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_3031784.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.52, per 1000 atoms: 0.45 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: 0.29 Conformation dependent library (CDL) restraints added in 106.4 milliseconds Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 395 0.89 - 1.15: 1224 1.15 - 1.41: 630 1.41 - 1.67: 858 1.67 - 1.93: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.608 -0.146 7.70e-03 1.69e+04 3.58e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.172 0.206 1.10e-02 8.26e+03 3.52e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.034 0.204 1.10e-02 8.26e+03 3.42e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.040 0.193 1.08e-02 8.57e+03 3.18e+02 bond pdb=" CA ASP A 60 " pdb=" C ASP A 60 " ideal model delta sigma weight residual 1.524 1.745 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 3113 4.46 - 8.92: 1829 8.92 - 13.38: 687 13.38 - 17.84: 133 17.84 - 22.30: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ARG A 98 " pdb=" C ARG A 98 " pdb=" O ARG A 98 " ideal model delta sigma weight residual 119.43 137.78 -18.35 1.21e+00 6.83e-01 2.30e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 136.28 -13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 135.83 -13.76 1.03e+00 9.43e-01 1.78e+02 angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta sigma weight residual 110.62 124.46 -13.84 1.05e+00 9.07e-01 1.74e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 120.19 134.73 -14.54 1.15e+00 7.56e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 924 16.65 - 33.30: 130 33.30 - 49.95: 36 49.95 - 66.59: 19 66.59 - 83.24: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " pdb=" HE1 HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " pdb=" CA BGLU A 96 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 98 0.213 - 0.427: 68 0.427 - 0.640: 44 0.640 - 0.853: 27 0.853 - 1.066: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.49 1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.089 2.00e-02 2.50e+03 5.87e-02 1.04e+02 pdb=" CG PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.29e-02 8.91e+01 pdb=" CG HIS A 126 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.094 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.060 9.50e-02 1.11e+02 6.44e-02 8.46e+01 pdb=" NE ARG A 5 " -0.090 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.050 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.102 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1120 2.33 - 2.90: 8110 2.90 - 3.47: 10544 3.47 - 4.03: 15209 4.03 - 4.60: 21683 Nonbonded interactions: 56666 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.763 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.823 2.100 nonbonded pdb=" O ILE A 102 " pdb=" H ALEU A 153 " model vdw 1.838 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.838 1.850 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.842 1.850 ... (remaining 56661 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_3031784_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= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795445 | | target function (ml) not normalized (work): 232877.368734 | | target function (ml) not normalized (free): 11855.589639 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3036 0.2009 7.0953 4.9331| | 2: 3.57 - 2.84 1.00 2876 122 0.2429 0.1865 4.3467 4.3474| | 3: 2.84 - 2.48 1.00 2833 165 0.2379 0.1678 4.124 4.1414| | 4: 2.47 - 2.25 1.00 2825 136 0.2351 0.1486 3.8281 3.821| | 5: 2.25 - 2.09 1.00 2756 127 0.2419 0.1579 3.7909 3.8137| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1752 3.4605 3.5289| | 7: 1.97 - 1.87 1.00 2787 165 0.2566 0.1865 3.1449 3.189| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1905 3.0876 3.1358| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.2118 2.9019 3.0009| | 10: 1.72 - 1.66 1.00 2789 158 0.2417 0.1900 2.8059 2.8726| | 11: 1.66 - 1.61 1.00 2740 147 0.2543 0.2011 2.7681 2.8502| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.2203 2.645 2.7258| | 13: 1.56 - 1.52 1.00 2745 130 0.2592 0.1965 2.5986 2.6429| | 14: 1.52 - 1.48 1.00 2803 134 0.2558 0.1822 2.5003 2.5199| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2220 2.4246 2.5406| | 16: 1.45 - 1.42 1.00 2756 161 0.2606 0.2346 2.3909 2.4845| | 17: 1.42 - 1.39 1.00 2785 139 0.2662 0.2220 2.3425 2.4083| | 18: 1.39 - 1.36 1.00 2741 179 0.2693 0.2197 2.2822 2.3536| | 19: 1.36 - 1.34 1.00 2807 134 0.2694 0.2259 2.246 2.2614| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2164 2.204 2.1344| | 21: 1.32 - 1.30 1.00 2785 112 0.2696 0.2282 2.1568 2.1924| | 22: 1.29 - 1.27 1.00 2704 152 0.2799 0.2756 2.1367 2.2217| | 23: 1.27 - 1.26 1.00 2802 156 0.2778 0.2470 2.1006 2.2166| | 24: 1.26 - 1.24 1.00 2744 132 0.2757 0.2231 2.0833 2.0711| | 25: 1.24 - 1.22 1.00 2734 148 0.2791 0.2647 2.0446 2.0998| | 26: 1.22 - 1.21 1.00 2727 135 0.2810 0.2275 2.0048 2.0668| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2849 2.0006 2.0257| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2843 2.0012 1.9928| | 29: 1.18 - 1.16 1.00 2800 134 0.2964 0.2789 1.9569 2.0639| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.3025 1.9336 1.9737| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.74 0.76 0.23 1455.13| | 2: 3.57 - 2.84 2876 122 0.81 25.86 1.27 0.23 1455.13| | 3: 2.84 - 2.48 2833 165 0.74 31.80 1.25 0.23 1207.37| | 4: 2.47 - 2.25 2825 136 0.81 25.40 1.26 0.25 564.40| | 5: 2.25 - 2.09 2756 127 0.78 29.00 1.27 0.25 564.40| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.29 0.25 310.87| | 7: 1.97 - 1.87 2787 165 0.90 16.85 1.29 0.26 94.64| | 8: 1.87 - 1.79 2789 144 0.85 21.41 1.24 0.26 94.64| | 9: 1.79 - 1.72 2745 138 0.87 19.18 1.22 0.25 58.37| | 10: 1.72 - 1.66 2789 158 0.86 20.84 1.23 0.25 51.10| | 11: 1.66 - 1.61 2740 147 0.85 22.15 1.25 0.25 49.40| | 12: 1.61 - 1.56 2787 146 0.88 19.31 1.23 0.25 32.17| | 13: 1.56 - 1.52 2745 130 0.86 21.17 1.24 0.25 32.17| | 14: 1.52 - 1.48 2803 134 0.86 21.49 1.24 0.25 28.53| | 15: 1.48 - 1.45 2738 128 0.86 20.84 1.23 0.25 21.86| | 16: 1.45 - 1.42 2756 161 0.85 22.17 1.23 0.25 21.86| | 17: 1.42 - 1.39 2785 139 0.86 21.17 1.23 0.25 18.26| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.23 0.25 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.51 1.22 0.25 16.17| | 20: 1.34 - 1.32 2696 147 0.87 20.97 1.21 0.24 12.99| | 21: 1.32 - 1.30 2785 112 0.86 21.90 1.21 0.24 12.77| | 22: 1.29 - 1.27 2704 152 0.85 22.67 1.21 0.24 12.51| | 23: 1.27 - 1.26 2802 156 0.85 22.39 1.21 0.24 11.18| | 24: 1.26 - 1.24 2744 132 0.85 22.80 1.19 0.24 11.18| | 25: 1.24 - 1.22 2734 148 0.84 23.60 1.19 0.24 10.69| | 26: 1.22 - 1.21 2727 135 0.84 24.25 1.19 0.23 10.14| | 27: 1.21 - 1.19 2814 148 0.83 25.36 1.20 0.23 10.14| | 28: 1.19 - 1.18 2671 147 0.82 25.81 1.17 0.23 9.66| | 29: 1.18 - 1.16 2800 134 0.82 26.27 1.17 0.22 9.48| | 30: 1.16 - 1.15 2740 148 0.80 27.94 1.15 0.22 9.48| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.48 max = 1455.13 mean = 212.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.93| |phase err.(test): min = 0.00 max = 89.82 mean = 22.83| |-----------------------------------------------------------------------------| ----------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 0.232 1557 Z= 5.599 Angle : 5.167 19.341 2118 Z= 3.645 Chirality : 0.398 1.066 243 Planarity : 0.030 0.086 284 Dihedral : 14.193 83.240 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 1.86 % Favored : 94.41 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.53), residues: 224 helix: -2.16 (0.45), residues: 102 sheet: -1.71 (0.83), residues: 30 loop : 0.61 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.016 ARG A 27 TYR 0.089 0.035 TYR A 141 PHE 0.108 0.037 PHE A 162 HIS 0.084 0.030 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= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795445 | | target function (ml) not normalized (work): 232877.368734 | | target function (ml) not normalized (free): 11855.589639 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1983 0.1963 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2009 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1638 0.1796 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1637 0.1796 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3812 386.282 356.300 0.663 1.003 0.401 11.894-9.307 98.04 96 4 0.1730 616.081 590.305 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.2146 501.842 492.572 0.963 1.004 0.364 7.162-5.571 100.00 427 22 0.2262 376.604 363.041 0.929 1.004 0.297 5.546-4.326 100.00 867 58 0.1259 516.985 510.847 0.962 1.003 0.224 4.315-3.360 100.00 1859 96 0.1143 491.656 488.366 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1450 322.993 319.633 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1337 214.115 212.218 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1662 104.562 103.830 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.367 45.080 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2582 29.215 26.933 0.975 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1796 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1642 r_free=0.1798 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.500787 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1997.973589 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 0.1679 0.1784 0.0105 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1532 0.1661 0.0129 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1457 0.1610 0.0153 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1394 0.1564 0.0171 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1370 0.1556 0.0187 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1361 0.1549 0.0188 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1291 0.1503 0.0213 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1260 0.1478 0.0218 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1482 0.0227 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1247 0.1481 0.0234 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1240 0.1476 0.0236 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1237 0.1472 0.0235 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1231 0.1468 0.0237 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1228 0.1466 0.0238 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1226 0.1465 0.0239 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1467 0.0241 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1223 0.1469 0.0246 0.007 0.9 3.2 0.5 0.6 0 12.000 0.1221 0.1469 0.0248 0.008 1.0 4.2 0.5 0.6 0 13.750 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1465 0.0239 0.006 0.9 3.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.65 2.39 3.013 19.068 1997.974 0.017 12.26 14.64 2.38 2.989 19.068 59.939 0.017 12.33 14.61 2.28 2.666 19.067 249.747 0.017 12.68 15.29 2.61 2.740 19.228 998.987 0.016 12.49 15.42 2.93 3.124 19.520 1997.974 0.016 12.44 15.42 2.98 3.284 19.625 2996.960 0.015 12.35 15.44 3.08 3.358 19.651 3995.947 0.015 12.29 15.41 3.12 3.290 19.607 4994.934 0.015 12.19 15.39 3.21 3.375 19.654 5993.921 0.015 12.24 15.48 3.24 3.412 19.665 6992.908 0.015 12.24 15.51 3.27 3.355 19.617 7991.894 0.015 12.23 15.55 3.33 3.571 19.732 8990.881 0.015 12.24 15.63 3.39 3.637 19.755 9989.868 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: 249.747 Accepted refinement result: 12.33 14.61 2.28 2.666 19.067 249.747 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.09 3.31 0 1785 Protein: 9.07 114.98 17.00 3.31 0 1519 Water: 11.47 119.44 38.24 N/A 0 258 Other: 19.72 26.59 22.07 N/A 0 8 Chain A: 9.07 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1461 r_work=0.1235 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1464 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 = 0.1227 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1227 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016698 | | target function (ls_wunit_k1) not normalized (work): 1390.874364 | | target function (ls_wunit_k1) not normalized (free): 109.028356 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1238 0.1227 0.1457 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1673 0.1674 0.1686 n_refl.: 87592 remove outliers: r(all,work,free)=0.1673 0.1674 0.1686 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1678 0.1680 0.1690 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1452 n_refl.: 87592 remove outliers: r(all,work,free)=0.1236 0.1225 0.1452 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3551 301.178 281.088 0.641 1.003 0.376 11.894-9.307 98.04 96 4 0.1551 484.428 472.304 0.932 1.003 0.373 9.237-7.194 100.00 213 7 0.1887 394.601 388.701 0.963 1.003 0.360 7.162-5.571 100.00 427 22 0.1833 296.126 290.256 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.1003 406.508 403.528 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.0868 386.592 385.512 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1173 253.971 252.805 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1016 168.360 167.621 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.218 82.415 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.459 35.967 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.972 21.461 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=0.0475 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1452 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=0.1226 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1453 | n_water=258 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1233 r_free=0.1451 | n_water=251 | time (s): 21.550 (total time: 23.340) Filter (q & B) r_work=0.1236 r_free=0.1451 | n_water=248 | time (s): 3.290 (total time: 26.630) Compute maps r_work=0.1236 r_free=0.1451 | n_water=248 | time (s): 1.540 (total time: 28.170) Filter (map) r_work=0.1253 r_free=0.1460 | n_water=227 | time (s): 3.130 (total time: 31.300) Find peaks r_work=0.1253 r_free=0.1460 | n_water=227 | time (s): 0.590 (total time: 31.890) Add new water r_work=0.1397 r_free=0.1636 | n_water=434 | time (s): 2.770 (total time: 34.660) Refine new water occ: r_work=0.1300 r_free=0.1495 adp: r_work=0.1224 r_free=0.1445 occ: r_work=0.1237 r_free=0.1425 adp: r_work=0.1204 r_free=0.1417 occ: r_work=0.1207 r_free=0.1400 adp: r_work=0.1198 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1404 r_work=0.1198 r_free=0.1404 | n_water=434 | time (s): 63.420 (total time: 98.080) Filter (q & B) r_work=0.1202 r_free=0.1407 | n_water=416 | time (s): 2.830 (total time: 100.910) Filter (dist only) r_work=0.1202 r_free=0.1405 | n_water=415 | time (s): 34.200 (total time: 135.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.581105 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1516.175844 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 0.1665 0.1779 0.0114 0.001 0.4 7.0 0.0 0.0 0 0.125 0.1535 0.1667 0.0132 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1417 0.1577 0.0160 0.001 0.4 5.1 0.0 0.0 0 0.500 0.1341 0.1516 0.0174 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1330 0.1515 0.0185 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1316 0.1500 0.0184 0.002 0.5 4.2 0.0 0.0 0 1.000 0.1254 0.1449 0.0195 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1228 0.1434 0.0206 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1216 0.1426 0.0210 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1209 0.1419 0.0210 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1200 0.1413 0.0213 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1199 0.1410 0.0211 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1197 0.1409 0.0213 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1193 0.1414 0.0221 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1192 0.1410 0.0218 0.006 0.8 4.2 0.5 0.0 0 10.000 0.1190 0.1413 0.0223 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1191 0.1415 0.0224 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1188 0.1413 0.0225 0.008 0.9 4.8 0.5 0.6 0 13.791 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1409 0.0213 0.005 0.8 3.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 14.09 2.13 3.774 21.746 1516.176 0.016 11.97 14.09 2.13 3.774 21.746 45.485 0.016 11.97 14.09 2.13 3.774 21.746 189.522 0.016 12.17 14.54 2.37 3.617 21.752 758.088 0.016 12.13 14.86 2.73 3.451 21.982 1516.176 0.015 11.99 14.79 2.80 3.465 22.119 2274.264 0.015 11.88 14.82 2.94 3.495 21.903 3032.352 0.014 11.82 14.82 3.00 3.518 21.893 3790.440 0.014 11.81 14.79 2.98 3.494 22.084 4548.528 0.014 11.80 14.90 3.11 3.511 22.027 5306.615 0.014 11.82 15.00 3.17 3.556 22.132 6064.703 0.014 11.76 14.92 3.16 3.575 22.173 6822.791 0.014 11.74 14.94 3.20 3.595 22.190 7580.879 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 45.485 Accepted refinement result: 11.97 14.09 2.13 3.774 21.746 45.485 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 22.12 3.31 188 1754 Protein: 9.11 115.01 17.03 3.31 0 1519 Water: 10.47 76.69 40.75 N/A 188 227 Other: 19.76 26.62 22.10 N/A 0 8 Chain A: 9.11 115.01 19.48 N/A 0 1754 Chain S: 10.47 60.00 46.72 N/A 188 0 Histogram: Values Number of atoms 9.11 - 19.70 1258 19.70 - 30.29 245 30.29 - 40.88 167 40.88 - 51.47 133 51.47 - 62.06 116 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=0.1197 r_free=0.1409 r_work=0.1197 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1413 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1198 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015296 | | target function (ls_wunit_k1) not normalized (work): 1274.075957 | | target function (ls_wunit_k1) not normalized (free): 102.036636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1198 0.1413 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1588 0.1587 0.1628 n_refl.: 87591 remove outliers: r(all,work,free)=0.1588 0.1587 0.1628 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1589 0.1629 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1195 0.1407 n_refl.: 87591 remove outliers: r(all,work,free)=0.1203 0.1193 0.1407 n_refl.: 87588 ======================== 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 0.3328 297.085 275.220 0.591 1.003 0.350 11.894-9.307 98.04 96 4 0.1611 484.428 476.054 0.924 1.003 0.333 9.237-7.194 100.00 213 7 0.1702 394.601 394.212 0.978 1.003 0.290 7.162-5.571 100.00 427 22 0.1625 296.126 291.516 0.933 1.003 0.230 5.546-4.326 100.00 867 58 0.0915 406.508 403.146 0.961 1.003 0.220 4.315-3.360 100.00 1859 96 0.0798 386.592 385.610 1.005 1.003 0.180 3.356-2.611 100.00 3867 181 0.1089 253.971 253.018 1.011 1.002 0.120 2.608-2.026 99.99 8198 413 0.1014 168.360 167.799 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.218 82.427 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.459 35.983 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2258 22.972 21.481 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0122 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1407 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1407 | n_water=415 | time (s): 2.090 (total time: 2.090) Filter (dist) r_work=0.1192 r_free=0.1408 | n_water=414 | time (s): 39.190 (total time: 41.280) Filter (q & B) r_work=0.1192 r_free=0.1408 | n_water=414 | time (s): 1.190 (total time: 42.470) Compute maps r_work=0.1192 r_free=0.1408 | n_water=414 | time (s): 1.400 (total time: 43.870) Filter (map) r_work=0.1232 r_free=0.1397 | n_water=279 | time (s): 3.880 (total time: 47.750) Find peaks r_work=0.1232 r_free=0.1397 | n_water=279 | time (s): 0.650 (total time: 48.400) Add new water r_work=0.1345 r_free=0.1506 | n_water=452 | time (s): 2.790 (total time: 51.190) Refine new water occ: r_work=0.1248 r_free=0.1415 adp: r_work=0.1249 r_free=0.1416 occ: r_work=0.1228 r_free=0.1395 adp: r_work=0.1227 r_free=0.1394 occ: r_work=0.1213 r_free=0.1377 adp: r_work=0.1208 r_free=0.1374 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1374 r_work=0.1208 r_free=0.1374 | n_water=452 | time (s): 220.750 (total time: 271.940) Filter (q & B) r_work=0.1212 r_free=0.1378 | n_water=427 | time (s): 2.800 (total time: 274.740) Filter (dist only) r_work=0.1212 r_free=0.1377 | n_water=426 | time (s): 38.170 (total time: 312.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.739373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.312244 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 0.1241 0.1347 0.0106 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1189 0.1311 0.0122 0.003 0.7 3.5 0.5 0.0 0 0.261 0.1173 0.1302 0.0130 0.004 0.8 3.5 0.5 0.0 0 0.522 0.1165 0.1298 0.0133 0.005 0.9 3.2 0.5 0.0 0 0.783 0.1161 0.1300 0.0139 0.006 1.0 3.5 0.5 0.0 0 1.044 0.1158 0.1296 0.0139 0.007 1.0 3.8 0.5 0.0 0 1.305 0.1155 0.1299 0.0144 0.007 1.0 4.2 0.5 0.0 0 1.565 0.1153 0.1299 0.0146 0.008 1.1 4.5 0.5 0.0 0 1.826 0.1163 0.1299 0.0135 0.005 0.9 3.2 0.5 0.0 0 0.870 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1296 0.0139 0.007 1.0 3.8 0.5 0.0 0 1.305 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 12.96 1.39 3.777 21.193 44.312 3.618 11.58 12.96 1.39 3.777 21.193 1.329 3.618 11.58 12.97 1.39 3.766 21.193 5.539 3.618 11.62 13.06 1.44 3.709 21.183 22.156 3.612 11.61 13.13 1.52 3.739 21.159 44.312 3.612 11.56 13.13 1.57 3.756 21.140 66.468 3.606 11.50 13.09 1.59 3.773 21.136 88.624 3.602 11.47 13.07 1.60 3.784 21.131 110.781 3.598 11.45 13.09 1.63 3.796 21.126 132.937 3.597 11.47 13.11 1.65 3.816 21.109 155.093 3.597 11.44 13.09 1.65 3.826 21.107 177.249 3.595 11.41 13.06 1.64 3.829 21.110 199.405 3.593 11.41 13.07 1.66 3.836 21.107 221.561 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.329 Accepted refinement result: 11.58 12.96 1.39 3.777 21.193 1.329 3.618 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.10 3.31 202 1751 Protein: 9.11 115.02 17.04 3.31 0 1519 Water: 10.48 76.70 35.58 N/A 202 224 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.11 115.02 19.45 N/A 0 1751 Chain S: 10.48 60.01 35.43 N/A 202 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 286 30.29 - 40.89 203 40.89 - 51.48 122 51.48 - 62.07 54 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1296 r_work=0.1158 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1296 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1301 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1149 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611260 | | target function (ml) not normalized (work): 300789.090772 | | target function (ml) not normalized (free): 15825.165525 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1149 0.1301 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1494 0.1495 0.1520 n_refl.: 87588 remove outliers: r(all,work,free)=0.1494 0.1495 0.1520 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1493 0.1494 0.1519 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1297 n_refl.: 87588 remove outliers: r(all,work,free)=0.1150 0.1143 0.1297 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3950 291.639 268.834 0.495 1.001 0.309 11.894-9.307 97.06 95 4 0.2291 484.574 468.103 0.881 1.002 0.301 9.237-7.194 98.18 209 7 0.2314 386.082 387.388 0.945 1.002 0.240 7.162-5.571 100.00 427 22 0.2080 296.126 285.702 0.922 1.002 0.180 5.546-4.326 100.00 867 58 0.1123 406.508 402.019 0.963 1.002 0.153 4.315-3.360 100.00 1859 96 0.0925 386.592 384.292 1.005 1.002 0.137 3.356-2.611 100.00 3867 181 0.1133 253.971 251.953 1.009 1.002 0.043 2.608-2.026 99.99 8198 413 0.0928 168.360 167.508 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.218 82.515 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1258 36.459 36.036 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 22.972 21.506 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0149 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1297 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=0.1146 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1299 | n_water=426 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1149 r_free=0.1300 | n_water=423 | time (s): 46.240 (total time: 48.780) Filter (q & B) r_work=0.1150 r_free=0.1302 | n_water=420 | time (s): 3.980 (total time: 52.760) Compute maps r_work=0.1150 r_free=0.1302 | n_water=420 | time (s): 1.880 (total time: 54.640) Filter (map) r_work=0.1170 r_free=0.1298 | n_water=320 | time (s): 3.980 (total time: 58.620) Find peaks r_work=0.1170 r_free=0.1298 | n_water=320 | time (s): 0.750 (total time: 59.370) Add new water r_work=0.1238 r_free=0.1371 | n_water=491 | time (s): 3.940 (total time: 63.310) Refine new water occ: r_work=0.1169 r_free=0.1301 adp: r_work=0.1169 r_free=0.1305 occ: r_work=0.1152 r_free=0.1289 adp: r_work=0.1151 r_free=0.1292 occ: r_work=0.1139 r_free=0.1285 adp: r_work=0.1136 r_free=0.1285 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1285 r_work=0.1136 r_free=0.1285 | n_water=491 | time (s): 250.370 (total time: 313.680) Filter (q & B) r_work=0.1144 r_free=0.1292 | n_water=449 | time (s): 4.080 (total time: 317.760) Filter (dist only) r_work=0.1144 r_free=0.1291 | n_water=448 | time (s): 47.360 (total time: 365.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705013 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.670388 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1326 0.0124 0.002 0.6 4.5 0.5 0.0 0 0.085 0.1165 0.1308 0.0143 0.003 0.7 3.5 0.5 0.0 0 0.256 0.1149 0.1300 0.0151 0.005 0.9 3.8 0.5 0.0 0 0.512 0.1143 0.1297 0.0154 0.005 0.9 3.8 0.5 0.0 0 0.767 0.1139 0.1295 0.0156 0.006 1.0 3.5 0.5 0.0 0 1.023 0.1136 0.1296 0.0160 0.007 1.0 3.5 0.5 0.0 0 1.279 0.1134 0.1296 0.0162 0.008 1.1 3.5 0.5 0.0 0 1.535 0.1133 0.1294 0.0162 0.008 1.1 3.8 0.5 0.0 0 1.790 0.1142 0.1296 0.0155 0.006 1.0 3.8 0.5 0.0 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1294 0.0162 0.008 1.1 3.8 0.5 0.0 0 1.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.94 1.62 3.778 21.274 47.670 3.604 11.33 12.94 1.62 3.778 21.274 1.430 3.604 11.33 12.95 1.62 3.767 21.274 5.959 3.604 11.38 13.04 1.66 3.712 21.261 23.835 3.600 11.35 13.06 1.71 3.740 21.243 47.670 3.598 11.33 13.08 1.75 3.763 21.223 71.506 3.594 11.31 13.07 1.76 3.777 21.216 95.341 3.591 11.25 13.00 1.75 3.786 21.218 119.176 3.587 11.26 13.06 1.79 3.809 21.200 143.011 3.587 11.24 13.03 1.80 3.819 21.198 166.846 3.585 11.23 13.03 1.80 3.832 21.192 190.682 3.585 11.23 13.05 1.82 3.842 21.187 214.517 3.584 11.21 13.04 1.82 3.849 21.188 238.352 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.430 Accepted refinement result: 11.33 12.94 1.62 3.778 21.274 1.430 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.25 3.31 225 1750 Protein: 9.11 115.01 17.03 3.31 0 1519 Water: 10.47 76.70 35.54 N/A 225 223 Other: 19.76 26.62 22.10 N/A 0 8 Chain A: 9.11 115.01 19.44 N/A 0 1750 Chain S: 10.47 60.00 35.34 N/A 225 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 294 30.29 - 40.88 212 40.88 - 51.47 127 51.47 - 62.06 54 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=0.1133 r_free=0.1294 r_work=0.1133 r_free=0.1294 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1294 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1292 target_work(ml) = 3.602 | | 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.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1292 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602022 | | target function (ml) not normalized (work): 299998.042596 | | target function (ml) not normalized (free): 15809.986338 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1127 0.1292 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1469 0.1469 0.1509 n_refl.: 87582 remove outliers: r(all,work,free)=0.1469 0.1469 0.1509 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1468 0.1467 0.1508 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1127 0.1295 n_refl.: 87582 remove outliers: r(all,work,free)=0.1133 0.1124 0.1295 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 0.3954 285.690 253.034 0.448 1.000 0.290 11.894-9.307 95.10 93 4 0.2356 481.046 468.368 0.870 1.001 0.277 9.237-7.194 98.18 209 7 0.2367 386.082 379.780 0.920 1.002 0.190 7.162-5.571 100.00 427 22 0.2064 296.126 286.246 0.912 1.002 0.160 5.546-4.326 100.00 867 58 0.1116 406.508 401.720 0.952 1.002 0.118 4.315-3.360 100.00 1859 96 0.0915 386.592 384.332 0.994 1.002 0.100 3.356-2.611 100.00 3867 181 0.1098 253.971 252.197 1.000 1.002 0.024 2.608-2.026 99.99 8198 413 0.0906 168.360 167.705 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.218 82.570 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.459 36.067 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 22.972 21.526 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0189 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1124 r_free=0.1295 After: r_work=0.1126 r_free=0.1294 ================================== NQH flips ================================== r_work=0.1126 r_free=0.1294 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1126 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1126 r_free=0.1294 | n_water=448 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1126 r_free=0.1294 | n_water=448 | time (s): 42.860 (total time: 45.310) Filter (q & B) r_work=0.1127 r_free=0.1294 | n_water=446 | time (s): 4.020 (total time: 49.330) Compute maps r_work=0.1127 r_free=0.1294 | n_water=446 | time (s): 1.870 (total time: 51.200) Filter (map) r_work=0.1152 r_free=0.1284 | n_water=364 | time (s): 4.000 (total time: 55.200) Find peaks r_work=0.1152 r_free=0.1284 | n_water=364 | time (s): 0.770 (total time: 55.970) Add new water r_work=0.1198 r_free=0.1328 | n_water=511 | time (s): 3.820 (total time: 59.790) Refine new water occ: r_work=0.1141 r_free=0.1291 adp: r_work=0.1142 r_free=0.1292 occ: r_work=0.1130 r_free=0.1284 adp: r_work=0.1129 r_free=0.1285 occ: r_work=0.1121 r_free=0.1280 adp: r_work=0.1118 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1118 r_free=0.1279 r_work=0.1118 r_free=0.1279 | n_water=511 | time (s): 259.910 (total time: 319.700) Filter (q & B) r_work=0.1126 r_free=0.1287 | n_water=469 | time (s): 4.030 (total time: 323.730) Filter (dist only) r_work=0.1126 r_free=0.1285 | n_water=468 | time (s): 50.660 (total time: 374.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.708545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.427797 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 0.1211 0.1336 0.0124 0.004 0.7 6.1 0.0 0.0 0 0.085 0.1164 0.1310 0.0146 0.004 0.8 5.8 0.0 0.0 0 0.256 0.1146 0.1299 0.0153 0.005 0.9 5.1 0.5 0.0 0 0.513 0.1139 0.1294 0.0155 0.005 1.0 5.1 0.5 0.0 0 0.769 0.1132 0.1289 0.0157 0.006 1.1 4.8 0.5 0.0 0 1.025 0.1128 0.1286 0.0158 0.007 1.1 4.5 0.5 0.0 0 1.281 0.1127 0.1285 0.0159 0.008 1.1 4.5 0.5 0.0 0 1.538 0.1126 0.1285 0.0159 0.008 1.1 4.5 0.5 0.0 0 1.794 0.1135 0.1291 0.0156 0.006 1.0 4.8 0.5 0.0 0 0.854 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1285 0.0159 0.008 1.1 4.5 0.5 0.0 0 1.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.85 1.59 3.777 21.335 34.428 3.600 11.26 12.85 1.59 3.777 21.335 1.033 3.600 11.26 12.85 1.59 3.777 21.335 4.303 3.600 11.31 12.90 1.58 3.705 21.330 17.214 3.597 11.34 13.00 1.66 3.726 21.312 34.428 3.598 11.31 13.02 1.71 3.745 21.296 51.642 3.595 11.27 13.01 1.75 3.759 21.290 68.856 3.592 11.24 13.00 1.76 3.768 21.285 86.069 3.588 11.22 12.99 1.77 3.777 21.284 103.283 3.587 11.19 12.96 1.77 3.787 21.282 120.497 3.584 11.18 12.96 1.79 3.796 21.280 137.711 3.584 11.18 12.98 1.80 3.810 21.273 154.925 3.583 11.17 12.99 1.82 3.820 21.268 172.139 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.033 Accepted refinement result: 11.26 12.85 1.59 3.777 21.335 1.033 3.600 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 21.37 3.31 246 1749 Protein: 9.10 115.01 17.03 3.31 0 1519 Water: 10.46 76.69 35.46 N/A 246 222 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.10 115.01 19.42 N/A 0 1749 Chain S: 10.46 60.00 35.26 N/A 246 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.28 301 30.28 - 40.87 218 40.87 - 51.46 132 51.46 - 62.05 55 62.05 - 72.64 12 72.64 - 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=0.1126 r_free=0.1285 r_work=0.1126 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1285 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1285 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598747 | | target function (ml) not normalized (work): 299707.273994 | | target function (ml) not normalized (free): 15790.684160 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1315 0.1325 5.6282 5.5965| | 2: 3.57 - 2.84 1.00 2888 124 0.1044 0.1401 5.1494 5.2193| | 3: 2.83 - 2.48 1.00 2820 163 0.1090 0.1197 4.9381 4.9673| | 4: 2.47 - 2.25 1.00 2825 136 0.0887 0.1024 4.6207 4.6735| | 5: 2.25 - 2.09 1.00 2756 127 0.0859 0.0951 4.5689 4.6204| | 6: 2.09 - 1.97 1.00 2846 113 0.0845 0.1011 4.2549 4.3558| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1131 3.9695 4.0848| | 8: 1.87 - 1.79 1.00 2789 144 0.0912 0.1083 3.882 3.9761| | 9: 1.79 - 1.72 1.00 2745 138 0.0867 0.1158 3.6378 3.8204| | 10: 1.72 - 1.66 1.00 2831 160 0.0910 0.1165 3.5579 3.6946| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1041 3.4879 3.5649| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1124 3.3237 3.4435| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1037 3.3025 3.3961| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1052 3.2324 3.3139| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1244 3.1475 3.2725| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1218 3.1308 3.2295| | 17: 1.42 - 1.39 1.00 2785 139 0.1139 0.1303 3.1155 3.229| | 18: 1.39 - 1.36 1.00 2741 179 0.1190 0.1339 3.1005 3.2389| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1549 3.112 3.2605| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1470 3.1109 3.1524| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1503 3.1117 3.1007| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1988 3.1232 3.2972| | 23: 1.27 - 1.26 1.00 2802 156 0.1644 0.1789 3.1309 3.2013| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1846 3.1266 3.23| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2140 3.142 3.2555| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1766 3.1475 3.2034| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2158 3.1722 3.1598| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2292 3.1649 3.172| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2386 3.1476 3.2314| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2443 3.1424 3.167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.59 1.00 0.98 5667.68| | 2: 3.57 - 2.84 2888 124 0.93 12.42 1.01 0.98 5667.68| | 3: 2.83 - 2.48 2820 163 0.90 16.40 0.99 0.98 4733.83| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.99 2325.72| | 5: 2.25 - 2.09 2756 127 0.90 15.50 1.01 0.99 2325.72| | 6: 2.09 - 1.97 2846 113 0.93 12.25 1.02 0.99 1341.26| | 7: 1.97 - 1.87 2787 165 0.95 9.17 1.02 0.99 501.64| | 8: 1.87 - 1.79 2789 144 0.93 12.50 1.00 0.99 501.64| | 9: 1.79 - 1.72 2745 138 0.94 9.92 0.98 0.98 283.87| | 10: 1.72 - 1.66 2831 160 0.94 10.97 0.98 0.98 240.26| | 11: 1.66 - 1.61 2712 147 0.94 11.58 0.98 0.98 230.20| | 12: 1.61 - 1.56 2773 144 0.96 8.77 0.99 0.98 135.24| | 13: 1.56 - 1.52 2745 130 0.95 10.29 1.03 0.98 135.24| | 14: 1.52 - 1.48 2803 134 0.94 10.68 1.02 0.99 121.52| | 15: 1.48 - 1.45 2738 128 0.95 9.78 1.02 0.99 96.40| | 16: 1.45 - 1.42 2756 161 0.94 11.01 1.02 0.99 96.40| | 17: 1.42 - 1.39 2785 139 0.95 10.85 1.01 0.99 88.16| | 18: 1.39 - 1.36 2741 179 0.94 11.49 1.01 0.99 83.38| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.99 83.38| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 79.65| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.97 79.39| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.97 79.84| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.95 82.13| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.13| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.95 84.13| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.03 0.94 86.35| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.94 86.35| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.94 90.09| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 91.50| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.93 91.50| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.39 max = 5667.68 mean = 874.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.38| |phase err.(test): min = 0.00 max = 89.41 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1123 0.1285 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1442 0.1440 0.1503 n_refl.: 87577 remove outliers: r(all,work,free)=0.1442 0.1440 0.1503 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1441 0.1439 0.1503 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1130 0.1122 0.1287 n_refl.: 87577 remove outliers: r(all,work,free)=0.1129 0.1121 0.1287 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 0.4033 288.291 247.803 0.445 1.000 0.298 11.894-9.307 94.12 92 4 0.2415 485.047 468.103 0.874 1.002 0.231 9.237-7.194 98.18 209 7 0.2355 386.082 379.532 0.930 1.002 0.179 7.162-5.571 100.00 427 22 0.2056 296.126 286.404 0.918 1.003 0.140 5.546-4.326 100.00 867 58 0.1113 406.508 401.766 0.962 1.003 0.118 4.315-3.360 100.00 1859 96 0.0899 386.592 384.708 1.004 1.002 0.100 3.356-2.611 100.00 3867 181 0.1087 253.971 252.069 1.009 1.002 0.019 2.608-2.026 99.99 8198 413 0.0902 168.360 167.702 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.218 82.581 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.459 36.075 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.972 21.534 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0165 ================= 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 : 0.2608 0.1963 0.083 5.167 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1796 0.083 5.167 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1796 0.083 5.167 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1798 0.083 5.167 9.1 119.5 20.1 258 0.003 1_weight: 0.1642 0.1798 0.083 5.167 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1226 0.1465 0.006 0.886 9.1 119.5 20.1 258 0.130 1_adp: 0.1233 0.1461 0.006 0.886 9.1 119.4 20.1 258 0.130 1_regHadp: 0.1235 0.1464 0.006 0.886 9.1 119.4 20.1 258 0.130 1_occ: 0.1227 0.1457 0.006 0.886 9.1 119.4 20.1 258 0.130 2_bss: 0.1225 0.1452 0.006 0.886 9.1 119.5 20.1 258 0.130 2_settarget: 0.1225 0.1452 0.006 0.886 9.1 119.5 20.1 258 0.130 2_updatecdl: 0.1225 0.1452 0.006 0.891 9.1 119.5 20.1 258 0.130 2_nqh: 0.1226 0.1453 0.006 0.891 9.1 119.5 20.1 258 0.133 2_sol: 0.1202 0.1405 0.006 0.891 9.1 115.0 22.1 415 n/a 2_weight: 0.1202 0.1405 0.006 0.891 9.1 115.0 22.1 415 n/a 2_xyzrec: 0.1197 0.1409 0.005 0.796 9.1 115.0 22.1 415 n/a 2_adp: 0.1197 0.1409 0.005 0.796 9.1 115.0 22.1 415 n/a 2_regHadp: 0.1197 0.1410 0.005 0.796 9.1 115.0 22.1 415 n/a 2_occ: 0.1198 0.1413 0.005 0.796 9.1 115.0 22.1 415 n/a 3_bss: 0.1193 0.1407 0.005 0.796 9.1 115.0 22.1 415 n/a 3_settarget: 0.1193 0.1407 0.005 0.796 9.1 115.0 22.1 415 n/a 3_updatecdl: 0.1193 0.1407 0.005 0.800 9.1 115.0 22.1 415 n/a 3_nqh: 0.1193 0.1407 0.005 0.800 9.1 115.0 22.1 415 n/a 3_sol: 0.1212 0.1377 0.005 0.800 9.1 115.0 21.1 426 n/a 3_weight: 0.1212 0.1377 0.005 0.800 9.1 115.0 21.1 426 n/a 3_xyzrec: 0.1158 0.1296 0.007 1.005 9.1 115.0 21.1 426 n/a 3_adp: 0.1158 0.1296 0.007 1.005 9.1 115.0 21.1 426 n/a 3_regHadp: 0.1158 0.1296 0.007 1.005 9.1 115.0 21.1 426 n/a 3_occ: 0.1149 0.1301 0.007 1.005 9.1 115.0 21.1 426 n/a 4_bss: 0.1143 0.1297 0.007 1.005 9.1 115.0 21.1 426 n/a 4_settarget: 0.1143 0.1297 0.007 1.005 9.1 115.0 21.1 426 n/a 4_updatecdl: 0.1143 0.1297 0.007 1.006 9.1 115.0 21.1 426 n/a 4_nqh: 0.1146 0.1299 0.007 1.006 9.1 115.0 21.1 426 n/a 4_sol: 0.1144 0.1291 0.007 1.006 9.1 115.0 21.3 448 n/a 4_weight: 0.1144 0.1291 0.007 1.006 9.1 115.0 21.3 448 n/a 4_xyzrec: 0.1133 0.1294 0.008 1.113 9.1 115.0 21.3 448 n/a 4_adp: 0.1133 0.1294 0.008 1.113 9.1 115.0 21.3 448 n/a 4_regHadp: 0.1133 0.1294 0.008 1.113 9.1 115.0 21.3 448 n/a 4_occ: 0.1127 0.1292 0.008 1.113 9.1 115.0 21.3 448 n/a 5_bss: 0.1124 0.1295 0.008 1.113 9.1 115.0 21.2 448 n/a 5_settarget: 0.1124 0.1295 0.008 1.113 9.1 115.0 21.2 448 n/a 5_updatecdl: 0.1124 0.1295 0.008 1.114 9.1 115.0 21.2 448 n/a 5_setrh: 0.1126 0.1294 0.008 1.114 9.1 115.0 21.2 448 n/a 5_nqh: 0.1126 0.1294 0.008 1.114 9.1 115.0 21.2 448 n/a 5_sol: 0.1126 0.1285 0.008 1.114 9.1 115.0 21.4 468 n/a 5_weight: 0.1126 0.1285 0.008 1.114 9.1 115.0 21.4 468 n/a 5_xyzrec: 0.1126 0.1285 0.008 1.117 9.1 115.0 21.4 468 n/a 5_adp: 0.1126 0.1285 0.008 1.117 9.1 115.0 21.4 468 n/a 5_regHadp: 0.1126 0.1285 0.008 1.117 9.1 115.0 21.4 468 n/a 5_occ: 0.1123 0.1285 0.008 1.117 9.1 115.0 21.4 468 n/a end: 0.1121 0.1287 0.008 1.117 9.1 115.0 21.4 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3031784_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3031784_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1100 Refinement macro-cycles (run) : 14020.6000 Write final files (write_after_run_outputs) : 92.1600 Total : 14115.8700 Total CPU time: 3.93 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:14:38 PST -0800 (1735366478.45 s) Start R-work = 0.1637, R-free = 0.1796 Final R-work = 0.1121, R-free = 0.1287 =============================================================================== Job complete usr+sys time: 14288.70 seconds wall clock time: 258 minutes 41.95 seconds (15521.95 seconds total)