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_8565654.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.59, per 1000 atoms: 0.47 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: 0.29 Conformation dependent library (CDL) restraints added in 106.8 milliseconds Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 605 0.93 - 1.19: 1066 1.19 - 1.46: 792 1.46 - 1.73: 674 1.73 - 2.00: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.090 0.236 1.10e-02 8.26e+03 4.59e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.553 -0.227 1.10e-02 8.26e+03 4.25e+02 bond pdb=" N ALA A 129 " pdb=" CA ALA A 129 " ideal model delta sigma weight residual 1.456 1.213 0.243 1.31e-02 5.83e+03 3.45e+02 bond pdb=" N GLN A 95 " pdb=" CA GLN A 95 " ideal model delta sigma weight residual 1.459 1.676 -0.217 1.17e-02 7.31e+03 3.45e+02 bond pdb=" N GLU A 116 " pdb=" CA GLU A 116 " ideal model delta sigma weight residual 1.462 1.728 -0.266 1.46e-02 4.69e+03 3.33e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3279 4.95 - 9.89: 1859 9.89 - 14.84: 558 14.84 - 19.79: 75 19.79 - 24.73: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.63 -14.43 9.00e-01 1.23e+00 2.57e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.29 111.06 11.23 8.10e-01 1.52e+00 1.92e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 107.28 15.99 1.16e+00 7.43e-01 1.90e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.28 -15.07 1.17e+00 7.31e-01 1.66e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.87 106.77 13.10 1.04e+00 9.25e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 954 17.39 - 34.77: 102 34.77 - 52.15: 37 52.15 - 69.54: 14 69.54 - 86.92: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -149.99 -30.01 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.242: 107 0.242 - 0.482: 79 0.482 - 0.723: 40 0.723 - 0.964: 14 0.964 - 1.204: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.69 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -1.56 -1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.166 9.50e-02 1.11e+02 9.29e-02 1.29e+02 pdb=" NE ARG A 28 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.104 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.142 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.047 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.021 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.117 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.120 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.041 2.00e-02 2.50e+03 6.26e-02 8.81e+01 pdb=" CG HIS A 138 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.148 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 716 2.26 - 2.85: 7771 2.85 - 3.43: 10628 3.43 - 4.02: 15312 4.02 - 4.60: 22148 Nonbonded interactions: 56575 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.681 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.810 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.813 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.833 1.850 ... (remaining 56570 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_8565654_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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787316 | | target function (ml) not normalized (work): 232200.118767 | | target function (ml) not normalized (free): 11802.585392 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2142 7.023 4.9604| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1707 4.3526 4.3208| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1681 4.1316 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2303 0.1514 3.8378 3.8499| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1611 3.8013 3.8362| | 6: 2.09 - 1.97 1.00 2846 113 0.2542 0.1801 3.4696 3.5433| | 7: 1.97 - 1.87 1.00 2787 165 0.2495 0.1809 3.1271 3.1989| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.1888 3.0523 3.1192| | 9: 1.79 - 1.72 1.00 2745 138 0.2427 0.1969 2.8965 2.9568| | 10: 1.72 - 1.66 1.00 2789 158 0.2423 0.1806 2.8051 2.8389| | 11: 1.66 - 1.61 1.00 2740 147 0.2510 0.1902 2.7489 2.7482| | 12: 1.61 - 1.56 1.00 2787 146 0.2521 0.2122 2.6333 2.7213| | 13: 1.56 - 1.52 1.00 2745 130 0.2530 0.1919 2.5602 2.6354| | 14: 1.52 - 1.48 1.00 2803 134 0.2580 0.1795 2.5067 2.5139| | 15: 1.48 - 1.45 1.00 2738 128 0.2596 0.2171 2.4389 2.5198| | 16: 1.45 - 1.42 1.00 2756 161 0.2671 0.2031 2.3991 2.4184| | 17: 1.42 - 1.39 1.00 2785 139 0.2655 0.2343 2.3282 2.4425| | 18: 1.39 - 1.36 1.00 2741 179 0.2684 0.2247 2.2738 2.3654| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2270 2.2379 2.283| | 20: 1.34 - 1.32 1.00 2696 147 0.2637 0.2188 2.1835 2.1568| | 21: 1.32 - 1.30 1.00 2785 112 0.2767 0.2424 2.1685 2.2311| | 22: 1.29 - 1.27 1.00 2704 152 0.2699 0.2440 2.1249 2.1768| | 23: 1.27 - 1.26 1.00 2802 156 0.2695 0.2417 2.0861 2.1662| | 24: 1.26 - 1.24 1.00 2744 132 0.2754 0.2341 2.0674 2.1522| | 25: 1.24 - 1.22 1.00 2734 148 0.2816 0.2395 2.0361 2.0154| | 26: 1.22 - 1.21 1.00 2727 135 0.2843 0.2131 2.0058 2.0304| | 27: 1.21 - 1.19 1.00 2814 148 0.2994 0.2731 2.001 2.0289| | 28: 1.19 - 1.18 1.00 2671 147 0.3004 0.2508 1.9829 1.9276| | 29: 1.18 - 1.16 1.00 2800 134 0.3000 0.2606 1.9604 1.9988| | 30: 1.16 - 1.15 1.00 2740 148 0.3034 0.2918 1.9242 1.9655| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1504.75| | 2: 3.57 - 2.84 2876 122 0.80 26.32 1.27 0.23 1504.75| | 3: 2.84 - 2.48 2833 165 0.74 32.29 1.25 0.23 1247.77| | 4: 2.47 - 2.25 2825 136 0.81 25.81 1.25 0.25 580.84| | 5: 2.25 - 2.09 2756 127 0.77 29.61 1.28 0.25 580.84| | 6: 2.09 - 1.97 2846 113 0.83 22.87 1.29 0.25 317.77| | 7: 1.97 - 1.87 2787 165 0.90 16.86 1.27 0.25 93.41| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 93.41| | 9: 1.79 - 1.72 2745 138 0.88 18.59 1.23 0.25 55.67| | 10: 1.72 - 1.66 2789 158 0.87 20.10 1.22 0.25 48.11| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 46.45| | 12: 1.61 - 1.56 2787 146 0.88 18.51 1.23 0.25 29.58| | 13: 1.56 - 1.52 2745 130 0.87 20.41 1.24 0.25 29.58| | 14: 1.52 - 1.48 2803 134 0.87 20.59 1.24 0.25 26.37| | 15: 1.48 - 1.45 2738 128 0.87 20.08 1.22 0.25 20.49| | 16: 1.45 - 1.42 2756 161 0.86 21.54 1.24 0.25 20.49| | 17: 1.42 - 1.39 2785 139 0.86 20.90 1.23 0.25 17.57| | 18: 1.39 - 1.36 2741 179 0.86 21.34 1.23 0.25 15.87| | 19: 1.36 - 1.34 2807 134 0.85 22.29 1.22 0.25 15.87| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.21 0.25 13.06| | 21: 1.32 - 1.30 2785 112 0.86 22.08 1.21 0.25 12.86| | 22: 1.29 - 1.27 2704 152 0.86 22.24 1.21 0.25 12.53| | 23: 1.27 - 1.26 2802 156 0.86 21.56 1.21 0.24 10.84| | 24: 1.26 - 1.24 2744 132 0.85 22.45 1.20 0.24 10.84| | 25: 1.24 - 1.22 2734 148 0.85 23.00 1.20 0.24 10.11| | 26: 1.22 - 1.21 2727 135 0.85 23.02 1.20 0.23 9.30| | 27: 1.21 - 1.19 2814 148 0.84 23.87 1.21 0.23 9.30| | 28: 1.19 - 1.18 2671 147 0.84 24.21 1.19 0.23 8.57| | 29: 1.18 - 1.16 2800 134 0.84 24.54 1.16 0.23 8.29| | 30: 1.16 - 1.15 2740 148 0.82 25.73 1.15 0.23 8.29| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.29 max = 1504.75 mean = 218.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.46| |phase err.(test): min = 0.00 max = 89.65 mean = 22.21| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.266 1557 Z= 5.534 Angle : 5.258 23.015 2118 Z= 3.666 Chirality : 0.408 1.204 243 Planarity : 0.033 0.139 284 Dihedral : 14.100 86.919 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.48), residues: 224 helix: -3.20 (0.32), residues: 109 sheet: -0.60 (0.84), residues: 38 loop : -1.00 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 98 TYR 0.083 0.039 TYR A 141 PHE 0.141 0.039 PHE A 119 HIS 0.104 0.040 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787316 | | target function (ml) not normalized (work): 232200.118767 | | target function (ml) not normalized (free): 11802.585392 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2599 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2599 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1970 0.1974 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1994 0.1998 0.1958 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1626 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1626 0.1765 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 0.3841 386.325 356.727 0.723 0.913 0.401 11.894-9.307 99.02 97 4 0.1797 613.658 592.762 1.015 0.914 0.375 9.237-7.194 100.00 213 7 0.2199 501.897 490.401 1.055 0.915 0.370 7.162-5.571 100.00 427 22 0.2126 376.646 364.898 1.023 0.916 0.310 5.546-4.326 100.00 867 58 0.1287 517.041 511.674 1.054 0.917 0.214 4.315-3.360 100.00 1859 96 0.1152 491.710 488.246 1.097 0.918 0.189 3.356-2.611 100.00 3867 181 0.1431 323.028 319.349 1.088 0.920 0.109 2.608-2.026 99.99 8198 413 0.1328 214.138 211.996 1.093 0.923 0.000 2.025-1.573 100.00 17313 902 0.1627 104.574 103.786 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2056 46.372 45.138 1.067 0.936 0.000 1.221-1.150 99.97 13689 708 0.2598 29.218 27.049 1.032 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1765 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.279087 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2013.235035 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 0.1750 0.1874 0.0123 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1593 0.1737 0.0143 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1437 0.1608 0.0170 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1384 0.1577 0.0193 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1363 0.1563 0.0200 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1343 0.1543 0.0200 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1292 0.1508 0.0216 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1269 0.1495 0.0226 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1478 0.0224 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1241 0.1473 0.0232 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1240 0.1471 0.0232 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1473 0.0237 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1235 0.1475 0.0240 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1228 0.1473 0.0245 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1225 0.1465 0.0241 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1224 0.1478 0.0253 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1223 0.1474 0.0251 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1220 0.1475 0.0255 0.007 1.0 3.8 0.5 0.6 0 13.140 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1225 0.1465 0.0241 0.006 0.9 4.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.65 2.41 3.012 19.053 2013.235 0.017 12.25 14.65 2.41 3.011 19.053 60.397 0.017 12.31 14.63 2.31 2.668 19.052 251.654 0.017 12.67 15.25 2.58 2.742 19.214 1006.618 0.016 12.55 15.43 2.89 3.230 19.564 2013.235 0.016 12.39 15.43 3.04 3.350 19.654 3019.853 0.015 12.32 15.36 3.04 3.334 19.631 4026.470 0.015 12.29 15.38 3.09 3.343 19.617 5033.088 0.015 12.26 15.44 3.18 3.357 19.627 6039.705 0.015 12.19 15.36 3.17 3.365 19.612 7046.323 0.015 12.17 15.32 3.15 3.326 19.585 8052.940 0.015 12.17 15.37 3.21 3.375 19.601 9059.558 0.015 12.15 15.39 3.23 3.364 19.574 10066.175 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: 251.654 Accepted refinement result: 12.31 14.63 2.31 2.668 19.052 251.654 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.44 20.08 3.31 0 1785 Protein: 9.05 114.99 16.99 3.32 0 1519 Water: 11.46 119.44 38.22 N/A 0 258 Other: 19.72 26.60 22.05 N/A 0 8 Chain A: 9.05 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1463 r_work=0.1233 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 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= 0.1230 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017006 | | target function (ls_wunit_k1) not normalized (work): 1416.573190 | | target function (ls_wunit_k1) not normalized (free): 111.140178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1673 0.1675 0.1687 n_refl.: 87593 remove outliers: r(all,work,free)=0.1673 0.1675 0.1687 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1680 0.1682 0.1691 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1452 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1229 0.1452 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 0.3636 301.515 282.247 0.636 1.002 0.375 11.894-9.307 99.02 97 4 0.1716 483.010 470.153 0.917 1.003 0.371 9.237-7.194 100.00 213 7 0.1889 395.043 389.490 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1867 296.458 289.859 0.936 1.003 0.253 5.546-4.326 100.00 867 58 0.1021 406.963 403.757 0.962 1.003 0.199 4.315-3.360 100.00 1859 96 0.0872 387.025 385.983 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1173 254.255 253.132 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1020 168.548 167.839 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1111 82.310 82.494 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.500 36.004 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.997 21.478 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0558 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1452 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=0.1230 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1453 | n_water=258 | time (s): 1.590 (total time: 1.590) Filter (dist) r_work=0.1240 r_free=0.1450 | n_water=251 | time (s): 21.960 (total time: 23.550) Filter (q & B) r_work=0.1243 r_free=0.1450 | n_water=248 | time (s): 3.090 (total time: 26.640) Compute maps r_work=0.1243 r_free=0.1450 | n_water=248 | time (s): 1.150 (total time: 27.790) Filter (map) r_work=0.1256 r_free=0.1457 | n_water=227 | time (s): 2.420 (total time: 30.210) Find peaks r_work=0.1256 r_free=0.1457 | n_water=227 | time (s): 0.490 (total time: 30.700) Add new water r_work=0.1397 r_free=0.1628 | n_water=434 | time (s): 3.070 (total time: 33.770) Refine new water occ: r_work=0.1305 r_free=0.1492 adp: r_work=0.1225 r_free=0.1435 occ: r_work=0.1236 r_free=0.1423 adp: r_work=0.1205 r_free=0.1404 occ: r_work=0.1208 r_free=0.1396 adp: r_work=0.1198 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1395 r_work=0.1198 r_free=0.1395 | n_water=434 | time (s): 52.130 (total time: 85.900) Filter (q & B) r_work=0.1201 r_free=0.1400 | n_water=418 | time (s): 3.500 (total time: 89.400) Filter (dist only) r_work=0.1202 r_free=0.1399 | n_water=417 | time (s): 32.310 (total time: 121.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.231226 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1472.550505 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 0.1663 0.1787 0.0124 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1524 0.1662 0.0138 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1408 0.1567 0.0159 0.002 0.4 4.8 0.0 0.0 0 0.500 0.1359 0.1527 0.0168 0.002 0.4 4.5 0.0 0.0 0 0.750 0.1299 0.1479 0.0180 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1314 0.1493 0.0179 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1253 0.1455 0.0202 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1231 0.1449 0.0218 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1216 0.1435 0.0218 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1211 0.1431 0.0221 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1205 0.1427 0.0222 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1200 0.1423 0.0223 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1195 0.1418 0.0223 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1193 0.1420 0.0227 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1192 0.1416 0.0224 0.006 0.8 4.2 0.5 0.0 0 10.000 0.1190 0.1416 0.0226 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1188 0.1413 0.0225 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1186 0.1414 0.0228 0.008 0.9 4.2 0.5 0.6 0 13.000 0.1184 0.1412 0.0228 0.008 0.9 5.1 0.5 0.6 0 14.116 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1184 0.1412 0.0228 0.008 0.9 5.1 0.5 0.6 0 14.116 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 14.12 2.28 3.775 21.756 1472.551 0.016 11.84 14.12 2.28 3.775 21.756 44.177 0.016 11.84 14.12 2.28 3.775 21.756 184.069 0.016 11.97 14.44 2.47 3.645 21.753 736.275 0.015 12.04 14.82 2.78 3.483 22.087 1472.551 0.015 11.85 14.75 2.91 3.456 22.072 2208.826 0.014 11.71 14.71 3.00 3.536 21.866 2945.101 0.014 11.71 14.74 3.03 3.497 22.092 3681.376 0.014 11.65 14.68 3.03 3.511 22.069 4417.652 0.014 11.68 14.85 3.17 3.544 22.085 5153.927 0.014 11.58 14.71 3.13 3.542 22.123 5890.202 0.014 11.60 14.80 3.20 3.570 22.146 6626.477 0.014 11.57 14.80 3.24 3.573 22.083 7362.753 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: 44.177 Accepted refinement result: 11.84 14.12 2.28 3.775 21.756 44.177 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 22.15 3.31 190 1754 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.49 76.68 40.82 N/A 190 227 Other: 19.76 26.64 22.09 N/A 0 8 Chain A: 9.09 115.03 19.48 N/A 0 1754 Chain S: 11.91 60.00 46.83 N/A 190 0 Histogram: Values Number of atoms 9.09 - 19.68 1261 19.68 - 30.28 244 30.28 - 40.87 164 40.87 - 51.46 131 51.46 - 62.06 121 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1412 r_work=0.1184 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 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 = 0.1182 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.17 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= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014878 | | target function (ls_wunit_k1) not normalized (work): 1239.318474 | | target function (ls_wunit_k1) not normalized (free): 104.134943 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1182 0.1412 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1577 0.1575 0.1634 n_refl.: 87592 remove outliers: r(all,work,free)=0.1577 0.1575 0.1634 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1579 0.1577 0.1636 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1179 0.1404 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1404 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3381 297.418 274.913 0.580 1.002 0.350 11.894-9.307 99.02 97 4 0.1742 483.010 474.229 0.912 1.003 0.330 9.237-7.194 100.00 213 7 0.1666 395.043 394.808 0.984 1.003 0.270 7.162-5.571 100.00 427 22 0.1548 296.458 292.897 0.938 1.003 0.230 5.546-4.326 100.00 867 58 0.0888 406.963 403.694 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0758 387.025 386.118 1.006 1.003 0.190 3.356-2.611 100.00 3867 181 0.1082 254.255 253.463 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1002 168.548 168.005 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.310 82.519 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.500 36.029 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.997 21.501 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1404 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=0.1178 r_free=0.1404 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1404 | n_water=417 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1178 r_free=0.1406 | n_water=414 | time (s): 37.110 (total time: 39.080) Filter (q & B) r_work=0.1178 r_free=0.1404 | n_water=413 | time (s): 2.940 (total time: 42.020) Compute maps r_work=0.1178 r_free=0.1404 | n_water=413 | time (s): 1.270 (total time: 43.290) Filter (map) r_work=0.1220 r_free=0.1384 | n_water=288 | time (s): 2.650 (total time: 45.940) Find peaks r_work=0.1220 r_free=0.1384 | n_water=288 | time (s): 0.610 (total time: 46.550) Add new water r_work=0.1330 r_free=0.1490 | n_water=471 | time (s): 3.150 (total time: 49.700) Refine new water occ: r_work=0.1236 r_free=0.1413 adp: r_work=0.1238 r_free=0.1412 occ: r_work=0.1215 r_free=0.1400 adp: r_work=0.1214 r_free=0.1398 occ: r_work=0.1198 r_free=0.1389 adp: r_work=0.1193 r_free=0.1383 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1383 r_work=0.1193 r_free=0.1383 | n_water=471 | time (s): 237.160 (total time: 286.860) Filter (q & B) r_work=0.1199 r_free=0.1390 | n_water=438 | time (s): 2.380 (total time: 289.240) Filter (dist only) r_work=0.1200 r_free=0.1389 | n_water=437 | time (s): 40.640 (total time: 329.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.653749 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.182162 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 0.1367 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.083 0.1192 0.1329 0.0138 0.003 0.7 3.5 0.5 0.0 0 0.248 0.1176 0.1320 0.0144 0.004 0.8 3.2 0.5 0.0 0 0.496 0.1168 0.1317 0.0150 0.005 0.9 3.2 0.5 0.0 0 0.744 0.1163 0.1317 0.0154 0.006 1.0 3.2 0.5 0.0 0 0.992 0.1160 0.1316 0.0156 0.007 1.0 3.8 0.5 0.0 0 1.240 0.1157 0.1311 0.0155 0.007 1.0 3.8 0.5 0.6 0 1.488 0.1156 0.1312 0.0156 0.008 1.1 3.8 0.5 0.6 0 1.736 0.1165 0.1316 0.0151 0.005 0.9 3.2 0.5 0.0 0 0.827 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1311 0.0155 0.007 1.0 3.8 0.5 0.6 0 1.488 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.11 1.55 3.779 21.263 45.182 3.621 11.57 13.11 1.55 3.779 21.263 1.355 3.621 11.58 13.11 1.54 3.764 21.263 5.648 3.621 11.62 13.17 1.55 3.712 21.248 22.591 3.615 11.63 13.25 1.61 3.730 21.216 45.182 3.614 11.53 13.20 1.67 3.761 21.209 67.773 3.608 11.51 13.22 1.71 3.777 21.199 90.364 3.605 11.48 13.21 1.73 3.788 21.192 112.955 3.602 11.46 13.22 1.76 3.803 21.181 135.546 3.601 11.45 13.22 1.78 3.819 21.175 158.138 3.600 11.43 13.20 1.77 3.829 21.171 180.729 3.598 11.42 13.18 1.76 3.836 21.167 203.320 3.597 11.41 13.18 1.77 3.843 21.167 225.911 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.355 Accepted refinement result: 11.57 13.11 1.55 3.779 21.263 1.355 3.621 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.24 3.31 213 1751 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.51 76.70 35.82 N/A 213 224 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.10 115.04 19.45 N/A 0 1751 Chain S: 11.92 60.01 35.93 N/A 213 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 284 30.29 - 40.88 213 40.88 - 51.48 127 51.48 - 62.07 53 62.07 - 72.66 12 72.66 - 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=0.1157 r_free=0.1311 r_work=0.1157 r_free=0.1311 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1311 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1306 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1144 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611586 | | target function (ml) not normalized (work): 300819.805326 | | target function (ml) not normalized (free): 15839.389709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1306 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1488 0.1488 0.1533 n_refl.: 87589 remove outliers: r(all,work,free)=0.1488 0.1488 0.1533 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1488 0.1488 0.1533 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1140 0.1308 n_refl.: 87589 remove outliers: r(all,work,free)=0.1147 0.1139 0.1308 n_refl.: 87586 ======================== 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 0.3961 297.418 276.804 0.496 0.998 0.295 11.894-9.307 98.04 96 4 0.2383 483.135 467.254 0.873 1.000 0.277 9.237-7.194 99.09 211 7 0.2311 389.537 389.211 0.960 1.001 0.180 7.162-5.571 100.00 427 22 0.2080 296.458 286.214 0.922 1.001 0.170 5.546-4.326 100.00 867 58 0.1112 406.963 401.734 0.963 1.001 0.160 4.315-3.360 100.00 1859 96 0.0922 387.025 384.581 1.003 1.001 0.160 3.356-2.611 100.00 3867 181 0.1124 254.255 252.354 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0925 168.548 167.854 1.022 1.002 0.000 2.025-1.573 100.00 17313 902 0.0894 82.310 82.653 1.032 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.500 36.087 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2169 22.997 21.463 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0016 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1308 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=0.1308 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1308 | n_water=437 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1139 r_free=0.1307 | n_water=434 | time (s): 47.910 (total time: 50.410) Filter (q & B) r_work=0.1140 r_free=0.1308 | n_water=433 | time (s): 3.480 (total time: 53.890) Compute maps r_work=0.1140 r_free=0.1308 | n_water=433 | time (s): 1.700 (total time: 55.590) Filter (map) r_work=0.1162 r_free=0.1304 | n_water=328 | time (s): 3.880 (total time: 59.470) Find peaks r_work=0.1162 r_free=0.1304 | n_water=328 | time (s): 0.690 (total time: 60.160) Add new water r_work=0.1233 r_free=0.1361 | n_water=485 | time (s): 3.620 (total time: 63.780) Refine new water occ: r_work=0.1167 r_free=0.1304 adp: r_work=0.1168 r_free=0.1306 occ: r_work=0.1152 r_free=0.1289 adp: r_work=0.1150 r_free=0.1291 occ: r_work=0.1140 r_free=0.1279 adp: r_work=0.1135 r_free=0.1280 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1280 r_work=0.1135 r_free=0.1280 | n_water=485 | time (s): 244.530 (total time: 308.310) Filter (q & B) r_work=0.1140 r_free=0.1284 | n_water=451 | time (s): 3.920 (total time: 312.230) Filter (dist only) r_work=0.1147 r_free=0.1283 | n_water=449 | time (s): 47.920 (total time: 360.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.782969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.871208 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 0.1210 0.1323 0.0113 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1171 0.1298 0.0127 0.003 0.8 3.2 0.5 0.0 0 0.267 0.1156 0.1285 0.0129 0.005 0.9 5.8 0.5 0.6 0 0.535 0.1150 0.1285 0.0135 0.006 1.0 3.8 0.5 0.0 0 0.802 0.1147 0.1289 0.0142 0.007 1.0 3.8 0.5 0.0 0 1.070 0.1144 0.1285 0.0141 0.007 1.1 3.8 0.5 0.0 0 1.337 0.1143 0.1287 0.0145 0.008 1.1 3.8 0.5 0.0 0 1.605 0.1140 0.1285 0.0145 0.009 1.1 3.8 0.5 0.0 0 1.872 0.1150 0.1290 0.0140 0.006 1.0 3.5 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1285 0.0129 0.005 0.9 5.8 0.5 0.6 0 0.535 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 12.85 1.29 3.780 21.275 35.871 3.617 11.56 12.85 1.29 3.780 21.275 1.076 3.617 11.56 12.85 1.29 3.779 21.275 4.484 3.617 11.60 12.87 1.27 3.707 21.272 17.936 3.613 11.63 12.96 1.33 3.724 21.256 35.871 3.613 11.63 13.02 1.39 3.734 21.239 53.807 3.612 11.55 12.98 1.42 3.753 21.235 71.742 3.607 11.52 12.97 1.45 3.764 21.233 89.678 3.604 11.51 12.98 1.47 3.769 21.228 107.614 3.602 11.48 12.96 1.48 3.778 21.226 125.549 3.600 11.47 12.97 1.50 3.789 21.224 143.485 3.599 11.46 12.97 1.51 3.801 21.216 161.420 3.598 11.46 12.99 1.52 3.809 21.214 179.356 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.484 Accepted refinement result: 11.56 12.85 1.29 3.779 21.275 4.484 3.617 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.26 3.31 227 1749 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.51 76.70 35.53 N/A 227 222 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.10 115.03 19.42 N/A 0 1749 Chain S: 11.92 60.01 35.39 N/A 227 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.29 293 30.29 - 40.88 222 40.88 - 51.47 124 51.47 - 62.07 51 62.07 - 72.66 12 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=0.1156 r_free=0.1285 r_work=0.1156 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1285 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1284 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87586 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614437 | | target function (ml) not normalized (work): 301046.440692 | | target function (ml) not normalized (free): 15814.626997 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1157 0.1150 0.1284 n_refl.: 87586 re-set all scales: r(all,work,free)=0.1479 0.1479 0.1503 n_refl.: 87586 remove outliers: r(all,work,free)=0.1479 0.1479 0.1503 n_refl.: 87586 overall B=-0.00 to atoms: r(all,work,free)=0.1479 0.1479 0.1503 n_refl.: 87586 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1150 0.1287 n_refl.: 87586 remove outliers: r(all,work,free)=0.1153 0.1146 0.1287 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 89.58 81 5 0.3980 296.778 252.818 0.461 0.998 0.314 11.894-9.307 94.12 92 4 0.2292 471.250 460.376 0.862 1.000 0.243 9.237-7.194 98.18 209 7 0.2322 386.514 384.610 0.938 1.000 0.180 7.162-5.571 100.00 427 22 0.2146 296.458 286.491 0.914 1.001 0.164 5.546-4.326 100.00 867 58 0.1125 406.963 401.585 0.961 1.001 0.128 4.315-3.360 100.00 1859 96 0.0926 387.025 385.093 1.005 1.001 0.107 3.356-2.611 100.00 3867 181 0.1113 254.255 252.484 1.011 1.001 0.024 2.608-2.026 99.99 8198 413 0.0928 168.548 167.874 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0910 82.310 82.651 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1273 36.500 36.086 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2181 22.997 21.454 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=0.0014 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1146 r_free=0.1287 After: r_work=0.1146 r_free=0.1287 ================================== NQH flips ================================== r_work=0.1146 r_free=0.1287 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=0.1287 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1287 | n_water=449 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1147 r_free=0.1288 | n_water=448 | time (s): 47.230 (total time: 49.710) Filter (q & B) r_work=0.1147 r_free=0.1290 | n_water=446 | time (s): 3.980 (total time: 53.690) Compute maps r_work=0.1147 r_free=0.1290 | n_water=446 | time (s): 1.900 (total time: 55.590) Filter (map) r_work=0.1172 r_free=0.1310 | n_water=346 | time (s): 4.350 (total time: 59.940) Find peaks r_work=0.1172 r_free=0.1310 | n_water=346 | time (s): 0.690 (total time: 60.630) Add new water r_work=0.1221 r_free=0.1361 | n_water=486 | time (s): 3.780 (total time: 64.410) Refine new water occ: r_work=0.1167 r_free=0.1303 adp: r_work=0.1168 r_free=0.1305 occ: r_work=0.1156 r_free=0.1289 adp: r_work=0.1155 r_free=0.1291 occ: r_work=0.1148 r_free=0.1279 adp: r_work=0.1145 r_free=0.1280 ADP+occupancy (water only), MIN, final r_work=0.1145 r_free=0.1280 r_work=0.1145 r_free=0.1280 | n_water=486 | time (s): 154.780 (total time: 219.190) Filter (q & B) r_work=0.1151 r_free=0.1282 | n_water=449 | time (s): 3.980 (total time: 223.170) Filter (dist only) r_work=0.1151 r_free=0.1283 | n_water=447 | time (s): 47.020 (total time: 270.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850077 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.462944 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 0.1215 0.1322 0.0108 0.003 0.7 6.4 0.0 0.0 0 0.093 0.1172 0.1295 0.0123 0.005 0.8 5.8 0.0 0.0 0 0.278 0.1151 0.1283 0.0133 0.005 0.9 5.1 0.5 0.6 0 0.555 0.1148 0.1282 0.0135 0.006 1.0 5.1 0.5 0.0 0 0.833 0.1145 0.1281 0.0136 0.007 1.0 4.8 0.5 0.0 0 1.110 0.1143 0.1280 0.0138 0.007 1.1 4.8 0.5 0.0 0 1.388 0.1141 0.1280 0.0139 0.008 1.1 4.8 0.5 0.0 0 1.665 0.1140 0.1281 0.0141 0.009 1.1 5.1 0.5 0.0 0 1.943 0.1147 0.1282 0.0135 0.006 1.0 5.1 0.5 0.0 0 0.925 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1280 0.0139 0.008 1.1 4.8 0.5 0.0 0 1.665 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.80 1.39 3.779 21.215 41.463 3.607 11.41 12.80 1.39 3.779 21.215 1.244 3.607 11.41 12.80 1.39 3.779 21.215 5.183 3.606 11.44 12.83 1.38 3.710 21.210 20.731 3.601 11.51 12.98 1.47 3.725 21.181 41.463 3.605 11.44 12.96 1.52 3.748 21.170 62.194 3.599 11.38 12.91 1.53 3.765 21.167 82.926 3.595 11.36 12.91 1.55 3.775 21.165 103.657 3.593 11.33 12.90 1.57 3.785 21.162 124.389 3.591 11.34 12.94 1.60 3.800 21.151 145.120 3.590 11.31 12.91 1.60 3.808 21.154 165.852 3.589 11.30 12.91 1.60 3.817 21.148 186.583 3.588 11.29 12.90 1.60 3.821 21.147 207.315 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.183 Accepted refinement result: 11.41 12.80 1.39 3.779 21.215 5.183 3.606 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.15 3.31 226 1748 Protein: 9.10 115.03 17.03 3.31 0 1519 Water: 11.51 76.70 35.11 N/A 226 221 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.10 115.03 19.40 N/A 0 1748 Chain S: 11.92 60.01 34.64 N/A 226 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 299 30.29 - 40.88 213 40.88 - 51.47 126 51.47 - 62.06 49 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1280 r_work=0.1141 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1280 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1277 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1137 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604758 | | target function (ml) not normalized (work): 300207.886336 | | target function (ml) not normalized (free): 15802.726646 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1344 0.1332 5.6499 5.6175| | 2: 3.57 - 2.84 1.00 2888 124 0.1071 0.1349 5.1596 5.1969| | 3: 2.83 - 2.48 1.00 2820 163 0.1101 0.1172 4.9401 4.9634| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.0959 4.6223 4.6502| | 5: 2.25 - 2.09 1.00 2756 127 0.0873 0.0964 4.571 4.6245| | 6: 2.09 - 1.97 1.00 2846 113 0.0858 0.1059 4.2648 4.3739| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1083 3.9773 4.0649| | 8: 1.87 - 1.79 1.00 2789 144 0.0923 0.1115 3.8898 3.9889| | 9: 1.79 - 1.72 1.00 2745 138 0.0879 0.1150 3.649 3.8172| | 10: 1.72 - 1.66 1.00 2831 160 0.0931 0.1200 3.5735 3.7261| | 11: 1.66 - 1.61 1.00 2712 147 0.0872 0.0998 3.4986 3.5505| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1109 3.3332 3.4389| | 13: 1.56 - 1.52 1.00 2745 130 0.0950 0.1044 3.3053 3.3946| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1042 3.2388 3.3199| | 15: 1.48 - 1.45 1.00 2738 128 0.1008 0.1228 3.1559 3.2695| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1267 3.134 3.2554| | 17: 1.42 - 1.39 1.00 2785 139 0.1146 0.1326 3.1234 3.2433| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1330 3.1063 3.2437| | 19: 1.36 - 1.34 1.00 2807 134 0.1264 0.1579 3.1163 3.2689| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1472 3.1136 3.1593| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1508 3.1149 3.1095| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1983 3.1255 3.2971| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1786 3.1358 3.1982| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1839 3.1289 3.228| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2191 3.145 3.2725| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1774 3.1507 3.2023| | 27: 1.21 - 1.19 1.00 2814 148 0.2082 0.2179 3.174 3.1599| | 28: 1.19 - 1.18 1.00 2671 147 0.2212 0.2317 3.1681 3.1765| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2392 3.148 3.228| | 30: 1.16 - 1.15 1.00 2739 148 0.2452 0.2438 3.1452 3.1662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.33 0.99 0.97 5611.69| | 2: 3.57 - 2.84 2888 124 0.93 12.27 1.01 0.97 5611.69| | 3: 2.83 - 2.48 2820 163 0.90 16.25 0.99 0.98 4689.23| | 4: 2.47 - 2.25 2825 136 0.92 13.29 1.00 0.98 2310.51| | 5: 2.25 - 2.09 2756 127 0.90 15.44 1.01 0.98 2310.51| | 6: 2.09 - 1.97 2846 113 0.93 12.22 1.02 0.98 1336.18| | 7: 1.97 - 1.87 2787 165 0.95 9.12 1.02 0.98 505.21| | 8: 1.87 - 1.79 2789 144 0.93 12.50 1.00 0.98 505.21| | 9: 1.79 - 1.72 2745 138 0.94 9.99 0.98 0.98 287.71| | 10: 1.72 - 1.66 2831 160 0.94 11.07 0.98 0.98 244.15| | 11: 1.66 - 1.61 2712 147 0.94 11.66 0.98 0.98 233.82| | 12: 1.61 - 1.56 2773 144 0.96 8.84 0.99 0.98 136.42| | 13: 1.56 - 1.52 2745 130 0.95 10.35 1.03 0.98 136.42| | 14: 1.52 - 1.48 2803 134 0.94 10.71 1.02 0.98 122.91| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.99 98.17| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.99 98.17| | 17: 1.42 - 1.39 2785 139 0.95 10.98 1.01 0.99 89.81| | 18: 1.39 - 1.36 2741 179 0.94 11.63 1.01 0.99 84.98| | 19: 1.36 - 1.34 2807 134 0.94 11.98 1.00 0.99 84.98| | 20: 1.34 - 1.32 2696 147 0.94 12.23 0.98 0.97 81.08| | 21: 1.32 - 1.30 2785 112 0.94 13.22 0.98 0.97 80.81| | 22: 1.29 - 1.27 2704 152 0.93 13.75 0.98 0.96 81.16| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.97 0.95 82.98| | 24: 1.26 - 1.24 2744 132 0.92 14.92 0.96 0.95 82.98| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.82| | 26: 1.22 - 1.21 2727 135 0.90 18.18 1.03 0.93 86.87| | 27: 1.21 - 1.19 2814 148 0.89 18.88 1.03 0.93 86.87| | 28: 1.19 - 1.18 2671 147 0.88 20.48 1.01 0.93 90.43| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 91.77| | 30: 1.16 - 1.15 2739 148 0.86 22.09 0.98 0.93 91.77| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.81 max = 5611.69 mean = 869.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.42| |phase err.(test): min = 0.00 max = 89.96 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1137 0.1277 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1458 0.1458 0.1496 n_refl.: 87577 remove outliers: r(all,work,free)=0.1458 0.1458 0.1496 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1458 0.1457 0.1495 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1137 0.1279 n_refl.: 87577 remove outliers: r(all,work,free)=0.1143 0.1136 0.1279 n_refl.: 87575 ======================== 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 0.4078 292.100 255.437 0.456 0.999 0.303 11.894-9.307 93.14 91 4 0.2316 475.189 458.573 0.850 1.001 0.223 9.237-7.194 98.18 209 7 0.2394 386.514 380.481 0.922 1.001 0.160 7.162-5.571 100.00 427 22 0.2165 296.458 285.554 0.906 1.002 0.140 5.546-4.326 100.00 867 58 0.1137 406.963 401.801 0.960 1.002 0.109 4.315-3.360 100.00 1859 96 0.0926 387.025 384.816 1.003 1.002 0.090 3.356-2.611 100.00 3867 181 0.1112 254.255 252.673 1.012 1.001 0.014 2.608-2.026 99.99 8198 413 0.0911 168.548 167.938 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.310 82.658 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.500 36.099 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.997 21.536 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=-0.0127 ================= 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 : 0.2598 0.1946 0.083 5.258 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_weight: 0.1626 0.1765 0.083 5.258 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1225 0.1465 0.006 0.880 9.0 119.5 20.1 258 0.134 1_adp: 0.1231 0.1463 0.006 0.880 9.1 119.4 20.1 258 0.134 1_regHadp: 0.1233 0.1467 0.006 0.880 9.1 119.4 20.1 258 0.134 1_occ: 0.1230 0.1461 0.006 0.880 9.1 119.4 20.1 258 0.134 2_bss: 0.1229 0.1452 0.006 0.880 9.1 119.5 20.1 258 0.134 2_settarget: 0.1229 0.1452 0.006 0.880 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1229 0.1452 0.006 0.891 9.1 119.5 20.1 258 0.134 2_nqh: 0.1230 0.1453 0.006 0.891 9.1 119.5 20.1 258 0.137 2_sol: 0.1202 0.1399 0.006 0.891 9.1 115.0 22.1 417 n/a 2_weight: 0.1202 0.1399 0.006 0.891 9.1 115.0 22.1 417 n/a 2_xyzrec: 0.1184 0.1412 0.008 0.940 9.1 115.0 22.1 417 n/a 2_adp: 0.1184 0.1412 0.008 0.940 9.1 115.0 22.1 417 n/a 2_regHadp: 0.1184 0.1412 0.008 0.940 9.1 115.0 22.1 417 n/a 2_occ: 0.1182 0.1412 0.008 0.940 9.1 115.0 22.1 417 n/a 3_bss: 0.1178 0.1404 0.008 0.940 9.1 115.0 22.2 417 n/a 3_settarget: 0.1178 0.1404 0.008 0.940 9.1 115.0 22.2 417 n/a 3_updatecdl: 0.1178 0.1404 0.008 0.939 9.1 115.0 22.2 417 n/a 3_nqh: 0.1178 0.1404 0.008 0.939 9.1 115.0 22.2 417 n/a 3_sol: 0.1200 0.1389 0.008 0.939 9.1 115.0 21.2 437 n/a 3_weight: 0.1200 0.1389 0.008 0.939 9.1 115.0 21.2 437 n/a 3_xyzrec: 0.1157 0.1311 0.007 1.043 9.1 115.0 21.2 437 n/a 3_adp: 0.1157 0.1311 0.007 1.043 9.1 115.0 21.2 437 n/a 3_regHadp: 0.1157 0.1311 0.007 1.043 9.1 115.0 21.2 437 n/a 3_occ: 0.1144 0.1306 0.007 1.043 9.1 115.0 21.2 437 n/a 4_bss: 0.1139 0.1308 0.007 1.043 9.1 115.0 21.2 437 n/a 4_settarget: 0.1139 0.1308 0.007 1.043 9.1 115.0 21.2 437 n/a 4_updatecdl: 0.1139 0.1308 0.007 1.046 9.1 115.0 21.2 437 n/a 4_nqh: 0.1139 0.1308 0.007 1.046 9.1 115.0 21.2 437 n/a 4_sol: 0.1147 0.1283 0.007 1.046 9.1 115.0 21.3 449 n/a 4_weight: 0.1147 0.1283 0.007 1.046 9.1 115.0 21.3 449 n/a 4_xyzrec: 0.1156 0.1285 0.005 0.910 9.1 115.0 21.3 449 n/a 4_adp: 0.1156 0.1285 0.005 0.910 9.1 115.0 21.3 449 n/a 4_regHadp: 0.1156 0.1285 0.005 0.910 9.1 115.0 21.3 449 n/a 4_occ: 0.1150 0.1284 0.005 0.910 9.1 115.0 21.3 449 n/a 5_bss: 0.1146 0.1287 0.005 0.910 9.1 115.0 21.3 449 n/a 5_settarget: 0.1146 0.1287 0.005 0.910 9.1 115.0 21.3 449 n/a 5_updatecdl: 0.1146 0.1287 0.005 0.912 9.1 115.0 21.3 449 n/a 5_setrh: 0.1146 0.1287 0.005 0.912 9.1 115.0 21.3 449 n/a 5_nqh: 0.1146 0.1287 0.005 0.912 9.1 115.0 21.3 449 n/a 5_sol: 0.1151 0.1283 0.005 0.912 9.1 115.0 21.1 447 n/a 5_weight: 0.1151 0.1283 0.005 0.912 9.1 115.0 21.1 447 n/a 5_xyzrec: 0.1141 0.1280 0.008 1.105 9.1 115.0 21.1 447 n/a 5_adp: 0.1141 0.1280 0.008 1.105 9.1 115.0 21.1 447 n/a 5_regHadp: 0.1141 0.1280 0.008 1.105 9.1 115.0 21.1 447 n/a 5_occ: 0.1137 0.1277 0.008 1.105 9.1 115.0 21.1 447 n/a end: 0.1136 0.1279 0.008 1.105 9.1 115.0 21.1 447 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8565654_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8565654_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1000 Refinement macro-cycles (run) : 13646.3200 Write final files (write_after_run_outputs) : 92.1000 Total : 13741.5200 Total CPU time: 3.82 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:08:26 PST -0800 (1735366106.78 s) Start R-work = 0.1626, R-free = 0.1765 Final R-work = 0.1136, R-free = 0.1279 =============================================================================== Job complete usr+sys time: 13919.47 seconds wall clock time: 252 minutes 35.51 seconds (15155.51 seconds total)