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_7798058.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_7798058.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7798058.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.12, per 1000 atoms: 0.63 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: 0.45 Conformation dependent library (CDL) restraints added in 189.5 milliseconds Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.92: 590 0.92 - 1.21: 1105 1.21 - 1.49: 885 1.49 - 1.78: 562 1.78 - 2.06: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 1.330 1.069 0.262 1.38e-02 5.25e+03 3.59e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.417 -0.182 1.02e-02 9.61e+03 3.20e+02 bond pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 1.523 1.283 0.240 1.35e-02 5.49e+03 3.16e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.236 1.043 0.193 1.09e-02 8.42e+03 3.13e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.668 -0.211 1.20e-02 6.94e+03 3.09e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2906 4.17 - 8.33: 1891 8.33 - 12.49: 756 12.49 - 16.65: 197 16.65 - 20.81: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 136.07 -13.40 1.02e+00 9.61e-01 1.73e+02 angle pdb=" O ALA A 114 " pdb=" C ALA A 114 " pdb=" N HIS A 115 " ideal model delta sigma weight residual 122.12 135.44 -13.32 1.06e+00 8.90e-01 1.58e+02 angle pdb=" CA AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 117.39 102.01 15.38 1.24e+00 6.50e-01 1.54e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 109.34 12.16 1.00e+00 1.00e+00 1.48e+02 angle pdb=" O ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 122.59 138.13 -15.54 1.33e+00 5.65e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 927 16.49 - 32.99: 130 32.99 - 49.48: 36 49.48 - 65.97: 16 65.97 - 82.46: 2 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 180.00 155.97 24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR A 139 " pdb=" C TYR A 139 " pdb=" N THR A 140 " pdb=" CA THR A 140 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.194: 104 0.194 - 0.384: 58 0.384 - 0.574: 37 0.574 - 0.764: 37 0.764 - 0.954: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.40 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.037 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG PHE A 162 " 0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.063 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.046 2.00e-02 2.50e+03 6.51e-02 1.27e+02 pdb=" CG TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.090 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.104 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.024 2.00e-02 2.50e+03 6.37e-02 1.22e+02 pdb=" CG TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.097 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.32: 1068 2.32 - 2.89: 8155 2.89 - 3.46: 10516 3.46 - 4.03: 15147 4.03 - 4.60: 21742 Nonbonded interactions: 56628 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.756 2.100 nonbonded pdb=" HD2 LYS A 32 " pdb=" HZ2 LYS A 32 " model vdw 1.796 2.270 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.818 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.826 1.850 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 1.850 ... (remaining 56623 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_7798058_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= 0.2603 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781375 | | target function (ml) not normalized (work): 231705.259508 | | target function (ml) not normalized (free): 11816.983228 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2115 7.0178 4.956| | 2: 3.57 - 2.84 1.00 2876 122 0.2442 0.1788 4.3525 4.3468| | 3: 2.84 - 2.48 1.00 2833 165 0.2334 0.1599 4.131 4.159| | 4: 2.47 - 2.25 1.00 2825 136 0.2352 0.1485 3.839 3.8298| | 5: 2.25 - 2.09 1.00 2756 127 0.2473 0.1519 3.8057 3.8205| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1690 3.4502 3.5376| | 7: 1.97 - 1.87 1.00 2787 165 0.2560 0.1718 3.1262 3.1709| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1747 3.0349 3.096| | 9: 1.79 - 1.72 1.00 2745 138 0.2428 0.1825 2.8812 2.9387| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.2006 2.7955 2.8858| | 11: 1.66 - 1.61 1.00 2740 147 0.2483 0.1865 2.7336 2.7597| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2122 2.6354 2.7387| | 13: 1.56 - 1.52 1.00 2745 130 0.2540 0.1847 2.5587 2.6164| | 14: 1.52 - 1.48 1.00 2803 134 0.2599 0.1782 2.4888 2.4966| | 15: 1.48 - 1.45 1.00 2738 128 0.2531 0.2090 2.4098 2.4656| | 16: 1.45 - 1.42 1.00 2756 161 0.2621 0.2187 2.3755 2.4786| | 17: 1.42 - 1.39 1.00 2785 139 0.2671 0.2044 2.3323 2.3652| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.2357 2.2697 2.3617| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2449 2.2361 2.3653| | 20: 1.34 - 1.32 1.00 2696 147 0.2653 0.2284 2.1894 2.2046| | 21: 1.32 - 1.30 1.00 2785 112 0.2652 0.2195 2.1392 2.184| | 22: 1.29 - 1.27 1.00 2704 152 0.2720 0.2651 2.1098 2.2435| | 23: 1.27 - 1.26 1.00 2802 156 0.2761 0.2561 2.1022 2.2087| | 24: 1.26 - 1.24 1.00 2744 132 0.2792 0.2497 2.0692 2.1653| | 25: 1.24 - 1.22 1.00 2734 148 0.2833 0.2699 2.0398 2.0754| | 26: 1.22 - 1.21 1.00 2727 135 0.2777 0.2220 1.9923 2.0484| | 27: 1.21 - 1.19 1.00 2814 148 0.2920 0.2326 1.9913 1.909| | 28: 1.19 - 1.18 1.00 2671 147 0.2949 0.2810 1.983 2.0056| | 29: 1.18 - 1.16 1.00 2800 134 0.2938 0.2729 1.9567 2.0088| | 30: 1.16 - 1.15 1.00 2740 148 0.3108 0.2633 1.9395 1.9125| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.07 0.76 0.23 1514.80| | 2: 3.57 - 2.84 2876 122 0.80 26.35 1.27 0.23 1514.80| | 3: 2.84 - 2.48 2833 165 0.74 32.33 1.24 0.24 1254.39| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 578.58| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 578.58| | 6: 2.09 - 1.97 2846 113 0.83 22.66 1.29 0.25 313.61| | 7: 1.97 - 1.87 2787 165 0.90 16.20 1.29 0.26 87.63| | 8: 1.87 - 1.79 2789 144 0.86 20.71 1.25 0.26 87.63| | 9: 1.79 - 1.72 2745 138 0.88 18.45 1.24 0.25 53.54| | 10: 1.72 - 1.66 2789 158 0.87 19.76 1.23 0.25 46.71| | 11: 1.66 - 1.61 2740 147 0.86 21.27 1.24 0.25 45.18| | 12: 1.61 - 1.56 2787 146 0.88 18.73 1.23 0.25 29.66| | 13: 1.56 - 1.52 2745 130 0.86 20.56 1.24 0.25 29.66| | 14: 1.52 - 1.48 2803 134 0.86 20.89 1.25 0.25 26.52| | 15: 1.48 - 1.45 2738 128 0.87 20.20 1.22 0.25 20.78| | 16: 1.45 - 1.42 2756 161 0.86 21.48 1.23 0.25 20.78| | 17: 1.42 - 1.39 2785 139 0.86 21.29 1.23 0.25 17.80| | 18: 1.39 - 1.36 2741 179 0.86 21.46 1.23 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.39 1.22 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.21 0.24 13.28| | 21: 1.32 - 1.30 2785 112 0.85 22.57 1.20 0.24 13.08| | 22: 1.29 - 1.27 2704 152 0.85 22.88 1.22 0.24 12.76| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.21 0.24 11.16| | 24: 1.26 - 1.24 2744 132 0.85 23.05 1.21 0.24 11.16| | 25: 1.24 - 1.22 2734 148 0.84 23.62 1.20 0.24 10.49| | 26: 1.22 - 1.21 2727 135 0.84 23.58 1.20 0.23 9.74| | 27: 1.21 - 1.19 2814 148 0.83 24.52 1.20 0.23 9.74| | 28: 1.19 - 1.18 2671 147 0.84 24.41 1.18 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.84 24.66 1.17 0.23 8.68| | 30: 1.16 - 1.15 2740 148 0.82 26.35 1.16 0.23 8.68| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.68 max = 1514.80 mean = 218.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.60| |phase err.(test): min = 0.00 max = 89.94 mean = 22.34| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.262 1557 Z= 5.405 Angle : 5.160 17.447 2118 Z= 3.572 Chirality : 0.380 0.954 243 Planarity : 0.030 0.097 284 Dihedral : 13.674 82.465 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 24.86 % 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: -2.66 (0.47), residues: 224 helix: -2.44 (0.36), residues: 108 sheet: -1.19 (0.71), residues: 38 loop : -0.58 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.025 ARG A 98 TYR 0.098 0.044 TYR A 141 PHE 0.121 0.043 PHE A 162 HIS 0.060 0.029 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= 0.2603 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781375 | | target function (ml) not normalized (work): 231705.259508 | | target function (ml) not normalized (free): 11816.983228 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2604 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2604 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1975 0.1927 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1998 0.2003 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1627 0.1759 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1759 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 0.3893 386.331 357.759 0.739 0.911 0.407 11.894-9.307 99.02 97 4 0.1865 613.668 595.718 1.023 0.912 0.390 9.237-7.194 100.00 213 7 0.2131 501.905 491.090 1.043 0.913 0.354 7.162-5.571 100.00 427 22 0.2213 376.652 365.906 1.016 0.913 0.330 5.546-4.326 100.00 867 58 0.1298 517.050 509.693 1.055 0.914 0.224 4.315-3.360 100.00 1859 96 0.1125 491.718 488.109 1.100 0.915 0.199 3.356-2.611 100.00 3867 181 0.1416 323.033 319.536 1.087 0.917 0.099 2.608-2.026 99.99 8198 413 0.1370 214.142 211.703 1.093 0.920 0.000 2.025-1.573 100.00 17313 902 0.1628 104.576 103.862 1.094 0.925 0.000 1.573-1.221 100.00 36679 1900 0.2038 46.373 45.087 1.071 0.934 0.000 1.221-1.150 99.97 13689 708 0.2574 29.218 27.005 1.030 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0502 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1759 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.185368 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.074101 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 0.1730 0.1853 0.0123 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1594 0.1736 0.0142 0.002 0.4 4.5 0.0 0.0 0 0.250 0.1445 0.1622 0.0177 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1385 0.1576 0.0192 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1355 0.1560 0.0206 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1349 0.1549 0.0200 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1293 0.1511 0.0218 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1270 0.1494 0.0224 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1256 0.1488 0.0231 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1248 0.1483 0.0235 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1239 0.1475 0.0236 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1235 0.1472 0.0237 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1231 0.1466 0.0235 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1229 0.1467 0.0237 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1225 0.1467 0.0242 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1226 0.1469 0.0243 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1224 0.1473 0.0248 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1222 0.1470 0.0248 0.007 1.0 3.8 0.5 0.6 0 13.093 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1466 0.0235 0.005 0.8 4.5 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.66 2.35 3.013 19.078 2026.074 0.018 12.31 14.66 2.35 3.009 19.078 60.782 0.018 12.38 14.62 2.24 2.669 19.077 253.259 0.017 12.73 15.28 2.56 2.746 19.244 1013.037 0.017 12.54 15.42 2.88 3.172 19.562 2026.074 0.016 12.45 15.48 3.03 3.327 19.657 3039.111 0.015 12.45 15.55 3.10 3.471 19.715 4052.148 0.015 12.32 15.40 3.08 3.317 19.623 5065.185 0.015 12.28 15.40 3.12 3.360 19.642 6078.222 0.015 12.28 15.44 3.17 3.286 19.598 7091.259 0.015 12.22 15.40 3.18 3.266 19.577 8104.296 0.015 12.24 15.49 3.25 3.302 19.582 9117.333 0.015 12.20 15.44 3.24 3.436 19.656 10130.371 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: 253.259 Accepted refinement result: 12.38 14.62 2.24 2.669 19.077 253.259 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.31 0 1785 Protein: 9.08 115.02 17.01 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1462 r_work=0.1240 r_free=0.1465 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1465 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 = 0.1234 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1234 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016994 | | target function (ls_wunit_k1) not normalized (work): 1415.576387 | | target function (ls_wunit_k1) not normalized (free): 110.094728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1682 0.1683 0.1698 n_refl.: 87593 remove outliers: r(all,work,free)=0.1682 0.1683 0.1698 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1687 0.1688 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1233 0.1456 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1233 0.1456 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 0.3590 303.446 279.361 0.660 1.002 0.390 11.894-9.307 99.02 97 4 0.1627 482.008 469.250 0.926 1.003 0.365 9.237-7.194 100.00 213 7 0.1884 394.224 388.876 0.962 1.003 0.326 7.162-5.571 100.00 427 22 0.1827 295.843 290.203 0.934 1.003 0.266 5.546-4.326 100.00 867 58 0.1012 406.119 403.202 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0885 386.222 385.003 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1178 253.728 252.570 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1025 168.198 167.480 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.139 82.321 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1456 36.424 35.923 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2258 22.950 21.429 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0412 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1456 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=0.1234 r_free=0.1458 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1458 | n_water=258 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1241 r_free=0.1458 | n_water=251 | time (s): 21.910 (total time: 23.590) Filter (q & B) r_work=0.1243 r_free=0.1456 | n_water=248 | time (s): 2.950 (total time: 26.540) Compute maps r_work=0.1243 r_free=0.1456 | n_water=248 | time (s): 1.340 (total time: 27.880) Filter (map) r_work=0.1264 r_free=0.1470 | n_water=224 | time (s): 3.350 (total time: 31.230) Find peaks r_work=0.1264 r_free=0.1470 | n_water=224 | time (s): 0.590 (total time: 31.820) Add new water r_work=0.1415 r_free=0.1648 | n_water=433 | time (s): 3.270 (total time: 35.090) Refine new water occ: r_work=0.1316 r_free=0.1515 adp: r_work=0.1236 r_free=0.1454 occ: r_work=0.1248 r_free=0.1440 adp: r_work=0.1214 r_free=0.1423 occ: r_work=0.1216 r_free=0.1415 adp: r_work=0.1207 r_free=0.1411 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1411 r_work=0.1207 r_free=0.1411 | n_water=433 | time (s): 61.560 (total time: 96.650) Filter (q & B) r_work=0.1211 r_free=0.1415 | n_water=419 | time (s): 2.740 (total time: 99.390) Filter (dist only) r_work=0.1211 r_free=0.1413 | n_water=418 | time (s): 37.040 (total time: 136.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.835045 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1482.542633 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 0.1685 0.1794 0.0109 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1564 0.1688 0.0125 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1431 0.1582 0.0150 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1366 0.1530 0.0164 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1321 0.1491 0.0171 0.002 0.5 6.4 0.0 0.0 0 1.000 0.1327 0.1500 0.0173 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1250 0.1440 0.0190 0.002 0.6 5.8 0.5 0.0 0 2.000 0.1230 0.1448 0.0218 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1215 0.1436 0.0221 0.003 0.7 5.8 0.5 0.0 0 4.000 0.1205 0.1425 0.0220 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1203 0.1430 0.0227 0.004 0.7 5.4 0.5 0.0 0 6.000 0.1198 0.1419 0.0221 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1197 0.1425 0.0228 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1194 0.1417 0.0223 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1193 0.1420 0.0228 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1412 0.0222 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1189 0.1417 0.0227 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1185 0.1413 0.0228 0.008 0.9 4.8 0.5 0.0 0 13.918 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1412 0.0222 0.007 0.9 5.1 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 14.12 2.22 3.778 21.788 1482.543 0.016 11.90 14.12 2.22 3.778 21.788 44.476 0.016 11.90 14.12 2.22 3.777 21.788 185.318 0.016 12.10 14.54 2.44 3.619 21.799 741.271 0.015 12.11 14.83 2.72 3.550 21.861 1482.543 0.015 11.96 14.81 2.86 3.453 22.159 2223.814 0.014 11.86 14.76 2.90 3.476 22.197 2965.085 0.014 11.77 14.71 2.94 3.465 22.145 3706.357 0.014 11.77 14.71 2.95 3.494 22.159 4447.628 0.014 11.76 14.76 3.01 3.517 22.201 5188.899 0.014 11.72 14.80 3.08 3.530 22.216 5930.171 0.014 11.70 14.78 3.08 3.551 22.220 6671.442 0.014 11.68 14.78 3.10 3.553 22.170 7412.713 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.318 Accepted refinement result: 11.90 14.12 2.22 3.777 21.788 185.318 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 22.19 3.31 194 1751 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.69 40.92 N/A 194 224 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.45 N/A 0 1751 Chain S: 13.05 60.00 46.91 N/A 194 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.30 244 30.30 - 40.89 165 40.89 - 51.48 131 51.48 - 62.08 122 62.08 - 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=0.1190 r_free=0.1412 r_work=0.1190 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 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 = 0.1192 r_free = 0.1415 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1192 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015236 | | target function (ls_wunit_k1) not normalized (work): 1269.129818 | | target function (ls_wunit_k1) not normalized (free): 105.212126 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1192 0.1415 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1595 0.1596 0.1612 n_refl.: 87593 remove outliers: r(all,work,free)=0.1595 0.1596 0.1612 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1596 0.1597 0.1613 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1188 0.1410 n_refl.: 87593 remove outliers: r(all,work,free)=0.1198 0.1187 0.1410 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 0.3506 299.487 275.423 0.601 1.003 0.359 11.894-9.307 99.02 97 4 0.1559 482.008 473.682 0.917 1.004 0.337 9.237-7.194 100.00 213 7 0.1705 394.224 395.456 0.979 1.004 0.264 7.162-5.571 100.00 427 22 0.1602 295.843 291.878 0.933 1.004 0.240 5.546-4.326 100.00 867 58 0.0891 406.119 402.678 0.960 1.003 0.220 4.315-3.360 100.00 1859 96 0.0789 386.222 385.573 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1091 253.728 252.922 1.008 1.002 0.120 2.608-2.026 99.99 8198 413 0.1013 168.198 167.603 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1099 82.139 82.346 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.424 35.946 1.026 0.996 0.000 1.221-1.150 99.97 13689 708 0.2250 22.950 21.454 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=0.0089 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1410 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1410 | n_water=418 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1186 r_free=0.1404 | n_water=413 | time (s): 37.650 (total time: 39.830) Filter (q & B) r_work=0.1187 r_free=0.1405 | n_water=412 | time (s): 3.090 (total time: 42.920) Compute maps r_work=0.1187 r_free=0.1405 | n_water=412 | time (s): 1.470 (total time: 44.390) Filter (map) r_work=0.1219 r_free=0.1404 | n_water=280 | time (s): 3.160 (total time: 47.550) Find peaks r_work=0.1219 r_free=0.1404 | n_water=280 | time (s): 0.500 (total time: 48.050) Add new water r_work=0.1337 r_free=0.1538 | n_water=465 | time (s): 2.520 (total time: 50.570) Refine new water occ: r_work=0.1245 r_free=0.1455 adp: r_work=0.1247 r_free=0.1458 occ: r_work=0.1223 r_free=0.1430 adp: r_work=0.1222 r_free=0.1432 occ: r_work=0.1205 r_free=0.1406 adp: r_work=0.1201 r_free=0.1407 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1407 r_work=0.1201 r_free=0.1407 | n_water=465 | time (s): 192.150 (total time: 242.720) Filter (q & B) r_work=0.1207 r_free=0.1408 | n_water=435 | time (s): 3.090 (total time: 245.810) Filter (dist only) r_work=0.1207 r_free=0.1405 | n_water=434 | time (s): 37.390 (total time: 283.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.750733 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.895402 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 0.1240 0.1383 0.0143 0.002 0.6 3.8 0.5 0.0 0 0.088 0.1197 0.1349 0.0152 0.003 0.7 3.2 0.5 0.0 0 0.263 0.1176 0.1335 0.0159 0.004 0.8 3.5 0.5 0.0 0 0.525 0.1168 0.1333 0.0165 0.005 0.9 3.8 0.5 0.0 0 0.788 0.1165 0.1331 0.0166 0.006 1.0 3.5 0.5 0.0 0 1.050 0.1162 0.1332 0.0169 0.007 1.0 3.5 0.5 0.0 0 1.313 0.1161 0.1331 0.0170 0.007 1.1 3.8 0.5 0.0 0 1.576 0.1159 0.1329 0.0171 0.008 1.1 4.2 0.5 0.0 0 1.838 0.1168 0.1334 0.0165 0.005 0.9 3.5 0.5 0.0 0 0.875 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1329 0.0171 0.008 1.1 4.2 0.5 0.0 0 1.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.29 1.71 3.779 21.201 35.895 3.619 11.59 13.29 1.71 3.779 21.201 1.077 3.619 11.59 13.29 1.71 3.779 21.201 4.487 3.619 11.63 13.34 1.70 3.707 21.195 17.948 3.613 11.74 13.49 1.74 3.720 21.165 35.895 3.619 11.66 13.46 1.81 3.741 21.148 53.843 3.612 11.57 13.41 1.84 3.761 21.145 71.791 3.606 11.54 13.39 1.85 3.770 21.140 89.739 3.603 11.53 13.40 1.87 3.779 21.129 107.686 3.601 11.49 13.38 1.89 3.789 21.122 125.634 3.598 11.47 13.36 1.89 3.793 21.128 143.582 3.597 11.49 13.39 1.90 3.812 21.098 161.529 3.597 11.48 13.39 1.91 3.821 21.098 179.477 3.597 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.487 Accepted refinement result: 11.59 13.29 1.71 3.779 21.201 4.487 3.619 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.11 3.31 213 1748 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.52 76.70 35.34 N/A 213 221 Other: 19.76 26.66 22.11 N/A 0 8 Chain A: 9.12 115.05 19.40 N/A 0 1748 Chain S: 13.05 60.01 35.18 N/A 213 0 Histogram: Values Number of atoms 9.12 - 19.71 1266 19.71 - 30.30 287 30.30 - 40.90 209 40.90 - 51.49 126 51.49 - 62.08 50 62.08 - 72.67 12 72.67 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1329 r_work=0.1159 r_free=0.1329 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1329 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1308 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.18 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= 0.1146 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610070 | | target function (ml) not normalized (work): 300697.180123 | | target function (ml) not normalized (free): 15838.022528 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1308 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1502 0.1502 0.1528 n_refl.: 87590 remove outliers: r(all,work,free)=0.1502 0.1502 0.1528 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1501 0.1501 0.1527 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1142 0.1299 n_refl.: 87590 remove outliers: r(all,work,free)=0.1147 0.1139 0.1299 n_refl.: 87584 ======================== 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 0.3765 299.008 268.011 0.500 1.001 0.324 11.894-9.307 99.02 97 4 0.2371 482.008 470.377 0.870 1.002 0.320 9.237-7.194 98.18 209 7 0.2216 385.712 387.008 0.947 1.003 0.214 7.162-5.571 100.00 427 22 0.2072 295.843 285.428 0.911 1.003 0.200 5.546-4.326 100.00 867 58 0.1095 406.119 401.593 0.955 1.003 0.170 4.315-3.360 100.00 1859 96 0.0922 386.222 383.604 0.993 1.003 0.170 3.356-2.611 100.00 3867 181 0.1151 253.728 251.616 0.997 1.002 0.043 2.608-2.026 99.99 8198 413 0.0931 168.198 167.394 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.139 82.407 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.424 36.003 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.950 21.487 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1299 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1139 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1299 | n_water=434 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1140 r_free=0.1298 | n_water=432 | time (s): 44.020 (total time: 46.530) Filter (q & B) r_work=0.1141 r_free=0.1300 | n_water=429 | time (s): 3.850 (total time: 50.380) Compute maps r_work=0.1141 r_free=0.1300 | n_water=429 | time (s): 1.860 (total time: 52.240) Filter (map) r_work=0.1166 r_free=0.1310 | n_water=314 | time (s): 3.950 (total time: 56.190) Find peaks r_work=0.1166 r_free=0.1310 | n_water=314 | time (s): 0.680 (total time: 56.870) Add new water r_work=0.1241 r_free=0.1399 | n_water=472 | time (s): 3.820 (total time: 60.690) Refine new water occ: r_work=0.1168 r_free=0.1328 adp: r_work=0.1168 r_free=0.1331 occ: r_work=0.1152 r_free=0.1313 adp: r_work=0.1151 r_free=0.1315 occ: r_work=0.1139 r_free=0.1301 adp: r_work=0.1135 r_free=0.1301 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1301 r_work=0.1135 r_free=0.1301 | n_water=472 | time (s): 361.150 (total time: 421.840) Filter (q & B) r_work=0.1141 r_free=0.1306 | n_water=438 | time (s): 4.030 (total time: 425.870) Filter (dist only) r_work=0.1141 r_free=0.1305 | n_water=436 | time (s): 43.800 (total time: 469.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.800752 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.526166 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1338 0.0133 0.002 0.6 3.8 0.5 0.0 0 0.090 0.1169 0.1316 0.0147 0.003 0.7 2.6 0.5 0.0 0 0.270 0.1154 0.1310 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.540 0.1148 0.1308 0.0160 0.006 0.9 3.5 0.5 0.0 0 0.810 0.1145 0.1308 0.0163 0.006 1.0 3.2 0.5 0.0 0 1.080 0.1141 0.1307 0.0166 0.007 1.1 3.5 0.5 0.0 0 1.351 0.1139 0.1308 0.0168 0.008 1.1 3.8 0.5 0.0 0 1.621 0.1138 0.1307 0.0170 0.008 1.1 3.8 0.5 0.0 0 1.891 0.1147 0.1309 0.0162 0.006 1.0 3.5 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1307 0.0166 0.007 1.1 3.5 0.5 0.0 0 1.351 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 13.07 1.66 3.780 21.142 42.526 3.607 11.41 13.07 1.66 3.780 21.142 1.276 3.607 11.41 13.07 1.66 3.779 21.142 5.316 3.607 11.45 13.10 1.65 3.711 21.135 21.263 3.602 11.52 13.24 1.72 3.732 21.104 42.526 3.605 11.45 13.22 1.77 3.757 21.093 63.789 3.599 11.39 13.18 1.79 3.772 21.090 85.052 3.595 11.35 13.13 1.78 3.779 21.090 106.315 3.592 11.34 13.16 1.81 3.793 21.083 127.578 3.591 11.34 13.17 1.83 3.808 21.070 148.842 3.589 11.34 13.19 1.85 3.821 21.066 170.105 3.589 11.33 13.18 1.86 3.829 21.064 191.368 3.588 11.30 13.16 1.85 3.832 21.066 212.631 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.316 Accepted refinement result: 11.41 13.07 1.66 3.779 21.142 5.316 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.01 3.31 216 1747 Protein: 9.11 115.03 17.04 3.31 0 1519 Water: 11.51 76.69 34.84 N/A 216 220 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.03 19.39 N/A 0 1747 Chain S: 13.04 59.44 34.14 N/A 216 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 292 30.29 - 40.89 215 40.89 - 51.48 122 51.48 - 62.07 46 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1307 r_work=0.1141 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1307 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1301 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1137 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604954 | | target function (ml) not normalized (work): 300249.372214 | | target function (ml) not normalized (free): 15809.497263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1137 0.1301 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1475 0.1475 0.1502 n_refl.: 87584 remove outliers: r(all,work,free)=0.1475 0.1475 0.1502 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1474 0.1474 0.1501 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1301 n_refl.: 87584 remove outliers: r(all,work,free)=0.1142 0.1134 0.1301 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3828 301.673 259.829 0.488 1.000 0.330 11.894-9.307 96.08 94 4 0.2451 475.384 458.794 0.861 1.002 0.249 9.237-7.194 98.18 209 7 0.2340 385.712 379.042 0.927 1.003 0.195 7.162-5.571 100.00 427 22 0.2191 295.843 285.339 0.916 1.003 0.190 5.546-4.326 100.00 867 58 0.1143 406.119 401.444 0.963 1.003 0.130 4.315-3.360 100.00 1859 96 0.0919 386.222 384.360 1.004 1.003 0.130 3.356-2.611 100.00 3867 181 0.1113 253.728 251.918 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0909 168.198 167.594 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.139 82.497 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.424 36.041 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.950 21.511 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0185 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1134 r_free=0.1301 After: r_work=0.1135 r_free=0.1301 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1301 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1135 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1301 | n_water=436 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1135 r_free=0.1301 | n_water=436 | time (s): 41.720 (total time: 44.270) Filter (q & B) r_work=0.1135 r_free=0.1301 | n_water=435 | time (s): 3.970 (total time: 48.240) Compute maps r_work=0.1135 r_free=0.1301 | n_water=435 | time (s): 1.860 (total time: 50.100) Filter (map) r_work=0.1162 r_free=0.1312 | n_water=340 | time (s): 4.070 (total time: 54.170) Find peaks r_work=0.1162 r_free=0.1312 | n_water=340 | time (s): 0.730 (total time: 54.900) Add new water r_work=0.1215 r_free=0.1364 | n_water=487 | time (s): 3.830 (total time: 58.730) Refine new water occ: r_work=0.1154 r_free=0.1301 adp: r_work=0.1155 r_free=0.1304 occ: r_work=0.1142 r_free=0.1289 adp: r_work=0.1141 r_free=0.1291 occ: r_work=0.1133 r_free=0.1281 adp: r_work=0.1130 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1281 r_work=0.1130 r_free=0.1281 | n_water=487 | time (s): 249.330 (total time: 308.060) Filter (q & B) r_work=0.1137 r_free=0.1288 | n_water=448 | time (s): 3.980 (total time: 312.040) Filter (dist only) r_work=0.1137 r_free=0.1287 | n_water=446 | time (s): 47.470 (total time: 359.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.723730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.824186 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 0.1229 0.1344 0.0115 0.004 0.7 6.4 0.0 0.0 0 0.086 0.1184 0.1313 0.0128 0.004 0.8 5.4 0.0 0.0 0 0.259 0.1161 0.1300 0.0138 0.005 0.9 6.7 0.5 0.0 0 0.517 0.1156 0.1297 0.0142 0.006 1.0 6.7 0.5 0.0 0 0.776 0.1147 0.1292 0.0145 0.007 1.1 7.0 0.5 0.0 0 1.034 0.1139 0.1286 0.0147 0.008 1.1 7.7 0.5 0.0 0 1.293 0.1136 0.1286 0.0150 0.008 1.1 7.7 0.5 0.0 0 1.551 0.1135 0.1285 0.0151 0.009 1.2 7.7 0.5 0.0 0 1.810 0.1151 0.1294 0.0143 0.006 1.0 7.4 0.5 0.0 0 0.862 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1285 0.0151 0.009 1.2 7.7 0.5 0.0 0 1.810 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.85 1.51 3.779 21.142 46.824 3.601 11.35 12.85 1.51 3.779 21.142 1.405 3.601 11.35 12.85 1.50 3.768 21.142 5.853 3.601 11.42 12.95 1.53 3.712 21.129 23.412 3.598 11.41 13.01 1.60 3.740 21.104 46.824 3.596 11.36 13.00 1.64 3.760 21.094 70.236 3.592 11.30 12.95 1.66 3.775 21.092 93.648 3.587 11.26 12.92 1.66 3.778 21.095 117.060 3.584 11.28 12.99 1.72 3.802 21.078 140.473 3.585 11.26 12.99 1.73 3.816 21.073 163.885 3.584 11.25 12.97 1.72 3.823 21.072 187.297 3.582 11.24 12.97 1.73 3.832 21.069 210.709 3.581 11.22 12.95 1.73 3.835 21.071 234.121 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.853 Accepted refinement result: 11.35 12.85 1.50 3.768 21.142 5.853 3.601 Individual atomic B min max mean iso aniso Overall: 9.12 114.91 21.02 3.28 227 1746 Protein: 9.12 114.91 17.03 3.28 0 1519 Water: 11.51 76.68 34.59 N/A 227 219 Other: 19.71 26.60 22.09 N/A 0 8 Chain A: 9.12 114.91 19.36 N/A 0 1746 Chain S: 13.03 59.43 33.75 N/A 227 0 Histogram: Values Number of atoms 9.12 - 19.70 1266 19.70 - 30.27 300 30.27 - 40.85 218 40.85 - 51.43 122 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=0.1135 r_free=0.1285 r_work=0.1135 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1285 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1281 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598685 | | target function (ml) not normalized (work): 299712.854570 | | target function (ml) not normalized (free): 15780.339891 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1348 0.1331 5.6607 5.6027| | 2: 3.57 - 2.84 1.00 2888 124 0.1064 0.1437 5.1594 5.2293| | 3: 2.83 - 2.48 1.00 2820 163 0.1090 0.1161 4.9419 4.9714| | 4: 2.47 - 2.25 1.00 2825 136 0.0901 0.0970 4.6285 4.6381| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0970 4.5734 4.6194| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.0994 4.2545 4.3581| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1083 3.961 4.0635| | 8: 1.87 - 1.79 1.00 2789 144 0.0904 0.1111 3.8722 3.9855| | 9: 1.79 - 1.72 1.00 2745 138 0.0868 0.1161 3.6331 3.8006| | 10: 1.72 - 1.66 1.00 2831 160 0.0911 0.1194 3.5523 3.7043| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1011 3.4858 3.5434| | 12: 1.61 - 1.56 1.00 2773 144 0.0898 0.1143 3.3218 3.4586| | 13: 1.56 - 1.52 1.00 2745 130 0.0939 0.1020 3.3 3.3791| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1067 3.2324 3.3248| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1213 3.1485 3.2625| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1250 3.13 3.241| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1295 3.1161 3.2258| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1329 3.0978 3.2371| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1550 3.1078 3.254| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1451 3.1088 3.1468| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1494 3.111 3.0945| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1986 3.1189 3.2934| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1812 3.1307 3.2055| | 24: 1.26 - 1.24 1.00 2744 132 0.1700 0.1835 3.124 3.2283| | 25: 1.24 - 1.22 1.00 2733 148 0.1871 0.2148 3.1388 3.2625| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1755 3.1456 3.196| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2155 3.1681 3.1601| | 28: 1.19 - 1.18 1.00 2671 147 0.2198 0.2288 3.1637 3.171| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2373 3.1457 3.2253| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2459 3.1408 3.1674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2922 171 0.95 8.50 1.00 0.97 5739.06| | 2: 3.57 - 2.84 2888 124 0.93 12.51 1.01 0.97 5739.06| | 3: 2.83 - 2.48 2820 163 0.89 16.48 0.99 0.97 4789.19| | 4: 2.47 - 2.25 2825 136 0.92 13.37 1.00 0.98 2339.77| | 5: 2.25 - 2.09 2756 127 0.90 15.60 1.01 0.98 2339.77| | 6: 2.09 - 1.97 2846 113 0.93 12.24 1.02 0.98 1342.21| | 7: 1.97 - 1.87 2787 165 0.95 9.12 1.02 0.98 491.42| | 8: 1.87 - 1.79 2789 144 0.93 12.32 1.00 0.98 491.42| | 9: 1.79 - 1.72 2745 138 0.95 9.83 0.98 0.97 280.04| | 10: 1.72 - 1.66 2831 160 0.94 10.91 0.98 0.97 237.70| | 11: 1.66 - 1.61 2712 147 0.94 11.51 0.98 0.97 227.87| | 12: 1.61 - 1.56 2773 144 0.96 8.80 0.99 0.97 135.12| | 13: 1.56 - 1.52 2745 130 0.95 10.29 1.03 0.97 135.12| | 14: 1.52 - 1.48 2803 134 0.94 10.66 1.02 0.98 121.56| | 15: 1.48 - 1.45 2738 128 0.95 9.83 1.02 0.98 96.74| | 16: 1.45 - 1.42 2756 161 0.94 11.02 1.02 0.98 96.74| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.25| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.98 83.33| | 19: 1.36 - 1.34 2807 134 0.94 11.83 1.00 0.98 83.33| | 20: 1.34 - 1.32 2696 147 0.94 12.06 0.98 0.97 79.40| | 21: 1.32 - 1.30 2785 112 0.94 13.02 0.98 0.96 79.12| | 22: 1.29 - 1.27 2704 152 0.93 13.61 0.98 0.96 79.56| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 81.79| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 81.79| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 83.80| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.03 0.93 86.04| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.04| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 89.76| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 91.16| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.93 91.16| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.12 max = 5739.06 mean = 881.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.37| |phase err.(test): min = 0.00 max = 89.85 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1131 0.1281 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1459 0.1458 0.1504 n_refl.: 87580 remove outliers: r(all,work,free)=0.1459 0.1458 0.1504 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1458 0.1457 0.1503 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1131 0.1284 n_refl.: 87580 remove outliers: r(all,work,free)=0.1138 0.1130 0.1284 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3998 291.495 257.082 0.463 0.999 0.303 11.894-9.307 96.08 94 4 0.2416 475.384 461.006 0.850 1.001 0.290 9.237-7.194 98.18 209 7 0.2399 385.712 378.222 0.915 1.002 0.180 7.162-5.571 100.00 427 22 0.2197 295.843 285.278 0.899 1.002 0.140 5.546-4.326 100.00 867 58 0.1130 406.119 401.564 0.955 1.002 0.127 4.315-3.360 100.00 1859 96 0.0922 386.222 384.179 0.993 1.002 0.093 3.356-2.611 100.00 3867 181 0.1101 253.728 251.818 1.000 1.002 0.040 2.608-2.026 99.99 8198 413 0.0910 168.198 167.515 1.016 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.139 82.453 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.424 36.020 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.950 21.497 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0190 ================= 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 : 0.2603 0.1926 0.081 5.160 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1759 0.081 5.160 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1231 0.1466 0.005 0.824 9.1 119.5 20.1 258 0.131 1_adp: 0.1238 0.1462 0.005 0.824 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1240 0.1465 0.005 0.824 9.1 119.5 20.1 258 0.131 1_occ: 0.1234 0.1464 0.005 0.824 9.1 119.5 20.1 258 0.131 2_bss: 0.1233 0.1456 0.005 0.824 9.1 119.5 20.1 258 0.131 2_settarget: 0.1233 0.1456 0.005 0.824 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1233 0.1456 0.006 0.834 9.1 119.5 20.1 258 0.131 2_nqh: 0.1234 0.1458 0.006 0.834 9.1 119.5 20.1 258 0.134 2_sol: 0.1211 0.1413 0.006 0.834 9.1 115.0 22.2 418 n/a 2_weight: 0.1211 0.1413 0.006 0.834 9.1 115.0 22.2 418 n/a 2_xyzrec: 0.1190 0.1412 0.007 0.875 9.1 115.0 22.2 418 n/a 2_adp: 0.1190 0.1412 0.007 0.875 9.1 115.0 22.2 418 n/a 2_regHadp: 0.1190 0.1412 0.007 0.875 9.1 115.0 22.2 418 n/a 2_occ: 0.1192 0.1415 0.007 0.875 9.1 115.0 22.2 418 n/a 3_bss: 0.1187 0.1410 0.007 0.875 9.1 115.0 22.2 418 n/a 3_settarget: 0.1187 0.1410 0.007 0.875 9.1 115.0 22.2 418 n/a 3_updatecdl: 0.1187 0.1410 0.007 0.875 9.1 115.0 22.2 418 n/a 3_nqh: 0.1187 0.1410 0.007 0.875 9.1 115.0 22.2 418 n/a 3_sol: 0.1207 0.1405 0.007 0.875 9.1 115.0 21.1 434 n/a 3_weight: 0.1207 0.1405 0.007 0.875 9.1 115.0 21.1 434 n/a 3_xyzrec: 0.1159 0.1329 0.008 1.086 9.1 115.0 21.1 434 n/a 3_adp: 0.1159 0.1329 0.008 1.086 9.1 115.0 21.1 434 n/a 3_regHadp: 0.1159 0.1329 0.008 1.086 9.1 115.0 21.1 434 n/a 3_occ: 0.1146 0.1308 0.008 1.086 9.1 115.0 21.1 434 n/a 4_bss: 0.1139 0.1299 0.008 1.086 9.1 115.0 21.1 434 n/a 4_settarget: 0.1139 0.1299 0.008 1.086 9.1 115.0 21.1 434 n/a 4_updatecdl: 0.1139 0.1299 0.008 1.089 9.1 115.0 21.1 434 n/a 4_nqh: 0.1139 0.1299 0.008 1.089 9.1 115.0 21.1 434 n/a 4_sol: 0.1141 0.1305 0.008 1.089 9.1 115.0 21.0 436 n/a 4_weight: 0.1141 0.1305 0.008 1.089 9.1 115.0 21.0 436 n/a 4_xyzrec: 0.1141 0.1307 0.007 1.054 9.1 115.0 21.0 436 n/a 4_adp: 0.1141 0.1307 0.007 1.054 9.1 115.0 21.0 436 n/a 4_regHadp: 0.1141 0.1307 0.007 1.054 9.1 115.0 21.0 436 n/a 4_occ: 0.1137 0.1301 0.007 1.054 9.1 115.0 21.0 436 n/a 5_bss: 0.1134 0.1301 0.007 1.054 9.1 115.0 21.0 436 n/a 5_settarget: 0.1134 0.1301 0.007 1.054 9.1 115.0 21.0 436 n/a 5_updatecdl: 0.1134 0.1301 0.007 1.055 9.1 115.0 21.0 436 n/a 5_setrh: 0.1135 0.1301 0.007 1.055 9.1 115.0 21.0 436 n/a 5_nqh: 0.1135 0.1301 0.007 1.055 9.1 115.0 21.0 436 n/a 5_sol: 0.1137 0.1287 0.007 1.055 9.1 115.0 21.0 446 n/a 5_weight: 0.1137 0.1287 0.007 1.055 9.1 115.0 21.0 446 n/a 5_xyzrec: 0.1135 0.1285 0.009 1.150 9.1 115.0 21.0 446 n/a 5_adp: 0.1135 0.1285 0.009 1.150 9.1 114.9 21.0 446 n/a 5_regHadp: 0.1135 0.1285 0.009 1.150 9.1 114.9 21.0 446 n/a 5_occ: 0.1131 0.1281 0.009 1.150 9.1 114.9 21.0 446 n/a end: 0.1130 0.1284 0.009 1.150 9.1 114.9 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7798058_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7798058_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9200 Refinement macro-cycles (run) : 14378.6100 Write final files (write_after_run_outputs) : 67.8200 Total : 14449.3500 Total CPU time: 4.02 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:21:04 PST -0800 (1735366864.64 s) Start R-work = 0.1626, R-free = 0.1759 Final R-work = 0.1130, R-free = 0.1284 =============================================================================== Job complete usr+sys time: 14588.53 seconds wall clock time: 264 minutes 30.85 seconds (15870.85 seconds total)