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_4912670.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_4912670.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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: 1.24, per 1000 atoms: 0.37 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: 0.39 Conformation dependent library (CDL) restraints added in 106.7 milliseconds Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 731 0.94 - 1.21: 965 1.21 - 1.47: 787 1.47 - 1.74: 658 1.74 - 2.01: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.340 1.189 0.151 6.60e-03 2.30e+04 5.24e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.519 1.303 0.216 1.04e-02 9.25e+03 4.30e+02 bond pdb=" C ASP A 149 " pdb=" O ASP A 149 " ideal model delta sigma weight residual 1.235 1.020 0.215 1.14e-02 7.69e+03 3.55e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.234 1.026 0.209 1.11e-02 8.12e+03 3.53e+02 bond pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 1.330 1.087 0.243 1.30e-02 5.92e+03 3.49e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3018 4.49 - 8.97: 1903 8.97 - 13.46: 684 13.46 - 17.95: 152 17.95 - 22.44: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 113.83 7.24 3.60e-01 7.72e+00 4.04e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 106.42 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" CA VAL A 23 " pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 121.27 135.78 -14.51 1.04e+00 9.25e-01 1.95e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 126.44 -13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 108.37 14.83 1.08e+00 8.57e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 925 16.17 - 32.33: 121 32.33 - 48.50: 42 48.50 - 64.67: 19 64.67 - 80.83: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.92 20.08 0 5.00e+00 4.00e-02 1.61e+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 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.207: 102 0.207 - 0.412: 72 0.412 - 0.616: 45 0.616 - 0.821: 22 0.821 - 1.026: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA VAL A 181 " pdb=" N VAL A 181 " pdb=" C VAL A 181 " pdb=" CB VAL A 181 " both_signs ideal model delta sigma weight residual False 2.44 3.26 -0.82 2.00e-01 2.50e+01 1.68e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.119 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.132 9.50e-02 1.11e+02 8.48e-02 1.20e+02 pdb=" NE ARG A 5 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.105 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.069 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.106 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.050 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.107 2.00e-02 2.50e+03 5.45e-02 8.92e+01 pdb=" CG ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.013 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 635 2.26 - 2.84: 7701 2.84 - 3.43: 10630 3.43 - 4.01: 15493 4.01 - 4.60: 22152 Nonbonded interactions: 56611 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.673 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 1.850 nonbonded pdb=" HG3BGLU A 90 " pdb=" O HOH A 373 " model vdw 1.848 2.620 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.851 1.850 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.855 1.850 ... (remaining 56606 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_4912670_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= 0.2612 r_free= 0.1911 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793428 | | target function (ml) not normalized (work): 232709.303819 | | target function (ml) not normalized (free): 11808.384591 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3031 0.2038 7.1204 4.9365| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1728 4.3445 4.3334| | 3: 2.84 - 2.48 1.00 2833 165 0.2354 0.1635 4.1198 4.1455| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1453 3.8277 3.8263| | 5: 2.25 - 2.09 1.00 2756 127 0.2492 0.1498 3.7913 3.8047| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1712 3.4539 3.5946| | 7: 1.97 - 1.87 1.00 2787 165 0.2584 0.1852 3.1437 3.1889| | 8: 1.87 - 1.79 1.00 2789 144 0.2429 0.1757 3.0534 3.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.2392 0.1739 2.9012 2.8788| | 10: 1.72 - 1.66 1.00 2789 158 0.2396 0.1892 2.8017 2.8562| | 11: 1.66 - 1.61 1.00 2740 147 0.2529 0.1820 2.744 2.7311| | 12: 1.61 - 1.56 1.00 2787 146 0.2492 0.1945 2.6216 2.6455| | 13: 1.56 - 1.52 1.00 2745 130 0.2599 0.1988 2.577 2.647| | 14: 1.52 - 1.48 1.00 2803 134 0.2544 0.1822 2.5096 2.4728| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.1820 2.446 2.3654| | 16: 1.45 - 1.42 1.00 2756 161 0.2632 0.2286 2.3684 2.4752| | 17: 1.42 - 1.39 1.00 2785 139 0.2659 0.2184 2.3201 2.3949| | 18: 1.39 - 1.36 1.00 2741 179 0.2763 0.2341 2.2832 2.3951| | 19: 1.36 - 1.34 1.00 2807 134 0.2691 0.2592 2.2577 2.3424| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2328 2.2146 2.2498| | 21: 1.32 - 1.30 1.00 2785 112 0.2724 0.2218 2.1682 2.1623| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2612 2.1369 2.2332| | 23: 1.27 - 1.26 1.00 2802 156 0.2756 0.2491 2.1052 2.1711| | 24: 1.26 - 1.24 1.00 2744 132 0.2805 0.2475 2.0843 2.1278| | 25: 1.24 - 1.22 1.00 2734 148 0.2787 0.2472 2.0517 2.0806| | 26: 1.22 - 1.21 1.00 2727 135 0.2873 0.2268 2.0087 2.0875| | 27: 1.21 - 1.19 1.00 2814 148 0.2996 0.2995 2.0167 2.1091| | 28: 1.19 - 1.18 1.00 2671 147 0.2982 0.2575 1.9838 1.9492| | 29: 1.18 - 1.16 1.00 2800 134 0.2954 0.2666 1.9603 2.0135| | 30: 1.16 - 1.15 1.00 2740 148 0.3108 0.2952 1.9291 1.9807| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.49 0.76 0.23 1441.40| | 2: 3.57 - 2.84 2876 122 0.81 25.85 1.27 0.23 1441.40| | 3: 2.84 - 2.48 2833 165 0.74 31.70 1.24 0.23 1195.94| | 4: 2.47 - 2.25 2825 136 0.82 25.27 1.26 0.25 558.94| | 5: 2.25 - 2.09 2756 127 0.78 28.94 1.29 0.25 558.94| | 6: 2.09 - 1.97 2846 113 0.84 22.50 1.29 0.25 306.75| | 7: 1.97 - 1.87 2787 165 0.90 16.81 1.29 0.25 91.67| | 8: 1.87 - 1.79 2789 144 0.86 21.23 1.24 0.25 91.67| | 9: 1.79 - 1.72 2745 138 0.88 18.09 1.22 0.25 53.16| | 10: 1.72 - 1.66 2789 158 0.87 19.71 1.21 0.25 45.44| | 11: 1.66 - 1.61 2740 147 0.86 20.82 1.24 0.25 43.92| | 12: 1.61 - 1.56 2787 146 0.89 18.04 1.23 0.25 28.45| | 13: 1.56 - 1.52 2745 130 0.87 20.09 1.24 0.25 28.45| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.22 0.25 25.67| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.23 0.25 20.57| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.24 0.25 20.57| | 17: 1.42 - 1.39 2785 139 0.86 21.45 1.23 0.25 18.00| | 18: 1.39 - 1.36 2741 179 0.86 21.95 1.24 0.24 16.50| | 19: 1.36 - 1.34 2807 134 0.85 22.81 1.22 0.24 16.50| | 20: 1.34 - 1.32 2696 147 0.86 21.91 1.20 0.24 13.82| | 21: 1.32 - 1.30 2785 112 0.85 22.78 1.20 0.24 13.63| | 22: 1.29 - 1.27 2704 152 0.84 23.69 1.22 0.24 13.32| | 23: 1.27 - 1.26 2802 156 0.85 22.92 1.21 0.24 11.71| | 24: 1.26 - 1.24 2744 132 0.84 23.78 1.20 0.24 11.71| | 25: 1.24 - 1.22 2734 148 0.84 23.94 1.19 0.24 11.02| | 26: 1.22 - 1.21 2727 135 0.83 24.62 1.20 0.23 10.26| | 27: 1.21 - 1.19 2814 148 0.83 25.29 1.20 0.23 10.26| | 28: 1.19 - 1.18 2671 147 0.83 25.16 1.18 0.23 9.29| | 29: 1.18 - 1.16 2800 134 0.83 25.27 1.16 0.23 8.92| | 30: 1.16 - 1.15 2740 148 0.81 27.05 1.17 0.23 8.92| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.92 max = 1441.40 mean = 209.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.74| |phase err.(test): min = 0.00 max = 89.47 mean = 22.63| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.243 1557 Z= 5.444 Angle : 5.386 18.870 2118 Z= 3.769 Chirality : 0.364 1.026 243 Planarity : 0.031 0.082 284 Dihedral : 14.033 80.833 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -2.70 (0.47), residues: 224 helix: -2.91 (0.33), residues: 102 sheet: -0.96 (0.72), residues: 38 loop : -0.27 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.013 ARG A 145 TYR 0.073 0.030 TYR A 139 PHE 0.111 0.049 PHE A 119 HIS 0.079 0.048 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= 0.2612 r_free= 0.1911 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793428 | | target function (ml) not normalized (work): 232709.303819 | | target function (ml) not normalized (free): 11808.384591 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1911 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1911 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1991 0.1911 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2008 0.2014 0.1925 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1644 0.1744 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1644 0.1744 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 0.3830 386.266 357.617 0.682 1.003 0.411 11.894-9.307 99.02 97 4 0.1827 613.565 594.155 0.934 1.003 0.378 9.237-7.194 100.00 213 7 0.2184 501.821 490.231 0.960 1.003 0.339 7.162-5.571 100.00 427 22 0.2240 376.589 362.430 0.931 1.003 0.288 5.546-4.326 100.00 867 58 0.1275 516.963 511.494 0.965 1.003 0.234 4.315-3.360 100.00 1859 96 0.1132 491.636 488.487 1.009 1.003 0.209 3.356-2.611 100.00 3867 181 0.1447 322.979 319.149 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.1358 214.106 212.192 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1650 104.558 103.908 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2085 46.365 45.007 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2588 29.213 26.919 0.977 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1744 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1645 r_free=0.1745 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.665950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2028.521615 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1450 0.0242 0.008 1.0 2.6 0.5 0.6 0 13.833 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.50 2.42 3.013 19.052 2028.522 0.017 12.08 14.50 2.42 3.013 19.052 60.856 0.017 12.15 14.47 2.33 2.686 19.050 253.565 0.017 12.50 15.13 2.63 2.712 19.172 1014.261 0.016 12.38 15.31 2.93 3.265 19.557 2028.522 0.015 12.29 15.37 3.08 3.291 19.574 3042.782 0.015 12.24 15.39 3.16 3.373 19.608 4057.043 0.015 12.14 15.33 3.20 3.336 19.582 5071.304 0.015 12.12 15.37 3.24 3.428 19.634 6085.565 0.015 12.10 15.38 3.28 3.480 19.647 7099.826 0.015 12.01 15.28 3.27 3.356 19.569 8114.086 0.015 12.00 15.30 3.31 3.365 19.566 9128.347 0.015 11.98 15.29 3.31 3.334 19.545 10142.608 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: 253.565 Accepted refinement result: 12.15 14.47 2.33 2.686 19.050 253.565 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.07 3.35 0 1785 Protein: 9.06 115.16 16.98 3.35 0 1519 Water: 11.46 119.44 38.22 N/A 0 258 Other: 19.66 26.60 22.03 N/A 0 8 Chain A: 9.06 119.44 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.17 125 42.17 - 53.21 95 53.21 - 64.25 41 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1447 r_work=0.1216 r_free=0.1451 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1451 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 = 0.1210 r_free = 0.1444 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1444 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016547 | | target function (ls_wunit_k1) not normalized (work): 1378.353544 | | target function (ls_wunit_k1) not normalized (free): 108.959934 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1210 0.1444 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1658 0.1660 0.1668 n_refl.: 87593 remove outliers: r(all,work,free)=0.1658 0.1660 0.1668 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1665 0.1667 0.1672 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1208 0.1435 n_refl.: 87593 remove outliers: r(all,work,free)=0.1217 0.1206 0.1435 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3450 300.332 281.260 0.629 1.003 0.370 11.894-9.307 98.04 96 4 0.1605 485.405 467.454 0.917 1.003 0.367 9.237-7.194 100.00 213 7 0.1913 395.397 389.305 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1882 296.724 290.375 0.934 1.003 0.264 5.546-4.326 100.00 867 58 0.1012 407.328 403.935 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0864 387.372 386.302 1.009 1.003 0.180 3.356-2.611 100.00 3867 181 0.1142 254.483 253.450 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.0988 168.699 168.065 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1083 82.384 82.637 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1433 36.532 36.060 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 23.018 21.505 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0576 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1435 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=0.1208 r_free=0.1437 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1208 r_free=0.1437 | n_water=258 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1215 r_free=0.1435 | n_water=252 | time (s): 22.230 (total time: 24.160) Filter (q & B) r_work=0.1217 r_free=0.1435 | n_water=249 | time (s): 2.820 (total time: 26.980) Compute maps r_work=0.1217 r_free=0.1435 | n_water=249 | time (s): 1.710 (total time: 28.690) Filter (map) r_work=0.1227 r_free=0.1442 | n_water=239 | time (s): 2.830 (total time: 31.520) Find peaks r_work=0.1227 r_free=0.1442 | n_water=239 | time (s): 0.560 (total time: 32.080) Add new water r_work=0.1364 r_free=0.1599 | n_water=447 | time (s): 3.150 (total time: 35.230) Refine new water occ: r_work=0.1275 r_free=0.1463 adp: r_work=0.1201 r_free=0.1411 occ: r_work=0.1215 r_free=0.1401 adp: r_work=0.1180 r_free=0.1386 occ: r_work=0.1184 r_free=0.1378 adp: r_work=0.1173 r_free=0.1379 ADP+occupancy (water only), MIN, final r_work=0.1173 r_free=0.1379 r_work=0.1173 r_free=0.1379 | n_water=447 | time (s): 49.520 (total time: 84.750) Filter (q & B) r_work=0.1178 r_free=0.1387 | n_water=426 | time (s): 3.490 (total time: 88.240) Filter (dist only) r_work=0.1179 r_free=0.1384 | n_water=425 | time (s): 34.860 (total time: 123.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.658061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.105184 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 0.1651 0.1784 0.0132 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1534 0.1679 0.0145 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1395 0.1561 0.0166 0.002 0.4 5.1 0.0 0.0 0 0.500 0.1324 0.1501 0.0177 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1301 0.1482 0.0181 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1293 0.1476 0.0183 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1237 0.1437 0.0199 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1220 0.1431 0.0211 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1210 0.1426 0.0216 0.003 0.6 5.1 0.5 0.0 0 4.000 0.1199 0.1411 0.0212 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1195 0.1410 0.0216 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1191 0.1408 0.0217 0.005 0.8 6.1 0.5 0.0 0 7.000 0.1188 0.1407 0.0219 0.005 0.8 6.1 0.5 0.0 0 8.000 0.1185 0.1403 0.0218 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1183 0.1405 0.0222 0.006 0.9 6.4 0.5 0.0 0 10.000 0.1184 0.1409 0.0225 0.007 0.9 6.4 0.5 0.0 0 11.000 0.1180 0.1403 0.0223 0.007 0.9 7.0 0.5 0.0 0 12.000 0.1176 0.1399 0.0223 0.007 0.9 7.4 0.5 0.0 0 13.000 0.1176 0.1405 0.0229 0.008 0.9 6.7 0.5 0.6 0 14.329 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1176 0.1399 0.0223 0.007 0.9 7.4 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 13.99 2.23 3.791 21.881 1483.105 0.015 11.76 13.99 2.23 3.791 21.881 44.493 0.015 11.76 13.99 2.23 3.791 21.881 185.388 0.015 11.96 14.43 2.46 3.627 21.895 741.553 0.015 11.97 14.74 2.78 3.446 22.150 1483.105 0.014 11.83 14.73 2.90 3.450 22.223 2224.658 0.014 11.73 14.70 2.98 3.489 22.070 2966.210 0.014 11.62 14.56 2.94 3.483 22.188 3707.763 0.014 11.55 14.54 2.99 3.498 22.108 4449.316 0.013 11.66 14.80 3.14 3.546 22.300 5190.868 0.013 11.57 14.69 3.12 3.528 22.192 5932.421 0.013 11.57 14.70 3.13 3.555 22.287 6673.973 0.013 11.53 14.68 3.15 3.559 22.228 7415.526 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: 185.388 Accepted refinement result: 11.76 13.99 2.23 3.791 21.881 185.388 0.015 Individual atomic B min max mean iso aniso Overall: 9.10 115.20 22.38 3.35 186 1766 Protein: 9.10 115.20 17.02 3.35 0 1519 Water: 11.50 79.15 41.53 N/A 186 239 Other: 19.70 26.63 22.07 N/A 0 8 Chain A: 9.10 115.20 19.69 N/A 0 1766 Chain S: 17.41 60.00 47.87 N/A 186 0 Histogram: Values Number of atoms 9.10 - 19.71 1261 19.71 - 30.32 242 30.32 - 40.93 156 40.93 - 51.54 143 51.54 - 62.15 125 62.15 - 72.76 13 72.76 - 83.37 6 83.37 - 93.98 4 93.98 - 104.59 0 104.59 - 115.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1399 r_work=0.1176 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1399 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1403 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1179 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014520 | | target function (ls_wunit_k1) not normalized (work): 1209.378238 | | target function (ls_wunit_k1) not normalized (free): 97.515349 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1179 0.1403 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1533 0.1532 0.1604 n_refl.: 87589 remove outliers: r(all,work,free)=0.1533 0.1532 0.1604 n_refl.: 87589 overall B=0.01 to atoms: r(all,work,free)=0.1536 0.1534 0.1605 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1176 0.1398 n_refl.: 87589 remove outliers: r(all,work,free)=0.1187 0.1176 0.1398 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 0.3320 297.684 279.373 0.600 1.002 0.350 11.894-9.307 98.04 96 4 0.1488 485.405 479.281 0.927 1.003 0.314 9.237-7.194 100.00 213 7 0.1607 395.397 397.152 0.987 1.003 0.280 7.162-5.571 100.00 427 22 0.1579 296.724 292.314 0.935 1.003 0.228 5.546-4.326 100.00 867 58 0.0905 407.328 404.578 0.962 1.003 0.220 4.315-3.360 100.00 1859 96 0.0776 387.372 386.391 1.004 1.002 0.180 3.356-2.611 100.00 3867 181 0.1083 254.483 253.454 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1001 168.699 168.164 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.384 82.620 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1434 36.532 36.063 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 23.018 21.520 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1398 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1178 r_free=0.1397 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1397 | n_water=425 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1178 r_free=0.1394 | n_water=421 | time (s): 36.480 (total time: 38.320) Filter (q & B) r_work=0.1178 r_free=0.1394 | n_water=421 | time (s): 0.790 (total time: 39.110) Compute maps r_work=0.1178 r_free=0.1394 | n_water=421 | time (s): 1.310 (total time: 40.420) Filter (map) r_work=0.1219 r_free=0.1416 | n_water=285 | time (s): 2.710 (total time: 43.130) Find peaks r_work=0.1219 r_free=0.1416 | n_water=285 | time (s): 0.450 (total time: 43.580) Add new water r_work=0.1333 r_free=0.1526 | n_water=468 | time (s): 2.480 (total time: 46.060) Refine new water occ: r_work=0.1240 r_free=0.1434 adp: r_work=0.1241 r_free=0.1436 occ: r_work=0.1217 r_free=0.1416 adp: r_work=0.1216 r_free=0.1416 occ: r_work=0.1199 r_free=0.1407 adp: r_work=0.1194 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1404 r_work=0.1194 r_free=0.1404 | n_water=468 | time (s): 202.950 (total time: 249.010) Filter (q & B) r_work=0.1199 r_free=0.1407 | n_water=437 | time (s): 2.630 (total time: 251.640) Filter (dist only) r_work=0.1200 r_free=0.1407 | n_water=435 | time (s): 36.530 (total time: 288.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.700906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.799059 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 0.1230 0.1382 0.0151 0.002 0.6 3.8 0.5 0.0 0 0.085 0.1189 0.1345 0.0155 0.003 0.7 3.2 0.5 0.0 0 0.255 0.1171 0.1330 0.0159 0.004 0.8 3.2 0.5 0.0 0 0.510 0.1165 0.1327 0.0162 0.005 0.9 2.9 0.5 0.0 0 0.765 0.1160 0.1325 0.0165 0.006 1.0 3.2 0.5 0.0 0 1.021 0.1156 0.1322 0.0166 0.007 1.0 3.2 0.5 0.0 0 1.276 0.1155 0.1323 0.0169 0.007 1.0 3.5 0.5 0.0 0 1.531 0.1152 0.1323 0.0171 0.008 1.1 3.5 0.5 0.0 0 1.786 0.1162 0.1327 0.0164 0.005 0.9 3.2 0.5 0.0 0 0.850 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1322 0.0166 0.007 1.0 3.2 0.5 0.0 0 1.276 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.22 1.66 3.794 21.254 43.799 3.622 11.56 13.22 1.66 3.794 21.254 1.314 3.622 11.56 13.22 1.66 3.780 21.254 5.475 3.622 11.62 13.30 1.69 3.720 21.241 21.900 3.618 11.63 13.38 1.75 3.741 21.216 43.799 3.617 11.56 13.37 1.81 3.764 21.204 65.699 3.611 11.52 13.37 1.84 3.777 21.194 87.598 3.608 11.50 13.36 1.86 3.788 21.188 109.498 3.605 11.47 13.34 1.87 3.804 21.178 131.397 3.603 11.47 13.33 1.86 3.814 21.168 153.297 3.602 11.44 13.33 1.88 3.827 21.168 175.196 3.601 11.43 13.32 1.89 3.837 21.163 197.096 3.600 11.41 13.30 1.90 3.838 21.169 218.995 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.314 Accepted refinement result: 11.56 13.22 1.66 3.794 21.254 1.314 3.622 Individual atomic B min max mean iso aniso Overall: 9.11 115.22 21.22 3.35 206 1756 Protein: 9.11 115.22 17.03 3.35 0 1519 Water: 11.51 76.71 35.82 N/A 206 229 Other: 19.71 26.65 22.08 N/A 0 8 Chain A: 9.11 115.22 19.50 N/A 0 1756 Chain S: 16.23 60.01 35.87 N/A 206 0 Histogram: Values Number of atoms 9.11 - 19.72 1264 19.72 - 30.33 294 30.33 - 40.94 191 40.94 - 51.55 138 51.55 - 62.16 51 62.16 - 72.77 13 72.77 - 83.38 5 83.38 - 93.99 4 93.99 - 104.60 0 104.60 - 115.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1322 r_work=0.1156 r_free=0.1322 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1322 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1312 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.19 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= 0.1146 r_free= 0.1312 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614567 | | target function (ml) not normalized (work): 301064.506776 | | target function (ml) not normalized (free): 15846.540790 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1312 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1492 0.1491 0.1540 n_refl.: 87588 remove outliers: r(all,work,free)=0.1492 0.1491 0.1540 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1491 0.1490 0.1539 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1298 n_refl.: 87588 remove outliers: r(all,work,free)=0.1146 0.1138 0.1298 n_refl.: 87580 ======================== 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 0.3757 297.044 263.434 0.495 1.001 0.330 11.894-9.307 97.06 95 4 0.2309 478.624 470.602 0.881 1.002 0.259 9.237-7.194 98.18 209 7 0.2256 386.860 389.201 0.953 1.002 0.210 7.162-5.571 100.00 427 22 0.2048 296.724 286.593 0.916 1.002 0.210 5.546-4.326 100.00 867 58 0.1114 407.328 402.932 0.964 1.002 0.170 4.315-3.360 100.00 1859 96 0.0922 387.372 385.115 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1132 254.483 252.160 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0923 168.699 167.885 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.384 82.656 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.532 36.105 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 23.018 21.540 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0067 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1298 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=0.1138 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1298 | n_water=435 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1138 r_free=0.1296 | n_water=434 | time (s): 38.370 (total time: 40.180) Filter (q & B) r_work=0.1139 r_free=0.1296 | n_water=433 | time (s): 2.930 (total time: 43.110) Compute maps r_work=0.1139 r_free=0.1296 | n_water=433 | time (s): 1.200 (total time: 44.310) Filter (map) r_work=0.1159 r_free=0.1302 | n_water=334 | time (s): 3.310 (total time: 47.620) Find peaks r_work=0.1159 r_free=0.1302 | n_water=334 | time (s): 0.680 (total time: 48.300) Add new water r_work=0.1226 r_free=0.1377 | n_water=489 | time (s): 2.900 (total time: 51.200) Refine new water occ: r_work=0.1162 r_free=0.1315 adp: r_work=0.1162 r_free=0.1317 occ: r_work=0.1148 r_free=0.1302 adp: r_work=0.1147 r_free=0.1304 occ: r_work=0.1136 r_free=0.1291 adp: r_work=0.1132 r_free=0.1292 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1292 r_work=0.1132 r_free=0.1292 | n_water=489 | time (s): 179.260 (total time: 230.460) Filter (q & B) r_work=0.1137 r_free=0.1292 | n_water=456 | time (s): 3.400 (total time: 233.860) Filter (dist only) r_work=0.1137 r_free=0.1292 | n_water=454 | time (s): 39.620 (total time: 273.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.764350 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.040800 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1336 0.0136 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1159 0.1305 0.0146 0.003 0.8 3.2 0.5 0.0 0 0.265 0.1146 0.1301 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.529 0.1140 0.1295 0.0156 0.006 0.9 3.5 0.5 0.0 0 0.794 0.1135 0.1296 0.0161 0.006 1.0 3.8 0.5 0.0 0 1.059 0.1132 0.1295 0.0162 0.007 1.1 4.2 0.5 0.0 0 1.323 0.1130 0.1296 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.588 0.1130 0.1292 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.853 0.1138 0.1296 0.0158 0.006 1.0 3.8 0.5 0.0 0 0.882 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1292 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.853 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.92 1.62 3.795 21.294 44.041 3.604 11.30 12.92 1.62 3.795 21.294 1.321 3.604 11.30 12.92 1.62 3.785 21.294 5.505 3.604 11.37 13.02 1.65 3.721 21.280 22.020 3.602 11.38 13.09 1.71 3.745 21.258 44.041 3.601 11.33 13.09 1.76 3.765 21.246 66.061 3.597 11.28 13.07 1.79 3.781 21.242 88.082 3.592 11.26 13.07 1.81 3.791 21.233 110.102 3.590 11.24 13.08 1.83 3.805 21.225 132.122 3.588 11.23 13.08 1.85 3.819 21.222 154.143 3.587 11.21 13.06 1.85 3.827 21.221 176.163 3.586 11.20 13.06 1.85 3.837 21.214 198.184 3.585 11.18 13.03 1.86 3.840 21.218 220.204 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.321 Accepted refinement result: 11.30 12.92 1.62 3.795 21.294 1.321 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.21 21.29 3.35 225 1756 Protein: 9.11 115.21 17.03 3.35 0 1519 Water: 11.51 76.71 35.53 N/A 225 229 Other: 19.71 26.64 22.08 N/A 0 8 Chain A: 9.11 115.21 19.50 N/A 0 1756 Chain S: 16.23 60.01 35.29 N/A 225 0 Histogram: Values Number of atoms 9.11 - 19.72 1265 19.72 - 30.33 300 30.33 - 40.94 202 40.94 - 51.55 143 51.55 - 62.16 47 62.16 - 72.77 13 72.77 - 83.38 5 83.38 - 93.99 4 93.99 - 104.60 0 104.60 - 115.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1292 r_work=0.1130 r_free=0.1292 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1292 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1122 r_free = 0.1289 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1122 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600705 | | target function (ml) not normalized (work): 299881.094634 | | target function (ml) not normalized (free): 15809.712463 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1122 0.1289 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1456 0.1454 0.1508 n_refl.: 87580 remove outliers: r(all,work,free)=0.1456 0.1454 0.1508 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1455 0.1454 0.1508 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1121 0.1288 n_refl.: 87580 remove outliers: r(all,work,free)=0.1128 0.1120 0.1288 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 0.4108 297.044 262.355 0.474 1.001 0.302 11.894-9.307 94.12 92 4 0.2261 482.729 459.520 0.860 1.002 0.248 9.237-7.194 98.18 209 7 0.2234 386.860 384.555 0.934 1.002 0.210 7.162-5.571 100.00 427 22 0.1969 296.724 287.656 0.916 1.003 0.171 5.546-4.326 100.00 867 58 0.1109 407.328 402.411 0.965 1.003 0.140 4.315-3.360 100.00 1859 96 0.0903 387.372 385.426 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1106 254.483 252.569 1.009 1.002 0.024 2.608-2.026 99.99 8198 413 0.0905 168.699 168.170 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0877 82.384 82.752 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.532 36.149 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.018 21.569 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0113 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1120 r_free=0.1288 After: r_work=0.1122 r_free=0.1288 ================================== NQH flips ================================== r_work=0.1122 r_free=0.1288 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=0.1122 r_free=0.1288 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1122 r_free=0.1288 | n_water=454 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1122 r_free=0.1288 | n_water=454 | time (s): 43.280 (total time: 45.710) Filter (q & B) r_work=0.1122 r_free=0.1289 | n_water=449 | time (s): 3.860 (total time: 49.570) Compute maps r_work=0.1122 r_free=0.1289 | n_water=449 | time (s): 1.820 (total time: 51.390) Filter (map) r_work=0.1147 r_free=0.1299 | n_water=351 | time (s): 3.610 (total time: 55.000) Find peaks r_work=0.1147 r_free=0.1299 | n_water=351 | time (s): 0.690 (total time: 55.690) Add new water r_work=0.1200 r_free=0.1352 | n_water=505 | time (s): 3.870 (total time: 59.560) Refine new water occ: r_work=0.1142 r_free=0.1289 adp: r_work=0.1143 r_free=0.1292 occ: r_work=0.1130 r_free=0.1280 adp: r_work=0.1129 r_free=0.1282 occ: r_work=0.1120 r_free=0.1271 adp: r_work=0.1117 r_free=0.1274 ADP+occupancy (water only), MIN, final r_work=0.1117 r_free=0.1274 r_work=0.1117 r_free=0.1274 | n_water=505 | time (s): 166.710 (total time: 226.270) Filter (q & B) r_work=0.1124 r_free=0.1276 | n_water=467 | time (s): 3.770 (total time: 230.040) Filter (dist only) r_work=0.1124 r_free=0.1275 | n_water=466 | time (s): 48.630 (total time: 278.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.724962 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.072971 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 0.1210 0.1334 0.0123 0.004 0.7 6.7 0.0 0.0 0 0.086 0.1162 0.1301 0.0139 0.004 0.8 7.0 0.0 0.0 0 0.259 0.1146 0.1290 0.0144 0.005 0.9 6.4 0.5 0.0 0 0.517 0.1136 0.1283 0.0147 0.006 1.0 6.7 0.5 0.0 0 0.776 0.1131 0.1279 0.0148 0.006 1.1 6.7 0.5 0.0 0 1.035 0.1127 0.1277 0.0150 0.007 1.1 6.4 0.5 0.0 0 1.294 0.1125 0.1275 0.0151 0.008 1.1 6.4 0.5 0.0 0 1.552 0.1124 0.1275 0.0151 0.008 1.1 6.4 0.5 0.0 0 1.811 0.1133 0.1281 0.0148 0.006 1.0 6.7 0.5 0.0 0 0.862 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1275 0.0151 0.008 1.1 6.4 0.5 0.0 0 1.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 12.75 1.51 3.795 21.329 35.073 3.602 11.24 12.75 1.51 3.795 21.329 1.052 3.602 11.24 12.75 1.51 3.795 21.329 4.384 3.602 11.28 12.79 1.51 3.720 21.324 17.536 3.598 11.39 12.96 1.57 3.724 21.301 35.073 3.604 11.28 12.92 1.64 3.757 21.289 52.609 3.597 11.21 12.87 1.66 3.767 21.289 70.146 3.591 11.24 12.93 1.69 3.778 21.274 87.682 3.591 11.21 12.92 1.71 3.791 21.274 105.219 3.589 11.18 12.89 1.71 3.800 21.269 122.755 3.587 11.15 12.85 1.71 3.803 21.273 140.292 3.585 11.15 12.89 1.74 3.817 21.266 157.828 3.584 11.17 12.91 1.75 3.834 21.254 175.365 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.052 Accepted refinement result: 11.24 12.75 1.51 3.795 21.329 1.052 3.602 Individual atomic B min max mean iso aniso Overall: 9.10 115.21 21.36 3.35 237 1756 Protein: 9.10 115.21 17.03 3.35 0 1519 Water: 11.50 76.70 35.46 N/A 237 229 Other: 19.70 26.64 22.07 N/A 0 8 Chain A: 9.10 115.21 19.49 N/A 0 1756 Chain S: 16.22 60.01 35.17 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.71 1264 19.71 - 30.32 310 30.32 - 40.93 204 40.93 - 51.55 141 51.55 - 62.16 50 62.16 - 72.77 13 72.77 - 83.38 5 83.38 - 93.99 4 93.99 - 104.60 0 104.60 - 115.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1124 r_free=0.1275 r_work=0.1124 r_free=0.1275 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1124 r_free = 0.1275 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1119 r_free = 0.1272 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1119 r_free= 0.1272 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599603 | | target function (ml) not normalized (work): 299778.564321 | | target function (ml) not normalized (free): 15795.340178 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1313 0.1307 5.6277 5.6049| | 2: 3.57 - 2.84 1.00 2888 124 0.1038 0.1359 5.1474 5.2048| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1241 4.9392 4.9814| | 4: 2.47 - 2.25 1.00 2825 136 0.0878 0.0933 4.6222 4.6374| | 5: 2.25 - 2.09 1.00 2756 127 0.0854 0.0927 4.5697 4.6163| | 6: 2.09 - 1.97 1.00 2846 113 0.0838 0.1026 4.2553 4.37| | 7: 1.97 - 1.87 1.00 2787 165 0.0872 0.1102 3.9673 4.0721| | 8: 1.87 - 1.79 1.00 2789 144 0.0908 0.1108 3.8788 3.9909| | 9: 1.79 - 1.72 1.00 2745 138 0.0867 0.1148 3.6405 3.8015| | 10: 1.72 - 1.66 1.00 2831 160 0.0906 0.1159 3.5552 3.7082| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1019 3.4894 3.5694| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1097 3.3259 3.4532| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1048 3.3028 3.402| | 14: 1.52 - 1.48 1.00 2803 134 0.0971 0.1064 3.234 3.3143| | 15: 1.48 - 1.45 1.00 2738 128 0.0991 0.1219 3.1495 3.2686| | 16: 1.45 - 1.42 1.00 2756 161 0.1049 0.1239 3.1319 3.2457| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1307 3.1189 3.2355| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1334 3.1037 3.2354| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1555 3.1107 3.2697| | 20: 1.34 - 1.32 1.00 2696 147 0.1363 0.1452 3.1109 3.15| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1498 3.1152 3.1026| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1971 3.1233 3.2929| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1793 3.1322 3.2016| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1839 3.128 3.2311| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2133 3.1435 3.2564| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1770 3.1489 3.2029| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2163 3.1726 3.1646| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2281 3.1676 3.1703| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2393 3.1491 3.2327| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2458 3.1442 3.1693| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.31 1.00 0.97 5697.53| | 2: 3.57 - 2.84 2888 124 0.93 12.53 1.01 0.97 5697.53| | 3: 2.83 - 2.48 2820 163 0.90 16.40 0.99 0.97 4757.60| | 4: 2.47 - 2.25 2825 136 0.92 13.28 1.00 0.98 2333.83| | 5: 2.25 - 2.09 2756 127 0.90 15.52 1.01 0.98 2333.83| | 6: 2.09 - 1.97 2846 113 0.93 12.16 1.02 0.98 1344.33| | 7: 1.97 - 1.87 2787 165 0.95 9.12 1.02 0.98 500.42| | 8: 1.87 - 1.79 2789 144 0.93 12.45 0.99 0.98 500.42| | 9: 1.79 - 1.72 2745 138 0.94 9.92 0.98 0.98 284.54| | 10: 1.72 - 1.66 2831 160 0.94 10.99 0.98 0.98 241.31| | 11: 1.66 - 1.61 2712 147 0.94 11.62 0.98 0.98 231.26| | 12: 1.61 - 1.56 2773 144 0.96 8.81 0.99 0.98 136.47| | 13: 1.56 - 1.52 2745 130 0.95 10.29 1.03 0.98 136.47| | 14: 1.52 - 1.48 2803 134 0.94 10.70 1.02 0.98 122.60| | 15: 1.48 - 1.45 2738 128 0.95 9.82 1.02 0.99 97.19| | 16: 1.45 - 1.42 2756 161 0.94 11.04 1.02 0.99 97.19| | 17: 1.42 - 1.39 2785 139 0.95 10.86 1.01 0.99 88.76| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.88| | 19: 1.36 - 1.34 2807 134 0.94 11.84 0.99 0.98 83.88| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 80.04| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.97 79.77| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.96 80.19| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.95 82.31| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.31| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.29| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.93 86.50| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.50| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 90.26| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 91.68| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.93 91.68| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.77 max = 5697.53 mean = 878.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.37| |phase err.(test): min = 0.00 max = 89.03 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1127 0.1119 0.1272 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1444 0.1440 0.1527 n_refl.: 87577 remove outliers: r(all,work,free)=0.1444 0.1440 0.1527 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1443 0.1440 0.1527 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1119 0.1274 n_refl.: 87577 remove outliers: r(all,work,free)=0.1125 0.1117 0.1274 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 88.54 80 5 0.4055 292.363 258.996 0.453 0.999 0.285 11.894-9.307 92.16 90 4 0.2353 480.183 464.882 0.867 1.002 0.233 9.237-7.194 97.73 208 7 0.2247 387.946 383.343 0.920 1.002 0.210 7.162-5.571 100.00 427 22 0.2071 296.724 286.643 0.911 1.002 0.136 5.546-4.326 100.00 867 58 0.1117 407.328 402.696 0.966 1.002 0.130 4.315-3.360 100.00 1859 96 0.0899 387.372 385.447 1.003 1.002 0.110 3.356-2.611 100.00 3867 181 0.1089 254.483 252.497 1.010 1.002 0.014 2.608-2.026 99.99 8198 413 0.0892 168.699 168.117 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.384 82.720 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.532 36.130 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2169 23.018 21.556 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 : 0.2612 0.1911 0.081 5.386 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1744 0.081 5.386 9.0 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1744 0.081 5.386 9.0 119.5 20.1 258 0.000 1_nqh: 0.1645 0.1745 0.081 5.386 9.0 119.5 20.1 258 0.003 1_weight: 0.1645 0.1745 0.081 5.386 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1208 0.1450 0.008 0.963 9.0 119.5 20.1 258 0.126 1_adp: 0.1215 0.1447 0.008 0.963 9.1 119.4 20.1 258 0.126 1_regHadp: 0.1216 0.1451 0.008 0.963 9.1 119.4 20.1 258 0.126 1_occ: 0.1210 0.1444 0.008 0.963 9.1 119.4 20.1 258 0.126 2_bss: 0.1206 0.1435 0.008 0.963 9.1 119.5 20.1 258 0.126 2_settarget: 0.1206 0.1435 0.008 0.963 9.1 119.5 20.1 258 0.126 2_updatecdl: 0.1206 0.1435 0.008 0.975 9.1 119.5 20.1 258 0.126 2_nqh: 0.1208 0.1437 0.008 0.975 9.1 119.5 20.1 258 0.128 2_sol: 0.1179 0.1384 0.008 0.975 9.1 115.2 22.4 425 n/a 2_weight: 0.1179 0.1384 0.008 0.975 9.1 115.2 22.4 425 n/a 2_xyzrec: 0.1176 0.1399 0.007 0.918 9.1 115.2 22.4 425 n/a 2_adp: 0.1176 0.1399 0.007 0.918 9.1 115.2 22.4 425 n/a 2_regHadp: 0.1176 0.1399 0.007 0.918 9.1 115.2 22.4 425 n/a 2_occ: 0.1179 0.1403 0.007 0.918 9.1 115.2 22.4 425 n/a 3_bss: 0.1176 0.1398 0.007 0.918 9.1 115.2 22.4 425 n/a 3_settarget: 0.1176 0.1398 0.007 0.918 9.1 115.2 22.4 425 n/a 3_updatecdl: 0.1176 0.1398 0.007 0.917 9.1 115.2 22.4 425 n/a 3_nqh: 0.1178 0.1397 0.007 0.917 9.1 115.2 22.4 425 n/a 3_sol: 0.1200 0.1407 0.007 0.917 9.1 115.2 21.2 435 n/a 3_weight: 0.1200 0.1407 0.007 0.917 9.1 115.2 21.2 435 n/a 3_xyzrec: 0.1156 0.1322 0.007 1.007 9.1 115.2 21.2 435 n/a 3_adp: 0.1156 0.1322 0.007 1.007 9.1 115.2 21.2 435 n/a 3_regHadp: 0.1156 0.1322 0.007 1.007 9.1 115.2 21.2 435 n/a 3_occ: 0.1146 0.1312 0.007 1.007 9.1 115.2 21.2 435 n/a 4_bss: 0.1138 0.1298 0.007 1.007 9.1 115.2 21.2 435 n/a 4_settarget: 0.1138 0.1298 0.007 1.007 9.1 115.2 21.2 435 n/a 4_updatecdl: 0.1138 0.1298 0.007 1.008 9.1 115.2 21.2 435 n/a 4_nqh: 0.1138 0.1298 0.007 1.008 9.1 115.2 21.2 435 n/a 4_sol: 0.1137 0.1292 0.007 1.008 9.1 115.2 21.3 454 n/a 4_weight: 0.1137 0.1292 0.007 1.008 9.1 115.2 21.3 454 n/a 4_xyzrec: 0.1130 0.1292 0.008 1.125 9.1 115.2 21.3 454 n/a 4_adp: 0.1130 0.1292 0.008 1.125 9.1 115.2 21.3 454 n/a 4_regHadp: 0.1130 0.1292 0.008 1.125 9.1 115.2 21.3 454 n/a 4_occ: 0.1122 0.1289 0.008 1.125 9.1 115.2 21.3 454 n/a 5_bss: 0.1120 0.1288 0.008 1.125 9.1 115.2 21.3 454 n/a 5_settarget: 0.1120 0.1288 0.008 1.125 9.1 115.2 21.3 454 n/a 5_updatecdl: 0.1120 0.1288 0.008 1.126 9.1 115.2 21.3 454 n/a 5_setrh: 0.1122 0.1288 0.008 1.126 9.1 115.2 21.3 454 n/a 5_nqh: 0.1122 0.1288 0.008 1.126 9.1 115.2 21.3 454 n/a 5_sol: 0.1124 0.1275 0.008 1.126 9.1 115.2 21.4 466 n/a 5_weight: 0.1124 0.1275 0.008 1.126 9.1 115.2 21.4 466 n/a 5_xyzrec: 0.1124 0.1275 0.008 1.133 9.1 115.2 21.4 466 n/a 5_adp: 0.1124 0.1275 0.008 1.133 9.1 115.2 21.4 466 n/a 5_regHadp: 0.1124 0.1275 0.008 1.133 9.1 115.2 21.4 466 n/a 5_occ: 0.1119 0.1272 0.008 1.133 9.1 115.2 21.4 466 n/a end: 0.1117 0.1274 0.008 1.133 9.1 115.2 21.4 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4912670_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4912670_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7100 Refinement macro-cycles (run) : 11157.3600 Write final files (write_after_run_outputs) : 92.1700 Total : 11253.2400 Total CPU time: 3.13 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:19:36 PST -0800 (1735363176.13 s) Start R-work = 0.1644, R-free = 0.1744 Final R-work = 0.1117, R-free = 0.1274 =============================================================================== Job complete usr+sys time: 11431.07 seconds wall clock time: 204 minutes 11.50 seconds (12251.50 seconds total)