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_1617309.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_1617309.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1617309.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.36, per 1000 atoms: 0.40 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: 0.47 Conformation dependent library (CDL) restraints added in 167.9 milliseconds Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 550 0.91 - 1.17: 1095 1.17 - 1.42: 641 1.42 - 1.67: 828 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.400 0.137 5.00e-03 4.00e+04 7.49e+02 bond pdb=" CA TYR A 141 " pdb=" C TYR A 141 " ideal model delta sigma weight residual 1.524 1.275 0.249 1.31e-02 5.83e+03 3.61e+02 bond pdb=" C BGLN A 80 " pdb=" O BGLN A 80 " ideal model delta sigma weight residual 1.236 1.020 0.216 1.15e-02 7.56e+03 3.53e+02 bond pdb=" C GLN A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 1.334 1.563 -0.229 1.25e-02 6.40e+03 3.35e+02 bond pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta sigma weight residual 1.458 1.671 -0.213 1.17e-02 7.31e+03 3.32e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 3470 5.34 - 10.68: 1850 10.68 - 16.02: 409 16.02 - 21.36: 45 21.36 - 26.71: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 104.35 14.85 9.00e-01 1.23e+00 2.72e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 138.56 -15.38 1.05e+00 9.07e-01 2.15e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.63 134.55 -13.92 1.08e+00 8.57e-01 1.66e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 109.84 12.76 1.00e+00 1.00e+00 1.63e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 128.37 -7.95 6.40e-01 2.44e+00 1.54e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.45: 938 17.45 - 34.89: 117 34.89 - 52.33: 39 52.33 - 69.78: 15 69.78 - 87.22: 2 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 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+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 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.211: 98 0.211 - 0.419: 75 0.419 - 0.628: 53 0.628 - 0.837: 12 0.837 - 1.046: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG PHE A 164 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.048 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG PHE A 162 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.070 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.109 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1240 2.34 - 2.91: 8270 2.91 - 3.47: 10441 3.47 - 4.04: 15154 4.04 - 4.60: 21532 Nonbonded interactions: 56637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.781 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.810 1.850 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.811 1.850 nonbonded pdb=" O GLN A 95 " pdb=" H BGLY A 100 " model vdw 1.826 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.840 1.850 ... (remaining 56632 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_1617309_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= 0.2605 r_free= 0.1927 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792367 | | target function (ml) not normalized (work): 232620.918292 | | target function (ml) not normalized (free): 11806.674244 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3027 0.2013 7.1352 4.9365| | 2: 3.57 - 2.84 1.00 2876 122 0.2455 0.1858 4.3436 4.336| | 3: 2.84 - 2.48 1.00 2833 165 0.2346 0.1740 4.1212 4.1811| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1474 3.8277 3.8186| | 5: 2.25 - 2.09 1.00 2756 127 0.2445 0.1486 3.7945 3.8267| | 6: 2.09 - 1.97 1.00 2846 113 0.2544 0.1592 3.4756 3.5415| | 7: 1.97 - 1.87 1.00 2787 165 0.2523 0.1879 3.1388 3.227| | 8: 1.87 - 1.79 1.00 2789 144 0.2555 0.1923 3.0781 3.1416| | 9: 1.79 - 1.72 1.00 2745 138 0.2376 0.1861 2.8947 2.9812| | 10: 1.72 - 1.66 1.00 2789 158 0.2384 0.1793 2.7997 2.8347| | 11: 1.66 - 1.61 1.00 2740 147 0.2486 0.1794 2.7347 2.7418| | 12: 1.61 - 1.56 1.00 2787 146 0.2482 0.1874 2.6183 2.6396| | 13: 1.56 - 1.52 1.00 2745 130 0.2551 0.2135 2.5562 2.6942| | 14: 1.52 - 1.48 1.00 2803 134 0.2585 0.1815 2.4936 2.4652| | 15: 1.48 - 1.45 1.00 2738 128 0.2609 0.2121 2.4232 2.446| | 16: 1.45 - 1.42 1.00 2756 161 0.2716 0.2166 2.3867 2.4417| | 17: 1.42 - 1.39 1.00 2785 139 0.2642 0.2241 2.3389 2.3784| | 18: 1.39 - 1.36 1.00 2741 179 0.2624 0.2086 2.2785 2.2884| | 19: 1.36 - 1.34 1.00 2807 134 0.2642 0.2377 2.2392 2.3286| | 20: 1.34 - 1.32 1.00 2696 147 0.2609 0.2222 2.198 2.1968| | 21: 1.32 - 1.30 1.00 2785 112 0.2730 0.2221 2.1532 2.1643| | 22: 1.29 - 1.27 1.00 2704 152 0.2746 0.2464 2.1482 2.1649| | 23: 1.27 - 1.26 1.00 2802 156 0.2740 0.2395 2.1036 2.1491| | 24: 1.26 - 1.24 1.00 2744 132 0.2777 0.2597 2.0729 2.1921| | 25: 1.24 - 1.22 1.00 2734 148 0.2852 0.2562 2.0482 2.0973| | 26: 1.22 - 1.21 1.00 2727 135 0.2897 0.2089 2.0116 2.0136| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2840 2.0139 2.059| | 28: 1.19 - 1.18 1.00 2671 147 0.2978 0.2828 1.9868 1.9973| | 29: 1.18 - 1.16 1.00 2800 134 0.2951 0.2844 1.9569 2.0322| | 30: 1.16 - 1.15 1.00 2740 148 0.3079 0.2930 1.9395 1.9908| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1453.18| | 2: 3.57 - 2.84 2876 122 0.81 25.83 1.27 0.23 1453.18| | 3: 2.84 - 2.48 2833 165 0.74 31.63 1.25 0.24 1206.28| | 4: 2.47 - 2.25 2825 136 0.81 25.58 1.26 0.25 565.54| | 5: 2.25 - 2.09 2756 127 0.77 29.15 1.28 0.25 565.54| | 6: 2.09 - 1.97 2846 113 0.83 22.84 1.29 0.25 311.64| | 7: 1.97 - 1.87 2787 165 0.89 17.21 1.27 0.25 95.09| | 8: 1.87 - 1.79 2789 144 0.85 21.60 1.26 0.25 95.09| | 9: 1.79 - 1.72 2745 138 0.88 18.79 1.23 0.25 56.69| | 10: 1.72 - 1.66 2789 158 0.86 20.26 1.22 0.25 49.00| | 11: 1.66 - 1.61 2740 147 0.85 21.75 1.24 0.25 47.21| | 12: 1.61 - 1.56 2787 146 0.89 18.20 1.24 0.25 29.03| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.24 0.25 29.03| | 14: 1.52 - 1.48 2803 134 0.87 20.56 1.24 0.25 25.82| | 15: 1.48 - 1.45 2738 128 0.87 19.96 1.24 0.25 19.94| | 16: 1.45 - 1.42 2756 161 0.86 21.23 1.25 0.25 19.94| | 17: 1.42 - 1.39 2785 139 0.87 20.27 1.22 0.25 17.14| | 18: 1.39 - 1.36 2741 179 0.87 20.83 1.22 0.25 15.52| | 19: 1.36 - 1.34 2807 134 0.86 21.74 1.22 0.25 15.52| | 20: 1.34 - 1.32 2696 147 0.87 20.81 1.19 0.25 12.91| | 21: 1.32 - 1.30 2785 112 0.86 21.98 1.22 0.25 12.73| | 22: 1.29 - 1.27 2704 152 0.86 22.17 1.20 0.25 12.48| | 23: 1.27 - 1.26 2802 156 0.86 22.23 1.21 0.24 11.22| | 24: 1.26 - 1.24 2744 132 0.84 23.24 1.20 0.24 11.22| | 25: 1.24 - 1.22 2734 148 0.84 24.11 1.20 0.23 10.74| | 26: 1.22 - 1.21 2727 135 0.83 24.67 1.20 0.23 10.21| | 27: 1.21 - 1.19 2814 148 0.83 25.39 1.20 0.23 10.21| | 28: 1.19 - 1.18 2671 147 0.82 26.34 1.18 0.22 9.87| | 29: 1.18 - 1.16 2800 134 0.81 26.90 1.16 0.22 9.74| | 30: 1.16 - 1.15 2740 148 0.79 28.64 1.14 0.22 9.74| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.74 max = 1453.18 mean = 212.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.76| |phase err.(test): min = 0.00 max = 89.83 mean = 22.71| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.249 1557 Z= 5.572 Angle : 5.349 20.777 2118 Z= 3.757 Chirality : 0.370 1.046 243 Planarity : 0.033 0.089 284 Dihedral : 13.847 87.219 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.89 % 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: -1.93 (0.51), residues: 224 helix: -2.69 (0.40), residues: 101 sheet: 0.90 (0.96), residues: 28 loop : -0.02 (0.61), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.021 ARG A 27 TYR 0.102 0.046 TYR A 139 PHE 0.115 0.051 PHE A 164 HIS 0.086 0.045 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1927 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792367 | | target function (ml) not normalized (work): 232620.918292 | | target function (ml) not normalized (free): 11806.674244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2606 0.1928 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2606 0.1928 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1982 0.1928 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2002 0.2007 0.1941 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1640 0.1763 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1639 0.1763 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 0.3835 386.113 358.559 0.673 1.004 0.411 11.894-9.307 99.02 97 4 0.1841 613.322 593.360 0.925 1.004 0.380 9.237-7.194 100.00 213 7 0.2104 501.622 490.673 0.959 1.004 0.363 7.162-5.571 100.00 427 22 0.2158 376.439 364.326 0.933 1.004 0.293 5.546-4.326 100.00 867 58 0.1280 516.758 511.565 0.961 1.003 0.228 4.315-3.360 100.00 1859 96 0.1153 491.441 486.660 1.007 1.003 0.199 3.356-2.611 100.00 3867 181 0.1449 322.851 319.483 0.997 1.002 0.119 2.608-2.026 99.99 8198 413 0.1357 214.021 211.939 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.517 103.900 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2066 46.347 45.014 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2595 29.202 26.880 0.975 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1639 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1646 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.760211 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1990.950718 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 0.1619 0.1739 0.0120 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1492 0.1633 0.0141 0.001 0.5 4.2 0.0 0.0 0 0.250 0.1424 0.1578 0.0154 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1361 0.1538 0.0177 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1358 0.1547 0.0188 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1342 0.1534 0.0192 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1273 0.1484 0.0211 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1278 0.1510 0.0232 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1484 0.0230 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1250 0.1486 0.0236 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1237 0.1473 0.0236 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1237 0.1475 0.0238 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1234 0.1475 0.0241 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1475 0.0242 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1232 0.1477 0.0245 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1468 0.0242 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1224 0.1471 0.0247 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1222 0.1468 0.0246 0.008 1.0 3.8 0.5 0.6 0 13.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1222 0.1468 0.0246 0.008 1.0 3.8 0.5 0.6 0 13.880 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.68 2.46 3.013 19.064 1990.951 0.017 12.22 14.68 2.46 2.989 19.064 59.729 0.017 12.29 14.67 2.37 2.668 19.063 248.869 0.017 12.61 15.29 2.68 2.733 19.218 995.475 0.016 12.44 15.41 2.97 2.989 19.412 1990.951 0.016 12.41 15.50 3.09 3.313 19.625 2986.426 0.015 12.31 15.48 3.17 3.381 19.657 3981.901 0.015 12.13 15.36 3.23 3.168 19.545 4977.377 0.015 12.15 15.37 3.22 3.287 19.592 5972.852 0.015 12.15 15.37 3.22 3.179 19.517 6968.328 0.015 12.14 15.43 3.29 3.373 19.622 7963.803 0.015 12.10 15.40 3.30 3.395 19.621 8959.278 0.015 12.16 15.55 3.38 3.555 19.697 9954.754 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: 248.869 Accepted refinement result: 12.29 14.67 2.37 2.668 19.063 248.869 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.45 20.09 3.31 0 1785 Protein: 9.06 115.00 17.00 3.32 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.70 26.61 22.06 N/A 0 8 Chain A: 9.06 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 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 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1467 r_work=0.1231 r_free=0.1470 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1470 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 = 0.1225 r_free = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1225 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016795 | | target function (ls_wunit_k1) not normalized (work): 1398.970728 | | target function (ls_wunit_k1) not normalized (free): 110.329609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1225 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1699 n_refl.: 87593 remove outliers: r(all,work,free)=0.1669 0.1670 0.1699 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1675 0.1676 0.1703 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1234 0.1223 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1234 0.1223 0.1455 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3590 304.148 279.771 0.660 1.003 0.385 11.894-9.307 99.02 97 4 0.1640 483.125 470.917 0.923 1.003 0.381 9.237-7.194 100.00 213 7 0.1910 395.136 388.762 0.964 1.003 0.350 7.162-5.571 100.00 427 22 0.1827 296.528 290.672 0.935 1.003 0.254 5.546-4.326 100.00 867 58 0.0993 407.060 404.148 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0867 387.116 386.067 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1172 254.315 253.147 1.009 1.002 0.053 2.608-2.026 99.99 8198 413 0.1020 168.588 167.838 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.330 82.534 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1443 36.508 36.016 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2244 23.003 21.489 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1455 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=0.1223 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1455 | n_water=258 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1235 r_free=0.1450 | n_water=250 | time (s): 19.780 (total time: 21.770) Filter (q & B) r_work=0.1237 r_free=0.1450 | n_water=247 | time (s): 2.330 (total time: 24.100) Compute maps r_work=0.1237 r_free=0.1450 | n_water=247 | time (s): 1.430 (total time: 25.530) Filter (map) r_work=0.1260 r_free=0.1448 | n_water=220 | time (s): 2.960 (total time: 28.490) Find peaks r_work=0.1260 r_free=0.1448 | n_water=220 | time (s): 0.510 (total time: 29.000) Add new water r_work=0.1407 r_free=0.1611 | n_water=423 | time (s): 2.290 (total time: 31.290) Refine new water occ: r_work=0.1308 r_free=0.1486 adp: r_work=0.1226 r_free=0.1432 occ: r_work=0.1238 r_free=0.1416 adp: r_work=0.1203 r_free=0.1402 occ: r_work=0.1205 r_free=0.1388 adp: r_work=0.1196 r_free=0.1388 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1388 r_work=0.1196 r_free=0.1388 | n_water=423 | time (s): 58.500 (total time: 89.790) Filter (q & B) r_work=0.1198 r_free=0.1390 | n_water=412 | time (s): 2.810 (total time: 92.600) Filter (dist only) r_work=0.1199 r_free=0.1390 | n_water=410 | time (s): 34.170 (total time: 126.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.016722 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1499.351984 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 0.1649 0.1756 0.0106 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1488 0.1616 0.0128 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1399 0.1546 0.0147 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1355 0.1515 0.0160 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1312 0.1481 0.0169 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1314 0.1484 0.0170 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1262 0.1457 0.0195 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1231 0.1438 0.0206 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1217 0.1423 0.0207 0.003 0.7 5.4 0.5 0.0 0 4.000 0.1207 0.1418 0.0211 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1206 0.1422 0.0216 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1200 0.1416 0.0216 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1196 0.1414 0.0218 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1192 0.1417 0.0224 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1189 0.1414 0.0225 0.006 0.9 4.8 0.5 0.6 0 10.000 0.1188 0.1421 0.0233 0.007 0.9 4.8 0.5 0.6 0 11.000 0.1186 0.1421 0.0234 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1189 0.1436 0.0247 0.007 0.9 4.5 0.5 0.6 0 13.000 0.1185 0.1418 0.0233 0.008 1.0 5.1 0.5 0.6 0 14.508 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1414 0.0218 0.005 0.8 4.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.14 2.18 3.776 21.719 1499.352 0.016 11.96 14.14 2.18 3.776 21.719 44.981 0.016 11.96 14.14 2.18 3.776 21.719 187.419 0.016 12.20 14.68 2.47 3.585 21.746 749.676 0.016 12.13 14.89 2.76 3.450 21.965 1499.352 0.015 11.95 14.71 2.76 3.457 22.040 2249.028 0.015 11.84 14.81 2.97 3.514 21.834 2998.704 0.014 11.81 14.87 3.06 3.504 21.885 3748.380 0.014 11.79 14.76 2.96 3.496 22.019 4498.056 0.014 11.76 14.84 3.08 3.509 21.985 5247.732 0.014 11.77 14.90 3.13 3.534 22.046 5997.408 0.014 11.74 14.89 3.15 3.550 22.048 6747.084 0.014 11.71 14.85 3.14 3.562 22.060 7496.760 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: 187.419 Accepted refinement result: 11.96 14.14 2.18 3.776 21.719 187.419 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 22.08 3.31 190 1747 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.50 76.70 40.78 N/A 190 220 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.03 19.37 N/A 0 1747 Chain S: 15.07 60.00 46.99 N/A 190 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 246 30.28 - 40.88 167 40.88 - 51.47 122 51.47 - 62.07 120 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=0.1196 r_free=0.1414 r_work=0.1196 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1414 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1193 r_free= 0.1412 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015223 | | target function (ls_wunit_k1) not normalized (work): 1268.013441 | | target function (ls_wunit_k1) not normalized (free): 104.426207 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1193 0.1412 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1594 0.1593 0.1652 n_refl.: 87593 remove outliers: r(all,work,free)=0.1594 0.1593 0.1652 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1596 0.1594 0.1653 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1191 0.1409 n_refl.: 87593 remove outliers: r(all,work,free)=0.1200 0.1189 0.1409 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3395 297.488 278.236 0.595 1.003 0.350 11.894-9.307 99.02 97 4 0.1659 483.125 475.008 0.912 1.003 0.333 9.237-7.194 100.00 213 7 0.1686 395.136 393.985 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1580 296.528 292.014 0.939 1.003 0.240 5.546-4.326 100.00 867 58 0.0888 407.060 403.935 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0781 387.116 386.007 1.006 1.003 0.200 3.356-2.611 100.00 3867 181 0.1092 254.315 253.427 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1015 168.588 168.016 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.330 82.556 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.508 36.046 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.003 21.520 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1409 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1409 | n_water=410 | time (s): 1.510 (total time: 1.510) Filter (dist) r_work=0.1191 r_free=0.1411 | n_water=409 | time (s): 35.760 (total time: 37.270) Filter (q & B) r_work=0.1191 r_free=0.1411 | n_water=409 | time (s): 0.760 (total time: 38.030) Compute maps r_work=0.1191 r_free=0.1411 | n_water=409 | time (s): 1.220 (total time: 39.250) Filter (map) r_work=0.1235 r_free=0.1411 | n_water=278 | time (s): 3.370 (total time: 42.620) Find peaks r_work=0.1235 r_free=0.1411 | n_water=278 | time (s): 0.600 (total time: 43.220) Add new water r_work=0.1350 r_free=0.1549 | n_water=456 | time (s): 3.010 (total time: 46.230) Refine new water occ: r_work=0.1256 r_free=0.1443 adp: r_work=0.1257 r_free=0.1448 occ: r_work=0.1236 r_free=0.1417 adp: r_work=0.1235 r_free=0.1421 occ: r_work=0.1221 r_free=0.1391 adp: r_work=0.1216 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1393 r_work=0.1216 r_free=0.1393 | n_water=456 | time (s): 187.090 (total time: 233.320) Filter (q & B) r_work=0.1221 r_free=0.1401 | n_water=425 | time (s): 2.760 (total time: 236.080) Filter (dist only) r_work=0.1221 r_free=0.1398 | n_water=424 | time (s): 35.360 (total time: 271.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.753355 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.425602 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 0.1244 0.1369 0.0125 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1204 0.1333 0.0129 0.003 0.7 3.5 0.5 0.0 0 0.263 0.1184 0.1322 0.0138 0.004 0.8 3.2 0.5 0.0 0 0.526 0.1175 0.1318 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.789 0.1171 0.1315 0.0145 0.006 1.0 3.2 0.5 0.0 0 1.052 0.1168 0.1315 0.0146 0.006 1.0 3.8 0.5 0.0 0 1.315 0.1167 0.1315 0.0148 0.007 1.0 4.5 0.5 0.0 0 1.578 0.1164 0.1315 0.0150 0.008 1.1 4.5 0.5 0.0 0 1.841 0.1174 0.1316 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1167 0.1315 0.0148 0.007 1.0 4.5 0.5 0.0 0 1.578 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 13.15 1.48 3.779 21.162 37.426 3.623 11.67 13.15 1.48 3.779 21.162 1.123 3.623 11.67 13.15 1.48 3.777 21.162 4.678 3.623 11.70 13.20 1.50 3.710 21.156 18.713 3.617 11.78 13.37 1.60 3.729 21.126 37.426 3.623 11.67 13.33 1.66 3.754 21.113 56.138 3.615 11.62 13.31 1.69 3.769 21.105 74.851 3.611 11.59 13.30 1.71 3.779 21.101 93.564 3.608 11.57 13.29 1.72 3.788 21.097 112.277 3.605 11.55 13.28 1.72 3.798 21.090 130.990 3.603 11.54 13.28 1.74 3.811 21.083 149.702 3.602 11.56 13.30 1.74 3.826 21.069 168.415 3.602 11.53 13.28 1.75 3.834 21.070 187.128 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.123 Accepted refinement result: 11.67 13.15 1.48 3.779 21.162 1.123 3.623 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.05 3.31 207 1744 Protein: 9.11 115.04 17.04 3.32 0 1519 Water: 11.51 76.71 35.39 N/A 207 217 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.32 N/A 0 1744 Chain S: 15.09 60.01 35.60 N/A 207 0 Histogram: Values Number of atoms 9.11 - 19.70 1261 19.70 - 30.29 292 30.29 - 40.89 205 40.89 - 51.48 118 51.48 - 62.08 52 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1315 r_work=0.1167 r_free=0.1315 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1315 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1156 r_free = 0.1306 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.13 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= 0.1156 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615168 | | target function (ml) not normalized (work): 301118.181392 | | target function (ml) not normalized (free): 15847.975621 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1156 0.1306 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1498 0.1499 0.1518 n_refl.: 87589 remove outliers: r(all,work,free)=0.1498 0.1499 0.1518 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1498 0.1517 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1151 0.1300 n_refl.: 87589 remove outliers: r(all,work,free)=0.1155 0.1147 0.1300 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 91.67 83 5 0.3803 294.219 269.063 0.485 1.000 0.300 11.894-9.307 97.06 95 4 0.2294 476.454 462.621 0.862 1.002 0.287 9.237-7.194 97.73 208 7 0.2369 387.690 385.135 0.953 1.002 0.200 7.162-5.571 100.00 427 22 0.2167 296.528 284.550 0.918 1.002 0.177 5.546-4.326 100.00 867 58 0.1106 407.060 402.369 0.963 1.002 0.149 4.315-3.360 100.00 1859 96 0.0952 387.116 384.509 1.005 1.002 0.133 3.356-2.611 100.00 3867 181 0.1143 254.315 252.163 1.008 1.002 0.038 2.608-2.026 99.99 8198 413 0.0932 168.588 167.856 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.330 82.610 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1258 36.508 36.084 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 23.003 21.536 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=-0.0164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1300 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1151 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1301 | n_water=424 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1152 r_free=0.1299 | n_water=422 | time (s): 46.260 (total time: 48.520) Filter (q & B) r_work=0.1152 r_free=0.1301 | n_water=420 | time (s): 3.770 (total time: 52.290) Compute maps r_work=0.1152 r_free=0.1301 | n_water=420 | time (s): 1.780 (total time: 54.070) Filter (map) r_work=0.1181 r_free=0.1316 | n_water=315 | time (s): 3.720 (total time: 57.790) Find peaks r_work=0.1181 r_free=0.1316 | n_water=315 | time (s): 0.680 (total time: 58.470) Add new water r_work=0.1242 r_free=0.1383 | n_water=475 | time (s): 3.630 (total time: 62.100) Refine new water occ: r_work=0.1169 r_free=0.1331 adp: r_work=0.1169 r_free=0.1333 occ: r_work=0.1155 r_free=0.1318 adp: r_work=0.1154 r_free=0.1319 occ: r_work=0.1144 r_free=0.1310 adp: r_work=0.1141 r_free=0.1307 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1307 r_work=0.1141 r_free=0.1307 | n_water=475 | time (s): 229.440 (total time: 291.540) Filter (q & B) r_work=0.1150 r_free=0.1317 | n_water=434 | time (s): 3.800 (total time: 295.340) Filter (dist only) r_work=0.1150 r_free=0.1315 | n_water=433 | time (s): 44.490 (total time: 339.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.752116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.196012 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 0.1213 0.1350 0.0138 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1169 0.1323 0.0154 0.003 0.8 4.2 0.5 0.0 0 0.263 0.1159 0.1315 0.0156 0.005 0.9 3.8 0.5 0.0 0 0.526 0.1153 0.1312 0.0160 0.005 0.9 3.5 0.5 0.0 0 0.788 0.1149 0.1312 0.0163 0.006 1.0 3.8 0.5 0.0 0 1.051 0.1146 0.1311 0.0165 0.007 1.0 3.8 0.5 0.0 0 1.314 0.1145 0.1311 0.0167 0.008 1.1 4.2 0.5 0.0 0 1.577 0.1143 0.1311 0.0167 0.008 1.1 4.2 0.5 0.0 0 1.840 0.1151 0.1312 0.0161 0.006 1.0 3.5 0.5 0.0 0 0.876 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1143 0.1311 0.0167 0.008 1.1 4.2 0.5 0.0 0 1.840 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 13.11 1.67 3.780 21.115 40.196 3.611 11.43 13.11 1.67 3.780 21.115 1.206 3.611 11.43 13.11 1.67 3.778 21.115 5.025 3.611 11.47 13.16 1.69 3.713 21.106 20.098 3.606 11.57 13.32 1.75 3.731 21.074 40.196 3.612 11.50 13.29 1.79 3.751 21.062 60.294 3.605 11.42 13.23 1.81 3.773 21.058 80.392 3.599 11.39 13.21 1.82 3.784 21.057 100.490 3.597 11.37 13.19 1.82 3.794 21.054 120.588 3.595 11.35 13.19 1.84 3.803 21.049 140.686 3.594 11.37 13.24 1.87 3.822 21.032 160.784 3.594 11.34 13.21 1.87 3.830 21.033 180.882 3.592 11.32 13.20 1.88 3.832 21.037 200.980 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.206 Accepted refinement result: 11.43 13.11 1.67 3.780 21.115 1.206 3.611 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 20.97 3.31 217 1743 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 34.75 N/A 217 216 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.04 19.31 N/A 0 1743 Chain S: 15.08 60.00 34.25 N/A 217 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.29 300 30.29 - 40.88 212 40.88 - 51.48 117 51.48 - 62.07 44 62.07 - 72.66 12 72.66 - 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=0.1143 r_free=0.1311 r_work=0.1143 r_free=0.1311 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1311 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1309 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1309 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608966 | | target function (ml) not normalized (work): 300572.739042 | | target function (ml) not normalized (free): 15842.284514 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1140 0.1309 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1474 0.1473 0.1509 n_refl.: 87581 remove outliers: r(all,work,free)=0.1474 0.1473 0.1509 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1473 0.1473 0.1508 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1309 n_refl.: 87581 remove outliers: r(all,work,free)=0.1147 0.1139 0.1309 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4067 291.240 258.702 0.445 1.000 0.290 11.894-9.307 95.10 93 4 0.2421 477.642 457.302 0.846 1.002 0.277 9.237-7.194 97.73 208 7 0.2402 387.690 377.077 0.926 1.002 0.180 7.162-5.571 100.00 427 22 0.2205 296.528 284.661 0.909 1.002 0.160 5.546-4.326 100.00 867 58 0.1121 407.060 402.731 0.963 1.003 0.119 4.315-3.360 100.00 1859 96 0.0940 387.116 384.958 1.004 1.002 0.103 3.356-2.611 100.00 3867 181 0.1126 254.315 252.618 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0912 168.588 168.015 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.330 82.682 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.508 36.111 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 23.003 21.543 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0124 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1139 r_free=0.1309 After: r_work=0.1140 r_free=0.1309 ================================== NQH flips ================================== r_work=0.1140 r_free=0.1309 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1140 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1309 | n_water=433 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1140 r_free=0.1309 | n_water=433 | time (s): 43.160 (total time: 45.420) Filter (q & B) r_work=0.1140 r_free=0.1309 | n_water=433 | time (s): 1.300 (total time: 46.720) Compute maps r_work=0.1140 r_free=0.1309 | n_water=433 | time (s): 1.800 (total time: 48.520) Filter (map) r_work=0.1159 r_free=0.1308 | n_water=346 | time (s): 3.720 (total time: 52.240) Find peaks r_work=0.1159 r_free=0.1308 | n_water=346 | time (s): 0.640 (total time: 52.880) Add new water r_work=0.1206 r_free=0.1369 | n_water=487 | time (s): 3.750 (total time: 56.630) Refine new water occ: r_work=0.1154 r_free=0.1317 adp: r_work=0.1154 r_free=0.1320 occ: r_work=0.1143 r_free=0.1301 adp: r_work=0.1142 r_free=0.1304 occ: r_work=0.1134 r_free=0.1287 adp: r_work=0.1132 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1288 r_work=0.1132 r_free=0.1288 | n_water=487 | time (s): 217.990 (total time: 274.620) Filter (q & B) r_work=0.1139 r_free=0.1301 | n_water=447 | time (s): 3.860 (total time: 278.480) Filter (dist only) r_work=0.1139 r_free=0.1299 | n_water=446 | time (s): 46.430 (total time: 324.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.219177 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 0.1220 0.1345 0.0125 0.004 0.7 5.8 0.0 0.0 0 0.088 0.1169 0.1314 0.0145 0.004 0.8 4.5 0.5 0.0 0 0.265 0.1156 0.1306 0.0150 0.005 0.9 4.5 0.5 0.0 0 0.530 0.1147 0.1301 0.0154 0.006 1.0 4.2 0.5 0.0 0 0.795 0.1143 0.1299 0.0155 0.007 1.1 4.2 0.5 0.0 0 1.060 0.1141 0.1298 0.0158 0.008 1.1 4.2 0.5 0.0 0 1.325 0.1139 0.1299 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.590 0.1139 0.1299 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.855 0.1145 0.1300 0.0155 0.006 1.1 4.2 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1298 0.0158 0.008 1.1 4.2 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 12.98 1.58 3.780 21.157 36.219 3.608 11.41 12.98 1.58 3.780 21.157 1.087 3.608 11.41 12.98 1.58 3.780 21.157 4.527 3.608 11.44 13.02 1.58 3.711 21.149 18.110 3.604 11.56 13.20 1.64 3.729 21.119 36.219 3.611 11.46 13.15 1.69 3.754 21.106 54.329 3.603 11.40 13.10 1.71 3.770 21.103 72.438 3.598 11.37 13.08 1.72 3.782 21.098 90.548 3.595 11.33 13.05 1.72 3.785 21.101 108.658 3.592 11.33 13.07 1.74 3.799 21.092 126.767 3.591 11.35 13.14 1.79 3.818 21.077 144.877 3.592 11.32 13.09 1.77 3.822 21.082 162.986 3.590 11.33 13.13 1.81 3.837 21.073 181.096 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.087 Accepted refinement result: 11.41 12.98 1.58 3.780 21.157 1.087 3.608 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.05 3.31 230 1743 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.50 76.70 34.72 N/A 230 216 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.10 115.03 19.31 N/A 0 1743 Chain S: 15.07 60.00 34.24 N/A 230 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.28 306 30.28 - 40.88 213 40.88 - 51.47 125 51.47 - 62.07 43 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=0.1141 r_free=0.1298 r_work=0.1141 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1298 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1296 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1138 r_free= 0.1296 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606588 | | target function (ml) not normalized (work): 300360.237406 | | target function (ml) not normalized (free): 15818.451549 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1351 0.1363 5.6582 5.6084| | 2: 3.57 - 2.84 1.00 2888 124 0.1078 0.1429 5.1737 5.261| | 3: 2.83 - 2.48 1.00 2820 163 0.1102 0.1224 4.9558 4.9872| | 4: 2.47 - 2.25 1.00 2825 136 0.0898 0.1017 4.637 4.6687| | 5: 2.25 - 2.09 1.00 2756 127 0.0863 0.0937 4.5869 4.6334| | 6: 2.09 - 1.97 1.00 2846 113 0.0848 0.0996 4.2699 4.3673| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1113 3.9794 4.0912| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1073 3.8849 3.976| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1158 3.6434 3.8141| | 10: 1.72 - 1.66 1.00 2831 160 0.0920 0.1190 3.56 3.7093| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1036 3.4915 3.5628| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1138 3.3283 3.4526| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1042 3.3055 3.4075| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1068 3.2416 3.3225| | 15: 1.48 - 1.45 1.00 2738 128 0.1006 0.1233 3.1552 3.2711| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1228 3.1397 3.2407| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1316 3.1201 3.2354| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1315 3.1061 3.232| | 19: 1.36 - 1.34 1.00 2807 134 0.1268 0.1581 3.1173 3.2783| | 20: 1.34 - 1.32 1.00 2696 147 0.1373 0.1480 3.1149 3.1648| | 21: 1.32 - 1.30 1.00 2785 112 0.1475 0.1504 3.1163 3.1075| | 22: 1.29 - 1.27 1.00 2704 152 0.1571 0.1992 3.1283 3.2964| | 23: 1.27 - 1.26 1.00 2802 156 0.1651 0.1792 3.1356 3.2013| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1836 3.1291 3.2332| | 25: 1.24 - 1.22 1.00 2733 148 0.1893 0.2158 3.1461 3.2636| | 26: 1.22 - 1.21 1.00 2727 135 0.1916 0.1777 3.1516 3.2087| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2164 3.1741 3.162| | 28: 1.19 - 1.18 1.00 2671 147 0.2206 0.2297 3.168 3.1738| | 29: 1.18 - 1.16 1.00 2800 134 0.2270 0.2385 3.1495 3.2292| | 30: 1.16 - 1.15 1.00 2739 148 0.2452 0.2450 3.1445 3.1677| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.83 1.00 0.97 5953.54| | 2: 3.57 - 2.84 2888 124 0.92 12.83 1.01 0.97 5953.54| | 3: 2.83 - 2.48 2820 163 0.89 16.84 0.99 0.97 4967.41| | 4: 2.47 - 2.25 2825 136 0.92 13.67 1.00 0.98 2424.48| | 5: 2.25 - 2.09 2756 127 0.90 15.82 1.01 0.98 2424.48| | 6: 2.09 - 1.97 2846 113 0.92 12.44 1.02 0.98 1388.71| | 7: 1.97 - 1.87 2787 165 0.95 9.24 1.02 0.97 505.33| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.97 505.33| | 9: 1.79 - 1.72 2745 138 0.94 9.95 0.98 0.97 285.44| | 10: 1.72 - 1.66 2831 160 0.94 11.01 0.98 0.97 241.41| | 11: 1.66 - 1.61 2712 147 0.94 11.62 0.98 0.97 231.35| | 12: 1.61 - 1.56 2773 144 0.96 8.83 0.99 0.97 136.51| | 13: 1.56 - 1.52 2745 130 0.95 10.39 1.03 0.97 136.51| | 14: 1.52 - 1.48 2803 134 0.94 10.71 1.02 0.98 122.90| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.98 97.98| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.98 97.98| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.44| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 84.50| | 19: 1.36 - 1.34 2807 134 0.94 11.92 0.99 0.98 84.50| | 20: 1.34 - 1.32 2696 147 0.94 12.22 0.98 0.96 80.77| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 80.51| | 22: 1.29 - 1.27 2704 152 0.93 13.72 0.98 0.96 80.90| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.97 0.94 82.87| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.96 0.94 82.87| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.96 0.94 84.78| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.93 86.90| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.93 86.90| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.93 90.33| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.92 91.62| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.98 0.92 91.62| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.51 max = 5953.54 mean = 911.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.50| |phase err.(test): min = 0.00 max = 89.61 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1138 0.1296 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1460 0.1461 0.1481 n_refl.: 87577 remove outliers: r(all,work,free)=0.1460 0.1461 0.1481 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1460 0.1480 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1138 0.1299 n_refl.: 87577 remove outliers: r(all,work,free)=0.1146 0.1138 0.1299 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4155 291.240 252.435 0.428 1.000 0.294 11.894-9.307 95.10 93 4 0.2363 477.642 464.426 0.856 1.002 0.240 9.237-7.194 97.73 208 7 0.2439 387.690 377.756 0.921 1.002 0.162 7.162-5.571 100.00 427 22 0.2186 296.528 284.699 0.904 1.003 0.133 5.546-4.326 100.00 867 58 0.1125 407.060 402.382 0.962 1.003 0.106 4.315-3.360 100.00 1859 96 0.0938 387.116 385.056 1.004 1.002 0.090 3.356-2.611 100.00 3867 181 0.1116 254.315 252.475 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0908 168.588 167.980 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.330 82.676 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.508 36.099 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2174 23.003 21.529 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0088 ================= 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 : 0.2605 0.1927 0.082 5.349 8.8 119.3 19.9 258 0.000 1_bss: 0.1639 0.1763 0.082 5.349 9.1 119.5 20.1 258 0.000 1_settarget: 0.1639 0.1763 0.082 5.349 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1772 0.082 5.349 9.1 119.5 20.1 258 0.006 1_weight: 0.1646 0.1772 0.082 5.349 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1222 0.1468 0.008 0.972 9.1 119.5 20.1 258 0.137 1_adp: 0.1229 0.1467 0.008 0.972 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1231 0.1470 0.008 0.972 9.1 119.4 20.1 258 0.137 1_occ: 0.1225 0.1463 0.008 0.972 9.1 119.4 20.1 258 0.137 2_bss: 0.1223 0.1455 0.008 0.972 9.1 119.5 20.1 258 0.137 2_settarget: 0.1223 0.1455 0.008 0.972 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1223 0.1455 0.008 0.976 9.1 119.5 20.1 258 0.137 2_nqh: 0.1223 0.1455 0.008 0.976 9.1 119.5 20.1 258 0.137 2_sol: 0.1199 0.1390 0.008 0.976 9.1 115.0 22.1 410 n/a 2_weight: 0.1199 0.1390 0.008 0.976 9.1 115.0 22.1 410 n/a 2_xyzrec: 0.1196 0.1414 0.005 0.812 9.1 115.0 22.1 410 n/a 2_adp: 0.1196 0.1414 0.005 0.812 9.1 115.0 22.1 410 n/a 2_regHadp: 0.1196 0.1414 0.005 0.812 9.1 115.0 22.1 410 n/a 2_occ: 0.1193 0.1412 0.005 0.812 9.1 115.0 22.1 410 n/a 3_bss: 0.1189 0.1409 0.005 0.812 9.1 115.0 22.1 410 n/a 3_settarget: 0.1189 0.1409 0.005 0.812 9.1 115.0 22.1 410 n/a 3_updatecdl: 0.1189 0.1409 0.005 0.812 9.1 115.0 22.1 410 n/a 3_nqh: 0.1189 0.1409 0.005 0.812 9.1 115.0 22.1 410 n/a 3_sol: 0.1221 0.1398 0.005 0.812 9.1 115.0 21.0 424 n/a 3_weight: 0.1221 0.1398 0.005 0.812 9.1 115.0 21.0 424 n/a 3_xyzrec: 0.1167 0.1315 0.007 1.043 9.1 115.0 21.0 424 n/a 3_adp: 0.1167 0.1315 0.007 1.043 9.1 115.0 21.0 424 n/a 3_regHadp: 0.1167 0.1315 0.007 1.043 9.1 115.0 21.0 424 n/a 3_occ: 0.1156 0.1306 0.007 1.043 9.1 115.0 21.0 424 n/a 4_bss: 0.1147 0.1300 0.007 1.043 9.1 115.0 21.0 424 n/a 4_settarget: 0.1147 0.1300 0.007 1.043 9.1 115.0 21.0 424 n/a 4_updatecdl: 0.1147 0.1300 0.007 1.045 9.1 115.0 21.0 424 n/a 4_nqh: 0.1151 0.1301 0.007 1.045 9.1 115.0 21.0 424 n/a 4_sol: 0.1150 0.1315 0.007 1.045 9.1 115.0 21.0 433 n/a 4_weight: 0.1150 0.1315 0.007 1.045 9.1 115.0 21.0 433 n/a 4_xyzrec: 0.1143 0.1311 0.008 1.122 9.1 115.0 21.0 433 n/a 4_adp: 0.1143 0.1311 0.008 1.122 9.1 115.0 21.0 433 n/a 4_regHadp: 0.1143 0.1311 0.008 1.122 9.1 115.0 21.0 433 n/a 4_occ: 0.1140 0.1309 0.008 1.122 9.1 115.0 21.0 433 n/a 5_bss: 0.1139 0.1309 0.008 1.122 9.1 115.0 21.0 433 n/a 5_settarget: 0.1139 0.1309 0.008 1.122 9.1 115.0 21.0 433 n/a 5_updatecdl: 0.1139 0.1309 0.008 1.121 9.1 115.0 21.0 433 n/a 5_setrh: 0.1140 0.1309 0.008 1.121 9.1 115.0 21.0 433 n/a 5_nqh: 0.1140 0.1309 0.008 1.121 9.1 115.0 21.0 433 n/a 5_sol: 0.1139 0.1299 0.008 1.121 9.1 115.0 21.0 446 n/a 5_weight: 0.1139 0.1299 0.008 1.121 9.1 115.0 21.0 446 n/a 5_xyzrec: 0.1141 0.1298 0.008 1.111 9.1 115.0 21.0 446 n/a 5_adp: 0.1141 0.1298 0.008 1.111 9.1 115.0 21.0 446 n/a 5_regHadp: 0.1141 0.1298 0.008 1.111 9.1 115.0 21.0 446 n/a 5_occ: 0.1138 0.1296 0.008 1.111 9.1 115.0 21.0 446 n/a end: 0.1138 0.1299 0.008 1.111 9.1 115.0 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1617309_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1617309_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 12868.9500 Write final files (write_after_run_outputs) : 93.1600 Total : 12965.2600 Total CPU time: 3.61 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:58:18 PST -0800 (1735365498.08 s) Start R-work = 0.1639, R-free = 0.1763 Final R-work = 0.1138, R-free = 0.1299 =============================================================================== Job complete usr+sys time: 13141.67 seconds wall clock time: 242 minutes 48.72 seconds (14568.72 seconds total)