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_7766834.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_7766834.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.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 2 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: 1.31, per 1000 atoms: 0.39 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: 0.44 Conformation dependent library (CDL) restraints added in 106.7 milliseconds Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 429 0.90 - 1.17: 1199 1.17 - 1.43: 682 1.43 - 1.70: 820 1.70 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta sigma weight residual 1.456 1.671 -0.215 1.16e-02 7.43e+03 3.43e+02 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.460 1.675 -0.216 1.21e-02 6.83e+03 3.18e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.20e-02 6.94e+03 2.98e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.490 -0.169 1.00e-02 1.00e+04 2.85e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.422 -0.185 1.12e-02 7.97e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 2988 4.38 - 8.76: 1875 8.76 - 13.14: 725 13.14 - 17.52: 160 17.52 - 21.91: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.45 -14.25 9.00e-01 1.23e+00 2.51e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.77 -12.54 8.10e-01 1.52e+00 2.40e+02 angle pdb=" O VAL A 177 " pdb=" C VAL A 177 " pdb=" N ALA A 178 " ideal model delta sigma weight residual 121.94 136.04 -14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.74 12.46 9.00e-01 1.23e+00 1.92e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.61 8.68 6.50e-01 2.37e+00 1.78e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.66: 953 17.66 - 35.30: 105 35.30 - 52.95: 38 52.95 - 70.60: 11 70.60 - 88.25: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 85 0.182 - 0.363: 73 0.363 - 0.544: 45 0.544 - 0.726: 33 0.726 - 0.907: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.50 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.69 -0.90 2.00e-01 2.50e+01 2.01e+01 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 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.118 2.00e-02 2.50e+03 7.88e-02 1.86e+02 pdb=" CG PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.138 2.00e-02 2.50e+03 7.86e-02 1.85e+02 pdb=" CG PHE A 164 " 0.165 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 123 " -0.040 2.00e-02 2.50e+03 9.05e-02 8.19e+01 pdb=" C VAL A 123 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL A 123 " -0.064 2.00e-02 2.50e+03 pdb=" N THR A 124 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 700 2.26 - 2.85: 7720 2.85 - 3.43: 10601 3.43 - 4.02: 15338 4.02 - 4.60: 22374 Nonbonded interactions: 56733 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.677 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HA3BGLY A 65 " pdb=" HA BPRO A 66 " model vdw 1.830 2.440 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.832 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56728 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_7766834_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= 0.2603 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791744 | | target function (ml) not normalized (work): 232569.009453 | | target function (ml) not normalized (free): 11795.763004 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3048 0.2004 7.1171 4.9295| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1840 4.3439 4.3481| | 3: 2.84 - 2.48 1.00 2833 165 0.2332 0.1519 4.1187 4.1289| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1338 3.8243 3.8039| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1603 3.7866 3.8193| | 6: 2.09 - 1.97 1.00 2846 113 0.2545 0.1893 3.4534 3.5836| | 7: 1.97 - 1.87 1.00 2787 165 0.2532 0.1756 3.1389 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2479 0.1757 3.052 3.121| | 9: 1.79 - 1.72 1.00 2745 138 0.2432 0.2074 2.8867 2.9335| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1882 2.8056 2.8668| | 11: 1.66 - 1.61 1.00 2740 147 0.2480 0.1935 2.7526 2.8202| | 12: 1.61 - 1.56 1.00 2787 146 0.2451 0.2170 2.6244 2.7102| | 13: 1.56 - 1.52 1.00 2745 130 0.2583 0.1895 2.5928 2.6479| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1777 2.509 2.5164| | 15: 1.48 - 1.45 1.00 2738 128 0.2563 0.2089 2.4298 2.5657| | 16: 1.45 - 1.42 1.00 2756 161 0.2626 0.2165 2.3831 2.4326| | 17: 1.42 - 1.39 1.00 2785 139 0.2672 0.1966 2.3237 2.3101| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.2120 2.2717 2.3121| | 19: 1.36 - 1.34 1.00 2807 134 0.2669 0.2224 2.2514 2.2802| | 20: 1.34 - 1.32 1.00 2696 147 0.2657 0.2158 2.1964 2.1622| | 21: 1.32 - 1.30 1.00 2785 112 0.2754 0.2159 2.1785 2.1042| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2545 2.1477 2.1861| | 23: 1.27 - 1.26 1.00 2802 156 0.2808 0.2303 2.1058 2.1232| | 24: 1.26 - 1.24 1.00 2744 132 0.2717 0.2672 2.0589 2.1663| | 25: 1.24 - 1.22 1.00 2734 148 0.2881 0.2689 2.0495 2.0976| | 26: 1.22 - 1.21 1.00 2727 135 0.2862 0.2142 2.0111 2.057| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2613 1.9973 2.0047| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2781 1.9822 1.9853| | 29: 1.18 - 1.16 1.00 2800 134 0.2949 0.2878 1.966 2.0517| | 30: 1.16 - 1.15 1.00 2740 148 0.3085 0.2915 1.9348 1.9989| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.63 0.76 0.23 1454.19| | 2: 3.57 - 2.84 2876 122 0.81 25.77 1.27 0.23 1454.19| | 3: 2.84 - 2.48 2833 165 0.74 31.72 1.24 0.24 1205.51| | 4: 2.47 - 2.25 2825 136 0.81 25.29 1.26 0.25 560.14| | 5: 2.25 - 2.09 2756 127 0.78 29.00 1.28 0.25 560.14| | 6: 2.09 - 1.97 2846 113 0.84 22.43 1.29 0.25 306.39| | 7: 1.97 - 1.87 2787 165 0.90 16.26 1.28 0.26 89.98| | 8: 1.87 - 1.79 2789 144 0.86 20.88 1.25 0.26 89.98| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.24 0.26 55.61| | 10: 1.72 - 1.66 2789 158 0.86 20.32 1.22 0.26 48.73| | 11: 1.66 - 1.61 2740 147 0.86 21.38 1.24 0.26 47.08| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.31| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.24 0.25 30.31| | 14: 1.52 - 1.48 2803 134 0.86 20.87 1.24 0.25 26.89| | 15: 1.48 - 1.45 2738 128 0.87 20.03 1.23 0.25 20.62| | 16: 1.45 - 1.42 2756 161 0.86 21.48 1.23 0.25 20.62| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.24 0.25 17.32| | 18: 1.39 - 1.36 2741 179 0.87 20.88 1.23 0.25 15.41| | 19: 1.36 - 1.34 2807 134 0.86 21.64 1.22 0.25 15.41| | 20: 1.34 - 1.32 2696 147 0.87 20.25 1.20 0.25 12.61| | 21: 1.32 - 1.30 2785 112 0.86 21.34 1.21 0.25 12.41| | 22: 1.29 - 1.27 2704 152 0.86 22.03 1.20 0.25 12.13| | 23: 1.27 - 1.26 2802 156 0.86 21.70 1.22 0.24 10.69| | 24: 1.26 - 1.24 2744 132 0.86 22.11 1.20 0.24 10.69| | 25: 1.24 - 1.22 2734 148 0.84 23.55 1.21 0.24 10.28| | 26: 1.22 - 1.21 2727 135 0.84 23.81 1.20 0.23 9.83| | 27: 1.21 - 1.19 2814 148 0.83 24.66 1.20 0.23 9.83| | 28: 1.19 - 1.18 2671 147 0.83 25.48 1.18 0.23 9.44| | 29: 1.18 - 1.16 2800 134 0.82 25.96 1.15 0.22 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.77 1.14 0.22 9.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1454.19 mean = 211.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.46| |phase err.(test): min = 0.00 max = 89.88 mean = 22.34| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.449 Angle : 5.364 17.071 2118 Z= 3.752 Chirality : 0.368 0.907 243 Planarity : 0.031 0.104 284 Dihedral : 14.050 88.249 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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 (0.50), residues: 224 helix: -2.64 (0.36), residues: 109 sheet: -0.60 (0.93), residues: 28 loop : 0.28 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.016 ARG A 28 TYR 0.074 0.023 TYR A 139 PHE 0.168 0.053 PHE A 164 HIS 0.084 0.036 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= 0.2603 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791744 | | target function (ml) not normalized (work): 232569.009453 | | target function (ml) not normalized (free): 11795.763004 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1907 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1907 n_refl.: 87602 remove outliers: r(all,work,free)=0.1973 0.1978 0.1907 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1999 0.2005 0.1921 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1633 0.1749 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1633 0.1749 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 0.3844 386.112 369.228 0.689 1.001 0.401 11.894-9.307 99.02 97 4 0.1784 613.321 592.677 0.926 1.001 0.380 9.237-7.194 100.00 213 7 0.2168 501.621 490.329 0.952 1.002 0.370 7.162-5.571 100.00 427 22 0.2212 376.439 366.686 0.935 1.002 0.288 5.546-4.326 100.00 867 58 0.1277 516.757 510.195 0.965 1.002 0.229 4.315-3.360 100.00 1859 96 0.1149 491.440 487.795 1.005 1.002 0.209 3.356-2.611 100.00 3867 181 0.1439 322.850 319.562 0.995 1.002 0.048 2.608-2.026 99.99 8198 413 0.1329 214.020 211.874 1.004 1.002 0.000 2.025-1.573 100.00 17313 902 0.1639 104.516 103.974 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.347 45.108 0.999 1.003 0.000 1.221-1.150 99.97 13689 708 0.2592 29.202 26.825 0.961 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0494 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1749 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=0.1635 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.314791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1977.162417 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 0.1724 0.1845 0.0121 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1555 0.1698 0.0143 0.001 0.4 3.8 0.0 0.0 0 0.250 0.1450 0.1623 0.0172 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1372 0.1563 0.0191 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1361 0.1561 0.0200 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1368 0.1575 0.0206 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1304 0.1522 0.0218 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1274 0.1499 0.0224 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1261 0.1484 0.0224 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1248 0.1479 0.0231 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1247 0.1474 0.0228 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1235 0.1465 0.0230 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1235 0.1470 0.0235 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1232 0.1469 0.0237 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1231 0.1468 0.0237 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1230 0.1472 0.0242 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1471 0.0245 0.007 0.9 3.2 0.5 0.6 0 12.000 0.1225 0.1476 0.0252 0.007 0.9 3.5 0.5 0.6 0 13.157 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1465 0.0230 0.005 0.8 4.2 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.65 2.30 3.013 19.074 1977.162 0.018 12.35 14.64 2.29 2.989 19.074 59.315 0.018 12.42 14.61 2.20 2.665 19.073 247.145 0.018 12.76 15.27 2.51 2.744 19.229 988.581 0.017 12.61 15.45 2.84 3.214 19.562 1977.162 0.016 12.51 15.47 2.96 3.340 19.663 2965.744 0.016 12.48 15.52 3.03 3.441 19.684 3954.325 0.015 12.37 15.44 3.07 3.346 19.617 4942.906 0.015 12.31 15.43 3.12 3.414 19.665 5931.487 0.015 12.26 15.34 3.09 3.191 19.525 6920.068 0.015 12.25 15.38 3.12 3.366 19.607 7908.650 0.015 12.19 15.29 3.10 3.182 19.500 8897.231 0.015 12.24 15.47 3.23 3.434 19.620 9885.812 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: 247.145 Accepted refinement result: 12.42 14.61 2.20 2.665 19.073 247.145 0.018 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.30 0 1785 Protein: 9.08 114.98 17.01 3.31 0 1519 Water: 11.47 119.46 38.24 N/A 0 258 Other: 19.73 26.62 22.07 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.19 125 42.19 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1461 r_work=0.1243 r_free=0.1465 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1465 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1238 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1238 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.017173 | | target function (ls_wunit_k1) not normalized (work): 1430.479609 | | target function (ls_wunit_k1) not normalized (free): 109.610407 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1248 0.1238 0.1460 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1681 0.1682 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1681 0.1682 0.1693 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1686 0.1687 0.1696 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1245 0.1235 0.1452 n_refl.: 87593 remove outliers: r(all,work,free)=0.1245 0.1234 0.1452 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 0.3548 301.106 280.282 0.648 1.003 0.380 11.894-9.307 99.02 97 4 0.1655 482.356 470.727 0.922 1.003 0.372 9.237-7.194 100.00 213 7 0.1928 394.508 387.378 0.961 1.003 0.353 7.162-5.571 100.00 427 22 0.1840 296.056 290.199 0.937 1.003 0.259 5.546-4.326 100.00 867 58 0.1017 406.412 403.332 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0886 386.501 385.331 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1179 253.911 252.744 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1027 168.320 167.568 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1117 82.199 82.380 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1456 36.450 35.951 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2258 22.966 21.448 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0432 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 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=0.1234 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1452 | n_water=258 | time (s): 1.720 (total time: 1.720) Filter (dist) r_work=0.1242 r_free=0.1448 | n_water=251 | time (s): 21.450 (total time: 23.170) Filter (q & B) r_work=0.1244 r_free=0.1448 | n_water=248 | time (s): 2.730 (total time: 25.900) Compute maps r_work=0.1244 r_free=0.1448 | n_water=248 | time (s): 1.240 (total time: 27.140) Filter (map) r_work=0.1261 r_free=0.1457 | n_water=228 | time (s): 2.640 (total time: 29.780) Find peaks r_work=0.1261 r_free=0.1457 | n_water=228 | time (s): 0.450 (total time: 30.230) Add new water r_work=0.1405 r_free=0.1645 | n_water=439 | time (s): 2.530 (total time: 32.760) Refine new water occ: r_work=0.1307 r_free=0.1495 adp: r_work=0.1227 r_free=0.1439 occ: r_work=0.1240 r_free=0.1416 adp: r_work=0.1206 r_free=0.1405 occ: r_work=0.1210 r_free=0.1393 adp: r_work=0.1199 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1389 r_work=0.1199 r_free=0.1389 | n_water=439 | time (s): 51.140 (total time: 83.900) Filter (q & B) r_work=0.1204 r_free=0.1390 | n_water=422 | time (s): 2.760 (total time: 86.660) Filter (dist only) r_work=0.1204 r_free=0.1388 | n_water=421 | time (s): 34.490 (total time: 121.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.456193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1505.964082 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 0.1704 0.1811 0.0107 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1551 0.1677 0.0126 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1414 0.1566 0.0152 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1351 0.1518 0.0167 0.002 0.4 5.1 0.0 0.0 0 0.750 0.1322 0.1499 0.0177 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1334 0.1511 0.0177 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1250 0.1448 0.0198 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1225 0.1436 0.0211 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1214 0.1426 0.0212 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1208 0.1423 0.0215 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1197 0.1409 0.0212 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1193 0.1406 0.0213 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1193 0.1411 0.0218 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1191 0.1403 0.0212 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1188 0.1410 0.0221 0.006 0.8 4.5 0.5 0.0 0 10.000 0.1186 0.1407 0.0221 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1187 0.1403 0.0216 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1186 0.1405 0.0219 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1182 0.1392 0.0210 0.008 1.0 3.8 0.5 0.0 0 14.728 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1392 0.0210 0.008 1.0 3.8 0.5 0.0 0 14.728 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 13.92 2.10 3.774 21.832 1505.964 0.016 11.82 13.92 2.10 3.774 21.832 45.179 0.016 11.82 13.92 2.10 3.774 21.832 188.246 0.016 12.06 14.48 2.42 3.580 21.872 752.982 0.015 11.98 14.61 2.63 3.519 21.939 1505.964 0.015 11.88 14.72 2.83 3.503 21.996 2258.946 0.014 11.76 14.65 2.89 3.512 21.992 3011.928 0.014 11.70 14.58 2.87 3.524 22.149 3764.910 0.014 11.67 14.60 2.93 3.513 22.128 4517.892 0.014 11.65 14.59 2.95 3.554 22.222 5270.874 0.014 11.57 14.50 2.93 3.559 22.198 6023.856 0.014 11.58 14.53 2.96 3.585 22.227 6776.838 0.013 11.55 14.58 3.03 3.583 22.148 7529.820 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: 45.179 Accepted refinement result: 11.82 13.92 2.10 3.774 21.832 45.179 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 22.27 3.30 193 1755 Protein: 9.11 115.00 17.04 3.31 0 1519 Water: 11.50 76.69 41.18 N/A 193 228 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.11 115.00 19.51 N/A 0 1755 Chain S: 16.59 60.00 47.39 N/A 193 0 Histogram: Values Number of atoms 9.11 - 19.70 1257 19.70 - 30.29 245 30.29 - 40.88 162 40.88 - 51.47 134 51.47 - 62.06 127 62.06 - 72.65 12 72.65 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1392 r_work=0.1182 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1392 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 = 0.1180 r_free = 0.1395 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1180 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014743 | | target function (ls_wunit_k1) not normalized (work): 1228.058663 | | target function (ls_wunit_k1) not normalized (free): 96.407334 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1180 0.1395 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1575 0.1574 0.1614 n_refl.: 87592 remove outliers: r(all,work,free)=0.1575 0.1574 0.1614 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1576 0.1575 0.1614 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1177 0.1391 n_refl.: 87592 remove outliers: r(all,work,free)=0.1186 0.1175 0.1391 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 0.3333 297.015 273.348 0.599 1.003 0.360 11.894-9.307 99.02 97 4 0.1544 482.356 476.574 0.926 1.003 0.360 9.237-7.194 100.00 213 7 0.1625 394.508 394.069 0.983 1.004 0.274 7.162-5.571 100.00 427 22 0.1579 296.056 291.041 0.938 1.003 0.240 5.546-4.326 100.00 867 58 0.0870 406.412 403.248 0.959 1.003 0.200 4.315-3.360 100.00 1859 96 0.0775 386.501 385.615 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1071 253.911 253.019 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1004 168.320 167.824 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1093 82.199 82.427 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.450 35.985 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 22.966 21.477 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0095 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1175 r_free=0.1391 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=0.1176 r_free=0.1393 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1176 r_free=0.1393 | n_water=421 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1176 r_free=0.1391 | n_water=417 | time (s): 38.550 (total time: 40.230) Filter (q & B) r_work=0.1176 r_free=0.1391 | n_water=417 | time (s): 0.920 (total time: 41.150) Compute maps r_work=0.1176 r_free=0.1391 | n_water=417 | time (s): 1.240 (total time: 42.390) Filter (map) r_work=0.1223 r_free=0.1405 | n_water=280 | time (s): 2.800 (total time: 45.190) Find peaks r_work=0.1223 r_free=0.1405 | n_water=280 | time (s): 0.450 (total time: 45.640) Add new water r_work=0.1345 r_free=0.1526 | n_water=471 | time (s): 2.410 (total time: 48.050) Refine new water occ: r_work=0.1245 r_free=0.1443 adp: r_work=0.1246 r_free=0.1444 occ: r_work=0.1221 r_free=0.1430 adp: r_work=0.1221 r_free=0.1427 occ: r_work=0.1203 r_free=0.1413 adp: r_work=0.1199 r_free=0.1408 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1408 r_work=0.1199 r_free=0.1408 | n_water=471 | time (s): 183.070 (total time: 231.120) Filter (q & B) r_work=0.1204 r_free=0.1407 | n_water=437 | time (s): 2.840 (total time: 233.960) Filter (dist only) r_work=0.1204 r_free=0.1406 | n_water=436 | time (s): 38.560 (total time: 272.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.762497 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.346460 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 0.1373 0.0141 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1195 0.1336 0.0141 0.003 0.7 3.5 0.5 0.0 0 0.264 0.1176 0.1325 0.0148 0.004 0.8 3.5 0.5 0.0 0 0.529 0.1169 0.1325 0.0157 0.005 0.9 3.2 0.5 0.0 0 0.793 0.1163 0.1326 0.0163 0.006 1.0 3.5 0.5 0.0 0 1.057 0.1162 0.1327 0.0165 0.007 1.0 3.8 0.5 0.0 0 1.322 0.1160 0.1329 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.586 0.1158 0.1329 0.0171 0.008 1.1 4.2 0.5 0.0 0 1.851 0.1168 0.1328 0.0160 0.005 0.9 3.2 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1176 0.1325 0.0148 0.004 0.8 3.5 0.5 0.0 0 0.529 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 13.25 1.48 3.776 21.271 46.346 3.633 11.76 13.25 1.48 3.776 21.271 1.390 3.633 11.77 13.25 1.48 3.765 21.271 5.793 3.633 11.83 13.38 1.55 3.708 21.257 23.173 3.628 11.82 13.47 1.65 3.725 21.230 46.346 3.626 11.75 13.45 1.70 3.747 21.219 69.520 3.621 11.70 13.40 1.71 3.764 21.215 92.693 3.616 11.66 13.36 1.70 3.776 21.208 115.866 3.612 11.63 13.34 1.71 3.788 21.206 139.039 3.610 11.63 13.36 1.74 3.804 21.192 162.213 3.610 11.62 13.37 1.74 3.814 21.188 185.386 3.609 11.61 13.34 1.74 3.821 21.187 208.559 3.607 11.59 13.31 1.72 3.825 21.187 231.732 3.605 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.390 Accepted refinement result: 11.76 13.25 1.48 3.776 21.271 1.390 3.633 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.24 3.30 215 1748 Protein: 9.11 115.01 17.04 3.31 0 1519 Water: 11.50 76.70 35.87 N/A 215 221 Other: 19.76 26.66 22.11 N/A 0 8 Chain A: 9.11 115.01 19.40 N/A 0 1748 Chain S: 16.59 60.01 36.26 N/A 215 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.29 288 30.29 - 40.88 213 40.88 - 51.47 123 51.47 - 62.06 56 62.06 - 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=0.1176 r_free=0.1325 r_work=0.1176 r_free=0.1325 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1325 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1169 r_free = 0.1318 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1169 r_free= 0.1318 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.626449 | | target function (ml) not normalized (work): 302057.799741 | | target function (ml) not normalized (free): 15872.630576 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1176 0.1169 0.1318 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1502 0.1503 0.1523 n_refl.: 87589 remove outliers: r(all,work,free)=0.1502 0.1503 0.1523 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1501 0.1502 0.1522 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1171 0.1164 0.1311 n_refl.: 87589 remove outliers: r(all,work,free)=0.1170 0.1162 0.1311 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3899 297.015 268.223 0.504 1.002 0.327 11.894-9.307 98.04 96 4 0.2214 475.638 467.671 0.887 1.003 0.326 9.237-7.194 98.64 210 7 0.2323 386.996 383.345 0.954 1.003 0.200 7.162-5.571 100.00 427 22 0.2138 296.056 284.104 0.920 1.003 0.184 5.546-4.326 100.00 867 58 0.1128 406.412 401.879 0.962 1.003 0.170 4.315-3.360 100.00 1859 96 0.0942 386.501 383.859 1.005 1.003 0.150 3.356-2.611 100.00 3867 181 0.1141 253.911 251.923 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0952 168.320 167.495 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0930 82.199 82.438 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1282 36.450 36.015 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2177 22.966 21.492 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0140 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1162 r_free=0.1311 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=0.1162 r_free=0.1311 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1162 r_free=0.1311 | n_water=436 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1162 r_free=0.1311 | n_water=436 | time (s): 42.600 (total time: 45.060) Filter (q & B) r_work=0.1163 r_free=0.1312 | n_water=435 | time (s): 4.010 (total time: 49.070) Compute maps r_work=0.1163 r_free=0.1312 | n_water=435 | time (s): 1.850 (total time: 50.920) Filter (map) r_work=0.1189 r_free=0.1325 | n_water=320 | time (s): 3.870 (total time: 54.790) Find peaks r_work=0.1189 r_free=0.1325 | n_water=320 | time (s): 0.690 (total time: 55.480) Add new water r_work=0.1259 r_free=0.1406 | n_water=480 | time (s): 3.670 (total time: 59.150) Refine new water occ: r_work=0.1184 r_free=0.1341 adp: r_work=0.1185 r_free=0.1343 occ: r_work=0.1169 r_free=0.1319 adp: r_work=0.1169 r_free=0.1321 occ: r_work=0.1158 r_free=0.1300 adp: r_work=0.1155 r_free=0.1303 ADP+occupancy (water only), MIN, final r_work=0.1155 r_free=0.1303 r_work=0.1155 r_free=0.1303 | n_water=480 | time (s): 259.320 (total time: 318.470) Filter (q & B) r_work=0.1162 r_free=0.1303 | n_water=443 | time (s): 3.790 (total time: 322.260) Filter (dist only) r_work=0.1168 r_free=0.1301 | n_water=440 | time (s): 45.680 (total time: 367.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.825701 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.593393 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1338 0.0125 0.002 0.6 4.8 0.5 0.0 0 0.091 0.1175 0.1314 0.0139 0.003 0.7 3.2 0.5 0.0 0 0.274 0.1159 0.1299 0.0141 0.005 0.9 3.5 0.5 0.0 0 0.548 0.1153 0.1299 0.0145 0.006 1.0 3.2 0.5 0.0 0 0.822 0.1152 0.1300 0.0148 0.006 1.0 3.2 0.5 0.0 0 1.095 0.1148 0.1297 0.0150 0.007 1.1 3.2 0.5 0.0 0 1.369 0.1146 0.1297 0.0151 0.008 1.1 3.2 0.5 0.0 0 1.643 0.1145 0.1296 0.0152 0.009 1.1 3.2 0.5 0.0 0 1.917 0.1152 0.1298 0.0146 0.006 1.0 3.2 0.5 0.0 0 0.913 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1296 0.0152 0.009 1.1 3.2 0.5 0.0 0 1.917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.96 1.52 3.777 21.153 40.593 3.608 11.45 12.96 1.52 3.777 21.153 1.218 3.608 11.45 12.96 1.52 3.775 21.153 5.074 3.608 11.48 13.01 1.53 3.708 21.146 20.297 3.603 11.56 13.18 1.62 3.725 21.116 40.593 3.607 11.48 13.13 1.65 3.751 21.105 60.890 3.601 11.42 13.08 1.66 3.766 21.100 81.187 3.595 11.38 13.04 1.66 3.774 21.101 101.483 3.592 11.36 13.04 1.68 3.783 21.096 121.780 3.590 11.35 13.05 1.70 3.794 21.092 142.077 3.589 11.37 13.09 1.73 3.815 21.074 162.374 3.589 11.35 13.07 1.72 3.820 21.070 182.670 3.588 11.33 13.05 1.72 3.826 21.073 202.967 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: 5.074 Accepted refinement result: 11.45 12.96 1.52 3.775 21.153 5.074 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 114.98 21.03 3.30 223 1744 Protein: 9.11 114.98 17.04 3.30 0 1519 Water: 11.50 76.69 34.81 N/A 223 217 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.11 114.98 19.35 N/A 0 1744 Chain S: 15.95 60.00 34.22 N/A 223 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.29 306 30.29 - 40.87 211 40.87 - 51.46 119 51.46 - 62.05 46 62.05 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.39 0 104.39 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1296 r_work=0.1145 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1296 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1139 r_free = 0.1294 target_work(ml) = 3.605 | | 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.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1139 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604959 | | target function (ml) not normalized (work): 300253.424450 | | target function (ml) not normalized (free): 15817.575372 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1147 0.1139 0.1294 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1479 0.1478 0.1527 n_refl.: 87585 remove outliers: r(all,work,free)=0.1479 0.1478 0.1527 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1478 0.1476 0.1526 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1297 n_refl.: 87585 remove outliers: r(all,work,free)=0.1145 0.1137 0.1297 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 0.4041 294.149 254.680 0.465 0.999 0.318 11.894-9.307 97.06 95 4 0.2477 475.696 456.450 0.842 1.002 0.310 9.237-7.194 98.18 209 7 0.2405 385.990 378.369 0.915 1.002 0.197 7.162-5.571 100.00 427 22 0.2122 296.056 285.132 0.906 1.002 0.170 5.546-4.326 100.00 867 58 0.1152 406.412 402.046 0.955 1.002 0.140 4.315-3.360 100.00 1859 96 0.0912 386.501 384.396 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1133 253.911 252.063 1.001 1.002 0.029 2.608-2.026 99.99 8198 413 0.0920 168.320 167.681 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.199 82.519 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.450 36.058 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.966 21.523 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=-0.0197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1297 After: r_work=0.1138 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1138 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=0.1138 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1297 | n_water=440 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1138 r_free=0.1297 | n_water=440 | time (s): 43.870 (total time: 46.280) Filter (q & B) r_work=0.1138 r_free=0.1297 | n_water=440 | time (s): 1.430 (total time: 47.710) Compute maps r_work=0.1138 r_free=0.1297 | n_water=440 | time (s): 1.850 (total time: 49.560) Filter (map) r_work=0.1159 r_free=0.1301 | n_water=345 | time (s): 3.910 (total time: 53.470) Find peaks r_work=0.1159 r_free=0.1301 | n_water=345 | time (s): 0.690 (total time: 54.160) Add new water r_work=0.1220 r_free=0.1366 | n_water=491 | time (s): 3.650 (total time: 57.810) Refine new water occ: r_work=0.1163 r_free=0.1310 adp: r_work=0.1163 r_free=0.1311 occ: r_work=0.1150 r_free=0.1300 adp: r_work=0.1149 r_free=0.1299 occ: r_work=0.1140 r_free=0.1294 adp: r_work=0.1137 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1290 r_work=0.1137 r_free=0.1290 | n_water=491 | time (s): 327.570 (total time: 385.380) Filter (q & B) r_work=0.1144 r_free=0.1300 | n_water=453 | time (s): 3.630 (total time: 389.010) Filter (dist only) r_work=0.1144 r_free=0.1298 | n_water=451 | time (s): 47.610 (total time: 436.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.722161 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.460693 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 0.1221 0.1345 0.0124 0.004 0.7 4.5 0.0 0.0 0 0.086 0.1175 0.1313 0.0138 0.004 0.8 3.8 0.0 0.0 0 0.258 0.1158 0.1302 0.0144 0.005 1.0 3.2 0.5 0.0 0 0.517 0.1153 0.1300 0.0147 0.006 1.0 3.2 0.5 0.0 0 0.775 0.1149 0.1299 0.0150 0.007 1.1 3.2 0.5 0.0 0 1.033 0.1147 0.1298 0.0151 0.008 1.1 3.2 0.5 0.0 0 1.292 0.1144 0.1298 0.0154 0.008 1.1 3.2 0.5 0.0 0 1.550 0.1144 0.1298 0.0154 0.008 1.1 3.2 0.5 0.0 0 1.808 0.1152 0.1299 0.0147 0.006 1.0 3.2 0.5 0.0 0 0.861 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1298 0.0151 0.008 1.1 3.2 0.5 0.0 0 1.292 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 12.98 1.51 3.773 21.208 34.461 3.609 11.47 12.98 1.51 3.773 21.208 1.034 3.609 11.47 12.98 1.51 3.773 21.208 4.308 3.609 11.51 13.02 1.51 3.702 21.202 17.230 3.606 11.50 13.09 1.59 3.721 21.189 34.461 3.604 11.50 13.16 1.65 3.743 21.166 51.691 3.603 11.47 13.14 1.67 3.754 21.159 68.921 3.600 11.42 13.09 1.67 3.767 21.158 86.152 3.596 11.41 13.09 1.68 3.775 21.155 103.382 3.594 11.38 13.07 1.68 3.784 21.153 120.612 3.592 11.37 13.07 1.70 3.794 21.149 137.843 3.591 11.37 13.09 1.72 3.808 21.140 155.073 3.590 11.37 13.09 1.72 3.817 21.137 172.303 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.034 Accepted refinement result: 11.47 12.98 1.51 3.773 21.208 1.034 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 114.97 21.14 3.30 235 1743 Protein: 9.11 114.97 17.03 3.30 0 1519 Water: 11.49 76.68 34.97 N/A 235 216 Other: 19.74 26.64 22.10 N/A 0 8 Chain A: 9.11 114.97 19.32 N/A 0 1743 Chain S: 15.10 59.99 34.63 N/A 235 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.28 307 30.28 - 40.87 209 40.87 - 51.45 127 51.45 - 62.04 49 62.04 - 72.62 12 72.62 - 83.21 5 83.21 - 93.80 4 93.80 - 104.38 0 104.38 - 114.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1298 r_work=0.1147 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1298 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1296 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1296 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606897 | | target function (ml) not normalized (work): 300400.381791 | | target function (ml) not normalized (free): 15810.956104 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1370 0.1346 5.6729 5.6328| | 2: 3.57 - 2.84 1.00 2888 124 0.1076 0.1456 5.1862 5.2519| | 3: 2.83 - 2.48 1.00 2820 163 0.1109 0.1247 4.9701 5.0073| | 4: 2.47 - 2.25 1.00 2825 136 0.0900 0.0990 4.6484 4.678| | 5: 2.25 - 2.09 1.00 2756 127 0.0875 0.0954 4.599 4.6451| | 6: 2.09 - 1.97 1.00 2846 113 0.0868 0.0978 4.2761 4.3783| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1122 3.9742 4.0769| | 8: 1.87 - 1.79 1.00 2789 144 0.0918 0.1093 3.8834 3.9862| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1171 3.6398 3.8091| | 10: 1.72 - 1.66 1.00 2831 160 0.0919 0.1191 3.5606 3.7077| | 11: 1.66 - 1.61 1.00 2712 147 0.0867 0.1010 3.4911 3.5547| | 12: 1.61 - 1.56 1.00 2773 144 0.0900 0.1134 3.3259 3.4517| | 13: 1.56 - 1.52 1.00 2745 130 0.0954 0.1058 3.3041 3.3975| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1017 3.2374 3.3081| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1230 3.1512 3.2532| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1243 3.1325 3.2332| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1289 3.1175 3.2261| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1323 3.1045 3.2365| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1549 3.1108 3.2574| | 20: 1.34 - 1.32 1.00 2696 147 0.1375 0.1461 3.1143 3.1525| | 21: 1.32 - 1.30 1.00 2785 112 0.1477 0.1508 3.115 3.1094| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1982 3.123 3.2964| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1798 3.1333 3.2049| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1835 3.1257 3.2259| | 25: 1.24 - 1.22 1.00 2733 148 0.1887 0.2149 3.1442 3.2554| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1764 3.1482 3.2006| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2165 3.171 3.1626| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2298 3.1656 3.1722| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2394 3.1473 3.2275| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2461 3.1431 3.1678| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2923 171 0.95 8.97 1.00 0.98 6174.42| | 2: 3.57 - 2.84 2888 124 0.92 13.13 1.01 0.98 6174.42| | 3: 2.83 - 2.48 2820 163 0.89 17.00 0.99 0.98 5146.18| | 4: 2.47 - 2.25 2825 136 0.91 13.93 1.00 0.99 2494.66| | 5: 2.25 - 2.09 2756 127 0.90 16.09 1.01 0.99 2494.66| | 6: 2.09 - 1.97 2846 113 0.92 12.53 1.02 0.99 1419.25| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.99 502.07| | 8: 1.87 - 1.79 2789 144 0.93 12.50 1.00 0.99 502.07| | 9: 1.79 - 1.72 2745 138 0.94 9.96 0.98 0.98 284.43| | 10: 1.72 - 1.66 2831 160 0.94 10.98 0.98 0.98 240.85| | 11: 1.66 - 1.61 2712 147 0.94 11.61 0.98 0.98 230.74| | 12: 1.61 - 1.56 2773 144 0.96 8.78 0.99 0.98 135.42| | 13: 1.56 - 1.52 2745 130 0.95 10.30 1.03 0.98 135.42| | 14: 1.52 - 1.48 2803 134 0.94 10.63 1.02 0.99 121.57| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.99 96.19| | 16: 1.45 - 1.42 2756 161 0.94 10.95 1.02 0.99 96.19| | 17: 1.42 - 1.39 2785 139 0.95 10.87 1.01 0.99 88.03| | 18: 1.39 - 1.36 2741 179 0.94 11.48 1.01 0.99 83.31| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.99 83.31| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 79.77| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.97 79.52| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.97 79.97| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 82.28| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.95 82.28| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.95 84.24| | 26: 1.22 - 1.21 2727 135 0.90 18.16 1.02 0.94 86.43| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.94 86.43| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.08| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.98 0.93 91.45| | 30: 1.16 - 1.15 2739 148 0.86 22.04 0.98 0.93 91.45| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.52 max = 6174.42 mean = 938.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.50| |phase err.(test): min = 0.00 max = 89.82 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1143 0.1296 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1474 0.1474 0.1510 n_refl.: 87581 remove outliers: r(all,work,free)=0.1474 0.1474 0.1510 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1474 0.1473 0.1510 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1296 n_refl.: 87581 remove outliers: r(all,work,free)=0.1148 0.1140 0.1296 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 88.54 80 5 0.4037 292.990 246.347 0.453 1.000 0.328 11.894-9.307 95.10 93 4 0.2625 469.509 453.884 0.854 1.002 0.238 9.237-7.194 98.18 209 7 0.2425 385.990 378.526 0.915 1.002 0.160 7.162-5.571 100.00 427 22 0.2176 296.056 284.883 0.910 1.002 0.150 5.546-4.326 100.00 867 58 0.1151 406.412 401.361 0.963 1.003 0.125 4.315-3.360 100.00 1859 96 0.0921 386.501 384.378 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1115 253.911 252.138 1.011 1.002 0.034 2.608-2.026 99.99 8198 413 0.0917 168.320 167.709 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.199 82.534 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.450 36.055 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 22.966 21.511 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0111 ================= 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 : 0.2603 0.1906 0.082 5.364 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1749 0.082 5.364 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1749 0.082 5.364 9.1 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1754 0.082 5.364 9.1 119.5 20.1 258 0.003 1_weight: 0.1635 0.1754 0.082 5.364 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1235 0.1465 0.005 0.789 9.1 119.5 20.1 258 0.132 1_adp: 0.1242 0.1461 0.005 0.789 9.1 119.5 20.1 258 0.132 1_regHadp: 0.1243 0.1465 0.005 0.789 9.1 119.5 20.1 258 0.132 1_occ: 0.1238 0.1460 0.005 0.789 9.1 119.5 20.1 258 0.132 2_bss: 0.1234 0.1452 0.005 0.789 9.1 119.5 20.1 258 0.132 2_settarget: 0.1234 0.1452 0.005 0.789 9.1 119.5 20.1 258 0.132 2_updatecdl: 0.1234 0.1452 0.005 0.817 9.1 119.5 20.1 258 0.132 2_nqh: 0.1234 0.1452 0.005 0.817 9.1 119.5 20.1 258 0.132 2_sol: 0.1204 0.1388 0.005 0.817 9.1 115.0 22.3 421 n/a 2_weight: 0.1204 0.1388 0.005 0.817 9.1 115.0 22.3 421 n/a 2_xyzrec: 0.1182 0.1392 0.008 0.950 9.1 115.0 22.3 421 n/a 2_adp: 0.1182 0.1392 0.008 0.950 9.1 115.0 22.3 421 n/a 2_regHadp: 0.1182 0.1392 0.008 0.950 9.1 115.0 22.3 421 n/a 2_occ: 0.1180 0.1395 0.008 0.950 9.1 115.0 22.3 421 n/a 3_bss: 0.1175 0.1391 0.008 0.950 9.1 115.0 22.3 421 n/a 3_settarget: 0.1175 0.1391 0.008 0.950 9.1 115.0 22.3 421 n/a 3_updatecdl: 0.1175 0.1391 0.008 0.951 9.1 115.0 22.3 421 n/a 3_nqh: 0.1176 0.1393 0.008 0.951 9.1 115.0 22.3 421 n/a 3_sol: 0.1204 0.1406 0.008 0.951 9.1 115.0 21.2 436 n/a 3_weight: 0.1204 0.1406 0.008 0.951 9.1 115.0 21.2 436 n/a 3_xyzrec: 0.1176 0.1325 0.004 0.833 9.1 115.0 21.2 436 n/a 3_adp: 0.1176 0.1325 0.004 0.833 9.1 115.0 21.2 436 n/a 3_regHadp: 0.1176 0.1325 0.004 0.833 9.1 115.0 21.2 436 n/a 3_occ: 0.1169 0.1318 0.004 0.833 9.1 115.0 21.2 436 n/a 4_bss: 0.1162 0.1311 0.004 0.833 9.1 115.0 21.2 436 n/a 4_settarget: 0.1162 0.1311 0.004 0.833 9.1 115.0 21.2 436 n/a 4_updatecdl: 0.1162 0.1311 0.004 0.836 9.1 115.0 21.2 436 n/a 4_nqh: 0.1162 0.1311 0.004 0.836 9.1 115.0 21.2 436 n/a 4_sol: 0.1168 0.1301 0.004 0.836 9.1 115.0 21.0 440 n/a 4_weight: 0.1168 0.1301 0.004 0.836 9.1 115.0 21.0 440 n/a 4_xyzrec: 0.1145 0.1296 0.009 1.132 9.1 115.0 21.0 440 n/a 4_adp: 0.1145 0.1296 0.009 1.132 9.1 115.0 21.0 440 n/a 4_regHadp: 0.1145 0.1296 0.009 1.132 9.1 115.0 21.0 440 n/a 4_occ: 0.1139 0.1294 0.009 1.132 9.1 115.0 21.0 440 n/a 5_bss: 0.1137 0.1297 0.009 1.132 9.1 115.0 21.0 440 n/a 5_settarget: 0.1137 0.1297 0.009 1.132 9.1 115.0 21.0 440 n/a 5_updatecdl: 0.1137 0.1297 0.009 1.134 9.1 115.0 21.0 440 n/a 5_setrh: 0.1138 0.1297 0.009 1.134 9.1 115.0 21.0 440 n/a 5_nqh: 0.1138 0.1297 0.009 1.134 9.1 115.0 21.0 440 n/a 5_sol: 0.1144 0.1298 0.009 1.134 9.1 115.0 21.1 451 n/a 5_weight: 0.1144 0.1298 0.009 1.134 9.1 115.0 21.1 451 n/a 5_xyzrec: 0.1147 0.1298 0.008 1.112 9.1 115.0 21.1 451 n/a 5_adp: 0.1147 0.1298 0.008 1.112 9.1 115.0 21.1 451 n/a 5_regHadp: 0.1147 0.1298 0.008 1.112 9.1 115.0 21.1 451 n/a 5_occ: 0.1143 0.1296 0.008 1.112 9.1 115.0 21.1 451 n/a end: 0.1140 0.1296 0.008 1.112 9.1 115.0 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7766834_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7766834_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 13892.2200 Write final files (write_after_run_outputs) : 96.8700 Total : 13992.4100 Total CPU time: 3.89 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:12:35 PST -0800 (1735366355.21 s) Start R-work = 0.1633, R-free = 0.1749 Final R-work = 0.1140, R-free = 0.1296 =============================================================================== Job complete usr+sys time: 14169.18 seconds wall clock time: 256 minutes 44.34 seconds (15404.34 seconds total)