Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.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_2514713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.56, per 1000 atoms: 0.46 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: 0.58 Conformation dependent library (CDL) restraints added in 206.1 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.42: 642 1.42 - 1.67: 817 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.444 1.695 -0.251 1.38e-02 5.25e+03 3.31e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.529 -0.193 1.11e-02 8.12e+03 3.01e+02 bond pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 1.459 1.235 0.224 1.32e-02 5.74e+03 2.88e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.17e-02 7.31e+03 2.65e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.652 -0.193 1.21e-02 6.83e+03 2.53e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 3049 4.68 - 9.35: 1933 9.35 - 14.03: 681 14.03 - 18.71: 104 18.71 - 23.38: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 120.55 138.65 -18.10 1.06e+00 8.90e-01 2.92e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.63 -14.51 1.06e+00 8.90e-01 1.87e+02 angle pdb=" O ALA A 61 " pdb=" C ALA A 61 " pdb=" N LYS A 62 " ideal model delta sigma weight residual 122.33 140.46 -18.13 1.34e+00 5.57e-01 1.83e+02 angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 117.30 102.08 15.22 1.16e+00 7.43e-01 1.72e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.55 106.79 13.76 1.06e+00 8.90e-01 1.68e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 918 16.43 - 32.87: 137 32.87 - 49.30: 40 49.30 - 65.73: 13 65.73 - 82.16: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.251: 103 0.251 - 0.500: 86 0.500 - 0.750: 42 0.750 - 0.999: 9 0.999 - 1.248: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 178 " pdb=" N ALA A 178 " pdb=" C ALA A 178 " pdb=" CB ALA A 178 " both_signs ideal model delta sigma weight residual False 2.48 3.73 -1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.095 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.147 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.001 2.00e-02 2.50e+03 5.66e-02 9.60e+01 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.071 2.00e-02 2.50e+03 5.58e-02 9.33e+01 pdb=" CG PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 782 2.28 - 2.86: 7820 2.86 - 3.44: 10665 3.44 - 4.02: 15303 4.02 - 4.60: 22068 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.700 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.806 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.822 1.850 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.833 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.839 2.100 ... (remaining 56633 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_2514713_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= 0.2613 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793216 | | target function (ml) not normalized (work): 232691.668698 | | target function (ml) not normalized (free): 11788.630217 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2052 7.099 4.9369| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1769 4.3431 4.3477| | 3: 2.84 - 2.48 1.00 2833 165 0.2382 0.1711 4.1241 4.1616| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1463 3.8298 3.8312| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1719 3.7935 3.8161| | 6: 2.09 - 1.97 1.00 2846 113 0.2538 0.1728 3.4681 3.5016| | 7: 1.97 - 1.87 1.00 2787 165 0.2528 0.1881 3.1387 3.2411| | 8: 1.87 - 1.79 1.00 2789 144 0.2448 0.1895 3.0576 3.1572| | 9: 1.79 - 1.72 1.00 2745 138 0.2434 0.1715 2.9107 2.864| | 10: 1.72 - 1.66 1.00 2789 158 0.2415 0.1949 2.7981 2.8895| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1864 2.7379 2.7625| | 12: 1.61 - 1.56 1.00 2787 146 0.2524 0.1778 2.6319 2.5503| | 13: 1.56 - 1.52 1.00 2745 130 0.2557 0.1802 2.5834 2.5962| | 14: 1.52 - 1.48 1.00 2803 134 0.2596 0.2132 2.4957 2.5883| | 15: 1.48 - 1.45 1.00 2738 128 0.2575 0.2108 2.4387 2.5288| | 16: 1.45 - 1.42 1.00 2756 161 0.2712 0.2136 2.4137 2.4306| | 17: 1.42 - 1.39 1.00 2785 139 0.2687 0.2096 2.3306 2.3396| | 18: 1.39 - 1.36 1.00 2741 179 0.2739 0.2143 2.2817 2.3264| | 19: 1.36 - 1.34 1.00 2807 134 0.2690 0.2179 2.2469 2.2508| | 20: 1.34 - 1.32 1.00 2696 147 0.2678 0.2099 2.1958 2.1896| | 21: 1.32 - 1.30 1.00 2785 112 0.2735 0.2192 2.1623 2.1604| | 22: 1.29 - 1.27 1.00 2704 152 0.2780 0.2775 2.135 2.2447| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2433 2.0809 2.1748| | 24: 1.26 - 1.24 1.00 2744 132 0.2796 0.2591 2.0763 2.1499| | 25: 1.24 - 1.22 1.00 2734 148 0.2881 0.2492 2.0494 2.0459| | 26: 1.22 - 1.21 1.00 2727 135 0.2875 0.2239 2.017 2.0928| | 27: 1.21 - 1.19 1.00 2814 148 0.2997 0.2569 2.0135 1.9962| | 28: 1.19 - 1.18 1.00 2671 147 0.3012 0.2965 1.9924 2.0469| | 29: 1.18 - 1.16 1.00 2800 134 0.2932 0.2555 1.9538 2.0057| | 30: 1.16 - 1.15 1.00 2740 148 0.3130 0.2746 1.9401 1.9273| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1466.21| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1466.21| | 3: 2.84 - 2.48 2833 165 0.74 31.90 1.24 0.24 1216.55| | 4: 2.47 - 2.25 2825 136 0.81 25.41 1.26 0.25 568.64| | 5: 2.25 - 2.09 2756 127 0.77 29.23 1.28 0.25 568.64| | 6: 2.09 - 1.97 2846 113 0.83 22.63 1.29 0.25 311.98| | 7: 1.97 - 1.87 2787 165 0.90 16.71 1.28 0.26 93.09| | 8: 1.87 - 1.79 2789 144 0.85 21.39 1.24 0.26 93.09| | 9: 1.79 - 1.72 2745 138 0.88 18.42 1.23 0.25 55.32| | 10: 1.72 - 1.66 2789 158 0.87 20.06 1.22 0.25 47.75| | 11: 1.66 - 1.61 2740 147 0.86 21.32 1.24 0.25 46.04| | 12: 1.61 - 1.56 2787 146 0.88 18.40 1.23 0.25 28.73| | 13: 1.56 - 1.52 2745 130 0.87 19.93 1.24 0.25 28.73| | 14: 1.52 - 1.48 2803 134 0.86 20.62 1.24 0.25 25.81| | 15: 1.48 - 1.45 2738 128 0.87 19.98 1.22 0.25 20.46| | 16: 1.45 - 1.42 2756 161 0.86 21.34 1.24 0.25 20.46| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.24 0.25 17.25| | 18: 1.39 - 1.36 2741 179 0.87 21.01 1.24 0.25 15.39| | 19: 1.36 - 1.34 2807 134 0.86 21.86 1.22 0.25 15.39| | 20: 1.34 - 1.32 2696 147 0.87 20.79 1.21 0.25 12.72| | 21: 1.32 - 1.30 2785 112 0.86 21.60 1.21 0.25 12.53| | 22: 1.29 - 1.27 2704 152 0.86 22.19 1.22 0.24 12.25| | 23: 1.27 - 1.26 2802 156 0.86 22.07 1.23 0.24 10.82| | 24: 1.26 - 1.24 2744 132 0.85 22.40 1.21 0.24 10.82| | 25: 1.24 - 1.22 2734 148 0.85 23.36 1.21 0.24 10.31| | 26: 1.22 - 1.21 2727 135 0.85 23.50 1.20 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.83 24.63 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 24.96 1.19 0.23 9.11| | 29: 1.18 - 1.16 2800 134 0.83 24.95 1.16 0.23 8.87| | 30: 1.16 - 1.15 2740 148 0.81 26.98 1.16 0.23 8.87| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.87 max = 1466.21 mean = 213.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.43| |phase err.(test): min = 0.00 max = 89.90 mean = 22.31| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.251 1557 Z= 5.405 Angle : 5.461 18.127 2118 Z= 3.839 Chirality : 0.407 1.248 243 Planarity : 0.033 0.095 284 Dihedral : 13.777 82.164 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 37.84 % 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: -2.79 (0.46), residues: 224 helix: -2.69 (0.38), residues: 109 sheet: -1.93 (0.70), residues: 30 loop : -0.19 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.029 ARG A 5 TYR 0.078 0.038 TYR A 139 PHE 0.145 0.050 PHE A 119 HIS 0.079 0.041 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= 0.2613 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793216 | | target function (ml) not normalized (work): 232691.668698 | | target function (ml) not normalized (free): 11788.630217 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2613 0.1933 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2613 0.1933 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1933 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2010 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1635 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1641 0.1635 0.1755 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 0.3857 386.469 359.071 0.737 0.914 0.408 11.894-9.307 99.02 97 4 0.1839 613.887 595.206 1.016 0.915 0.385 9.237-7.194 100.00 213 7 0.2166 502.084 490.718 1.037 0.916 0.349 7.162-5.571 100.00 427 22 0.2197 376.786 363.390 1.017 0.916 0.278 5.546-4.326 100.00 867 58 0.1253 517.234 511.251 1.052 0.917 0.239 4.315-3.360 100.00 1859 96 0.1133 491.894 487.873 1.101 0.918 0.209 3.356-2.611 100.00 3867 181 0.1436 323.149 319.487 1.086 0.919 0.089 2.608-2.026 99.99 8198 413 0.1350 214.218 211.984 1.094 0.922 0.000 2.025-1.573 100.00 17313 902 0.1637 104.613 103.939 1.091 0.925 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.390 45.098 1.074 0.932 0.000 1.221-1.150 99.97 13689 708 0.2606 29.229 27.002 1.036 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0456 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1637 r_free=0.1758 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.780343 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2009.992458 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 0.1617 0.1726 0.0110 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1524 0.1650 0.0125 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1428 0.1578 0.0150 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1396 0.1562 0.0166 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1360 0.1541 0.0181 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1350 0.1532 0.0183 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1280 0.1488 0.0208 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1273 0.1492 0.0220 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1257 0.1479 0.0223 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1475 0.0229 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1246 0.1482 0.0236 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1240 0.1475 0.0235 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1233 0.1466 0.0233 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1469 0.0236 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1229 0.1469 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1230 0.1467 0.0237 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1468 0.0242 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1224 0.1469 0.0245 0.008 1.0 3.8 0.5 0.6 0 13.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1466 0.0233 0.005 0.8 3.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.66 2.33 3.013 19.058 2009.992 0.018 12.33 14.65 2.32 2.989 19.057 60.300 0.018 12.39 14.63 2.24 2.669 19.057 251.249 0.017 12.73 15.32 2.59 2.745 19.227 1004.996 0.017 12.62 15.51 2.89 3.357 19.644 2009.992 0.016 12.50 15.54 3.04 3.354 19.646 3014.989 0.016 12.45 15.60 3.14 3.501 19.709 4019.985 0.015 12.34 15.48 3.14 3.393 19.636 5024.981 0.015 12.30 15.46 3.16 3.379 19.624 6029.977 0.015 12.23 15.43 3.20 3.137 19.492 7034.974 0.015 12.20 15.45 3.25 3.370 19.586 8039.970 0.015 12.26 15.54 3.28 3.538 19.679 9044.966 0.015 12.24 15.53 3.29 3.519 19.646 10049.962 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: 251.249 Accepted refinement result: 12.39 14.63 2.24 2.669 19.057 251.249 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.43 20.08 3.31 0 1785 Protein: 9.08 115.00 16.99 3.32 0 1519 Water: 11.46 119.43 38.22 N/A 0 258 Other: 19.71 26.61 22.06 N/A 0 8 Chain A: 9.08 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1463 r_work=0.1241 r_free=0.1466 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1241 r_free = 0.1466 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 = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016982 | | target function (ls_wunit_k1) not normalized (work): 1414.512858 | | target function (ls_wunit_k1) not normalized (free): 110.610129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1678 0.1680 0.1697 n_refl.: 87593 remove outliers: r(all,work,free)=0.1678 0.1680 0.1697 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1684 0.1686 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1233 0.1456 n_refl.: 87593 remove outliers: r(all,work,free)=0.1244 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 0.3566 304.040 279.828 0.652 1.003 0.384 11.894-9.307 99.02 97 4 0.1635 482.953 470.214 0.926 1.003 0.380 9.237-7.194 100.00 213 7 0.1873 394.996 388.935 0.963 1.003 0.351 7.162-5.571 100.00 427 22 0.1856 296.423 290.392 0.934 1.003 0.256 5.546-4.326 100.00 867 58 0.1021 406.915 403.794 0.965 1.003 0.220 4.315-3.360 100.00 1859 96 0.0877 386.979 385.815 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1177 254.225 253.016 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1028 168.528 167.765 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1118 82.300 82.491 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1457 36.495 35.992 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 22.995 21.476 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0501 ============================ 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 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1233 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1456 | n_water=258 | time (s): 1.860 (total time: 1.860) Filter (dist) r_work=0.1241 r_free=0.1455 | n_water=251 | time (s): 22.490 (total time: 24.350) Filter (q & B) r_work=0.1243 r_free=0.1455 | n_water=248 | time (s): 2.450 (total time: 26.800) Compute maps r_work=0.1243 r_free=0.1455 | n_water=248 | time (s): 1.410 (total time: 28.210) Filter (map) r_work=0.1261 r_free=0.1458 | n_water=227 | time (s): 2.460 (total time: 30.670) Find peaks r_work=0.1261 r_free=0.1458 | n_water=227 | time (s): 0.650 (total time: 31.320) Add new water r_work=0.1409 r_free=0.1630 | n_water=437 | time (s): 2.400 (total time: 33.720) Refine new water occ: r_work=0.1313 r_free=0.1501 adp: r_work=0.1231 r_free=0.1440 occ: r_work=0.1243 r_free=0.1431 adp: r_work=0.1211 r_free=0.1414 occ: r_work=0.1214 r_free=0.1404 adp: r_work=0.1205 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1400 r_work=0.1205 r_free=0.1400 | n_water=437 | time (s): 63.470 (total time: 97.190) Filter (q & B) r_work=0.1208 r_free=0.1399 | n_water=423 | time (s): 2.810 (total time: 100.000) Filter (dist only) r_work=0.1208 r_free=0.1397 | n_water=422 | time (s): 36.460 (total time: 136.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.945391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1461.207642 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 0.1613 0.1724 0.0112 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1524 0.1650 0.0126 0.001 0.4 5.8 0.0 0.0 0 0.250 0.1403 0.1551 0.0148 0.001 0.4 4.8 0.0 0.0 0 0.500 0.1344 0.1501 0.0156 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1330 0.1505 0.0175 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1312 0.1490 0.0178 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1253 0.1454 0.0202 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1221 0.1432 0.0211 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1213 0.1425 0.0211 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1208 0.1424 0.0216 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1200 0.1419 0.0219 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1196 0.1421 0.0225 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1194 0.1414 0.0220 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1191 0.1413 0.0222 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1188 0.1405 0.0217 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1186 0.1408 0.0223 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1183 0.1413 0.0229 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1182 0.1415 0.0233 0.008 0.9 4.2 0.5 0.0 0 13.973 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1188 0.1405 0.0217 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 11.88 14.05 2.17 3.776 21.804 1461.208 0.016 11.88 14.05 2.17 3.776 21.804 43.836 0.016 11.88 14.05 2.17 3.776 21.804 182.651 0.016 12.03 14.41 2.38 3.633 21.805 730.604 0.015 12.08 14.81 2.73 3.543 21.878 1461.208 0.015 11.93 14.71 2.78 3.459 22.182 2191.811 0.014 11.82 14.66 2.84 3.480 22.186 2922.415 0.014 11.74 14.67 2.93 3.491 21.999 3653.019 0.014 11.75 14.72 2.97 3.492 22.104 4383.623 0.014 11.76 14.77 3.01 3.559 22.246 5114.227 0.014 11.71 14.73 3.03 3.533 22.124 5844.831 0.014 11.69 14.71 3.02 3.576 22.231 6575.434 0.014 11.67 14.73 3.06 3.580 22.177 7306.038 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: 182.651 Accepted refinement result: 11.88 14.05 2.17 3.776 21.804 182.651 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 22.23 3.31 195 1754 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.50 76.69 40.99 N/A 195 227 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.11 115.03 19.49 N/A 0 1754 Chain S: 13.77 60.00 46.95 N/A 195 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.29 244 30.29 - 40.89 166 40.89 - 51.48 133 51.48 - 62.07 122 62.07 - 72.66 13 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=0.1188 r_free=0.1405 r_work=0.1188 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1405 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 = 0.1187 r_free = 0.1403 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 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= 0.1187 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015035 | | target function (ls_wunit_k1) not normalized (work): 1252.334896 | | target function (ls_wunit_k1) not normalized (free): 100.302811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1187 0.1403 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1591 0.1591 0.1618 n_refl.: 87593 remove outliers: r(all,work,free)=0.1591 0.1591 0.1618 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1594 0.1594 0.1620 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1184 0.1400 n_refl.: 87593 remove outliers: r(all,work,free)=0.1193 0.1183 0.1400 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 0.3411 297.383 274.448 0.602 1.001 0.360 11.894-9.307 99.02 97 4 0.1474 482.953 475.495 0.920 1.002 0.324 9.237-7.194 100.00 213 7 0.1665 394.996 395.829 0.982 1.002 0.290 7.162-5.571 100.00 427 22 0.1624 296.423 291.776 0.934 1.002 0.225 5.546-4.326 100.00 867 58 0.0891 406.915 403.874 0.959 1.002 0.199 4.315-3.360 100.00 1859 96 0.0776 386.979 386.057 1.004 1.002 0.180 3.356-2.611 100.00 3867 181 0.1077 254.225 253.426 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1007 168.528 168.025 1.018 1.002 0.000 2.025-1.573 100.00 17313 902 0.1103 82.300 82.552 1.028 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.495 36.010 1.018 1.001 0.000 1.221-1.150 99.97 13689 708 0.2252 22.995 21.387 0.976 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0290 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1400 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=0.1183 r_free=0.1400 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1400 | n_water=422 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1184 r_free=0.1404 | n_water=418 | time (s): 32.720 (total time: 34.880) Filter (q & B) r_work=0.1184 r_free=0.1404 | n_water=418 | time (s): 0.880 (total time: 35.760) Compute maps r_work=0.1184 r_free=0.1404 | n_water=418 | time (s): 1.340 (total time: 37.100) Filter (map) r_work=0.1225 r_free=0.1388 | n_water=289 | time (s): 2.740 (total time: 39.840) Find peaks r_work=0.1225 r_free=0.1388 | n_water=289 | time (s): 0.580 (total time: 40.420) Add new water r_work=0.1343 r_free=0.1488 | n_water=478 | time (s): 3.360 (total time: 43.780) Refine new water occ: r_work=0.1247 r_free=0.1413 adp: r_work=0.1248 r_free=0.1414 occ: r_work=0.1224 r_free=0.1399 adp: r_work=0.1221 r_free=0.1398 occ: r_work=0.1206 r_free=0.1392 adp: r_work=0.1199 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1389 r_work=0.1199 r_free=0.1389 | n_water=478 | time (s): 175.490 (total time: 219.270) Filter (q & B) r_work=0.1204 r_free=0.1390 | n_water=447 | time (s): 3.020 (total time: 222.290) Filter (dist only) r_work=0.1204 r_free=0.1390 | n_water=447 | time (s): 34.800 (total time: 257.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.721258 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.938707 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 0.1233 0.1361 0.0128 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1184 0.1321 0.0137 0.003 0.7 3.8 0.5 0.0 0 0.258 0.1168 0.1310 0.0141 0.004 0.8 3.5 0.5 0.0 0 0.516 0.1159 0.1308 0.0149 0.005 0.9 3.8 0.5 0.0 0 0.775 0.1155 0.1309 0.0154 0.006 1.0 3.2 0.5 0.0 0 1.033 0.1153 0.1311 0.0158 0.007 1.0 3.2 0.5 0.0 0 1.291 0.1150 0.1309 0.0159 0.007 1.1 3.5 0.5 0.0 0 1.549 0.1147 0.1309 0.0162 0.008 1.1 3.8 0.5 0.0 0 1.807 0.1159 0.1309 0.0151 0.005 0.9 3.2 0.5 0.0 0 0.861 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1308 0.0149 0.005 0.9 3.8 0.5 0.0 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.08 1.49 3.779 21.367 43.939 3.625 11.59 13.08 1.49 3.779 21.367 1.318 3.625 11.59 13.08 1.48 3.769 21.367 5.492 3.625 11.61 13.14 1.53 3.710 21.361 21.969 3.617 11.67 13.28 1.61 3.718 21.329 43.939 3.619 11.58 13.23 1.65 3.751 21.318 65.908 3.613 11.52 13.19 1.67 3.765 21.315 87.877 3.608 11.50 13.18 1.68 3.774 21.306 109.847 3.605 11.47 13.17 1.70 3.785 21.303 131.816 3.603 11.46 13.19 1.72 3.801 21.290 153.785 3.603 11.45 13.18 1.73 3.811 21.286 175.755 3.601 11.45 13.19 1.73 3.821 21.281 197.724 3.601 11.43 13.17 1.73 3.828 21.281 219.694 3.600 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.318 Accepted refinement result: 11.59 13.08 1.49 3.779 21.367 1.318 3.625 Individual atomic B min max mean iso aniso Overall: 9.13 115.05 21.42 3.31 226 1748 Protein: 9.13 115.05 17.04 3.32 0 1519 Water: 11.52 76.70 36.28 N/A 226 221 Other: 19.77 26.66 22.11 N/A 0 8 Chain A: 9.13 115.05 19.41 N/A 0 1748 Chain S: 13.79 60.02 37.00 N/A 226 0 Histogram: Values Number of atoms 9.13 - 19.72 1264 19.72 - 30.31 285 30.31 - 40.91 209 40.91 - 51.50 135 51.50 - 62.09 57 62.09 - 72.68 13 72.68 - 83.28 5 83.28 - 93.87 4 93.87 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1308 r_work=0.1159 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1308 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1318 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.13 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= 0.1151 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618897 | | target function (ml) not normalized (work): 301428.812531 | | target function (ml) not normalized (free): 15856.969654 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1151 0.1318 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1500 0.1499 0.1555 n_refl.: 87589 remove outliers: r(all,work,free)=0.1500 0.1499 0.1555 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1499 0.1497 0.1554 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1148 0.1316 n_refl.: 87589 remove outliers: r(all,work,free)=0.1154 0.1146 0.1316 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 92.71 84 5 0.3890 297.383 272.936 0.506 1.001 0.311 11.894-9.307 97.06 95 4 0.2219 476.285 461.994 0.884 1.002 0.297 9.237-7.194 98.64 210 7 0.2182 388.498 390.465 0.964 1.002 0.220 7.162-5.571 100.00 427 22 0.1972 296.423 287.736 0.926 1.002 0.190 5.546-4.326 100.00 867 58 0.1086 406.915 401.992 0.966 1.002 0.180 4.315-3.360 100.00 1859 96 0.0914 386.979 384.586 1.005 1.002 0.170 3.356-2.611 100.00 3867 181 0.1145 254.225 252.119 1.008 1.002 0.038 2.608-2.026 99.99 8198 413 0.0943 168.528 167.753 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0915 82.300 82.558 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1272 36.495 36.074 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.995 21.534 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=-0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1316 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=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1316 | n_water=447 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1146 r_free=0.1317 | n_water=445 | time (s): 48.570 (total time: 51.050) Filter (q & B) r_work=0.1146 r_free=0.1317 | n_water=443 | time (s): 3.940 (total time: 54.990) Compute maps r_work=0.1146 r_free=0.1317 | n_water=443 | time (s): 1.860 (total time: 56.850) Filter (map) r_work=0.1169 r_free=0.1290 | n_water=339 | time (s): 3.780 (total time: 60.630) Find peaks r_work=0.1169 r_free=0.1290 | n_water=339 | time (s): 0.660 (total time: 61.290) Add new water r_work=0.1241 r_free=0.1360 | n_water=490 | time (s): 3.630 (total time: 64.920) Refine new water occ: r_work=0.1172 r_free=0.1305 adp: r_work=0.1172 r_free=0.1305 occ: r_work=0.1157 r_free=0.1293 adp: r_work=0.1155 r_free=0.1292 occ: r_work=0.1145 r_free=0.1287 adp: r_work=0.1141 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1283 r_work=0.1141 r_free=0.1283 | n_water=490 | time (s): 249.720 (total time: 314.640) Filter (q & B) r_work=0.1147 r_free=0.1290 | n_water=455 | time (s): 4.060 (total time: 318.700) Filter (dist only) r_work=0.1153 r_free=0.1287 | n_water=453 | time (s): 47.670 (total time: 366.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.731196 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.340524 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 0.1209 0.1329 0.0120 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1170 0.1305 0.0135 0.003 0.7 3.8 0.5 0.0 0 0.260 0.1156 0.1300 0.0144 0.005 0.9 3.8 0.5 0.0 0 0.519 0.1149 0.1296 0.0146 0.006 0.9 3.8 0.5 0.0 0 0.779 0.1145 0.1289 0.0144 0.006 1.0 4.2 0.5 0.0 0 1.039 0.1142 0.1293 0.0151 0.007 1.0 3.8 0.5 0.0 0 1.298 0.1141 0.1289 0.0148 0.008 1.1 3.8 0.5 0.0 0 1.558 0.1139 0.1293 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.818 0.1147 0.1294 0.0147 0.006 1.0 3.8 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1289 0.0148 0.008 1.1 3.8 0.5 0.0 0 1.558 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.89 1.48 3.781 21.334 36.341 3.609 11.41 12.89 1.48 3.781 21.334 1.090 3.609 11.41 12.89 1.48 3.781 21.334 4.543 3.609 11.44 12.95 1.51 3.709 21.328 18.170 3.605 11.46 13.06 1.60 3.728 21.313 36.341 3.605 11.46 13.11 1.65 3.745 21.294 54.511 3.604 11.39 13.05 1.67 3.760 21.291 72.681 3.599 11.35 13.02 1.67 3.770 21.288 90.851 3.595 11.34 13.02 1.68 3.777 21.286 109.022 3.594 11.32 13.02 1.70 3.786 21.283 127.192 3.592 11.33 13.07 1.74 3.802 21.273 145.362 3.593 11.32 13.06 1.75 3.809 21.271 163.532 3.592 11.30 13.04 1.74 3.815 21.270 181.703 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.090 Accepted refinement result: 11.41 12.89 1.48 3.781 21.334 1.090 3.609 Individual atomic B min max mean iso aniso Overall: 9.12 115.05 21.36 3.31 235 1745 Protein: 9.12 115.05 17.04 3.32 0 1519 Water: 11.51 76.70 35.85 N/A 235 218 Other: 19.76 26.66 22.10 N/A 0 8 Chain A: 9.12 115.05 19.37 N/A 0 1745 Chain S: 13.78 60.01 36.14 N/A 235 0 Histogram: Values Number of atoms 9.12 - 19.71 1265 19.71 - 30.31 287 30.31 - 40.90 220 40.90 - 51.49 132 51.49 - 62.08 52 62.08 - 72.68 13 72.68 - 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=0.1141 r_free=0.1289 r_work=0.1141 r_free=0.1289 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1289 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1289 target_work(ml) = 3.606 | | 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.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606275 | | target function (ml) not normalized (work): 300359.454435 | | target function (ml) not normalized (free): 15822.335800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1134 0.1289 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1484 0.1482 0.1541 n_refl.: 87584 remove outliers: r(all,work,free)=0.1484 0.1482 0.1541 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1483 0.1481 0.1540 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1132 0.1290 n_refl.: 87584 remove outliers: r(all,work,free)=0.1137 0.1129 0.1290 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 0.3797 290.723 262.246 0.475 1.000 0.312 11.894-9.307 94.12 92 4 0.2266 471.194 452.295 0.858 1.002 0.249 9.237-7.194 98.18 209 7 0.2238 386.468 384.825 0.942 1.002 0.200 7.162-5.571 100.00 427 22 0.2039 296.423 287.637 0.920 1.002 0.170 5.546-4.326 100.00 867 58 0.1103 406.915 402.024 0.965 1.002 0.145 4.315-3.360 100.00 1859 96 0.0903 386.979 385.049 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1112 254.225 252.313 1.010 1.002 0.014 2.608-2.026 99.99 8198 413 0.0924 168.528 167.916 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.300 82.628 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.495 36.098 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.995 21.546 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0168 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1129 r_free=0.1290 After: r_work=0.1130 r_free=0.1291 ================================== NQH flips ================================== r_work=0.1130 r_free=0.1291 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=0.1130 r_free=0.1291 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1130 r_free=0.1291 | n_water=453 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1131 r_free=0.1292 | n_water=452 | time (s): 49.790 (total time: 52.300) Filter (q & B) r_work=0.1131 r_free=0.1290 | n_water=451 | time (s): 3.930 (total time: 56.230) Compute maps r_work=0.1131 r_free=0.1290 | n_water=451 | time (s): 1.870 (total time: 58.100) Filter (map) r_work=0.1153 r_free=0.1281 | n_water=363 | time (s): 3.940 (total time: 62.040) Find peaks r_work=0.1153 r_free=0.1281 | n_water=363 | time (s): 0.730 (total time: 62.770) Add new water r_work=0.1205 r_free=0.1325 | n_water=507 | time (s): 4.080 (total time: 66.850) Refine new water occ: r_work=0.1152 r_free=0.1282 adp: r_work=0.1152 r_free=0.1283 occ: r_work=0.1142 r_free=0.1273 adp: r_work=0.1140 r_free=0.1273 occ: r_work=0.1133 r_free=0.1268 adp: r_work=0.1130 r_free=0.1267 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1267 r_work=0.1130 r_free=0.1267 | n_water=507 | time (s): 305.550 (total time: 372.400) Filter (q & B) r_work=0.1136 r_free=0.1275 | n_water=468 | time (s): 4.050 (total time: 376.450) Filter (dist only) r_work=0.1136 r_free=0.1273 | n_water=467 | time (s): 49.690 (total time: 426.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850180 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.644012 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 0.1231 0.1338 0.0106 0.003 0.7 6.4 0.5 0.0 0 0.093 0.1173 0.1296 0.0123 0.004 0.8 7.0 0.0 0.0 0 0.278 0.1156 0.1283 0.0128 0.005 0.9 7.0 0.5 0.0 0 0.555 0.1145 0.1276 0.0131 0.006 1.0 7.0 0.5 0.0 0 0.833 0.1140 0.1273 0.0133 0.007 1.1 6.7 0.5 0.0 0 1.110 0.1137 0.1273 0.0136 0.008 1.1 6.7 0.5 0.0 0 1.388 0.1136 0.1273 0.0136 0.008 1.1 6.4 0.5 0.0 0 1.665 0.1136 0.1272 0.0137 0.008 1.1 6.7 0.5 0.0 0 1.943 0.1144 0.1275 0.0131 0.006 1.0 7.0 0.5 0.0 0 0.925 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1272 0.0137 0.008 1.1 6.7 0.5 0.0 0 1.943 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.72 1.37 3.780 21.367 48.644 3.605 11.36 12.72 1.37 3.780 21.367 1.459 3.605 11.36 12.73 1.36 3.770 21.367 6.081 3.605 11.41 12.84 1.43 3.715 21.353 24.322 3.601 11.41 12.96 1.55 3.736 21.327 48.644 3.601 11.33 12.89 1.56 3.763 21.320 72.966 3.595 11.29 12.84 1.55 3.774 21.318 97.288 3.591 11.27 12.85 1.58 3.786 21.314 121.610 3.588 11.25 12.85 1.60 3.800 21.310 145.932 3.587 11.25 12.89 1.63 3.816 21.301 170.254 3.587 11.23 12.87 1.64 3.820 21.302 194.576 3.585 11.22 12.86 1.64 3.829 21.301 218.898 3.584 11.20 12.83 1.63 3.831 21.302 243.220 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.459 Accepted refinement result: 11.36 12.72 1.37 3.780 21.367 1.459 3.605 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.43 3.31 249 1745 Protein: 9.12 115.04 17.03 3.32 0 1519 Water: 11.50 76.69 35.71 N/A 249 218 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.12 115.04 19.37 N/A 0 1745 Chain S: 13.78 60.01 35.87 N/A 249 0 Histogram: Values Number of atoms 9.12 - 19.71 1267 19.71 - 30.30 295 30.30 - 40.89 216 40.89 - 51.48 140 51.48 - 62.08 52 62.08 - 72.67 13 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=0.1136 r_free=0.1272 r_work=0.1136 r_free=0.1272 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1272 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1270 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1270 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603172 | | target function (ml) not normalized (work): 300075.751781 | | target function (ml) not normalized (free): 15807.779168 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1317 0.1297 5.6346 5.6093| | 2: 3.57 - 2.84 1.00 2888 124 0.1061 0.1295 5.1516 5.182| | 3: 2.83 - 2.48 1.00 2820 163 0.1104 0.1200 4.9377 4.9715| | 4: 2.47 - 2.25 1.00 2825 136 0.0893 0.0989 4.6206 4.6559| | 5: 2.25 - 2.09 1.00 2756 127 0.0887 0.0965 4.5714 4.6266| | 6: 2.09 - 1.97 1.00 2846 113 0.0862 0.1008 4.2617 4.3694| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1098 3.9747 4.0783| | 8: 1.87 - 1.79 1.00 2789 144 0.0920 0.1103 3.8835 3.9788| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1197 3.6429 3.8278| | 10: 1.72 - 1.66 1.00 2831 160 0.0920 0.1175 3.563 3.7084| | 11: 1.66 - 1.61 1.00 2712 147 0.0874 0.1024 3.4984 3.5669| | 12: 1.61 - 1.56 1.00 2773 144 0.0910 0.1176 3.3363 3.4772| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1061 3.3116 3.4095| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1042 3.2451 3.3308| | 15: 1.48 - 1.45 1.00 2738 128 0.1013 0.1237 3.1611 3.2719| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1269 3.1383 3.25| | 17: 1.42 - 1.39 1.00 2785 139 0.1145 0.1309 3.1241 3.24| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1323 3.1068 3.2368| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1567 3.1156 3.2692| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1463 3.114 3.1522| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1513 3.1152 3.112| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1976 3.1246 3.2907| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1785 3.1336 3.2005| | 24: 1.26 - 1.24 1.00 2744 132 0.1703 0.1856 3.1266 3.2316| | 25: 1.24 - 1.22 1.00 2733 148 0.1874 0.2142 3.1425 3.2579| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1779 3.148 3.206| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2168 3.1713 3.1667| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2299 3.1664 3.1737| | 29: 1.18 - 1.16 1.00 2800 134 0.2260 0.2387 3.1475 3.2274| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2450 3.1438 3.1663| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1.00 0.97 5576.43| | 2: 3.57 - 2.84 2888 124 0.93 12.32 1.01 0.97 5576.43| | 3: 2.83 - 2.48 2820 163 0.90 16.20 0.99 0.97 4658.41| | 4: 2.47 - 2.25 2825 136 0.92 13.21 1.00 0.98 2291.13| | 5: 2.25 - 2.09 2756 127 0.91 15.30 1.01 0.98 2291.13| | 6: 2.09 - 1.97 2846 113 0.93 12.13 1.02 0.98 1323.90| | 7: 1.97 - 1.87 2787 165 0.95 9.13 1.02 0.98 498.98| | 8: 1.87 - 1.79 2789 144 0.93 12.40 1.00 0.98 498.98| | 9: 1.79 - 1.72 2745 138 0.94 9.97 0.98 0.98 285.97| | 10: 1.72 - 1.66 2831 160 0.94 11.07 0.98 0.98 243.31| | 11: 1.66 - 1.61 2712 147 0.94 11.66 0.98 0.97 233.34| | 12: 1.61 - 1.56 2773 144 0.95 9.02 0.99 0.97 139.23| | 13: 1.56 - 1.52 2745 130 0.95 10.50 1.03 0.97 139.23| | 14: 1.52 - 1.48 2803 134 0.94 10.89 1.02 0.98 125.20| | 15: 1.48 - 1.45 2738 128 0.95 10.06 1.02 0.98 99.50| | 16: 1.45 - 1.42 2756 161 0.94 11.22 1.02 0.98 99.50| | 17: 1.42 - 1.39 2785 139 0.95 11.02 1.01 0.98 90.38| | 18: 1.39 - 1.36 2741 179 0.94 11.61 1.01 0.98 85.11| | 19: 1.36 - 1.34 2807 134 0.94 11.96 1.00 0.98 85.11| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.97 80.59| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 80.27| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.61| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.36| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.36| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.23| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.03 0.93 86.32| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.32| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 89.84| | 29: 1.18 - 1.16 2800 134 0.88 20.43 0.99 0.93 91.16| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 91.16| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 80.27 max = 5576.43 mean = 863.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.40| |phase err.(test): min = 0.00 max = 89.61 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1132 0.1270 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1451 0.1449 0.1510 n_refl.: 87577 remove outliers: r(all,work,free)=0.1451 0.1449 0.1510 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1450 0.1447 0.1509 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1273 n_refl.: 87577 remove outliers: r(all,work,free)=0.1135 0.1128 0.1273 n_refl.: 87570 ======================== 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 86.46 78 5 0.3927 286.009 253.482 0.448 1.000 0.313 11.894-9.307 92.16 90 4 0.2319 476.445 459.844 0.865 1.002 0.237 9.237-7.194 97.27 207 7 0.2240 387.717 382.917 0.926 1.002 0.179 7.162-5.571 100.00 427 22 0.2081 296.423 286.811 0.912 1.002 0.130 5.546-4.326 100.00 867 58 0.1106 406.915 401.952 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0905 386.979 384.904 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1111 254.225 252.390 1.011 1.001 0.020 2.608-2.026 99.99 8198 413 0.0914 168.528 167.938 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.300 82.635 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.495 36.098 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.995 21.547 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0165 ================= 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 : 0.2613 0.1934 0.082 5.461 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1755 0.082 5.461 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1755 0.082 5.461 9.0 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1758 0.082 5.461 9.0 119.5 20.1 258 0.003 1_weight: 0.1637 0.1758 0.082 5.461 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1233 0.1466 0.005 0.838 9.0 119.5 20.1 258 0.128 1_adp: 0.1239 0.1463 0.005 0.838 9.1 119.4 20.1 258 0.128 1_regHadp: 0.1241 0.1466 0.005 0.838 9.1 119.4 20.1 258 0.128 1_occ: 0.1234 0.1462 0.005 0.838 9.1 119.4 20.1 258 0.128 2_bss: 0.1233 0.1456 0.005 0.838 9.1 119.5 20.1 258 0.128 2_settarget: 0.1233 0.1456 0.005 0.838 9.1 119.5 20.1 258 0.128 2_updatecdl: 0.1233 0.1456 0.005 0.842 9.1 119.5 20.1 258 0.128 2_nqh: 0.1233 0.1456 0.005 0.842 9.1 119.5 20.1 258 0.128 2_sol: 0.1208 0.1397 0.005 0.842 9.1 115.0 22.2 422 n/a 2_weight: 0.1208 0.1397 0.005 0.842 9.1 115.0 22.2 422 n/a 2_xyzrec: 0.1188 0.1405 0.006 0.852 9.1 115.0 22.2 422 n/a 2_adp: 0.1188 0.1405 0.006 0.852 9.1 115.0 22.2 422 n/a 2_regHadp: 0.1188 0.1405 0.006 0.852 9.1 115.0 22.2 422 n/a 2_occ: 0.1187 0.1403 0.006 0.852 9.1 115.0 22.2 422 n/a 3_bss: 0.1183 0.1400 0.006 0.852 9.1 115.1 22.3 422 n/a 3_settarget: 0.1183 0.1400 0.006 0.852 9.1 115.1 22.3 422 n/a 3_updatecdl: 0.1183 0.1400 0.006 0.852 9.1 115.1 22.3 422 n/a 3_nqh: 0.1183 0.1400 0.006 0.852 9.1 115.1 22.3 422 n/a 3_sol: 0.1204 0.1390 0.006 0.852 9.1 115.1 21.4 447 n/a 3_weight: 0.1204 0.1390 0.006 0.852 9.1 115.1 21.4 447 n/a 3_xyzrec: 0.1159 0.1308 0.005 0.911 9.1 115.1 21.4 447 n/a 3_adp: 0.1159 0.1308 0.005 0.911 9.1 115.1 21.4 447 n/a 3_regHadp: 0.1159 0.1308 0.005 0.911 9.1 115.1 21.4 447 n/a 3_occ: 0.1151 0.1318 0.005 0.911 9.1 115.1 21.4 447 n/a 4_bss: 0.1146 0.1316 0.005 0.911 9.1 115.0 21.4 447 n/a 4_settarget: 0.1146 0.1316 0.005 0.911 9.1 115.0 21.4 447 n/a 4_updatecdl: 0.1146 0.1316 0.005 0.911 9.1 115.0 21.4 447 n/a 4_nqh: 0.1146 0.1316 0.005 0.911 9.1 115.0 21.4 447 n/a 4_sol: 0.1153 0.1287 0.005 0.911 9.1 115.0 21.4 453 n/a 4_weight: 0.1153 0.1287 0.005 0.911 9.1 115.0 21.4 453 n/a 4_xyzrec: 0.1141 0.1289 0.008 1.089 9.1 115.0 21.4 453 n/a 4_adp: 0.1141 0.1289 0.008 1.089 9.1 115.0 21.4 453 n/a 4_regHadp: 0.1141 0.1289 0.008 1.089 9.1 115.0 21.4 453 n/a 4_occ: 0.1134 0.1289 0.008 1.089 9.1 115.0 21.4 453 n/a 5_bss: 0.1129 0.1290 0.008 1.089 9.1 115.0 21.4 453 n/a 5_settarget: 0.1129 0.1290 0.008 1.089 9.1 115.0 21.4 453 n/a 5_updatecdl: 0.1129 0.1290 0.008 1.089 9.1 115.0 21.4 453 n/a 5_setrh: 0.1130 0.1291 0.008 1.089 9.1 115.0 21.4 453 n/a 5_nqh: 0.1130 0.1291 0.008 1.089 9.1 115.0 21.4 453 n/a 5_sol: 0.1136 0.1273 0.008 1.089 9.1 115.0 21.4 467 n/a 5_weight: 0.1136 0.1273 0.008 1.089 9.1 115.0 21.4 467 n/a 5_xyzrec: 0.1136 0.1272 0.008 1.117 9.1 115.0 21.4 467 n/a 5_adp: 0.1136 0.1272 0.008 1.117 9.1 115.0 21.4 467 n/a 5_regHadp: 0.1136 0.1272 0.008 1.117 9.1 115.0 21.4 467 n/a 5_occ: 0.1132 0.1270 0.008 1.117 9.1 115.0 21.4 467 n/a end: 0.1128 0.1273 0.008 1.117 9.1 115.0 21.4 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2514713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2514713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9600 Refinement macro-cycles (run) : 14403.4800 Write final files (write_after_run_outputs) : 68.2100 Total : 14474.6500 Total CPU time: 4.03 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:21:30 PST -0800 (1735366890.54 s) Start R-work = 0.1635, R-free = 0.1755 Final R-work = 0.1128, R-free = 0.1273 =============================================================================== Job complete usr+sys time: 14615.47 seconds wall clock time: 264 minutes 58.78 seconds (15898.78 seconds total)