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_8315495.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_8315495.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.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 2 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: 1.51, per 1000 atoms: 0.45 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: 0.46 Conformation dependent library (CDL) restraints added in 211.0 milliseconds Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 547 0.91 - 1.17: 1097 1.17 - 1.42: 632 1.42 - 1.68: 839 1.68 - 1.94: 38 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.725 -0.271 1.18e-02 7.18e+03 5.28e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.277 0.246 1.19e-02 7.06e+03 4.27e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.545 -0.219 1.10e-02 8.26e+03 3.97e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.236 1.056 0.181 1.02e-02 9.61e+03 3.14e+02 bond pdb=" C SER A 57 " pdb=" O SER A 57 " ideal model delta sigma weight residual 1.234 1.447 -0.213 1.23e-02 6.61e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3263 4.85 - 9.70: 1816 9.70 - 14.55: 612 14.55 - 19.40: 79 19.40 - 24.25: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.32 -9.90 6.40e-01 2.44e+00 2.39e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 105.90 14.65 9.50e-01 1.11e+00 2.38e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 107.07 15.05 1.06e+00 8.90e-01 2.02e+02 angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.77 135.47 -13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 108.48 13.29 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 949 17.65 - 35.30: 108 35.30 - 52.95: 40 52.95 - 70.61: 12 70.61 - 88.26: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 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 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 105 0.216 - 0.431: 72 0.431 - 0.646: 41 0.646 - 0.862: 22 0.862 - 1.077: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.32 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.100 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.067 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.125 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.011 9.50e-02 1.11e+02 6.69e-02 1.00e+02 pdb=" NE ARG A 28 " -0.106 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.082 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1025 2.31 - 2.88: 8054 2.88 - 3.46: 10574 3.46 - 4.03: 15124 4.03 - 4.60: 21875 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.741 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.743 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.787 1.850 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.788 2.100 ... (remaining 56647 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_8315495_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= 0.2611 r_free= 0.1937 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797706 | | target function (ml) not normalized (work): 233065.657431 | | target function (ml) not normalized (free): 11838.006266 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2101 7.1545 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2450 0.1661 4.3381 4.3078| | 3: 2.84 - 2.48 1.00 2833 165 0.2333 0.1723 4.1195 4.1382| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1445 3.8259 3.8277| | 5: 2.25 - 2.09 1.00 2756 127 0.2484 0.1612 3.7907 3.8144| | 6: 2.09 - 1.97 1.00 2846 113 0.2530 0.1767 3.4628 3.5538| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1822 3.1444 3.2132| | 8: 1.87 - 1.79 1.00 2789 144 0.2498 0.1756 3.0661 3.1126| | 9: 1.79 - 1.72 1.00 2745 138 0.2410 0.2035 2.8917 3.0375| | 10: 1.72 - 1.66 1.00 2789 158 0.2405 0.1899 2.8052 2.8841| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1914 2.7461 2.8037| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2148 2.6345 2.6988| | 13: 1.56 - 1.52 1.00 2745 130 0.2577 0.1750 2.5932 2.595| | 14: 1.52 - 1.48 1.00 2803 134 0.2633 0.1924 2.5198 2.5528| | 15: 1.48 - 1.45 1.00 2738 128 0.2641 0.2050 2.4525 2.4721| | 16: 1.45 - 1.42 1.00 2756 161 0.2660 0.2049 2.3961 2.4267| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.1992 2.331 2.3006| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2146 2.2653 2.3283| | 19: 1.36 - 1.34 1.00 2807 134 0.2615 0.2320 2.2375 2.3035| | 20: 1.34 - 1.32 1.00 2696 147 0.2719 0.2127 2.2167 2.1868| | 21: 1.32 - 1.30 1.00 2785 112 0.2703 0.2223 2.1703 2.1857| | 22: 1.29 - 1.27 1.00 2704 152 0.2706 0.2764 2.129 2.2638| | 23: 1.27 - 1.26 1.00 2802 156 0.2815 0.2513 2.1161 2.1343| | 24: 1.26 - 1.24 1.00 2744 132 0.2789 0.2554 2.0877 2.1727| | 25: 1.24 - 1.22 1.00 2734 148 0.2933 0.2721 2.0469 2.1316| | 26: 1.22 - 1.21 1.00 2727 135 0.2915 0.2374 2.0282 2.0656| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2695 2.0082 2.0295| | 28: 1.19 - 1.18 1.00 2671 147 0.3041 0.2740 1.9927 1.9933| | 29: 1.18 - 1.16 1.00 2800 134 0.3030 0.2588 1.9667 2.0255| | 30: 1.16 - 1.15 1.00 2740 148 0.3110 0.3020 1.9345 2.0038| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.46 0.76 0.23 1435.35| | 2: 3.57 - 2.84 2876 122 0.81 25.68 1.27 0.23 1435.35| | 3: 2.84 - 2.48 2833 165 0.75 31.35 1.24 0.24 1191.38| | 4: 2.47 - 2.25 2825 136 0.81 25.34 1.25 0.25 558.24| | 5: 2.25 - 2.09 2756 127 0.78 28.98 1.28 0.25 558.24| | 6: 2.09 - 1.97 2846 113 0.83 22.65 1.29 0.25 307.77| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.28 0.25 94.16| | 8: 1.87 - 1.79 2789 144 0.85 21.63 1.25 0.25 94.16| | 9: 1.79 - 1.72 2745 138 0.88 18.98 1.23 0.25 57.44| | 10: 1.72 - 1.66 2789 158 0.86 20.67 1.22 0.25 50.09| | 11: 1.66 - 1.61 2740 147 0.85 21.88 1.24 0.25 48.25| | 12: 1.61 - 1.56 2787 146 0.88 18.60 1.23 0.25 29.67| | 13: 1.56 - 1.52 2745 130 0.87 20.36 1.24 0.25 29.67| | 14: 1.52 - 1.48 2803 134 0.87 20.59 1.24 0.25 26.30| | 15: 1.48 - 1.45 2738 128 0.87 19.78 1.23 0.25 20.13| | 16: 1.45 - 1.42 2756 161 0.86 21.46 1.23 0.25 20.13| | 17: 1.42 - 1.39 2785 139 0.87 20.26 1.23 0.25 17.01| | 18: 1.39 - 1.36 2741 179 0.87 20.94 1.23 0.25 15.20| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.21 0.25 15.20| | 20: 1.34 - 1.32 2696 147 0.87 20.79 1.21 0.24 12.93| | 21: 1.32 - 1.30 2785 112 0.86 21.75 1.20 0.24 12.77| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.20 0.24 12.55| | 23: 1.27 - 1.26 2802 156 0.85 22.78 1.21 0.24 11.45| | 24: 1.26 - 1.24 2744 132 0.84 23.27 1.20 0.24 11.45| | 25: 1.24 - 1.22 2734 148 0.83 24.51 1.22 0.24 11.00| | 26: 1.22 - 1.21 2727 135 0.83 24.78 1.20 0.23 10.50| | 27: 1.21 - 1.19 2814 148 0.83 25.41 1.21 0.23 10.50| | 28: 1.19 - 1.18 2671 147 0.82 26.22 1.19 0.23 9.83| | 29: 1.18 - 1.16 2800 134 0.81 26.53 1.17 0.23 9.57| | 30: 1.16 - 1.15 2740 148 0.80 27.96 1.16 0.23 9.57| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.57 max = 1435.35 mean = 209.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.75| |phase err.(test): min = 0.00 max = 89.49 mean = 22.55| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.271 1557 Z= 5.557 Angle : 5.380 22.608 2118 Z= 3.810 Chirality : 0.381 1.077 243 Planarity : 0.033 0.126 284 Dihedral : 13.949 88.257 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 24.86 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.47), residues: 224 helix: -2.24 (0.40), residues: 102 sheet: -0.68 (0.82), residues: 28 loop : 0.15 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.018 ARG A 28 TYR 0.116 0.041 TYR A 141 PHE 0.113 0.040 PHE A 119 HIS 0.067 0.033 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= 0.2611 r_free= 0.1937 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797706 | | target function (ml) not normalized (work): 233065.657431 | | target function (ml) not normalized (free): 11838.006266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1937 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1937 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1990 0.1937 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2006 0.2012 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1642 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1755 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 98.94 88 5 0.3833 386.610 359.778 0.675 1.002 0.411 11.894-9.307 98.04 96 4 0.1724 616.604 592.192 0.929 1.003 0.379 9.237-7.194 100.00 213 7 0.2139 502.268 492.781 0.966 1.003 0.363 7.162-5.571 100.00 427 22 0.2218 376.924 366.425 0.935 1.003 0.330 5.546-4.326 100.00 867 58 0.1289 517.424 511.342 0.964 1.003 0.222 4.315-3.360 100.00 1859 96 0.1144 492.073 488.377 1.007 1.003 0.189 3.356-2.611 100.00 3867 181 0.1434 323.267 320.107 1.002 1.002 0.099 2.608-2.026 99.99 8198 413 0.1360 214.296 212.214 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.651 104.035 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2087 46.407 45.107 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2614 29.239 26.977 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1640 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.971598 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.782406 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 0.1634 0.1751 0.0118 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1531 0.1664 0.0133 0.001 0.5 3.8 0.0 0.0 0 0.250 0.1425 0.1581 0.0157 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1378 0.1555 0.0176 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1345 0.1533 0.0188 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1338 0.1528 0.0189 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1293 0.1508 0.0215 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1270 0.1497 0.0227 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1258 0.1490 0.0232 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1255 0.1489 0.0234 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1241 0.1480 0.0239 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1241 0.1482 0.0241 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1232 0.1470 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1470 0.0239 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1229 0.1470 0.0241 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1470 0.0242 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1470 0.0244 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1220 0.1463 0.0243 0.008 1.0 3.8 0.5 0.6 0 13.986 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1220 0.1463 0.0243 0.008 1.0 3.8 0.5 0.6 0 13.986 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.20 14.63 2.43 3.013 19.034 2011.782 0.017 12.20 14.62 2.43 3.008 19.034 60.353 0.017 12.27 14.59 2.31 2.666 19.033 251.473 0.017 12.63 15.22 2.59 2.755 19.207 1005.891 0.016 12.49 15.41 2.92 3.274 19.589 2011.782 0.015 12.39 15.34 2.96 3.274 19.593 3017.674 0.015 12.28 15.33 3.05 3.330 19.613 4023.565 0.015 12.28 15.44 3.16 3.406 19.645 5029.456 0.015 12.20 15.37 3.18 3.404 19.641 6035.347 0.015 12.20 15.41 3.21 3.308 19.580 7041.238 0.015 12.20 15.45 3.26 3.446 19.643 8047.130 0.015 12.15 15.45 3.29 3.486 19.650 9053.021 0.015 12.10 15.40 3.30 3.434 19.611 10058.912 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: 251.473 Accepted refinement result: 12.27 14.59 2.31 2.666 19.033 251.473 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.06 3.31 0 1785 Protein: 9.05 114.95 16.97 3.31 0 1519 Water: 11.44 119.42 38.20 N/A 0 258 Other: 19.68 26.57 22.03 N/A 0 8 Chain A: 9.05 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.34 4 97.34 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1459 r_work=0.1229 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1462 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 = 0.1223 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1223 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016579 | | target function (ls_wunit_k1) not normalized (work): 1380.946197 | | target function (ls_wunit_k1) not normalized (free): 109.835179 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1223 0.1461 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1665 0.1666 0.1686 n_refl.: 87592 remove outliers: r(all,work,free)=0.1665 0.1666 0.1686 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1672 0.1673 0.1692 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1220 0.1451 n_refl.: 87592 remove outliers: r(all,work,free)=0.1231 0.1220 0.1451 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 96.88 88 5 0.3547 304.635 283.730 0.658 1.002 0.387 11.894-9.307 98.04 96 4 0.1569 485.861 473.584 0.930 1.003 0.355 9.237-7.194 100.00 213 7 0.1855 395.769 390.700 0.969 1.003 0.340 7.162-5.571 100.00 427 22 0.1824 297.002 291.145 0.936 1.003 0.300 5.546-4.326 100.00 867 58 0.1011 407.711 404.358 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0863 387.736 386.647 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1163 254.722 253.613 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1015 168.858 168.161 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.461 82.671 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.567 36.074 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 23.040 21.522 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0623 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1451 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1222 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1452 | n_water=258 | time (s): 1.550 (total time: 1.550) Filter (dist) r_work=0.1229 r_free=0.1453 | n_water=252 | time (s): 24.080 (total time: 25.630) Filter (q & B) r_work=0.1232 r_free=0.1454 | n_water=249 | time (s): 3.380 (total time: 29.010) Compute maps r_work=0.1232 r_free=0.1454 | n_water=249 | time (s): 1.410 (total time: 30.420) Filter (map) r_work=0.1250 r_free=0.1460 | n_water=223 | time (s): 3.360 (total time: 33.780) Find peaks r_work=0.1250 r_free=0.1460 | n_water=223 | time (s): 0.570 (total time: 34.350) Add new water r_work=0.1395 r_free=0.1609 | n_water=428 | time (s): 2.280 (total time: 36.630) Refine new water occ: r_work=0.1301 r_free=0.1481 adp: r_work=0.1221 r_free=0.1423 occ: r_work=0.1232 r_free=0.1422 adp: r_work=0.1200 r_free=0.1404 occ: r_work=0.1203 r_free=0.1398 adp: r_work=0.1192 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1395 r_work=0.1192 r_free=0.1395 | n_water=428 | time (s): 123.250 (total time: 159.880) Filter (q & B) r_work=0.1196 r_free=0.1393 | n_water=417 | time (s): 2.990 (total time: 162.870) Filter (dist only) r_work=0.1197 r_free=0.1393 | n_water=416 | time (s): 35.950 (total time: 198.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.508987 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.701057 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 0.1684 0.1784 0.0101 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1541 0.1659 0.0118 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1417 0.1556 0.0139 0.001 0.4 5.1 0.0 0.0 0 0.500 0.1350 0.1504 0.0155 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1316 0.1485 0.0170 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1304 0.1476 0.0172 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1252 0.1441 0.0189 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1228 0.1431 0.0202 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1215 0.1418 0.0203 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1210 0.1414 0.0204 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1207 0.1418 0.0211 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1202 0.1407 0.0205 0.005 0.8 5.4 0.5 0.0 0 7.000 0.1200 0.1411 0.0210 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1198 0.1407 0.0209 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1196 0.1405 0.0210 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1191 0.1406 0.0216 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1188 0.1408 0.0220 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1189 0.1415 0.0226 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1187 0.1420 0.0233 0.008 0.9 5.8 0.5 0.6 0 14.254 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1405 0.0210 0.006 0.9 5.4 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.05 2.10 3.771 21.717 1485.701 0.016 11.96 14.05 2.10 3.771 21.717 44.571 0.016 11.96 14.05 2.10 3.771 21.717 185.713 0.016 12.13 14.42 2.30 3.626 21.721 742.851 0.016 12.16 14.81 2.65 3.434 21.993 1485.701 0.015 12.03 14.79 2.76 3.435 22.067 2228.552 0.015 11.94 14.78 2.84 3.504 21.870 2971.402 0.014 11.84 14.77 2.93 3.495 21.912 3714.253 0.014 11.86 14.84 2.98 3.501 22.125 4457.103 0.014 11.81 14.81 3.00 3.511 22.115 5199.954 0.014 11.79 14.83 3.03 3.516 22.049 5942.804 0.014 11.76 14.83 3.07 3.574 22.204 6685.655 0.014 11.75 14.87 3.12 3.573 22.125 7428.505 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.713 Accepted refinement result: 11.96 14.05 2.10 3.771 21.717 185.713 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.99 22.10 3.31 193 1750 Protein: 9.09 114.99 17.01 3.31 0 1519 Water: 11.48 76.67 40.67 N/A 193 223 Other: 19.72 26.61 22.07 N/A 0 8 Chain A: 9.09 114.99 19.39 N/A 0 1750 Chain S: 11.74 60.00 46.63 N/A 193 0 Histogram: Values Number of atoms 9.09 - 19.68 1259 19.68 - 30.27 247 30.27 - 40.86 167 40.86 - 51.45 129 51.45 - 62.04 118 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1405 r_work=0.1196 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1405 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1398 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 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= 0.1195 r_free= 0.1398 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015102 | | target function (ls_wunit_k1) not normalized (work): 1257.959433 | | target function (ls_wunit_k1) not normalized (free): 100.079261 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1195 0.1398 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1594 0.1595 0.1599 n_refl.: 87592 remove outliers: r(all,work,free)=0.1594 0.1595 0.1599 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1597 0.1598 0.1601 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1192 0.1391 n_refl.: 87592 remove outliers: r(all,work,free)=0.1200 0.1190 0.1391 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 92.71 84 5 0.3373 297.964 277.659 0.605 1.003 0.360 11.894-9.307 98.04 96 4 0.1439 485.861 478.470 0.933 1.003 0.324 9.237-7.194 100.00 213 7 0.1698 395.769 395.400 0.985 1.003 0.290 7.162-5.571 100.00 427 22 0.1668 297.002 291.679 0.934 1.003 0.230 5.546-4.326 100.00 867 58 0.0888 407.711 404.527 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0794 387.736 387.008 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1095 254.722 253.700 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1014 168.858 168.358 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1105 82.461 82.668 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.567 36.087 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 23.040 21.543 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0242 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1391 | n_water=416 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1191 r_free=0.1394 | n_water=411 | time (s): 37.770 (total time: 40.010) Filter (q & B) r_work=0.1191 r_free=0.1394 | n_water=411 | time (s): 0.900 (total time: 40.910) Compute maps r_work=0.1191 r_free=0.1394 | n_water=411 | time (s): 1.290 (total time: 42.200) Filter (map) r_work=0.1227 r_free=0.1394 | n_water=281 | time (s): 2.780 (total time: 44.980) Find peaks r_work=0.1227 r_free=0.1394 | n_water=281 | time (s): 0.480 (total time: 45.460) Add new water r_work=0.1351 r_free=0.1528 | n_water=472 | time (s): 2.820 (total time: 48.280) Refine new water occ: r_work=0.1258 r_free=0.1440 adp: r_work=0.1260 r_free=0.1442 occ: r_work=0.1235 r_free=0.1414 adp: r_work=0.1235 r_free=0.1416 occ: r_work=0.1217 r_free=0.1391 adp: r_work=0.1212 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1212 r_free=0.1391 r_work=0.1212 r_free=0.1391 | n_water=472 | time (s): 163.680 (total time: 211.960) Filter (q & B) r_work=0.1217 r_free=0.1395 | n_water=441 | time (s): 3.500 (total time: 215.460) Filter (dist only) r_work=0.1217 r_free=0.1394 | n_water=440 | time (s): 41.130 (total time: 256.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.680541 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.146868 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 0.1375 0.0130 0.002 0.6 3.8 0.5 0.0 0 0.084 0.1200 0.1340 0.0140 0.003 0.7 3.5 0.5 0.0 0 0.252 0.1183 0.1328 0.0145 0.004 0.8 3.5 0.5 0.0 0 0.504 0.1174 0.1325 0.0151 0.005 0.9 3.8 0.5 0.0 0 0.756 0.1169 0.1322 0.0153 0.006 1.0 3.5 0.5 0.0 0 1.008 0.1167 0.1322 0.0155 0.006 1.0 3.5 0.5 0.0 0 1.260 0.1164 0.1321 0.0157 0.007 1.0 4.2 0.5 0.0 0 1.512 0.1165 0.1321 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.765 0.1173 0.1325 0.0152 0.005 0.9 3.8 0.5 0.0 0 0.840 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1321 0.0157 0.007 1.0 4.2 0.5 0.0 0 1.512 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 13.21 1.57 3.775 21.208 48.147 3.627 11.64 13.21 1.57 3.775 21.208 1.444 3.627 11.65 13.21 1.57 3.760 21.208 6.018 3.627 11.72 13.33 1.62 3.710 21.191 24.073 3.622 11.70 13.38 1.68 3.737 21.162 48.147 3.619 11.63 13.36 1.73 3.758 21.153 72.220 3.613 11.62 13.39 1.77 3.768 21.141 96.294 3.611 11.57 13.35 1.78 3.784 21.139 120.367 3.608 11.57 13.39 1.81 3.803 21.123 144.441 3.607 11.55 13.36 1.81 3.813 21.119 168.514 3.605 11.53 13.34 1.81 3.820 21.121 192.587 3.604 11.52 13.33 1.81 3.827 21.119 216.661 3.603 11.50 13.31 1.81 3.833 21.116 240.734 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.444 Accepted refinement result: 11.64 13.21 1.57 3.775 21.208 1.444 3.627 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 21.15 3.31 220 1747 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.49 76.69 35.38 N/A 220 220 Other: 19.74 26.62 22.09 N/A 0 8 Chain A: 9.10 115.00 19.34 N/A 0 1747 Chain S: 11.76 60.02 35.52 N/A 220 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.28 298 30.28 - 40.87 208 40.87 - 51.46 118 51.46 - 62.05 54 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1321 r_work=0.1164 r_free=0.1321 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1321 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1313 target_work(ml) = 3.619 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1154 r_free= 0.1313 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618799 | | target function (ml) not normalized (work): 301416.985878 | | target function (ml) not normalized (free): 15868.069557 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1313 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1491 0.1492 0.1508 n_refl.: 87588 remove outliers: r(all,work,free)=0.1491 0.1492 0.1508 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1490 0.1491 0.1508 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1300 n_refl.: 87588 remove outliers: r(all,work,free)=0.1153 0.1146 0.1300 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3948 294.681 260.673 0.478 1.001 0.309 11.894-9.307 96.08 94 4 0.2311 479.152 464.668 0.878 1.002 0.293 9.237-7.194 97.73 208 7 0.2243 388.310 386.660 0.953 1.002 0.210 7.162-5.571 100.00 427 22 0.2156 297.002 286.388 0.920 1.002 0.171 5.546-4.326 100.00 867 58 0.1108 407.711 403.035 0.963 1.002 0.148 4.315-3.360 100.00 1859 96 0.0944 387.736 385.220 1.004 1.002 0.133 3.356-2.611 100.00 3867 181 0.1139 254.722 252.459 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.0935 168.858 168.040 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.461 82.764 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.567 36.149 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2165 23.040 21.574 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1300 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1146 r_free=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1300 | n_water=440 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1148 r_free=0.1302 | n_water=437 | time (s): 45.320 (total time: 47.850) Filter (q & B) r_work=0.1149 r_free=0.1303 | n_water=434 | time (s): 4.320 (total time: 52.170) Compute maps r_work=0.1149 r_free=0.1303 | n_water=434 | time (s): 1.940 (total time: 54.110) Filter (map) r_work=0.1170 r_free=0.1305 | n_water=324 | time (s): 3.900 (total time: 58.010) Find peaks r_work=0.1170 r_free=0.1305 | n_water=324 | time (s): 0.740 (total time: 58.750) Add new water r_work=0.1232 r_free=0.1401 | n_water=483 | time (s): 3.930 (total time: 62.680) Refine new water occ: r_work=0.1164 r_free=0.1326 adp: r_work=0.1165 r_free=0.1328 occ: r_work=0.1151 r_free=0.1310 adp: r_work=0.1151 r_free=0.1312 occ: r_work=0.1141 r_free=0.1300 adp: r_work=0.1139 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1300 r_work=0.1139 r_free=0.1300 | n_water=483 | time (s): 271.780 (total time: 334.460) Filter (q & B) r_work=0.1147 r_free=0.1308 | n_water=442 | time (s): 4.010 (total time: 338.470) Filter (dist only) r_work=0.1154 r_free=0.1307 | n_water=440 | time (s): 46.920 (total time: 385.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.855272 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.659524 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 0.1216 0.1345 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.093 0.1179 0.1322 0.0143 0.003 0.8 2.9 0.5 0.0 0 0.278 0.1164 0.1314 0.0150 0.005 0.9 3.2 0.5 0.0 0 0.557 0.1158 0.1310 0.0152 0.006 1.0 3.2 0.5 0.0 0 0.835 0.1154 0.1308 0.0154 0.007 1.0 2.9 0.5 0.0 0 1.113 0.1152 0.1308 0.0157 0.007 1.1 2.9 0.5 0.0 0 1.391 0.1150 0.1305 0.0155 0.008 1.1 3.5 0.5 0.0 0 1.670 0.1148 0.1306 0.0158 0.009 1.1 3.2 0.5 0.0 0 1.948 0.1156 0.1307 0.0151 0.006 1.0 3.5 0.5 0.0 0 0.928 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1150 0.1305 0.0155 0.008 1.1 3.5 0.5 0.0 0 1.670 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 13.05 1.55 3.776 21.128 37.660 3.613 11.50 13.05 1.55 3.776 21.128 1.130 3.613 11.50 13.05 1.55 3.776 21.128 4.707 3.613 11.54 13.09 1.55 3.708 21.123 18.830 3.608 11.65 13.26 1.61 3.721 21.095 37.660 3.614 11.56 13.23 1.67 3.746 21.082 56.489 3.608 11.50 13.20 1.69 3.763 21.077 75.319 3.603 11.47 13.17 1.70 3.774 21.075 94.149 3.600 11.47 13.19 1.72 3.785 21.069 112.979 3.599 11.42 13.14 1.71 3.790 21.071 131.808 3.596 11.42 13.15 1.74 3.801 21.067 150.638 3.595 11.44 13.21 1.77 3.818 21.051 169.468 3.596 11.43 13.20 1.76 3.824 21.051 188.298 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.130 Accepted refinement result: 11.50 13.05 1.55 3.776 21.128 1.130 3.613 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 21.01 3.31 223 1744 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.49 76.68 34.74 N/A 223 217 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.10 115.00 19.31 N/A 0 1744 Chain S: 11.75 60.01 34.24 N/A 223 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.28 307 30.28 - 40.87 213 40.87 - 51.46 113 51.46 - 62.05 48 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1150 r_free=0.1305 r_work=0.1150 r_free=0.1305 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1150 r_free = 0.1305 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1299 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1145 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611083 | | target function (ml) not normalized (work): 300741.823962 | | target function (ml) not normalized (free): 15835.288050 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1145 0.1299 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1468 0.1467 0.1506 n_refl.: 87579 remove outliers: r(all,work,free)=0.1468 0.1467 0.1506 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1467 0.1466 0.1506 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1144 0.1300 n_refl.: 87579 remove outliers: r(all,work,free)=0.1151 0.1143 0.1300 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4129 297.324 254.579 0.449 1.000 0.308 11.894-9.307 95.10 93 4 0.2440 479.203 458.393 0.866 1.002 0.238 9.237-7.194 97.73 208 7 0.2366 388.310 381.192 0.927 1.002 0.180 7.162-5.571 100.00 427 22 0.2216 297.002 286.249 0.909 1.002 0.140 5.546-4.326 100.00 867 58 0.1158 407.711 402.398 0.962 1.002 0.111 4.315-3.360 100.00 1859 96 0.0942 387.736 385.888 1.004 1.002 0.100 3.356-2.611 100.00 3867 181 0.1123 254.722 252.885 1.011 1.002 0.034 2.608-2.026 99.99 8198 413 0.0918 168.858 168.233 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.461 82.818 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.567 36.177 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.040 21.590 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=-0.0101 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1143 r_free=0.1300 After: r_work=0.1144 r_free=0.1300 ================================== NQH flips ================================== r_work=0.1144 r_free=0.1300 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=0.1144 r_free=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1300 | n_water=440 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1144 r_free=0.1302 | n_water=439 | time (s): 45.860 (total time: 48.270) Filter (q & B) r_work=0.1145 r_free=0.1302 | n_water=438 | time (s): 3.920 (total time: 52.190) Compute maps r_work=0.1145 r_free=0.1302 | n_water=438 | time (s): 1.790 (total time: 53.980) Filter (map) r_work=0.1168 r_free=0.1295 | n_water=352 | time (s): 3.950 (total time: 57.930) Find peaks r_work=0.1168 r_free=0.1295 | n_water=352 | time (s): 0.690 (total time: 58.620) Add new water r_work=0.1212 r_free=0.1358 | n_water=492 | time (s): 3.720 (total time: 62.340) Refine new water occ: r_work=0.1159 r_free=0.1295 adp: r_work=0.1159 r_free=0.1297 occ: r_work=0.1148 r_free=0.1286 adp: r_work=0.1148 r_free=0.1287 occ: r_work=0.1140 r_free=0.1280 adp: r_work=0.1138 r_free=0.1278 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1278 r_work=0.1138 r_free=0.1278 | n_water=492 | time (s): 298.870 (total time: 361.210) Filter (q & B) r_work=0.1144 r_free=0.1284 | n_water=455 | time (s): 3.930 (total time: 365.140) Filter (dist only) r_work=0.1144 r_free=0.1283 | n_water=454 | time (s): 48.060 (total time: 413.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.770495 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.406811 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 0.1226 0.1336 0.0110 0.004 0.7 4.8 0.0 0.0 0 0.089 0.1173 0.1300 0.0127 0.004 0.8 3.8 0.0 0.0 0 0.266 0.1160 0.1291 0.0131 0.005 0.9 3.8 0.5 0.0 0 0.531 0.1151 0.1285 0.0134 0.006 1.0 4.2 0.5 0.0 0 0.797 0.1148 0.1284 0.0136 0.007 1.1 4.2 0.5 0.0 0 1.062 0.1145 0.1282 0.0137 0.008 1.1 4.2 0.5 0.0 0 1.328 0.1144 0.1283 0.0138 0.008 1.1 4.2 0.5 0.0 0 1.593 0.1144 0.1282 0.0138 0.008 1.1 4.2 0.5 0.0 0 1.859 0.1150 0.1284 0.0135 0.006 1.0 4.2 0.5 0.0 0 0.885 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1282 0.0137 0.008 1.1 4.2 0.5 0.0 0 1.328 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.82 1.37 3.776 21.184 36.407 3.609 11.45 12.82 1.37 3.776 21.184 1.092 3.609 11.45 12.82 1.37 3.776 21.184 4.551 3.609 11.49 12.88 1.39 3.706 21.179 18.203 3.605 11.60 13.05 1.44 3.721 21.153 36.407 3.611 11.51 13.01 1.49 3.744 21.139 54.610 3.604 11.44 12.96 1.52 3.761 21.136 72.814 3.599 11.42 12.95 1.53 3.769 21.132 91.017 3.596 11.38 12.90 1.52 3.777 21.134 109.220 3.593 11.35 12.88 1.53 3.782 21.134 127.424 3.591 11.35 12.92 1.57 3.796 21.126 145.627 3.591 11.37 12.97 1.60 3.814 21.114 163.831 3.591 11.35 12.95 1.60 3.818 21.115 182.034 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.092 Accepted refinement result: 11.45 12.82 1.37 3.776 21.184 1.092 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 115.00 21.11 3.31 238 1743 Protein: 9.10 115.00 17.02 3.31 0 1519 Water: 11.49 76.68 34.79 N/A 238 216 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.10 115.00 19.29 N/A 0 1743 Chain S: 11.75 60.01 34.42 N/A 238 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 309 30.28 - 40.87 214 40.87 - 51.46 126 51.46 - 62.05 45 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1282 r_work=0.1145 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1282 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1281 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608255 | | target function (ml) not normalized (work): 300499.057864 | | target function (ml) not normalized (free): 15810.336291 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1361 0.1354 5.6649 5.6327| | 2: 3.57 - 2.84 1.00 2888 124 0.1075 0.1369 5.1724 5.2053| | 3: 2.83 - 2.48 1.00 2820 163 0.1107 0.1202 4.9511 4.9789| | 4: 2.47 - 2.25 1.00 2825 136 0.0916 0.0964 4.6372 4.6558| | 5: 2.25 - 2.09 1.00 2756 127 0.0876 0.0931 4.5813 4.6216| | 6: 2.09 - 1.97 1.00 2846 113 0.0855 0.0991 4.2697 4.3624| | 7: 1.97 - 1.87 1.00 2787 165 0.0887 0.1084 3.9768 4.0755| | 8: 1.87 - 1.79 1.00 2789 144 0.0922 0.1081 3.8849 3.9749| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1180 3.6455 3.8285| | 10: 1.72 - 1.66 1.00 2831 160 0.0926 0.1202 3.5677 3.7258| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1026 3.4972 3.5683| | 12: 1.61 - 1.56 1.00 2773 144 0.0913 0.1133 3.3385 3.461| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1047 3.3126 3.3985| | 14: 1.52 - 1.48 1.00 2803 134 0.0990 0.1045 3.2471 3.33| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1224 3.1576 3.2665| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1240 3.1395 3.2402| | 17: 1.42 - 1.39 1.00 2785 139 0.1146 0.1306 3.1259 3.2405| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1336 3.1081 3.239| | 19: 1.36 - 1.34 1.00 2807 134 0.1264 0.1558 3.1172 3.2642| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1467 3.1162 3.159| | 21: 1.32 - 1.30 1.00 2785 112 0.1480 0.1492 3.1185 3.0979| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.1972 3.127 3.2884| | 23: 1.27 - 1.26 1.00 2802 156 0.1652 0.1792 3.1363 3.2053| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1833 3.1313 3.2319| | 25: 1.24 - 1.22 1.00 2733 148 0.1886 0.2155 3.1462 3.2602| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1763 3.1509 3.2021| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2172 3.1751 3.1646| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2282 3.1686 3.1754| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2375 3.1507 3.2298| | 30: 1.16 - 1.15 1.00 2739 148 0.2450 0.2445 3.1461 3.168| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.59 1.00 0.97 5839.34| | 2: 3.57 - 2.84 2888 124 0.93 12.66 1.01 0.97 5839.34| | 3: 2.83 - 2.48 2820 163 0.89 16.57 0.99 0.97 4871.12| | 4: 2.47 - 2.25 2825 136 0.92 13.47 1.00 0.98 2374.38| | 5: 2.25 - 2.09 2756 127 0.90 15.64 1.01 0.98 2374.38| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.98 1359.90| | 7: 1.97 - 1.87 2787 165 0.95 9.03 1.02 0.98 494.68| | 8: 1.87 - 1.79 2789 144 0.93 12.29 0.99 0.98 494.68| | 9: 1.79 - 1.72 2745 138 0.94 9.90 0.98 0.98 284.88| | 10: 1.72 - 1.66 2831 160 0.94 10.98 0.97 0.98 242.86| | 11: 1.66 - 1.61 2712 147 0.94 11.64 0.98 0.98 232.85| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.98 138.45| | 13: 1.56 - 1.52 2745 130 0.95 10.42 1.03 0.98 138.45| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 124.28| | 15: 1.48 - 1.45 2738 128 0.95 9.89 1.02 0.99 98.33| | 16: 1.45 - 1.42 2756 161 0.94 11.12 1.02 0.99 98.33| | 17: 1.42 - 1.39 2785 139 0.95 10.94 1.01 0.99 89.46| | 18: 1.39 - 1.36 2741 179 0.94 11.55 1.01 0.99 84.33| | 19: 1.36 - 1.34 2807 134 0.94 11.85 0.99 0.99 84.33| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 80.13| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.97 79.83| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 80.24| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 82.28| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.95 82.28| | 25: 1.24 - 1.22 2733 148 0.91 16.28 0.96 0.94 84.26| | 26: 1.22 - 1.21 2727 135 0.90 18.05 1.02 0.93 86.44| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.44| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 90.16| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.98 0.93 91.56| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.97 0.93 91.56| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.83 max = 5839.34 mean = 895.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.90 mean = 13.41| |phase err.(test): min = 0.00 max = 89.48 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1143 0.1281 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1457 0.1457 0.1478 n_refl.: 87577 remove outliers: r(all,work,free)=0.1457 0.1457 0.1478 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1457 0.1457 0.1478 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1282 n_refl.: 87577 remove outliers: r(all,work,free)=0.1148 0.1142 0.1282 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 0.4066 293.926 256.330 0.452 1.000 0.308 11.894-9.307 95.10 93 4 0.2412 479.203 464.256 0.875 1.002 0.228 9.237-7.194 97.73 208 7 0.2379 388.310 380.204 0.917 1.002 0.161 7.162-5.571 100.00 427 22 0.2196 297.002 286.775 0.903 1.003 0.120 5.546-4.326 100.00 867 58 0.1164 407.711 402.801 0.962 1.003 0.105 4.315-3.360 100.00 1859 96 0.0928 387.736 385.747 1.004 1.003 0.100 3.356-2.611 100.00 3867 181 0.1117 254.722 252.820 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0920 168.858 168.190 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0892 82.461 82.807 1.034 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.567 36.163 1.027 0.996 0.000 1.221-1.150 99.97 13689 708 0.2169 23.040 21.578 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0025 ================= 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 : 0.2611 0.1937 0.082 5.380 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_weight: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1220 0.1463 0.008 0.971 9.0 119.5 20.1 258 0.131 1_adp: 0.1227 0.1459 0.008 0.971 9.0 119.4 20.1 258 0.131 1_regHadp: 0.1229 0.1462 0.008 0.971 9.0 119.4 20.1 258 0.131 1_occ: 0.1223 0.1461 0.008 0.971 9.0 119.4 20.1 258 0.131 2_bss: 0.1220 0.1451 0.008 0.971 9.1 119.5 20.1 258 0.131 2_settarget: 0.1220 0.1451 0.008 0.971 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1220 0.1451 0.008 0.984 9.1 119.5 20.1 258 0.131 2_nqh: 0.1222 0.1452 0.008 0.984 9.1 119.5 20.1 258 0.134 2_sol: 0.1197 0.1393 0.008 0.984 9.1 115.0 22.1 416 n/a 2_weight: 0.1197 0.1393 0.008 0.984 9.1 115.0 22.1 416 n/a 2_xyzrec: 0.1196 0.1405 0.006 0.860 9.1 115.0 22.1 416 n/a 2_adp: 0.1196 0.1405 0.006 0.860 9.1 115.0 22.1 416 n/a 2_regHadp: 0.1196 0.1405 0.006 0.860 9.1 115.0 22.1 416 n/a 2_occ: 0.1195 0.1398 0.006 0.860 9.1 115.0 22.1 416 n/a 3_bss: 0.1190 0.1391 0.006 0.860 9.1 115.0 22.1 416 n/a 3_settarget: 0.1190 0.1391 0.006 0.860 9.1 115.0 22.1 416 n/a 3_updatecdl: 0.1190 0.1391 0.006 0.861 9.1 115.0 22.1 416 n/a 3_nqh: 0.1190 0.1391 0.006 0.861 9.1 115.0 22.1 416 n/a 3_sol: 0.1217 0.1394 0.006 0.861 9.1 115.0 21.1 440 n/a 3_weight: 0.1217 0.1394 0.006 0.861 9.1 115.0 21.1 440 n/a 3_xyzrec: 0.1164 0.1321 0.007 1.046 9.1 115.0 21.1 440 n/a 3_adp: 0.1164 0.1321 0.007 1.046 9.1 115.0 21.1 440 n/a 3_regHadp: 0.1164 0.1321 0.007 1.046 9.1 115.0 21.1 440 n/a 3_occ: 0.1154 0.1313 0.007 1.046 9.1 115.0 21.1 440 n/a 4_bss: 0.1146 0.1300 0.007 1.046 9.1 115.0 21.1 440 n/a 4_settarget: 0.1146 0.1300 0.007 1.046 9.1 115.0 21.1 440 n/a 4_updatecdl: 0.1146 0.1300 0.007 1.046 9.1 115.0 21.1 440 n/a 4_nqh: 0.1146 0.1300 0.007 1.046 9.1 115.0 21.1 440 n/a 4_sol: 0.1154 0.1307 0.007 1.046 9.1 115.0 21.0 440 n/a 4_weight: 0.1154 0.1307 0.007 1.046 9.1 115.0 21.0 440 n/a 4_xyzrec: 0.1150 0.1305 0.008 1.102 9.1 115.0 21.0 440 n/a 4_adp: 0.1150 0.1305 0.008 1.102 9.1 115.0 21.0 440 n/a 4_regHadp: 0.1150 0.1305 0.008 1.102 9.1 115.0 21.0 440 n/a 4_occ: 0.1145 0.1299 0.008 1.102 9.1 115.0 21.0 440 n/a 5_bss: 0.1143 0.1300 0.008 1.102 9.1 115.0 21.0 440 n/a 5_settarget: 0.1143 0.1300 0.008 1.102 9.1 115.0 21.0 440 n/a 5_updatecdl: 0.1143 0.1300 0.008 1.104 9.1 115.0 21.0 440 n/a 5_setrh: 0.1144 0.1300 0.008 1.104 9.1 115.0 21.0 440 n/a 5_nqh: 0.1144 0.1300 0.008 1.104 9.1 115.0 21.0 440 n/a 5_sol: 0.1144 0.1283 0.008 1.104 9.1 115.0 21.1 454 n/a 5_weight: 0.1144 0.1283 0.008 1.104 9.1 115.0 21.1 454 n/a 5_xyzrec: 0.1145 0.1282 0.008 1.099 9.1 115.0 21.1 454 n/a 5_adp: 0.1145 0.1282 0.008 1.099 9.1 115.0 21.1 454 n/a 5_regHadp: 0.1145 0.1282 0.008 1.099 9.1 115.0 21.1 454 n/a 5_occ: 0.1143 0.1281 0.008 1.099 9.1 115.0 21.1 454 n/a end: 0.1142 0.1282 0.008 1.099 9.1 115.0 21.1 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8315495_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8315495_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0500 Refinement macro-cycles (run) : 13955.5200 Write final files (write_after_run_outputs) : 95.3500 Total : 14053.9200 Total CPU time: 3.91 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:13:40 PST -0800 (1735366420.58 s) Start R-work = 0.1640, R-free = 0.1755 Final R-work = 0.1142, R-free = 0.1282 =============================================================================== Job complete usr+sys time: 14228.60 seconds wall clock time: 257 minutes 44.15 seconds (15464.15 seconds total)