Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 0.56 Conformation dependent library (CDL) restraints added in 202.5 milliseconds Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 524 0.92 - 1.17: 1131 1.17 - 1.42: 627 1.42 - 1.68: 838 1.68 - 1.93: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.463 1.722 -0.259 1.14e-02 7.69e+03 5.15e+02 bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.179 0.160 7.50e-03 1.78e+04 4.57e+02 bond pdb=" C PRO A 43 " pdb=" O PRO A 43 " ideal model delta sigma weight residual 1.233 1.004 0.229 1.10e-02 8.26e+03 4.33e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.234 1.001 0.233 1.16e-02 7.43e+03 4.02e+02 bond pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.20e-02 6.94e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3172 4.79 - 9.58: 1880 9.58 - 14.36: 609 14.36 - 19.15: 107 19.15 - 23.93: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " ideal model delta sigma weight residual 122.07 138.06 -15.99 1.03e+00 9.43e-01 2.41e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.18 107.34 15.84 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 129.76 -9.69 7.10e-01 1.98e+00 1.86e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 121.00 110.11 10.89 8.30e-01 1.45e+00 1.72e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 109.79 12.81 1.00e+00 1.00e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 927 16.05 - 32.10: 118 32.10 - 48.15: 45 48.15 - 64.20: 19 64.20 - 80.25: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+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 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 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 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.231: 103 0.231 - 0.460: 79 0.460 - 0.690: 47 0.690 - 0.919: 10 0.919 - 1.148: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.59 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" CA APRO A 66 " pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CB APRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 6.86e-02 1.41e+02 pdb=" CG PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.110 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.061 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.090 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CD GLN A 45 " -0.116 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " -0.072 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1007 2.31 - 2.88: 7997 2.88 - 3.46: 10546 3.46 - 4.03: 15328 4.03 - 4.60: 21693 Nonbonded interactions: 56571 Sorted by model distance: nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.741 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.743 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.788 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.803 1.850 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.811 1.850 ... (remaining 56566 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_7848743_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792487 | | target function (ml) not normalized (work): 232630.945006 | | target function (ml) not normalized (free): 11809.152330 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2097 6.9973 4.9487| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1954 4.3585 4.3594| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1631 4.1334 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2338 0.1524 3.8391 3.8528| | 5: 2.25 - 2.09 1.00 2756 127 0.2488 0.1588 3.8089 3.8221| | 6: 2.09 - 1.97 1.00 2846 113 0.2557 0.1833 3.4751 3.563| | 7: 1.97 - 1.87 1.00 2787 165 0.2525 0.1824 3.1401 3.1689| | 8: 1.87 - 1.79 1.00 2789 144 0.2503 0.1903 3.0613 3.1479| | 9: 1.79 - 1.72 1.00 2745 138 0.2401 0.1914 2.9049 2.9989| | 10: 1.72 - 1.66 1.00 2789 158 0.2348 0.1918 2.8023 2.8936| | 11: 1.66 - 1.61 1.00 2740 147 0.2484 0.2101 2.7578 2.8428| | 12: 1.61 - 1.56 1.00 2787 146 0.2496 0.1827 2.6475 2.5759| | 13: 1.56 - 1.52 1.00 2745 130 0.2509 0.2024 2.581 2.6867| | 14: 1.52 - 1.48 1.00 2803 134 0.2538 0.1953 2.5073 2.5349| | 15: 1.48 - 1.45 1.00 2738 128 0.2526 0.2146 2.4281 2.4946| | 16: 1.45 - 1.42 1.00 2756 161 0.2699 0.2231 2.3916 2.45| | 17: 1.42 - 1.39 1.00 2785 139 0.2710 0.2282 2.3353 2.4231| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2068 2.2738 2.313| | 19: 1.36 - 1.34 1.00 2807 134 0.2658 0.2201 2.2498 2.2335| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2296 2.1912 2.1891| | 21: 1.32 - 1.30 1.00 2785 112 0.2747 0.2321 2.1753 2.204| | 22: 1.29 - 1.27 1.00 2704 152 0.2743 0.2472 2.1326 2.1687| | 23: 1.27 - 1.26 1.00 2802 156 0.2835 0.2234 2.1096 2.1083| | 24: 1.26 - 1.24 1.00 2744 132 0.2788 0.2355 2.0724 2.1065| | 25: 1.24 - 1.22 1.00 2734 148 0.2863 0.2664 2.0336 2.1029| | 26: 1.22 - 1.21 1.00 2727 135 0.2906 0.2152 2.0131 2.0447| | 27: 1.21 - 1.19 1.00 2814 148 0.3054 0.2501 2.0287 2.0125| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.2737 1.9889 1.9878| | 29: 1.18 - 1.16 1.00 2800 134 0.2978 0.2549 1.9527 2.0079| | 30: 1.16 - 1.15 1.00 2740 148 0.3086 0.2870 1.93 1.9393| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.08 0.76 0.23 1513.06| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1513.06| | 3: 2.84 - 2.48 2833 165 0.73 32.47 1.25 0.23 1254.31| | 4: 2.47 - 2.25 2825 136 0.81 25.88 1.26 0.25 582.82| | 5: 2.25 - 2.09 2756 127 0.77 29.60 1.28 0.25 582.82| | 6: 2.09 - 1.97 2846 113 0.83 22.82 1.29 0.25 318.61| | 7: 1.97 - 1.87 2787 165 0.90 16.71 1.28 0.25 93.27| | 8: 1.87 - 1.79 2789 144 0.85 21.48 1.25 0.25 93.27| | 9: 1.79 - 1.72 2745 138 0.87 19.23 1.23 0.25 57.66| | 10: 1.72 - 1.66 2789 158 0.86 20.74 1.21 0.25 50.53| | 11: 1.66 - 1.61 2740 147 0.85 21.87 1.24 0.25 48.76| | 12: 1.61 - 1.56 2787 146 0.88 18.97 1.23 0.25 30.87| | 13: 1.56 - 1.52 2745 130 0.86 20.88 1.23 0.25 30.87| | 14: 1.52 - 1.48 2803 134 0.86 21.09 1.23 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.87 20.19 1.22 0.25 21.11| | 16: 1.45 - 1.42 2756 161 0.85 21.80 1.24 0.25 21.11| | 17: 1.42 - 1.39 2785 139 0.87 20.86 1.24 0.25 17.75| | 18: 1.39 - 1.36 2741 179 0.87 20.92 1.22 0.25 15.80| | 19: 1.36 - 1.34 2807 134 0.85 22.04 1.22 0.25 15.80| | 20: 1.34 - 1.32 2696 147 0.87 20.54 1.21 0.25 12.71| | 21: 1.32 - 1.30 2785 112 0.86 21.46 1.21 0.25 12.50| | 22: 1.29 - 1.27 2704 152 0.86 21.87 1.21 0.25 12.17| | 23: 1.27 - 1.26 2802 156 0.86 21.65 1.22 0.24 10.52| | 24: 1.26 - 1.24 2744 132 0.86 21.89 1.20 0.24 10.52| | 25: 1.24 - 1.22 2734 148 0.85 23.13 1.22 0.24 10.02| | 26: 1.22 - 1.21 2727 135 0.85 23.38 1.20 0.24 9.47| | 27: 1.21 - 1.19 2814 148 0.84 24.01 1.21 0.24 9.47| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.18 0.23 8.99| | 29: 1.18 - 1.16 2800 134 0.83 25.04 1.17 0.23 8.81| | 30: 1.16 - 1.15 2740 148 0.81 26.70 1.16 0.23 8.81| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.81 max = 1513.06 mean = 219.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.59| |phase err.(test): min = 0.00 max = 89.88 mean = 22.60| |-----------------------------------------------------------------------------| ----------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 0.259 1557 Z= 5.513 Angle : 5.384 15.993 2118 Z= 3.813 Chirality : 0.384 1.148 243 Planarity : 0.032 0.100 284 Dihedral : 13.568 80.246 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.49), residues: 224 helix: -2.99 (0.35), residues: 108 sheet: -0.53 (0.99), residues: 30 loop : -0.40 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 27 TYR 0.071 0.033 TYR A 141 PHE 0.121 0.046 PHE A 164 HIS 0.054 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792487 | | target function (ml) not normalized (work): 232630.945006 | | target function (ml) not normalized (free): 11809.152330 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2608 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2608 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1963 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2008 0.1979 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1638 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1788 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 0.3855 386.460 354.778 0.716 0.921 0.397 11.894-9.307 99.02 97 4 0.1831 613.872 594.149 1.001 0.922 0.380 9.237-7.194 100.00 213 7 0.2135 502.072 491.628 1.041 0.922 0.370 7.162-5.571 100.00 427 22 0.2204 376.777 364.805 1.011 0.922 0.290 5.546-4.326 100.00 867 58 0.1291 517.222 511.737 1.048 0.922 0.218 4.315-3.360 100.00 1859 96 0.1128 491.881 487.777 1.094 0.922 0.189 3.356-2.611 100.00 3867 181 0.1438 323.141 319.535 1.084 0.921 0.129 2.608-2.026 99.99 8198 413 0.1367 214.213 212.207 1.096 0.920 0.000 2.025-1.573 100.00 17313 902 0.1649 104.610 103.933 1.100 0.918 0.000 1.573-1.221 100.00 36679 1900 0.2052 46.388 44.979 1.091 0.915 0.000 1.221-1.150 99.97 13689 708 0.2613 29.228 26.984 1.068 0.913 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1642 r_free=0.1793 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.702002 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.531414 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 0.1567 0.1685 0.0119 0.001 0.5 4.2 0.0 0.0 0 0.125 0.1537 0.1668 0.0131 0.001 0.5 3.8 0.0 0.0 0 0.250 0.1436 0.1591 0.0155 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1384 0.1563 0.0179 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1345 0.1535 0.0190 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1347 0.1539 0.0192 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1291 0.1503 0.0212 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1268 0.1493 0.0225 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1246 0.1471 0.0225 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1247 0.1480 0.0233 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1239 0.1474 0.0235 0.005 0.8 3.5 0.5 0.0 0 6.000 0.1235 0.1471 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1229 0.1462 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1228 0.1466 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1228 0.1468 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1224 0.1465 0.0240 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1223 0.1464 0.0240 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1221 0.1466 0.0246 0.008 1.0 4.2 0.5 0.6 0 13.851 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1462 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.62 2.34 3.013 19.057 1992.531 0.017 12.29 14.62 2.33 2.989 19.057 59.776 0.017 12.36 14.59 2.22 2.657 19.057 249.066 0.017 12.72 15.29 2.57 2.832 19.292 996.266 0.017 12.58 15.44 2.86 3.280 19.602 1992.531 0.016 12.47 15.46 2.98 3.385 19.671 2988.797 0.016 12.38 15.42 3.04 3.420 19.682 3985.063 0.015 12.32 15.39 3.07 3.344 19.625 4981.329 0.015 12.32 15.47 3.15 3.512 19.707 5977.594 0.015 12.30 15.51 3.21 3.530 19.715 6973.860 0.015 12.20 15.38 3.18 3.454 19.671 7970.126 0.015 12.18 15.40 3.22 3.480 19.676 8966.391 0.015 12.21 15.47 3.27 3.554 19.696 9962.657 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 249.066 Accepted refinement result: 12.36 14.59 2.22 2.657 19.057 249.066 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.43 20.08 3.29 0 1785 Protein: 9.07 114.88 16.99 3.29 0 1519 Water: 11.47 119.43 38.22 N/A 0 258 Other: 19.72 26.60 22.06 N/A 0 8 Chain A: 9.07 119.43 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1459 r_work=0.1238 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 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 = 0.1230 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016976 | | target function (ls_wunit_k1) not normalized (work): 1414.010100 | | target function (ls_wunit_k1) not normalized (free): 108.741199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1457 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1692 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1696 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1231 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1231 0.1453 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3549 304.228 280.898 0.661 1.002 0.388 11.894-9.307 99.02 97 4 0.1613 483.251 471.290 0.922 1.003 0.365 9.237-7.194 100.00 213 7 0.1876 395.240 389.416 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1853 296.606 290.704 0.935 1.003 0.263 5.546-4.326 100.00 867 58 0.1015 407.166 404.009 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0883 387.218 386.014 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1172 254.382 253.262 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 168.632 167.907 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.351 82.548 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.518 36.015 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.009 21.489 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0516 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A Total number of N/Q/H flips: 1 r_work=0.1230 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1453 | n_water=258 | time (s): 1.850 (total time: 1.850) Filter (dist) r_work=0.1238 r_free=0.1449 | n_water=251 | time (s): 22.980 (total time: 24.830) Filter (q & B) r_work=0.1240 r_free=0.1449 | n_water=248 | time (s): 3.190 (total time: 28.020) Compute maps r_work=0.1240 r_free=0.1449 | n_water=248 | time (s): 1.540 (total time: 29.560) Filter (map) r_work=0.1261 r_free=0.1465 | n_water=224 | time (s): 3.090 (total time: 32.650) Find peaks r_work=0.1261 r_free=0.1465 | n_water=224 | time (s): 0.550 (total time: 33.200) Add new water r_work=0.1412 r_free=0.1634 | n_water=434 | time (s): 3.090 (total time: 36.290) Refine new water occ: r_work=0.1314 r_free=0.1490 adp: r_work=0.1231 r_free=0.1434 occ: r_work=0.1244 r_free=0.1420 adp: r_work=0.1210 r_free=0.1404 occ: r_work=0.1212 r_free=0.1393 adp: r_work=0.1202 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1389 r_work=0.1202 r_free=0.1389 | n_water=434 | time (s): 65.540 (total time: 101.830) Filter (q & B) r_work=0.1207 r_free=0.1395 | n_water=419 | time (s): 3.430 (total time: 105.260) Filter (dist only) r_work=0.1207 r_free=0.1394 | n_water=418 | time (s): 36.280 (total time: 141.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.209442 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1495.118805 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 0.1679 0.1781 0.0103 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1558 0.1680 0.0122 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1413 0.1562 0.0149 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1345 0.1512 0.0167 0.001 0.4 5.4 0.0 0.0 0 0.750 0.1311 0.1491 0.0180 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1311 0.1487 0.0177 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1253 0.1456 0.0204 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1224 0.1434 0.0209 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1211 0.1429 0.0218 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1204 0.1422 0.0218 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1203 0.1424 0.0222 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1198 0.1422 0.0224 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1192 0.1421 0.0229 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1188 0.1418 0.0230 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1185 0.1421 0.0236 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1186 0.1421 0.0235 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1185 0.1416 0.0232 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1183 0.1414 0.0232 0.008 0.9 4.5 0.5 0.0 0 13.000 0.1180 0.1410 0.0230 0.008 0.9 4.8 0.5 0.0 0 14.605 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1180 0.1410 0.0230 0.008 0.9 4.8 0.5 0.0 0 14.605 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 14.10 2.30 3.765 21.808 1495.119 0.015 11.80 14.10 2.30 3.765 21.808 44.854 0.015 11.80 14.10 2.30 3.765 21.808 186.890 0.015 11.94 14.47 2.53 3.635 21.802 747.559 0.015 12.02 14.83 2.81 3.448 22.076 1495.119 0.014 11.87 14.79 2.92 3.496 21.934 2242.678 0.014 11.74 14.78 3.04 3.510 21.933 2990.238 0.014 11.74 14.76 3.02 3.489 22.181 3737.797 0.014 11.73 14.91 3.18 3.509 22.059 4485.356 0.014 11.65 14.81 3.16 3.517 22.030 5232.916 0.013 11.62 14.73 3.11 3.538 22.188 5980.475 0.013 11.61 14.75 3.15 3.543 22.135 6728.035 0.013 11.64 14.89 3.25 3.596 22.237 7475.594 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 186.890 Accepted refinement result: 11.80 14.10 2.30 3.765 21.808 186.890 0.015 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 22.24 3.29 194 1751 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.50 76.67 41.20 N/A 194 224 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.11 114.91 19.42 N/A 0 1751 Chain S: 14.34 60.00 47.67 N/A 194 0 Histogram: Values Number of atoms 9.11 - 19.69 1257 19.69 - 30.27 247 30.27 - 40.85 157 40.85 - 51.43 136 51.43 - 62.01 125 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1410 r_work=0.1180 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1410 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1403 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1180 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014661 | | target function (ls_wunit_k1) not normalized (work): 1221.249903 | | target function (ls_wunit_k1) not normalized (free): 100.303548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1180 0.1403 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1580 0.1580 0.1611 n_refl.: 87593 remove outliers: r(all,work,free)=0.1580 0.1580 0.1611 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1582 0.1582 0.1613 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1177 0.1399 n_refl.: 87593 remove outliers: r(all,work,free)=0.1187 0.1176 0.1399 n_refl.: 87591 ======================== 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 94.79 86 5 0.3460 303.672 277.103 0.614 1.002 0.370 11.894-9.307 99.02 97 4 0.1564 483.251 476.022 0.920 1.003 0.321 9.237-7.194 100.00 213 7 0.1636 395.240 396.300 0.977 1.003 0.284 7.162-5.571 100.00 427 22 0.1577 296.606 292.217 0.935 1.003 0.224 5.546-4.326 100.00 867 58 0.0885 407.166 403.904 0.958 1.003 0.194 4.315-3.360 100.00 1859 96 0.0785 387.218 386.436 1.004 1.003 0.180 3.356-2.611 100.00 3867 181 0.1062 254.382 253.527 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.0995 168.632 168.122 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1096 82.351 82.624 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.518 36.063 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 23.009 21.525 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1399 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1178 r_free=0.1400 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1400 | n_water=418 | time (s): 1.850 (total time: 1.850) Filter (dist) r_work=0.1177 r_free=0.1403 | n_water=414 | time (s): 35.730 (total time: 37.580) Filter (q & B) r_work=0.1177 r_free=0.1403 | n_water=414 | time (s): 1.230 (total time: 38.810) Compute maps r_work=0.1177 r_free=0.1403 | n_water=414 | time (s): 1.540 (total time: 40.350) Filter (map) r_work=0.1221 r_free=0.1406 | n_water=282 | time (s): 3.060 (total time: 43.410) Find peaks r_work=0.1221 r_free=0.1406 | n_water=282 | time (s): 0.640 (total time: 44.050) Add new water r_work=0.1344 r_free=0.1525 | n_water=483 | time (s): 2.620 (total time: 46.670) Refine new water occ: r_work=0.1248 r_free=0.1441 adp: r_work=0.1249 r_free=0.1441 occ: r_work=0.1225 r_free=0.1418 adp: r_work=0.1224 r_free=0.1417 occ: r_work=0.1206 r_free=0.1393 adp: r_work=0.1201 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1391 r_work=0.1201 r_free=0.1391 | n_water=483 | time (s): 230.860 (total time: 277.530) Filter (q & B) r_work=0.1206 r_free=0.1395 | n_water=447 | time (s): 3.310 (total time: 280.840) Filter (dist only) r_work=0.1206 r_free=0.1394 | n_water=445 | time (s): 38.070 (total time: 318.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.803154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.482064 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 0.1236 0.1363 0.0126 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1192 0.1329 0.0137 0.003 0.7 3.2 0.5 0.0 0 0.270 0.1177 0.1317 0.0140 0.004 0.8 2.9 0.5 0.0 0 0.541 0.1173 0.1318 0.0145 0.005 0.9 2.9 0.5 0.0 0 0.811 0.1169 0.1316 0.0148 0.006 1.0 2.6 0.5 0.0 0 1.082 0.1167 0.1316 0.0149 0.007 1.0 2.6 0.5 0.0 0 1.352 0.1165 0.1315 0.0150 0.007 1.1 2.9 0.5 0.0 0 1.623 0.1162 0.1314 0.0152 0.008 1.1 2.9 0.5 0.0 0 1.893 0.1169 0.1315 0.0146 0.005 0.9 2.9 0.5 0.0 0 0.902 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1314 0.0152 0.008 1.1 2.9 0.5 0.0 0 1.893 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.14 1.52 3.768 21.268 35.482 3.625 11.62 13.14 1.52 3.768 21.268 1.064 3.625 11.62 13.14 1.52 3.768 21.268 4.435 3.625 11.67 13.17 1.51 3.700 21.261 17.741 3.619 11.75 13.35 1.60 3.723 21.233 35.482 3.624 11.64 13.31 1.67 3.745 21.216 53.223 3.615 11.59 13.29 1.70 3.761 21.210 70.964 3.611 11.58 13.29 1.71 3.772 21.201 88.705 3.608 11.53 13.25 1.72 3.780 21.201 106.446 3.605 11.54 13.28 1.74 3.796 21.185 124.187 3.604 11.54 13.31 1.77 3.812 21.173 141.928 3.604 11.53 13.29 1.77 3.821 21.171 159.669 3.603 11.51 13.26 1.75 3.826 21.169 177.410 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: 1.064 Accepted refinement result: 11.62 13.14 1.52 3.768 21.268 1.064 3.625 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 21.25 3.29 225 1747 Protein: 9.12 114.92 17.04 3.29 0 1519 Water: 11.51 76.68 35.61 N/A 225 220 Other: 19.76 26.65 22.11 N/A 0 8 Chain A: 9.12 114.92 19.34 N/A 0 1747 Chain S: 14.35 60.01 36.04 N/A 225 0 Histogram: Values Number of atoms 9.12 - 19.70 1261 19.70 - 30.28 291 30.28 - 40.86 211 40.86 - 51.44 136 51.44 - 62.02 51 62.02 - 72.60 11 72.60 - 83.18 5 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1314 r_work=0.1162 r_free=0.1314 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1314 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1311 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1152 r_free= 0.1311 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616568 | | target function (ml) not normalized (work): 301242.072285 | | target function (ml) not normalized (free): 15856.500439 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1311 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1488 0.1487 0.1535 n_refl.: 87591 remove outliers: r(all,work,free)=0.1488 0.1487 0.1535 n_refl.: 87591 overall B=-0.01 to atoms: r(all,work,free)=0.1487 0.1486 0.1534 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1146 0.1309 n_refl.: 87591 remove outliers: r(all,work,free)=0.1151 0.1143 0.1309 n_refl.: 87583 ======================== 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 0.3969 292.112 270.261 0.500 1.000 0.324 11.894-9.307 98.04 96 4 0.2286 483.376 464.882 0.872 1.002 0.320 9.237-7.194 98.18 209 7 0.2261 386.707 387.871 0.955 1.002 0.210 7.162-5.571 100.00 427 22 0.2073 296.606 285.271 0.917 1.002 0.160 5.546-4.326 100.00 867 58 0.1115 407.166 401.928 0.964 1.002 0.150 4.315-3.360 100.00 1859 96 0.0935 387.218 384.741 1.005 1.002 0.150 3.356-2.611 100.00 3867 181 0.1140 254.382 252.126 1.007 1.002 0.070 2.608-2.026 99.99 8198 413 0.0936 168.632 167.802 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.351 82.621 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.518 36.090 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.009 21.541 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1309 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=0.1143 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1309 | n_water=445 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1143 r_free=0.1308 | n_water=444 | time (s): 46.960 (total time: 49.460) Filter (q & B) r_work=0.1144 r_free=0.1310 | n_water=442 | time (s): 3.960 (total time: 53.420) Compute maps r_work=0.1144 r_free=0.1310 | n_water=442 | time (s): 1.850 (total time: 55.270) Filter (map) r_work=0.1177 r_free=0.1304 | n_water=328 | time (s): 3.960 (total time: 59.230) Find peaks r_work=0.1177 r_free=0.1304 | n_water=328 | time (s): 0.740 (total time: 59.970) Add new water r_work=0.1245 r_free=0.1387 | n_water=493 | time (s): 3.930 (total time: 63.900) Refine new water occ: r_work=0.1166 r_free=0.1323 adp: r_work=0.1167 r_free=0.1325 occ: r_work=0.1151 r_free=0.1306 adp: r_work=0.1151 r_free=0.1308 occ: r_work=0.1139 r_free=0.1290 adp: r_work=0.1136 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1291 r_work=0.1136 r_free=0.1291 | n_water=493 | time (s): 235.980 (total time: 299.880) Filter (q & B) r_work=0.1143 r_free=0.1296 | n_water=449 | time (s): 4.350 (total time: 304.230) Filter (dist only) r_work=0.1143 r_free=0.1295 | n_water=448 | time (s): 49.810 (total time: 354.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.797344 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.359128 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 0.1205 0.1334 0.0129 0.002 0.6 3.8 0.5 0.0 0 0.090 0.1170 0.1311 0.0140 0.003 0.7 2.9 0.5 0.0 0 0.270 0.1154 0.1297 0.0143 0.005 0.9 3.2 0.5 0.0 0 0.539 0.1148 0.1298 0.0150 0.006 0.9 2.9 0.5 0.0 0 0.809 0.1145 0.1300 0.0155 0.006 1.0 2.9 0.5 0.0 0 1.078 0.1143 0.1294 0.0151 0.007 1.1 2.9 0.5 0.0 0 1.348 0.1140 0.1298 0.0157 0.008 1.1 2.9 0.5 0.0 0 1.618 0.1139 0.1298 0.0159 0.008 1.1 2.9 0.5 0.0 0 1.887 0.1147 0.1299 0.0151 0.006 1.0 2.9 0.5 0.0 0 0.899 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1294 0.0151 0.007 1.1 2.9 0.5 0.0 0 1.348 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 12.94 1.51 3.769 21.185 43.359 3.611 11.43 12.94 1.51 3.769 21.185 1.301 3.611 11.43 12.94 1.51 3.766 21.185 5.420 3.611 11.46 13.00 1.54 3.705 21.177 21.680 3.605 11.52 13.17 1.65 3.730 21.144 43.359 3.609 11.42 13.11 1.69 3.754 21.138 65.039 3.601 11.40 13.11 1.71 3.767 21.131 86.718 3.598 11.34 13.05 1.70 3.774 21.132 108.398 3.594 11.33 13.06 1.73 3.786 21.128 130.077 3.593 11.34 13.11 1.77 3.808 21.113 151.757 3.594 11.33 13.11 1.78 3.818 21.109 173.437 3.592 11.31 13.09 1.78 3.824 21.107 195.116 3.591 11.30 13.08 1.78 3.829 21.108 216.796 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: 1.301 Accepted refinement result: 11.43 12.94 1.51 3.769 21.185 1.301 3.611 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.10 3.29 231 1744 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.51 76.68 34.88 N/A 231 217 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.11 114.91 19.31 N/A 0 1744 Chain S: 14.35 60.00 34.60 N/A 231 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.27 299 30.27 - 40.85 223 40.85 - 51.43 124 51.43 - 62.01 45 62.01 - 72.59 11 72.59 - 83.17 5 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1294 r_work=0.1143 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1294 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1289 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608031 | | target function (ml) not normalized (work): 300502.116358 | | target function (ml) not normalized (free): 15813.693689 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1136 0.1289 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1470 0.1470 0.1500 n_refl.: 87583 remove outliers: r(all,work,free)=0.1470 0.1470 0.1500 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1470 0.1470 0.1499 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1135 0.1289 n_refl.: 87583 remove outliers: r(all,work,free)=0.1139 0.1131 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 87.50 79 5 0.3880 288.757 249.290 0.438 1.000 0.285 11.894-9.307 94.12 92 4 0.2391 479.745 459.113 0.861 1.002 0.267 9.237-7.194 98.18 209 7 0.2361 386.707 381.134 0.923 1.002 0.180 7.162-5.571 100.00 427 22 0.2149 296.606 285.649 0.909 1.002 0.134 5.546-4.326 100.00 867 58 0.1133 407.166 402.340 0.964 1.002 0.120 4.315-3.360 100.00 1859 96 0.0904 387.218 385.166 1.005 1.002 0.120 3.356-2.611 100.00 3867 181 0.1107 254.382 252.687 1.009 1.002 0.024 2.608-2.026 99.99 8198 413 0.0911 168.632 168.011 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.351 82.720 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.518 36.129 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 23.009 21.555 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0128 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1289 After: r_work=0.1132 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1289 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=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1289 | n_water=448 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1132 r_free=0.1289 | n_water=448 | time (s): 43.820 (total time: 46.190) Filter (q & B) r_work=0.1133 r_free=0.1289 | n_water=447 | time (s): 4.070 (total time: 50.260) Compute maps r_work=0.1133 r_free=0.1289 | n_water=447 | time (s): 1.840 (total time: 52.100) Filter (map) r_work=0.1161 r_free=0.1294 | n_water=352 | time (s): 3.980 (total time: 56.080) Find peaks r_work=0.1161 r_free=0.1294 | n_water=352 | time (s): 0.690 (total time: 56.770) Add new water r_work=0.1207 r_free=0.1330 | n_water=497 | time (s): 3.750 (total time: 60.520) Refine new water occ: r_work=0.1148 r_free=0.1285 adp: r_work=0.1149 r_free=0.1286 occ: r_work=0.1137 r_free=0.1278 adp: r_work=0.1136 r_free=0.1278 occ: r_work=0.1129 r_free=0.1275 adp: r_work=0.1126 r_free=0.1273 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1273 r_work=0.1126 r_free=0.1273 | n_water=497 | time (s): 253.210 (total time: 313.730) Filter (q & B) r_work=0.1133 r_free=0.1283 | n_water=459 | time (s): 4.060 (total time: 317.790) Filter (dist only) r_work=0.1133 r_free=0.1282 | n_water=458 | time (s): 49.610 (total time: 367.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.920233 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.605358 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 0.1217 0.1344 0.0127 0.004 0.7 8.0 0.5 0.0 0 0.096 0.1181 0.1314 0.0133 0.004 0.8 8.0 0.0 0.0 0 0.288 0.1161 0.1300 0.0140 0.005 0.9 7.7 0.5 0.0 0 0.576 0.1149 0.1293 0.0144 0.006 1.0 8.6 0.5 0.0 0 0.864 0.1137 0.1285 0.0148 0.007 1.1 8.0 0.5 0.0 0 1.152 0.1133 0.1283 0.0150 0.008 1.1 8.3 0.5 0.0 0 1.440 0.1131 0.1282 0.0150 0.008 1.1 8.0 0.5 0.0 0 1.728 0.1130 0.1282 0.0151 0.009 1.1 8.0 0.5 0.0 0 2.016 0.1147 0.1292 0.0145 0.007 1.0 8.6 0.5 0.0 0 0.960 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1282 0.0150 0.008 1.1 8.0 0.5 0.0 0 1.728 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.82 1.50 3.768 21.201 37.605 3.603 11.31 12.82 1.50 3.768 21.201 1.128 3.603 11.31 12.82 1.50 3.768 21.201 4.701 3.603 11.34 12.86 1.52 3.703 21.196 18.803 3.598 11.45 13.07 1.62 3.718 21.166 37.605 3.604 11.36 13.03 1.67 3.739 21.154 56.408 3.597 11.29 12.99 1.69 3.761 21.149 75.211 3.592 11.25 12.95 1.70 3.771 21.149 94.013 3.589 11.23 12.94 1.71 3.780 21.144 112.816 3.586 11.24 13.00 1.76 3.798 21.133 131.619 3.587 11.21 12.96 1.75 3.804 21.133 150.421 3.585 11.20 12.97 1.77 3.816 21.129 169.224 3.584 11.20 12.96 1.76 3.822 21.127 188.027 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.701 Accepted refinement result: 11.31 12.82 1.50 3.768 21.201 4.701 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.13 3.29 242 1743 Protein: 9.11 114.91 17.02 3.29 0 1519 Water: 11.50 76.67 34.74 N/A 242 216 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.11 114.91 19.29 N/A 0 1743 Chain S: 14.34 60.00 34.42 N/A 242 0 Histogram: Values Number of atoms 9.11 - 19.69 1265 19.69 - 30.27 302 30.27 - 40.85 227 40.85 - 51.43 121 51.43 - 62.01 48 62.01 - 72.59 11 72.59 - 83.17 5 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1282 r_work=0.1131 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1282 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1280 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602263 | | target function (ml) not normalized (work): 299992.864148 | | target function (ml) not normalized (free): 15799.078363 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1327 0.1303 5.6426 5.5691| | 2: 3.57 - 2.84 1.00 2888 124 0.1055 0.1453 5.1528 5.2569| | 3: 2.83 - 2.48 1.00 2820 163 0.1099 0.1162 4.9388 4.9648| | 4: 2.47 - 2.25 1.00 2825 136 0.0894 0.0998 4.6237 4.6533| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0968 4.5705 4.6277| | 6: 2.09 - 1.97 1.00 2846 113 0.0845 0.1005 4.2587 4.3666| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1100 3.9723 4.0817| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1084 3.8823 3.9857| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1170 3.6416 3.8014| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1169 3.5611 3.7037| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1043 3.4934 3.57| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1118 3.3299 3.4478| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1024 3.3048 3.3944| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1042 3.2366 3.322| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1258 3.1538 3.2904| | 16: 1.45 - 1.42 1.00 2756 161 0.1057 0.1255 3.1369 3.2399| | 17: 1.42 - 1.39 1.00 2785 139 0.1145 0.1295 3.1221 3.2268| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1338 3.1076 3.2393| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1573 3.1135 3.2685| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1456 3.1132 3.1601| | 21: 1.32 - 1.30 1.00 2785 112 0.1474 0.1510 3.1152 3.1035| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1983 3.1235 3.2937| | 23: 1.27 - 1.26 1.00 2802 156 0.1650 0.1794 3.1351 3.2029| | 24: 1.26 - 1.24 1.00 2744 132 0.1714 0.1807 3.1284 3.2236| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2142 3.1442 3.2619| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1779 3.15 3.2052| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2162 3.1725 3.1628| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2291 3.1666 3.1729| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2384 3.1495 3.2286| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2465 3.145 3.1735| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.45 1.00 0.97 5648.11| | 2: 3.57 - 2.84 2888 124 0.93 12.43 1.01 0.97 5648.11| | 3: 2.83 - 2.48 2820 163 0.90 16.32 0.99 0.97 4718.22| | 4: 2.47 - 2.25 2825 136 0.92 13.28 1.00 0.98 2320.32| | 5: 2.25 - 2.09 2756 127 0.90 15.48 1.01 0.98 2320.32| | 6: 2.09 - 1.97 2846 113 0.93 12.24 1.02 0.98 1339.94| | 7: 1.97 - 1.87 2787 165 0.95 9.16 1.02 0.98 503.81| | 8: 1.87 - 1.79 2789 144 0.93 12.47 0.99 0.98 503.81| | 9: 1.79 - 1.72 2745 138 0.94 9.95 0.98 0.98 285.99| | 10: 1.72 - 1.66 2831 160 0.94 11.03 0.98 0.98 242.37| | 11: 1.66 - 1.61 2712 147 0.94 11.65 0.98 0.98 232.35| | 12: 1.61 - 1.56 2773 144 0.96 8.87 0.99 0.97 137.82| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.02 0.97 137.82| | 14: 1.52 - 1.48 2803 134 0.94 10.77 1.02 0.98 123.90| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.98 98.40| | 16: 1.45 - 1.42 2756 161 0.94 11.12 1.02 0.98 98.40| | 17: 1.42 - 1.39 2785 139 0.95 10.98 1.01 0.98 89.56| | 18: 1.39 - 1.36 2741 179 0.94 11.57 1.01 0.98 84.45| | 19: 1.36 - 1.34 2807 134 0.94 11.90 0.99 0.98 84.45| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.34| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.96 80.06| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.43| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 82.33| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.33| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.37| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.64| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.64| | 28: 1.19 - 1.18 2671 147 0.88 20.43 1.01 0.93 90.49| | 29: 1.18 - 1.16 2800 134 0.88 20.54 0.99 0.92 91.94| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.98 0.92 91.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.06 max = 5648.11 mean = 873.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.87 mean = 13.41| |phase err.(test): min = 0.00 max = 89.01 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1280 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1448 0.1447 0.1499 n_refl.: 87575 remove outliers: r(all,work,free)=0.1448 0.1447 0.1499 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1448 0.1446 0.1499 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1282 n_refl.: 87575 remove outliers: r(all,work,free)=0.1135 0.1128 0.1282 n_refl.: 87573 ======================== 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 87.50 79 5 0.4085 288.757 253.201 0.434 0.999 0.284 11.894-9.307 93.14 91 4 0.2463 473.417 459.434 0.870 1.001 0.224 9.237-7.194 97.73 208 7 0.2283 388.431 379.393 0.919 1.002 0.170 7.162-5.571 100.00 427 22 0.2114 296.606 286.274 0.908 1.003 0.140 5.546-4.326 100.00 867 58 0.1129 407.166 402.480 0.962 1.003 0.113 4.315-3.360 100.00 1859 96 0.0917 387.218 385.158 1.003 1.002 0.083 3.356-2.611 100.00 3867 181 0.1097 254.382 252.377 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0907 168.632 167.994 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.351 82.688 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.518 36.114 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2171 23.009 21.545 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0080 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1963 0.082 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1788 0.082 5.384 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1788 0.082 5.384 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1793 0.082 5.384 9.0 119.5 20.1 258 0.007 1_weight: 0.1642 0.1793 0.082 5.384 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1229 0.1462 0.005 0.826 9.0 119.5 20.1 258 0.132 1_adp: 0.1236 0.1459 0.005 0.826 9.1 119.4 20.1 258 0.132 1_regHadp: 0.1238 0.1462 0.005 0.826 9.1 119.4 20.1 258 0.132 1_occ: 0.1230 0.1457 0.005 0.826 9.1 119.4 20.1 258 0.132 2_bss: 0.1231 0.1453 0.005 0.826 9.1 119.5 20.1 258 0.132 2_settarget: 0.1231 0.1453 0.005 0.826 9.1 119.5 20.1 258 0.132 2_updatecdl: 0.1231 0.1453 0.005 0.834 9.1 119.5 20.1 258 0.132 2_nqh: 0.1230 0.1453 0.005 0.834 9.1 119.5 20.1 258 0.129 2_sol: 0.1207 0.1394 0.005 0.834 9.1 114.9 22.2 418 n/a 2_weight: 0.1207 0.1394 0.005 0.834 9.1 114.9 22.2 418 n/a 2_xyzrec: 0.1180 0.1410 0.008 0.946 9.1 114.9 22.2 418 n/a 2_adp: 0.1180 0.1410 0.008 0.946 9.1 114.9 22.2 418 n/a 2_regHadp: 0.1180 0.1410 0.008 0.946 9.1 114.9 22.2 418 n/a 2_occ: 0.1180 0.1403 0.008 0.946 9.1 114.9 22.2 418 n/a 3_bss: 0.1176 0.1399 0.008 0.946 9.1 114.9 22.3 418 n/a 3_settarget: 0.1176 0.1399 0.008 0.946 9.1 114.9 22.3 418 n/a 3_updatecdl: 0.1176 0.1399 0.008 0.948 9.1 114.9 22.3 418 n/a 3_nqh: 0.1178 0.1400 0.008 0.948 9.1 114.9 22.3 418 n/a 3_sol: 0.1206 0.1394 0.008 0.948 9.1 114.9 21.2 445 n/a 3_weight: 0.1206 0.1394 0.008 0.948 9.1 114.9 21.2 445 n/a 3_xyzrec: 0.1162 0.1314 0.008 1.084 9.1 114.9 21.2 445 n/a 3_adp: 0.1162 0.1314 0.008 1.084 9.1 114.9 21.2 445 n/a 3_regHadp: 0.1162 0.1314 0.008 1.084 9.1 114.9 21.2 445 n/a 3_occ: 0.1152 0.1311 0.008 1.084 9.1 114.9 21.2 445 n/a 4_bss: 0.1143 0.1309 0.008 1.084 9.1 114.9 21.2 445 n/a 4_settarget: 0.1143 0.1309 0.008 1.084 9.1 114.9 21.2 445 n/a 4_updatecdl: 0.1143 0.1309 0.008 1.085 9.1 114.9 21.2 445 n/a 4_nqh: 0.1143 0.1309 0.008 1.085 9.1 114.9 21.2 445 n/a 4_sol: 0.1143 0.1295 0.008 1.085 9.1 114.9 21.1 448 n/a 4_weight: 0.1143 0.1295 0.008 1.085 9.1 114.9 21.1 448 n/a 4_xyzrec: 0.1143 0.1294 0.007 1.052 9.1 114.9 21.1 448 n/a 4_adp: 0.1143 0.1294 0.007 1.052 9.1 114.9 21.1 448 n/a 4_regHadp: 0.1143 0.1294 0.007 1.052 9.1 114.9 21.1 448 n/a 4_occ: 0.1136 0.1289 0.007 1.052 9.1 114.9 21.1 448 n/a 5_bss: 0.1131 0.1289 0.007 1.052 9.1 114.9 21.1 448 n/a 5_settarget: 0.1131 0.1289 0.007 1.052 9.1 114.9 21.1 448 n/a 5_updatecdl: 0.1131 0.1289 0.007 1.051 9.1 114.9 21.1 448 n/a 5_setrh: 0.1132 0.1289 0.007 1.051 9.1 114.9 21.1 448 n/a 5_nqh: 0.1132 0.1289 0.007 1.051 9.1 114.9 21.1 448 n/a 5_sol: 0.1133 0.1282 0.007 1.051 9.1 114.9 21.1 458 n/a 5_weight: 0.1133 0.1282 0.007 1.051 9.1 114.9 21.1 458 n/a 5_xyzrec: 0.1131 0.1282 0.008 1.132 9.1 114.9 21.1 458 n/a 5_adp: 0.1131 0.1282 0.008 1.132 9.1 114.9 21.1 458 n/a 5_regHadp: 0.1131 0.1282 0.008 1.132 9.1 114.9 21.1 458 n/a 5_occ: 0.1128 0.1280 0.008 1.132 9.1 114.9 21.1 458 n/a end: 0.1128 0.1282 0.008 1.132 9.1 114.9 21.1 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7848743_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7848743_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8100 Refinement macro-cycles (run) : 14114.5400 Write final files (write_after_run_outputs) : 79.6300 Total : 14196.9800 Total CPU time: 3.95 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:16:40 PST -0800 (1735366600.18 s) Start R-work = 0.1638, R-free = 0.1788 Final R-work = 0.1128, R-free = 0.1282 =============================================================================== Job complete usr+sys time: 14344.76 seconds wall clock time: 260 minutes 17.83 seconds (15617.83 seconds total)