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_8008321.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8008321.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" } 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 3 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: 1.59, per 1000 atoms: 0.47 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: 0.35 Conformation dependent library (CDL) restraints added in 120.0 milliseconds Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 533 0.92 - 1.17: 1104 1.17 - 1.43: 667 1.43 - 1.69: 824 1.69 - 1.94: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta sigma weight residual 1.455 1.703 -0.248 1.25e-02 6.40e+03 3.95e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.246 1.419 -0.173 9.20e-03 1.18e+04 3.52e+02 bond pdb=" N THR A 34 " pdb=" CA THR A 34 " ideal model delta sigma weight residual 1.458 1.241 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 1.242 1.091 0.151 8.60e-03 1.35e+04 3.07e+02 bond pdb=" C ARG A 98 " pdb=" N ALYS A 99 " ideal model delta sigma weight residual 1.333 1.566 -0.233 1.38e-02 5.25e+03 2.85e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3184 4.72 - 9.43: 1852 9.43 - 14.15: 610 14.15 - 18.87: 118 18.87 - 23.59: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 137.50 -16.68 1.05e+00 9.07e-01 2.52e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 134.89 -13.54 9.20e-01 1.18e+00 2.17e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.53 109.25 12.28 8.70e-01 1.32e+00 1.99e+02 angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.15 106.84 15.31 1.14e+00 7.69e-01 1.80e+02 angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.79 13.21 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.44: 949 18.44 - 36.88: 120 36.88 - 55.31: 30 55.31 - 73.75: 10 73.75 - 92.19: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 95 0.222 - 0.440: 77 0.440 - 0.658: 49 0.658 - 0.877: 16 0.877 - 1.095: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 3.61 -1.09 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA ALA A 56 " pdb=" N ALA A 56 " pdb=" C ALA A 56 " pdb=" CB ALA A 56 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.057 2.00e-02 2.50e+03 7.67e-02 1.77e+02 pdb=" CG PHE A 162 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.076 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.098 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.111 2.00e-02 2.50e+03 6.98e-02 1.46e+02 pdb=" CG PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.022 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG ATYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.055 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1194 2.34 - 2.90: 8151 2.90 - 3.47: 10475 3.47 - 4.03: 15175 4.03 - 4.60: 21550 Nonbonded interactions: 56545 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.792 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.815 2.100 nonbonded pdb=" O ALA A 6 " pdb=" H THR A 34 " model vdw 1.830 1.850 nonbonded pdb=" H CYS A 46 " pdb=" O VAL A 50 " model vdw 1.849 1.850 ... (remaining 56540 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_8008321_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= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794815 | | target function (ml) not normalized (work): 232824.818337 | | target function (ml) not normalized (free): 11876.937492 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2090 7.0691 4.9474| | 2: 3.57 - 2.84 1.00 2876 122 0.2427 0.1709 4.3461 4.3296| | 3: 2.84 - 2.48 1.00 2833 165 0.2342 0.1781 4.127 4.1822| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1369 3.8288 3.8421| | 5: 2.25 - 2.09 1.00 2756 127 0.2519 0.1379 3.7969 3.8051| | 6: 2.09 - 1.97 1.00 2846 113 0.2562 0.1741 3.4585 3.549| | 7: 1.97 - 1.87 1.00 2787 165 0.2604 0.1899 3.1494 3.1835| | 8: 1.87 - 1.79 1.00 2789 144 0.2463 0.2053 3.048 3.1722| | 9: 1.79 - 1.72 1.00 2745 138 0.2418 0.1781 2.9081 2.9368| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.2018 2.8188 2.91| | 11: 1.66 - 1.61 1.00 2740 147 0.2493 0.2015 2.751 2.8205| | 12: 1.61 - 1.56 1.00 2787 146 0.2558 0.1942 2.6507 2.6445| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.2022 2.5787 2.651| | 14: 1.52 - 1.48 1.00 2803 134 0.2552 0.1792 2.5144 2.487| | 15: 1.48 - 1.45 1.00 2738 128 0.2600 0.2265 2.4437 2.5492| | 16: 1.45 - 1.42 1.00 2756 161 0.2684 0.2249 2.3873 2.4291| | 17: 1.42 - 1.39 1.00 2785 139 0.2639 0.2322 2.3354 2.4593| | 18: 1.39 - 1.36 1.00 2741 179 0.2689 0.2051 2.2763 2.2963| | 19: 1.36 - 1.34 1.00 2807 134 0.2686 0.2414 2.2493 2.2562| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2279 2.1998 2.1957| | 21: 1.32 - 1.30 1.00 2785 112 0.2751 0.2406 2.1845 2.2095| | 22: 1.29 - 1.27 1.00 2704 152 0.2747 0.2437 2.1367 2.1821| | 23: 1.27 - 1.26 1.00 2802 156 0.2727 0.2571 2.1006 2.2086| | 24: 1.26 - 1.24 1.00 2744 132 0.2765 0.2624 2.065 2.1648| | 25: 1.24 - 1.22 1.00 2734 148 0.2803 0.2692 2.0369 2.1188| | 26: 1.22 - 1.21 1.00 2727 135 0.2878 0.2428 2.0192 2.1504| | 27: 1.21 - 1.19 1.00 2814 148 0.2985 0.2672 2.016 2.0397| | 28: 1.19 - 1.18 1.00 2671 147 0.2989 0.2756 1.9901 2.015| | 29: 1.18 - 1.16 1.00 2800 134 0.2980 0.2975 1.9647 2.0796| | 30: 1.16 - 1.15 1.00 2740 148 0.3064 0.2825 1.9376 1.9912| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.76 0.76 0.23 1469.95| | 2: 3.57 - 2.84 2876 122 0.80 25.99 1.27 0.23 1469.95| | 3: 2.84 - 2.48 2833 165 0.74 31.93 1.24 0.23 1219.61| | 4: 2.47 - 2.25 2825 136 0.81 25.70 1.25 0.25 569.92| | 5: 2.25 - 2.09 2756 127 0.77 29.52 1.28 0.25 569.92| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.30 0.25 313.40| | 7: 1.97 - 1.87 2787 165 0.90 17.01 1.29 0.26 94.61| | 8: 1.87 - 1.79 2789 144 0.85 21.71 1.25 0.26 94.61| | 9: 1.79 - 1.72 2745 138 0.88 18.84 1.23 0.25 56.95| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.23 0.25 49.41| | 11: 1.66 - 1.61 2740 147 0.85 21.61 1.24 0.25 47.70| | 12: 1.61 - 1.56 2787 146 0.88 18.51 1.24 0.25 30.31| | 13: 1.56 - 1.52 2745 130 0.86 20.57 1.24 0.25 30.31| | 14: 1.52 - 1.48 2803 134 0.86 20.83 1.23 0.25 26.92| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.22 0.25 20.73| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.24 0.25 20.73| | 17: 1.42 - 1.39 2785 139 0.87 20.82 1.21 0.25 17.91| | 18: 1.39 - 1.36 2741 179 0.86 21.78 1.22 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.49 1.22 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.51 1.21 0.25 13.61| | 21: 1.32 - 1.30 2785 112 0.85 22.31 1.20 0.25 13.42| | 22: 1.29 - 1.27 2704 152 0.85 22.90 1.21 0.25 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.74 1.21 0.24 11.91| | 24: 1.26 - 1.24 2744 132 0.84 23.91 1.20 0.24 11.91| | 25: 1.24 - 1.22 2734 148 0.83 24.85 1.20 0.24 11.44| | 26: 1.22 - 1.21 2727 135 0.83 25.26 1.20 0.23 10.92| | 27: 1.21 - 1.19 2814 148 0.81 26.29 1.21 0.23 10.92| | 28: 1.19 - 1.18 2671 147 0.81 27.17 1.18 0.23 10.47| | 29: 1.18 - 1.16 2800 134 0.80 27.83 1.17 0.22 10.30| | 30: 1.16 - 1.15 2740 148 0.78 29.27 1.16 0.22 10.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.30 max = 1469.95 mean = 214.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 23.16| |phase err.(test): min = 0.00 max = 89.63 mean = 23.00| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.248 1557 Z= 5.441 Angle : 5.290 21.328 2118 Z= 3.740 Chirality : 0.390 1.095 243 Planarity : 0.030 0.100 284 Dihedral : 14.300 92.188 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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: -2.21 (0.48), residues: 224 helix: -2.26 (0.39), residues: 108 sheet: -0.87 (0.87), residues: 28 loop : -0.24 (0.58), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.019 ARG A 156 TYR 0.064 0.029 TYR A 139 PHE 0.119 0.062 PHE A 164 HIS 0.045 0.027 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2613 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794815 | | target function (ml) not normalized (work): 232824.818337 | | target function (ml) not normalized (free): 11876.937492 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2614 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1986 0.1952 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2008 0.2012 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1637 0.1769 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1637 0.1769 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 0.3787 386.373 358.004 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1804 613.735 591.609 0.928 1.003 0.380 9.237-7.194 100.00 213 7 0.2158 501.960 491.967 0.954 1.003 0.370 7.162-5.571 100.00 427 22 0.2171 376.693 364.251 0.936 1.003 0.310 5.546-4.326 100.00 867 58 0.1281 517.107 510.768 0.962 1.003 0.229 4.315-3.360 100.00 1859 96 0.1145 491.772 488.069 1.004 1.003 0.209 3.356-2.611 100.00 3867 181 0.1427 323.069 319.521 0.993 1.002 0.043 2.608-2.026 99.99 8198 413 0.1365 214.165 211.780 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1638 104.587 103.984 1.016 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.378 44.954 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2599 29.221 26.930 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0474 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1769 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1638 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.904284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1972.129387 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1651 0.1770 0.0118 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1562 0.1693 0.0131 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1435 0.1588 0.0153 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1367 0.1541 0.0174 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1339 0.1524 0.0185 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1361 0.1544 0.0183 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1301 0.1515 0.0213 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1272 0.1494 0.0222 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1259 0.1489 0.0230 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1252 0.1484 0.0232 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1246 0.1482 0.0236 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1238 0.1474 0.0236 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1236 0.1474 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1235 0.1476 0.0241 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1229 0.1467 0.0238 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1231 0.1472 0.0242 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1229 0.1471 0.0242 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1224 0.1468 0.0244 0.008 1.0 3.5 0.5 0.6 0 13.952 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1467 0.0238 0.006 0.9 3.2 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.67 2.38 3.013 19.066 1972.129 0.017 12.30 14.67 2.37 2.989 19.065 59.164 0.017 12.36 14.65 2.29 2.669 19.065 246.516 0.017 12.69 15.31 2.62 2.796 19.281 986.065 0.017 12.64 15.53 2.89 3.428 19.687 1972.129 0.016 12.49 15.52 3.03 3.366 19.664 2958.194 0.016 12.32 15.41 3.09 3.313 19.619 3944.259 0.015 12.26 15.37 3.11 3.003 19.442 4930.323 0.015 12.24 15.40 3.17 3.302 19.597 5916.388 0.015 12.22 15.44 3.22 3.359 19.620 6902.453 0.015 12.22 15.51 3.30 3.475 19.678 7888.518 0.015 12.20 15.52 3.33 3.511 19.687 8874.582 0.015 12.20 15.55 3.35 3.518 19.678 9860.647 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: 246.516 Accepted refinement result: 12.36 14.65 2.29 2.669 19.065 246.516 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.09 3.31 0 1785 Protein: 9.06 115.00 17.00 3.32 0 1519 Water: 11.49 119.44 38.23 N/A 0 258 Other: 19.69 26.59 22.06 N/A 0 8 Chain A: 9.06 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1465 r_work=0.1237 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1468 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 = 0.1230 r_free = 0.1462 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016985 | | target function (ls_wunit_k1) not normalized (work): 1414.836314 | | target function (ls_wunit_k1) not normalized (free): 109.361740 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1674 0.1676 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1674 0.1676 0.1689 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1681 0.1693 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1227 0.1452 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1452 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 0.3589 303.793 280.356 0.660 1.002 0.388 11.894-9.307 99.02 97 4 0.1649 482.561 470.661 0.926 1.003 0.380 9.237-7.194 100.00 213 7 0.1945 394.676 388.229 0.961 1.003 0.323 7.162-5.571 100.00 427 22 0.1829 296.182 290.429 0.934 1.003 0.263 5.546-4.326 100.00 867 58 0.1001 406.585 403.555 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0873 386.665 385.585 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1175 254.019 252.858 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1021 168.391 167.665 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.234 82.441 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.466 35.971 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.976 21.464 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=0.0470 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1452 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=0.1227 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1452 | n_water=258 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1237 r_free=0.1446 | n_water=249 | time (s): 23.270 (total time: 25.020) Filter (q & B) r_work=0.1240 r_free=0.1446 | n_water=246 | time (s): 2.540 (total time: 27.560) Compute maps r_work=0.1240 r_free=0.1446 | n_water=246 | time (s): 1.450 (total time: 29.010) Filter (map) r_work=0.1260 r_free=0.1452 | n_water=222 | time (s): 3.330 (total time: 32.340) Find peaks r_work=0.1260 r_free=0.1452 | n_water=222 | time (s): 0.490 (total time: 32.830) Add new water r_work=0.1412 r_free=0.1629 | n_water=432 | time (s): 2.470 (total time: 35.300) Refine new water occ: r_work=0.1315 r_free=0.1472 adp: r_work=0.1229 r_free=0.1414 occ: r_work=0.1241 r_free=0.1399 adp: r_work=0.1207 r_free=0.1387 occ: r_work=0.1209 r_free=0.1374 adp: r_work=0.1199 r_free=0.1373 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1373 r_work=0.1199 r_free=0.1373 | n_water=432 | time (s): 60.540 (total time: 95.840) Filter (q & B) r_work=0.1203 r_free=0.1375 | n_water=419 | time (s): 3.030 (total time: 98.870) Filter (dist only) r_work=0.1203 r_free=0.1372 | n_water=418 | time (s): 34.130 (total time: 133.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.623820 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1495.471890 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 0.1630 0.1727 0.0097 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1558 0.1665 0.0107 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1390 0.1523 0.0133 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1353 0.1500 0.0147 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1322 0.1480 0.0158 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1320 0.1478 0.0158 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1253 0.1437 0.0184 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1226 0.1421 0.0195 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1214 0.1418 0.0205 0.004 0.7 4.2 0.5 0.0 0 4.000 0.1206 0.1414 0.0208 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1205 0.1412 0.0208 0.005 0.7 4.2 0.5 0.0 0 6.000 0.1199 0.1407 0.0209 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1193 0.1405 0.0212 0.006 0.8 4.5 0.5 0.0 0 8.000 0.1193 0.1403 0.0210 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1191 0.1407 0.0216 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1190 0.1408 0.0218 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1187 0.1403 0.0215 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1189 0.1413 0.0224 0.008 1.0 5.1 0.5 0.6 0 13.812 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1403 0.0215 0.007 0.9 5.1 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.03 2.15 3.776 21.829 1495.472 0.016 11.87 14.03 2.15 3.776 21.829 44.864 0.016 11.87 14.03 2.15 3.776 21.829 186.934 0.016 12.06 14.43 2.37 3.611 21.847 747.736 0.015 12.02 14.65 2.63 3.476 21.991 1495.472 0.014 11.92 14.66 2.74 3.456 22.189 2243.208 0.014 11.80 14.56 2.76 3.466 22.192 2990.944 0.014 11.72 14.60 2.88 3.510 22.005 3738.680 0.014 11.70 14.57 2.86 3.514 22.172 4486.416 0.014 11.70 14.61 2.91 3.537 22.204 5234.152 0.014 11.68 14.62 2.95 3.551 22.207 5981.888 0.013 11.67 14.64 2.97 3.573 22.224 6729.624 0.013 11.63 14.68 3.05 3.611 22.306 7477.359 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.864 Accepted refinement result: 11.87 14.03 2.15 3.776 21.829 44.864 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 22.27 3.31 196 1749 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.52 76.69 41.33 N/A 196 222 Other: 19.72 26.62 22.09 N/A 0 8 Chain A: 9.09 115.03 19.39 N/A 0 1749 Chain S: 13.77 60.00 47.99 N/A 196 0 Histogram: Values Number of atoms 9.09 - 19.68 1259 19.68 - 30.28 241 30.28 - 40.87 164 40.87 - 51.47 130 51.47 - 62.06 128 62.06 - 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=0.1187 r_free=0.1403 r_work=0.1187 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1403 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 = 0.1186 r_free = 0.1399 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 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= 0.1186 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014736 | | target function (ls_wunit_k1) not normalized (work): 1227.471525 | | target function (ls_wunit_k1) not normalized (free): 100.596556 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1186 0.1399 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1586 0.1584 0.1661 n_refl.: 87593 remove outliers: r(all,work,free)=0.1586 0.1584 0.1661 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1588 0.1585 0.1662 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1184 0.1395 n_refl.: 87593 remove outliers: r(all,work,free)=0.1193 0.1182 0.1395 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3361 299.784 276.904 0.612 1.002 0.360 11.894-9.307 99.02 97 4 0.1547 482.561 478.649 0.924 1.003 0.337 9.237-7.194 100.00 213 7 0.1615 394.676 395.711 0.984 1.003 0.270 7.162-5.571 100.00 427 22 0.1552 296.182 291.830 0.943 1.003 0.250 5.546-4.326 100.00 867 58 0.0884 406.585 403.850 0.958 1.003 0.200 4.315-3.360 100.00 1859 96 0.0776 386.665 385.850 1.006 1.002 0.190 3.356-2.611 100.00 3867 181 0.1083 254.019 253.111 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1017 168.391 167.768 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.234 82.445 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.466 35.996 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.976 21.487 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0144 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1395 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=0.1182 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1395 | n_water=418 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1182 r_free=0.1393 | n_water=413 | time (s): 36.380 (total time: 38.120) Filter (q & B) r_work=0.1182 r_free=0.1393 | n_water=413 | time (s): 0.830 (total time: 38.950) Compute maps r_work=0.1182 r_free=0.1393 | n_water=413 | time (s): 1.300 (total time: 40.250) Filter (map) r_work=0.1221 r_free=0.1395 | n_water=284 | time (s): 3.150 (total time: 43.400) Find peaks r_work=0.1221 r_free=0.1395 | n_water=284 | time (s): 0.680 (total time: 44.080) Add new water r_work=0.1342 r_free=0.1539 | n_water=465 | time (s): 3.050 (total time: 47.130) Refine new water occ: r_work=0.1251 r_free=0.1456 adp: r_work=0.1253 r_free=0.1455 occ: r_work=0.1227 r_free=0.1428 adp: r_work=0.1227 r_free=0.1428 occ: r_work=0.1209 r_free=0.1407 adp: r_work=0.1204 r_free=0.1403 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1403 r_work=0.1204 r_free=0.1403 | n_water=465 | time (s): 181.020 (total time: 228.150) Filter (q & B) r_work=0.1207 r_free=0.1409 | n_water=438 | time (s): 3.040 (total time: 231.190) Filter (dist only) r_work=0.1207 r_free=0.1407 | n_water=437 | time (s): 37.940 (total time: 269.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.821238 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.903550 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 0.1245 0.1384 0.0139 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1194 0.1345 0.0151 0.003 0.7 3.2 0.5 0.0 0 0.273 0.1177 0.1332 0.0155 0.004 0.8 2.9 0.5 0.0 0 0.546 0.1171 0.1333 0.0163 0.005 0.9 3.2 0.5 0.0 0 0.820 0.1165 0.1329 0.0163 0.006 1.0 2.9 0.5 0.0 0 1.093 0.1163 0.1332 0.0169 0.007 1.0 2.9 0.5 0.0 0 1.366 0.1160 0.1332 0.0171 0.007 1.1 3.2 0.5 0.0 0 1.639 0.1159 0.1331 0.0172 0.008 1.1 3.5 0.5 0.0 0 1.912 0.1168 0.1331 0.0163 0.006 0.9 3.2 0.5 0.0 0 0.911 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1165 0.1329 0.0163 0.006 1.0 2.9 0.5 0.0 0 1.093 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 13.29 1.63 3.779 21.271 50.904 3.624 11.65 13.29 1.63 3.779 21.271 1.527 3.624 11.66 13.29 1.63 3.769 21.271 6.363 3.624 11.71 13.38 1.66 3.713 21.256 25.452 3.618 11.68 13.40 1.72 3.741 21.230 50.904 3.615 11.62 13.38 1.75 3.759 21.218 76.355 3.610 11.58 13.35 1.76 3.768 21.211 101.807 3.605 11.55 13.34 1.79 3.783 21.205 127.259 3.603 11.55 13.38 1.83 3.801 21.192 152.711 3.603 11.53 13.37 1.83 3.813 21.184 178.162 3.601 11.52 13.35 1.83 3.822 21.180 203.614 3.600 11.51 13.34 1.84 3.827 21.183 229.066 3.599 11.49 13.31 1.82 3.834 21.179 254.518 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.527 Accepted refinement result: 11.65 13.29 1.63 3.779 21.271 1.527 3.624 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.25 3.31 219 1745 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.53 76.70 35.86 N/A 219 218 Other: 19.73 26.63 22.10 N/A 0 8 Chain A: 9.10 115.04 19.33 N/A 0 1745 Chain S: 13.78 60.01 36.54 N/A 219 0 Histogram: Values Number of atoms 9.10 - 19.69 1262 19.69 - 30.28 286 30.28 - 40.88 213 40.88 - 51.47 122 51.47 - 62.07 58 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=0.1165 r_free=0.1329 r_work=0.1165 r_free=0.1329 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1329 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1157 r_free = 0.1318 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1157 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616988 | | target function (ml) not normalized (work): 301273.431293 | | target function (ml) not normalized (free): 15851.020722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1157 0.1318 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1501 0.1501 0.1537 n_refl.: 87590 remove outliers: r(all,work,free)=0.1501 0.1501 0.1537 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1501 0.1500 0.1537 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1159 0.1152 0.1307 n_refl.: 87590 remove outliers: r(all,work,free)=0.1156 0.1148 0.1307 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 90.62 82 5 0.3722 288.329 271.426 0.499 0.999 0.320 11.894-9.307 97.06 95 4 0.2278 482.244 465.955 0.872 1.000 0.320 9.237-7.194 98.18 209 7 0.2338 386.155 386.308 0.959 1.001 0.195 7.162-5.571 100.00 427 22 0.2089 296.182 285.289 0.920 1.001 0.190 5.546-4.326 100.00 867 58 0.1124 406.585 401.365 0.962 1.001 0.155 4.315-3.360 100.00 1859 96 0.0931 386.665 384.015 1.005 1.001 0.143 3.356-2.611 100.00 3867 181 0.1138 254.019 251.915 1.007 1.002 0.120 2.608-2.026 99.99 8198 413 0.0943 168.391 167.549 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0906 82.234 82.507 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1264 36.466 36.019 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2168 22.976 21.413 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0026 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1307 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=0.1148 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1307 | n_water=437 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1149 r_free=0.1308 | n_water=435 | time (s): 47.500 (total time: 49.720) Filter (q & B) r_work=0.1149 r_free=0.1308 | n_water=433 | time (s): 3.580 (total time: 53.300) Compute maps r_work=0.1149 r_free=0.1308 | n_water=433 | time (s): 1.820 (total time: 55.120) Filter (map) r_work=0.1175 r_free=0.1312 | n_water=326 | time (s): 3.940 (total time: 59.060) Find peaks r_work=0.1175 r_free=0.1312 | n_water=326 | time (s): 0.740 (total time: 59.800) Add new water r_work=0.1244 r_free=0.1387 | n_water=490 | time (s): 3.840 (total time: 63.640) Refine new water occ: r_work=0.1173 r_free=0.1324 adp: r_work=0.1174 r_free=0.1325 occ: r_work=0.1159 r_free=0.1312 adp: r_work=0.1158 r_free=0.1313 occ: r_work=0.1148 r_free=0.1301 adp: r_work=0.1144 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1300 r_work=0.1144 r_free=0.1300 | n_water=490 | time (s): 298.220 (total time: 361.860) Filter (q & B) r_work=0.1150 r_free=0.1309 | n_water=448 | time (s): 3.770 (total time: 365.630) Filter (dist only) r_work=0.1150 r_free=0.1309 | n_water=446 | time (s): 46.590 (total time: 412.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.819791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.422480 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1349 0.0141 0.002 0.6 4.2 0.5 0.0 0 0.091 0.1171 0.1321 0.0150 0.003 0.7 2.9 0.5 0.0 0 0.273 0.1155 0.1312 0.0156 0.005 0.9 3.2 0.5 0.0 0 0.546 0.1150 0.1311 0.0161 0.006 1.0 3.2 0.5 0.0 0 0.819 0.1146 0.1309 0.0163 0.007 1.0 2.9 0.5 0.0 0 1.092 0.1144 0.1310 0.0167 0.007 1.1 2.9 0.5 0.0 0 1.365 0.1142 0.1307 0.0165 0.008 1.1 2.9 0.5 0.0 0 1.638 0.1140 0.1308 0.0168 0.009 1.1 2.9 0.5 0.0 0 1.911 0.1149 0.1308 0.0158 0.006 1.0 2.9 0.5 0.0 0 0.910 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1142 0.1307 0.0165 0.008 1.1 2.9 0.5 0.0 0 1.638 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.42 13.07 1.65 3.780 21.233 43.422 3.609 11.42 13.07 1.65 3.780 21.233 1.303 3.609 11.43 13.07 1.64 3.778 21.233 5.428 3.609 11.47 13.14 1.67 3.712 21.224 21.711 3.604 11.53 13.29 1.77 3.732 21.195 43.422 3.607 11.43 13.24 1.81 3.757 21.188 65.134 3.600 11.39 13.22 1.83 3.769 21.183 86.845 3.596 11.37 13.20 1.83 3.777 21.181 108.556 3.594 11.34 13.18 1.84 3.788 21.177 130.267 3.592 11.36 13.24 1.88 3.807 21.161 151.979 3.592 11.33 13.22 1.89 3.816 21.161 173.690 3.591 11.31 13.20 1.89 3.822 21.160 195.401 3.589 11.31 13.20 1.89 3.829 21.160 217.112 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.428 Accepted refinement result: 11.43 13.07 1.64 3.778 21.233 5.428 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 21.18 3.30 230 1743 Protein: 9.10 115.01 17.04 3.31 0 1519 Water: 11.53 76.70 35.26 N/A 230 216 Other: 19.72 26.62 22.09 N/A 0 8 Chain A: 9.10 115.01 19.30 N/A 0 1743 Chain S: 13.77 60.01 35.38 N/A 230 0 Histogram: Values Number of atoms 9.10 - 19.69 1265 19.69 - 30.28 289 30.28 - 40.87 224 40.87 - 51.46 123 51.46 - 62.05 49 62.05 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1143 r_free=0.1307 r_work=0.1143 r_free=0.1307 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1143 r_free = 0.1307 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1302 target_work(ml) = 3.606 | | 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= 0.1137 r_free= 0.1302 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605932 | | target function (ml) not normalized (work): 300320.044266 | | target function (ml) not normalized (free): 15820.917263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1145 0.1137 0.1302 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1481 0.1480 0.1518 n_refl.: 87581 remove outliers: r(all,work,free)=0.1481 0.1480 0.1518 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1480 0.1479 0.1517 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1143 0.1135 0.1301 n_refl.: 87581 remove outliers: r(all,work,free)=0.1142 0.1134 0.1301 n_refl.: 87578 ======================== 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 0.3851 286.161 251.513 0.443 1.001 0.317 11.894-9.307 96.08 94 4 0.2373 475.383 465.602 0.846 1.002 0.314 9.237-7.194 98.18 209 7 0.2348 386.155 380.832 0.919 1.002 0.164 7.162-5.571 100.00 427 22 0.2142 296.182 284.919 0.901 1.003 0.150 5.546-4.326 100.00 867 58 0.1132 406.585 401.939 0.953 1.003 0.140 4.315-3.360 100.00 1859 96 0.0923 386.665 384.558 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1115 254.019 252.071 0.999 1.002 0.080 2.608-2.026 99.99 8198 413 0.0920 168.391 167.671 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.234 82.562 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.466 36.058 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.976 21.514 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1134 r_free=0.1301 After: r_work=0.1135 r_free=0.1301 ================================== NQH flips ================================== r_work=0.1135 r_free=0.1301 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=0.1135 r_free=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1301 | n_water=446 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1135 r_free=0.1301 | n_water=446 | time (s): 43.050 (total time: 45.600) Filter (q & B) r_work=0.1135 r_free=0.1301 | n_water=446 | time (s): 1.440 (total time: 47.040) Compute maps r_work=0.1135 r_free=0.1301 | n_water=446 | time (s): 1.930 (total time: 48.970) Filter (map) r_work=0.1160 r_free=0.1307 | n_water=350 | time (s): 3.970 (total time: 52.940) Find peaks r_work=0.1160 r_free=0.1307 | n_water=350 | time (s): 0.750 (total time: 53.690) Add new water r_work=0.1213 r_free=0.1361 | n_water=494 | time (s): 3.930 (total time: 57.620) Refine new water occ: r_work=0.1154 r_free=0.1291 adp: r_work=0.1155 r_free=0.1294 occ: r_work=0.1141 r_free=0.1279 adp: r_work=0.1141 r_free=0.1281 occ: r_work=0.1132 r_free=0.1273 adp: r_work=0.1129 r_free=0.1273 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1273 r_work=0.1129 r_free=0.1273 | n_water=494 | time (s): 261.210 (total time: 318.830) Filter (q & B) r_work=0.1135 r_free=0.1283 | n_water=459 | time (s): 4.020 (total time: 322.850) Filter (dist only) r_work=0.1135 r_free=0.1283 | n_water=457 | time (s): 48.890 (total time: 371.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.803646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.370263 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 0.1225 0.1343 0.0117 0.003 0.7 5.1 0.0 0.0 0 0.090 0.1173 0.1306 0.0133 0.004 0.8 4.5 0.0 0.0 0 0.271 0.1152 0.1292 0.0140 0.005 0.9 3.8 0.5 0.0 0 0.541 0.1144 0.1287 0.0143 0.006 1.0 4.2 0.5 0.0 0 0.812 0.1141 0.1286 0.0145 0.006 1.1 4.2 0.5 0.0 0 1.082 0.1137 0.1284 0.0147 0.007 1.1 4.2 0.5 0.0 0 1.353 0.1135 0.1283 0.0148 0.008 1.1 4.2 0.5 0.0 0 1.623 0.1134 0.1283 0.0149 0.009 1.1 4.2 0.5 0.0 0 1.894 0.1142 0.1286 0.0144 0.006 1.0 4.2 0.5 0.0 0 0.902 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1283 0.0149 0.009 1.1 4.2 0.5 0.0 0 1.894 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.83 1.49 3.776 21.248 43.370 3.602 11.34 12.83 1.49 3.776 21.248 1.301 3.602 11.34 12.83 1.49 3.776 21.248 5.421 3.602 11.37 12.89 1.52 3.709 21.241 21.685 3.598 11.44 13.06 1.62 3.730 21.212 43.370 3.601 11.35 13.01 1.66 3.754 21.202 65.055 3.595 11.30 12.97 1.68 3.768 21.199 86.741 3.590 11.28 12.95 1.67 3.777 21.198 108.426 3.588 11.26 12.95 1.69 3.790 21.193 130.111 3.586 11.26 12.98 1.72 3.807 21.181 151.796 3.586 11.23 12.95 1.71 3.812 21.183 173.481 3.583 11.22 12.94 1.72 3.821 21.180 195.166 3.583 11.21 12.93 1.73 3.826 21.181 216.851 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.421 Accepted refinement result: 11.34 12.83 1.49 3.776 21.248 5.421 3.602 Individual atomic B min max mean iso aniso Overall: 9.09 115.00 21.21 3.30 242 1742 Protein: 9.09 115.00 17.03 3.31 0 1519 Water: 11.52 76.69 35.09 N/A 242 215 Other: 19.72 26.61 22.09 N/A 0 8 Chain A: 9.09 115.00 19.26 N/A 0 1742 Chain S: 13.76 60.00 35.23 N/A 242 0 Histogram: Values Number of atoms 9.09 - 19.68 1265 19.68 - 30.27 296 30.27 - 40.86 224 40.86 - 51.45 127 51.45 - 62.05 50 62.05 - 72.64 12 72.64 - 83.23 4 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1283 r_work=0.1134 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1283 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1279 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599666 | | target function (ml) not normalized (work): 299787.369512 | | target function (ml) not normalized (free): 15788.726041 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1327 0.1331 5.6364 5.5965| | 2: 3.57 - 2.84 1.00 2888 124 0.1058 0.1352 5.1558 5.2157| | 3: 2.83 - 2.48 1.00 2820 163 0.1098 0.1219 4.9411 4.9763| | 4: 2.47 - 2.25 1.00 2825 136 0.0901 0.0965 4.6232 4.657| | 5: 2.25 - 2.09 1.00 2756 127 0.0865 0.0961 4.5712 4.6183| | 6: 2.09 - 1.97 1.00 2846 113 0.0855 0.0983 4.261 4.3455| | 7: 1.97 - 1.87 1.00 2787 165 0.0877 0.1113 3.9697 4.0831| | 8: 1.87 - 1.79 1.00 2789 144 0.0904 0.1100 3.8748 3.9799| | 9: 1.79 - 1.72 1.00 2745 138 0.0864 0.1184 3.6354 3.8304| | 10: 1.72 - 1.66 1.00 2831 160 0.0914 0.1194 3.5573 3.6998| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1018 3.4903 3.5637| | 12: 1.61 - 1.56 1.00 2773 144 0.0901 0.1122 3.3263 3.4425| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1065 3.3039 3.4103| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1046 3.2361 3.3256| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1242 3.1523 3.2762| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1243 3.1337 3.2348| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1281 3.1171 3.2181| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1308 3.1005 3.2262| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1554 3.1104 3.2619| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1463 3.1087 3.1512| | 21: 1.32 - 1.30 1.00 2785 112 0.1467 0.1516 3.1121 3.1023| | 22: 1.29 - 1.27 1.00 2704 152 0.1552 0.1980 3.1181 3.2902| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1776 3.1314 3.1979| | 24: 1.26 - 1.24 1.00 2744 132 0.1706 0.1828 3.125 3.2222| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2140 3.1416 3.2545| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1771 3.1469 3.2019| | 27: 1.21 - 1.19 1.00 2814 148 0.2074 0.2139 3.17 3.1577| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2307 3.165 3.1762| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2391 3.1474 3.2282| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2460 3.1431 3.1702| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.33 1.00 0.98 5666.67| | 2: 3.57 - 2.84 2888 124 0.93 12.41 1.01 0.98 5666.67| | 3: 2.83 - 2.48 2820 163 0.90 16.34 0.99 0.98 4731.78| | 4: 2.47 - 2.25 2825 136 0.92 13.38 1.00 0.99 2321.02| | 5: 2.25 - 2.09 2756 127 0.90 15.46 1.01 0.99 2321.02| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.99 1337.11| | 7: 1.97 - 1.87 2787 165 0.95 9.10 1.02 0.98 497.96| | 8: 1.87 - 1.79 2789 144 0.93 12.44 1.00 0.98 497.96| | 9: 1.79 - 1.72 2745 138 0.95 9.91 0.98 0.98 284.27| | 10: 1.72 - 1.66 2831 160 0.94 11.04 0.98 0.98 241.48| | 11: 1.66 - 1.61 2712 147 0.94 11.63 0.98 0.98 231.48| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.98 137.14| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.98 137.14| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.99 123.24| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.99 97.77| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.99 97.77| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.99 88.72| | 18: 1.39 - 1.36 2741 179 0.94 11.49 1.01 0.99 83.48| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.99 83.48| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 79.38| | 21: 1.32 - 1.30 2785 112 0.94 13.01 0.98 0.97 79.10| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.97 79.50| | 23: 1.27 - 1.26 2802 156 0.92 14.76 0.97 0.95 81.55| | 24: 1.26 - 1.24 2744 132 0.93 14.80 0.96 0.95 81.55| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.95 83.76| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.94 86.22| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.94 86.22| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.94 90.33| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.93 91.88| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.93 91.88| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.10 max = 5666.67 mean = 874.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.86 mean = 13.39| |phase err.(test): min = 0.00 max = 89.33 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1279 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1470 0.1470 0.1496 n_refl.: 87578 remove outliers: r(all,work,free)=0.1470 0.1470 0.1496 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1469 0.1469 0.1495 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1278 n_refl.: 87578 remove outliers: r(all,work,free)=0.1135 0.1128 0.1278 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 87.50 79 5 0.3893 288.345 246.138 0.438 1.000 0.308 11.894-9.307 96.08 94 4 0.2495 475.383 463.509 0.850 1.002 0.300 9.237-7.194 98.18 209 7 0.2289 386.155 380.022 0.932 1.002 0.180 7.162-5.571 100.00 427 22 0.2106 296.182 285.444 0.909 1.003 0.150 5.546-4.326 100.00 867 58 0.1127 406.585 401.833 0.962 1.003 0.130 4.315-3.360 100.00 1859 96 0.0916 386.665 384.507 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1098 254.019 252.236 1.010 1.002 0.080 2.608-2.026 99.99 8198 413 0.0914 168.391 167.774 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.234 82.585 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.466 36.066 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.976 21.519 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0150 ================= 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 : 0.2613 0.1952 0.080 5.290 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1769 0.080 5.290 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1769 0.080 5.290 9.1 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1770 0.080 5.290 9.1 119.5 20.1 258 0.003 1_weight: 0.1638 0.1770 0.080 5.290 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1229 0.1467 0.006 0.894 9.1 119.5 20.1 258 0.128 1_adp: 0.1236 0.1465 0.006 0.894 9.1 119.4 20.1 258 0.128 1_regHadp: 0.1237 0.1468 0.006 0.894 9.1 119.4 20.1 258 0.128 1_occ: 0.1230 0.1462 0.006 0.894 9.1 119.4 20.1 258 0.128 2_bss: 0.1227 0.1452 0.006 0.894 9.1 119.5 20.1 258 0.128 2_settarget: 0.1227 0.1452 0.006 0.894 9.1 119.5 20.1 258 0.128 2_updatecdl: 0.1227 0.1452 0.006 0.898 9.1 119.5 20.1 258 0.128 2_nqh: 0.1227 0.1452 0.006 0.898 9.1 119.5 20.1 258 0.128 2_sol: 0.1203 0.1372 0.006 0.898 9.1 115.0 22.3 418 n/a 2_weight: 0.1203 0.1372 0.006 0.898 9.1 115.0 22.3 418 n/a 2_xyzrec: 0.1187 0.1403 0.007 0.911 9.1 115.0 22.3 418 n/a 2_adp: 0.1187 0.1403 0.007 0.911 9.1 115.0 22.3 418 n/a 2_regHadp: 0.1187 0.1403 0.007 0.911 9.1 115.0 22.3 418 n/a 2_occ: 0.1186 0.1399 0.007 0.911 9.1 115.0 22.3 418 n/a 3_bss: 0.1182 0.1395 0.007 0.911 9.1 115.0 22.3 418 n/a 3_settarget: 0.1182 0.1395 0.007 0.911 9.1 115.0 22.3 418 n/a 3_updatecdl: 0.1182 0.1395 0.007 0.911 9.1 115.0 22.3 418 n/a 3_nqh: 0.1182 0.1395 0.007 0.911 9.1 115.0 22.3 418 n/a 3_sol: 0.1207 0.1407 0.007 0.911 9.1 115.0 21.2 437 n/a 3_weight: 0.1207 0.1407 0.007 0.911 9.1 115.0 21.2 437 n/a 3_xyzrec: 0.1165 0.1329 0.006 0.980 9.1 115.0 21.2 437 n/a 3_adp: 0.1165 0.1329 0.006 0.980 9.1 115.0 21.2 437 n/a 3_regHadp: 0.1165 0.1329 0.006 0.980 9.1 115.0 21.2 437 n/a 3_occ: 0.1157 0.1318 0.006 0.980 9.1 115.0 21.2 437 n/a 4_bss: 0.1148 0.1307 0.006 0.980 9.1 115.0 21.2 437 n/a 4_settarget: 0.1148 0.1307 0.006 0.980 9.1 115.0 21.2 437 n/a 4_updatecdl: 0.1148 0.1307 0.006 0.981 9.1 115.0 21.2 437 n/a 4_nqh: 0.1148 0.1307 0.006 0.981 9.1 115.0 21.2 437 n/a 4_sol: 0.1150 0.1309 0.006 0.981 9.1 115.0 21.2 446 n/a 4_weight: 0.1150 0.1309 0.006 0.981 9.1 115.0 21.2 446 n/a 4_xyzrec: 0.1142 0.1307 0.008 1.103 9.1 115.0 21.2 446 n/a 4_adp: 0.1143 0.1307 0.008 1.103 9.1 115.0 21.2 446 n/a 4_regHadp: 0.1143 0.1307 0.008 1.103 9.1 115.0 21.2 446 n/a 4_occ: 0.1137 0.1302 0.008 1.103 9.1 115.0 21.2 446 n/a 5_bss: 0.1134 0.1301 0.008 1.103 9.1 115.0 21.2 446 n/a 5_settarget: 0.1134 0.1301 0.008 1.103 9.1 115.0 21.2 446 n/a 5_updatecdl: 0.1134 0.1301 0.008 1.104 9.1 115.0 21.2 446 n/a 5_setrh: 0.1135 0.1301 0.008 1.104 9.1 115.0 21.2 446 n/a 5_nqh: 0.1135 0.1301 0.008 1.104 9.1 115.0 21.2 446 n/a 5_sol: 0.1135 0.1283 0.008 1.104 9.1 115.0 21.2 457 n/a 5_weight: 0.1135 0.1283 0.008 1.104 9.1 115.0 21.2 457 n/a 5_xyzrec: 0.1134 0.1283 0.009 1.144 9.1 115.0 21.2 457 n/a 5_adp: 0.1134 0.1283 0.009 1.144 9.1 115.0 21.2 457 n/a 5_regHadp: 0.1134 0.1283 0.009 1.144 9.1 115.0 21.2 457 n/a 5_occ: 0.1128 0.1279 0.009 1.144 9.1 115.0 21.2 457 n/a end: 0.1128 0.1278 0.009 1.144 9.1 115.0 21.2 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8008321_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8008321_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7600 Refinement macro-cycles (run) : 13509.9600 Write final files (write_after_run_outputs) : 94.6400 Total : 13608.3600 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:57 PST -0800 (1735366077.56 s) Start R-work = 0.1637, R-free = 0.1769 Final R-work = 0.1128, R-free = 0.1278 =============================================================================== Job complete usr+sys time: 13784.22 seconds wall clock time: 252 minutes 5.27 seconds (15125.27 seconds total)