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_6024882.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 6 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: 1.61, per 1000 atoms: 0.48 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 192.2 milliseconds Time building geometry restraints manager: 0.56 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: 489 0.91 - 1.16: 1142 1.16 - 1.41: 599 1.41 - 1.65: 864 1.65 - 1.90: 59 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.444 1.641 -0.198 8.80e-03 1.29e+04 5.05e+02 bond pdb=" CA GLY A 108 " pdb=" C GLY A 108 " ideal model delta sigma weight residual 1.511 1.385 0.126 6.90e-03 2.10e+04 3.35e+02 bond pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta sigma weight residual 1.533 1.325 0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.267 0.179 9.90e-03 1.02e+04 3.28e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.14e-02 7.69e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3154 4.69 - 9.37: 1888 9.37 - 14.06: 613 14.06 - 18.75: 109 18.75 - 23.44: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 110.85 10.22 3.60e-01 7.72e+00 8.05e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" O GLY A 74 " ideal model delta sigma weight residual 121.28 137.77 -16.49 1.01e+00 9.80e-01 2.67e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.71 107.68 12.03 8.10e-01 1.52e+00 2.20e+02 angle pdb=" OD1 ASN A 173 " pdb=" CG ASN A 173 " pdb=" ND2 ASN A 173 " ideal model delta sigma weight residual 122.60 108.37 14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 105.54 15.56 1.10e+00 8.26e-01 2.00e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 21.37: 999 21.37 - 42.72: 84 42.72 - 64.07: 22 64.07 - 85.43: 4 85.43 - 106.78: 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 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.233: 113 0.233 - 0.462: 76 0.462 - 0.692: 35 0.692 - 0.922: 13 0.922 - 1.151: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.66 -1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA LEU A 128 " pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CB LEU A 128 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.134 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG PHE A 119 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.063 9.50e-02 1.11e+02 7.48e-02 1.16e+02 pdb=" NE ARG A 98 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.100 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.108 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1176 2.34 - 2.91: 8301 2.91 - 3.47: 10440 3.47 - 4.04: 15158 4.04 - 4.60: 21573 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.777 2.100 nonbonded pdb=" OE2 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.836 1.850 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.837 1.850 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.841 2.100 ... (remaining 56643 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_6024882_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= 0.2610 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788184 | | target function (ml) not normalized (work): 232272.451099 | | target function (ml) not normalized (free): 11793.114391 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3031 0.2065 7.0541 4.9477| | 2: 3.57 - 2.84 1.00 2876 122 0.2448 0.1800 4.3516 4.3374| | 3: 2.84 - 2.48 1.00 2833 165 0.2337 0.1741 4.1244 4.1652| | 4: 2.47 - 2.25 1.00 2825 136 0.2350 0.1410 3.8311 3.8081| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1542 3.7955 3.8012| | 6: 2.09 - 1.97 1.00 2846 113 0.2576 0.1793 3.4607 3.5704| | 7: 1.97 - 1.87 1.00 2787 165 0.2477 0.1738 3.1167 3.1674| | 8: 1.87 - 1.79 1.00 2789 144 0.2492 0.1802 3.0487 3.1187| | 9: 1.79 - 1.72 1.00 2745 138 0.2434 0.1812 2.8938 2.908| | 10: 1.72 - 1.66 1.00 2789 158 0.2360 0.2042 2.7924 2.9151| | 11: 1.66 - 1.61 1.00 2740 147 0.2494 0.1849 2.7329 2.7266| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.1794 2.6279 2.5434| | 13: 1.56 - 1.52 1.00 2745 130 0.2588 0.2049 2.5587 2.7548| | 14: 1.52 - 1.48 1.00 2803 134 0.2546 0.1858 2.5002 2.5217| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.2173 2.4268 2.5063| | 16: 1.45 - 1.42 1.00 2756 161 0.2650 0.2271 2.3834 2.4523| | 17: 1.42 - 1.39 1.00 2785 139 0.2701 0.2102 2.3341 2.362| | 18: 1.39 - 1.36 1.00 2741 179 0.2727 0.2167 2.2911 2.321| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2047 2.2511 2.2149| | 20: 1.34 - 1.32 1.00 2696 147 0.2725 0.2300 2.2047 2.2533| | 21: 1.32 - 1.30 1.00 2785 112 0.2696 0.2308 2.1527 2.1539| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2491 2.1313 2.169| | 23: 1.27 - 1.26 1.00 2802 156 0.2805 0.2433 2.1187 2.1486| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2552 2.0695 2.1697| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2664 2.0511 2.125| | 26: 1.22 - 1.21 1.00 2727 135 0.2875 0.2540 2.0088 2.1315| | 27: 1.21 - 1.19 1.00 2814 148 0.2943 0.2553 2.0065 1.9815| | 28: 1.19 - 1.18 1.00 2671 147 0.2953 0.2639 1.9763 1.9624| | 29: 1.18 - 1.16 1.00 2800 134 0.2956 0.2658 1.968 2.0231| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2759 1.9265 1.9575| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.87 0.76 0.23 1474.51| | 2: 3.57 - 2.84 2876 122 0.80 26.10 1.27 0.23 1474.51| | 3: 2.84 - 2.48 2833 165 0.74 31.91 1.24 0.23 1221.30| | 4: 2.47 - 2.25 2825 136 0.81 25.32 1.26 0.25 564.16| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.29 0.25 564.16| | 6: 2.09 - 1.97 2846 113 0.84 22.18 1.30 0.25 305.97| | 7: 1.97 - 1.87 2787 165 0.90 15.92 1.27 0.26 85.77| | 8: 1.87 - 1.79 2789 144 0.87 20.29 1.25 0.26 85.77| | 9: 1.79 - 1.72 2745 138 0.88 18.38 1.23 0.26 52.93| | 10: 1.72 - 1.66 2789 158 0.87 19.74 1.22 0.25 46.35| | 11: 1.66 - 1.61 2740 147 0.86 20.87 1.25 0.25 44.79| | 12: 1.61 - 1.56 2787 146 0.89 18.21 1.23 0.25 28.98| | 13: 1.56 - 1.52 2745 130 0.86 20.46 1.25 0.25 28.98| | 14: 1.52 - 1.48 2803 134 0.86 20.85 1.23 0.25 26.11| | 15: 1.48 - 1.45 2738 128 0.87 20.18 1.22 0.25 20.87| | 16: 1.45 - 1.42 2756 161 0.85 21.89 1.24 0.25 20.87| | 17: 1.42 - 1.39 2785 139 0.86 21.01 1.23 0.25 17.63| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.23 0.25 15.76| | 19: 1.36 - 1.34 2807 134 0.85 22.09 1.21 0.25 15.76| | 20: 1.34 - 1.32 2696 147 0.87 20.97 1.22 0.24 12.97| | 21: 1.32 - 1.30 2785 112 0.86 21.91 1.20 0.24 12.78| | 22: 1.29 - 1.27 2704 152 0.85 22.57 1.21 0.24 12.49| | 23: 1.27 - 1.26 2802 156 0.86 21.89 1.22 0.24 11.01| | 24: 1.26 - 1.24 2744 132 0.85 22.83 1.20 0.24 11.01| | 25: 1.24 - 1.22 2734 148 0.84 23.78 1.20 0.24 10.44| | 26: 1.22 - 1.21 2727 135 0.84 23.92 1.20 0.23 9.81| | 27: 1.21 - 1.19 2814 148 0.83 24.62 1.20 0.23 9.81| | 28: 1.19 - 1.18 2671 147 0.83 24.90 1.18 0.23 9.02| | 29: 1.18 - 1.16 2800 134 0.83 24.77 1.15 0.23 8.72| | 30: 1.16 - 1.15 2740 148 0.81 26.73 1.15 0.23 8.72| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.72 max = 1474.51 mean = 212.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.45| |phase err.(test): min = 0.00 max = 89.46 mean = 22.32| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.226 1557 Z= 5.599 Angle : 5.311 18.178 2118 Z= 3.853 Chirality : 0.388 1.151 243 Planarity : 0.032 0.111 284 Dihedral : 14.207 106.782 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % 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: -2.70 (0.48), residues: 224 helix: -2.67 (0.37), residues: 109 sheet: -0.75 (0.80), residues: 38 loop : -0.49 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.016 ARG A 98 TYR 0.077 0.032 TYR A 141 PHE 0.127 0.044 PHE A 119 HIS 0.040 0.023 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= 0.2610 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788184 | | target function (ml) not normalized (work): 232272.451099 | | target function (ml) not normalized (free): 11793.114391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2611 0.1931 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2611 0.1931 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1982 0.1931 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2008 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1634 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1633 0.1761 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 0.3818 386.333 358.967 0.677 1.002 0.413 11.894-9.307 99.02 97 4 0.1757 613.671 594.432 0.930 1.003 0.379 9.237-7.194 100.00 213 7 0.2105 501.907 490.587 0.954 1.003 0.349 7.162-5.571 100.00 427 22 0.2159 376.653 364.589 0.932 1.003 0.340 5.546-4.326 100.00 867 58 0.1265 517.052 511.774 0.964 1.003 0.223 4.315-3.360 100.00 1859 96 0.1125 491.720 487.888 1.004 1.003 0.189 3.356-2.611 100.00 3867 181 0.1451 323.035 319.557 0.995 1.002 0.038 2.608-2.026 99.99 8198 413 0.1351 214.142 212.160 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1637 104.576 103.962 1.010 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2069 46.373 45.059 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2597 29.218 26.984 0.972 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.1642 r_free=0.1776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.875804 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2034.726664 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 0.1590 0.1718 0.0129 0.002 0.5 3.5 0.0 0.0 0 0.125 0.1481 0.1629 0.0147 0.002 0.5 3.5 0.0 0.0 0 0.250 0.1392 0.1556 0.0164 0.002 0.5 3.2 0.0 0.0 0 0.500 0.1360 0.1537 0.0177 0.002 0.5 2.9 0.0 0.0 0 0.750 0.1325 0.1513 0.0188 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1335 0.1523 0.0189 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1282 0.1494 0.0213 0.002 0.6 2.6 0.5 0.0 0 2.000 0.1274 0.1500 0.0226 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1256 0.1486 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1241 0.1475 0.0234 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1243 0.1481 0.0238 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1237 0.1480 0.0243 0.005 0.8 2.9 0.5 0.0 0 7.000 0.1233 0.1473 0.0240 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1230 0.1476 0.0246 0.006 0.9 2.6 0.5 0.0 0 9.000 0.1227 0.1472 0.0245 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1226 0.1475 0.0249 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1225 0.1472 0.0247 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1222 0.1476 0.0254 0.007 1.0 3.5 0.5 0.0 0 13.000 0.1222 0.1473 0.0252 0.008 1.0 3.5 0.5 0.0 0 14.438 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1472 0.0245 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 12.27 14.72 2.45 3.012 19.065 2034.727 0.017 12.27 14.71 2.44 2.988 19.065 61.042 0.017 12.35 14.69 2.34 2.656 19.064 254.341 0.017 12.73 15.43 2.70 2.910 19.348 1017.363 0.017 12.61 15.58 2.98 3.234 19.578 2034.727 0.016 12.47 15.54 3.08 3.291 19.630 3052.090 0.016 12.33 15.46 3.13 3.325 19.644 4069.453 0.015 12.28 15.48 3.20 3.370 19.669 5086.817 0.015 12.28 15.50 3.22 3.339 19.637 6104.180 0.015 12.21 15.47 3.26 3.429 19.674 7121.543 0.015 12.23 15.50 3.28 3.264 19.569 8138.907 0.015 12.24 15.58 3.34 3.602 19.748 9156.270 0.015 12.15 15.48 3.33 3.484 19.675 10173.633 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: 254.341 Accepted refinement result: 12.35 14.69 2.34 2.656 19.064 254.341 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.09 3.29 0 1785 Protein: 9.06 114.87 17.00 3.29 0 1519 Water: 11.47 119.44 38.23 N/A 0 258 Other: 19.74 26.61 22.08 N/A 0 8 Chain A: 9.06 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1270 20.10 - 31.14 229 31.14 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1469 r_work=0.1237 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1472 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 = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016949 | | target function (ls_wunit_k1) not normalized (work): 1411.832404 | | target function (ls_wunit_k1) not normalized (free): 109.150488 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1230 0.1468 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1698 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1698 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1683 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1456 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1456 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3515 301.313 281.654 0.651 1.003 0.380 11.894-9.307 99.02 97 4 0.1639 482.687 470.122 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.1913 394.779 389.217 0.961 1.003 0.323 7.162-5.571 100.00 427 22 0.1843 296.259 290.207 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1014 406.691 403.426 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0870 386.766 385.735 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1171 254.085 252.936 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1022 168.435 167.681 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.255 82.452 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.475 35.978 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.982 21.469 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1456 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** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1227 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1456 | n_water=258 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1237 r_free=0.1452 | n_water=251 | time (s): 20.850 (total time: 22.540) Filter (q & B) r_work=0.1239 r_free=0.1452 | n_water=248 | time (s): 2.250 (total time: 24.790) Compute maps r_work=0.1239 r_free=0.1452 | n_water=248 | time (s): 1.310 (total time: 26.100) Filter (map) r_work=0.1260 r_free=0.1442 | n_water=226 | time (s): 2.390 (total time: 28.490) Find peaks r_work=0.1260 r_free=0.1442 | n_water=226 | time (s): 0.530 (total time: 29.020) Add new water r_work=0.1407 r_free=0.1615 | n_water=443 | time (s): 3.460 (total time: 32.480) Refine new water occ: r_work=0.1312 r_free=0.1488 adp: r_work=0.1223 r_free=0.1427 occ: r_work=0.1238 r_free=0.1412 adp: r_work=0.1201 r_free=0.1397 occ: r_work=0.1204 r_free=0.1387 adp: r_work=0.1195 r_free=0.1385 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1385 r_work=0.1195 r_free=0.1385 | n_water=443 | time (s): 57.720 (total time: 90.200) Filter (q & B) r_work=0.1199 r_free=0.1388 | n_water=424 | time (s): 3.380 (total time: 93.580) Filter (dist only) r_work=0.1199 r_free=0.1387 | n_water=423 | time (s): 35.610 (total time: 129.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.050490 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1490.294038 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 0.1681 0.1780 0.0099 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1486 0.1613 0.0127 0.001 0.4 5.4 0.0 0.0 0 0.250 0.1427 0.1565 0.0138 0.001 0.4 4.8 0.0 0.0 0 0.500 0.1339 0.1495 0.0156 0.001 0.4 4.8 0.0 0.0 0 0.750 0.1297 0.1467 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1322 0.1493 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1241 0.1435 0.0194 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1218 0.1427 0.0209 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1202 0.1419 0.0218 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1195 0.1416 0.0221 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1190 0.1418 0.0227 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1188 0.1418 0.0230 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1187 0.1419 0.0232 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1183 0.1411 0.0228 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1180 0.1404 0.0224 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1179 0.1408 0.0229 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1178 0.1406 0.0229 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1178 0.1407 0.0228 0.008 0.9 3.8 0.5 0.0 0 13.000 0.1177 0.1413 0.0236 0.008 0.9 3.8 0.5 0.0 0 14.025 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1180 0.1404 0.0224 0.006 0.9 4.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 14.04 2.24 3.765 21.821 1490.294 0.016 11.80 14.04 2.24 3.765 21.821 44.709 0.016 11.80 14.04 2.24 3.765 21.821 186.287 0.016 11.94 14.47 2.53 3.627 21.821 745.147 0.015 11.98 14.82 2.84 3.528 21.900 1490.294 0.015 11.77 14.60 2.84 3.455 22.189 2235.441 0.014 11.71 14.70 2.98 3.483 21.978 2980.588 0.014 11.64 14.65 3.01 3.483 22.002 3725.735 0.014 11.65 14.70 3.05 3.478 22.182 4470.882 0.014 11.70 14.88 3.19 3.544 22.253 5216.029 0.014 11.62 14.79 3.18 3.521 22.124 5961.176 0.013 11.58 14.76 3.18 3.546 22.207 6706.323 0.013 11.60 14.89 3.28 3.594 22.297 7451.470 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: 186.287 Accepted refinement result: 11.80 14.04 2.24 3.765 21.821 186.287 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.91 22.26 3.29 197 1753 Protein: 9.09 114.91 17.03 3.29 0 1519 Water: 11.50 76.68 41.04 N/A 197 226 Other: 19.77 26.64 22.11 N/A 0 8 Chain A: 9.09 114.91 19.49 N/A 0 1753 Chain S: 13.25 60.00 46.89 N/A 197 0 Histogram: Values Number of atoms 9.09 - 19.67 1258 19.67 - 30.26 247 30.26 - 40.84 165 40.84 - 51.42 134 51.42 - 62.00 122 62.00 - 72.58 12 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1404 r_work=0.1180 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1180 r_free = 0.1404 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 = 0.1178 r_free = 0.1404 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1178 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014862 | | target function (ls_wunit_k1) not normalized (work): 1237.914539 | | target function (ls_wunit_k1) not normalized (free): 103.177235 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1178 0.1404 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1576 0.1575 0.1642 n_refl.: 87592 remove outliers: r(all,work,free)=0.1576 0.1575 0.1642 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1578 0.1576 0.1643 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1176 0.1399 n_refl.: 87592 remove outliers: r(all,work,free)=0.1185 0.1174 0.1399 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 0.3381 297.219 275.051 0.590 1.003 0.350 11.894-9.307 99.02 97 4 0.1625 482.687 475.845 0.922 1.003 0.333 9.237-7.194 100.00 213 7 0.1665 394.779 395.739 0.981 1.003 0.269 7.162-5.571 100.00 427 22 0.1609 296.259 290.476 0.932 1.003 0.240 5.546-4.326 100.00 867 58 0.0881 406.691 403.270 0.961 1.003 0.209 4.315-3.360 100.00 1859 96 0.0780 386.766 386.063 1.004 1.002 0.190 3.356-2.611 100.00 3867 181 0.1063 254.085 253.304 1.011 1.002 0.043 2.608-2.026 99.99 8198 413 0.0990 168.435 167.928 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1091 82.255 82.482 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.475 36.001 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.982 21.487 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=0.0163 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1174 r_free=0.1399 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1174 r_free=0.1399 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1399 | n_water=423 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1173 r_free=0.1400 | n_water=420 | time (s): 33.800 (total time: 35.550) Filter (q & B) r_work=0.1173 r_free=0.1400 | n_water=420 | time (s): 0.770 (total time: 36.320) Compute maps r_work=0.1173 r_free=0.1400 | n_water=420 | time (s): 1.190 (total time: 37.510) Filter (map) r_work=0.1216 r_free=0.1388 | n_water=288 | time (s): 2.480 (total time: 39.990) Find peaks r_work=0.1216 r_free=0.1388 | n_water=288 | time (s): 0.450 (total time: 40.440) Add new water r_work=0.1333 r_free=0.1504 | n_water=483 | time (s): 3.060 (total time: 43.500) Refine new water occ: r_work=0.1239 r_free=0.1416 adp: r_work=0.1241 r_free=0.1416 occ: r_work=0.1217 r_free=0.1400 adp: r_work=0.1215 r_free=0.1398 occ: r_work=0.1201 r_free=0.1390 adp: r_work=0.1201 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1390 r_work=0.1201 r_free=0.1390 | n_water=483 | time (s): 220.090 (total time: 263.590) Filter (q & B) r_work=0.1205 r_free=0.1393 | n_water=449 | time (s): 2.930 (total time: 266.520) Filter (dist only) r_work=0.1205 r_free=0.1391 | n_water=447 | time (s): 34.800 (total time: 301.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.727296 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.401150 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 0.1232 0.1365 0.0132 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1190 0.1330 0.0140 0.003 0.7 3.5 0.5 0.0 0 0.259 0.1172 0.1314 0.0142 0.004 0.8 3.5 0.5 0.0 0 0.518 0.1166 0.1310 0.0144 0.005 0.9 3.5 0.5 0.0 0 0.777 0.1160 0.1308 0.0148 0.006 1.0 3.2 0.5 0.0 0 1.036 0.1158 0.1308 0.0150 0.007 1.0 3.5 0.5 0.0 0 1.295 0.1157 0.1309 0.0153 0.007 1.0 3.5 0.5 0.0 0 1.555 0.1155 0.1309 0.0154 0.008 1.1 3.5 0.5 0.0 0 1.814 0.1165 0.1310 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.864 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1308 0.0148 0.006 1.0 3.2 0.5 0.0 0 1.036 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.08 1.48 3.768 21.110 42.401 3.622 11.60 13.08 1.48 3.768 21.110 1.272 3.622 11.60 13.08 1.48 3.765 21.110 5.300 3.622 11.64 13.16 1.52 3.702 21.104 21.201 3.615 11.69 13.34 1.64 3.718 21.082 42.401 3.618 11.60 13.28 1.68 3.749 21.071 63.602 3.612 11.54 13.24 1.70 3.766 21.069 84.802 3.607 11.51 13.22 1.71 3.777 21.070 106.003 3.604 11.49 13.22 1.73 3.794 21.066 127.203 3.602 11.48 13.20 1.73 3.806 21.065 148.404 3.600 11.45 13.19 1.73 3.813 21.064 169.605 3.599 11.44 13.18 1.74 3.820 21.064 190.805 3.597 11.43 13.17 1.74 3.831 21.068 212.006 3.597 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.272 Accepted refinement result: 11.60 13.08 1.48 3.768 21.110 1.272 3.622 Individual atomic B min max mean iso aniso Overall: 9.10 114.92 20.95 3.29 225 1749 Protein: 9.10 114.92 17.04 3.29 0 1519 Water: 11.51 76.69 34.23 N/A 225 222 Other: 19.78 26.65 22.12 N/A 0 8 Chain A: 9.10 114.92 19.44 N/A 0 1749 Chain S: 13.26 60.01 32.76 N/A 225 0 Histogram: Values Number of atoms 9.10 - 19.68 1260 19.68 - 30.27 330 30.27 - 40.85 202 40.85 - 51.43 108 51.43 - 62.01 50 62.01 - 72.59 12 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1308 r_work=0.1160 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1308 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1158 r_free = 0.1310 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.19 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= 0.1158 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.618003 | | target function (ml) not normalized (work): 301354.310934 | | target function (ml) not normalized (free): 15853.177554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1158 0.1310 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1491 0.1489 0.1546 n_refl.: 87589 remove outliers: r(all,work,free)=0.1491 0.1489 0.1546 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1489 0.1487 0.1545 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1150 0.1297 n_refl.: 87589 remove outliers: r(all,work,free)=0.1155 0.1148 0.1297 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3811 294.351 265.744 0.476 1.001 0.314 11.894-9.307 98.04 96 4 0.2540 482.812 463.977 0.847 1.002 0.310 9.237-7.194 98.64 210 7 0.2370 388.815 388.556 0.941 1.002 0.167 7.162-5.571 100.00 427 22 0.2151 296.259 284.876 0.903 1.003 0.160 5.546-4.326 100.00 867 58 0.1113 406.691 401.988 0.954 1.002 0.145 4.315-3.360 100.00 1859 96 0.0927 386.766 384.066 0.996 1.002 0.140 3.356-2.611 100.00 3867 181 0.1128 254.085 252.090 0.999 1.002 0.080 2.608-2.026 99.99 8198 413 0.0936 168.435 167.659 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0906 82.255 82.556 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1261 36.475 36.069 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.982 21.532 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1297 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=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1297 | n_water=447 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1148 r_free=0.1296 | n_water=446 | time (s): 45.530 (total time: 47.880) Filter (q & B) r_work=0.1148 r_free=0.1298 | n_water=443 | time (s): 3.770 (total time: 51.650) Compute maps r_work=0.1148 r_free=0.1298 | n_water=443 | time (s): 1.860 (total time: 53.510) Filter (map) r_work=0.1165 r_free=0.1299 | n_water=337 | time (s): 3.870 (total time: 57.380) Find peaks r_work=0.1165 r_free=0.1299 | n_water=337 | time (s): 0.690 (total time: 58.070) Add new water r_work=0.1230 r_free=0.1364 | n_water=500 | time (s): 3.730 (total time: 61.800) Refine new water occ: r_work=0.1165 r_free=0.1298 adp: r_work=0.1165 r_free=0.1300 occ: r_work=0.1150 r_free=0.1286 adp: r_work=0.1148 r_free=0.1285 occ: r_work=0.1139 r_free=0.1281 adp: r_work=0.1135 r_free=0.1278 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1278 r_work=0.1135 r_free=0.1278 | n_water=500 | time (s): 162.270 (total time: 224.070) Filter (q & B) r_work=0.1142 r_free=0.1288 | n_water=461 | time (s): 4.030 (total time: 228.100) Filter (dist only) r_work=0.1142 r_free=0.1287 | n_water=459 | time (s): 46.690 (total time: 274.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.783151 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.391449 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 0.1200 0.1326 0.0126 0.002 0.6 3.8 0.5 0.0 0 0.089 0.1162 0.1302 0.0140 0.003 0.7 2.6 0.5 0.0 0 0.267 0.1147 0.1291 0.0144 0.005 0.9 2.9 0.5 0.0 0 0.535 0.1142 0.1291 0.0149 0.006 0.9 2.6 0.5 0.0 0 0.802 0.1137 0.1289 0.0152 0.006 1.0 2.6 0.5 0.0 0 1.070 0.1135 0.1287 0.0151 0.007 1.1 2.9 0.5 0.0 0 1.337 0.1133 0.1288 0.0155 0.008 1.1 2.9 0.5 0.0 0 1.605 0.1131 0.1287 0.0156 0.008 1.1 2.9 0.5 0.0 0 1.872 0.1140 0.1289 0.0149 0.006 1.0 2.6 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1287 0.0151 0.007 1.1 2.9 0.5 0.0 0 1.337 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 12.87 1.51 3.769 21.272 42.391 3.606 11.35 12.87 1.51 3.769 21.272 1.272 3.606 11.35 12.87 1.51 3.769 21.272 5.299 3.606 11.38 12.92 1.55 3.708 21.267 21.196 3.601 11.47 13.12 1.65 3.728 21.233 42.391 3.606 11.40 13.09 1.70 3.748 21.223 63.587 3.600 11.33 13.05 1.72 3.767 21.220 84.783 3.595 11.30 13.02 1.72 3.776 21.218 105.979 3.592 11.30 13.03 1.74 3.795 21.207 127.174 3.591 11.26 13.00 1.74 3.800 21.211 148.370 3.589 11.27 13.03 1.76 3.818 21.198 169.566 3.588 11.26 13.03 1.76 3.828 21.196 190.762 3.587 11.24 13.00 1.76 3.832 21.197 211.957 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.299 Accepted refinement result: 11.35 12.87 1.51 3.769 21.272 5.299 3.606 Individual atomic B min max mean iso aniso Overall: 9.09 114.91 21.25 3.29 238 1748 Protein: 9.09 114.91 17.03 3.29 0 1519 Water: 11.51 76.68 35.21 N/A 238 221 Other: 19.77 26.64 22.11 N/A 0 8 Chain A: 9.09 114.91 19.41 N/A 0 1748 Chain S: 13.25 60.00 34.80 N/A 238 0 Histogram: Values Number of atoms 9.09 - 19.68 1260 19.68 - 30.26 312 30.26 - 40.84 211 40.84 - 51.42 125 51.42 - 62.00 54 62.00 - 72.58 12 72.58 - 83.16 6 83.16 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1287 r_work=0.1135 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1287 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1280 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1280 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603911 | | target function (ml) not normalized (work): 300158.917268 | | target function (ml) not normalized (free): 15796.388026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1280 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1463 0.1463 0.1505 n_refl.: 87583 remove outliers: r(all,work,free)=0.1463 0.1463 0.1505 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1462 0.1461 0.1505 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1281 n_refl.: 87583 remove outliers: r(all,work,free)=0.1135 0.1127 0.1281 n_refl.: 87575 ======================== 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 0.4019 288.420 248.832 0.455 1.000 0.313 11.894-9.307 95.10 93 4 0.2567 469.831 459.248 0.853 1.002 0.243 9.237-7.194 97.73 208 7 0.2349 385.775 383.013 0.933 1.002 0.180 7.162-5.571 100.00 427 22 0.2126 296.259 285.794 0.907 1.003 0.130 5.546-4.326 100.00 867 58 0.1114 406.691 402.150 0.964 1.003 0.120 4.315-3.360 100.00 1859 96 0.0911 386.766 384.426 1.006 1.002 0.120 3.356-2.611 100.00 3867 181 0.1097 254.085 252.081 1.010 1.002 0.060 2.608-2.026 99.99 8198 413 0.0905 168.435 167.734 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.255 82.573 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.475 36.068 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.982 21.528 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1127 r_free=0.1281 After: r_work=0.1128 r_free=0.1281 ================================== NQH flips ================================== r_work=0.1128 r_free=0.1281 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1128 r_free=0.1281 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1128 r_free=0.1281 | n_water=459 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1128 r_free=0.1282 | n_water=458 | time (s): 49.940 (total time: 52.340) Filter (q & B) r_work=0.1128 r_free=0.1282 | n_water=457 | time (s): 4.310 (total time: 56.650) Compute maps r_work=0.1128 r_free=0.1282 | n_water=457 | time (s): 1.890 (total time: 58.540) Filter (map) r_work=0.1152 r_free=0.1299 | n_water=355 | time (s): 3.990 (total time: 62.530) Find peaks r_work=0.1152 r_free=0.1299 | n_water=355 | time (s): 0.690 (total time: 63.220) Add new water r_work=0.1198 r_free=0.1334 | n_water=499 | time (s): 3.790 (total time: 67.010) Refine new water occ: r_work=0.1146 r_free=0.1276 adp: r_work=0.1146 r_free=0.1278 occ: r_work=0.1135 r_free=0.1263 adp: r_work=0.1133 r_free=0.1265 occ: r_work=0.1126 r_free=0.1253 adp: r_work=0.1123 r_free=0.1253 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1253 r_work=0.1123 r_free=0.1253 | n_water=499 | time (s): 255.090 (total time: 322.100) Filter (q & B) r_work=0.1132 r_free=0.1268 | n_water=457 | time (s): 4.060 (total time: 326.160) Filter (dist only) r_work=0.1132 r_free=0.1266 | n_water=455 | time (s): 47.300 (total time: 373.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.805880 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.436577 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 0.1204 0.1308 0.0104 0.003 0.7 4.2 0.0 0.0 0 0.090 0.1160 0.1281 0.0121 0.004 0.8 3.5 0.5 0.0 0 0.271 0.1142 0.1271 0.0129 0.005 1.0 2.9 0.5 0.0 0 0.542 0.1135 0.1267 0.0132 0.006 1.0 2.9 0.5 0.0 0 0.813 0.1133 0.1266 0.0133 0.007 1.1 2.9 0.5 0.0 0 1.084 0.1132 0.1266 0.0134 0.007 1.1 2.9 0.5 0.0 0 1.354 0.1132 0.1266 0.0134 0.007 1.1 2.9 0.5 0.0 0 1.625 0.1131 0.1266 0.0135 0.008 1.1 2.9 0.5 0.0 0 1.896 0.1134 0.1266 0.0132 0.007 1.0 2.9 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1266 0.0135 0.008 1.1 2.9 0.5 0.0 0 1.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.66 1.35 3.768 21.238 40.437 3.600 11.31 12.66 1.35 3.768 21.238 1.213 3.600 11.31 12.66 1.35 3.768 21.238 5.055 3.600 11.34 12.71 1.37 3.706 21.232 20.218 3.595 11.43 12.91 1.48 3.722 21.199 40.437 3.601 11.35 12.88 1.52 3.747 21.188 60.655 3.595 11.28 12.82 1.54 3.765 21.185 80.873 3.590 11.25 12.80 1.55 3.775 21.184 101.091 3.587 11.23 12.78 1.56 3.785 21.181 121.310 3.585 11.21 12.78 1.56 3.797 21.177 141.528 3.584 11.21 12.79 1.58 3.814 21.166 161.746 3.583 11.19 12.77 1.58 3.822 21.164 181.965 3.581 11.19 12.77 1.58 3.829 21.164 202.183 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.213 Accepted refinement result: 11.31 12.66 1.35 3.768 21.238 1.213 3.600 Individual atomic B min max mean iso aniso Overall: 9.09 114.90 21.20 3.29 234 1748 Protein: 9.09 114.90 17.03 3.29 0 1519 Water: 11.50 76.68 35.10 N/A 234 221 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.09 114.90 19.40 N/A 0 1748 Chain S: 13.24 60.00 34.59 N/A 234 0 Histogram: Values Number of atoms 9.09 - 19.67 1260 19.67 - 30.25 315 30.25 - 40.83 208 40.83 - 51.41 124 51.41 - 62.00 51 62.00 - 72.58 12 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1266 r_work=0.1131 r_free=0.1266 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1266 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1259 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1259 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598113 | | target function (ml) not normalized (work): 299647.290393 | | target function (ml) not normalized (free): 15771.914262 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1302 0.1227 5.6249 5.5441| | 2: 3.57 - 2.84 1.00 2888 124 0.1061 0.1363 5.1357 5.2026| | 3: 2.83 - 2.48 1.00 2820 163 0.1110 0.1225 4.9223 4.9604| | 4: 2.47 - 2.25 1.00 2825 136 0.0898 0.0955 4.6021 4.6255| | 5: 2.25 - 2.09 1.00 2756 127 0.0867 0.0964 4.548 4.5941| | 6: 2.09 - 1.97 1.00 2846 113 0.0852 0.0985 4.2469 4.3451| | 7: 1.97 - 1.87 1.00 2787 165 0.0887 0.1103 3.9724 4.0834| | 8: 1.87 - 1.79 1.00 2789 144 0.0909 0.1076 3.8762 3.9667| | 9: 1.79 - 1.72 1.00 2745 138 0.0882 0.1182 3.6432 3.8171| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1165 3.5571 3.6955| | 11: 1.66 - 1.61 1.00 2712 147 0.0875 0.1037 3.494 3.5633| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1131 3.3286 3.4582| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1047 3.3051 3.4092| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1069 3.2384 3.323| | 15: 1.48 - 1.45 1.00 2738 128 0.1010 0.1240 3.1565 3.2678| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1243 3.1386 3.2412| | 17: 1.42 - 1.39 1.00 2785 139 0.1145 0.1303 3.1214 3.2275| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1337 3.1038 3.2385| | 19: 1.36 - 1.34 1.00 2807 134 0.1264 0.1572 3.1153 3.2746| | 20: 1.34 - 1.32 1.00 2696 147 0.1370 0.1446 3.1131 3.1504| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1528 3.1133 3.1125| | 22: 1.29 - 1.27 1.00 2704 152 0.1567 0.1961 3.1258 3.2859| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1795 3.1344 3.1984| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1835 3.1268 3.2258| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2161 3.1427 3.2636| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1762 3.1489 3.1987| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2141 3.1721 3.1574| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2316 3.1664 3.1782| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2387 3.1469 3.2271| | 30: 1.16 - 1.15 1.00 2739 148 0.2450 0.2435 3.1436 3.1657| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 7.96 1.00 0.97 5242.33| | 2: 3.57 - 2.84 2888 124 0.93 11.88 1.01 0.97 5242.33| | 3: 2.83 - 2.48 2820 163 0.90 15.74 0.99 0.97 4385.73| | 4: 2.47 - 2.25 2825 136 0.92 12.86 1.00 0.98 2176.85| | 5: 2.25 - 2.09 2756 127 0.91 14.93 1.01 0.98 2176.85| | 6: 2.09 - 1.97 2846 113 0.93 11.93 1.02 0.98 1269.15| | 7: 1.97 - 1.87 2787 165 0.95 9.07 1.02 0.97 495.01| | 8: 1.87 - 1.79 2789 144 0.93 12.41 1.00 0.97 495.01| | 9: 1.79 - 1.72 2745 138 0.94 9.92 0.98 0.97 282.96| | 10: 1.72 - 1.66 2831 160 0.94 10.95 0.98 0.97 240.50| | 11: 1.66 - 1.61 2712 147 0.94 11.61 0.98 0.97 230.58| | 12: 1.61 - 1.56 2773 144 0.96 8.81 0.99 0.97 137.05| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 137.05| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 123.31| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.98 98.14| | 16: 1.45 - 1.42 2756 161 0.94 11.14 1.02 0.98 98.14| | 17: 1.42 - 1.39 2785 139 0.95 10.96 1.01 0.98 89.40| | 18: 1.39 - 1.36 2741 179 0.94 11.58 1.01 0.98 84.33| | 19: 1.36 - 1.34 2807 134 0.94 11.90 0.99 0.98 84.33| | 20: 1.34 - 1.32 2696 147 0.94 12.16 0.98 0.96 80.09| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.80| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.17| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.94 82.07| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 82.07| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.08| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.03 0.93 86.32| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.02 0.93 86.32| | 28: 1.19 - 1.18 2671 147 0.88 20.45 1.01 0.92 90.28| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.92 91.77| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.92 91.77| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.80 max = 5242.33 mean = 820.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.87 mean = 13.30| |phase err.(test): min = 0.00 max = 88.39 mean = 13.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1127 0.1259 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1493 n_refl.: 87575 remove outliers: r(all,work,free)=0.1449 0.1448 0.1493 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1449 0.1447 0.1493 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1128 0.1259 n_refl.: 87575 remove outliers: r(all,work,free)=0.1133 0.1126 0.1259 n_refl.: 87572 ======================== 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 86.46 78 5 0.4021 290.542 249.130 0.428 1.000 0.269 11.894-9.307 93.14 91 4 0.2410 469.870 454.792 0.853 1.002 0.261 9.237-7.194 97.73 208 7 0.2263 385.775 382.500 0.931 1.002 0.182 7.162-5.571 100.00 427 22 0.2075 296.259 286.290 0.909 1.002 0.140 5.546-4.326 100.00 867 58 0.1088 406.691 402.492 0.965 1.002 0.130 4.315-3.360 100.00 1859 96 0.0905 386.766 384.761 1.006 1.002 0.130 3.356-2.611 100.00 3867 181 0.1109 254.085 252.173 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0913 168.435 167.784 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.255 82.603 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.475 36.076 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2166 22.982 21.534 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0115 ================= 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 : 0.2610 0.1931 0.083 5.311 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1761 0.083 5.311 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1761 0.083 5.311 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1776 0.083 5.311 9.1 119.5 20.1 258 0.010 1_weight: 0.1642 0.1776 0.083 5.311 9.1 119.5 20.1 258 0.010 1_xyzrec: 0.1227 0.1472 0.006 0.876 9.1 119.5 20.1 258 0.132 1_adp: 0.1235 0.1469 0.006 0.876 9.1 119.4 20.1 258 0.132 1_regHadp: 0.1237 0.1472 0.006 0.876 9.1 119.4 20.1 258 0.132 1_occ: 0.1230 0.1468 0.006 0.876 9.1 119.4 20.1 258 0.132 2_bss: 0.1227 0.1456 0.006 0.876 9.1 119.5 20.1 258 0.132 2_settarget: 0.1227 0.1456 0.006 0.876 9.1 119.5 20.1 258 0.132 2_updatecdl: 0.1227 0.1456 0.006 0.890 9.1 119.5 20.1 258 0.132 2_nqh: 0.1227 0.1456 0.006 0.890 9.1 119.5 20.1 258 0.129 2_sol: 0.1199 0.1387 0.006 0.890 9.1 114.9 22.3 423 n/a 2_weight: 0.1199 0.1387 0.006 0.890 9.1 114.9 22.3 423 n/a 2_xyzrec: 0.1180 0.1404 0.006 0.850 9.1 114.9 22.3 423 n/a 2_adp: 0.1180 0.1404 0.006 0.850 9.1 114.9 22.3 423 n/a 2_regHadp: 0.1180 0.1404 0.006 0.850 9.1 114.9 22.3 423 n/a 2_occ: 0.1178 0.1404 0.006 0.850 9.1 114.9 22.3 423 n/a 3_bss: 0.1174 0.1399 0.006 0.850 9.1 114.9 22.3 423 n/a 3_settarget: 0.1174 0.1399 0.006 0.850 9.1 114.9 22.3 423 n/a 3_updatecdl: 0.1174 0.1399 0.006 0.852 9.1 114.9 22.3 423 n/a 3_nqh: 0.1174 0.1399 0.006 0.852 9.1 114.9 22.3 423 n/a 3_sol: 0.1205 0.1391 0.006 0.852 9.1 114.9 21.0 447 n/a 3_weight: 0.1205 0.1391 0.006 0.852 9.1 114.9 21.0 447 n/a 3_xyzrec: 0.1160 0.1308 0.006 0.961 9.1 114.9 21.0 447 n/a 3_adp: 0.1160 0.1308 0.006 0.961 9.1 114.9 21.0 447 n/a 3_regHadp: 0.1160 0.1308 0.006 0.961 9.1 114.9 21.0 447 n/a 3_occ: 0.1158 0.1310 0.006 0.961 9.1 114.9 21.0 447 n/a 4_bss: 0.1148 0.1297 0.006 0.961 9.1 114.9 20.9 447 n/a 4_settarget: 0.1148 0.1297 0.006 0.961 9.1 114.9 20.9 447 n/a 4_updatecdl: 0.1148 0.1297 0.006 0.962 9.1 114.9 20.9 447 n/a 4_nqh: 0.1148 0.1297 0.006 0.962 9.1 114.9 20.9 447 n/a 4_sol: 0.1142 0.1287 0.006 0.962 9.1 114.9 21.3 459 n/a 4_weight: 0.1142 0.1287 0.006 0.962 9.1 114.9 21.3 459 n/a 4_xyzrec: 0.1135 0.1287 0.007 1.054 9.1 114.9 21.3 459 n/a 4_adp: 0.1135 0.1287 0.007 1.054 9.1 114.9 21.3 459 n/a 4_regHadp: 0.1135 0.1287 0.007 1.054 9.1 114.9 21.3 459 n/a 4_occ: 0.1132 0.1280 0.007 1.054 9.1 114.9 21.3 459 n/a 5_bss: 0.1127 0.1281 0.007 1.054 9.1 114.9 21.2 459 n/a 5_settarget: 0.1127 0.1281 0.007 1.054 9.1 114.9 21.2 459 n/a 5_updatecdl: 0.1127 0.1281 0.007 1.055 9.1 114.9 21.2 459 n/a 5_setrh: 0.1128 0.1281 0.007 1.055 9.1 114.9 21.2 459 n/a 5_nqh: 0.1128 0.1281 0.007 1.055 9.1 114.9 21.2 459 n/a 5_sol: 0.1132 0.1266 0.007 1.055 9.1 114.9 21.2 455 n/a 5_weight: 0.1132 0.1266 0.007 1.055 9.1 114.9 21.2 455 n/a 5_xyzrec: 0.1131 0.1266 0.008 1.089 9.1 114.9 21.2 455 n/a 5_adp: 0.1131 0.1266 0.008 1.089 9.1 114.9 21.2 455 n/a 5_regHadp: 0.1131 0.1266 0.008 1.089 9.1 114.9 21.2 455 n/a 5_occ: 0.1127 0.1259 0.008 1.089 9.1 114.9 21.2 455 n/a end: 0.1126 0.1259 0.008 1.089 9.1 114.9 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6024882_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6024882_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1100 Refinement macro-cycles (run) : 13344.5000 Write final files (write_after_run_outputs) : 96.6100 Total : 13445.2200 Total CPU time: 3.74 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:50 PST -0800 (1735366010.09 s) Start R-work = 0.1633, R-free = 0.1761 Final R-work = 0.1126, R-free = 0.1259 =============================================================================== Job complete usr+sys time: 13629.61 seconds wall clock time: 251 minutes 7.30 seconds (15067.30 seconds total)