Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.63, per 1000 atoms: 0.48 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: 0.60 Conformation dependent library (CDL) restraints added in 205.6 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 722 0.94 - 1.20: 976 1.20 - 1.46: 712 1.46 - 1.71: 720 1.71 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.515 -0.194 1.00e-02 1.00e+04 3.77e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.775 -0.235 1.29e-02 6.01e+03 3.33e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.424 -0.187 1.13e-02 7.83e+03 2.74e+02 bond pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 1.235 1.430 -0.194 1.19e-02 7.06e+03 2.67e+02 bond pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 1.456 1.250 0.205 1.26e-02 6.30e+03 2.65e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3198 4.76 - 9.52: 1843 9.52 - 14.28: 618 14.28 - 19.03: 108 19.03 - 23.79: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 104.39 14.81 9.00e-01 1.23e+00 2.71e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 137.81 -15.21 1.00e+00 1.00e+00 2.31e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 132.19 -12.99 9.00e-01 1.23e+00 2.08e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 116.37 132.58 -16.21 1.19e+00 7.06e-01 1.85e+02 angle pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 120.63 106.13 14.50 1.08e+00 8.57e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 923 16.26 - 32.51: 127 32.51 - 48.77: 36 48.77 - 65.03: 21 65.03 - 81.28: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.185: 66 0.185 - 0.368: 79 0.368 - 0.551: 54 0.551 - 0.734: 30 0.734 - 0.917: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 103 " pdb=" N ALA A 103 " pdb=" C ALA A 103 " pdb=" CB ALA A 103 " both_signs ideal model delta sigma weight residual False 2.48 1.57 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LEU A 77 " pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CB LEU A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA VAL A 169 " pdb=" N VAL A 169 " pdb=" C VAL A 169 " pdb=" CB VAL A 169 " both_signs ideal model delta sigma weight residual False 2.44 3.35 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.062 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.133 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.040 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.017 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.060 2.00e-02 2.50e+03 5.74e-02 9.89e+01 pdb=" CG PHE A 162 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1001 2.31 - 2.88: 8055 2.88 - 3.46: 10524 3.46 - 4.03: 15242 4.03 - 4.60: 21875 Nonbonded interactions: 56697 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.739 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.792 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.812 1.850 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.821 2.270 ... (remaining 56692 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_2226169_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= 0.2595 r_free= 0.1930 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784553 | | target function (ml) not normalized (work): 231969.967499 | | target function (ml) not normalized (free): 11774.106116 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2087 7.0825 4.9576| | 2: 3.57 - 2.84 1.00 2876 122 0.2435 0.1793 4.3449 4.3317| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1706 4.1332 4.1585| | 4: 2.47 - 2.25 1.00 2825 136 0.2302 0.1466 3.8284 3.8188| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1634 3.8 3.8198| | 6: 2.09 - 1.97 1.00 2846 113 0.2525 0.1655 3.4722 3.4798| | 7: 1.97 - 1.87 1.00 2787 165 0.2517 0.1871 3.1091 3.2356| | 8: 1.87 - 1.79 1.00 2789 144 0.2432 0.1815 3.0491 3.1207| | 9: 1.79 - 1.72 1.00 2745 138 0.2385 0.1858 2.8763 2.9341| | 10: 1.72 - 1.66 1.00 2789 158 0.2375 0.1704 2.7858 2.7693| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1953 2.7233 2.7733| | 12: 1.61 - 1.56 1.00 2787 146 0.2471 0.1784 2.5993 2.5734| | 13: 1.56 - 1.52 1.00 2745 130 0.2528 0.1825 2.5617 2.5662| | 14: 1.52 - 1.48 1.00 2803 134 0.2572 0.1947 2.4959 2.5582| | 15: 1.48 - 1.45 1.00 2738 128 0.2574 0.1962 2.4184 2.4754| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2187 2.3778 2.4679| | 17: 1.42 - 1.39 1.00 2785 139 0.2662 0.2313 2.3334 2.3777| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2153 2.2554 2.3023| | 19: 1.36 - 1.34 1.00 2807 134 0.2649 0.2162 2.2343 2.257| | 20: 1.34 - 1.32 1.00 2696 147 0.2679 0.2437 2.1873 2.286| | 21: 1.32 - 1.30 1.00 2785 112 0.2692 0.2204 2.1687 2.1588| | 22: 1.29 - 1.27 1.00 2704 152 0.2721 0.2490 2.1382 2.1933| | 23: 1.27 - 1.26 1.00 2802 156 0.2791 0.2350 2.1076 2.11| | 24: 1.26 - 1.24 1.00 2744 132 0.2772 0.2519 2.0727 2.1792| | 25: 1.24 - 1.22 1.00 2734 148 0.2781 0.2598 2.0343 2.1157| | 26: 1.22 - 1.21 1.00 2727 135 0.2900 0.2358 2.0179 2.1186| | 27: 1.21 - 1.19 1.00 2814 148 0.2893 0.2541 1.9892 1.9795| | 28: 1.19 - 1.18 1.00 2671 147 0.2990 0.2705 1.9888 1.9534| | 29: 1.18 - 1.16 1.00 2800 134 0.3033 0.2828 1.9593 2.0502| | 30: 1.16 - 1.15 1.00 2740 148 0.3099 0.2694 1.9334 1.941| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.80 0.76 0.23 1491.17| | 2: 3.57 - 2.84 2876 122 0.80 26.09 1.27 0.23 1491.17| | 3: 2.84 - 2.48 2833 165 0.74 31.97 1.24 0.24 1236.00| | 4: 2.47 - 2.25 2825 136 0.81 25.51 1.25 0.25 573.80| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 573.80| | 6: 2.09 - 1.97 2846 113 0.84 22.51 1.29 0.25 312.42| | 7: 1.97 - 1.87 2787 165 0.90 16.32 1.28 0.26 89.50| | 8: 1.87 - 1.79 2789 144 0.86 20.82 1.24 0.26 89.50| | 9: 1.79 - 1.72 2745 138 0.88 18.17 1.23 0.26 52.84| | 10: 1.72 - 1.66 2789 158 0.87 19.48 1.22 0.25 45.50| | 11: 1.66 - 1.61 2740 147 0.86 20.75 1.25 0.25 43.92| | 12: 1.61 - 1.56 2787 146 0.89 17.83 1.24 0.25 27.93| | 13: 1.56 - 1.52 2745 130 0.87 19.73 1.24 0.25 27.93| | 14: 1.52 - 1.48 2803 134 0.87 20.42 1.24 0.25 25.26| | 15: 1.48 - 1.45 2738 128 0.87 20.04 1.23 0.25 20.39| | 16: 1.45 - 1.42 2756 161 0.86 21.51 1.24 0.25 20.39| | 17: 1.42 - 1.39 2785 139 0.87 20.65 1.23 0.25 17.55| | 18: 1.39 - 1.36 2741 179 0.86 21.45 1.23 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.85 22.42 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.86 21.58 1.22 0.24 13.40| | 21: 1.32 - 1.30 2785 112 0.85 22.30 1.19 0.24 13.23| | 22: 1.29 - 1.27 2704 152 0.85 22.76 1.20 0.24 12.92| | 23: 1.27 - 1.26 2802 156 0.85 22.70 1.20 0.24 11.34| | 24: 1.26 - 1.24 2744 132 0.84 23.43 1.20 0.24 11.34| | 25: 1.24 - 1.22 2734 148 0.84 23.84 1.19 0.23 10.73| | 26: 1.22 - 1.21 2727 135 0.84 24.42 1.21 0.23 10.07| | 27: 1.21 - 1.19 2814 148 0.83 24.91 1.20 0.23 10.07| | 28: 1.19 - 1.18 2671 147 0.83 25.03 1.17 0.23 9.13| | 29: 1.18 - 1.16 2800 134 0.82 25.62 1.18 0.23 8.78| | 30: 1.16 - 1.15 2740 148 0.81 26.65 1.16 0.23 8.78| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.78 max = 1491.17 mean = 215.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.56| |phase err.(test): min = 0.00 max = 89.67 mean = 22.56| |-----------------------------------------------------------------------------| ----------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 0.235 1557 Z= 5.403 Angle : 5.373 18.971 2118 Z= 3.821 Chirality : 0.404 0.917 243 Planarity : 0.031 0.107 284 Dihedral : 13.852 81.283 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.43 (0.48), residues: 224 helix: -2.67 (0.36), residues: 108 sheet: 0.02 (0.93), residues: 28 loop : -0.40 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.019 ARG A 48 TYR 0.080 0.032 TYR A 141 PHE 0.117 0.042 PHE A 162 HIS 0.086 0.038 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= 0.2595 r_free= 0.1930 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784553 | | target function (ml) not normalized (work): 231969.967499 | | target function (ml) not normalized (free): 11774.106116 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2554 0.2595 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2554 0.2595 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1963 0.1967 0.1931 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1987 0.1991 0.1942 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1630 0.1623 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1629 0.1623 0.1756 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 0.3882 386.134 356.576 0.674 1.003 0.409 11.894-9.307 99.02 97 4 0.1836 613.356 596.841 0.925 1.004 0.401 9.237-7.194 100.00 213 7 0.2085 501.649 491.609 0.960 1.004 0.344 7.162-5.571 100.00 427 22 0.2188 376.460 364.210 0.927 1.004 0.283 5.546-4.326 100.00 867 58 0.1289 516.787 510.301 0.967 1.004 0.222 4.315-3.360 100.00 1859 96 0.1143 491.468 487.644 1.006 1.004 0.205 3.356-2.611 100.00 3867 181 0.1441 322.869 319.446 0.999 1.003 0.052 2.608-2.026 99.99 8198 413 0.1324 214.033 211.986 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1616 104.522 103.919 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.349 45.048 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2578 29.203 26.941 0.980 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0458 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1756 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=0.1623 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.199430 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2053.650246 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 0.1707 0.1812 0.0105 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1574 0.1707 0.0134 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1439 0.1610 0.0171 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1404 0.1600 0.0195 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1367 0.1573 0.0206 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1363 0.1567 0.0205 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1304 0.1526 0.0222 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1273 0.1504 0.0231 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1257 0.1490 0.0232 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1250 0.1483 0.0233 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1481 0.0236 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1239 0.1475 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1235 0.1475 0.0240 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1470 0.0238 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1229 0.1468 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1229 0.1470 0.0242 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1226 0.1473 0.0247 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1223 0.1473 0.0251 0.007 1.0 3.5 0.5 0.6 0 13.100 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1468 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.68 2.40 3.013 19.058 2053.650 0.017 12.29 14.68 2.39 2.989 19.058 61.610 0.017 12.35 14.65 2.30 2.668 19.057 256.706 0.017 12.73 15.30 2.57 2.769 19.225 1026.825 0.017 12.58 15.51 2.93 3.274 19.585 2053.650 0.016 12.39 15.40 3.01 3.284 19.605 3080.475 0.015 12.40 15.50 3.10 3.436 19.674 4107.300 0.015 12.27 15.35 3.08 3.310 19.598 5134.126 0.015 12.19 15.35 3.16 3.355 19.628 6160.951 0.015 12.21 15.39 3.18 3.400 19.633 7187.776 0.015 12.19 15.41 3.21 3.400 19.626 8214.601 0.015 12.18 15.44 3.26 3.521 19.684 9241.426 0.015 12.12 15.35 3.23 3.424 19.616 10268.251 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: 256.706 Accepted refinement result: 12.35 14.65 2.30 2.668 19.057 256.706 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.31 0 1785 Protein: 9.07 115.00 16.99 3.32 0 1519 Water: 11.47 119.44 38.22 N/A 0 258 Other: 19.73 26.61 22.06 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.10 1272 20.10 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1465 r_work=0.1237 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 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 = 0.1232 r_free = 0.1459 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 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= 0.1232 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016932 | | target function (ls_wunit_k1) not normalized (work): 1410.417973 | | target function (ls_wunit_k1) not normalized (free): 110.629873 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1459 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1687 n_refl.: 87593 remove outliers: r(all,work,free)=0.1673 0.1674 0.1687 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1679 0.1681 0.1692 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1450 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1229 0.1450 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 0.3550 301.659 283.373 0.642 1.002 0.376 11.894-9.307 99.02 97 4 0.1700 483.241 470.031 0.919 1.003 0.373 9.237-7.194 100.00 213 7 0.1919 395.231 389.094 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1842 296.599 290.550 0.938 1.003 0.259 5.546-4.326 100.00 867 58 0.1002 407.157 404.453 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 387.210 386.092 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1173 254.377 253.288 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1022 168.628 167.919 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.349 82.534 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.517 36.027 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 23.008 21.492 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0547 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1450 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=0.1230 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1451 | n_water=258 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1238 r_free=0.1448 | n_water=252 | time (s): 20.780 (total time: 22.340) Filter (q & B) r_work=0.1240 r_free=0.1449 | n_water=249 | time (s): 3.040 (total time: 25.380) Compute maps r_work=0.1240 r_free=0.1449 | n_water=249 | time (s): 1.570 (total time: 26.950) Filter (map) r_work=0.1261 r_free=0.1458 | n_water=224 | time (s): 2.610 (total time: 29.560) Find peaks r_work=0.1261 r_free=0.1458 | n_water=224 | time (s): 0.570 (total time: 30.130) Add new water r_work=0.1406 r_free=0.1635 | n_water=433 | time (s): 2.560 (total time: 32.690) Refine new water occ: r_work=0.1315 r_free=0.1484 adp: r_work=0.1229 r_free=0.1430 occ: r_work=0.1242 r_free=0.1418 adp: r_work=0.1207 r_free=0.1404 occ: r_work=0.1209 r_free=0.1395 adp: r_work=0.1200 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1395 r_work=0.1200 r_free=0.1395 | n_water=433 | time (s): 48.920 (total time: 81.610) Filter (q & B) r_work=0.1203 r_free=0.1397 | n_water=419 | time (s): 2.740 (total time: 84.350) Filter (dist only) r_work=0.1203 r_free=0.1395 | n_water=418 | time (s): 35.790 (total time: 120.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.818841 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1486.303661 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 0.1532 0.1665 0.0134 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1457 0.1600 0.0143 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1406 0.1556 0.0151 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1357 0.1520 0.0163 0.001 0.4 5.1 0.0 0.0 0 0.750 0.1323 0.1498 0.0175 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1318 0.1487 0.0169 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1254 0.1454 0.0200 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1225 0.1440 0.0215 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1215 0.1437 0.0222 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1205 0.1429 0.0225 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1200 0.1429 0.0228 0.004 0.7 5.4 0.5 0.0 0 6.000 0.1198 0.1431 0.0233 0.005 0.8 5.8 0.5 0.0 0 7.000 0.1192 0.1426 0.0233 0.005 0.8 6.4 0.5 0.0 0 8.000 0.1188 0.1423 0.0235 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1187 0.1424 0.0237 0.006 0.8 6.1 0.5 0.0 0 10.000 0.1186 0.1422 0.0236 0.007 0.9 6.1 0.5 0.0 0 11.000 0.1184 0.1415 0.0231 0.007 0.9 6.4 0.5 0.0 0 12.000 0.1182 0.1409 0.0227 0.007 0.9 5.8 0.5 0.0 0 13.000 0.1180 0.1417 0.0237 0.008 0.9 6.1 0.5 0.0 0 14.409 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1409 0.0227 0.007 0.9 5.8 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 14.09 2.27 3.776 21.738 1486.304 0.015 11.82 14.09 2.27 3.776 21.738 44.589 0.015 11.82 14.09 2.27 3.776 21.738 185.788 0.015 11.96 14.44 2.48 3.643 21.737 743.152 0.015 12.02 14.81 2.79 3.472 22.028 1486.304 0.014 11.80 14.63 2.84 3.475 22.052 2229.455 0.014 11.77 14.73 2.96 3.511 22.038 2972.607 0.014 11.71 14.75 3.04 3.530 21.897 3715.759 0.014 11.65 14.62 2.98 3.508 22.058 4458.911 0.014 11.65 14.73 3.08 3.530 21.968 5202.063 0.013 11.61 14.69 3.08 3.544 22.111 5945.215 0.013 11.54 14.64 3.10 3.549 22.016 6688.366 0.013 11.56 14.67 3.11 3.561 22.046 7431.518 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: 185.788 Accepted refinement result: 11.82 14.09 2.27 3.776 21.738 185.788 0.015 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 22.11 3.31 194 1751 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 40.60 N/A 194 224 Other: 19.77 26.65 22.09 N/A 0 8 Chain A: 9.10 115.04 19.42 N/A 0 1751 Chain S: 14.10 60.00 46.45 N/A 194 0 Histogram: Values Number of atoms 9.10 - 19.70 1262 19.70 - 30.29 248 30.29 - 40.88 165 40.88 - 51.48 126 51.48 - 62.07 122 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1409 r_work=0.1182 r_free=0.1409 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1406 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= 0.1180 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014735 | | target function (ls_wunit_k1) not normalized (work): 1227.331276 | | target function (ls_wunit_k1) not normalized (free): 100.972587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1180 0.1406 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1581 0.1581 0.1617 n_refl.: 87592 remove outliers: r(all,work,free)=0.1581 0.1581 0.1617 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1583 0.1583 0.1618 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1177 0.1401 n_refl.: 87592 remove outliers: r(all,work,free)=0.1187 0.1176 0.1401 n_refl.: 87590 ======================== 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 0.3402 300.206 277.171 0.604 1.003 0.360 11.894-9.307 99.02 97 4 0.1594 483.241 477.104 0.919 1.003 0.358 9.237-7.194 100.00 213 7 0.1643 395.231 393.413 0.986 1.003 0.280 7.162-5.571 100.00 427 22 0.1550 296.599 292.483 0.942 1.003 0.250 5.546-4.326 100.00 867 58 0.0883 407.157 404.421 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0773 387.210 386.342 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1065 254.377 253.577 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1001 168.628 168.065 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1097 82.349 82.562 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1440 36.517 36.060 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 23.008 21.526 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0152 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1176 r_free=0.1401 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=0.1403 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1403 | n_water=418 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1179 r_free=0.1399 | n_water=415 | time (s): 37.270 (total time: 39.450) Filter (q & B) r_work=0.1179 r_free=0.1399 | n_water=415 | time (s): 1.270 (total time: 40.720) Compute maps r_work=0.1179 r_free=0.1399 | n_water=415 | time (s): 1.550 (total time: 42.270) Filter (map) r_work=0.1220 r_free=0.1391 | n_water=286 | time (s): 2.360 (total time: 44.630) Find peaks r_work=0.1220 r_free=0.1391 | n_water=286 | time (s): 0.450 (total time: 45.080) Add new water r_work=0.1345 r_free=0.1519 | n_water=470 | time (s): 2.540 (total time: 47.620) Refine new water occ: r_work=0.1250 r_free=0.1433 adp: r_work=0.1251 r_free=0.1435 occ: r_work=0.1227 r_free=0.1405 adp: r_work=0.1225 r_free=0.1407 occ: r_work=0.1208 r_free=0.1387 adp: r_work=0.1203 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1385 r_work=0.1203 r_free=0.1385 | n_water=470 | time (s): 188.260 (total time: 235.880) Filter (q & B) r_work=0.1207 r_free=0.1399 | n_water=443 | time (s): 3.540 (total time: 239.420) Filter (dist only) r_work=0.1207 r_free=0.1398 | n_water=441 | time (s): 39.640 (total time: 279.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.818209 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.370114 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 0.1241 0.1382 0.0140 0.002 0.6 5.1 0.5 0.0 0 0.091 0.1193 0.1346 0.0153 0.003 0.7 3.8 0.5 0.0 0 0.273 0.1177 0.1340 0.0163 0.004 0.8 3.5 0.5 0.0 0 0.545 0.1168 0.1336 0.0169 0.005 0.9 3.8 0.5 0.0 0 0.818 0.1165 0.1336 0.0171 0.006 1.0 3.5 0.5 0.0 0 1.091 0.1162 0.1336 0.0174 0.007 1.0 3.8 0.5 0.0 0 1.364 0.1160 0.1337 0.0177 0.007 1.1 3.8 0.5 0.0 0 1.636 0.1158 0.1336 0.0178 0.008 1.1 3.8 0.5 0.0 0 1.909 0.1169 0.1341 0.0172 0.006 0.9 3.5 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1336 0.0178 0.008 1.1 3.8 0.5 0.0 0 1.909 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.36 1.78 3.779 21.302 35.370 3.624 11.58 13.36 1.78 3.779 21.302 1.061 3.624 11.58 13.36 1.78 3.778 21.302 4.421 3.624 11.63 13.40 1.77 3.708 21.295 17.685 3.619 11.74 13.55 1.80 3.724 21.267 35.370 3.624 11.65 13.52 1.87 3.739 21.249 53.055 3.616 11.59 13.49 1.90 3.761 21.243 70.740 3.612 11.57 13.50 1.92 3.772 21.237 88.425 3.609 11.54 13.47 1.93 3.781 21.232 106.110 3.607 11.51 13.44 1.94 3.791 21.230 123.795 3.604 11.50 13.46 1.96 3.804 21.220 141.480 3.603 11.51 13.45 1.94 3.817 21.202 159.166 3.602 11.48 13.44 1.97 3.822 21.210 176.851 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.421 Accepted refinement result: 11.58 13.36 1.78 3.778 21.302 4.421 3.624 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.31 3.31 221 1747 Protein: 9.11 115.04 17.04 3.31 0 1519 Water: 11.51 76.71 36.00 N/A 221 220 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.37 N/A 0 1747 Chain S: 14.11 60.01 36.63 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.71 1262 19.71 - 30.30 289 30.30 - 40.89 205 40.89 - 51.48 131 51.48 - 62.08 59 62.08 - 72.67 11 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1336 r_work=0.1158 r_free=0.1336 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1336 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1338 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1338 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618098 | | target function (ml) not normalized (work): 301365.896318 | | target function (ml) not normalized (free): 15886.844824 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1150 0.1338 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1495 0.1494 0.1556 n_refl.: 87590 remove outliers: r(all,work,free)=0.1495 0.1494 0.1556 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1495 0.1493 0.1556 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1153 0.1144 0.1333 n_refl.: 87590 remove outliers: r(all,work,free)=0.1151 0.1142 0.1333 n_refl.: 87585 ======================== 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 0.3829 297.560 273.764 0.519 1.001 0.330 11.894-9.307 98.04 96 4 0.2207 483.366 466.645 0.879 1.002 0.330 9.237-7.194 98.64 210 7 0.2204 388.730 388.912 0.961 1.002 0.191 7.162-5.571 100.00 427 22 0.2077 296.599 286.611 0.924 1.002 0.190 5.546-4.326 100.00 867 58 0.1108 407.157 402.165 0.963 1.002 0.160 4.315-3.360 100.00 1859 96 0.0942 387.210 384.678 1.004 1.002 0.160 3.356-2.611 100.00 3867 181 0.1144 254.377 252.215 1.007 1.002 0.034 2.608-2.026 99.99 8198 413 0.0938 168.628 167.854 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.349 82.639 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.517 36.098 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 23.008 21.548 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=-0.0137 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1333 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=0.1142 r_free=0.1333 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1333 | n_water=441 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1145 r_free=0.1335 | n_water=439 | time (s): 46.830 (total time: 49.250) Filter (q & B) r_work=0.1145 r_free=0.1335 | n_water=439 | time (s): 1.330 (total time: 50.580) Compute maps r_work=0.1145 r_free=0.1335 | n_water=439 | time (s): 1.940 (total time: 52.520) Filter (map) r_work=0.1175 r_free=0.1309 | n_water=323 | time (s): 3.920 (total time: 56.440) Find peaks r_work=0.1175 r_free=0.1309 | n_water=323 | time (s): 0.720 (total time: 57.160) Add new water r_work=0.1252 r_free=0.1386 | n_water=501 | time (s): 3.850 (total time: 61.010) Refine new water occ: r_work=0.1169 r_free=0.1333 adp: r_work=0.1170 r_free=0.1333 occ: r_work=0.1151 r_free=0.1322 adp: r_work=0.1150 r_free=0.1321 occ: r_work=0.1137 r_free=0.1314 adp: r_work=0.1133 r_free=0.1311 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1311 r_work=0.1133 r_free=0.1311 | n_water=501 | time (s): 278.650 (total time: 339.660) Filter (q & B) r_work=0.1139 r_free=0.1319 | n_water=459 | time (s): 3.860 (total time: 343.520) Filter (dist only) r_work=0.1140 r_free=0.1318 | n_water=458 | time (s): 47.340 (total time: 390.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766961 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.231708 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 0.1361 0.0153 0.002 0.6 5.1 0.5 0.0 0 0.088 0.1170 0.1334 0.0164 0.003 0.7 3.8 0.5 0.0 0 0.265 0.1155 0.1323 0.0169 0.004 0.9 4.2 0.5 0.0 0 0.530 0.1150 0.1324 0.0175 0.005 0.9 3.8 0.5 0.0 0 0.795 0.1144 0.1320 0.0176 0.006 1.0 4.2 0.5 0.0 0 1.060 0.1141 0.1318 0.0177 0.007 1.1 4.5 0.5 0.0 0 1.325 0.1141 0.1322 0.0181 0.008 1.1 4.5 0.5 0.0 0 1.590 0.1138 0.1319 0.0180 0.008 1.1 4.5 0.5 0.0 0 1.855 0.1147 0.1322 0.0175 0.006 1.0 3.8 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1318 0.0177 0.007 1.1 4.5 0.5 0.0 0 1.325 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 13.18 1.77 3.779 21.290 43.232 3.615 11.41 13.18 1.77 3.779 21.290 1.297 3.615 11.41 13.18 1.77 3.777 21.290 5.404 3.614 11.46 13.23 1.77 3.713 21.282 21.616 3.609 11.54 13.37 1.83 3.732 21.252 43.232 3.613 11.47 13.34 1.87 3.752 21.242 64.848 3.607 11.39 13.29 1.89 3.771 21.239 86.463 3.601 11.36 13.26 1.89 3.778 21.238 108.079 3.599 11.34 13.26 1.91 3.788 21.237 129.695 3.597 11.36 13.33 1.96 3.808 21.219 151.311 3.598 11.33 13.29 1.96 3.815 21.220 172.927 3.596 11.31 13.27 1.96 3.820 21.220 194.543 3.595 11.31 13.29 1.98 3.832 21.214 216.159 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.297 Accepted refinement result: 11.41 13.18 1.77 3.779 21.290 1.297 3.615 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.29 3.31 241 1744 Protein: 9.11 115.03 17.03 3.31 0 1519 Water: 11.51 76.70 35.39 N/A 241 217 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.03 19.35 N/A 0 1744 Chain S: 14.10 60.00 35.29 N/A 241 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 294 30.29 - 40.89 219 40.89 - 51.48 131 51.48 - 62.07 53 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1318 r_work=0.1141 r_free=0.1318 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1318 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1316 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1134 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611456 | | target function (ml) not normalized (work): 300794.564899 | | target function (ml) not normalized (free): 15859.030990 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1134 0.1316 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1529 n_refl.: 87585 remove outliers: r(all,work,free)=0.1470 0.1468 0.1529 n_refl.: 87585 overall B=-0.00 to atoms: r(all,work,free)=0.1470 0.1468 0.1529 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1133 0.1316 n_refl.: 87585 remove outliers: r(all,work,free)=0.1140 0.1131 0.1316 n_refl.: 87581 ======================== 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 0.3719 293.527 256.996 0.460 1.000 0.314 11.894-9.307 98.04 96 4 0.2503 483.366 467.997 0.874 1.001 0.310 9.237-7.194 98.64 210 7 0.2286 388.730 384.674 0.937 1.001 0.165 7.162-5.571 100.00 427 22 0.2134 296.599 285.972 0.918 1.001 0.160 5.546-4.326 100.00 867 58 0.1129 407.157 401.421 0.961 1.001 0.114 4.315-3.360 100.00 1859 96 0.0916 387.210 385.443 1.004 1.001 0.097 3.356-2.611 100.00 3867 181 0.1106 254.377 252.520 1.009 1.001 0.024 2.608-2.026 99.99 8198 413 0.0913 168.628 168.019 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.349 82.706 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.517 36.121 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2170 23.008 21.480 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0031 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1316 After: r_work=0.1132 r_free=0.1316 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1316 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1132 r_free=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1316 | n_water=458 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1132 r_free=0.1316 | n_water=458 | time (s): 46.500 (total time: 48.870) Filter (q & B) r_work=0.1134 r_free=0.1315 | n_water=454 | time (s): 3.960 (total time: 52.830) Compute maps r_work=0.1134 r_free=0.1315 | n_water=454 | time (s): 1.870 (total time: 54.700) Filter (map) r_work=0.1162 r_free=0.1309 | n_water=353 | time (s): 3.970 (total time: 58.670) Find peaks r_work=0.1162 r_free=0.1309 | n_water=353 | time (s): 0.680 (total time: 59.350) Add new water r_work=0.1205 r_free=0.1355 | n_water=499 | time (s): 3.580 (total time: 62.930) Refine new water occ: r_work=0.1148 r_free=0.1294 adp: r_work=0.1149 r_free=0.1298 occ: r_work=0.1138 r_free=0.1279 adp: r_work=0.1137 r_free=0.1283 occ: r_work=0.1129 r_free=0.1268 adp: r_work=0.1127 r_free=0.1271 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1271 r_work=0.1127 r_free=0.1271 | n_water=499 | time (s): 327.410 (total time: 390.340) Filter (q & B) r_work=0.1134 r_free=0.1281 | n_water=458 | time (s): 3.920 (total time: 394.260) Filter (dist only) r_work=0.1134 r_free=0.1281 | n_water=457 | time (s): 47.700 (total time: 441.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.817444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.035043 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 0.1218 0.1334 0.0115 0.004 0.7 8.0 0.0 0.0 0 0.091 0.1173 0.1303 0.0130 0.004 0.8 7.7 0.0 0.0 0 0.273 0.1149 0.1288 0.0139 0.005 0.9 7.4 0.5 0.0 0 0.545 0.1139 0.1282 0.0144 0.006 1.0 7.4 0.5 0.0 0 0.818 0.1135 0.1281 0.0146 0.007 1.1 7.0 0.5 0.0 0 1.090 0.1134 0.1281 0.0147 0.007 1.1 7.0 0.5 0.0 0 1.363 0.1133 0.1280 0.0147 0.007 1.1 7.0 0.5 0.0 0 1.636 0.1132 0.1280 0.0148 0.008 1.1 7.0 0.5 0.0 0 1.908 0.1138 0.1282 0.0144 0.006 1.0 7.4 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1280 0.0148 0.008 1.1 7.0 0.5 0.0 0 1.908 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.80 1.48 3.779 21.264 46.035 3.606 11.32 12.80 1.48 3.778 21.264 1.381 3.606 11.32 12.80 1.47 3.768 21.264 5.754 3.606 11.35 12.85 1.50 3.716 21.256 23.018 3.600 11.37 12.94 1.57 3.742 21.230 46.035 3.601 11.35 12.98 1.63 3.759 21.213 69.053 3.597 11.28 12.93 1.64 3.776 21.211 92.070 3.592 11.25 12.91 1.66 3.785 21.211 115.088 3.590 11.26 12.96 1.70 3.805 21.196 138.105 3.590 11.23 12.95 1.71 3.814 21.196 161.123 3.588 11.23 12.95 1.72 3.826 21.190 184.140 3.587 11.21 12.93 1.72 3.834 21.188 207.158 3.586 11.20 12.92 1.71 3.839 21.188 230.175 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: 1.381 Accepted refinement result: 11.32 12.80 1.48 3.778 21.264 1.381 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.24 3.31 241 1743 Protein: 9.11 115.03 17.03 3.31 0 1519 Water: 11.51 76.70 35.23 N/A 241 216 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.03 19.33 N/A 0 1743 Chain S: 14.10 60.00 35.05 N/A 241 0 Histogram: Values Number of atoms 9.11 - 19.70 1267 19.70 - 30.29 299 30.29 - 40.88 215 40.88 - 51.48 128 51.48 - 62.07 53 62.07 - 72.66 11 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1280 r_work=0.1132 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1280 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1274 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1274 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603560 | | target function (ml) not normalized (work): 300122.474097 | | target function (ml) not normalized (free): 15812.921969 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1319 0.1290 5.6471 5.5999| | 2: 3.57 - 2.84 1.00 2888 124 0.1058 0.1347 5.1581 5.2251| | 3: 2.83 - 2.48 1.00 2820 163 0.1100 0.1231 4.9409 4.9844| | 4: 2.47 - 2.25 1.00 2825 136 0.0895 0.0992 4.6249 4.667| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0944 4.5737 4.6292| | 6: 2.09 - 1.97 1.00 2846 113 0.0844 0.0996 4.2613 4.3571| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1106 3.9749 4.0819| | 8: 1.87 - 1.79 1.00 2789 144 0.0908 0.1092 3.8862 3.9902| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1182 3.6426 3.8269| | 10: 1.72 - 1.66 1.00 2831 160 0.0920 0.1178 3.5634 3.7068| | 11: 1.66 - 1.61 1.00 2712 147 0.0862 0.1010 3.4923 3.5626| | 12: 1.61 - 1.56 1.00 2773 144 0.0901 0.1160 3.3293 3.4681| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1032 3.3088 3.3881| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1060 3.2398 3.3267| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1241 3.1543 3.2763| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1256 3.1372 3.2417| | 17: 1.42 - 1.39 1.00 2785 139 0.1142 0.1305 3.1215 3.2297| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1330 3.1055 3.2433| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1573 3.1133 3.2733| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1457 3.1132 3.1519| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1510 3.1147 3.1025| | 22: 1.29 - 1.27 1.00 2704 152 0.1560 0.1996 3.1232 3.3028| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1796 3.1338 3.205| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1847 3.1294 3.2326| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2150 3.1446 3.2651| | 26: 1.22 - 1.21 1.00 2727 135 0.1913 0.1773 3.1515 3.2055| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2173 3.1733 3.1645| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2297 3.1672 3.173| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2385 3.1494 3.2305| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2454 3.1445 3.1678| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2923 171 0.95 8.48 1.00 0.97 5685.43| | 2: 3.57 - 2.84 2888 124 0.93 12.47 1.01 0.97 5685.43| | 3: 2.83 - 2.48 2820 163 0.90 16.41 0.99 0.97 4750.16| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.98 2338.40| | 5: 2.25 - 2.09 2756 127 0.90 15.54 1.01 0.98 2338.40| | 6: 2.09 - 1.97 2846 113 0.93 12.25 1.02 0.98 1351.27| | 7: 1.97 - 1.87 2787 165 0.95 9.24 1.02 0.98 509.38| | 8: 1.87 - 1.79 2789 144 0.93 12.60 1.00 0.98 509.38| | 9: 1.79 - 1.72 2745 138 0.94 10.00 0.98 0.98 288.71| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.98 244.52| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.98 234.24| | 12: 1.61 - 1.56 2773 144 0.95 8.88 0.99 0.98 137.34| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.98 137.34| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.98 123.41| | 15: 1.48 - 1.45 2738 128 0.95 9.91 1.02 0.99 97.90| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.99 97.90| | 17: 1.42 - 1.39 2785 139 0.95 10.94 1.01 0.98 89.30| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.33| | 19: 1.36 - 1.34 2807 134 0.94 11.88 0.99 0.98 84.33| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.52| | 21: 1.32 - 1.30 2785 112 0.94 13.14 0.98 0.96 80.25| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 80.68| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.97 0.95 82.83| | 24: 1.26 - 1.24 2744 132 0.92 14.90 0.96 0.95 82.83| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.75| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.03 0.93 86.88| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.03 0.93 86.88| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.33| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.62| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.93 91.62| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.25 max = 5685.43 mean = 879.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.43| |phase err.(test): min = 0.00 max = 89.03 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1128 0.1274 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1492 n_refl.: 87581 remove outliers: r(all,work,free)=0.1449 0.1448 0.1492 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1448 0.1447 0.1492 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1127 0.1274 n_refl.: 87581 remove outliers: r(all,work,free)=0.1134 0.1126 0.1274 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3907 288.751 255.471 0.462 1.001 0.302 11.894-9.307 97.06 95 4 0.2429 476.569 464.903 0.868 1.002 0.290 9.237-7.194 98.64 210 7 0.2289 388.730 384.129 0.933 1.002 0.160 7.162-5.571 100.00 427 22 0.2109 296.599 286.468 0.918 1.002 0.160 5.546-4.326 100.00 867 58 0.1125 407.157 402.282 0.960 1.002 0.108 4.315-3.360 100.00 1859 96 0.0904 387.210 385.019 1.003 1.002 0.087 3.356-2.611 100.00 3867 181 0.1102 254.377 252.409 1.010 1.002 0.014 2.608-2.026 99.99 8198 413 0.0908 168.628 168.001 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.349 82.665 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.517 36.110 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.008 21.547 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0092 ================= 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 : 0.2595 0.1930 0.081 5.373 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1756 0.081 5.373 9.0 119.5 20.1 258 0.000 1_settarget: 0.1623 0.1756 0.081 5.373 9.0 119.5 20.1 258 0.000 1_nqh: 0.1623 0.1759 0.081 5.373 9.0 119.5 20.1 258 0.003 1_weight: 0.1623 0.1759 0.081 5.373 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1229 0.1468 0.006 0.878 9.0 119.5 20.1 258 0.140 1_adp: 0.1235 0.1465 0.006 0.878 9.1 119.4 20.1 258 0.140 1_regHadp: 0.1237 0.1469 0.006 0.878 9.1 119.4 20.1 258 0.140 1_occ: 0.1232 0.1459 0.006 0.878 9.1 119.4 20.1 258 0.140 2_bss: 0.1229 0.1450 0.006 0.878 9.1 119.5 20.1 258 0.140 2_settarget: 0.1229 0.1450 0.006 0.878 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1229 0.1450 0.006 0.885 9.1 119.5 20.1 258 0.140 2_nqh: 0.1230 0.1451 0.006 0.885 9.1 119.5 20.1 258 0.143 2_sol: 0.1203 0.1395 0.006 0.885 9.1 115.0 22.1 418 n/a 2_weight: 0.1203 0.1395 0.006 0.885 9.1 115.0 22.1 418 n/a 2_xyzrec: 0.1182 0.1409 0.007 0.918 9.1 115.0 22.1 418 n/a 2_adp: 0.1182 0.1409 0.007 0.918 9.1 115.0 22.1 418 n/a 2_regHadp: 0.1182 0.1409 0.007 0.918 9.1 115.0 22.1 418 n/a 2_occ: 0.1180 0.1406 0.007 0.918 9.1 115.0 22.1 418 n/a 3_bss: 0.1176 0.1401 0.007 0.918 9.1 115.0 22.1 418 n/a 3_settarget: 0.1176 0.1401 0.007 0.918 9.1 115.0 22.1 418 n/a 3_updatecdl: 0.1176 0.1401 0.007 0.919 9.1 115.0 22.1 418 n/a 3_nqh: 0.1178 0.1403 0.007 0.919 9.1 115.0 22.1 418 n/a 3_sol: 0.1207 0.1398 0.007 0.919 9.1 115.0 21.3 441 n/a 3_weight: 0.1207 0.1398 0.007 0.919 9.1 115.0 21.3 441 n/a 3_xyzrec: 0.1158 0.1336 0.008 1.098 9.1 115.0 21.3 441 n/a 3_adp: 0.1158 0.1336 0.008 1.098 9.1 115.0 21.3 441 n/a 3_regHadp: 0.1158 0.1336 0.008 1.098 9.1 115.0 21.3 441 n/a 3_occ: 0.1150 0.1338 0.008 1.098 9.1 115.0 21.3 441 n/a 4_bss: 0.1142 0.1333 0.008 1.098 9.1 115.0 21.3 441 n/a 4_settarget: 0.1142 0.1333 0.008 1.098 9.1 115.0 21.3 441 n/a 4_updatecdl: 0.1142 0.1333 0.008 1.101 9.1 115.0 21.3 441 n/a 4_nqh: 0.1142 0.1333 0.008 1.101 9.1 115.0 21.3 441 n/a 4_sol: 0.1140 0.1318 0.008 1.101 9.1 115.0 21.3 458 n/a 4_weight: 0.1140 0.1318 0.008 1.101 9.1 115.0 21.3 458 n/a 4_xyzrec: 0.1141 0.1318 0.007 1.052 9.1 115.0 21.3 458 n/a 4_adp: 0.1141 0.1318 0.007 1.052 9.1 115.0 21.3 458 n/a 4_regHadp: 0.1141 0.1318 0.007 1.052 9.1 115.0 21.3 458 n/a 4_occ: 0.1134 0.1316 0.007 1.052 9.1 115.0 21.3 458 n/a 5_bss: 0.1131 0.1316 0.007 1.052 9.1 115.0 21.3 458 n/a 5_settarget: 0.1131 0.1316 0.007 1.052 9.1 115.0 21.3 458 n/a 5_updatecdl: 0.1131 0.1316 0.007 1.050 9.1 115.0 21.3 458 n/a 5_setrh: 0.1132 0.1316 0.007 1.050 9.1 115.0 21.3 458 n/a 5_nqh: 0.1132 0.1316 0.007 1.050 9.1 115.0 21.3 458 n/a 5_sol: 0.1134 0.1281 0.007 1.050 9.1 115.0 21.2 457 n/a 5_weight: 0.1134 0.1281 0.007 1.050 9.1 115.0 21.2 457 n/a 5_xyzrec: 0.1132 0.1280 0.008 1.097 9.1 115.0 21.2 457 n/a 5_adp: 0.1132 0.1280 0.008 1.097 9.1 115.0 21.2 457 n/a 5_regHadp: 0.1132 0.1280 0.008 1.097 9.1 115.0 21.2 457 n/a 5_occ: 0.1128 0.1274 0.008 1.097 9.1 115.0 21.2 457 n/a end: 0.1126 0.1274 0.008 1.097 9.1 115.0 21.2 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2226169_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2226169_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3100 Refinement macro-cycles (run) : 13604.6500 Write final files (write_after_run_outputs) : 91.2700 Total : 13699.2300 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:35 PST -0800 (1735366295.76 s) Start R-work = 0.1623, R-free = 0.1756 Final R-work = 0.1126, R-free = 0.1274 =============================================================================== Job complete usr+sys time: 13879.82 seconds wall clock time: 255 minutes 45.96 seconds (15345.96 seconds total)