Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.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_7326401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7326401.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 2 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: 1.62, per 1000 atoms: 0.48 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 186.0 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 467 0.90 - 1.15: 1156 1.15 - 1.40: 583 1.40 - 1.65: 876 1.65 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " ideal model delta sigma weight residual 1.521 1.296 0.226 1.17e-02 7.31e+03 3.72e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.176 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.215 0.241 1.32e-02 5.74e+03 3.33e+02 bond pdb=" CA VAL A 186 " pdb=" C VAL A 186 " ideal model delta sigma weight residual 1.523 1.739 -0.216 1.27e-02 6.20e+03 2.90e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.238 1.434 -0.197 1.17e-02 7.31e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.73: 3246 4.73 - 9.45: 1828 9.45 - 14.18: 583 14.18 - 18.90: 113 18.90 - 23.63: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 136.33 -15.94 1.05e+00 9.07e-01 2.31e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.63 -14.83 1.00e+00 1.00e+00 2.20e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 136.04 -14.13 9.80e-01 1.04e+00 2.08e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 134.80 -13.30 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.83: 979 19.83 - 39.66: 93 39.66 - 59.49: 34 59.49 - 79.32: 4 79.32 - 99.15: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.223: 95 0.223 - 0.442: 86 0.442 - 0.662: 42 0.662 - 0.881: 16 0.881 - 1.101: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.042 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.101 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.053 2.00e-02 2.50e+03 6.77e-02 1.38e+02 pdb=" CG TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.143 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.124 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.139 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 802 2.28 - 2.86: 7824 2.86 - 3.44: 10634 3.44 - 4.02: 15246 4.02 - 4.60: 22030 Nonbonded interactions: 56536 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.700 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.772 1.850 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.800 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.822 1.850 ... (remaining 56531 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_7326401_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= 0.2614 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792926 | | target function (ml) not normalized (work): 232667.511929 | | target function (ml) not normalized (free): 11841.761022 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3027 0.2111 7.0218 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1838 4.356 4.3531| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1695 4.1294 4.1866| | 4: 2.47 - 2.25 1.00 2825 136 0.2366 0.1405 3.8452 3.8257| | 5: 2.25 - 2.09 1.00 2756 127 0.2474 0.1779 3.8069 3.8307| | 6: 2.09 - 1.97 1.00 2846 113 0.2580 0.1761 3.4899 3.5475| | 7: 1.97 - 1.87 1.00 2787 165 0.2509 0.1896 3.1428 3.2383| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1853 3.0732 3.1339| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.2039 2.9176 3.0314| | 10: 1.72 - 1.66 1.00 2789 158 0.2451 0.2053 2.8294 2.8732| | 11: 1.66 - 1.61 1.00 2740 147 0.2530 0.1885 2.746 2.7529| | 12: 1.61 - 1.56 1.00 2787 146 0.2555 0.1879 2.6252 2.5864| | 13: 1.56 - 1.52 1.00 2745 130 0.2625 0.1944 2.5811 2.588| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.2038 2.4972 2.578| | 15: 1.48 - 1.45 1.00 2738 128 0.2610 0.2014 2.4118 2.4785| | 16: 1.45 - 1.42 1.00 2756 161 0.2614 0.2133 2.3797 2.4205| | 17: 1.42 - 1.39 1.00 2785 139 0.2657 0.2176 2.3316 2.3984| | 18: 1.39 - 1.36 1.00 2741 179 0.2675 0.2217 2.2752 2.3521| | 19: 1.36 - 1.34 1.00 2807 134 0.2696 0.2246 2.2481 2.2881| | 20: 1.34 - 1.32 1.00 2696 147 0.2675 0.1986 2.187 2.1392| | 21: 1.32 - 1.30 1.00 2785 112 0.2747 0.2313 2.1713 2.2311| | 22: 1.29 - 1.27 1.00 2704 152 0.2781 0.2788 2.1317 2.2787| | 23: 1.27 - 1.26 1.00 2802 156 0.2842 0.2344 2.1059 2.1607| | 24: 1.26 - 1.24 1.00 2744 132 0.2807 0.2334 2.0768 2.0688| | 25: 1.24 - 1.22 1.00 2734 148 0.2828 0.2534 2.0362 2.086| | 26: 1.22 - 1.21 1.00 2727 135 0.2910 0.2457 2.0364 2.1356| | 27: 1.21 - 1.19 1.00 2814 148 0.3001 0.2655 2.0182 2.0119| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2727 1.9839 2.0134| | 29: 1.18 - 1.16 1.00 2800 134 0.2935 0.2726 1.9481 2.0653| | 30: 1.16 - 1.15 1.00 2740 148 0.3046 0.2924 1.9292 1.955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.91 0.76 0.23 1488.69| | 2: 3.57 - 2.84 2876 122 0.80 26.18 1.27 0.23 1488.69| | 3: 2.84 - 2.48 2833 165 0.74 32.16 1.24 0.23 1236.13| | 4: 2.47 - 2.25 2825 136 0.81 25.75 1.26 0.25 580.71| | 5: 2.25 - 2.09 2756 127 0.77 29.39 1.28 0.25 580.71| | 6: 2.09 - 1.97 2846 113 0.83 23.13 1.29 0.25 320.14| | 7: 1.97 - 1.87 2787 165 0.89 17.28 1.28 0.25 97.91| | 8: 1.87 - 1.79 2789 144 0.85 22.08 1.25 0.25 97.91| | 9: 1.79 - 1.72 2745 138 0.88 18.76 1.23 0.25 57.97| | 10: 1.72 - 1.66 2789 158 0.86 20.54 1.23 0.25 49.98| | 11: 1.66 - 1.61 2740 147 0.85 21.86 1.25 0.25 48.08| | 12: 1.61 - 1.56 2787 146 0.88 18.49 1.24 0.25 28.86| | 13: 1.56 - 1.52 2745 130 0.87 20.35 1.25 0.25 28.86| | 14: 1.52 - 1.48 2803 134 0.86 20.72 1.23 0.25 25.89| | 15: 1.48 - 1.45 2738 128 0.87 19.95 1.24 0.25 20.45| | 16: 1.45 - 1.42 2756 161 0.86 21.30 1.23 0.25 20.45| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.23 0.25 17.38| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.22 0.25 15.61| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.22 0.25 15.61| | 20: 1.34 - 1.32 2696 147 0.87 20.78 1.22 0.24 13.07| | 21: 1.32 - 1.30 2785 112 0.86 22.21 1.21 0.24 12.89| | 22: 1.29 - 1.27 2704 152 0.85 22.60 1.22 0.24 12.62| | 23: 1.27 - 1.26 2802 156 0.85 22.40 1.22 0.24 11.24| | 24: 1.26 - 1.24 2744 132 0.85 23.11 1.21 0.24 11.24| | 25: 1.24 - 1.22 2734 148 0.84 23.89 1.21 0.24 10.77| | 26: 1.22 - 1.21 2727 135 0.84 24.21 1.20 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.83 25.31 1.22 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.82 25.90 1.18 0.23 9.68| | 29: 1.18 - 1.16 2800 134 0.82 26.35 1.17 0.23 9.46| | 30: 1.16 - 1.15 2740 148 0.80 27.64 1.16 0.23 9.46| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.46 max = 1488.69 mean = 217.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.83| |phase err.(test): min = 0.00 max = 89.74 mean = 22.78| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.261 1557 Z= 5.552 Angle : 5.318 21.366 2118 Z= 3.709 Chirality : 0.386 1.101 243 Planarity : 0.031 0.103 284 Dihedral : 13.847 99.154 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.32 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -2.10 (0.47), residues: 224 helix: -2.20 (0.38), residues: 102 sheet: -1.12 (0.86), residues: 28 loop : -0.19 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.150 0.035 ARG A 28 TYR 0.123 0.059 TYR A 141 PHE 0.085 0.028 PHE A 119 HIS 0.068 0.023 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2614 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792926 | | target function (ml) not normalized (work): 232667.511929 | | target function (ml) not normalized (free): 11841.761022 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2573 0.2614 0.1969 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2573 0.2614 0.1969 n_refl.: 87602 remove outliers: r(all,work,free)=0.1987 0.1990 0.1969 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2009 0.2012 0.1982 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1654 0.1646 0.1793 n_refl.: 87594 remove outliers: r(all,work,free)=0.1653 0.1646 0.1793 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 0.3819 386.663 370.025 0.694 0.999 0.407 11.894-9.307 99.02 97 4 0.1881 614.196 593.297 0.932 1.001 0.380 9.237-7.194 100.00 213 7 0.2086 502.337 490.972 0.964 1.001 0.370 7.162-5.571 100.00 427 22 0.2299 376.976 365.281 0.937 1.001 0.288 5.546-4.326 100.00 867 58 0.1291 517.495 511.688 0.963 1.001 0.224 4.315-3.360 100.00 1859 96 0.1147 492.141 488.416 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1451 323.311 319.699 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.1360 214.326 212.187 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1660 104.666 103.972 1.009 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.413 45.096 1.000 1.002 0.000 1.221-1.150 99.97 13689 708 0.2600 29.243 26.939 0.965 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0405 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1646 r_free=0.1793 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.442308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1981.558983 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 0.1687 0.1810 0.0123 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1626 0.1763 0.0138 0.002 0.4 5.1 0.0 0.0 0 0.250 0.1466 0.1627 0.0162 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1410 0.1592 0.0182 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1353 0.1546 0.0193 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1364 0.1562 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1299 0.1516 0.0217 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1268 0.1494 0.0226 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1261 0.1492 0.0231 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1248 0.1482 0.0235 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1474 0.0232 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1240 0.1479 0.0238 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1238 0.1475 0.0238 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1233 0.1471 0.0237 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1231 0.1472 0.0241 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1227 0.1469 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1227 0.1471 0.0244 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1222 0.1470 0.0248 0.008 1.0 3.8 0.5 0.6 0 13.221 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1469 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.69 2.42 3.013 19.036 1981.559 0.017 12.27 14.69 2.41 2.989 19.035 59.447 0.017 12.34 14.67 2.33 2.669 19.035 247.695 0.017 12.74 15.39 2.65 2.863 19.304 990.779 0.016 12.42 15.35 2.93 2.979 19.406 1981.559 0.016 12.43 15.49 3.05 3.343 19.623 2972.338 0.015 12.33 15.39 3.06 3.358 19.623 3963.118 0.015 12.28 15.45 3.17 3.414 19.643 4953.897 0.015 12.22 15.37 3.15 3.331 19.588 5944.677 0.015 12.18 15.38 3.20 3.351 19.588 6935.456 0.015 12.19 15.46 3.27 3.507 19.662 7926.236 0.015 12.11 15.38 3.27 3.418 19.601 8917.015 0.015 12.23 15.58 3.35 3.656 19.715 9907.795 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 247.695 Accepted refinement result: 12.34 14.67 2.33 2.669 19.035 247.695 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.43 20.06 3.31 0 1785 Protein: 9.06 114.98 16.97 3.32 0 1519 Water: 11.45 119.43 38.20 N/A 0 258 Other: 19.69 26.57 22.03 N/A 0 8 Chain A: 9.06 119.43 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.24 42 64.24 - 75.28 11 75.28 - 86.32 7 86.32 - 97.35 4 97.35 - 108.39 1 108.39 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1467 r_work=0.1236 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1471 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 = 0.1231 r_free = 0.1466 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 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= 0.1231 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016912 | | target function (ls_wunit_k1) not normalized (work): 1408.736917 | | target function (ls_wunit_k1) not normalized (free): 111.776752 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1466 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1669 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1669 0.1696 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1675 0.1676 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1459 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1459 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 0.3474 301.819 281.079 0.654 1.003 0.380 11.894-9.307 99.02 97 4 0.1636 483.497 470.642 0.924 1.003 0.365 9.237-7.194 100.00 213 7 0.1874 395.441 389.935 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1818 296.757 291.042 0.939 1.003 0.263 5.546-4.326 100.00 867 58 0.1008 407.373 404.395 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0880 387.415 386.286 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1177 254.512 253.369 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.1028 168.718 167.996 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.393 82.572 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.536 36.039 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2249 23.021 21.497 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0581 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1459 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** Total number of N/Q/H flips: 1 r_work=0.1229 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1459 | n_water=258 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1237 r_free=0.1456 | n_water=252 | time (s): 20.020 (total time: 22.100) Filter (q & B) r_work=0.1240 r_free=0.1456 | n_water=249 | time (s): 2.830 (total time: 24.930) Compute maps r_work=0.1240 r_free=0.1456 | n_water=249 | time (s): 1.190 (total time: 26.120) Filter (map) r_work=0.1254 r_free=0.1462 | n_water=226 | time (s): 2.820 (total time: 28.940) Find peaks r_work=0.1254 r_free=0.1462 | n_water=226 | time (s): 0.450 (total time: 29.390) Add new water r_work=0.1397 r_free=0.1631 | n_water=440 | time (s): 2.690 (total time: 32.080) Refine new water occ: r_work=0.1299 r_free=0.1479 adp: r_work=0.1223 r_free=0.1434 occ: r_work=0.1235 r_free=0.1413 adp: r_work=0.1203 r_free=0.1403 occ: r_work=0.1207 r_free=0.1396 adp: r_work=0.1196 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1394 r_work=0.1196 r_free=0.1394 | n_water=440 | time (s): 53.760 (total time: 85.840) Filter (q & B) r_work=0.1200 r_free=0.1398 | n_water=424 | time (s): 3.140 (total time: 88.980) Filter (dist only) r_work=0.1200 r_free=0.1397 | n_water=423 | time (s): 33.900 (total time: 122.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.011509 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1476.981930 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 0.1623 0.1738 0.0114 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1550 0.1673 0.0123 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1418 0.1564 0.0147 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1354 0.1516 0.0162 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1323 0.1494 0.0171 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1327 0.1497 0.0170 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1253 0.1447 0.0194 0.002 0.6 4.8 0.5 0.0 0 2.000 0.1228 0.1436 0.0208 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1215 0.1429 0.0214 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1207 0.1424 0.0217 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1201 0.1421 0.0220 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1196 0.1416 0.0220 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1192 0.1415 0.0224 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1190 0.1419 0.0230 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1190 0.1416 0.0226 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1185 0.1412 0.0227 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1185 0.1410 0.0226 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1185 0.1412 0.0227 0.008 0.9 4.2 0.5 0.6 0 13.000 0.1182 0.1407 0.0225 0.008 0.9 4.8 0.5 0.6 0 14.006 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1407 0.0225 0.008 0.9 4.8 0.5 0.6 0 14.006 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 14.07 2.25 3.774 21.815 1476.982 0.016 11.82 14.07 2.25 3.774 21.815 44.309 0.016 11.82 14.07 2.25 3.774 21.815 184.623 0.016 12.09 14.54 2.45 3.601 21.834 738.491 0.015 11.97 14.70 2.73 3.459 21.993 1476.982 0.015 11.83 14.63 2.80 3.454 22.148 2215.473 0.014 11.75 14.62 2.87 3.459 22.120 2953.964 0.014 11.72 14.75 3.03 3.504 21.999 3692.455 0.014 11.65 14.65 3.00 3.492 22.041 4430.946 0.014 11.60 14.64 3.03 3.503 22.034 5169.437 0.014 11.64 14.69 3.05 3.536 22.171 5907.928 0.014 11.60 14.67 3.07 3.545 22.159 6646.419 0.014 11.59 14.70 3.11 3.559 22.168 7384.910 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.309 Accepted refinement result: 11.82 14.07 2.25 3.774 21.815 44.309 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 22.27 3.31 197 1753 Protein: 9.10 115.02 17.01 3.32 0 1519 Water: 11.49 76.67 41.17 N/A 197 226 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.10 115.02 19.46 N/A 0 1753 Chain S: 17.13 60.00 47.26 N/A 197 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 245 30.28 - 40.87 161 40.87 - 51.46 138 51.46 - 62.06 125 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1407 r_work=0.1182 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1407 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 = 0.1182 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 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= 0.1182 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014791 | | target function (ls_wunit_k1) not normalized (work): 1231.992441 | | target function (ls_wunit_k1) not normalized (free): 105.478143 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1182 0.1409 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1581 0.1581 0.1615 n_refl.: 87592 remove outliers: r(all,work,free)=0.1581 0.1581 0.1615 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1583 0.1583 0.1616 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1179 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1402 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3353 301.246 275.657 0.608 1.003 0.360 11.894-9.307 99.02 97 4 0.1548 483.497 478.767 0.927 1.003 0.351 9.237-7.194 100.00 213 7 0.1704 395.441 394.494 0.983 1.003 0.280 7.162-5.571 100.00 427 22 0.1564 296.757 293.239 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0874 407.373 404.551 0.960 1.003 0.205 4.315-3.360 100.00 1859 96 0.0786 387.415 386.617 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1067 254.512 253.612 1.008 1.002 0.140 2.608-2.026 99.99 8198 413 0.1009 168.718 168.155 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.393 82.600 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.536 36.076 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 23.021 21.531 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1402 | n_water=423 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1177 r_free=0.1401 | n_water=416 | time (s): 38.640 (total time: 40.550) Filter (q & B) r_work=0.1177 r_free=0.1401 | n_water=416 | time (s): 1.160 (total time: 41.710) Compute maps r_work=0.1177 r_free=0.1401 | n_water=416 | time (s): 1.610 (total time: 43.320) Filter (map) r_work=0.1222 r_free=0.1399 | n_water=289 | time (s): 3.220 (total time: 46.540) Find peaks r_work=0.1222 r_free=0.1399 | n_water=289 | time (s): 0.540 (total time: 47.080) Add new water r_work=0.1345 r_free=0.1542 | n_water=478 | time (s): 3.070 (total time: 50.150) Refine new water occ: r_work=0.1249 r_free=0.1447 adp: r_work=0.1251 r_free=0.1450 occ: r_work=0.1226 r_free=0.1413 adp: r_work=0.1226 r_free=0.1417 occ: r_work=0.1207 r_free=0.1387 adp: r_work=0.1203 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1389 r_work=0.1203 r_free=0.1389 | n_water=478 | time (s): 255.820 (total time: 305.970) Filter (q & B) r_work=0.1208 r_free=0.1393 | n_water=445 | time (s): 2.790 (total time: 308.760) Filter (dist only) r_work=0.1208 r_free=0.1392 | n_water=444 | time (s): 37.830 (total time: 346.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.781241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.776640 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 0.1371 0.0133 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1200 0.1342 0.0142 0.003 0.7 3.5 0.5 0.0 0 0.267 0.1180 0.1327 0.0146 0.004 0.8 3.8 0.5 0.0 0 0.534 0.1173 0.1322 0.0149 0.005 0.9 3.8 0.5 0.0 0 0.802 0.1169 0.1318 0.0149 0.006 1.0 3.5 0.5 0.0 0 1.069 0.1166 0.1319 0.0153 0.007 1.0 3.8 0.5 0.0 0 1.336 0.1164 0.1318 0.0154 0.007 1.1 3.8 0.5 0.6 0 1.603 0.1162 0.1318 0.0157 0.008 1.1 4.5 0.5 0.6 0 1.870 0.1172 0.1320 0.0148 0.005 0.9 3.8 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1318 0.0149 0.006 1.0 3.5 0.5 0.0 0 1.069 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 13.18 1.49 3.777 21.272 41.777 3.627 11.69 13.18 1.49 3.777 21.272 1.253 3.627 11.69 13.18 1.50 3.775 21.272 5.222 3.627 11.72 13.24 1.52 3.705 21.266 20.888 3.620 11.78 13.38 1.60 3.717 21.239 41.777 3.623 11.69 13.34 1.66 3.742 21.227 62.665 3.616 11.63 13.31 1.68 3.757 21.222 83.553 3.611 11.60 13.29 1.68 3.766 21.216 104.442 3.608 11.58 13.29 1.71 3.778 21.208 125.330 3.607 11.56 13.29 1.73 3.790 21.202 146.218 3.605 11.55 13.28 1.74 3.800 21.196 167.107 3.604 11.56 13.30 1.75 3.812 21.184 187.995 3.604 11.53 13.27 1.74 3.816 21.190 208.883 3.603 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.253 Accepted refinement result: 11.69 13.18 1.49 3.777 21.272 1.253 3.627 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.27 3.31 223 1748 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.78 N/A 223 221 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.11 115.03 19.37 N/A 0 1748 Chain S: 15.33 60.01 36.11 N/A 223 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 294 30.29 - 40.88 202 40.88 - 51.48 133 51.48 - 62.07 57 62.07 - 72.66 11 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1169 r_free=0.1318 r_work=0.1169 r_free=0.1318 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1169 r_free = 0.1318 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1306 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.14 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= 0.1154 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618009 | | target function (ml) not normalized (work): 301358.447757 | | target function (ml) not normalized (free): 15858.176569 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1154 0.1306 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1497 0.1498 0.1508 n_refl.: 87590 remove outliers: r(all,work,free)=0.1497 0.1498 0.1508 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1497 0.1498 0.1508 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1298 n_refl.: 87590 remove outliers: r(all,work,free)=0.1154 0.1146 0.1298 n_refl.: 87582 ======================== 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 0.4031 297.717 272.055 0.495 1.001 0.313 11.894-9.307 97.06 95 4 0.2207 476.793 466.610 0.876 1.002 0.301 9.237-7.194 97.73 208 7 0.2198 387.989 387.552 0.958 1.002 0.230 7.162-5.571 100.00 427 22 0.2097 296.757 286.957 0.925 1.003 0.174 5.546-4.326 100.00 867 58 0.1091 407.373 403.064 0.963 1.003 0.160 4.315-3.360 100.00 1859 96 0.0929 387.415 384.872 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1147 254.512 252.353 1.007 1.002 0.038 2.608-2.026 99.99 8198 413 0.0937 168.718 167.934 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0907 82.393 82.674 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1265 36.536 36.120 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.021 21.557 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0089 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1298 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=0.1146 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1298 | n_water=444 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1146 r_free=0.1299 | n_water=442 | time (s): 48.470 (total time: 50.950) Filter (q & B) r_work=0.1147 r_free=0.1299 | n_water=438 | time (s): 3.880 (total time: 54.830) Compute maps r_work=0.1147 r_free=0.1299 | n_water=438 | time (s): 1.900 (total time: 56.730) Filter (map) r_work=0.1171 r_free=0.1305 | n_water=326 | time (s): 3.810 (total time: 60.540) Find peaks r_work=0.1171 r_free=0.1305 | n_water=326 | time (s): 0.700 (total time: 61.240) Add new water r_work=0.1240 r_free=0.1377 | n_water=491 | time (s): 3.710 (total time: 64.950) Refine new water occ: r_work=0.1173 r_free=0.1325 adp: r_work=0.1174 r_free=0.1328 occ: r_work=0.1158 r_free=0.1308 adp: r_work=0.1157 r_free=0.1312 occ: r_work=0.1146 r_free=0.1295 adp: r_work=0.1142 r_free=0.1297 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1297 r_work=0.1142 r_free=0.1297 | n_water=491 | time (s): 195.320 (total time: 260.270) Filter (q & B) r_work=0.1148 r_free=0.1298 | n_water=452 | time (s): 3.830 (total time: 264.100) Filter (dist only) r_work=0.1148 r_free=0.1297 | n_water=451 | time (s): 46.200 (total time: 310.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789997 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.125768 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1333 0.0126 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1169 0.1306 0.0137 0.003 0.8 3.5 0.5 0.0 0 0.268 0.1155 0.1299 0.0144 0.005 0.9 3.8 0.5 0.0 0 0.537 0.1149 0.1300 0.0151 0.006 0.9 3.5 0.5 0.0 0 0.805 0.1145 0.1303 0.0157 0.006 1.0 3.8 0.5 0.0 0 1.074 0.1142 0.1297 0.0155 0.007 1.1 3.5 0.5 0.0 0 1.342 0.1140 0.1300 0.0160 0.008 1.1 4.2 0.5 0.0 0 1.611 0.1138 0.1301 0.0163 0.009 1.1 4.2 0.5 0.0 0 1.879 0.1148 0.1300 0.0153 0.006 1.0 3.5 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1142 0.1297 0.0155 0.007 1.1 3.5 0.5 0.0 0 1.342 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.42 12.97 1.55 3.778 21.216 38.126 3.611 11.42 12.97 1.55 3.778 21.216 1.144 3.611 11.42 12.98 1.55 3.778 21.216 4.766 3.611 11.45 13.02 1.57 3.707 21.211 19.063 3.607 11.47 13.09 1.63 3.726 21.197 38.126 3.607 11.47 13.18 1.71 3.741 21.176 57.189 3.606 11.41 13.15 1.73 3.759 21.170 76.252 3.601 11.37 13.11 1.74 3.772 21.167 95.314 3.597 11.36 13.13 1.77 3.781 21.160 114.377 3.595 11.33 13.10 1.77 3.789 21.162 133.440 3.594 11.33 13.12 1.79 3.802 21.154 152.503 3.593 11.32 13.12 1.81 3.811 21.152 171.566 3.592 11.30 13.11 1.80 3.820 21.147 190.629 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.144 Accepted refinement result: 11.42 12.97 1.55 3.778 21.216 1.144 3.611 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.17 3.31 233 1745 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.13 N/A 233 218 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.10 115.03 19.30 N/A 0 1745 Chain S: 16.67 60.01 35.13 N/A 233 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.29 300 30.29 - 40.88 217 40.88 - 51.47 121 51.47 - 62.07 55 62.07 - 72.66 10 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=0.1142 r_free=0.1297 r_work=0.1142 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1297 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1294 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608455 | | target function (ml) not normalized (work): 300533.752857 | | target function (ml) not normalized (free): 15829.486104 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1136 0.1294 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1478 0.1478 0.1502 n_refl.: 87582 remove outliers: r(all,work,free)=0.1478 0.1478 0.1502 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1477 0.1477 0.1501 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1296 n_refl.: 87582 remove outliers: r(all,work,free)=0.1141 0.1133 0.1296 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.4099 294.845 260.878 0.464 1.000 0.320 11.894-9.307 95.10 93 4 0.2332 468.958 452.087 0.862 1.002 0.320 9.237-7.194 97.27 207 7 0.2280 389.727 382.163 0.934 1.002 0.174 7.162-5.571 100.00 427 22 0.2174 296.757 286.104 0.915 1.002 0.151 5.546-4.326 100.00 867 58 0.1118 407.373 402.360 0.964 1.002 0.124 4.315-3.360 100.00 1859 96 0.0920 387.415 385.519 1.004 1.002 0.107 3.356-2.611 100.00 3867 181 0.1115 254.512 252.649 1.009 1.002 0.024 2.608-2.026 99.99 8198 413 0.0912 168.718 168.172 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.393 82.766 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.536 36.156 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.021 21.579 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0111 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1133 r_free=0.1296 After: r_work=0.1134 r_free=0.1296 ================================== NQH flips ================================== r_work=0.1134 r_free=0.1296 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1134 r_free=0.1296 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1296 | n_water=451 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1134 r_free=0.1296 | n_water=450 | time (s): 46.000 (total time: 48.370) Filter (q & B) r_work=0.1135 r_free=0.1296 | n_water=447 | time (s): 3.800 (total time: 52.170) Compute maps r_work=0.1135 r_free=0.1296 | n_water=447 | time (s): 1.720 (total time: 53.890) Filter (map) r_work=0.1159 r_free=0.1302 | n_water=348 | time (s): 3.840 (total time: 57.730) Find peaks r_work=0.1159 r_free=0.1302 | n_water=348 | time (s): 0.670 (total time: 58.400) Add new water r_work=0.1211 r_free=0.1357 | n_water=495 | time (s): 3.620 (total time: 62.020) Refine new water occ: r_work=0.1155 r_free=0.1298 adp: r_work=0.1155 r_free=0.1301 occ: r_work=0.1143 r_free=0.1283 adp: r_work=0.1142 r_free=0.1285 occ: r_work=0.1135 r_free=0.1273 adp: r_work=0.1132 r_free=0.1273 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1273 r_work=0.1132 r_free=0.1273 | n_water=495 | time (s): 202.490 (total time: 264.510) Filter (q & B) r_work=0.1137 r_free=0.1278 | n_water=463 | time (s): 3.640 (total time: 268.150) Filter (dist only) r_work=0.1137 r_free=0.1277 | n_water=461 | time (s): 47.890 (total time: 316.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.803156 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.146684 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 0.1331 0.0107 0.004 0.7 6.1 0.5 0.0 0 0.090 0.1179 0.1300 0.0121 0.004 0.8 5.4 0.0 0.0 0 0.270 0.1158 0.1288 0.0130 0.005 0.9 6.1 0.5 0.0 0 0.541 0.1149 0.1283 0.0134 0.006 1.0 6.4 0.5 0.0 0 0.811 0.1141 0.1277 0.0137 0.007 1.1 6.4 0.5 0.0 0 1.082 0.1137 0.1277 0.0140 0.007 1.1 6.4 0.5 0.0 0 1.352 0.1136 0.1276 0.0140 0.008 1.1 6.1 0.5 0.0 0 1.623 0.1135 0.1276 0.0141 0.008 1.1 6.4 0.5 0.0 0 1.893 0.1144 0.1279 0.0135 0.006 1.0 6.7 0.5 0.0 0 0.902 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1276 0.0141 0.008 1.1 6.4 0.5 0.0 0 1.893 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.76 1.41 3.778 21.231 41.147 3.605 11.35 12.76 1.41 3.778 21.231 1.234 3.605 11.35 12.76 1.41 3.778 21.231 5.143 3.605 11.37 12.80 1.44 3.711 21.224 20.573 3.600 11.47 13.01 1.54 3.713 21.198 41.147 3.605 11.36 12.94 1.58 3.752 21.187 61.720 3.598 11.32 12.92 1.59 3.767 21.182 82.293 3.594 11.30 12.89 1.59 3.776 21.179 102.867 3.592 11.25 12.84 1.59 3.783 21.181 123.440 3.588 11.26 12.87 1.61 3.801 21.168 144.013 3.588 11.24 12.86 1.61 3.809 21.167 164.587 3.587 11.23 12.86 1.63 3.819 21.162 185.160 3.586 11.23 12.86 1.63 3.827 21.160 205.733 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.143 Accepted refinement result: 11.35 12.76 1.41 3.778 21.231 5.143 3.605 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 21.20 3.31 243 1745 Protein: 9.10 115.02 17.01 3.32 0 1519 Water: 11.50 76.67 34.97 N/A 243 218 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.10 115.02 19.30 N/A 0 1745 Chain S: 16.66 60.01 34.83 N/A 243 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 307 30.28 - 40.88 216 40.88 - 51.47 126 51.47 - 62.06 54 62.06 - 72.65 10 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1276 r_work=0.1135 r_free=0.1276 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1276 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1273 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1273 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603456 | | target function (ml) not normalized (work): 300099.441113 | | target function (ml) not normalized (free): 15800.478937 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1340 0.1339 5.6687 5.6211| | 2: 3.57 - 2.84 1.00 2888 124 0.1067 0.1288 5.1514 5.1798| | 3: 2.83 - 2.48 1.00 2820 163 0.1096 0.1168 4.9317 4.96| | 4: 2.47 - 2.25 1.00 2825 136 0.0894 0.1008 4.6183 4.6529| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0914 4.5635 4.6084| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.1013 4.2567 4.3449| | 7: 1.97 - 1.87 1.00 2787 165 0.0883 0.1100 3.9744 4.0774| | 8: 1.87 - 1.79 1.00 2789 144 0.0904 0.1109 3.8833 3.9939| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1187 3.6438 3.8271| | 10: 1.72 - 1.66 1.00 2831 160 0.0914 0.1200 3.563 3.7072| | 11: 1.66 - 1.61 1.00 2712 147 0.0873 0.1044 3.4997 3.5712| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1147 3.3309 3.4646| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1040 3.3084 3.3953| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1056 3.2427 3.3252| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1211 3.1569 3.2667| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1246 3.1389 3.2499| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1321 3.1208 3.2461| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1327 3.1063 3.2389| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1567 3.1153 3.2703| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1462 3.1154 3.1521| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1529 3.1159 3.1108| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1982 3.1249 3.2916| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1791 3.1346 3.1996| | 24: 1.26 - 1.24 1.00 2744 132 0.1702 0.1839 3.1285 3.2308| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2151 3.1439 3.2622| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1761 3.1502 3.2019| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2163 3.1715 3.1652| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2295 3.167 3.1744| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2377 3.1487 3.229| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2445 3.1442 3.1645| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.10 1.00 0.97 5525.95| | 2: 3.57 - 2.84 2888 124 0.93 12.25 1.01 0.97 5525.95| | 3: 2.83 - 2.48 2820 163 0.90 16.16 0.99 0.97 4619.31| | 4: 2.47 - 2.25 2825 136 0.92 13.15 1.00 0.98 2281.38| | 5: 2.25 - 2.09 2756 127 0.91 15.31 1.01 0.98 2281.38| | 6: 2.09 - 1.97 2846 113 0.93 12.14 1.02 0.98 1323.24| | 7: 1.97 - 1.87 2787 165 0.95 9.23 1.02 0.98 506.08| | 8: 1.87 - 1.79 2789 144 0.93 12.51 1.00 0.98 506.08| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.97 289.19| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.97 245.75| | 11: 1.66 - 1.61 2712 147 0.94 11.71 0.98 0.97 235.45| | 12: 1.61 - 1.56 2773 144 0.96 8.88 0.99 0.97 138.34| | 13: 1.56 - 1.52 2745 130 0.95 10.45 1.03 0.97 138.34| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.98 124.26| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 98.47| | 16: 1.45 - 1.42 2756 161 0.94 11.10 1.02 0.98 98.47| | 17: 1.42 - 1.39 2785 139 0.95 10.98 1.01 0.98 89.72| | 18: 1.39 - 1.36 2741 179 0.94 11.60 1.01 0.98 84.66| | 19: 1.36 - 1.34 2807 134 0.94 11.89 1.00 0.98 84.66| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.53| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 80.24| | 22: 1.29 - 1.27 2704 152 0.93 13.66 0.98 0.96 80.60| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 82.45| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.95 82.45| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.31| | 26: 1.22 - 1.21 2727 135 0.90 18.04 1.03 0.93 86.38| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.38| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.93 89.91| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.93 91.24| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.93 91.24| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.24 max = 5525.95 mean = 858.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.38| |phase err.(test): min = 0.00 max = 89.78 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1273 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1464 0.1465 0.1467 n_refl.: 87577 remove outliers: r(all,work,free)=0.1464 0.1465 0.1467 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1464 0.1465 0.1467 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1274 n_refl.: 87577 remove outliers: r(all,work,free)=0.1136 0.1129 0.1274 n_refl.: 87572 ======================== 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 89.58 81 5 0.4022 297.077 250.980 0.451 0.999 0.324 11.894-9.307 91.18 89 4 0.2219 465.427 444.213 0.856 1.002 0.245 9.237-7.194 97.27 207 7 0.2295 389.727 383.946 0.925 1.002 0.146 7.162-5.571 100.00 427 22 0.2177 296.757 286.132 0.910 1.003 0.121 5.546-4.326 100.00 867 58 0.1126 407.373 402.576 0.961 1.003 0.120 4.315-3.360 100.00 1859 96 0.0918 387.415 385.649 1.004 1.003 0.110 3.356-2.611 100.00 3867 181 0.1108 254.512 252.825 1.009 1.002 0.014 2.608-2.026 99.99 8198 413 0.0906 168.718 168.194 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.393 82.780 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.536 36.152 1.027 0.996 0.000 1.221-1.150 99.97 13689 708 0.2170 23.021 21.566 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0034 ================= 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 : 0.2614 0.1970 0.084 5.318 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.003 1_weight: 0.1646 0.1793 0.084 5.318 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1227 0.1469 0.007 0.910 9.0 119.5 20.1 258 0.138 1_adp: 0.1234 0.1467 0.007 0.910 9.1 119.4 20.1 258 0.138 1_regHadp: 0.1236 0.1471 0.007 0.910 9.1 119.4 20.1 258 0.138 1_occ: 0.1231 0.1466 0.007 0.910 9.1 119.4 20.1 258 0.138 2_bss: 0.1228 0.1459 0.007 0.910 9.1 119.5 20.1 258 0.138 2_settarget: 0.1228 0.1459 0.007 0.910 9.1 119.5 20.1 258 0.138 2_updatecdl: 0.1228 0.1459 0.007 0.920 9.1 119.5 20.1 258 0.138 2_nqh: 0.1229 0.1459 0.007 0.920 9.1 119.5 20.1 258 0.141 2_sol: 0.1200 0.1397 0.007 0.920 9.1 115.0 22.3 423 n/a 2_weight: 0.1200 0.1397 0.007 0.920 9.1 115.0 22.3 423 n/a 2_xyzrec: 0.1182 0.1407 0.008 0.940 9.1 115.0 22.3 423 n/a 2_adp: 0.1182 0.1407 0.008 0.940 9.1 115.0 22.3 423 n/a 2_regHadp: 0.1182 0.1407 0.008 0.940 9.1 115.0 22.3 423 n/a 2_occ: 0.1182 0.1409 0.008 0.940 9.1 115.0 22.3 423 n/a 3_bss: 0.1178 0.1402 0.008 0.940 9.1 115.0 22.3 423 n/a 3_settarget: 0.1178 0.1402 0.008 0.940 9.1 115.0 22.3 423 n/a 3_updatecdl: 0.1178 0.1402 0.008 0.941 9.1 115.0 22.3 423 n/a 3_nqh: 0.1178 0.1402 0.008 0.941 9.1 115.0 22.3 423 n/a 3_sol: 0.1208 0.1392 0.008 0.941 9.1 115.0 21.3 444 n/a 3_weight: 0.1208 0.1392 0.008 0.941 9.1 115.0 21.3 444 n/a 3_xyzrec: 0.1169 0.1318 0.006 0.974 9.1 115.0 21.3 444 n/a 3_adp: 0.1169 0.1318 0.006 0.974 9.1 115.0 21.3 444 n/a 3_regHadp: 0.1169 0.1318 0.006 0.974 9.1 115.0 21.3 444 n/a 3_occ: 0.1154 0.1306 0.006 0.974 9.1 115.0 21.3 444 n/a 4_bss: 0.1146 0.1298 0.006 0.974 9.1 115.0 21.3 444 n/a 4_settarget: 0.1146 0.1298 0.006 0.974 9.1 115.0 21.3 444 n/a 4_updatecdl: 0.1146 0.1298 0.006 0.975 9.1 115.0 21.3 444 n/a 4_nqh: 0.1146 0.1298 0.006 0.975 9.1 115.0 21.3 444 n/a 4_sol: 0.1148 0.1297 0.006 0.975 9.1 115.0 21.2 451 n/a 4_weight: 0.1148 0.1297 0.006 0.975 9.1 115.0 21.2 451 n/a 4_xyzrec: 0.1142 0.1297 0.007 1.051 9.1 115.0 21.2 451 n/a 4_adp: 0.1142 0.1297 0.007 1.051 9.1 115.0 21.2 451 n/a 4_regHadp: 0.1142 0.1297 0.007 1.051 9.1 115.0 21.2 451 n/a 4_occ: 0.1136 0.1294 0.007 1.051 9.1 115.0 21.2 451 n/a 5_bss: 0.1133 0.1296 0.007 1.051 9.1 115.0 21.2 451 n/a 5_settarget: 0.1133 0.1296 0.007 1.051 9.1 115.0 21.2 451 n/a 5_updatecdl: 0.1133 0.1296 0.007 1.051 9.1 115.0 21.2 451 n/a 5_setrh: 0.1134 0.1296 0.007 1.051 9.1 115.0 21.2 451 n/a 5_nqh: 0.1134 0.1296 0.007 1.051 9.1 115.0 21.2 451 n/a 5_sol: 0.1137 0.1277 0.007 1.051 9.1 115.0 21.2 461 n/a 5_weight: 0.1137 0.1277 0.007 1.051 9.1 115.0 21.2 461 n/a 5_xyzrec: 0.1135 0.1276 0.008 1.098 9.1 115.0 21.2 461 n/a 5_adp: 0.1135 0.1276 0.008 1.098 9.1 115.0 21.2 461 n/a 5_regHadp: 0.1135 0.1276 0.008 1.098 9.1 115.0 21.2 461 n/a 5_occ: 0.1132 0.1273 0.008 1.098 9.1 115.0 21.2 461 n/a end: 0.1129 0.1274 0.008 1.098 9.1 115.0 21.2 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7326401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7326401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0500 Refinement macro-cycles (run) : 13505.4600 Write final files (write_after_run_outputs) : 95.2400 Total : 13603.7500 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:04:56 PST -0800 (1735365896.67 s) Start R-work = 0.1646, R-free = 0.1793 Final R-work = 0.1129, R-free = 0.1274 =============================================================================== Job complete usr+sys time: 13783.27 seconds wall clock time: 249 minutes 10.04 seconds (14950.04 seconds total)