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_2353655.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 =============================================================================== 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: 1.50, per 1000 atoms: 0.44 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: 0.30 Conformation dependent library (CDL) restraints added in 104.4 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 532 0.91 - 1.16: 1109 1.16 - 1.42: 624 1.42 - 1.67: 838 1.67 - 1.92: 50 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.974 0.262 1.19e-02 7.06e+03 4.84e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.523 1.699 -0.176 9.20e-03 1.18e+04 3.64e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.011 0.226 1.19e-02 7.06e+03 3.59e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.132 0.189 1.00e-02 1.00e+04 3.57e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.639 -0.100 5.40e-03 3.43e+04 3.41e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 3034 4.38 - 8.76: 1829 8.76 - 13.13: 729 13.13 - 17.51: 159 17.51 - 21.89: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 134.62 -13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.15 137.09 -14.94 1.14e+00 7.69e-01 1.72e+02 angle pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " pdb=" CG PHE A 119 " ideal model delta sigma weight residual 113.80 126.88 -13.08 1.00e+00 1.00e+00 1.71e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 109.67 11.52 9.40e-01 1.13e+00 1.50e+02 angle pdb=" O PRO A 158 " pdb=" C PRO A 158 " pdb=" N GLY A 159 " ideal model delta sigma weight residual 122.23 136.92 -14.69 1.20e+00 6.94e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 924 16.75 - 33.50: 127 33.50 - 50.25: 43 50.25 - 67.00: 15 67.00 - 83.75: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 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 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+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 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 105 0.225 - 0.449: 85 0.449 - 0.673: 38 0.673 - 0.897: 8 0.897 - 1.122: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.61 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.090 9.50e-02 1.11e+02 7.28e-02 1.00e+02 pdb=" NE ARG A 156 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " -0.077 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.034 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " -0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG BTYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.114 2.00e-02 2.50e+03 6.49e-02 9.46e+01 pdb=" CG HIS A 138 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 984 2.31 - 2.88: 8064 2.88 - 3.46: 10527 3.46 - 4.03: 15145 4.03 - 4.60: 21916 Nonbonded interactions: 56636 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.738 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.766 2.100 nonbonded pdb=" HE3ALYS A 132 " pdb=" HO2ADTT A 201 " model vdw 1.792 2.270 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.808 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.832 1.850 ... (remaining 56631 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_2353655_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= 0.2594 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.780728 | | target function (ml) not normalized (work): 231651.315679 | | target function (ml) not normalized (free): 11805.514883 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3026 0.2092 7.0432 4.9518| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1746 4.3497 4.3356| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1634 4.1285 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2322 0.1559 3.8378 3.8479| | 5: 2.25 - 2.09 1.00 2756 127 0.2504 0.1553 3.7977 3.8116| | 6: 2.09 - 1.97 1.00 2846 113 0.2494 0.1680 3.4535 3.5476| | 7: 1.97 - 1.87 1.00 2787 165 0.2520 0.1820 3.1252 3.1758| | 8: 1.87 - 1.79 1.00 2789 144 0.2423 0.1840 3.037 3.1328| | 9: 1.79 - 1.72 1.00 2745 138 0.2374 0.1946 2.8905 2.9844| | 10: 1.72 - 1.66 1.00 2789 158 0.2368 0.1940 2.7972 2.884| | 11: 1.66 - 1.61 1.00 2740 147 0.2466 0.1964 2.7246 2.7751| | 12: 1.61 - 1.56 1.00 2787 146 0.2517 0.2007 2.594 2.5956| | 13: 1.56 - 1.52 1.00 2745 130 0.2549 0.1881 2.5565 2.5924| | 14: 1.52 - 1.48 1.00 2803 134 0.2576 0.2005 2.5203 2.5338| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.2299 2.4169 2.5561| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2065 2.3807 2.3974| | 17: 1.42 - 1.39 1.00 2785 139 0.2688 0.2074 2.321 2.3753| | 18: 1.39 - 1.36 1.00 2741 179 0.2673 0.2273 2.2538 2.3778| | 19: 1.36 - 1.34 1.00 2807 134 0.2617 0.2523 2.2223 2.3968| | 20: 1.34 - 1.32 1.00 2696 147 0.2637 0.2348 2.1852 2.254| | 21: 1.32 - 1.30 1.00 2785 112 0.2654 0.2189 2.1684 2.1299| | 22: 1.29 - 1.27 1.00 2704 152 0.2687 0.2645 2.1209 2.2453| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2285 2.0994 2.1076| | 24: 1.26 - 1.24 1.00 2744 132 0.2773 0.2330 2.0673 2.1016| | 25: 1.24 - 1.22 1.00 2734 148 0.2824 0.2512 2.0332 2.0254| | 26: 1.22 - 1.21 1.00 2727 135 0.2883 0.2233 2.0029 2.0798| | 27: 1.21 - 1.19 1.00 2814 148 0.2918 0.2435 1.9849 1.9532| | 28: 1.19 - 1.18 1.00 2671 147 0.2976 0.2800 1.9698 1.9874| | 29: 1.18 - 1.16 1.00 2800 134 0.2970 0.2779 1.955 2.0481| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2824 1.9277 1.9306| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.77 0.76 0.23 1495.94| | 2: 3.57 - 2.84 2876 122 0.80 26.15 1.27 0.23 1495.94| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.25 0.24 1239.86| | 4: 2.47 - 2.25 2825 136 0.81 25.63 1.25 0.25 575.28| | 5: 2.25 - 2.09 2756 127 0.77 29.48 1.29 0.25 575.28| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.29 0.25 313.50| | 7: 1.97 - 1.87 2787 165 0.90 16.55 1.28 0.25 90.24| | 8: 1.87 - 1.79 2789 144 0.86 21.11 1.25 0.25 90.24| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.23 0.25 55.01| | 10: 1.72 - 1.66 2789 158 0.87 20.09 1.22 0.25 47.95| | 11: 1.66 - 1.61 2740 147 0.86 21.39 1.24 0.25 46.28| | 12: 1.61 - 1.56 2787 146 0.88 18.65 1.24 0.25 29.32| | 13: 1.56 - 1.52 2745 130 0.87 20.35 1.24 0.25 29.32| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.23 0.25 26.39| | 15: 1.48 - 1.45 2738 128 0.87 20.33 1.24 0.25 21.02| | 16: 1.45 - 1.42 2756 161 0.85 21.82 1.24 0.25 21.02| | 17: 1.42 - 1.39 2785 139 0.86 20.99 1.24 0.25 17.90| | 18: 1.39 - 1.36 2741 179 0.86 21.43 1.24 0.25 16.09| | 19: 1.36 - 1.34 2807 134 0.85 22.27 1.22 0.25 16.09| | 20: 1.34 - 1.32 2696 147 0.86 21.12 1.20 0.25 13.25| | 21: 1.32 - 1.30 2785 112 0.86 22.00 1.19 0.25 13.05| | 22: 1.29 - 1.27 2704 152 0.85 22.53 1.21 0.24 12.69| | 23: 1.27 - 1.26 2802 156 0.86 21.81 1.20 0.24 10.83| | 24: 1.26 - 1.24 2744 132 0.85 22.61 1.20 0.24 10.83| | 25: 1.24 - 1.22 2734 148 0.85 23.30 1.21 0.24 10.23| | 26: 1.22 - 1.21 2727 135 0.84 23.67 1.21 0.23 9.57| | 27: 1.21 - 1.19 2814 148 0.83 24.49 1.21 0.23 9.57| | 28: 1.19 - 1.18 2671 147 0.83 24.88 1.19 0.23 9.03| | 29: 1.18 - 1.16 2800 134 0.83 25.11 1.17 0.23 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.85 1.15 0.23 8.83| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.83 max = 1495.94 mean = 216.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.59| |phase err.(test): min = 0.00 max = 89.79 mean = 22.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.262 1557 Z= 5.579 Angle : 5.302 19.172 2118 Z= 3.691 Chirality : 0.374 1.122 243 Planarity : 0.033 0.109 284 Dihedral : 13.894 83.747 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -1.96 (0.51), residues: 224 helix: -2.43 (0.37), residues: 108 sheet: 0.13 (0.94), residues: 28 loop : 0.11 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.027 ARG A 145 TYR 0.086 0.035 TYR A 141 PHE 0.103 0.033 PHE A 119 HIS 0.053 0.028 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= 0.2594 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.780728 | | target function (ml) not normalized (work): 231651.315679 | | target function (ml) not normalized (free): 11805.514883 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2552 0.2594 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2552 0.2594 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1965 0.1968 0.1941 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1987 0.1991 0.1952 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1626 0.1619 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1626 0.1619 0.1765 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3863 386.290 358.196 0.675 1.003 0.414 11.894-9.307 99.02 97 4 0.1842 613.603 592.725 0.931 1.004 0.400 9.237-7.194 100.00 213 7 0.2167 501.852 492.504 0.963 1.004 0.354 7.162-5.571 100.00 427 22 0.2183 376.612 364.362 0.930 1.004 0.293 5.546-4.326 100.00 867 58 0.1290 516.995 511.330 0.962 1.004 0.224 4.315-3.360 100.00 1859 96 0.1145 491.666 487.807 1.006 1.004 0.199 3.356-2.611 100.00 3867 181 0.1429 322.999 319.976 0.997 1.003 0.048 2.608-2.026 99.99 8198 413 0.1337 214.119 212.058 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1608 104.565 103.935 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2041 46.368 45.133 1.004 0.995 0.000 1.221-1.150 99.97 13689 708 0.2555 29.215 26.984 0.980 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0416 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1623 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.094862 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.566442 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 0.1628 0.1753 0.0125 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1515 0.1656 0.0141 0.001 0.5 3.5 0.0 0.0 0 0.250 0.1425 0.1587 0.0161 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1391 0.1569 0.0178 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1363 0.1553 0.0190 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1361 0.1553 0.0192 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1290 0.1502 0.0213 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1272 0.1496 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1486 0.0231 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1249 0.1487 0.0238 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1482 0.0240 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1238 0.1481 0.0243 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1235 0.1477 0.0242 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1233 0.1476 0.0243 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1227 0.1471 0.0244 0.006 0.9 4.2 0.5 0.6 0 10.000 0.1227 0.1471 0.0245 0.007 0.9 3.5 0.5 0.6 0 11.000 0.1223 0.1468 0.0244 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1222 0.1468 0.0246 0.007 1.0 3.8 0.5 0.6 0 13.000 0.1220 0.1468 0.0248 0.008 1.0 3.5 0.5 0.6 0 14.047 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1223 0.1468 0.0244 0.007 0.9 3.8 0.5 0.6 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 14.68 2.44 3.013 19.040 2014.566 0.017 12.24 14.67 2.43 2.989 19.040 60.437 0.017 12.31 14.65 2.34 2.669 19.039 251.821 0.017 12.64 15.27 2.63 2.728 19.194 1007.283 0.016 12.45 15.39 2.94 3.035 19.425 2014.566 0.016 12.40 15.46 3.06 3.364 19.638 3021.850 0.015 12.31 15.45 3.14 3.361 19.626 4029.133 0.015 12.23 15.37 3.14 3.300 19.572 5036.416 0.015 12.13 15.32 3.19 3.264 19.556 6043.699 0.015 12.13 15.30 3.17 3.220 19.528 7050.983 0.015 12.20 15.55 3.35 3.523 19.672 8058.266 0.015 12.22 15.58 3.36 3.600 19.706 9065.549 0.015 12.11 15.42 3.31 3.459 19.622 10072.832 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: 251.821 Accepted refinement result: 12.31 14.65 2.34 2.669 19.039 251.821 0.017 Individual atomic B min max mean iso aniso Overall: 9.03 119.42 20.06 3.31 0 1785 Protein: 9.03 114.98 16.97 3.32 0 1519 Water: 11.45 119.42 38.21 N/A 0 258 Other: 19.69 26.57 22.04 N/A 0 8 Chain A: 9.03 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.03 - 20.07 1272 20.07 - 31.11 227 31.11 - 42.15 125 42.15 - 53.19 94 53.19 - 64.23 42 64.23 - 75.27 11 75.27 - 86.30 7 86.30 - 97.34 4 97.34 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1465 r_work=0.1232 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1468 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 = 0.1225 r_free = 0.1465 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= 0.1225 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016646 | | target function (ls_wunit_k1) not normalized (work): 1386.582078 | | target function (ls_wunit_k1) not normalized (free): 111.351807 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1225 0.1465 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1671 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1671 0.1689 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1677 0.1678 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1235 0.1224 0.1457 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 0.3504 302.059 281.556 0.650 1.003 0.380 11.894-9.307 99.02 97 4 0.1621 483.883 471.680 0.925 1.003 0.373 9.237-7.194 100.00 213 7 0.1855 395.756 391.305 0.966 1.003 0.350 7.162-5.571 100.00 427 22 0.1793 296.993 291.412 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.0993 407.698 404.785 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0869 387.724 386.717 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1173 254.715 253.538 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.852 168.104 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.459 82.657 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.566 36.062 1.018 0.996 0.000 1.221-1.150 99.97 13689 708 0.2250 23.039 21.517 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0608 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1457 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 B A 144 ASN Total number of N/Q/H flips: 3 r_work=0.1224 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1456 | n_water=258 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1232 r_free=0.1456 | n_water=251 | time (s): 20.470 (total time: 22.550) Filter (q & B) r_work=0.1234 r_free=0.1455 | n_water=248 | time (s): 3.130 (total time: 25.680) Compute maps r_work=0.1234 r_free=0.1455 | n_water=248 | time (s): 1.430 (total time: 27.110) Filter (map) r_work=0.1266 r_free=0.1463 | n_water=221 | time (s): 2.450 (total time: 29.560) Find peaks r_work=0.1266 r_free=0.1463 | n_water=221 | time (s): 0.600 (total time: 30.160) Add new water r_work=0.1417 r_free=0.1651 | n_water=431 | time (s): 2.450 (total time: 32.610) Refine new water occ: r_work=0.1309 r_free=0.1499 adp: r_work=0.1228 r_free=0.1440 occ: r_work=0.1241 r_free=0.1422 adp: r_work=0.1206 r_free=0.1408 occ: r_work=0.1208 r_free=0.1393 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=431 | time (s): 71.680 (total time: 104.290) Filter (q & B) r_work=0.1204 r_free=0.1392 | n_water=414 | time (s): 3.020 (total time: 107.310) Filter (dist only) r_work=0.1204 r_free=0.1390 | n_water=413 | time (s): 35.750 (total time: 143.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.454541 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.060925 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 0.1631 0.1741 0.0110 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1551 0.1674 0.0123 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1431 0.1573 0.0142 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1368 0.1522 0.0155 0.001 0.5 4.8 0.0 0.0 0 0.750 0.1331 0.1501 0.0171 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1329 0.1499 0.0170 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1252 0.1444 0.0192 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1231 0.1437 0.0206 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1222 0.1432 0.0210 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1213 0.1428 0.0215 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1208 0.1424 0.0217 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1203 0.1417 0.0214 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1200 0.1416 0.0216 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1198 0.1419 0.0221 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1194 0.1415 0.0221 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1195 0.1426 0.0231 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1193 0.1418 0.0225 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1194 0.1427 0.0233 0.007 0.9 4.2 0.5 0.0 0 13.000 0.1188 0.1416 0.0229 0.008 0.9 3.8 0.5 0.0 0 14.227 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1415 0.0221 0.006 0.9 5.1 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 14.15 2.21 3.774 21.740 1498.061 0.016 11.94 14.15 2.21 3.774 21.740 44.942 0.016 11.94 14.15 2.21 3.774 21.740 187.258 0.016 12.07 14.53 2.46 3.645 21.734 749.030 0.016 12.12 14.86 2.74 3.528 21.830 1498.061 0.015 12.00 14.94 2.93 3.462 21.978 2247.091 0.015 11.83 14.78 2.94 3.498 21.895 2996.122 0.014 11.79 14.78 3.00 3.513 21.901 3745.152 0.014 11.82 14.87 3.05 3.495 22.094 4494.183 0.014 11.77 14.86 3.08 3.509 22.150 5243.213 0.014 11.73 14.82 3.10 3.524 22.171 5992.244 0.014 11.72 14.82 3.09 3.533 22.072 6741.274 0.014 11.67 14.79 3.11 3.543 22.097 7490.305 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: 44.942 Accepted refinement result: 11.94 14.15 2.21 3.774 21.740 44.942 0.016 Individual atomic B min max mean iso aniso Overall: 9.07 115.02 22.13 3.31 192 1748 Protein: 9.07 115.02 17.01 3.32 0 1519 Water: 11.49 76.67 40.97 N/A 192 221 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.07 115.02 19.41 N/A 0 1748 Chain S: 14.72 60.00 46.95 N/A 192 0 Histogram: Values Number of atoms 9.07 - 19.67 1257 19.67 - 30.26 239 30.26 - 40.86 167 40.86 - 51.45 137 51.45 - 62.05 117 62.05 - 72.64 12 72.64 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1415 r_work=0.1194 r_free=0.1415 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1415 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1422 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 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= 0.1196 r_free= 0.1422 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015390 | | target function (ls_wunit_k1) not normalized (work): 1281.941974 | | target function (ls_wunit_k1) not normalized (free): 100.910644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1196 0.1422 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1582 0.1580 0.1644 n_refl.: 87592 remove outliers: r(all,work,free)=0.1582 0.1580 0.1644 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1584 0.1583 0.1645 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1193 0.1415 n_refl.: 87592 remove outliers: r(all,work,free)=0.1203 0.1192 0.1415 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 0.3344 297.955 273.037 0.592 1.003 0.350 11.894-9.307 99.02 97 4 0.1609 483.883 477.042 0.922 1.003 0.333 9.237-7.194 100.00 213 7 0.1736 395.756 395.462 0.986 1.003 0.290 7.162-5.571 100.00 427 22 0.1601 296.993 292.071 0.931 1.003 0.230 5.546-4.326 100.00 867 58 0.0883 407.698 404.465 0.960 1.003 0.199 4.315-3.360 100.00 1859 96 0.0801 387.724 386.538 1.004 1.003 0.180 3.356-2.611 100.00 3867 181 0.1092 254.715 253.715 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 168.852 168.376 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.459 82.673 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.566 36.095 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 23.039 21.544 0.986 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0224 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1415 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=0.1192 r_free=0.1415 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1415 | n_water=413 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1193 r_free=0.1415 | n_water=409 | time (s): 35.010 (total time: 37.360) Filter (q & B) r_work=0.1193 r_free=0.1415 | n_water=409 | time (s): 1.160 (total time: 38.520) Compute maps r_work=0.1193 r_free=0.1415 | n_water=409 | time (s): 1.510 (total time: 40.030) Filter (map) r_work=0.1224 r_free=0.1404 | n_water=283 | time (s): 3.330 (total time: 43.360) Find peaks r_work=0.1224 r_free=0.1404 | n_water=283 | time (s): 0.650 (total time: 44.010) Add new water r_work=0.1341 r_free=0.1553 | n_water=484 | time (s): 3.330 (total time: 47.340) Refine new water occ: r_work=0.1249 r_free=0.1457 adp: r_work=0.1250 r_free=0.1460 occ: r_work=0.1226 r_free=0.1430 adp: r_work=0.1225 r_free=0.1433 occ: r_work=0.1210 r_free=0.1404 adp: r_work=0.1205 r_free=0.1405 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1405 r_work=0.1205 r_free=0.1405 | n_water=484 | time (s): 191.270 (total time: 238.610) Filter (q & B) r_work=0.1211 r_free=0.1409 | n_water=440 | time (s): 3.240 (total time: 241.850) Filter (dist only) r_work=0.1211 r_free=0.1409 | n_water=438 | time (s): 35.730 (total time: 277.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.768052 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.850709 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 0.1245 0.1381 0.0136 0.002 0.6 5.1 0.5 0.0 0 0.088 0.1193 0.1345 0.0152 0.003 0.7 4.2 0.5 0.0 0 0.265 0.1176 0.1334 0.0158 0.004 0.8 3.8 0.5 0.0 0 0.530 0.1168 0.1328 0.0159 0.005 0.9 3.8 0.5 0.0 0 0.796 0.1166 0.1328 0.0162 0.006 1.0 3.5 0.5 0.0 0 1.061 0.1163 0.1325 0.0163 0.007 1.0 3.8 0.5 0.0 0 1.326 0.1160 0.1327 0.0167 0.007 1.1 3.8 0.5 0.0 0 1.591 0.1159 0.1326 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.856 0.1169 0.1330 0.0162 0.005 0.9 3.5 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1325 0.0163 0.007 1.0 3.8 0.5 0.0 0 1.326 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 13.25 1.63 3.778 21.248 55.851 3.626 11.63 13.25 1.63 3.778 21.248 1.676 3.626 11.66 13.27 1.61 3.736 21.248 6.981 3.626 11.71 13.37 1.66 3.715 21.226 27.925 3.622 11.68 13.40 1.73 3.738 21.194 55.851 3.618 11.61 13.37 1.76 3.762 21.184 83.776 3.613 11.53 13.30 1.77 3.774 21.186 111.701 3.607 11.54 13.36 1.82 3.797 21.165 139.627 3.607 11.53 13.36 1.83 3.811 21.155 167.552 3.605 11.50 13.34 1.84 3.820 21.155 195.477 3.604 11.49 13.31 1.82 3.828 21.150 223.403 3.602 11.48 13.30 1.82 3.836 21.146 251.328 3.600 11.48 13.31 1.83 3.846 21.143 279.254 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: 1.676 Accepted refinement result: 11.63 13.25 1.63 3.778 21.248 1.676 3.626 Individual atomic B min max mean iso aniso Overall: 9.09 115.04 21.22 3.31 220 1745 Protein: 9.09 115.04 17.03 3.32 0 1519 Water: 11.50 76.69 35.74 N/A 220 218 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.09 115.04 19.37 N/A 0 1745 Chain S: 14.73 60.01 35.90 N/A 220 0 Histogram: Values Number of atoms 9.09 - 19.68 1259 19.68 - 30.28 286 30.28 - 40.87 211 40.87 - 51.47 136 51.47 - 62.06 50 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1325 r_work=0.1163 r_free=0.1325 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1325 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1316 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.17 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= 0.1154 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619829 | | target function (ml) not normalized (work): 301506.440115 | | target function (ml) not normalized (free): 15874.275813 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1316 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1497 0.1497 0.1519 n_refl.: 87589 remove outliers: r(all,work,free)=0.1497 0.1497 0.1519 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1497 0.1497 0.1519 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1150 0.1312 n_refl.: 87589 remove outliers: r(all,work,free)=0.1156 0.1148 0.1312 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.4180 292.493 262.099 0.493 1.001 0.324 11.894-9.307 97.06 95 4 0.2251 485.984 466.702 0.870 1.002 0.320 9.237-7.194 99.09 211 7 0.2356 390.241 386.482 0.951 1.003 0.210 7.162-5.571 100.00 427 22 0.2171 296.993 286.260 0.917 1.003 0.180 5.546-4.326 100.00 867 58 0.1087 407.698 403.274 0.963 1.003 0.165 4.315-3.360 100.00 1859 96 0.0935 387.724 385.535 1.003 1.003 0.129 3.356-2.611 100.00 3867 181 0.1135 254.715 252.569 1.008 1.002 0.048 2.608-2.026 99.99 8198 413 0.0937 168.852 168.058 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.459 82.750 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1263 36.566 36.147 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 23.039 21.565 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0061 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1312 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=0.1148 r_free=0.1312 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1312 | n_water=438 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1148 r_free=0.1310 | n_water=437 | time (s): 49.060 (total time: 51.570) Filter (q & B) r_work=0.1148 r_free=0.1312 | n_water=435 | time (s): 4.020 (total time: 55.590) Compute maps r_work=0.1148 r_free=0.1312 | n_water=435 | time (s): 1.900 (total time: 57.490) Filter (map) r_work=0.1165 r_free=0.1296 | n_water=335 | time (s): 3.880 (total time: 61.370) Find peaks r_work=0.1165 r_free=0.1296 | n_water=335 | time (s): 0.700 (total time: 62.070) Add new water r_work=0.1232 r_free=0.1360 | n_water=498 | time (s): 3.730 (total time: 65.800) Refine new water occ: r_work=0.1164 r_free=0.1304 adp: r_work=0.1164 r_free=0.1305 occ: r_work=0.1149 r_free=0.1294 adp: r_work=0.1148 r_free=0.1294 occ: r_work=0.1139 r_free=0.1287 adp: r_work=0.1135 r_free=0.1285 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1285 r_work=0.1135 r_free=0.1285 | n_water=498 | time (s): 177.850 (total time: 243.650) Filter (q & B) r_work=0.1143 r_free=0.1300 | n_water=458 | time (s): 3.650 (total time: 247.300) Filter (dist only) r_work=0.1143 r_free=0.1299 | n_water=457 | time (s): 48.690 (total time: 295.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.405817 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 0.1201 0.1339 0.0137 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1166 0.1318 0.0151 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1151 0.1305 0.0154 0.005 0.9 4.2 0.5 0.0 0 0.535 0.1146 0.1305 0.0160 0.006 1.0 3.8 0.5 0.0 0 0.803 0.1142 0.1303 0.0161 0.007 1.0 3.5 0.5 0.0 0 1.071 0.1139 0.1305 0.0166 0.007 1.1 3.8 0.5 0.0 0 1.338 0.1137 0.1305 0.0168 0.008 1.1 3.8 0.5 0.0 0 1.606 0.1135 0.1304 0.0169 0.008 1.1 3.8 0.5 0.0 0 1.873 0.1144 0.1303 0.0159 0.006 1.0 3.5 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1142 0.1303 0.0161 0.007 1.0 3.5 0.5 0.0 0 1.071 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.42 13.03 1.61 3.779 21.278 46.406 3.614 11.42 13.03 1.61 3.779 21.278 1.392 3.614 11.43 13.03 1.60 3.764 21.278 5.801 3.614 11.48 13.10 1.62 3.711 21.265 23.203 3.611 11.45 13.14 1.70 3.737 21.248 46.406 3.608 11.43 13.17 1.75 3.757 21.228 69.609 3.604 11.38 13.16 1.78 3.771 21.224 92.812 3.601 11.36 13.16 1.80 3.781 21.220 116.015 3.598 11.35 13.19 1.85 3.798 21.212 139.217 3.598 11.32 13.18 1.86 3.809 21.207 162.420 3.596 11.31 13.17 1.86 3.818 21.203 185.623 3.594 11.30 13.16 1.86 3.825 21.203 208.826 3.593 11.29 13.14 1.85 3.831 21.201 232.029 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: 1.392 Accepted refinement result: 11.42 13.03 1.61 3.779 21.278 1.392 3.614 Individual atomic B min max mean iso aniso Overall: 9.09 115.04 21.27 3.31 239 1745 Protein: 9.09 115.04 17.02 3.32 0 1519 Water: 11.50 76.69 35.38 N/A 239 218 Other: 19.74 26.62 22.09 N/A 0 8 Chain A: 9.09 115.04 19.36 N/A 0 1745 Chain S: 14.73 60.01 35.20 N/A 239 0 Histogram: Values Number of atoms 9.09 - 19.68 1260 19.68 - 30.28 301 30.28 - 40.87 222 40.87 - 51.47 124 51.47 - 62.06 54 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1303 r_work=0.1142 r_free=0.1303 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1303 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1295 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.17 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= 0.1135 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.610564 | | target function (ml) not normalized (work): 300716.613142 | | target function (ml) not normalized (free): 15836.632158 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1135 0.1295 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1475 0.1474 0.1508 n_refl.: 87584 remove outliers: r(all,work,free)=0.1475 0.1474 0.1508 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1474 0.1474 0.1508 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1134 0.1294 n_refl.: 87584 remove outliers: r(all,work,free)=0.1139 0.1131 0.1294 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4034 286.945 251.989 0.456 1.000 0.314 11.894-9.307 94.12 92 4 0.2127 483.158 467.356 0.879 1.002 0.253 9.237-7.194 98.18 209 7 0.2335 387.212 383.637 0.936 1.002 0.200 7.162-5.571 100.00 427 22 0.2116 296.993 286.969 0.912 1.003 0.170 5.546-4.326 100.00 867 58 0.1109 407.698 402.766 0.963 1.003 0.123 4.315-3.360 100.00 1859 96 0.0913 387.724 385.772 1.002 1.003 0.106 3.356-2.611 100.00 3867 181 0.1107 254.715 252.715 1.009 1.002 0.060 2.608-2.026 99.99 8198 413 0.0913 168.852 168.162 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.459 82.776 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.566 36.162 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2174 23.039 21.572 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0085 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1294 After: r_work=0.1132 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1295 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=0.1132 r_free=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1295 | n_water=457 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1132 r_free=0.1295 | n_water=457 | time (s): 45.980 (total time: 48.430) Filter (q & B) r_work=0.1132 r_free=0.1292 | n_water=454 | time (s): 4.010 (total time: 52.440) Compute maps r_work=0.1132 r_free=0.1292 | n_water=454 | time (s): 1.900 (total time: 54.340) Filter (map) r_work=0.1155 r_free=0.1293 | n_water=354 | time (s): 4.050 (total time: 58.390) Find peaks r_work=0.1155 r_free=0.1293 | n_water=354 | time (s): 0.710 (total time: 59.100) Add new water r_work=0.1209 r_free=0.1345 | n_water=503 | time (s): 3.780 (total time: 62.880) Refine new water occ: r_work=0.1154 r_free=0.1286 adp: r_work=0.1154 r_free=0.1289 occ: r_work=0.1141 r_free=0.1279 adp: r_work=0.1140 r_free=0.1280 occ: r_work=0.1132 r_free=0.1276 adp: r_work=0.1129 r_free=0.1274 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1274 r_work=0.1129 r_free=0.1274 | n_water=503 | time (s): 257.490 (total time: 320.370) Filter (q & B) r_work=0.1135 r_free=0.1289 | n_water=462 | time (s): 4.020 (total time: 324.390) Filter (dist only) r_work=0.1135 r_free=0.1289 | n_water=460 | time (s): 50.220 (total time: 374.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767805 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.924832 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 0.1222 0.1340 0.0118 0.004 0.7 6.1 0.0 0.0 0 0.088 0.1164 0.1305 0.0141 0.004 0.8 5.1 0.0 0.0 0 0.265 0.1146 0.1294 0.0148 0.005 0.9 5.1 0.5 0.0 0 0.530 0.1137 0.1289 0.0152 0.006 1.0 4.2 0.5 0.0 0 0.796 0.1135 0.1289 0.0153 0.006 1.0 4.2 0.5 0.0 0 1.061 0.1134 0.1288 0.0154 0.007 1.0 4.2 0.5 0.0 0 1.326 0.1133 0.1288 0.0155 0.007 1.1 4.2 0.5 0.0 0 1.591 0.1132 0.1288 0.0156 0.008 1.1 4.2 0.5 0.0 0 1.856 0.1136 0.1289 0.0153 0.006 1.0 4.2 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1288 0.0156 0.008 1.1 4.2 0.5 0.0 0 1.856 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.88 1.56 3.779 21.302 37.925 3.607 11.32 12.88 1.56 3.779 21.302 1.138 3.607 11.32 12.88 1.56 3.779 21.302 4.741 3.607 11.36 12.91 1.55 3.710 21.297 18.962 3.602 11.46 13.09 1.63 3.718 21.268 37.925 3.608 11.38 13.06 1.69 3.746 21.255 56.887 3.601 11.33 13.06 1.72 3.762 21.250 75.850 3.597 11.30 13.03 1.74 3.775 21.247 94.812 3.594 11.27 13.02 1.75 3.782 21.245 113.774 3.592 11.24 12.98 1.75 3.789 21.247 132.737 3.589 11.26 13.06 1.80 3.808 21.229 151.699 3.590 11.22 13.01 1.78 3.811 21.236 170.662 3.588 11.23 13.02 1.79 3.822 21.227 189.624 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: 4.741 Accepted refinement result: 11.32 12.88 1.56 3.779 21.302 4.741 3.607 Individual atomic B min max mean iso aniso Overall: 9.08 115.03 21.32 3.31 243 1744 Protein: 9.08 115.03 17.02 3.32 0 1519 Water: 11.50 76.68 35.49 N/A 243 217 Other: 19.74 26.61 22.08 N/A 0 8 Chain A: 9.08 115.03 19.34 N/A 0 1744 Chain S: 14.72 60.01 35.49 N/A 243 0 Histogram: Values Number of atoms 9.08 - 19.68 1262 19.68 - 30.27 291 30.27 - 40.87 226 40.87 - 51.46 136 51.46 - 62.06 49 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1288 r_work=0.1132 r_free=0.1288 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1288 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1285 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605342 | | target function (ml) not normalized (work): 300252.863230 | | target function (ml) not normalized (free): 15821.054211 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1308 0.1313 5.5976 5.611| | 2: 3.57 - 2.84 1.00 2888 124 0.1061 0.1451 5.1661 5.2517| | 3: 2.83 - 2.48 1.00 2820 163 0.1092 0.1169 4.9523 4.9836| | 4: 2.47 - 2.25 1.00 2825 136 0.0896 0.0987 4.6371 4.6584| | 5: 2.25 - 2.09 1.00 2756 127 0.0877 0.0978 4.5884 4.6441| | 6: 2.09 - 1.97 1.00 2846 113 0.0858 0.1033 4.2735 4.3768| | 7: 1.97 - 1.87 1.00 2787 165 0.0879 0.1114 3.9796 4.0912| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1094 3.8904 3.9926| | 9: 1.79 - 1.72 1.00 2745 138 0.0872 0.1172 3.6468 3.8115| | 10: 1.72 - 1.66 1.00 2831 160 0.0916 0.1176 3.5648 3.7078| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1015 3.4966 3.5524| | 12: 1.61 - 1.56 1.00 2773 144 0.0910 0.1159 3.3323 3.462| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1014 3.307 3.3845| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1050 3.2383 3.3212| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1219 3.1545 3.268| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1246 3.1373 3.2496| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1301 3.1209 3.2298| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1320 3.1075 3.2451| | 19: 1.36 - 1.34 1.00 2807 134 0.1267 0.1574 3.1171 3.2755| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1463 3.1168 3.1633| | 21: 1.32 - 1.30 1.00 2785 112 0.1476 0.1494 3.1189 3.1011| | 22: 1.29 - 1.27 1.00 2704 152 0.1571 0.1983 3.1299 3.2942| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1797 3.1371 3.2105| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1847 3.1312 3.2354| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2170 3.1452 3.27| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1761 3.151 3.2035| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2182 3.1742 3.1656| | 28: 1.19 - 1.18 1.00 2671 147 0.2205 0.2316 3.1692 3.1797| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2382 3.1511 3.2293| | 30: 1.16 - 1.15 1.00 2739 148 0.2451 0.2448 3.1465 3.1683| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.56 1.00 0.97 5909.39| | 2: 3.57 - 2.84 2888 124 0.92 12.70 1.01 0.97 5909.39| | 3: 2.83 - 2.48 2820 163 0.89 16.71 0.99 0.98 4933.82| | 4: 2.47 - 2.25 2825 136 0.92 13.64 1.00 0.98 2418.14| | 5: 2.25 - 2.09 2756 127 0.90 15.81 1.01 0.98 2418.14| | 6: 2.09 - 1.97 2846 113 0.92 12.46 1.02 0.98 1390.47| | 7: 1.97 - 1.87 2787 165 0.95 9.33 1.02 0.98 514.01| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.98 514.01| | 9: 1.79 - 1.72 2745 138 0.94 10.00 0.98 0.98 288.90| | 10: 1.72 - 1.66 2831 160 0.94 11.02 0.98 0.98 243.81| | 11: 1.66 - 1.61 2712 147 0.94 11.66 0.98 0.98 233.52| | 12: 1.61 - 1.56 2773 144 0.96 8.79 0.99 0.98 136.41| | 13: 1.56 - 1.52 2745 130 0.95 10.34 1.03 0.98 136.41| | 14: 1.52 - 1.48 2803 134 0.94 10.68 1.02 0.98 122.66| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.99 97.47| | 16: 1.45 - 1.42 2756 161 0.94 11.01 1.02 0.99 97.47| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.99 89.23| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 84.47| | 19: 1.36 - 1.34 2807 134 0.94 11.88 0.99 0.98 84.47| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.97 80.86| | 21: 1.32 - 1.30 2785 112 0.94 13.13 0.98 0.97 80.60| | 22: 1.29 - 1.27 2704 152 0.93 13.73 0.98 0.96 81.03| | 23: 1.27 - 1.26 2802 156 0.92 14.91 0.97 0.95 83.22| | 24: 1.26 - 1.24 2744 132 0.92 14.94 0.96 0.95 83.22| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 85.11| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.93 87.21| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 87.21| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.93 90.67| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.93 91.97| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.93 91.97| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.60 max = 5909.39 mean = 907.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.48| |phase err.(test): min = 0.00 max = 87.69 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1285 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1460 0.1460 0.1490 n_refl.: 87576 remove outliers: r(all,work,free)=0.1460 0.1460 0.1490 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1460 0.1490 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1128 0.1289 n_refl.: 87576 remove outliers: r(all,work,free)=0.1136 0.1128 0.1289 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4121 286.945 248.732 0.440 0.999 0.298 11.894-9.307 93.14 91 4 0.2268 484.404 466.710 0.877 1.002 0.233 9.237-7.194 98.18 209 7 0.2300 387.212 381.320 0.930 1.002 0.180 7.162-5.571 100.00 427 22 0.2105 296.993 287.152 0.907 1.003 0.130 5.546-4.326 100.00 867 58 0.1094 407.698 403.171 0.962 1.003 0.115 4.315-3.360 100.00 1859 96 0.0916 387.724 386.081 1.003 1.002 0.110 3.356-2.611 100.00 3867 181 0.1099 254.715 252.858 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0912 168.852 168.199 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.459 82.818 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.566 36.174 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 23.039 21.583 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0086 ================= 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 : 0.2594 0.1940 0.083 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1765 0.083 5.302 9.0 119.5 20.1 258 0.000 1_settarget: 0.1619 0.1765 0.083 5.302 9.0 119.5 20.1 258 0.000 1_nqh: 0.1623 0.1770 0.083 5.302 9.0 119.5 20.1 258 0.006 1_weight: 0.1623 0.1770 0.083 5.302 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1223 0.1468 0.007 0.940 9.0 119.5 20.1 258 0.134 1_adp: 0.1231 0.1465 0.007 0.940 9.0 119.4 20.1 258 0.134 1_regHadp: 0.1232 0.1468 0.007 0.940 9.0 119.4 20.1 258 0.134 1_occ: 0.1225 0.1465 0.007 0.940 9.0 119.4 20.1 258 0.134 2_bss: 0.1224 0.1457 0.007 0.940 9.1 119.5 20.1 258 0.134 2_settarget: 0.1224 0.1457 0.007 0.940 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1224 0.1457 0.007 0.945 9.1 119.5 20.1 258 0.134 2_nqh: 0.1224 0.1456 0.007 0.945 9.1 119.5 20.1 258 0.132 2_sol: 0.1204 0.1390 0.007 0.945 9.1 115.0 22.1 413 n/a 2_weight: 0.1204 0.1390 0.007 0.945 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1194 0.1415 0.006 0.851 9.1 115.0 22.1 413 n/a 2_adp: 0.1194 0.1415 0.006 0.851 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1194 0.1415 0.006 0.851 9.1 115.0 22.1 413 n/a 2_occ: 0.1196 0.1422 0.006 0.851 9.1 115.0 22.1 413 n/a 3_bss: 0.1192 0.1415 0.006 0.851 9.1 115.0 22.1 413 n/a 3_settarget: 0.1192 0.1415 0.006 0.851 9.1 115.0 22.1 413 n/a 3_updatecdl: 0.1192 0.1415 0.006 0.854 9.1 115.0 22.1 413 n/a 3_nqh: 0.1192 0.1415 0.006 0.854 9.1 115.0 22.1 413 n/a 3_sol: 0.1211 0.1409 0.006 0.854 9.1 115.0 21.2 438 n/a 3_weight: 0.1211 0.1409 0.006 0.854 9.1 115.0 21.2 438 n/a 3_xyzrec: 0.1163 0.1325 0.007 1.020 9.1 115.0 21.2 438 n/a 3_adp: 0.1163 0.1325 0.007 1.020 9.1 115.0 21.2 438 n/a 3_regHadp: 0.1163 0.1325 0.007 1.020 9.1 115.0 21.2 438 n/a 3_occ: 0.1154 0.1316 0.007 1.020 9.1 115.0 21.2 438 n/a 4_bss: 0.1148 0.1312 0.007 1.020 9.1 115.0 21.2 438 n/a 4_settarget: 0.1148 0.1312 0.007 1.020 9.1 115.0 21.2 438 n/a 4_updatecdl: 0.1148 0.1312 0.007 1.023 9.1 115.0 21.2 438 n/a 4_nqh: 0.1148 0.1312 0.007 1.023 9.1 115.0 21.2 438 n/a 4_sol: 0.1143 0.1299 0.007 1.023 9.1 115.0 21.3 457 n/a 4_weight: 0.1143 0.1299 0.007 1.023 9.1 115.0 21.3 457 n/a 4_xyzrec: 0.1142 0.1303 0.007 1.011 9.1 115.0 21.3 457 n/a 4_adp: 0.1142 0.1303 0.007 1.011 9.1 115.0 21.3 457 n/a 4_regHadp: 0.1142 0.1303 0.007 1.011 9.1 115.0 21.3 457 n/a 4_occ: 0.1135 0.1295 0.007 1.011 9.1 115.0 21.3 457 n/a 5_bss: 0.1131 0.1294 0.007 1.011 9.1 115.0 21.3 457 n/a 5_settarget: 0.1131 0.1294 0.007 1.011 9.1 115.0 21.3 457 n/a 5_updatecdl: 0.1131 0.1294 0.007 1.010 9.1 115.0 21.3 457 n/a 5_setrh: 0.1132 0.1295 0.007 1.010 9.1 115.0 21.3 457 n/a 5_nqh: 0.1132 0.1295 0.007 1.010 9.1 115.0 21.3 457 n/a 5_sol: 0.1135 0.1289 0.007 1.010 9.1 115.0 21.3 460 n/a 5_weight: 0.1135 0.1289 0.007 1.010 9.1 115.0 21.3 460 n/a 5_xyzrec: 0.1132 0.1288 0.008 1.075 9.1 115.0 21.3 460 n/a 5_adp: 0.1132 0.1288 0.008 1.075 9.1 115.0 21.3 460 n/a 5_regHadp: 0.1132 0.1288 0.008 1.075 9.1 115.0 21.3 460 n/a 5_occ: 0.1128 0.1285 0.008 1.075 9.1 115.0 21.3 460 n/a end: 0.1128 0.1289 0.008 1.075 9.1 115.0 21.3 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2353655_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2353655_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1600 Refinement macro-cycles (run) : 14293.4600 Write final files (write_after_run_outputs) : 71.6200 Total : 14369.2400 Total CPU time: 4.00 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:19:30 PST -0800 (1735366770.22 s) Start R-work = 0.1619, R-free = 0.1765 Final R-work = 0.1128, R-free = 0.1289 =============================================================================== Job complete usr+sys time: 14516.68 seconds wall clock time: 263 minutes 8.69 seconds (15788.69 seconds total)