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_8530424.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_8530424.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530424.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.22, per 1000 atoms: 0.36 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: 0.37 Conformation dependent library (CDL) restraints added in 119.5 milliseconds Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 556 0.91 - 1.16: 1074 1.16 - 1.40: 593 1.40 - 1.65: 869 1.65 - 1.89: 61 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.204 0.256 1.19e-02 7.06e+03 4.61e+02 bond pdb=" N LYS A 63 " pdb=" CA LYS A 63 " ideal model delta sigma weight residual 1.457 1.729 -0.272 1.33e-02 5.65e+03 4.18e+02 bond pdb=" CA HIS A 126 " pdb=" C HIS A 126 " ideal model delta sigma weight residual 1.528 1.729 -0.200 1.11e-02 8.12e+03 3.25e+02 bond pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 1.454 1.688 -0.234 1.33e-02 5.65e+03 3.09e+02 bond pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " ideal model delta sigma weight residual 1.523 1.757 -0.234 1.35e-02 5.49e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 2729 4.02 - 8.04: 1893 8.04 - 12.06: 872 12.06 - 16.08: 230 16.08 - 20.10: 53 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.83 138.67 -16.84 1.03e+00 9.43e-01 2.67e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH1 ARG A 28 " ideal model delta sigma weight residual 121.50 135.63 -14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 134.91 -13.41 1.00e+00 1.00e+00 1.80e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 135.98 -13.38 1.00e+00 1.00e+00 1.79e+02 angle pdb=" CA LYS A 130 " pdb=" C LYS A 130 " pdb=" O LYS A 130 " ideal model delta sigma weight residual 120.82 134.78 -13.96 1.05e+00 9.07e-01 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 935 16.66 - 33.32: 125 33.32 - 49.98: 33 49.98 - 66.63: 14 66.63 - 83.29: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " pdb=" HE1 HIS A 138 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 100 0.211 - 0.422: 81 0.422 - 0.633: 41 0.633 - 0.843: 16 0.843 - 1.054: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.067 2.00e-02 2.50e+03 6.69e-02 1.34e+02 pdb=" CG PHE A 119 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.100 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.048 2.00e-02 2.50e+03 6.63e-02 9.88e+01 pdb=" CG HIS A 138 " 0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.129 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.031 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1010 2.32 - 2.89: 8126 2.89 - 3.46: 10504 3.46 - 4.03: 15263 4.03 - 4.60: 21626 Nonbonded interactions: 56529 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.748 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.755 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.826 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 ... (remaining 56524 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_8530424_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= 0.2606 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792794 | | target function (ml) not normalized (work): 232656.523122 | | target function (ml) not normalized (free): 11819.249878 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2055 7.1077 4.9209| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1872 4.3393 4.335| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1819 4.1239 4.1631| | 4: 2.47 - 2.25 1.00 2825 136 0.2321 0.1517 3.8224 3.8427| | 5: 2.25 - 2.09 1.00 2756 127 0.2462 0.1617 3.7958 3.8201| | 6: 2.09 - 1.97 1.00 2846 113 0.2571 0.1810 3.4696 3.5209| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1852 3.1471 3.2048| | 8: 1.87 - 1.79 1.00 2789 144 0.2487 0.1962 3.0618 3.1452| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1814 2.8887 2.9363| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2156 2.8086 2.9311| | 11: 1.66 - 1.61 1.00 2740 147 0.2492 0.1957 2.7627 2.7952| | 12: 1.61 - 1.56 1.00 2787 146 0.2567 0.2168 2.6366 2.7079| | 13: 1.56 - 1.52 1.00 2745 130 0.2553 0.1711 2.5963 2.5787| | 14: 1.52 - 1.48 1.00 2803 134 0.2530 0.2002 2.5005 2.6095| | 15: 1.48 - 1.45 1.00 2738 128 0.2600 0.2168 2.4297 2.4502| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2022 2.3807 2.3845| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.2092 2.3374 2.3734| | 18: 1.39 - 1.36 1.00 2741 179 0.2703 0.2252 2.2668 2.3701| | 19: 1.36 - 1.34 1.00 2807 134 0.2631 0.2391 2.2535 2.3461| | 20: 1.34 - 1.32 1.00 2696 147 0.2739 0.2061 2.2184 2.1674| | 21: 1.32 - 1.30 1.00 2785 112 0.2737 0.2360 2.1693 2.2017| | 22: 1.29 - 1.27 1.00 2704 152 0.2733 0.2349 2.1337 2.1469| | 23: 1.27 - 1.26 1.00 2802 156 0.2745 0.2526 2.0947 2.184| | 24: 1.26 - 1.24 1.00 2744 132 0.2773 0.2438 2.0719 2.1498| | 25: 1.24 - 1.22 1.00 2734 148 0.2831 0.2818 2.0393 2.1188| | 26: 1.22 - 1.21 1.00 2727 135 0.2866 0.2242 1.9938 2.0448| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2566 2.009 1.9822| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2731 1.9827 1.9681| | 29: 1.18 - 1.16 1.00 2800 134 0.2936 0.2636 1.9496 2.023| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2861 1.9341 1.9578| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.60 0.76 0.23 1445.40| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1445.40| | 3: 2.84 - 2.48 2833 165 0.74 31.64 1.24 0.24 1199.64| | 4: 2.47 - 2.25 2825 136 0.81 25.37 1.26 0.25 561.84| | 5: 2.25 - 2.09 2756 127 0.78 28.95 1.28 0.25 561.84| | 6: 2.09 - 1.97 2846 113 0.83 22.68 1.29 0.25 309.70| | 7: 1.97 - 1.87 2787 165 0.90 16.87 1.29 0.26 94.66| | 8: 1.87 - 1.79 2789 144 0.85 21.55 1.25 0.26 94.66| | 9: 1.79 - 1.72 2745 138 0.87 19.28 1.23 0.25 58.05| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.25 50.71| | 11: 1.66 - 1.61 2740 147 0.85 21.73 1.23 0.25 48.93| | 12: 1.61 - 1.56 2787 146 0.88 19.08 1.24 0.25 30.85| | 13: 1.56 - 1.52 2745 130 0.86 20.88 1.23 0.25 30.85| | 14: 1.52 - 1.48 2803 134 0.86 21.19 1.23 0.25 27.48| | 15: 1.48 - 1.45 2738 128 0.86 20.67 1.23 0.25 21.31| | 16: 1.45 - 1.42 2756 161 0.85 22.12 1.24 0.25 21.31| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.23 0.25 18.01| | 18: 1.39 - 1.36 2741 179 0.86 21.62 1.24 0.25 16.10| | 19: 1.36 - 1.34 2807 134 0.85 22.13 1.21 0.25 16.10| | 20: 1.34 - 1.32 2696 147 0.87 21.03 1.21 0.25 13.23| | 21: 1.32 - 1.30 2785 112 0.86 21.94 1.20 0.25 13.03| | 22: 1.29 - 1.27 2704 152 0.86 22.31 1.21 0.25 12.72| | 23: 1.27 - 1.26 2802 156 0.86 22.10 1.21 0.24 11.18| | 24: 1.26 - 1.24 2744 132 0.85 22.71 1.21 0.24 11.18| | 25: 1.24 - 1.22 2734 148 0.85 23.39 1.21 0.24 10.53| | 26: 1.22 - 1.21 2727 135 0.84 23.74 1.21 0.24 9.80| | 27: 1.21 - 1.19 2814 148 0.83 24.65 1.20 0.24 9.80| | 28: 1.19 - 1.18 2671 147 0.84 24.52 1.19 0.23 8.96| | 29: 1.18 - 1.16 2800 134 0.84 24.61 1.17 0.23 8.65| | 30: 1.16 - 1.15 2740 148 0.82 26.35 1.15 0.23 8.65| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.65 max = 1445.40 mean = 211.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.64| |phase err.(test): min = 0.00 max = 89.82 mean = 22.65| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.272 1557 Z= 5.609 Angle : 5.432 16.836 2118 Z= 3.905 Chirality : 0.375 1.054 243 Planarity : 0.030 0.083 284 Dihedral : 14.044 83.291 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.04 (0.50), residues: 224 helix: -2.30 (0.39), residues: 109 sheet: -0.50 (0.86), residues: 30 loop : 0.07 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.031 ARG A 27 TYR 0.116 0.039 TYR A 141 PHE 0.113 0.044 PHE A 119 HIS 0.072 0.030 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792794 | | target function (ml) not normalized (work): 232656.523122 | | target function (ml) not normalized (free): 11819.249878 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1975 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1975 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1982 0.1975 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2007 0.1990 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1633 0.1789 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1632 0.1789 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3806 386.340 360.033 0.740 0.916 0.407 11.894-9.307 98.04 96 4 0.1735 616.173 590.293 1.013 0.917 0.390 9.237-7.194 100.00 213 7 0.2205 501.916 491.202 1.041 0.917 0.370 7.162-5.571 100.00 427 22 0.2233 376.660 364.544 1.023 0.918 0.288 5.546-4.326 100.00 867 58 0.1278 517.062 510.322 1.051 0.918 0.228 4.315-3.360 100.00 1859 96 0.1149 491.729 488.401 1.094 0.919 0.199 3.356-2.611 100.00 3867 181 0.1421 323.041 319.738 1.084 0.920 0.109 2.608-2.026 99.99 8198 413 0.1354 214.146 212.181 1.092 0.922 0.000 2.025-1.573 100.00 17313 902 0.1641 104.578 103.927 1.093 0.926 0.000 1.573-1.221 100.00 36679 1900 0.2055 46.374 45.008 1.071 0.932 0.000 1.221-1.150 99.97 13689 708 0.2583 29.219 26.977 1.038 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0464 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1633 r_free=0.1792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.788508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2001.444807 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 0.1721 0.1845 0.0124 0.002 0.4 5.1 0.0 0.0 0 0.125 0.1584 0.1729 0.0146 0.002 0.4 4.8 0.0 0.0 0 0.250 0.1439 0.1612 0.0172 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1385 0.1573 0.0187 0.002 0.5 4.2 0.0 0.0 0 0.750 0.1361 0.1566 0.0205 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1360 0.1561 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1298 0.1521 0.0222 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1270 0.1488 0.0217 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1256 0.1479 0.0222 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1250 0.1473 0.0223 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1469 0.0227 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1236 0.1463 0.0227 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1467 0.0233 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1463 0.0232 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1228 0.1465 0.0237 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1226 0.1465 0.0239 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1222 0.1466 0.0244 0.007 0.9 3.8 0.5 0.0 0 12.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1463 0.0232 0.006 0.9 4.2 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.63 2.32 3.013 19.061 2001.445 0.017 12.31 14.63 2.32 3.013 19.061 60.043 0.017 12.37 14.59 2.22 2.668 19.061 250.181 0.017 12.70 15.25 2.55 2.730 19.230 1000.722 0.016 12.57 15.43 2.86 3.386 19.687 2001.445 0.016 12.47 15.45 2.98 3.318 19.651 3002.167 0.015 12.41 15.51 3.10 3.438 19.702 4002.890 0.015 12.36 15.47 3.11 3.446 19.696 5003.612 0.015 12.21 15.30 3.09 3.299 19.614 6004.334 0.015 12.21 15.39 3.18 3.415 19.668 7005.057 0.015 12.19 15.41 3.22 3.402 19.646 8005.779 0.015 12.16 15.38 3.22 3.446 19.662 9006.502 0.015 12.22 15.53 3.31 3.581 19.717 10007.224 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: 250.181 Accepted refinement result: 12.37 14.59 2.22 2.668 19.061 250.181 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.44 20.09 3.31 0 1785 Protein: 9.08 115.00 17.00 3.32 0 1519 Water: 11.46 119.44 38.23 N/A 0 258 Other: 19.71 26.60 22.06 N/A 0 8 Chain A: 9.08 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.26 42 64.26 - 75.30 11 75.30 - 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=0.1237 r_free=0.1459 r_work=0.1239 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1454 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1454 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016897 | | target function (ls_wunit_k1) not normalized (work): 1407.448788 | | target function (ls_wunit_k1) not normalized (free): 108.505007 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1454 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1689 n_refl.: 87592 remove outliers: r(all,work,free)=0.1676 0.1677 0.1689 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1683 0.1693 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1231 0.1447 n_refl.: 87592 remove outliers: r(all,work,free)=0.1241 0.1231 0.1447 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3504 301.086 281.110 0.644 1.004 0.374 11.894-9.307 98.04 96 4 0.1567 484.281 473.340 0.932 1.003 0.370 9.237-7.194 100.00 213 7 0.1931 394.482 387.005 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1820 296.037 290.133 0.938 1.003 0.259 5.546-4.326 100.00 867 58 0.1005 406.385 403.376 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0875 386.475 385.343 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1179 253.894 252.736 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1026 168.309 167.596 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.193 82.370 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1454 36.448 35.952 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2260 22.965 21.443 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1447 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=0.1231 r_free=0.1447 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1447 | n_water=258 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1239 r_free=0.1443 | n_water=252 | time (s): 20.110 (total time: 21.710) Filter (q & B) r_work=0.1242 r_free=0.1443 | n_water=249 | time (s): 3.000 (total time: 24.710) Compute maps r_work=0.1242 r_free=0.1443 | n_water=249 | time (s): 1.120 (total time: 25.830) Filter (map) r_work=0.1265 r_free=0.1446 | n_water=223 | time (s): 2.690 (total time: 28.520) Find peaks r_work=0.1265 r_free=0.1446 | n_water=223 | time (s): 0.600 (total time: 29.120) Add new water r_work=0.1409 r_free=0.1597 | n_water=425 | time (s): 3.010 (total time: 32.130) Refine new water occ: r_work=0.1311 r_free=0.1483 adp: r_work=0.1231 r_free=0.1425 occ: r_work=0.1243 r_free=0.1420 adp: r_work=0.1209 r_free=0.1402 occ: r_work=0.1213 r_free=0.1395 adp: r_work=0.1202 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1393 r_work=0.1202 r_free=0.1393 | n_water=425 | time (s): 63.340 (total time: 95.470) Filter (q & B) r_work=0.1205 r_free=0.1395 | n_water=410 | time (s): 2.620 (total time: 98.090) Filter (dist only) r_work=0.1206 r_free=0.1395 | n_water=409 | time (s): 35.620 (total time: 133.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.823576 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.282852 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 0.1488 0.1621 0.0133 0.001 0.4 6.4 0.0 0.0 0 0.125 0.1514 0.1634 0.0120 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1431 0.1568 0.0137 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1355 0.1515 0.0159 0.001 0.4 4.8 0.0 0.0 0 0.750 0.1323 0.1491 0.0168 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1322 0.1490 0.0168 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1259 0.1447 0.0188 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1231 0.1429 0.0199 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1216 0.1422 0.0205 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1211 0.1418 0.0207 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1203 0.1409 0.0206 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1199 0.1412 0.0213 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1198 0.1408 0.0211 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1193 0.1407 0.0214 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1191 0.1399 0.0208 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1189 0.1397 0.0209 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1188 0.1398 0.0211 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1182 0.1399 0.0218 0.008 0.9 6.4 0.5 0.0 0 13.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1397 0.0209 0.007 0.9 4.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.97 2.09 3.776 21.704 1487.283 0.016 11.89 13.97 2.09 3.776 21.704 44.618 0.016 11.89 13.97 2.09 3.776 21.704 185.910 0.016 12.09 14.45 2.36 3.617 21.715 743.641 0.015 12.10 14.80 2.70 3.445 21.987 1487.283 0.015 11.90 14.67 2.78 3.465 22.085 2230.924 0.014 11.80 14.61 2.81 3.474 21.907 2974.566 0.014 11.77 14.67 2.91 3.532 21.849 3718.207 0.014 11.79 14.80 3.01 3.525 22.134 4461.849 0.014 11.77 14.80 3.03 3.525 22.035 5205.490 0.014 11.66 14.67 3.01 3.532 22.007 5949.131 0.014 11.71 14.80 3.08 3.583 22.135 6692.773 0.014 11.66 14.73 3.07 3.578 22.097 7436.414 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.618 Accepted refinement result: 11.89 13.97 2.09 3.776 21.704 44.618 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 22.05 3.31 186 1750 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 40.70 N/A 186 223 Other: 19.75 26.63 22.10 N/A 0 8 Chain A: 9.11 115.03 19.43 N/A 0 1750 Chain S: 12.10 60.00 46.75 N/A 186 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.30 244 30.30 - 40.89 160 40.89 - 51.48 130 51.48 - 62.07 119 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1397 r_work=0.1189 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1397 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1394 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.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1187 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014999 | | target function (ls_wunit_k1) not normalized (work): 1249.324316 | | target function (ls_wunit_k1) not normalized (free): 103.078335 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1187 0.1394 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1588 0.1587 0.1646 n_refl.: 87591 remove outliers: r(all,work,free)=0.1588 0.1587 0.1646 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1590 0.1588 0.1647 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1185 0.1387 n_refl.: 87591 remove outliers: r(all,work,free)=0.1194 0.1184 0.1387 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3356 300.515 276.320 0.630 0.939 0.350 11.894-9.307 98.04 96 4 0.1518 484.281 478.008 0.986 0.939 0.332 9.237-7.194 100.00 213 7 0.1676 394.482 394.788 1.051 0.939 0.290 7.162-5.571 100.00 427 22 0.1649 296.037 291.645 1.002 0.939 0.220 5.546-4.326 100.00 867 58 0.0900 406.385 403.322 1.025 0.939 0.200 4.315-3.360 100.00 1859 96 0.0783 386.475 385.646 1.072 0.940 0.190 3.356-2.611 100.00 3867 181 0.1085 253.894 253.120 1.076 0.940 0.110 2.608-2.026 99.99 8198 413 0.1011 168.309 167.822 1.085 0.941 0.000 2.025-1.573 100.00 17313 902 0.1091 82.193 82.408 1.091 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.448 35.980 1.078 0.947 0.000 1.221-1.150 99.97 13689 708 0.2255 22.965 21.476 1.035 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0131 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1387 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=0.1184 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1387 | n_water=409 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1184 r_free=0.1387 | n_water=407 | time (s): 35.250 (total time: 37.490) Filter (q & B) r_work=0.1184 r_free=0.1387 | n_water=407 | time (s): 1.270 (total time: 38.760) Compute maps r_work=0.1184 r_free=0.1387 | n_water=407 | time (s): 1.760 (total time: 40.520) Filter (map) r_work=0.1216 r_free=0.1378 | n_water=290 | time (s): 3.390 (total time: 43.910) Find peaks r_work=0.1216 r_free=0.1378 | n_water=290 | time (s): 0.710 (total time: 44.620) Add new water r_work=0.1329 r_free=0.1506 | n_water=473 | time (s): 3.030 (total time: 47.650) Refine new water occ: r_work=0.1241 r_free=0.1419 adp: r_work=0.1242 r_free=0.1420 occ: r_work=0.1220 r_free=0.1399 adp: r_work=0.1219 r_free=0.1400 occ: r_work=0.1203 r_free=0.1380 adp: r_work=0.1198 r_free=0.1379 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1379 r_work=0.1198 r_free=0.1379 | n_water=473 | time (s): 150.650 (total time: 198.300) Filter (q & B) r_work=0.1203 r_free=0.1390 | n_water=437 | time (s): 3.260 (total time: 201.560) Filter (dist only) r_work=0.1203 r_free=0.1388 | n_water=436 | time (s): 37.590 (total time: 239.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.802772 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.159782 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 0.1229 0.1349 0.0120 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1185 0.1317 0.0131 0.003 0.7 3.5 0.5 0.0 0 0.270 0.1172 0.1310 0.0138 0.004 0.8 3.5 0.5 0.0 0 0.541 0.1164 0.1306 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.811 0.1161 0.1304 0.0143 0.006 1.0 3.5 0.5 0.0 0 1.082 0.1157 0.1304 0.0147 0.007 1.0 3.8 0.5 0.0 0 1.352 0.1155 0.1305 0.0150 0.007 1.1 4.2 0.5 0.0 0 1.622 0.1154 0.1305 0.0151 0.008 1.1 4.2 0.5 0.0 0 1.893 0.1162 0.1304 0.0142 0.006 0.9 3.8 0.5 0.0 0 0.901 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1304 0.0142 0.006 0.9 3.8 0.5 0.0 0 0.901 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.04 1.42 3.779 21.249 49.160 3.621 11.62 13.04 1.42 3.779 21.249 1.475 3.621 11.63 13.04 1.42 3.768 21.249 6.145 3.621 11.68 13.13 1.45 3.711 21.235 24.580 3.616 11.69 13.22 1.52 3.726 21.206 49.160 3.615 11.61 13.18 1.57 3.754 21.196 73.740 3.609 11.59 13.20 1.61 3.765 21.185 98.320 3.606 11.55 13.19 1.64 3.784 21.177 122.899 3.603 11.51 13.16 1.65 3.795 21.178 147.479 3.600 11.50 13.17 1.67 3.810 21.166 172.059 3.599 11.48 13.14 1.67 3.815 21.167 196.639 3.597 11.47 13.13 1.66 3.822 21.164 221.219 3.596 11.45 13.11 1.66 3.829 21.159 245.799 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.475 Accepted refinement result: 11.62 13.04 1.42 3.779 21.249 1.475 3.621 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.21 3.31 214 1749 Protein: 9.12 115.04 17.04 3.32 0 1519 Water: 11.50 76.70 35.73 N/A 214 222 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.12 115.04 19.42 N/A 0 1749 Chain S: 12.10 60.01 35.85 N/A 214 0 Histogram: Values Number of atoms 9.12 - 19.71 1262 19.71 - 30.30 286 30.30 - 40.89 211 40.89 - 51.49 125 51.49 - 62.08 56 62.08 - 72.67 12 72.67 - 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=0.1162 r_free=0.1304 r_work=0.1162 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1304 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1297 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 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= 0.1153 r_free= 0.1297 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614447 | | target function (ml) not normalized (work): 301058.157136 | | target function (ml) not normalized (free): 15830.057721 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1153 0.1297 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1494 0.1494 0.1514 n_refl.: 87589 remove outliers: r(all,work,free)=0.1494 0.1494 0.1514 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1493 0.1493 0.1514 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1149 0.1294 n_refl.: 87589 remove outliers: r(all,work,free)=0.1152 0.1145 0.1294 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3838 293.731 273.146 0.493 1.001 0.298 11.894-9.307 95.10 93 4 0.2176 478.769 463.542 0.876 1.002 0.283 9.237-7.194 98.18 209 7 0.2299 385.965 384.869 0.952 1.002 0.207 7.162-5.571 100.00 427 22 0.2105 296.037 286.213 0.925 1.002 0.173 5.546-4.326 100.00 867 58 0.1088 406.385 401.964 0.963 1.002 0.143 4.315-3.360 100.00 1859 96 0.0937 386.475 383.969 1.004 1.002 0.127 3.356-2.611 100.00 3867 181 0.1131 253.894 251.903 1.008 1.002 0.048 2.608-2.026 99.99 8198 413 0.0934 168.309 167.530 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0907 82.193 82.475 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1267 36.448 36.031 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2171 22.965 21.504 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1294 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=0.1145 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1294 | n_water=436 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1145 r_free=0.1295 | n_water=431 | time (s): 45.090 (total time: 47.540) Filter (q & B) r_work=0.1146 r_free=0.1296 | n_water=430 | time (s): 3.930 (total time: 51.470) Compute maps r_work=0.1146 r_free=0.1296 | n_water=430 | time (s): 1.790 (total time: 53.260) Filter (map) r_work=0.1166 r_free=0.1300 | n_water=327 | time (s): 4.010 (total time: 57.270) Find peaks r_work=0.1166 r_free=0.1300 | n_water=327 | time (s): 0.700 (total time: 57.970) Add new water r_work=0.1231 r_free=0.1376 | n_water=490 | time (s): 3.750 (total time: 61.720) Refine new water occ: r_work=0.1166 r_free=0.1316 adp: r_work=0.1167 r_free=0.1318 occ: r_work=0.1151 r_free=0.1297 adp: r_work=0.1150 r_free=0.1299 occ: r_work=0.1139 r_free=0.1281 adp: r_work=0.1136 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1283 r_work=0.1136 r_free=0.1283 | n_water=490 | time (s): 272.740 (total time: 334.460) Filter (q & B) r_work=0.1143 r_free=0.1293 | n_water=449 | time (s): 3.930 (total time: 338.390) Filter (dist only) r_work=0.1143 r_free=0.1292 | n_water=448 | time (s): 46.240 (total time: 384.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.744556 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.671099 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 0.1331 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1165 0.1307 0.0141 0.003 0.7 3.2 0.5 0.0 0 0.262 0.1150 0.1299 0.0148 0.005 0.9 3.5 0.5 0.0 0 0.523 0.1144 0.1296 0.0152 0.006 0.9 3.2 0.5 0.0 0 0.785 0.1140 0.1292 0.0152 0.006 1.0 3.2 0.5 0.0 0 1.047 0.1137 0.1291 0.0154 0.007 1.0 3.2 0.5 0.0 0 1.308 0.1136 0.1289 0.0153 0.008 1.1 3.8 0.5 0.0 0 1.570 0.1133 0.1290 0.0156 0.008 1.1 3.5 0.5 0.0 0 1.832 0.1142 0.1292 0.0150 0.006 1.0 3.2 0.5 0.0 0 0.872 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1289 0.0153 0.008 1.1 3.8 0.5 0.0 0 1.570 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.89 1.53 3.779 21.234 39.671 3.606 11.36 12.89 1.53 3.779 21.234 1.190 3.606 11.36 12.89 1.53 3.779 21.234 4.959 3.605 11.39 12.94 1.55 3.711 21.228 19.836 3.600 11.52 13.14 1.62 3.721 21.200 39.671 3.607 11.41 13.07 1.66 3.750 21.189 59.507 3.598 11.37 13.05 1.68 3.763 21.182 79.342 3.594 11.33 13.01 1.68 3.776 21.182 99.178 3.591 11.31 13.00 1.69 3.784 21.178 119.013 3.589 11.30 13.02 1.72 3.799 21.169 138.849 3.588 11.28 13.01 1.73 3.808 21.166 158.684 3.587 11.27 13.00 1.73 3.818 21.162 178.520 3.586 11.27 12.99 1.72 3.826 21.158 198.355 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: 1.190 Accepted refinement result: 11.36 12.89 1.53 3.779 21.234 1.190 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.19 3.31 226 1749 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.49 76.70 35.26 N/A 226 222 Other: 19.75 26.63 22.10 N/A 0 8 Chain A: 9.11 115.03 19.41 N/A 0 1749 Chain S: 12.10 60.00 34.92 N/A 226 0 Histogram: Values Number of atoms 9.11 - 19.71 1262 19.71 - 30.30 299 30.30 - 40.89 217 40.89 - 51.48 119 51.48 - 62.07 55 62.07 - 72.66 12 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=0.1136 r_free=0.1289 r_work=0.1136 r_free=0.1289 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1289 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1284 target_work(ml) = 3.602 | | 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.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602307 | | target function (ml) not normalized (work): 300014.499663 | | target function (ml) not normalized (free): 15805.433042 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1130 0.1284 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1470 0.1471 0.1488 n_refl.: 87580 remove outliers: r(all,work,free)=0.1470 0.1471 0.1488 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1469 0.1470 0.1487 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1129 0.1284 n_refl.: 87580 remove outliers: r(all,work,free)=0.1135 0.1127 0.1284 n_refl.: 87574 ======================== 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 0.3853 292.970 255.403 0.447 1.000 0.285 11.894-9.307 92.16 90 4 0.2387 476.513 458.212 0.856 1.002 0.216 9.237-7.194 98.18 209 7 0.2380 385.965 379.913 0.931 1.002 0.170 7.162-5.571 100.00 427 22 0.2113 296.037 285.008 0.918 1.002 0.170 5.546-4.326 100.00 867 58 0.1124 406.385 401.917 0.963 1.002 0.121 4.315-3.360 100.00 1859 96 0.0900 386.475 384.462 1.004 1.002 0.107 3.356-2.611 100.00 3867 181 0.1105 253.894 252.197 1.010 1.002 0.038 2.608-2.026 99.99 8198 413 0.0906 168.309 167.695 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.193 82.556 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.448 36.060 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2170 22.965 21.515 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1127 r_free=0.1284 After: r_work=0.1128 r_free=0.1284 ================================== NQH flips ================================== r_work=0.1128 r_free=0.1284 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=0.1128 r_free=0.1284 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1128 r_free=0.1284 | n_water=448 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1128 r_free=0.1284 | n_water=447 | time (s): 47.650 (total time: 50.100) Filter (q & B) r_work=0.1129 r_free=0.1285 | n_water=446 | time (s): 3.820 (total time: 53.920) Compute maps r_work=0.1129 r_free=0.1285 | n_water=446 | time (s): 1.780 (total time: 55.700) Filter (map) r_work=0.1153 r_free=0.1300 | n_water=352 | time (s): 3.970 (total time: 59.670) Find peaks r_work=0.1153 r_free=0.1300 | n_water=352 | time (s): 0.750 (total time: 60.420) Add new water r_work=0.1197 r_free=0.1353 | n_water=499 | time (s): 3.830 (total time: 64.250) Refine new water occ: r_work=0.1142 r_free=0.1294 adp: r_work=0.1142 r_free=0.1295 occ: r_work=0.1131 r_free=0.1281 adp: r_work=0.1130 r_free=0.1282 occ: r_work=0.1122 r_free=0.1270 adp: r_work=0.1119 r_free=0.1270 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1270 r_work=0.1119 r_free=0.1270 | n_water=499 | time (s): 189.550 (total time: 253.800) Filter (q & B) r_work=0.1126 r_free=0.1276 | n_water=461 | time (s): 4.020 (total time: 257.820) Filter (dist only) r_work=0.1127 r_free=0.1275 | n_water=460 | time (s): 48.440 (total time: 306.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.740108 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.067234 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 0.1326 0.0117 0.004 0.7 5.1 0.0 0.0 0 0.087 0.1161 0.1294 0.0133 0.004 0.8 5.1 0.0 0.0 0 0.261 0.1144 0.1281 0.0138 0.005 0.9 5.1 0.5 0.0 0 0.522 0.1137 0.1278 0.0141 0.006 1.0 5.1 0.5 0.0 0 0.783 0.1131 0.1275 0.0144 0.007 1.0 4.8 0.5 0.0 0 1.044 0.1128 0.1274 0.0147 0.007 1.1 4.8 0.5 0.0 0 1.305 0.1127 0.1274 0.0148 0.008 1.1 4.8 0.5 0.0 0 1.566 0.1126 0.1274 0.0148 0.008 1.1 4.8 0.5 0.0 0 1.827 0.1135 0.1277 0.0142 0.006 1.0 5.1 0.5 0.0 0 0.870 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1274 0.0148 0.008 1.1 4.8 0.5 0.0 0 1.827 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.74 1.48 3.779 21.236 46.067 3.599 11.26 12.74 1.48 3.779 21.236 1.382 3.599 11.26 12.74 1.48 3.769 21.236 5.758 3.599 11.28 12.79 1.51 3.713 21.229 23.034 3.593 11.34 12.95 1.60 3.735 21.197 46.067 3.596 11.26 12.90 1.64 3.758 21.190 69.101 3.590 11.23 12.87 1.64 3.770 21.185 92.134 3.586 11.19 12.84 1.65 3.782 21.185 115.168 3.583 11.18 12.87 1.69 3.797 21.176 138.202 3.582 11.17 12.89 1.72 3.812 21.166 161.235 3.581 11.16 12.88 1.72 3.821 21.164 184.269 3.580 11.14 12.85 1.71 3.825 21.166 207.303 3.578 11.12 12.84 1.71 3.830 21.166 230.336 3.577 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.382 Accepted refinement result: 11.26 12.74 1.48 3.779 21.236 1.382 3.599 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.20 3.31 240 1747 Protein: 9.11 115.02 17.03 3.32 0 1519 Water: 11.49 76.69 34.95 N/A 240 220 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.11 115.02 19.37 N/A 0 1747 Chain S: 12.09 60.00 34.47 N/A 240 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 299 30.29 - 40.88 227 40.88 - 51.48 122 51.48 - 62.07 51 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1126 r_free=0.1274 r_work=0.1126 r_free=0.1274 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1274 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1122 r_free = 0.1268 target_work(ml) = 3.597 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1122 r_free= 0.1268 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597213 | | target function (ml) not normalized (work): 299568.745105 | | target function (ml) not normalized (free): 15779.388660 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1317 0.1292 5.6345 5.5873| | 2: 3.57 - 2.84 1.00 2888 124 0.1044 0.1329 5.1419 5.1963| | 3: 2.83 - 2.48 1.00 2820 163 0.1083 0.1160 4.9278 4.951| | 4: 2.47 - 2.25 1.00 2825 136 0.0886 0.0999 4.6116 4.6471| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.0977 4.5595 4.6161| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.1020 4.2526 4.3621| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1098 3.9634 4.0684| | 8: 1.87 - 1.79 1.00 2789 144 0.0908 0.1079 3.8768 3.9698| | 9: 1.79 - 1.72 1.00 2745 138 0.0866 0.1163 3.6367 3.7997| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1251 3.5555 3.7412| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1026 3.4879 3.5485| | 12: 1.61 - 1.56 1.00 2773 144 0.0896 0.1154 3.3212 3.4667| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1016 3.3004 3.3821| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1041 3.2343 3.3192| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1202 3.15 3.2592| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1240 3.1309 3.2386| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1311 3.1166 3.2312| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1307 3.1023 3.2262| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1580 3.1107 3.2779| | 20: 1.34 - 1.32 1.00 2696 147 0.1369 0.1453 3.1125 3.1492| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1511 3.1128 3.1036| | 22: 1.29 - 1.27 1.00 2704 152 0.1566 0.1997 3.1233 3.2953| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1774 3.1329 3.1947| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1858 3.126 3.2332| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2166 3.1408 3.2597| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1765 3.1475 3.198| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2170 3.1695 3.1635| | 28: 1.19 - 1.18 1.00 2671 147 0.2207 0.2303 3.1663 3.1712| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2386 3.1474 3.2268| | 30: 1.16 - 1.15 1.00 2739 148 0.2451 0.2437 3.1431 3.1643| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 8.22 1.00 0.97 5489.98| | 2: 3.57 - 2.84 2888 124 0.93 12.17 1.01 0.97 5489.98| | 3: 2.83 - 2.48 2820 163 0.90 16.10 0.99 0.97 4587.66| | 4: 2.47 - 2.25 2825 136 0.92 13.16 1.00 0.98 2260.85| | 5: 2.25 - 2.09 2756 127 0.91 15.26 1.01 0.98 2260.85| | 6: 2.09 - 1.97 2846 113 0.93 12.15 1.02 0.98 1308.47| | 7: 1.97 - 1.87 2787 165 0.95 9.09 1.02 0.98 496.22| | 8: 1.87 - 1.79 2789 144 0.93 12.40 1.00 0.98 496.22| | 9: 1.79 - 1.72 2745 138 0.95 9.85 0.98 0.97 282.41| | 10: 1.72 - 1.66 2831 160 0.94 10.95 0.98 0.97 239.59| | 11: 1.66 - 1.61 2712 147 0.94 11.56 0.98 0.97 229.65| | 12: 1.61 - 1.56 2773 144 0.96 8.83 0.99 0.97 135.88| | 13: 1.56 - 1.52 2745 130 0.95 10.34 1.02 0.97 135.88| | 14: 1.52 - 1.48 2803 134 0.94 10.71 1.02 0.98 122.13| | 15: 1.48 - 1.45 2738 128 0.95 9.88 1.02 0.98 96.95| | 16: 1.45 - 1.42 2756 161 0.94 11.01 1.02 0.98 96.95| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.44| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 83.51| | 19: 1.36 - 1.34 2807 134 0.94 11.83 0.99 0.98 83.51| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.96 79.85| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.96 79.60| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.01| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.13| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.13| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 84.05| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.18| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.18| | 28: 1.19 - 1.18 2671 147 0.88 20.34 1.01 0.93 89.56| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.99 0.92 90.83| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.83| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.60 max = 5489.98 mean = 851.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.33| |phase err.(test): min = 0.00 max = 89.55 mean = 13.31| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1122 0.1268 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1467 n_refl.: 87574 remove outliers: r(all,work,free)=0.1442 0.1442 0.1467 n_refl.: 87574 overall B=-0.00 to atoms: r(all,work,free)=0.1441 0.1441 0.1466 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1122 0.1269 n_refl.: 87574 remove outliers: r(all,work,free)=0.1128 0.1121 0.1269 n_refl.: 87571 ======================== 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 0.4010 288.203 257.689 0.434 1.000 0.273 11.894-9.307 91.18 89 4 0.2328 472.622 461.467 0.872 1.002 0.253 9.237-7.194 97.73 208 7 0.2342 387.047 378.569 0.925 1.002 0.150 7.162-5.571 100.00 427 22 0.2102 296.037 285.577 0.906 1.002 0.130 5.546-4.326 100.00 867 58 0.1123 406.385 401.622 0.963 1.002 0.110 4.315-3.360 100.00 1859 96 0.0904 386.475 384.447 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1084 253.894 252.185 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0899 168.309 167.663 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.193 82.546 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.448 36.058 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2169 22.965 21.519 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=-0.0137 ================= 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 : 0.2606 0.1975 0.084 5.432 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1789 0.084 5.432 9.0 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1789 0.084 5.432 9.0 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1792 0.084 5.432 9.0 119.5 20.1 258 0.003 1_weight: 0.1633 0.1792 0.084 5.432 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1231 0.1463 0.006 0.851 9.0 119.5 20.1 258 0.137 1_adp: 0.1237 0.1459 0.006 0.851 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1239 0.1462 0.006 0.851 9.1 119.4 20.1 258 0.137 1_occ: 0.1232 0.1454 0.006 0.851 9.1 119.4 20.1 258 0.137 2_bss: 0.1231 0.1447 0.006 0.851 9.1 119.5 20.1 258 0.137 2_settarget: 0.1231 0.1447 0.006 0.851 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1231 0.1447 0.006 0.855 9.1 119.5 20.1 258 0.137 2_nqh: 0.1231 0.1447 0.006 0.855 9.1 119.5 20.1 258 0.137 2_sol: 0.1206 0.1395 0.006 0.855 9.1 115.0 22.1 409 n/a 2_weight: 0.1206 0.1395 0.006 0.855 9.1 115.0 22.1 409 n/a 2_xyzrec: 0.1189 0.1397 0.007 0.876 9.1 115.0 22.1 409 n/a 2_adp: 0.1189 0.1397 0.007 0.876 9.1 115.0 22.1 409 n/a 2_regHadp: 0.1189 0.1397 0.007 0.876 9.1 115.0 22.1 409 n/a 2_occ: 0.1187 0.1394 0.007 0.876 9.1 115.0 22.1 409 n/a 3_bss: 0.1184 0.1387 0.007 0.876 9.1 115.0 22.1 409 n/a 3_settarget: 0.1184 0.1387 0.007 0.876 9.1 115.0 22.1 409 n/a 3_updatecdl: 0.1184 0.1387 0.007 0.876 9.1 115.0 22.1 409 n/a 3_nqh: 0.1184 0.1387 0.007 0.876 9.1 115.0 22.1 409 n/a 3_sol: 0.1203 0.1388 0.007 0.876 9.1 115.0 21.2 436 n/a 3_weight: 0.1203 0.1388 0.007 0.876 9.1 115.0 21.2 436 n/a 3_xyzrec: 0.1162 0.1304 0.006 0.936 9.1 115.0 21.2 436 n/a 3_adp: 0.1162 0.1304 0.006 0.936 9.1 115.0 21.2 436 n/a 3_regHadp: 0.1162 0.1304 0.006 0.936 9.1 115.0 21.2 436 n/a 3_occ: 0.1153 0.1297 0.006 0.936 9.1 115.0 21.2 436 n/a 4_bss: 0.1145 0.1294 0.006 0.936 9.1 115.0 21.2 436 n/a 4_settarget: 0.1145 0.1294 0.006 0.936 9.1 115.0 21.2 436 n/a 4_updatecdl: 0.1145 0.1294 0.006 0.937 9.1 115.0 21.2 436 n/a 4_nqh: 0.1145 0.1294 0.006 0.937 9.1 115.0 21.2 436 n/a 4_sol: 0.1143 0.1292 0.006 0.937 9.1 115.0 21.2 448 n/a 4_weight: 0.1143 0.1292 0.006 0.937 9.1 115.0 21.2 448 n/a 4_xyzrec: 0.1136 0.1289 0.008 1.083 9.1 115.0 21.2 448 n/a 4_adp: 0.1136 0.1289 0.008 1.083 9.1 115.0 21.2 448 n/a 4_regHadp: 0.1136 0.1289 0.008 1.083 9.1 115.0 21.2 448 n/a 4_occ: 0.1130 0.1284 0.008 1.083 9.1 115.0 21.2 448 n/a 5_bss: 0.1127 0.1284 0.008 1.083 9.1 115.0 21.2 448 n/a 5_settarget: 0.1127 0.1284 0.008 1.083 9.1 115.0 21.2 448 n/a 5_updatecdl: 0.1127 0.1284 0.008 1.084 9.1 115.0 21.2 448 n/a 5_setrh: 0.1128 0.1284 0.008 1.084 9.1 115.0 21.2 448 n/a 5_nqh: 0.1128 0.1284 0.008 1.084 9.1 115.0 21.2 448 n/a 5_sol: 0.1127 0.1275 0.008 1.084 9.1 115.0 21.2 460 n/a 5_weight: 0.1127 0.1275 0.008 1.084 9.1 115.0 21.2 460 n/a 5_xyzrec: 0.1126 0.1274 0.008 1.113 9.1 115.0 21.2 460 n/a 5_adp: 0.1126 0.1274 0.008 1.113 9.1 115.0 21.2 460 n/a 5_regHadp: 0.1126 0.1274 0.008 1.113 9.1 115.0 21.2 460 n/a 5_occ: 0.1122 0.1268 0.008 1.113 9.1 115.0 21.2 460 n/a end: 0.1121 0.1269 0.008 1.113 9.1 115.0 21.2 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8530424_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8530424_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8500 Refinement macro-cycles (run) : 13399.5300 Write final files (write_after_run_outputs) : 98.7400 Total : 13502.1200 Total CPU time: 3.76 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:04:09 PST -0800 (1735365849.61 s) Start R-work = 0.1632, R-free = 0.1789 Final R-work = 0.1121, R-free = 0.1269 =============================================================================== Job complete usr+sys time: 13689.29 seconds wall clock time: 248 minutes 40.17 seconds (14920.17 seconds total)