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_6446528.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.87, per 1000 atoms: 0.55 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: 0.59 Conformation dependent library (CDL) restraints added in 125.3 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: 0.65 - 0.92: 547 0.92 - 1.19: 1123 1.19 - 1.46: 744 1.46 - 1.73: 724 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.232 0.227 1.19e-02 7.06e+03 3.64e+02 bond pdb=" C SER A 121 " pdb=" O SER A 121 " ideal model delta sigma weight residual 1.234 1.455 -0.221 1.27e-02 6.20e+03 3.04e+02 bond pdb=" C ILE A 105 " pdb=" N CYS A 106 " ideal model delta sigma weight residual 1.332 1.574 -0.242 1.40e-02 5.10e+03 2.98e+02 bond pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " ideal model delta sigma weight residual 1.527 1.309 0.218 1.27e-02 6.20e+03 2.94e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.520 1.320 0.200 1.21e-02 6.83e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3315 4.95 - 9.90: 1822 9.90 - 14.85: 544 14.85 - 19.80: 87 19.80 - 24.75: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 141.59 -18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 106.92 15.75 1.09e+00 8.42e-01 2.09e+02 angle pdb=" O VAL A 8 " pdb=" C VAL A 8 " pdb=" N ILE A 9 " ideal model delta sigma weight residual 123.20 137.66 -14.46 1.06e+00 8.90e-01 1.86e+02 angle pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 120.55 134.58 -14.03 1.06e+00 8.90e-01 1.75e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 136.31 -13.28 1.11e+00 8.12e-01 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 18.03: 968 18.03 - 36.04: 86 36.04 - 54.05: 44 54.05 - 72.06: 10 72.06 - 90.07: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " ideal model delta harmonic sigma weight residual 0.00 -21.18 21.18 0 5.00e+00 4.00e-02 1.79e+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 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 96 0.231 - 0.460: 75 0.460 - 0.690: 53 0.690 - 0.919: 13 0.919 - 1.149: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.010 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.167 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.057 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.062 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 164 " 0.139 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.066 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.058 2.00e-02 2.50e+03 5.69e-02 9.71e+01 pdb=" CG PHE A 162 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1017 2.32 - 2.89: 8108 2.89 - 3.46: 10552 3.46 - 4.03: 15217 4.03 - 4.60: 21670 Nonbonded interactions: 56564 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.747 2.100 nonbonded pdb=" O LEU A 166 " pdb=" H GLU A 170 " model vdw 1.820 1.850 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.841 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.844 1.850 nonbonded pdb=" O GLU A 16 " pdb=" H VAL A 20 " model vdw 1.852 1.850 ... (remaining 56559 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_6446528_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= 0.2608 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784748 | | target function (ml) not normalized (work): 231986.208295 | | target function (ml) not normalized (free): 11772.415375 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2105 7.0587 4.95| | 2: 3.57 - 2.84 1.00 2876 122 0.2457 0.1792 4.3496 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1646 4.136 4.1621| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1417 3.8367 3.8321| | 5: 2.25 - 2.09 1.00 2756 127 0.2506 0.1666 3.8014 3.829| | 6: 2.09 - 1.97 1.00 2846 113 0.2542 0.1673 3.4617 3.5493| | 7: 1.97 - 1.87 1.00 2787 165 0.2550 0.1801 3.1368 3.1773| | 8: 1.87 - 1.79 1.00 2789 144 0.2513 0.1760 3.0394 3.0944| | 9: 1.79 - 1.72 1.00 2745 138 0.2430 0.2040 2.8816 3.0192| | 10: 1.72 - 1.66 1.00 2789 158 0.2349 0.1718 2.7889 2.7968| | 11: 1.66 - 1.61 1.00 2740 147 0.2525 0.1888 2.7308 2.7255| | 12: 1.61 - 1.56 1.00 2787 146 0.2549 0.1862 2.6311 2.5902| | 13: 1.56 - 1.52 1.00 2745 130 0.2536 0.1896 2.5616 2.5921| | 14: 1.52 - 1.48 1.00 2803 134 0.2594 0.1967 2.4899 2.5235| | 15: 1.48 - 1.45 1.00 2738 128 0.2532 0.1853 2.4507 2.3522| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2159 2.3697 2.4337| | 17: 1.42 - 1.39 1.00 2785 139 0.2633 0.2126 2.3148 2.3757| | 18: 1.39 - 1.36 1.00 2741 179 0.2629 0.2305 2.2494 2.381| | 19: 1.36 - 1.34 1.00 2807 134 0.2640 0.2093 2.2312 2.2269| | 20: 1.34 - 1.32 1.00 2696 147 0.2679 0.2473 2.1943 2.2749| | 21: 1.32 - 1.30 1.00 2785 112 0.2654 0.2248 2.1446 2.1713| | 22: 1.29 - 1.27 1.00 2704 152 0.2714 0.2552 2.1263 2.2166| | 23: 1.27 - 1.26 1.00 2802 156 0.2754 0.2291 2.104 2.1256| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2590 2.0739 2.2022| | 25: 1.24 - 1.22 1.00 2734 148 0.2847 0.2256 2.0308 2.0587| | 26: 1.22 - 1.21 1.00 2727 135 0.2906 0.2300 2.0156 2.0661| | 27: 1.21 - 1.19 1.00 2814 148 0.2981 0.2590 2.0143 1.994| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2715 1.9878 1.9747| | 29: 1.18 - 1.16 1.00 2800 134 0.2959 0.2801 1.9534 2.0404| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2953 1.9207 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 18.94 0.76 0.23 1508.99| | 2: 3.57 - 2.84 2876 122 0.80 26.32 1.27 0.23 1508.99| | 3: 2.84 - 2.48 2833 165 0.74 32.11 1.24 0.24 1249.81| | 4: 2.47 - 2.25 2825 136 0.81 25.53 1.26 0.25 577.20| | 5: 2.25 - 2.09 2756 127 0.77 29.43 1.28 0.25 577.20| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 312.54| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.28 0.26 86.83| | 8: 1.87 - 1.79 2789 144 0.86 20.78 1.26 0.26 86.83| | 9: 1.79 - 1.72 2745 138 0.88 18.13 1.23 0.25 52.54| | 10: 1.72 - 1.66 2789 158 0.87 19.47 1.21 0.25 45.68| | 11: 1.66 - 1.61 2740 147 0.86 20.91 1.25 0.25 44.06| | 12: 1.61 - 1.56 2787 146 0.89 17.72 1.24 0.25 27.62| | 13: 1.56 - 1.52 2745 130 0.87 19.57 1.24 0.25 27.62| | 14: 1.52 - 1.48 2803 134 0.87 20.07 1.23 0.25 24.97| | 15: 1.48 - 1.45 2738 128 0.88 19.34 1.21 0.25 20.11| | 16: 1.45 - 1.42 2756 161 0.86 21.19 1.24 0.25 20.11| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.23 0.25 17.43| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.25 15.88| | 19: 1.36 - 1.34 2807 134 0.86 21.90 1.22 0.25 15.88| | 20: 1.34 - 1.32 2696 147 0.86 21.27 1.21 0.25 13.32| | 21: 1.32 - 1.30 2785 112 0.86 21.95 1.20 0.25 13.15| | 22: 1.29 - 1.27 2704 152 0.85 22.42 1.21 0.25 12.84| | 23: 1.27 - 1.26 2802 156 0.86 22.09 1.21 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 22.83 1.21 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 23.95 1.20 0.24 10.65| | 26: 1.22 - 1.21 2727 135 0.84 24.07 1.20 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 24.84 1.21 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.83 25.35 1.18 0.23 9.39| | 29: 1.18 - 1.16 2800 134 0.82 25.82 1.16 0.23 9.17| | 30: 1.16 - 1.15 2740 148 0.80 27.67 1.16 0.23 9.17| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.17 max = 1508.99 mean = 217.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.47| |phase err.(test): min = 0.00 max = 89.62 mean = 22.48| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.242 1557 Z= 5.374 Angle : 5.219 18.992 2118 Z= 3.663 Chirality : 0.412 1.149 243 Planarity : 0.032 0.167 284 Dihedral : 13.668 90.066 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % 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: -2.24 (0.49), residues: 224 helix: -2.46 (0.40), residues: 109 sheet: -1.52 (0.69), residues: 30 loop : 0.37 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.013 ARG A 145 TYR 0.134 0.039 TYR A 141 PHE 0.134 0.055 PHE A 164 HIS 0.055 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784748 | | target function (ml) not normalized (work): 231986.208295 | | target function (ml) not normalized (free): 11772.415375 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1927 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1927 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1927 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2000 0.2005 0.1940 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1635 0.1740 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1635 0.1740 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 386.284 355.918 0.668 1.003 0.402 11.894-9.307 99.02 97 4 0.1876 613.594 594.747 0.922 1.003 0.380 9.237-7.194 100.00 213 7 0.2167 501.844 490.365 0.960 1.004 0.344 7.162-5.571 100.00 427 22 0.2227 376.606 363.891 0.933 1.004 0.273 5.546-4.326 100.00 867 58 0.1267 516.987 510.346 0.962 1.004 0.214 4.315-3.360 100.00 1859 96 0.1177 491.658 487.345 1.004 1.003 0.199 3.356-2.611 100.00 3867 181 0.1442 322.994 319.438 0.997 1.003 0.052 2.608-2.026 99.99 8198 413 0.1353 214.116 212.038 1.006 1.002 0.000 2.025-1.573 100.00 17313 902 0.1639 104.563 103.895 1.013 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.367 45.070 1.002 0.997 0.000 1.221-1.150 99.97 13689 708 0.2587 29.215 26.960 0.977 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0445 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1740 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1640 r_free=0.1751 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.308191 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.617701 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 0.1726 0.1841 0.0115 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1627 0.1756 0.0129 0.002 0.4 4.5 0.0 0.0 0 0.250 0.1467 0.1620 0.0152 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1413 0.1586 0.0173 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1364 0.1555 0.0190 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1364 0.1551 0.0186 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1303 0.1515 0.0212 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1278 0.1498 0.0220 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1265 0.1493 0.0229 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1473 0.0228 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1246 0.1478 0.0232 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1243 0.1479 0.0235 0.005 0.8 2.9 0.5 0.0 0 7.000 0.1238 0.1474 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1236 0.1473 0.0237 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1233 0.1474 0.0240 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1233 0.1475 0.0242 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1229 0.1470 0.0241 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1225 0.1475 0.0249 0.008 1.0 3.5 0.5 0.6 0 13.654 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1470 0.0241 0.007 0.9 3.2 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.70 2.41 3.013 19.053 1996.618 0.017 12.29 14.69 2.40 2.989 19.053 59.899 0.017 12.36 14.68 2.32 2.656 19.052 249.577 0.017 12.68 15.29 2.61 2.746 19.222 998.309 0.016 12.52 15.41 2.89 3.332 19.639 1996.618 0.016 12.44 15.45 3.01 3.325 19.633 2994.927 0.015 12.38 15.47 3.10 3.455 19.691 3993.235 0.015 12.27 15.36 3.09 3.306 19.597 4991.544 0.015 12.26 15.45 3.20 3.380 19.643 5989.853 0.015 12.16 15.35 3.19 3.355 19.625 6988.162 0.015 12.16 15.40 3.24 3.347 19.601 7986.471 0.015 12.12 15.33 3.21 3.189 19.507 8984.780 0.015 12.17 15.52 3.35 3.442 19.617 9983.089 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: 249.577 Accepted refinement result: 12.36 14.68 2.32 2.656 19.052 249.577 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.28 0 1785 Protein: 9.07 114.86 16.99 3.29 0 1519 Water: 11.44 119.44 38.22 N/A 0 258 Other: 19.74 26.59 22.06 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.10 1271 20.10 - 31.14 228 31.14 - 42.18 125 42.18 - 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=0.1236 r_free=0.1468 r_work=0.1237 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1471 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016757 | | target function (ls_wunit_k1) not normalized (work): 1395.840104 | | target function (ls_wunit_k1) not normalized (free): 110.337784 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1230 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1671 0.1672 0.1698 n_refl.: 87593 remove outliers: r(all,work,free)=0.1671 0.1672 0.1698 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1677 0.1678 0.1703 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1456 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1456 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 0.3530 301.644 280.950 0.646 1.003 0.374 11.894-9.307 99.02 97 4 0.1635 483.217 471.165 0.921 1.003 0.370 9.237-7.194 100.00 213 7 0.1862 395.212 391.110 0.965 1.003 0.320 7.162-5.571 100.00 427 22 0.1797 296.585 290.931 0.940 1.003 0.261 5.546-4.326 100.00 867 58 0.0988 407.138 404.401 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0870 387.191 386.180 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1176 254.364 253.188 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.1030 168.620 167.893 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1115 82.345 82.529 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.515 36.018 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 23.007 21.490 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0516 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 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** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1228 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1456 | n_water=258 | time (s): 1.530 (total time: 1.530) Filter (dist) r_work=0.1238 r_free=0.1452 | n_water=250 | time (s): 21.740 (total time: 23.270) Filter (q & B) r_work=0.1240 r_free=0.1453 | n_water=247 | time (s): 2.570 (total time: 25.840) Compute maps r_work=0.1240 r_free=0.1453 | n_water=247 | time (s): 1.350 (total time: 27.190) Filter (map) r_work=0.1253 r_free=0.1457 | n_water=225 | time (s): 2.360 (total time: 29.550) Find peaks r_work=0.1253 r_free=0.1457 | n_water=225 | time (s): 0.490 (total time: 30.040) Add new water r_work=0.1401 r_free=0.1615 | n_water=434 | time (s): 2.580 (total time: 32.620) Refine new water occ: r_work=0.1304 r_free=0.1482 adp: r_work=0.1223 r_free=0.1431 occ: r_work=0.1236 r_free=0.1422 adp: r_work=0.1202 r_free=0.1408 occ: r_work=0.1204 r_free=0.1401 adp: r_work=0.1194 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1399 r_work=0.1194 r_free=0.1399 | n_water=434 | time (s): 55.820 (total time: 88.440) Filter (q & B) r_work=0.1197 r_free=0.1403 | n_water=420 | time (s): 3.320 (total time: 91.760) Filter (dist only) r_work=0.1197 r_free=0.1403 | n_water=419 | time (s): 36.220 (total time: 127.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.515160 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1484.163221 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 0.1644 0.1768 0.0124 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1503 0.1646 0.0143 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1386 0.1553 0.0167 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1361 0.1533 0.0172 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1313 0.1495 0.0182 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1316 0.1500 0.0184 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1267 0.1474 0.0207 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1229 0.1447 0.0217 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1214 0.1437 0.0222 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1209 0.1432 0.0223 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1202 0.1429 0.0227 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1198 0.1422 0.0224 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1197 0.1421 0.0225 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1193 0.1420 0.0227 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1188 0.1410 0.0222 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1188 0.1416 0.0228 0.007 0.9 5.8 0.5 0.6 0 11.000 0.1186 0.1420 0.0233 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1184 0.1416 0.0232 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1183 0.1419 0.0236 0.008 1.0 5.8 0.5 0.6 0 14.258 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1188 0.1410 0.0222 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 14.10 2.22 3.763 21.774 1484.163 0.016 11.88 14.10 2.22 3.763 21.774 44.525 0.016 11.88 14.10 2.22 3.763 21.774 185.520 0.016 12.08 14.49 2.41 3.623 21.780 742.082 0.015 12.05 14.76 2.72 3.551 21.848 1484.163 0.015 11.89 14.62 2.73 3.455 22.140 2226.245 0.014 11.81 14.60 2.78 3.473 22.113 2968.326 0.014 11.72 14.65 2.94 3.520 21.934 3710.408 0.014 11.70 14.57 2.87 3.500 22.083 4452.490 0.014 11.71 14.64 2.93 3.523 22.152 5194.571 0.014 11.64 14.59 2.95 3.536 22.178 5936.653 0.014 11.64 14.63 2.99 3.544 22.134 6678.734 0.014 11.63 14.67 3.04 3.559 22.124 7420.816 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: 44.525 Accepted refinement result: 11.88 14.10 2.22 3.763 21.774 44.525 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.89 22.19 3.28 194 1752 Protein: 9.10 114.89 17.02 3.29 0 1519 Water: 11.48 76.68 40.91 N/A 194 225 Other: 19.77 26.62 22.09 N/A 0 8 Chain A: 9.10 114.89 19.44 N/A 0 1752 Chain S: 15.50 60.00 46.96 N/A 194 0 Histogram: Values Number of atoms 9.10 - 19.68 1259 19.68 - 30.26 247 30.26 - 40.84 164 40.84 - 51.42 126 51.42 - 62.00 127 62.00 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1410 r_work=0.1188 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1415 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1190 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015057 | | target function (ls_wunit_k1) not normalized (work): 1254.183844 | | target function (ls_wunit_k1) not normalized (free): 102.684205 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1190 0.1415 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1585 0.1583 0.1662 n_refl.: 87592 remove outliers: r(all,work,free)=0.1585 0.1583 0.1662 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1589 0.1586 0.1664 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1187 0.1412 n_refl.: 87592 remove outliers: r(all,work,free)=0.1196 0.1185 0.1412 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3141 294.275 275.151 0.595 1.001 0.350 11.894-9.307 99.02 97 4 0.1589 483.217 477.909 0.920 1.001 0.350 9.237-7.194 100.00 213 7 0.1732 395.212 394.743 0.986 1.001 0.250 7.162-5.571 100.00 427 22 0.1610 296.585 291.731 0.939 1.002 0.230 5.546-4.326 100.00 867 58 0.0873 407.138 404.113 0.961 1.002 0.215 4.315-3.360 100.00 1859 96 0.0788 387.191 386.043 1.004 1.002 0.210 3.356-2.611 100.00 3867 181 0.1081 254.364 253.427 1.008 1.002 0.120 2.608-2.026 99.99 8198 413 0.1018 168.620 168.089 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1099 82.345 82.593 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.515 36.023 1.018 1.001 0.000 1.221-1.150 99.97 13689 708 0.2255 23.007 21.391 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=0.0311 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1412 | n_water=419 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1185 r_free=0.1414 | n_water=412 | time (s): 36.640 (total time: 38.860) Filter (q & B) r_work=0.1185 r_free=0.1414 | n_water=412 | time (s): 0.950 (total time: 39.810) Compute maps r_work=0.1185 r_free=0.1414 | n_water=412 | time (s): 1.520 (total time: 41.330) Filter (map) r_work=0.1219 r_free=0.1399 | n_water=289 | time (s): 3.710 (total time: 45.040) Find peaks r_work=0.1219 r_free=0.1399 | n_water=289 | time (s): 0.700 (total time: 45.740) Add new water r_work=0.1330 r_free=0.1511 | n_water=469 | time (s): 3.190 (total time: 48.930) Refine new water occ: r_work=0.1244 r_free=0.1441 adp: r_work=0.1246 r_free=0.1440 occ: r_work=0.1222 r_free=0.1426 adp: r_work=0.1220 r_free=0.1422 occ: r_work=0.1205 r_free=0.1413 adp: r_work=0.1200 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1406 r_work=0.1200 r_free=0.1406 | n_water=469 | time (s): 195.920 (total time: 244.850) Filter (q & B) r_work=0.1204 r_free=0.1406 | n_water=441 | time (s): 2.580 (total time: 247.430) Filter (dist only) r_work=0.1204 r_free=0.1405 | n_water=440 | time (s): 38.400 (total time: 285.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.776610 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.309971 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1370 0.0141 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1185 0.1330 0.0145 0.003 0.7 4.5 0.5 0.0 0 0.266 0.1168 0.1320 0.0152 0.004 0.8 3.5 0.5 0.0 0 0.533 0.1161 0.1317 0.0156 0.005 0.9 3.2 0.5 0.0 0 0.799 0.1157 0.1315 0.0157 0.006 1.0 3.2 0.5 0.0 0 1.066 0.1154 0.1314 0.0160 0.007 1.0 3.8 0.5 0.0 0 1.332 0.1152 0.1312 0.0160 0.007 1.1 4.2 0.5 0.0 0 1.599 0.1150 0.1311 0.0161 0.008 1.1 4.2 0.5 0.0 0 1.865 0.1160 0.1316 0.0156 0.005 0.9 3.2 0.5 0.0 0 0.888 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1150 0.1311 0.0161 0.008 1.1 4.2 0.5 0.0 0 1.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 13.11 1.61 3.767 21.308 43.310 3.618 11.50 13.11 1.61 3.767 21.308 1.299 3.618 11.50 13.11 1.61 3.767 21.308 5.414 3.618 11.53 13.16 1.63 3.701 21.299 21.655 3.611 11.58 13.28 1.70 3.723 21.265 43.310 3.612 11.49 13.23 1.74 3.746 21.256 64.965 3.605 11.45 13.21 1.76 3.758 21.247 86.620 3.602 11.42 13.21 1.79 3.772 21.241 108.275 3.599 11.39 13.21 1.83 3.784 21.234 129.930 3.597 11.38 13.23 1.85 3.798 21.227 151.585 3.597 11.37 13.24 1.87 3.812 21.217 173.240 3.596 11.35 13.20 1.85 3.816 21.217 194.895 3.594 11.33 13.16 1.84 3.819 21.217 216.550 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.414 Accepted refinement result: 11.50 13.11 1.61 3.767 21.308 5.414 3.618 Individual atomic B min max mean iso aniso Overall: 9.12 114.91 21.32 3.28 216 1751 Protein: 9.12 114.91 17.04 3.29 0 1519 Water: 11.50 76.70 36.06 N/A 216 224 Other: 19.79 26.64 22.11 N/A 0 8 Chain A: 9.12 114.91 19.44 N/A 0 1751 Chain S: 15.52 60.02 36.51 N/A 216 0 Histogram: Values Number of atoms 9.12 - 19.70 1260 19.70 - 30.28 285 30.28 - 40.86 218 40.86 - 51.44 121 51.44 - 62.02 60 62.02 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1311 r_work=0.1150 r_free=0.1311 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1150 r_free = 0.1311 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1309 target_work(ml) = 3.611 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1140 r_free= 0.1309 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611464 | | target function (ml) not normalized (work): 300806.081931 | | target function (ml) not normalized (free): 15835.503573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1140 0.1309 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1494 0.1492 0.1550 n_refl.: 87588 remove outliers: r(all,work,free)=0.1494 0.1492 0.1550 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1493 0.1492 0.1549 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1299 n_refl.: 87588 remove outliers: r(all,work,free)=0.1142 0.1134 0.1299 n_refl.: 87581 ======================== 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 0.3633 290.882 261.504 0.506 1.000 0.330 11.894-9.307 98.04 96 4 0.2236 485.170 470.811 0.886 1.000 0.330 9.237-7.194 98.18 209 7 0.2213 386.680 388.874 0.959 1.001 0.216 7.162-5.571 100.00 427 22 0.2042 296.585 286.553 0.921 1.001 0.193 5.546-4.326 100.00 867 58 0.1096 407.138 402.583 0.966 1.001 0.180 4.315-3.360 100.00 1859 96 0.0924 387.191 384.810 1.003 1.001 0.170 3.356-2.611 100.00 3867 181 0.1129 254.364 251.964 1.007 1.001 0.080 2.608-2.026 99.99 8198 413 0.0918 168.620 167.890 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.345 82.654 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.515 36.091 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2166 23.007 21.465 0.981 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0076 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1134 r_free=0.1299 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1134 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1134 r_free=0.1299 | n_water=440 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1134 r_free=0.1298 | n_water=438 | time (s): 47.770 (total time: 50.290) Filter (q & B) r_work=0.1134 r_free=0.1298 | n_water=438 | time (s): 1.360 (total time: 51.650) Compute maps r_work=0.1134 r_free=0.1298 | n_water=438 | time (s): 1.930 (total time: 53.580) Filter (map) r_work=0.1154 r_free=0.1297 | n_water=339 | time (s): 3.960 (total time: 57.540) Find peaks r_work=0.1154 r_free=0.1297 | n_water=339 | time (s): 0.730 (total time: 58.270) Add new water r_work=0.1226 r_free=0.1387 | n_water=495 | time (s): 3.710 (total time: 61.980) Refine new water occ: r_work=0.1165 r_free=0.1324 adp: r_work=0.1165 r_free=0.1327 occ: r_work=0.1148 r_free=0.1303 adp: r_work=0.1148 r_free=0.1305 occ: r_work=0.1135 r_free=0.1287 adp: r_work=0.1131 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1288 r_work=0.1131 r_free=0.1288 | n_water=495 | time (s): 188.980 (total time: 250.960) Filter (q & B) r_work=0.1135 r_free=0.1289 | n_water=457 | time (s): 3.930 (total time: 254.890) Filter (dist only) r_work=0.1135 r_free=0.1287 | n_water=456 | time (s): 48.170 (total time: 303.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.768321 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.012436 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 0.1200 0.1334 0.0134 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1163 0.1302 0.0139 0.003 0.7 3.2 0.5 0.0 0 0.265 0.1149 0.1294 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.530 0.1141 0.1288 0.0147 0.006 1.0 3.5 0.5 0.0 0 0.796 0.1137 0.1287 0.0150 0.007 1.0 3.2 0.5 0.0 0 1.061 0.1135 0.1286 0.0151 0.007 1.1 3.5 0.5 0.0 0 1.326 0.1133 0.1287 0.0154 0.008 1.1 3.8 0.5 0.6 0 1.591 0.1131 0.1285 0.0155 0.009 1.1 3.8 0.5 0.6 0 1.857 0.1139 0.1288 0.0149 0.006 1.0 3.8 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1285 0.0155 0.009 1.1 3.8 0.5 0.6 0 1.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.85 1.55 3.768 21.308 33.012 3.605 11.31 12.85 1.55 3.768 21.308 0.990 3.605 11.31 12.85 1.55 3.768 21.308 4.127 3.605 11.34 12.87 1.53 3.701 21.302 16.506 3.601 11.37 12.96 1.58 3.718 21.286 33.012 3.601 11.36 13.00 1.64 3.739 21.265 49.519 3.600 11.32 12.99 1.67 3.753 21.259 66.025 3.596 11.28 12.97 1.69 3.764 21.256 82.531 3.592 11.25 12.95 1.70 3.771 21.255 99.037 3.590 11.23 12.96 1.73 3.780 21.251 115.544 3.588 11.21 12.95 1.74 3.786 21.251 132.050 3.587 11.21 12.98 1.77 3.802 21.241 148.556 3.587 11.22 13.01 1.79 3.815 21.232 165.062 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.127 Accepted refinement result: 11.31 12.85 1.55 3.768 21.308 4.127 3.605 Individual atomic B min max mean iso aniso Overall: 9.12 114.91 21.31 3.28 233 1750 Protein: 9.12 114.91 17.04 3.29 0 1519 Water: 11.49 76.69 35.54 N/A 233 223 Other: 19.79 26.64 22.11 N/A 0 8 Chain A: 9.12 114.91 19.42 N/A 0 1750 Chain S: 15.52 60.02 35.53 N/A 233 0 Histogram: Values Number of atoms 9.12 - 19.69 1261 19.69 - 30.27 301 30.27 - 40.85 217 40.85 - 51.43 125 51.43 - 62.01 56 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1285 r_work=0.1131 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1285 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1282 target_work(ml) = 3.603 | | 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.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1282 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602928 | | target function (ml) not normalized (work): 300069.854660 | | target function (ml) not normalized (free): 15806.495546 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1127 0.1282 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1458 0.1456 0.1504 n_refl.: 87581 remove outliers: r(all,work,free)=0.1458 0.1456 0.1504 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1456 0.1455 0.1503 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1123 0.1278 n_refl.: 87581 remove outliers: r(all,work,free)=0.1129 0.1121 0.1278 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 86.46 78 5 0.3669 286.166 255.673 0.470 1.001 0.320 11.894-9.307 95.10 93 4 0.2279 488.007 470.866 0.858 1.002 0.320 9.237-7.194 98.18 209 7 0.2279 386.680 383.028 0.926 1.002 0.164 7.162-5.571 100.00 427 22 0.2099 296.585 286.326 0.907 1.002 0.140 5.546-4.326 100.00 867 58 0.1114 407.138 402.557 0.956 1.002 0.130 4.315-3.360 100.00 1859 96 0.0906 387.191 385.064 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1107 254.364 252.367 0.999 1.002 0.060 2.608-2.026 99.99 8198 413 0.0901 168.620 167.978 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.345 82.726 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.515 36.140 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2165 23.007 21.575 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0246 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1121 r_free=0.1278 After: r_work=0.1123 r_free=0.1278 ================================== NQH flips ================================== r_work=0.1123 r_free=0.1278 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=0.1123 r_free=0.1278 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1123 r_free=0.1278 | n_water=456 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1123 r_free=0.1279 | n_water=455 | time (s): 49.950 (total time: 52.430) Filter (q & B) r_work=0.1123 r_free=0.1280 | n_water=454 | time (s): 3.980 (total time: 56.410) Compute maps r_work=0.1123 r_free=0.1280 | n_water=454 | time (s): 1.870 (total time: 58.280) Filter (map) r_work=0.1147 r_free=0.1287 | n_water=356 | time (s): 3.960 (total time: 62.240) Find peaks r_work=0.1147 r_free=0.1287 | n_water=356 | time (s): 0.690 (total time: 62.930) Add new water r_work=0.1202 r_free=0.1338 | n_water=515 | time (s): 3.820 (total time: 66.750) Refine new water occ: r_work=0.1145 r_free=0.1296 adp: r_work=0.1145 r_free=0.1297 occ: r_work=0.1131 r_free=0.1285 adp: r_work=0.1130 r_free=0.1285 occ: r_work=0.1121 r_free=0.1278 adp: r_work=0.1117 r_free=0.1275 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1275 r_work=0.1117 r_free=0.1275 | n_water=515 | time (s): 281.180 (total time: 347.930) Filter (q & B) r_work=0.1125 r_free=0.1274 | n_water=475 | time (s): 4.090 (total time: 352.020) Filter (dist only) r_work=0.1125 r_free=0.1272 | n_water=473 | time (s): 50.680 (total time: 402.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.812830 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.628515 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 0.1208 0.1326 0.0119 0.004 0.7 6.1 0.0 0.0 0 0.091 0.1160 0.1292 0.0132 0.004 0.8 5.4 0.0 0.0 0 0.272 0.1145 0.1282 0.0137 0.005 0.9 5.1 0.5 0.0 0 0.544 0.1134 0.1274 0.0141 0.006 1.0 4.8 0.5 0.0 0 0.816 0.1132 0.1274 0.0142 0.007 1.1 4.8 0.5 0.0 0 1.088 0.1128 0.1272 0.0145 0.008 1.1 4.8 0.5 0.0 0 1.360 0.1126 0.1272 0.0147 0.008 1.1 5.1 0.5 0.6 0 1.632 0.1125 0.1272 0.0147 0.009 1.1 5.1 0.5 0.6 0 1.903 0.1133 0.1274 0.0141 0.006 1.0 4.8 0.5 0.0 0 0.906 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1125 0.1272 0.0147 0.009 1.1 5.1 0.5 0.6 0 1.903 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 12.72 1.47 3.768 21.316 40.629 3.601 11.25 12.72 1.47 3.768 21.316 1.219 3.601 11.25 12.72 1.47 3.768 21.316 5.079 3.601 11.28 12.74 1.47 3.704 21.310 20.314 3.596 11.37 12.91 1.54 3.724 21.279 40.629 3.600 11.28 12.86 1.58 3.749 21.269 60.943 3.594 11.22 12.83 1.60 3.763 21.265 81.257 3.589 11.20 12.80 1.61 3.773 21.262 101.571 3.587 11.17 12.80 1.62 3.784 21.260 121.886 3.585 11.15 12.79 1.64 3.794 21.257 142.200 3.583 11.16 12.84 1.68 3.813 21.245 162.514 3.583 11.14 12.82 1.68 3.820 21.245 182.828 3.582 11.13 12.80 1.68 3.825 21.244 203.143 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.219 Accepted refinement result: 11.25 12.72 1.47 3.768 21.316 1.219 3.601 Individual atomic B min max mean iso aniso Overall: 9.11 114.90 21.34 3.28 251 1749 Protein: 9.11 114.90 17.03 3.29 0 1519 Water: 11.48 76.69 35.15 N/A 251 222 Other: 19.78 26.63 22.10 N/A 0 8 Chain A: 9.11 114.90 19.39 N/A 0 1749 Chain S: 15.51 60.01 34.87 N/A 251 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.26 304 30.26 - 40.84 229 40.84 - 51.42 131 51.42 - 62.00 50 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1272 r_work=0.1125 r_free=0.1272 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1125 r_free = 0.1272 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1271 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1271 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600283 | | target function (ml) not normalized (work): 299827.958763 | | target function (ml) not normalized (free): 15794.217623 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1314 0.1283 5.6354 5.5863| | 2: 3.57 - 2.84 1.00 2888 124 0.1053 0.1384 5.1509 5.213| | 3: 2.83 - 2.48 1.00 2820 163 0.1083 0.1171 4.9298 4.9454| | 4: 2.47 - 2.25 1.00 2825 136 0.0893 0.0977 4.6203 4.6443| | 5: 2.25 - 2.09 1.00 2756 127 0.0865 0.0984 4.5662 4.6277| | 6: 2.09 - 1.97 1.00 2846 113 0.0840 0.1006 4.2522 4.3352| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1107 3.9717 4.0884| | 8: 1.87 - 1.79 1.00 2789 144 0.0902 0.1072 3.8834 3.9826| | 9: 1.79 - 1.72 1.00 2745 138 0.0865 0.1203 3.6398 3.8433| | 10: 1.72 - 1.66 1.00 2831 160 0.0906 0.1194 3.5602 3.7278| | 11: 1.66 - 1.61 1.00 2712 147 0.0861 0.0978 3.4919 3.5523| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1201 3.3265 3.4902| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1014 3.3053 3.3784| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1065 3.2366 3.3271| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1211 3.153 3.2582| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1258 3.1335 3.2445| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1290 3.1194 3.223| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1321 3.1052 3.2337| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1568 3.1134 3.2742| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1452 3.1137 3.146| | 21: 1.32 - 1.30 1.00 2785 112 0.1464 0.1557 3.1134 3.1216| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1961 3.1227 3.2846| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1793 3.134 3.2026| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1848 3.128 3.2315| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2124 3.1433 3.2589| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1764 3.1481 3.2| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2157 3.1708 3.1616| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2299 3.1667 3.1722| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2378 3.1482 3.2299| | 30: 1.16 - 1.15 1.00 2739 148 0.2442 0.2433 3.1437 3.1669| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.22 1.00 0.98 5569.52| | 2: 3.57 - 2.84 2888 124 0.93 12.31 1.01 0.98 5569.52| | 3: 2.83 - 2.48 2820 163 0.90 16.26 0.99 0.98 4655.44| | 4: 2.47 - 2.25 2825 136 0.92 13.24 1.00 0.99 2298.32| | 5: 2.25 - 2.09 2756 127 0.90 15.41 1.01 0.99 2298.32| | 6: 2.09 - 1.97 2846 113 0.93 12.19 1.02 0.99 1332.45| | 7: 1.97 - 1.87 2787 165 0.95 9.32 1.02 0.99 508.69| | 8: 1.87 - 1.79 2789 144 0.93 12.58 1.00 0.99 508.69| | 9: 1.79 - 1.72 2745 138 0.94 10.02 0.98 0.98 289.28| | 10: 1.72 - 1.66 2831 160 0.94 11.14 0.98 0.98 245.34| | 11: 1.66 - 1.61 2712 147 0.93 11.78 0.98 0.98 235.01| | 12: 1.61 - 1.56 2773 144 0.96 8.84 0.99 0.98 137.59| | 13: 1.56 - 1.52 2745 130 0.95 10.39 1.02 0.98 137.59| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.99 123.31| | 15: 1.48 - 1.45 2738 128 0.95 9.81 1.02 0.99 97.16| | 16: 1.45 - 1.42 2756 161 0.94 10.98 1.02 0.99 97.16| | 17: 1.42 - 1.39 2785 139 0.95 10.82 1.01 0.99 88.61| | 18: 1.39 - 1.36 2741 179 0.94 11.46 1.01 0.99 83.66| | 19: 1.36 - 1.34 2807 134 0.94 11.82 0.99 0.99 83.66| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.98 79.89| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.97 79.63| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.97 80.03| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 82.11| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.95 82.11| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.95 84.03| | 26: 1.22 - 1.21 2727 135 0.90 18.04 1.02 0.94 86.16| | 27: 1.21 - 1.19 2814 148 0.89 18.69 1.02 0.94 86.16| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.94 89.74| | 29: 1.18 - 1.16 2800 134 0.88 20.40 0.99 0.93 91.08| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.93 91.08| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.63 max = 5569.52 mean = 863.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.36| |phase err.(test): min = 0.00 max = 89.77 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1123 0.1271 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1445 0.1443 0.1489 n_refl.: 87575 remove outliers: r(all,work,free)=0.1445 0.1443 0.1489 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1444 0.1442 0.1489 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1123 0.1269 n_refl.: 87575 remove outliers: r(all,work,free)=0.1129 0.1122 0.1269 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 86.46 78 5 0.4043 286.166 249.944 0.440 1.000 0.304 11.894-9.307 92.16 90 4 0.2320 483.171 465.960 0.873 1.002 0.228 9.237-7.194 98.18 209 7 0.2330 386.680 381.782 0.923 1.002 0.160 7.162-5.571 100.00 427 22 0.2111 296.585 286.706 0.913 1.003 0.145 5.546-4.326 100.00 867 58 0.1108 407.138 402.845 0.966 1.003 0.120 4.315-3.360 100.00 1859 96 0.0898 387.191 385.042 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1095 254.364 252.383 1.010 1.002 0.020 2.608-2.026 99.99 8198 413 0.0904 168.620 167.978 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.345 82.707 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.515 36.125 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.007 21.561 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=-0.0162 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1926 0.081 5.219 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1740 0.081 5.219 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1740 0.081 5.219 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1751 0.081 5.219 9.0 119.5 20.1 258 0.006 1_weight: 0.1640 0.1751 0.081 5.219 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1229 0.1470 0.007 0.922 9.0 119.5 20.1 258 0.142 1_adp: 0.1236 0.1468 0.007 0.922 9.1 119.4 20.1 258 0.142 1_regHadp: 0.1237 0.1471 0.007 0.922 9.1 119.4 20.1 258 0.142 1_occ: 0.1230 0.1464 0.007 0.922 9.1 119.4 20.1 258 0.142 2_bss: 0.1228 0.1456 0.007 0.922 9.1 119.5 20.1 258 0.142 2_settarget: 0.1228 0.1456 0.007 0.922 9.1 119.5 20.1 258 0.142 2_updatecdl: 0.1228 0.1456 0.007 0.929 9.1 119.5 20.1 258 0.142 2_nqh: 0.1228 0.1456 0.007 0.929 9.1 119.5 20.1 258 0.139 2_sol: 0.1197 0.1403 0.007 0.929 9.1 114.9 22.2 419 n/a 2_weight: 0.1197 0.1403 0.007 0.929 9.1 114.9 22.2 419 n/a 2_xyzrec: 0.1188 0.1410 0.006 0.865 9.1 114.9 22.2 419 n/a 2_adp: 0.1188 0.1410 0.006 0.865 9.1 114.9 22.2 419 n/a 2_regHadp: 0.1188 0.1410 0.006 0.865 9.1 114.9 22.2 419 n/a 2_occ: 0.1190 0.1415 0.006 0.865 9.1 114.9 22.2 419 n/a 3_bss: 0.1185 0.1412 0.006 0.865 9.1 114.9 22.2 419 n/a 3_settarget: 0.1185 0.1412 0.006 0.865 9.1 114.9 22.2 419 n/a 3_updatecdl: 0.1185 0.1412 0.006 0.866 9.1 114.9 22.2 419 n/a 3_nqh: 0.1185 0.1412 0.006 0.866 9.1 114.9 22.2 419 n/a 3_sol: 0.1204 0.1405 0.006 0.866 9.1 114.9 21.3 440 n/a 3_weight: 0.1204 0.1405 0.006 0.866 9.1 114.9 21.3 440 n/a 3_xyzrec: 0.1150 0.1311 0.008 1.095 9.1 114.9 21.3 440 n/a 3_adp: 0.1150 0.1311 0.008 1.095 9.1 114.9 21.3 440 n/a 3_regHadp: 0.1150 0.1311 0.008 1.095 9.1 114.9 21.3 440 n/a 3_occ: 0.1140 0.1309 0.008 1.095 9.1 114.9 21.3 440 n/a 4_bss: 0.1134 0.1299 0.008 1.095 9.1 114.9 21.3 440 n/a 4_settarget: 0.1134 0.1299 0.008 1.095 9.1 114.9 21.3 440 n/a 4_updatecdl: 0.1134 0.1299 0.008 1.098 9.1 114.9 21.3 440 n/a 4_nqh: 0.1134 0.1299 0.008 1.098 9.1 114.9 21.3 440 n/a 4_sol: 0.1135 0.1287 0.008 1.098 9.1 114.9 21.3 456 n/a 4_weight: 0.1135 0.1287 0.008 1.098 9.1 114.9 21.3 456 n/a 4_xyzrec: 0.1131 0.1285 0.009 1.130 9.1 114.9 21.3 456 n/a 4_adp: 0.1131 0.1285 0.009 1.130 9.1 114.9 21.3 456 n/a 4_regHadp: 0.1131 0.1285 0.009 1.130 9.1 114.9 21.3 456 n/a 4_occ: 0.1127 0.1282 0.009 1.130 9.1 114.9 21.3 456 n/a 5_bss: 0.1121 0.1278 0.009 1.130 9.1 114.9 21.3 456 n/a 5_settarget: 0.1121 0.1278 0.009 1.130 9.1 114.9 21.3 456 n/a 5_updatecdl: 0.1121 0.1278 0.009 1.129 9.1 114.9 21.3 456 n/a 5_setrh: 0.1123 0.1278 0.009 1.129 9.1 114.9 21.3 456 n/a 5_nqh: 0.1123 0.1278 0.009 1.129 9.1 114.9 21.3 456 n/a 5_sol: 0.1125 0.1272 0.009 1.129 9.1 114.9 21.3 473 n/a 5_weight: 0.1125 0.1272 0.009 1.129 9.1 114.9 21.3 473 n/a 5_xyzrec: 0.1125 0.1272 0.009 1.137 9.1 114.9 21.3 473 n/a 5_adp: 0.1125 0.1272 0.009 1.137 9.1 114.9 21.3 473 n/a 5_regHadp: 0.1125 0.1272 0.009 1.137 9.1 114.9 21.3 473 n/a 5_occ: 0.1123 0.1271 0.009 1.137 9.1 114.9 21.3 473 n/a end: 0.1122 0.1269 0.009 1.137 9.1 114.9 21.3 473 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6446528_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6446528_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2700 Refinement macro-cycles (run) : 14126.1300 Write final files (write_after_run_outputs) : 75.3500 Total : 14204.7500 Total CPU time: 3.95 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:17:16 PST -0800 (1735366636.43 s) Start R-work = 0.1635, R-free = 0.1740 Final R-work = 0.1122, R-free = 0.1269 =============================================================================== Job complete usr+sys time: 14349.21 seconds wall clock time: 260 minutes 47.35 seconds (15647.35 seconds total)