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_2686906.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_2686906.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2686906.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.38, per 1000 atoms: 0.41 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: 0.29 Conformation dependent library (CDL) restraints added in 107.0 milliseconds Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 531 0.91 - 1.16: 1106 1.16 - 1.41: 612 1.41 - 1.66: 849 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.117 0.209 1.10e-02 8.26e+03 3.63e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.449 0.088 5.00e-03 4.00e+04 3.07e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.409 -0.173 9.90e-03 1.02e+04 3.06e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.029 0.208 1.19e-02 7.06e+03 3.04e+02 bond pdb=" N PRO A 43 " pdb=" CD PRO A 43 " ideal model delta sigma weight residual 1.473 1.240 0.233 1.40e-02 5.10e+03 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 3001 4.29 - 8.58: 1829 8.58 - 12.86: 754 12.86 - 17.15: 172 17.15 - 21.44: 21 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 108.11 12.72 5.90e-01 2.87e+00 4.65e+02 angle pdb=" O LYS A 148 " pdb=" C LYS A 148 " pdb=" N ASP A 149 " ideal model delta sigma weight residual 123.31 104.50 18.81 1.17e+00 7.31e-01 2.58e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 109.20 10.09 6.50e-01 2.37e+00 2.41e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 120.04 -9.52 6.70e-01 2.23e+00 2.02e+02 angle pdb=" O GLY A 137 " pdb=" C GLY A 137 " pdb=" N HIS A 138 " ideal model delta sigma weight residual 122.51 133.94 -11.43 8.10e-01 1.52e+00 1.99e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 940 17.02 - 34.04: 119 34.04 - 51.06: 36 51.06 - 68.08: 13 68.08 - 85.10: 3 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 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta harmonic sigma weight residual 180.00 -158.18 -21.82 0 5.00e+00 4.00e-02 1.90e+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 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.197: 98 0.197 - 0.393: 74 0.393 - 0.588: 50 0.588 - 0.784: 17 0.784 - 0.979: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA GLU A 143 " pdb=" N GLU A 143 " pdb=" C GLU A 143 " pdb=" CB GLU A 143 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 3.35 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.114 2.00e-02 2.50e+03 6.83e-02 1.40e+02 pdb=" CG TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.028 2.00e-02 2.50e+03 6.07e-02 1.11e+02 pdb=" CG PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.114 2.00e-02 2.50e+03 6.03e-02 1.09e+02 pdb=" CG PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 828 2.29 - 2.87: 7894 2.87 - 3.44: 10636 3.44 - 4.02: 15268 4.02 - 4.60: 21897 Nonbonded interactions: 56523 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.711 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.751 1.850 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.823 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.851 1.850 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.852 1.850 ... (remaining 56518 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_2686906_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= 0.2609 r_free= 0.1983 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793941 | | target function (ml) not normalized (work): 232752.077972 | | target function (ml) not normalized (free): 11849.171916 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2116 7.011 4.9419| | 2: 3.57 - 2.84 1.00 2876 122 0.2446 0.1798 4.3586 4.347| | 3: 2.84 - 2.48 1.00 2833 165 0.2333 0.1832 4.1335 4.1771| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1455 3.8462 3.8343| | 5: 2.25 - 2.09 1.00 2756 127 0.2458 0.1546 3.8071 3.8365| | 6: 2.09 - 1.97 1.00 2846 113 0.2549 0.1808 3.4801 3.5477| | 7: 1.97 - 1.87 1.00 2787 165 0.2570 0.1963 3.1632 3.2588| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.2050 3.0974 3.2009| | 9: 1.79 - 1.72 1.00 2745 138 0.2403 0.1732 2.9112 2.9047| | 10: 1.72 - 1.66 1.00 2789 158 0.2429 0.2203 2.8133 2.9575| | 11: 1.66 - 1.61 1.00 2740 147 0.2454 0.1753 2.7588 2.744| | 12: 1.61 - 1.56 1.00 2787 146 0.2526 0.1847 2.6151 2.5872| | 13: 1.56 - 1.52 1.00 2745 130 0.2553 0.1947 2.5625 2.6244| | 14: 1.52 - 1.48 1.00 2803 134 0.2554 0.1927 2.5024 2.544| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2148 2.4293 2.4602| | 16: 1.45 - 1.42 1.00 2756 161 0.2649 0.2293 2.3795 2.4643| | 17: 1.42 - 1.39 1.00 2785 139 0.2696 0.1943 2.3285 2.3322| | 18: 1.39 - 1.36 1.00 2741 179 0.2736 0.2229 2.2812 2.3427| | 19: 1.36 - 1.34 1.00 2807 134 0.2699 0.2639 2.2692 2.3952| | 20: 1.34 - 1.32 1.00 2696 147 0.2703 0.2160 2.206 2.1867| | 21: 1.32 - 1.30 1.00 2785 112 0.2680 0.2421 2.1603 2.2414| | 22: 1.29 - 1.27 1.00 2704 152 0.2703 0.2570 2.1299 2.2129| | 23: 1.27 - 1.26 1.00 2802 156 0.2779 0.2608 2.114 2.2077| | 24: 1.26 - 1.24 1.00 2744 132 0.2725 0.2220 2.0649 2.0586| | 25: 1.24 - 1.22 1.00 2734 148 0.2841 0.2545 2.0501 2.0764| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2232 2.007 2.0675| | 27: 1.21 - 1.19 1.00 2814 148 0.2951 0.2793 2.0077 2.0148| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.3147 1.9873 2.0577| | 29: 1.18 - 1.16 1.00 2800 134 0.2985 0.2751 1.9635 1.9975| | 30: 1.16 - 1.15 1.00 2740 148 0.3066 0.2797 1.9249 1.9537| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1501.11| | 2: 3.57 - 2.84 2876 122 0.80 26.35 1.27 0.23 1501.11| | 3: 2.84 - 2.48 2833 165 0.74 32.23 1.24 0.23 1247.02| | 4: 2.47 - 2.25 2825 136 0.81 25.97 1.26 0.25 587.62| | 5: 2.25 - 2.09 2756 127 0.77 29.63 1.28 0.25 587.62| | 6: 2.09 - 1.97 2846 113 0.83 23.28 1.29 0.25 325.09| | 7: 1.97 - 1.87 2787 165 0.89 17.48 1.28 0.26 101.18| | 8: 1.87 - 1.79 2789 144 0.85 22.20 1.24 0.26 101.18| | 9: 1.79 - 1.72 2745 138 0.87 19.20 1.23 0.25 59.64| | 10: 1.72 - 1.66 2789 158 0.86 20.99 1.22 0.25 51.32| | 11: 1.66 - 1.61 2740 147 0.85 21.88 1.23 0.25 49.35| | 12: 1.61 - 1.56 2787 146 0.88 18.66 1.24 0.25 29.35| | 13: 1.56 - 1.52 2745 130 0.86 20.51 1.24 0.25 29.35| | 14: 1.52 - 1.48 2803 134 0.86 20.69 1.23 0.25 26.30| | 15: 1.48 - 1.45 2738 128 0.87 20.36 1.23 0.25 20.70| | 16: 1.45 - 1.42 2756 161 0.86 21.70 1.24 0.25 20.70| | 17: 1.42 - 1.39 2785 139 0.86 21.08 1.23 0.25 17.76| | 18: 1.39 - 1.36 2741 179 0.86 21.57 1.23 0.25 16.06| | 19: 1.36 - 1.34 2807 134 0.85 22.19 1.22 0.25 16.06| | 20: 1.34 - 1.32 2696 147 0.86 21.43 1.21 0.24 13.54| | 21: 1.32 - 1.30 2785 112 0.85 22.43 1.20 0.24 13.37| | 22: 1.29 - 1.27 2704 152 0.85 22.97 1.21 0.24 13.05| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.21 0.24 11.43| | 24: 1.26 - 1.24 2744 132 0.85 23.20 1.20 0.24 11.43| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.87| | 26: 1.22 - 1.21 2727 135 0.83 24.47 1.19 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.82 25.47 1.20 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.82 26.19 1.18 0.23 9.67| | 29: 1.18 - 1.16 2800 134 0.82 26.42 1.17 0.22 9.45| | 30: 1.16 - 1.15 2740 148 0.80 28.06 1.16 0.22 9.45| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.45 max = 1501.11 mean = 219.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.07| |phase err.(test): min = 0.00 max = 89.93 mean = 23.06| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.248 1557 Z= 5.529 Angle : 5.240 18.808 2118 Z= 3.762 Chirality : 0.353 0.979 243 Planarity : 0.034 0.118 284 Dihedral : 13.585 85.097 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 27.03 % 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: -3.08 (0.48), residues: 224 helix: -2.85 (0.38), residues: 109 sheet: -1.23 (0.83), residues: 28 loop : -0.84 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.017 ARG A 98 TYR 0.136 0.046 TYR A 141 PHE 0.093 0.046 PHE A 119 HIS 0.062 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2609 r_free= 0.1983 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793941 | | target function (ml) not normalized (work): 232752.077972 | | target function (ml) not normalized (free): 11849.171916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2610 0.1984 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2610 0.1984 n_refl.: 87602 remove outliers: r(all,work,free)=0.1989 0.1991 0.1984 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2014 0.2017 0.1998 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1644 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1643 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 0.3718 386.415 360.393 0.722 0.929 0.401 11.894-9.307 99.02 97 4 0.1850 613.801 591.909 1.000 0.930 0.380 9.237-7.194 100.00 213 7 0.2204 502.014 491.144 1.028 0.930 0.370 7.162-5.571 100.00 427 22 0.2199 376.733 364.706 1.007 0.930 0.320 5.546-4.326 100.00 867 58 0.1312 517.162 511.370 1.042 0.930 0.259 4.315-3.360 100.00 1859 96 0.1139 491.824 488.431 1.084 0.930 0.158 3.356-2.611 100.00 3867 181 0.1456 323.103 319.370 1.072 0.930 0.129 2.608-2.026 99.99 8198 413 0.1355 214.188 211.799 1.084 0.929 0.000 2.025-1.573 100.00 17313 902 0.1655 104.598 103.870 1.088 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.383 45.086 1.079 0.926 0.000 1.221-1.150 99.97 13689 708 0.2593 29.225 26.957 1.050 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0485 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 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 Total number of N/Q/H flips: 1 r_work=0.1647 r_free=0.1791 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.287818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1983.038123 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 0.1557 0.1683 0.0126 0.002 0.5 3.8 0.0 0.0 0 0.125 0.1519 0.1657 0.0138 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1435 0.1595 0.0159 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1364 0.1542 0.0178 0.002 0.5 2.9 0.0 0.0 0 0.750 0.1321 0.1509 0.0188 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1357 0.1549 0.0192 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1282 0.1496 0.0214 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1265 0.1489 0.0224 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1252 0.1486 0.0234 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1241 0.1481 0.0240 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1235 0.1477 0.0242 0.005 0.8 2.6 0.5 0.0 0 6.000 0.1237 0.1481 0.0245 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1232 0.1475 0.0243 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1228 0.1473 0.0246 0.006 0.9 2.9 0.5 0.0 0 9.000 0.1232 0.1480 0.0248 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1477 0.0249 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1473 0.0246 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1223 0.1471 0.0247 0.007 1.0 3.8 0.5 0.6 0 13.000 0.1221 0.1469 0.0248 0.008 1.0 4.2 0.5 0.6 0 14.144 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1469 0.0248 0.008 1.0 4.2 0.5 0.6 0 14.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.69 2.48 3.013 19.071 1983.038 0.017 12.21 14.68 2.47 3.008 19.071 59.491 0.017 12.27 14.66 2.39 2.694 19.068 247.880 0.017 12.66 15.33 2.67 2.761 19.229 991.519 0.016 12.47 15.49 3.02 3.196 19.553 1983.038 0.016 12.34 15.43 3.09 3.206 19.565 2974.557 0.015 12.27 15.43 3.16 3.367 19.654 3966.076 0.015 12.23 15.41 3.18 3.354 19.631 4957.595 0.015 12.22 15.48 3.26 3.340 19.621 5949.114 0.015 12.12 15.41 3.29 3.337 19.617 6940.633 0.015 12.08 15.36 3.28 3.337 19.605 7932.152 0.015 12.12 15.43 3.31 3.368 19.608 8923.672 0.015 12.07 15.41 3.35 3.446 19.644 9915.191 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: 247.880 Accepted refinement result: 12.27 14.66 2.39 2.694 19.068 247.880 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.47 20.09 3.36 0 1785 Protein: 9.08 115.25 17.00 3.37 0 1519 Water: 11.49 119.47 38.24 N/A 0 258 Other: 19.66 26.61 22.04 N/A 0 8 Chain A: 9.08 119.47 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1273 20.12 - 31.16 227 31.16 - 42.20 124 42.20 - 53.24 95 53.24 - 64.27 41 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1466 r_work=0.1228 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1228 r_free = 0.1469 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 = 0.1221 r_free = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1221 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016644 | | target function (ls_wunit_k1) not normalized (work): 1386.374112 | | target function (ls_wunit_k1) not normalized (free): 109.838561 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1221 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1672 0.1673 0.1701 n_refl.: 87593 remove outliers: r(all,work,free)=0.1672 0.1673 0.1701 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1678 0.1679 0.1705 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1232 0.1220 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1231 0.1220 0.1457 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3474 301.322 281.746 0.653 1.003 0.380 11.894-9.307 99.02 97 4 0.1655 482.702 470.473 0.922 1.003 0.371 9.237-7.194 100.00 213 7 0.1829 394.790 389.835 0.962 1.004 0.350 7.162-5.571 100.00 427 22 0.1806 296.268 290.535 0.939 1.003 0.276 5.546-4.326 100.00 867 58 0.0990 406.703 403.912 0.967 1.003 0.250 4.315-3.360 100.00 1859 96 0.0867 386.778 385.688 1.007 1.003 0.170 3.356-2.611 100.00 3867 181 0.1168 254.093 252.931 1.008 1.002 0.110 2.608-2.026 99.99 8198 413 0.1021 168.440 167.707 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.257 82.458 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.476 35.984 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2245 22.983 21.467 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0462 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1457 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1221 r_free=0.1457 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1457 | n_water=258 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1231 r_free=0.1455 | n_water=250 | time (s): 21.940 (total time: 23.670) Filter (q & B) r_work=0.1233 r_free=0.1454 | n_water=247 | time (s): 2.660 (total time: 26.330) Compute maps r_work=0.1233 r_free=0.1454 | n_water=247 | time (s): 1.250 (total time: 27.580) Filter (map) r_work=0.1248 r_free=0.1463 | n_water=224 | time (s): 2.850 (total time: 30.430) Find peaks r_work=0.1248 r_free=0.1463 | n_water=224 | time (s): 0.490 (total time: 30.920) Add new water r_work=0.1401 r_free=0.1636 | n_water=422 | time (s): 2.580 (total time: 33.500) Refine new water occ: r_work=0.1306 r_free=0.1503 adp: r_work=0.1224 r_free=0.1450 occ: r_work=0.1235 r_free=0.1431 adp: r_work=0.1201 r_free=0.1417 occ: r_work=0.1203 r_free=0.1405 adp: r_work=0.1192 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1404 r_work=0.1192 r_free=0.1404 | n_water=422 | time (s): 58.380 (total time: 91.880) Filter (q & B) r_work=0.1194 r_free=0.1404 | n_water=411 | time (s): 2.780 (total time: 94.660) Filter (dist only) r_work=0.1194 r_free=0.1403 | n_water=410 | time (s): 35.840 (total time: 130.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.642636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.097585 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 0.1705 0.1815 0.0110 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1526 0.1664 0.0138 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1409 0.1568 0.0160 0.002 0.5 6.7 0.0 0.0 0 0.500 0.1352 0.1524 0.0172 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1312 0.1496 0.0185 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1311 0.1494 0.0183 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1259 0.1468 0.0210 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1229 0.1450 0.0221 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1216 0.1439 0.0224 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1204 0.1430 0.0226 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1200 0.1432 0.0232 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1196 0.1432 0.0236 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1192 0.1431 0.0238 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1190 0.1431 0.0241 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1188 0.1424 0.0236 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1187 0.1422 0.0235 0.007 0.9 5.4 0.5 0.6 0 11.000 0.1185 0.1419 0.0234 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1184 0.1416 0.0232 0.008 0.9 5.4 0.5 0.6 0 13.000 0.1182 0.1412 0.0230 0.008 0.9 6.1 0.5 0.6 0 14.321 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1412 0.0230 0.008 0.9 6.1 0.5 0.6 0 14.321 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 14.12 2.30 3.799 21.720 1498.098 0.015 11.82 14.12 2.30 3.799 21.720 44.943 0.015 11.82 14.12 2.30 3.799 21.720 187.262 0.015 11.96 14.47 2.52 3.652 21.721 749.049 0.015 12.03 14.87 2.84 3.565 21.788 1498.098 0.015 11.83 14.75 2.92 3.478 22.068 2247.146 0.014 11.71 14.68 2.97 3.457 21.988 2996.195 0.014 11.71 14.76 3.05 3.482 22.045 3745.244 0.014 11.65 14.78 3.12 3.522 21.905 4494.293 0.014 11.66 14.85 3.19 3.534 22.041 5243.342 0.013 11.67 14.90 3.23 3.559 22.119 5992.390 0.013 11.59 14.77 3.18 3.539 21.983 6741.439 0.013 11.59 14.75 3.16 3.549 22.054 7490.488 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: 44.943 Accepted refinement result: 11.82 14.12 2.30 3.799 21.720 44.943 0.015 Individual atomic B min max mean iso aniso Overall: 9.11 115.28 22.07 3.36 186 1751 Protein: 9.11 115.28 17.03 3.37 0 1519 Water: 11.52 76.73 40.76 N/A 186 224 Other: 19.69 26.64 22.07 N/A 0 8 Chain A: 9.11 115.28 19.43 N/A 0 1751 Chain S: 16.86 60.00 46.95 N/A 186 0 Histogram: Values Number of atoms 9.11 - 19.73 1260 19.73 - 30.34 244 30.34 - 40.96 166 40.96 - 51.58 129 51.58 - 62.20 115 62.20 - 72.81 12 72.81 - 83.43 5 83.43 - 94.05 4 94.05 - 104.67 0 104.67 - 115.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1412 r_work=0.1182 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1416 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1181 r_free= 0.1416 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014757 | | target function (ls_wunit_k1) not normalized (work): 1229.198185 | | target function (ls_wunit_k1) not normalized (free): 103.116187 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1181 0.1416 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1594 0.1593 0.1632 n_refl.: 87592 remove outliers: r(all,work,free)=0.1594 0.1593 0.1632 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1595 0.1595 0.1633 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1177 0.1410 n_refl.: 87592 remove outliers: r(all,work,free)=0.1187 0.1176 0.1410 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3170 297.561 278.389 0.599 1.003 0.350 11.894-9.307 99.02 97 4 0.1605 482.702 475.358 0.920 1.003 0.330 9.237-7.194 100.00 213 7 0.1666 394.790 395.076 0.984 1.003 0.280 7.162-5.571 100.00 427 22 0.1592 296.268 292.473 0.944 1.003 0.240 5.546-4.326 100.00 867 58 0.0860 406.703 403.723 0.961 1.003 0.230 4.315-3.360 100.00 1859 96 0.0770 386.778 385.989 1.005 1.003 0.180 3.356-2.611 100.00 3867 181 0.1071 254.093 253.310 1.008 1.002 0.110 2.608-2.026 99.99 8198 413 0.1015 168.440 167.942 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1092 82.257 82.500 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1436 36.476 36.016 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 22.983 21.491 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0122 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1410 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1176 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1410 | n_water=410 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1177 r_free=0.1404 | n_water=406 | time (s): 35.770 (total time: 37.940) Filter (q & B) r_work=0.1177 r_free=0.1404 | n_water=406 | time (s): 1.170 (total time: 39.110) Compute maps r_work=0.1177 r_free=0.1404 | n_water=406 | time (s): 1.360 (total time: 40.470) Filter (map) r_work=0.1220 r_free=0.1392 | n_water=279 | time (s): 2.820 (total time: 43.290) Find peaks r_work=0.1220 r_free=0.1392 | n_water=279 | time (s): 0.500 (total time: 43.790) Add new water r_work=0.1345 r_free=0.1520 | n_water=466 | time (s): 2.460 (total time: 46.250) Refine new water occ: r_work=0.1243 r_free=0.1437 adp: r_work=0.1245 r_free=0.1440 occ: r_work=0.1218 r_free=0.1414 adp: r_work=0.1218 r_free=0.1416 occ: r_work=0.1198 r_free=0.1395 adp: r_work=0.1194 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1394 r_work=0.1194 r_free=0.1394 | n_water=466 | time (s): 163.610 (total time: 209.860) Filter (q & B) r_work=0.1198 r_free=0.1400 | n_water=441 | time (s): 3.430 (total time: 213.290) Filter (dist only) r_work=0.1198 r_free=0.1398 | n_water=439 | time (s): 37.810 (total time: 251.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.788044 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.037842 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 0.1228 0.1368 0.0140 0.002 0.6 5.1 0.5 0.0 0 0.089 0.1189 0.1331 0.0142 0.003 0.7 3.8 0.5 0.0 0 0.268 0.1172 0.1318 0.0146 0.004 0.8 3.5 0.5 0.0 0 0.536 0.1164 0.1314 0.0151 0.005 0.9 3.5 0.5 0.0 0 0.805 0.1159 0.1314 0.0154 0.006 1.0 3.8 0.5 0.0 0 1.073 0.1156 0.1312 0.0156 0.007 1.0 3.8 0.5 0.0 0 1.341 0.1155 0.1315 0.0161 0.007 1.1 3.5 0.5 0.0 0 1.609 0.1152 0.1312 0.0160 0.008 1.1 3.5 0.5 0.6 0 1.877 0.1162 0.1315 0.0153 0.005 0.9 3.5 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1312 0.0156 0.007 1.0 3.8 0.5 0.0 0 1.341 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.12 1.56 3.802 21.273 47.038 3.619 11.56 13.12 1.56 3.802 21.273 1.411 3.619 11.57 13.12 1.56 3.791 21.273 5.880 3.619 11.63 13.20 1.57 3.728 21.257 23.519 3.615 11.63 13.26 1.63 3.749 21.231 47.038 3.614 11.57 13.24 1.67 3.769 21.219 70.557 3.609 11.54 13.23 1.69 3.782 21.212 94.076 3.606 11.52 13.24 1.72 3.791 21.204 117.595 3.603 11.48 13.21 1.73 3.803 21.202 141.114 3.601 11.47 13.23 1.76 3.818 21.189 164.632 3.600 11.45 13.22 1.76 3.828 21.182 188.151 3.599 11.44 13.20 1.77 3.834 21.182 211.670 3.598 11.43 13.20 1.77 3.840 21.173 235.189 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.411 Accepted refinement result: 11.56 13.12 1.56 3.802 21.273 1.411 3.619 Individual atomic B min max mean iso aniso Overall: 9.12 115.29 21.25 3.36 220 1746 Protein: 9.12 115.29 17.04 3.37 0 1519 Water: 11.52 76.73 35.80 N/A 220 219 Other: 19.70 26.65 22.08 N/A 0 8 Chain A: 9.12 115.29 19.36 N/A 0 1746 Chain S: 16.58 60.01 36.25 N/A 220 0 Histogram: Values Number of atoms 9.12 - 19.73 1265 19.73 - 30.35 285 30.35 - 40.97 212 40.97 - 51.59 128 51.59 - 62.20 53 62.20 - 72.82 12 72.82 - 83.44 5 83.44 - 94.06 4 94.06 - 104.67 0 104.67 - 115.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1312 r_work=0.1156 r_free=0.1312 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1312 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1308 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1148 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613096 | | target function (ml) not normalized (work): 300945.607993 | | target function (ml) not normalized (free): 15843.338201 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1148 0.1308 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1492 0.1491 0.1538 n_refl.: 87589 remove outliers: r(all,work,free)=0.1492 0.1491 0.1538 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1491 0.1490 0.1537 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1144 0.1305 n_refl.: 87589 remove outliers: r(all,work,free)=0.1149 0.1141 0.1305 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 90.62 82 5 0.3817 296.567 268.041 0.502 1.001 0.324 11.894-9.307 99.02 97 4 0.2335 482.702 469.591 0.881 1.002 0.320 9.237-7.194 98.18 209 7 0.2227 386.267 385.859 0.960 1.002 0.214 7.162-5.571 100.00 427 22 0.2056 296.268 287.410 0.929 1.002 0.190 5.546-4.326 100.00 867 58 0.1113 406.703 402.167 0.964 1.002 0.170 4.315-3.360 100.00 1859 96 0.0938 386.778 384.327 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1124 254.093 252.012 1.007 1.002 0.038 2.608-2.026 99.99 8198 413 0.0932 168.440 167.626 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0902 82.257 82.547 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.476 36.058 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.983 21.522 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0151 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1305 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=0.1141 r_free=0.1305 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1305 | n_water=439 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1141 r_free=0.1305 | n_water=439 | time (s): 44.670 (total time: 47.260) Filter (q & B) r_work=0.1141 r_free=0.1305 | n_water=439 | time (s): 1.450 (total time: 48.710) Compute maps r_work=0.1141 r_free=0.1305 | n_water=439 | time (s): 2.020 (total time: 50.730) Filter (map) r_work=0.1161 r_free=0.1301 | n_water=333 | time (s): 3.910 (total time: 54.640) Find peaks r_work=0.1161 r_free=0.1301 | n_water=333 | time (s): 0.700 (total time: 55.340) Add new water r_work=0.1240 r_free=0.1385 | n_water=504 | time (s): 3.840 (total time: 59.180) Refine new water occ: r_work=0.1168 r_free=0.1321 adp: r_work=0.1169 r_free=0.1325 occ: r_work=0.1152 r_free=0.1302 adp: r_work=0.1151 r_free=0.1305 occ: r_work=0.1139 r_free=0.1286 adp: r_work=0.1135 r_free=0.1287 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1287 r_work=0.1135 r_free=0.1287 | n_water=504 | time (s): 254.660 (total time: 313.840) Filter (q & B) r_work=0.1141 r_free=0.1284 | n_water=464 | time (s): 4.030 (total time: 317.870) Filter (dist only) r_work=0.1141 r_free=0.1283 | n_water=463 | time (s): 49.130 (total time: 367.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.732368 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.521498 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 0.1202 0.1328 0.0126 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1166 0.1300 0.0134 0.003 0.7 3.8 0.5 0.0 0 0.260 0.1151 0.1290 0.0139 0.005 0.9 4.2 0.5 0.0 0 0.520 0.1146 0.1294 0.0148 0.006 0.9 4.2 0.5 0.0 0 0.780 0.1142 0.1289 0.0147 0.006 1.0 4.5 0.5 0.0 0 1.039 0.1139 0.1287 0.0148 0.007 1.0 4.5 0.5 0.0 0 1.299 0.1136 0.1285 0.0148 0.008 1.1 4.2 0.5 0.0 0 1.559 0.1135 0.1286 0.0151 0.008 1.1 4.5 0.5 0.0 0 1.819 0.1142 0.1284 0.0141 0.006 1.0 4.5 0.5 0.0 0 0.866 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1142 0.1284 0.0141 0.006 1.0 4.5 0.5 0.0 0 0.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.42 12.84 1.41 3.803 21.301 38.521 3.608 11.42 12.84 1.41 3.802 21.301 1.156 3.608 11.42 12.84 1.41 3.802 21.301 4.815 3.608 11.47 12.87 1.40 3.725 21.295 19.261 3.604 11.52 13.00 1.48 3.742 21.277 38.521 3.608 11.49 13.00 1.51 3.745 21.265 57.782 3.604 11.42 12.97 1.55 3.769 21.258 77.043 3.599 11.39 12.95 1.56 3.781 21.256 96.304 3.596 11.36 12.92 1.55 3.787 21.254 115.564 3.593 11.34 12.91 1.57 3.796 21.252 134.825 3.591 11.35 12.97 1.62 3.809 21.241 154.086 3.592 11.33 12.95 1.63 3.818 21.240 173.347 3.591 11.32 12.95 1.63 3.826 21.238 192.607 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: 4.815 Accepted refinement result: 11.42 12.84 1.41 3.802 21.301 4.815 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 115.28 21.30 3.36 244 1746 Protein: 9.11 115.28 17.03 3.37 0 1519 Water: 11.52 76.73 35.29 N/A 244 219 Other: 19.69 26.64 22.07 N/A 0 8 Chain A: 9.11 115.28 19.35 N/A 0 1746 Chain S: 16.87 60.00 35.26 N/A 244 0 Histogram: Values Number of atoms 9.11 - 19.73 1267 19.73 - 30.35 301 30.35 - 40.96 220 40.96 - 51.58 125 51.58 - 62.20 54 62.20 - 72.82 12 72.82 - 83.43 5 83.43 - 94.05 4 94.05 - 104.67 0 104.67 - 115.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1142 r_free=0.1284 r_work=0.1142 r_free=0.1284 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1142 r_free = 0.1284 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1281 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 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= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605053 | | target function (ml) not normalized (work): 300254.074116 | | target function (ml) not normalized (free): 15801.030359 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1136 0.1281 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1474 0.1474 0.1500 n_refl.: 87583 remove outliers: r(all,work,free)=0.1474 0.1474 0.1500 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1473 0.1473 0.1500 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1283 n_refl.: 87583 remove outliers: r(all,work,free)=0.1138 0.1130 0.1283 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 0.3816 288.429 257.209 0.463 1.000 0.307 11.894-9.307 93.14 91 4 0.2310 467.067 454.367 0.862 1.002 0.233 9.237-7.194 97.73 208 7 0.2321 387.350 378.962 0.932 1.002 0.180 7.162-5.571 100.00 427 22 0.2112 296.268 287.092 0.921 1.002 0.156 5.546-4.326 100.00 867 58 0.1134 406.703 402.533 0.964 1.002 0.145 4.315-3.360 100.00 1859 96 0.0909 386.778 384.847 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1107 254.093 252.175 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0911 168.440 167.807 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.257 82.606 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.476 36.083 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.983 21.526 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0112 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1130 r_free=0.1283 After: r_work=0.1131 r_free=0.1282 ================================== NQH flips ================================== r_work=0.1131 r_free=0.1282 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=0.1131 r_free=0.1282 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1131 r_free=0.1282 | n_water=463 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1131 r_free=0.1282 | n_water=463 | time (s): 47.090 (total time: 49.550) Filter (q & B) r_work=0.1131 r_free=0.1283 | n_water=462 | time (s): 3.730 (total time: 53.280) Compute maps r_work=0.1131 r_free=0.1283 | n_water=462 | time (s): 1.820 (total time: 55.100) Filter (map) r_work=0.1159 r_free=0.1301 | n_water=355 | time (s): 3.820 (total time: 58.920) Find peaks r_work=0.1159 r_free=0.1301 | n_water=355 | time (s): 0.700 (total time: 59.620) Add new water r_work=0.1215 r_free=0.1360 | n_water=512 | time (s): 3.730 (total time: 63.350) Refine new water occ: r_work=0.1156 r_free=0.1304 adp: r_work=0.1156 r_free=0.1307 occ: r_work=0.1143 r_free=0.1289 adp: r_work=0.1142 r_free=0.1292 occ: r_work=0.1133 r_free=0.1277 adp: r_work=0.1130 r_free=0.1278 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1278 r_work=0.1130 r_free=0.1278 | n_water=512 | time (s): 224.770 (total time: 288.120) Filter (q & B) r_work=0.1136 r_free=0.1282 | n_water=469 | time (s): 3.940 (total time: 292.060) Filter (dist only) r_work=0.1136 r_free=0.1282 | n_water=467 | time (s): 49.630 (total time: 341.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.814218 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.295427 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 0.1209 0.1328 0.0118 0.003 0.7 6.7 0.0 0.0 0 0.091 0.1162 0.1296 0.0133 0.004 0.8 5.8 0.0 0.0 0 0.272 0.1143 0.1283 0.0141 0.005 0.9 5.4 0.5 0.0 0 0.544 0.1137 0.1281 0.0144 0.006 1.0 5.4 0.5 0.0 0 0.816 0.1135 0.1281 0.0145 0.006 1.0 5.1 0.5 0.0 0 1.089 0.1134 0.1280 0.0147 0.007 1.0 5.1 0.5 0.0 0 1.361 0.1132 0.1280 0.0148 0.008 1.1 5.1 0.5 0.0 0 1.633 0.1131 0.1279 0.0149 0.008 1.1 5.1 0.5 0.0 0 1.905 0.1136 0.1281 0.0145 0.006 1.0 5.4 0.5 0.0 0 0.907 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1279 0.0149 0.008 1.1 5.1 0.5 0.0 0 1.905 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.79 1.49 3.802 21.268 38.295 3.600 11.31 12.79 1.49 3.802 21.268 1.149 3.600 11.31 12.79 1.49 3.801 21.268 4.787 3.600 11.34 12.83 1.49 3.728 21.263 19.148 3.596 11.41 12.96 1.55 3.742 21.242 38.295 3.601 11.37 12.98 1.61 3.754 21.228 57.443 3.597 11.30 12.92 1.62 3.773 21.223 76.591 3.591 11.27 12.90 1.63 3.783 21.221 95.739 3.589 11.24 12.88 1.64 3.790 21.220 114.886 3.586 11.22 12.87 1.65 3.799 21.218 134.034 3.585 11.22 12.90 1.68 3.811 21.210 153.182 3.584 11.20 12.89 1.69 3.818 21.208 172.329 3.583 11.19 12.89 1.70 3.826 21.208 191.477 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.149 Accepted refinement result: 11.31 12.79 1.49 3.802 21.268 1.149 3.600 Individual atomic B min max mean iso aniso Overall: 9.11 115.28 21.25 3.36 251 1743 Protein: 9.11 115.28 17.03 3.37 0 1519 Water: 11.51 76.72 34.95 N/A 251 216 Other: 19.69 26.64 22.07 N/A 0 8 Chain A: 9.11 115.28 19.28 N/A 0 1743 Chain S: 15.97 60.00 34.90 N/A 251 0 Histogram: Values Number of atoms 9.11 - 19.72 1267 19.72 - 30.34 305 30.34 - 40.96 223 40.96 - 51.58 128 51.58 - 62.19 49 62.19 - 72.81 11 72.81 - 83.43 5 83.43 - 94.05 4 94.05 - 104.66 0 104.66 - 115.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1279 r_work=0.1131 r_free=0.1279 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1279 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1276 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1276 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598203 | | target function (ml) not normalized (work): 299647.542810 | | target function (ml) not normalized (free): 15787.932549 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1327 0.1347 5.6341 5.6042| | 2: 3.57 - 2.84 1.00 2888 124 0.1053 0.1285 5.1508 5.1769| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1179 4.9313 4.9636| | 4: 2.47 - 2.25 1.00 2825 136 0.0896 0.1008 4.618 4.6513| | 5: 2.25 - 2.09 1.00 2756 127 0.0871 0.0966 4.5643 4.6175| | 6: 2.09 - 1.97 1.00 2846 113 0.0853 0.1035 4.2586 4.3552| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1088 3.9715 4.0807| | 8: 1.87 - 1.79 1.00 2789 144 0.0893 0.1126 3.8793 3.9995| | 9: 1.79 - 1.72 1.00 2745 138 0.0862 0.1140 3.6378 3.8006| | 10: 1.72 - 1.66 1.00 2831 160 0.0909 0.1192 3.5563 3.7035| | 11: 1.66 - 1.61 1.00 2712 147 0.0861 0.1020 3.4892 3.5667| | 12: 1.61 - 1.56 1.00 2773 144 0.0894 0.1130 3.3236 3.4535| | 13: 1.56 - 1.52 1.00 2745 130 0.0938 0.1027 3.3006 3.3863| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1026 3.2357 3.3206| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1210 3.1497 3.2569| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1280 3.1315 3.2569| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1290 3.1161 3.2242| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1332 3.1012 3.2379| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1558 3.1088 3.2644| | 20: 1.34 - 1.32 1.00 2696 147 0.1359 0.1455 3.1083 3.152| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1522 3.1133 3.1154| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1960 3.1199 3.2858| | 23: 1.27 - 1.26 1.00 2802 156 0.1640 0.1813 3.1312 3.2065| | 24: 1.26 - 1.24 1.00 2744 132 0.1704 0.1812 3.1247 3.221| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2147 3.1409 3.2604| | 26: 1.22 - 1.21 1.00 2727 135 0.1900 0.1775 3.1453 3.204| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2164 3.1682 3.1627| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2308 3.1657 3.1721| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2384 3.1472 3.2276| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2459 3.1429 3.1683| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2915 171 0.95 8.21 1.00 0.97 5521.12| | 2: 3.57 - 2.84 2888 124 0.93 12.14 1.01 0.97 5521.12| | 3: 2.83 - 2.48 2820 163 0.90 16.12 0.99 0.97 4616.15| | 4: 2.47 - 2.25 2825 136 0.92 13.21 1.00 0.98 2282.54| | 5: 2.25 - 2.09 2756 127 0.91 15.36 1.01 0.98 2282.54| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.98 1324.85| | 7: 1.97 - 1.87 2787 165 0.95 9.24 1.02 0.98 508.07| | 8: 1.87 - 1.79 2789 144 0.93 12.60 1.00 0.98 508.07| | 9: 1.79 - 1.72 2745 138 0.94 9.94 0.98 0.97 286.74| | 10: 1.72 - 1.66 2831 160 0.94 11.06 0.98 0.97 242.41| | 11: 1.66 - 1.61 2712 147 0.94 11.65 0.98 0.97 232.28| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.97 136.74| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.03 0.97 136.74| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 122.85| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.98 97.42| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.98 97.42| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 88.92| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.99| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 83.99| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.97 79.96| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.96 79.67| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.07| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.95 82.09| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.95 82.09| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.08| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.03 0.93 86.29| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.29| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.15| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 91.60| | 30: 1.16 - 1.15 2739 148 0.86 22.04 0.98 0.92 91.60| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.67 max = 5521.12 mean = 857.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.37| |phase err.(test): min = 0.00 max = 89.76 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1126 0.1276 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1445 0.1445 0.1480 n_refl.: 87573 remove outliers: r(all,work,free)=0.1445 0.1445 0.1480 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1444 0.1444 0.1479 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1126 0.1278 n_refl.: 87573 remove outliers: r(all,work,free)=0.1132 0.1125 0.1278 n_refl.: 87570 ======================== 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 0.3961 288.429 253.532 0.439 0.999 0.287 11.894-9.307 90.20 88 4 0.2185 469.608 449.262 0.848 1.001 0.209 9.237-7.194 97.73 208 7 0.2322 387.350 379.310 0.927 1.002 0.160 7.162-5.571 100.00 427 22 0.2147 296.268 286.754 0.916 1.002 0.147 5.546-4.326 100.00 867 58 0.1132 406.703 402.256 0.963 1.002 0.133 4.315-3.360 100.00 1859 96 0.0916 386.778 384.885 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1102 254.093 252.345 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0907 168.440 167.822 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.257 82.621 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.476 36.092 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 22.983 21.540 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0154 ================= 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 : 0.2609 0.1983 0.083 5.240 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1788 0.083 5.240 9.1 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1788 0.083 5.240 9.1 119.5 20.1 258 0.000 1_nqh: 0.1647 0.1791 0.083 5.240 9.1 119.5 20.1 258 0.003 1_weight: 0.1647 0.1791 0.083 5.240 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1221 0.1469 0.008 0.973 9.1 119.5 20.1 258 0.135 1_adp: 0.1227 0.1466 0.008 0.973 9.1 119.5 20.1 258 0.135 1_regHadp: 0.1228 0.1469 0.008 0.973 9.1 119.5 20.1 258 0.135 1_occ: 0.1221 0.1463 0.008 0.973 9.1 119.5 20.1 258 0.135 2_bss: 0.1220 0.1457 0.008 0.973 9.1 119.5 20.1 258 0.135 2_settarget: 0.1220 0.1457 0.008 0.973 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1220 0.1457 0.008 0.979 9.1 119.5 20.1 258 0.135 2_nqh: 0.1221 0.1457 0.008 0.979 9.1 119.5 20.1 258 0.138 2_sol: 0.1194 0.1403 0.008 0.979 9.1 115.3 22.1 410 n/a 2_weight: 0.1194 0.1403 0.008 0.979 9.1 115.3 22.1 410 n/a 2_xyzrec: 0.1182 0.1412 0.008 0.943 9.1 115.3 22.1 410 n/a 2_adp: 0.1182 0.1412 0.008 0.943 9.1 115.3 22.1 410 n/a 2_regHadp: 0.1182 0.1412 0.008 0.943 9.1 115.3 22.1 410 n/a 2_occ: 0.1181 0.1416 0.008 0.943 9.1 115.3 22.1 410 n/a 3_bss: 0.1176 0.1410 0.008 0.943 9.1 115.3 22.1 410 n/a 3_settarget: 0.1176 0.1410 0.008 0.943 9.1 115.3 22.1 410 n/a 3_updatecdl: 0.1176 0.1410 0.008 0.943 9.1 115.3 22.1 410 n/a 3_nqh: 0.1176 0.1410 0.008 0.943 9.1 115.3 22.1 410 n/a 3_sol: 0.1198 0.1398 0.008 0.943 9.1 115.3 21.2 439 n/a 3_weight: 0.1198 0.1398 0.008 0.943 9.1 115.3 21.2 439 n/a 3_xyzrec: 0.1156 0.1312 0.007 1.021 9.1 115.3 21.2 439 n/a 3_adp: 0.1156 0.1312 0.007 1.021 9.1 115.3 21.2 439 n/a 3_regHadp: 0.1156 0.1312 0.007 1.021 9.1 115.3 21.2 439 n/a 3_occ: 0.1148 0.1308 0.007 1.021 9.1 115.3 21.2 439 n/a 4_bss: 0.1141 0.1305 0.007 1.021 9.1 115.3 21.2 439 n/a 4_settarget: 0.1141 0.1305 0.007 1.021 9.1 115.3 21.2 439 n/a 4_updatecdl: 0.1141 0.1305 0.007 1.022 9.1 115.3 21.2 439 n/a 4_nqh: 0.1141 0.1305 0.007 1.022 9.1 115.3 21.2 439 n/a 4_sol: 0.1141 0.1283 0.007 1.022 9.1 115.3 21.3 463 n/a 4_weight: 0.1141 0.1283 0.007 1.022 9.1 115.3 21.3 463 n/a 4_xyzrec: 0.1142 0.1284 0.006 0.975 9.1 115.3 21.3 463 n/a 4_adp: 0.1142 0.1284 0.006 0.975 9.1 115.3 21.3 463 n/a 4_regHadp: 0.1142 0.1284 0.006 0.975 9.1 115.3 21.3 463 n/a 4_occ: 0.1136 0.1281 0.006 0.975 9.1 115.3 21.3 463 n/a 5_bss: 0.1130 0.1283 0.006 0.975 9.1 115.3 21.3 463 n/a 5_settarget: 0.1130 0.1283 0.006 0.975 9.1 115.3 21.3 463 n/a 5_updatecdl: 0.1130 0.1283 0.006 0.977 9.1 115.3 21.3 463 n/a 5_setrh: 0.1131 0.1282 0.006 0.977 9.1 115.3 21.3 463 n/a 5_nqh: 0.1131 0.1282 0.006 0.977 9.1 115.3 21.3 463 n/a 5_sol: 0.1136 0.1282 0.006 0.977 9.1 115.3 21.2 467 n/a 5_weight: 0.1136 0.1282 0.006 0.977 9.1 115.3 21.2 467 n/a 5_xyzrec: 0.1131 0.1279 0.008 1.113 9.1 115.3 21.2 467 n/a 5_adp: 0.1131 0.1279 0.008 1.113 9.1 115.3 21.2 467 n/a 5_regHadp: 0.1131 0.1279 0.008 1.113 9.1 115.3 21.2 467 n/a 5_occ: 0.1126 0.1276 0.008 1.113 9.1 115.3 21.2 467 n/a end: 0.1125 0.1278 0.008 1.113 9.1 115.3 21.2 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2686906_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2686906_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 14324.3600 Write final files (write_after_run_outputs) : 70.9000 Total : 14398.5800 Total CPU time: 4.01 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:20:34 PST -0800 (1735366834.89 s) Start R-work = 0.1643, R-free = 0.1788 Final R-work = 0.1125, R-free = 0.1278 =============================================================================== Job complete usr+sys time: 14542.20 seconds wall clock time: 264 minutes 8.79 seconds (15848.79 seconds total)