402.636 0.961 1.002 0.158 4.315-3.360 100.00 1859 96 0.0957 387.056 384.485 1.005 1.002 0.137 3.356-2.611 100.00 3867 181 0.1159 254.275 251.991 1.008 1.001 0.080 2.608-2.026 99.99 8198 413 0.0946 168.561 167.754 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.317 82.593 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.503 36.085 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.999 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=-0.0162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1322 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1152 r_free=0.1322 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1322 | n_water=424 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1152 r_free=0.1321 | n_water=421 | time (s): 46.440 (total time: 48.840) Filter (q & B) r_work=0.1152 r_free=0.1321 | n_water=421 | time (s): 1.260 (total time: 50.100) Compute maps r_work=0.1152 r_free=0.1321 | n_water=421 | time (s): 1.800 (total time: 51.900) Filter (map) r_work=0.1181 r_free=0.1314 | n_water=312 | time (s): 3.840 (total time: 55.740) Find peaks r_work=0.1181 r_free=0.1314 | n_water=312 | time (s): 0.690 (total time: 56.430) Add new water r_work=0.1247 r_free=0.1403 | n_water=464 | time (s): 3.600 (total time: 60.030) Refine new water occ: r_work=0.1173 r_free=0.1335 adp: r_work=0.1174 r_free=0.1337 occ: r_work=0.1160 r_free=0.1316 adp: r_work=0.1159 r_free=0.1317 occ: r_work=0.1149 r_free=0.1303 adp: r_work=0.1146 r_free=0.1302 ADP+occupancy (water only), MIN, final r_work=0.1146 r_free=0.1302 r_work=0.1146 r_free=0.1302 | n_water=464 | time (s): 263.250 (total time: 323.280) Filter (q & B) r_work=0.1153 r_free=0.1311 | n_water=426 | time (s): 3.940 (total time: 327.220) Filter (dist only) r_work=0.1153 r_free=0.1308 | n_water=425 | time (s): 45.000 (total time: 372.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.785237 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.739387 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 0.1223 0.1351 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1176 0.1315 0.0139 0.003 0.8 4.2 0.5 0.0 0 0.268 0.1166 0.1311 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.536 0.1159 0.1306 0.0147 0.006 1.0 3.5 0.5 0.0 0 0.803 0.1155 0.1306 0.0151 0.006 1.0 3.5 0.5 0.0 0 1.071 0.1153 0.1306 0.0153 0.007 1.1 3.5 0.5 0.0 0 1.339 0.1151 0.1305 0.0154 0.008 1.1 3.5 0.5 0.0 0 1.607 0.1149 0.1304 0.0156 0.008 1.1 3.5 0.5 0.0 0 1.874 0.1157 0.1307 0.0149 0.006 1.0 3.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1149 0.1304 0.0156 0.008 1.1 3.5 0.5 0.0 0 1.874 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.49 13.04 1.56 3.780 21.083 46.739 3.611 11.49 13.04 1.56 3.780 21.083 1.402 3.611 11.49 13.04 1.55 3.770 21.083 5.842 3.611 11.55 13.09 1.54 3.711 21.070 23.370 3.608 11.52 13.12 1.59 3.737 21.053 46.739 3.605 11.49 13.12 1.63 3.757 21.036 70.109 3.601 11.46 13.11 1.65 3.770 21.030 93.479 3.597 11.44 13.13 1.69 3.782 21.026 116.848 3.596 11.40 13.10 1.70 3.794 21.024 140.218 3.594 11.38 13.10 1.72 3.805 21.017 163.588 3.592 11.37 13.09 1.72 3.816 21.013 186.958 3.591 11.38 13.13 1.74 3.831 21.009 210.327 3.592 11.35 13.08 1.73 3.829 21.013 233.697 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.842 Accepted refinement result: 11.49 13.04 1.55 3.770 21.083 5.842 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 20.92 3.28 208 1744 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.50 76.69 34.79 N/A 208 217 Other: 19.72 26.59 22.08 N/A 0 8 Chain A: 9.11 114.91 19.36 N/A 0 1744 Chain S: 14.27 60.01 33.99 N/A 208 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.27 293 30.27 - 40.85 208 40.85 - 51.43 120 51.43 - 62.01 44 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1304 r_work=0.1149 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1304 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1300 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1142 r_free= 0.1300 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608193 | | target function (ml) not normalized (work): 300504.780825 | | target function (ml) not normalized (free): 15831.940116 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1142 0.1300 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1469 0.1468 0.1527 n_refl.: 87580 remove outliers: r(all,work,free)=0.1469 0.1468 0.1527 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1468 0.1467 0.1527 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1304 n_refl.: 87580 remove outliers: r(all,work,free)=0.1148 0.1140 0.1304 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4002 294.164 259.898 0.484 0.999 0.308 11.894-9.307 96.08 94 4 0.2292 476.410 464.078 0.864 1.001 0.264 9.237-7.194 97.73 208 7 0.2330 387.629 379.174 0.927 1.001 0.230 7.162-5.571 100.00 427 22 0.2232 296.481 285.205 0.914 1.002 0.160 5.546-4.326 100.00 867 58 0.1140 406.995 402.719 0.959 1.002 0.113 4.315-3.360 100.00 1859 96 0.0945 387.056 384.701 1.005 1.002 0.093 3.356-2.611 100.00 3867 181 0.1125 254.275 252.269 1.010 1.001 0.040 2.608-2.026 99.99 8198 413 0.0917 168.561 167.891 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.317 82.639 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.503 36.105 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.999 21.542 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0179 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1140 r_free=0.1304 After: r_work=0.1142 r_free=0.1304 ================================== NQH flips ================================== r_work=0.1142 r_free=0.1304 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1142 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1304 | n_water=425 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1142 r_free=0.1304 | n_water=425 | time (s): 40.610 (total time: 43.070) Filter (q & B) r_work=0.1142 r_free=0.1305 | n_water=424 | time (s): 4.440 (total time: 47.510) Compute maps r_work=0.1142 r_free=0.1305 | n_water=424 | time (s): 1.910 (total time: 49.420) Filter (map) r_work=0.1164 r_free=0.1309 | n_water=335 | time (s): 4.010 (total time: 53.430) Find peaks r_work=0.1164 r_free=0.1309 | n_water=335 | time (s): 0.690 (total time: 54.120) Add new water r_work=0.1217 r_free=0.1356 | n_water=484 | time (s): 3.670 (total time: 57.790) Refine new water occ: r_work=0.1161 r_free=0.1303 adp: r_work=0.1161 r_free=0.1305 occ: r_work=0.1149 r_free=0.1292 adp: r_work=0.1147 r_free=0.1293 occ: r_work=0.1139 r_free=0.1283 adp: r_work=0.1135 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1283 r_work=0.1135 r_free=0.1283 | n_water=484 | time (s): 215.230 (total time: 273.020) Filter (q & B) r_work=0.1142 r_free=0.1293 | n_water=447 | time (s): 4.060 (total time: 277.080) Filter (dist only) r_work=0.1142 r_free=0.1291 | n_water=446 | time (s): 45.920 (total time: 323.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.822663 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.407384 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1348 0.0116 0.004 0.7 6.7 0.0 0.0 0 0.091 0.1180 0.1313 0.0132 0.004 0.8 6.1 0.0 0.0 0 0.273 0.1164 0.1303 0.0139 0.005 0.9 5.4 0.5 0.0 0 0.547 0.1156 0.1299 0.0142 0.006 1.0 5.4 0.5 0.0 0 0.820 0.1148 0.1294 0.0145 0.007 1.1 5.8 0.5 0.0 0 1.094 0.1146 0.1292 0.0147 0.007 1.1 5.8 0.5 0.0 0 1.367 0.1143 0.1291 0.0148 0.008 1.1 5.4 0.5 0.0 0 1.640 0.1142 0.1291 0.0149 0.008 1.1 5.1 0.5 0.0 0 1.914 0.1151 0.1295 0.0144 0.006 1.0 5.8 0.5 0.0 0 0.911 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1291 0.0148 0.008 1.1 5.4 0.5 0.0 0 1.640 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.91 1.48 3.764 21.177 44.407 3.607 11.43 12.91 1.48 3.764 21.177 1.332 3.607 11.43 12.91 1.48 3.764 21.177 5.551 3.607 11.44 12.93 1.49 3.703 21.169 22.204 3.602 11.51 13.06 1.56 3.726 21.138 44.407 3.605 11.44 13.03 1.59 3.747 21.129 66.611 3.599 11.38 13.00 1.61 3.762 21.126 88.815 3.594 11.36 13.00 1.64 3.773 21.122 111.018 3.592 11.33 12.98 1.65 3.782 21.121 133.222 3.590 11.34 13.02 1.69 3.800 21.111 155.426 3.590 11.33 13.02 1.69 3.811 21.104 177.630 3.590 11.31 13.01 1.70 3.818 21.105 199.833 3.588 11.29 12.97 1.68 3.823 21.103 222.037 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: 1.332 Accepted refinement result: 11.43 12.91 1.48 3.764 21.177 1.332 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.09 3.28 229 1744 Protein: 9.11 114.91 17.02 3.29 0 1519 Water: 11.49 76.68 34.94 N/A 229 217 Other: 19.72 26.58 22.08 N/A 0 8 Chain A: 9.11 114.91 19.35 N/A 0 1744 Chain S: 14.27 60.00 34.37 N/A 229 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.27 309 30.27 - 40.85 200 40.85 - 51.43 127 51.43 - 62.01 50 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1291 r_work=0.1143 r_free=0.1291 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1291 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1289 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1139 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605583 | | target function (ml) not normalized (work): 300283.798465 | | target function (ml) not normalized (free): 15810.042100 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1352 0.1324 5.6719 5.587| | 2: 3.57 - 2.84 1.00 2888 124 0.1080 0.1350 5.1596 5.2092| | 3: 2.83 - 2.48 1.00 2820 163 0.1100 0.1248 4.9351 4.9675| | 4: 2.47 - 2.25 1.00 2825 136 0.0900 0.1008 4.6223 4.6531| | 5: 2.25 - 2.09 1.00 2756 127 0.0874 0.0966 4.5682 4.6245| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.1022 4.2653 4.3567| | 7: 1.97 - 1.87 1.00 2787 165 0.0890 0.1102 3.9852 4.087| | 8: 1.87 - 1.79 1.00 2789 144 0.0918 0.1131 3.8971 4.0039| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1216 3.6534 3.8492| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1200 3.571 3.7192| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1037 3.5021 3.5751| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1134 3.3341 3.4578| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1058 3.3102 3.4139| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1061 3.2413 3.3231| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1227 3.1562 3.2698| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1243 3.1362 3.2403| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1302 3.118 3.2246| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1325 3.105 3.2365| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1576 3.1117 3.2769| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1430 3.1143 3.141| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1538 3.1148 3.1122| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1966 3.124 3.2871| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1796 3.134 3.2012| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1837 3.1266 3.2355| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2159 3.1423 3.262| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1763 3.1497 3.2039| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2167 3.1716 3.1658| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2327 3.1673 3.182| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2383 3.1489 3.2254| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2471 3.1437 3.1741| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.30 1.00 0.97 5543.03| | 2: 3.57 - 2.84 2888 124 0.93 12.39 1.01 0.97 5543.03| | 3: 2.83 - 2.48 2820 163 0.90 16.20 0.99 0.97 4637.57| | 4: 2.47 - 2.25 2825 136 0.92 13.27 1.00 0.98 2302.70| | 5: 2.25 - 2.09 2756 127 0.90 15.43 1.01 0.98 2302.70| | 6: 2.09 - 1.97 2846 113 0.93 12.29 1.02 0.98 1341.97| | 7: 1.97 - 1.87 2787 165 0.95 9.45 1.02 0.98 522.59| | 8: 1.87 - 1.79 2789 144 0.92 12.83 1.00 0.98 522.59| | 9: 1.79 - 1.72 2745 138 0.94 10.21 0.98 0.97 296.44| | 10: 1.72 - 1.66 2831 160 0.94 11.33 0.98 0.97 251.15| | 11: 1.66 - 1.61 2712 147 0.93 11.97 0.98 0.97 240.42| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.97 139.20| | 13: 1.56 - 1.52 2745 130 0.95 10.49 1.02 0.97 139.20| | 14: 1.52 - 1.48 2803 134 0.94 10.83 1.02 0.98 124.72| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 98.19| | 16: 1.45 - 1.42 2756 161 0.94 11.15 1.02 0.98 98.19| | 17: 1.42 - 1.39 2785 139 0.95 10.88 1.01 0.98 89.13| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.89| | 19: 1.36 - 1.34 2807 134 0.94 11.84 0.99 0.98 83.89| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 80.00| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.96 79.73| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 80.16| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 82.34| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.34| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 84.49| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.93 86.89| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.89| | 28: 1.19 - 1.18 2671 147 0.88 20.50 1.01 0.93 90.80| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 92.27| | 30: 1.16 - 1.15 2739 148 0.86 22.16 0.98 0.92 92.27| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.73 max = 5543.03 mean = 864.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.89 mean = 13.46| |phase err.(test): min = 0.00 max = 89.83 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1139 0.1289 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1457 0.1455 0.1517 n_refl.: 87579 remove outliers: r(all,work,free)=0.1457 0.1455 0.1517 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1456 0.1454 0.1516 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1295 n_refl.: 87579 remove outliers: r(all,work,free)=0.1144 0.1137 0.1295 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 0.4014 286.032 257.792 0.446 0.998 0.280 11.894-9.307 94.12 92 4 0.2296 481.531 459.623 0.856 1.001 0.232 9.237-7.194 97.27 207 7 0.2386 387.151 381.459 0.923 1.001 0.200 7.162-5.571 100.00 427 22 0.2226 296.481 285.624 0.907 1.002 0.113 5.546-4.326 100.00 867 58 0.1121 406.995 402.455 0.960 1.002 0.091 4.315-3.360 100.00 1859 96 0.0929 387.056 384.811 1.005 1.002 0.077 3.356-2.611 100.00 3867 181 0.1117 254.275 252.196 1.012 1.002 0.014 2.608-2.026 99.99 8198 413 0.0912 168.561 167.921 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.317 82.654 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.503 36.108 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.999 21.544 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0162 ================= 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 0.1961 0.082 5.278 8.8 119.3 19.9 258 0.000 1_bss: 0.1649 0.1780 0.082 5.278 9.0 119.5 20.1 258 0.000 1_settarget: 0.1649 0.1780 0.082 5.278 9.0 119.5 20.1 258 0.000 1_nqh: 0.1651 0.1783 0.082 5.278 9.0 119.5 20.1 258 0.007 1_weight: 0.1651 0.1783 0.082 5.278 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1224 0.1467 0.007 0.931 9.0 119.5 20.1 258 0.136 1_adp: 0.1230 0.1464 0.007 0.931 9.1 119.4 20.1 258 0.136 1_regHadp: 0.1232 0.1467 0.007 0.931 9.1 119.4 20.1 258 0.136 1_occ: 0.1225 0.1461 0.007 0.931 9.1 119.4 20.1 258 0.136 2_bss: 0.1224 0.1457 0.007 0.931 9.1 119.5 20.1 258 0.136 2_settarget: 0.1224 0.1457 0.007 0.931 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1224 0.1457 0.007 0.942 9.1 119.5 20.1 258 0.136 2_nqh: 0.1225 0.1458 0.007 0.942 9.1 119.5 20.1 258 0.134 2_sol: 0.1203 0.1400 0.007 0.942 9.1 115.0 22.2 412 n/a 2_weight: 0.1203 0.1400 0.007 0.942 9.1 115.0 22.2 412 n/a 2_xyzrec: 0.1197 0.1412 0.006 0.841 9.1 115.0 22.2 412 n/a 2_adp: 0.1197 0.1412 0.006 0.841 9.1 115.0 22.2 412 n/a 2_regHadp: 0.1197 0.1412 0.006 0.841 9.1 115.0 22.2 412 n/a 2_occ: 0.1201 0.1412 0.006 0.841 9.1 115.0 22.2 412 n/a 3_bss: 0.1197 0.1407 0.006 0.841 9.1 115.0 22.2 412 n/a 3_settarget: 0.1197 0.1407 0.006 0.841 9.1 115.0 22.2 412 n/a 3_updatecdl: 0.1197 0.1407 0.006 0.840 9.1 115.0 22.2 412 n/a 3_nqh: 0.1197 0.1407 0.006 0.840 9.1 115.0 22.2 412 n/a 3_sol: 0.1227 0.1414 0.006 0.840 9.1 115.0 21.1 424 n/a 3_weight: 0.1227 0.1414 0.006 0.840 9.1 115.0 21.1 424 n/a 3_xyzrec: 0.1172 0.1334 0.008 1.072 9.1 115.0 21.1 424 n/a 3_adp: 0.1172 0.1334 0.008 1.072 9.1 115.0 21.1 424 n/a 3_regHadp: 0.1172 0.1334 0.008 1.072 9.1 115.0 21.1 424 n/a 3_occ: 0.1161 0.1336 0.008 1.072 9.1 115.0 21.1 424 n/a 4_bss: 0.1152 0.1322 0.008 1.072 9.1 115.0 21.1 424 n/a 4_settarget: 0.1152 0.1322 0.008 1.072 9.1 115.0 21.1 424 n/a 4_updatecdl: 0.1152 0.1322 0.008 1.074 9.1 115.0 21.1 424 n/a 4_nqh: 0.1152 0.1322 0.008 1.074 9.1 115.0 21.1 424 n/a 4_sol: 0.1153 0.1308 0.008 1.074 9.1 115.0 20.9 425 n/a 4_weight: 0.1153 0.1308 0.008 1.074 9.1 115.0 20.9 425 n/a 4_xyzrec: 0.1149 0.1304 0.008 1.125 9.1 115.0 20.9 425 n/a 4_adp: 0.1149 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 4_regHadp: 0.1149 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 4_occ: 0.1142 0.1300 0.008 1.125 9.1 114.9 20.9 425 n/a 5_bss: 0.1140 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 5_settarget: 0.1140 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 5_updatecdl: 0.1140 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 5_setrh: 0.1142 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 5_nqh: 0.1142 0.1304 0.008 1.125 9.1 114.9 20.9 425 n/a 5_sol: 0.1142 0.1291 0.008 1.125 9.1 114.9 21.1 446 n/a 5_weight: 0.1142 0.1291 0.008 1.125 9.1 114.9 21.1 446 n/a 5_xyzrec: 0.1143 0.1291 0.008 1.128 9.1 114.9 21.1 446 n/a 5_adp: 0.1143 0.1291 0.008 1.128 9.1 114.9 21.1 446 n/a 5_regHadp: 0.1143 0.1291 0.008 1.128 9.1 114.9 21.1 446 n/a 5_occ: 0.1139 0.1289 0.008 1.128 9.1 114.9 21.1 446 n/a end: 0.1137 0.1295 0.008 1.128 9.1 114.9 21.1 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5352376_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5352376_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0800 Refinement macro-cycles (run) : 14024.6000 Write final files (write_after_run_outputs) : 90.0100 Total : 14117.6900 Total CPU time: 3.93 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:15:26 PST -0800 (1735366526.23 s) Start R-work = 0.1649, R-free = 0.1780 Final R-work = 0.1137, R-free = 0.1295 =============================================================================== Job complete usr+sys time: 14281.61 seconds wall clock time: 259 minutes 21.08 seconds (15561.08 seconds total)