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_9049096.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.53, 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: 0.32 Conformation dependent library (CDL) restraints added in 105.1 milliseconds Time building geometry restraints manager: 0.45 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: 396 0.89 - 1.15: 1225 1.15 - 1.41: 621 1.41 - 1.67: 874 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.432 -0.195 9.70e-03 1.06e+04 4.05e+02 bond pdb=" C LYS A 122 " pdb=" O LYS A 122 " ideal model delta sigma weight residual 1.235 1.015 0.221 1.21e-02 6.83e+03 3.32e+02 bond pdb=" C LEU A 172 " pdb=" N ASN A 173 " ideal model delta sigma weight residual 1.332 1.581 -0.249 1.39e-02 5.18e+03 3.22e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.457 1.659 -0.202 1.14e-02 7.69e+03 3.13e+02 bond pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta sigma weight residual 1.537 1.331 0.206 1.17e-02 7.31e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 2954 4.32 - 8.63: 1867 8.63 - 12.95: 762 12.95 - 17.26: 172 17.26 - 21.58: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 108.55 10.74 6.50e-01 2.37e+00 2.73e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.74 95.89 14.85 9.10e-01 1.21e+00 2.66e+02 angle pdb=" C ALA A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 121.13 132.71 -11.58 7.30e-01 1.88e+00 2.52e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 135.02 -13.52 1.00e+00 1.00e+00 1.83e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.75 -10.52 8.10e-01 1.52e+00 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.49: 924 16.49 - 32.96: 120 32.96 - 49.44: 51 49.44 - 65.91: 14 65.91 - 82.39: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA A 11 " pdb=" C ALA A 11 " pdb=" N LYS A 12 " pdb=" CA LYS A 12 " ideal model delta harmonic sigma weight residual 180.00 161.39 18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.229: 92 0.229 - 0.454: 87 0.454 - 0.679: 45 0.679 - 0.904: 16 0.904 - 1.129: 3 Chirality restraints: 243 Sorted by residual: 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 -1.46 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 1.42 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 3.36 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.186 9.50e-02 1.11e+02 9.10e-02 1.03e+02 pdb=" NE ARG A 156 " -0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.030 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.026 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.046 9.50e-02 1.11e+02 6.85e-02 1.01e+02 pdb=" NE ARG A 48 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.122 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.009 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1220 2.35 - 2.91: 8224 2.91 - 3.47: 10514 3.47 - 4.04: 15150 4.04 - 4.60: 21582 Nonbonded interactions: 56690 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.783 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.840 2.270 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.852 1.816 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.852 1.850 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.852 2.100 ... (remaining 56685 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_9049096_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= 0.2601 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787510 | | target function (ml) not normalized (work): 232216.321120 | | target function (ml) not normalized (free): 11854.817596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2154 7.0133 4.9671| | 2: 3.57 - 2.84 1.00 2876 122 0.2416 0.1759 4.3516 4.3489| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1755 4.1359 4.1567| | 4: 2.47 - 2.25 1.00 2825 136 0.2339 0.1493 3.8387 3.8487| | 5: 2.25 - 2.09 1.00 2756 127 0.2472 0.1521 3.7969 3.8133| | 6: 2.09 - 1.97 1.00 2846 113 0.2559 0.1686 3.4687 3.579| | 7: 1.97 - 1.87 1.00 2787 165 0.2542 0.1855 3.1207 3.1802| | 8: 1.87 - 1.79 1.00 2789 144 0.2426 0.1921 3.0457 3.1565| | 9: 1.79 - 1.72 1.00 2745 138 0.2411 0.1796 2.8932 2.9474| | 10: 1.72 - 1.66 1.00 2789 158 0.2402 0.2131 2.8045 2.9472| | 11: 1.66 - 1.61 1.00 2740 147 0.2496 0.1903 2.7418 2.7911| | 12: 1.61 - 1.56 1.00 2787 146 0.2511 0.1934 2.61 2.6493| | 13: 1.56 - 1.52 1.00 2745 130 0.2513 0.1930 2.577 2.6045| | 14: 1.52 - 1.48 1.00 2803 134 0.2643 0.2115 2.5229 2.6081| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.1863 2.4246 2.4065| | 16: 1.45 - 1.42 1.00 2756 161 0.2576 0.2072 2.3743 2.4041| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.2171 2.3203 2.3813| | 18: 1.39 - 1.36 1.00 2741 179 0.2647 0.2149 2.2646 2.393| | 19: 1.36 - 1.34 1.00 2807 134 0.2686 0.2480 2.2474 2.3359| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2141 2.1968 2.1731| | 21: 1.32 - 1.30 1.00 2785 112 0.2724 0.2384 2.1529 2.1918| | 22: 1.29 - 1.27 1.00 2704 152 0.2759 0.2702 2.1425 2.2289| | 23: 1.27 - 1.26 1.00 2802 156 0.2776 0.2643 2.1085 2.2517| | 24: 1.26 - 1.24 1.00 2744 132 0.2772 0.2503 2.0875 2.1512| | 25: 1.24 - 1.22 1.00 2734 148 0.2856 0.2403 2.0626 2.06| | 26: 1.22 - 1.21 1.00 2727 135 0.2857 0.2614 2.0134 2.1611| | 27: 1.21 - 1.19 1.00 2814 148 0.2939 0.2359 2.0062 1.9232| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2679 1.9744 1.9866| | 29: 1.18 - 1.16 1.00 2800 134 0.2968 0.2647 1.9572 2.0055| | 30: 1.16 - 1.15 1.00 2740 148 0.3019 0.2790 1.9173 1.9701| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.01 0.76 0.23 1505.45| | 2: 3.57 - 2.84 2876 122 0.80 26.28 1.27 0.23 1505.45| | 3: 2.84 - 2.48 2833 165 0.74 32.15 1.25 0.24 1247.47| | 4: 2.47 - 2.25 2825 136 0.81 25.66 1.25 0.25 577.95| | 5: 2.25 - 2.09 2756 127 0.77 29.51 1.28 0.25 577.95| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 314.72| | 7: 1.97 - 1.87 2787 165 0.90 16.61 1.28 0.26 90.22| | 8: 1.87 - 1.79 2789 144 0.86 21.12 1.24 0.26 90.22| | 9: 1.79 - 1.72 2745 138 0.88 18.77 1.23 0.25 56.18| | 10: 1.72 - 1.66 2789 158 0.86 20.44 1.22 0.25 49.37| | 11: 1.66 - 1.61 2740 147 0.85 21.56 1.24 0.25 47.63| | 12: 1.61 - 1.56 2787 146 0.88 18.88 1.24 0.25 30.06| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.23 0.25 30.06| | 14: 1.52 - 1.48 2803 134 0.86 21.11 1.24 0.25 26.89| | 15: 1.48 - 1.45 2738 128 0.87 20.32 1.23 0.25 21.08| | 16: 1.45 - 1.42 2756 161 0.85 21.75 1.23 0.25 21.08| | 17: 1.42 - 1.39 2785 139 0.86 21.29 1.23 0.25 18.10| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.22 0.25 16.37| | 19: 1.36 - 1.34 2807 134 0.85 22.59 1.22 0.25 16.37| | 20: 1.34 - 1.32 2696 147 0.86 21.37 1.21 0.24 13.66| | 21: 1.32 - 1.30 2785 112 0.85 22.60 1.21 0.24 13.47| | 22: 1.29 - 1.27 2704 152 0.85 23.06 1.21 0.24 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.87 1.20 0.24 11.67| | 24: 1.26 - 1.24 2744 132 0.85 23.25 1.20 0.24 11.67| | 25: 1.24 - 1.22 2734 148 0.84 23.87 1.20 0.24 10.89| | 26: 1.22 - 1.21 2727 135 0.84 23.76 1.20 0.23 10.02| | 27: 1.21 - 1.19 2814 148 0.83 24.90 1.20 0.23 10.02| | 28: 1.19 - 1.18 2671 147 0.83 24.62 1.19 0.23 9.04| | 29: 1.18 - 1.16 2800 134 0.83 24.78 1.17 0.23 8.67| | 30: 1.16 - 1.15 2740 148 0.82 26.25 1.16 0.23 8.67| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.67 max = 1505.45 mean = 218.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.79| |phase err.(test): min = 0.00 max = 89.92 mean = 22.72| |-----------------------------------------------------------------------------| ----------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 0.250 1557 Z= 5.564 Angle : 5.272 17.218 2118 Z= 3.760 Chirality : 0.389 1.129 243 Planarity : 0.032 0.084 284 Dihedral : 13.915 82.386 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.44), residues: 224 helix: -2.86 (0.37), residues: 109 sheet: -0.74 (0.76), residues: 28 loop : -0.74 (0.51), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.025 ARG A 156 TYR 0.115 0.046 TYR A 141 PHE 0.110 0.045 PHE A 164 HIS 0.058 0.032 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= 0.2601 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787510 | | target function (ml) not normalized (work): 232216.321120 | | target function (ml) not normalized (free): 11854.817596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2601 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2601 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1974 0.1962 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1995 0.1998 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1626 0.1782 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1625 0.1782 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 0.3806 386.325 357.869 0.677 1.002 0.407 11.894-9.307 99.02 97 4 0.1825 613.659 594.412 0.932 1.003 0.390 9.237-7.194 100.00 213 7 0.2155 501.897 490.959 0.958 1.003 0.349 7.162-5.571 100.00 427 22 0.2194 376.646 365.226 0.933 1.003 0.283 5.546-4.326 100.00 867 58 0.1265 517.042 511.767 0.962 1.003 0.234 4.315-3.360 100.00 1859 96 0.1137 491.711 487.780 1.007 1.003 0.219 3.356-2.611 100.00 3867 181 0.1436 323.028 319.521 0.995 1.002 0.089 2.608-2.026 99.99 8198 413 0.1338 214.138 212.008 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1622 104.574 103.958 1.013 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.372 45.140 1.002 0.998 0.000 1.221-1.150 99.97 13689 708 0.2569 29.218 27.055 0.976 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0433 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1625 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.1636 r_free=0.1797 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.260586 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.800405 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 0.1650 0.1778 0.0129 0.002 0.4 4.2 0.0 0.0 0 0.125 0.1555 0.1694 0.0139 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1457 0.1615 0.0157 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1399 0.1573 0.0174 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1336 0.1531 0.0196 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1367 0.1556 0.0189 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1298 0.1516 0.0218 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1273 0.1496 0.0223 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1261 0.1492 0.0232 0.004 0.7 3.5 0.5 0.0 0 4.000 0.1249 0.1482 0.0233 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1243 0.1477 0.0235 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1238 0.1472 0.0235 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1235 0.1473 0.0238 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1471 0.0240 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1229 0.1470 0.0241 0.006 0.9 3.8 0.5 0.6 0 10.000 0.1228 0.1474 0.0246 0.007 0.9 3.8 0.5 0.6 0 11.000 0.1228 0.1471 0.0243 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1226 0.1476 0.0249 0.008 0.9 3.5 0.5 0.6 0 13.000 0.1224 0.1472 0.0248 0.008 1.0 3.5 0.5 0.6 0 14.130 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1470 0.0241 0.006 0.9 3.8 0.5 0.6 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.70 2.41 3.013 19.048 2018.800 0.017 12.29 14.70 2.41 3.012 19.048 60.564 0.017 12.36 14.67 2.31 2.665 19.047 252.350 0.017 12.69 15.30 2.61 2.738 19.215 1009.400 0.017 12.51 15.42 2.91 3.141 19.508 2018.800 0.016 12.47 15.50 3.03 3.337 19.627 3028.201 0.015 12.41 15.54 3.13 3.442 19.671 4037.601 0.015 12.30 15.47 3.17 3.395 19.638 5047.001 0.015 12.22 15.48 3.27 3.394 19.637 6056.401 0.015 12.22 15.42 3.20 3.352 19.596 7065.801 0.015 12.18 15.47 3.29 3.497 19.665 8075.202 0.015 12.17 15.46 3.29 3.478 19.647 9084.602 0.015 12.16 15.48 3.32 3.553 19.677 10094.002 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: 252.350 Accepted refinement result: 12.36 14.67 2.31 2.665 19.047 252.350 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.42 20.07 3.31 0 1785 Protein: 9.04 114.96 16.98 3.31 0 1519 Water: 11.45 119.42 38.21 N/A 0 258 Other: 19.71 26.58 22.05 N/A 0 8 Chain A: 9.04 119.42 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.15 125 42.15 - 53.19 94 53.19 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1467 r_work=0.1237 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1469 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1230 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016886 | | target function (ls_wunit_k1) not normalized (work): 1406.537995 | | target function (ls_wunit_k1) not normalized (free): 111.065010 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1461 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1671 0.1673 0.1685 n_refl.: 87593 remove outliers: r(all,work,free)=0.1671 0.1673 0.1685 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1678 0.1680 0.1689 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1228 0.1454 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 94.79 86 5 0.3545 298.091 281.578 0.644 1.002 0.380 11.894-9.307 99.02 97 4 0.1688 483.039 470.092 0.920 1.003 0.371 9.237-7.194 100.00 213 7 0.1891 395.067 388.733 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1848 296.476 290.112 0.935 1.003 0.254 5.546-4.326 100.00 867 58 0.1003 406.988 403.748 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0867 387.048 385.969 1.009 1.003 0.190 3.356-2.611 100.00 3867 181 0.1174 254.271 253.069 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1020 168.558 167.795 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.315 82.514 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1453 36.502 36.000 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.999 21.480 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0581 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1454 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** A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.1229 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1455 | n_water=258 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1236 r_free=0.1454 | n_water=251 | time (s): 22.100 (total time: 24.170) Filter (q & B) r_work=0.1239 r_free=0.1454 | n_water=248 | time (s): 2.510 (total time: 26.680) Compute maps r_work=0.1239 r_free=0.1454 | n_water=248 | time (s): 1.350 (total time: 28.030) Filter (map) r_work=0.1256 r_free=0.1462 | n_water=228 | time (s): 2.640 (total time: 30.670) Find peaks r_work=0.1256 r_free=0.1462 | n_water=228 | time (s): 0.490 (total time: 31.160) Add new water r_work=0.1400 r_free=0.1624 | n_water=439 | time (s): 3.260 (total time: 34.420) Refine new water occ: r_work=0.1303 r_free=0.1468 adp: r_work=0.1224 r_free=0.1425 occ: r_work=0.1235 r_free=0.1409 adp: r_work=0.1204 r_free=0.1402 occ: r_work=0.1207 r_free=0.1392 adp: r_work=0.1197 r_free=0.1392 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1392 r_work=0.1197 r_free=0.1392 | n_water=439 | time (s): 56.300 (total time: 90.720) Filter (q & B) r_work=0.1201 r_free=0.1393 | n_water=423 | time (s): 3.220 (total time: 93.940) Filter (dist only) r_work=0.1202 r_free=0.1392 | n_water=422 | time (s): 36.860 (total time: 130.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.771170 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.474435 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 0.1720 0.1827 0.0107 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1551 0.1677 0.0126 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1433 0.1582 0.0149 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1348 0.1517 0.0169 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1302 0.1480 0.0179 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1317 0.1497 0.0180 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1259 0.1460 0.0202 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1226 0.1437 0.0210 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1214 0.1428 0.0214 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1204 0.1424 0.0220 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1197 0.1417 0.0220 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1196 0.1419 0.0223 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1193 0.1410 0.0217 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1192 0.1409 0.0218 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1189 0.1408 0.0219 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1186 0.1406 0.0220 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1185 0.1410 0.0225 0.007 0.9 4.8 0.5 0.6 0 12.000 0.1182 0.1404 0.0222 0.008 0.9 6.1 0.5 0.6 0 13.000 0.1180 0.1406 0.0226 0.008 0.9 4.5 0.5 0.6 0 14.386 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1404 0.0222 0.008 0.9 6.1 0.5 0.6 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 14.04 2.22 3.772 21.776 1487.474 0.015 11.82 14.04 2.22 3.772 21.776 44.624 0.015 11.82 14.04 2.22 3.772 21.776 185.934 0.015 12.08 14.59 2.51 3.585 21.808 743.737 0.015 11.98 14.75 2.77 3.453 22.020 1487.474 0.014 11.92 14.87 2.95 3.497 21.943 2231.212 0.014 11.73 14.62 2.89 3.477 22.104 2974.949 0.014 11.66 14.62 2.96 3.510 21.934 3718.686 0.014 11.62 14.63 3.01 3.509 21.974 4462.423 0.014 11.69 14.79 3.10 3.567 22.212 5206.161 0.014 11.56 14.61 3.05 3.537 22.143 5949.898 0.013 11.60 14.67 3.07 3.570 22.177 6693.635 0.013 11.57 14.69 3.11 3.593 22.213 7437.372 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.624 Accepted refinement result: 11.82 14.04 2.22 3.772 21.776 44.624 0.015 Individual atomic B min max mean iso aniso Overall: 9.08 114.99 22.19 3.31 194 1755 Protein: 9.08 114.99 17.02 3.31 0 1519 Water: 11.09 76.68 40.80 N/A 194 228 Other: 19.75 26.62 22.08 N/A 0 8 Chain A: 9.08 114.99 19.50 N/A 0 1755 Chain S: 11.09 60.00 46.48 N/A 194 0 Histogram: Values Number of atoms 9.08 - 19.67 1258 19.67 - 30.26 246 30.26 - 40.85 169 40.85 - 51.44 136 51.44 - 62.04 116 62.04 - 72.63 13 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1182 r_free=0.1404 r_work=0.1182 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1404 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1399 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 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= 0.1182 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014679 | | target function (ls_wunit_k1) not normalized (work): 1222.659515 | | target function (ls_wunit_k1) not normalized (free): 99.630771 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1182 0.1399 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1578 0.1576 0.1637 n_refl.: 87591 remove outliers: r(all,work,free)=0.1578 0.1576 0.1637 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1580 0.1578 0.1638 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1179 0.1396 n_refl.: 87591 remove outliers: r(all,work,free)=0.1188 0.1178 0.1396 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 0.3269 297.436 273.691 0.590 1.002 0.350 11.894-9.307 99.02 97 4 0.1581 483.039 477.944 0.917 1.003 0.330 9.237-7.194 100.00 213 7 0.1665 395.067 395.190 0.980 1.003 0.280 7.162-5.571 100.00 427 22 0.1571 296.476 292.747 0.943 1.003 0.230 5.546-4.326 100.00 867 58 0.0866 406.988 403.803 0.960 1.003 0.204 4.315-3.360 100.00 1859 96 0.0800 387.048 386.043 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1068 254.271 253.461 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1003 168.558 168.051 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.315 82.541 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.502 36.045 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.999 21.512 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0170 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1396 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1396 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1396 | n_water=422 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1178 r_free=0.1396 | n_water=419 | time (s): 37.880 (total time: 39.540) Filter (q & B) r_work=0.1178 r_free=0.1396 | n_water=419 | time (s): 0.770 (total time: 40.310) Compute maps r_work=0.1178 r_free=0.1396 | n_water=419 | time (s): 1.210 (total time: 41.520) Filter (map) r_work=0.1219 r_free=0.1396 | n_water=286 | time (s): 3.470 (total time: 44.990) Find peaks r_work=0.1219 r_free=0.1396 | n_water=286 | time (s): 0.690 (total time: 45.680) Add new water r_work=0.1334 r_free=0.1497 | n_water=469 | time (s): 2.580 (total time: 48.260) Refine new water occ: r_work=0.1239 r_free=0.1420 adp: r_work=0.1240 r_free=0.1421 occ: r_work=0.1217 r_free=0.1404 adp: r_work=0.1216 r_free=0.1404 occ: r_work=0.1200 r_free=0.1396 adp: r_work=0.1195 r_free=0.1392 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1392 r_work=0.1195 r_free=0.1392 | n_water=469 | time (s): 186.300 (total time: 234.560) Filter (q & B) r_work=0.1200 r_free=0.1397 | n_water=438 | time (s): 2.820 (total time: 237.380) Filter (dist only) r_work=0.1200 r_free=0.1395 | n_water=436 | time (s): 37.970 (total time: 275.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.834091 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.461947 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 0.1233 0.1369 0.0135 0.002 0.6 4.8 0.5 0.0 0 0.092 0.1186 0.1335 0.0149 0.003 0.7 3.5 0.5 0.0 0 0.275 0.1170 0.1324 0.0153 0.004 0.8 3.2 0.5 0.0 0 0.550 0.1163 0.1325 0.0162 0.005 0.9 3.8 0.5 0.0 0 0.825 0.1158 0.1325 0.0166 0.006 1.0 3.5 0.5 0.0 0 1.100 0.1156 0.1327 0.0171 0.007 1.0 3.5 0.5 0.0 0 1.376 0.1155 0.1325 0.0170 0.007 1.1 3.8 0.5 0.6 0 1.651 0.1152 0.1324 0.0173 0.008 1.1 3.8 0.5 0.6 0 1.926 0.1162 0.1327 0.0165 0.006 0.9 3.5 0.5 0.0 0 0.917 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1170 0.1324 0.0153 0.004 0.8 3.2 0.5 0.0 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 13.24 1.53 3.776 21.282 46.462 3.629 11.70 13.24 1.53 3.776 21.282 1.394 3.629 11.71 13.24 1.53 3.761 21.282 5.808 3.629 11.76 13.36 1.60 3.705 21.272 23.231 3.624 11.75 13.45 1.70 3.726 21.247 46.462 3.623 11.68 13.42 1.74 3.748 21.236 69.693 3.617 11.65 13.39 1.74 3.755 21.229 92.924 3.613 11.61 13.37 1.76 3.772 21.225 116.155 3.610 11.60 13.39 1.80 3.787 21.211 139.386 3.609 11.58 13.39 1.81 3.799 21.209 162.617 3.607 11.56 13.36 1.81 3.807 21.207 185.848 3.606 11.55 13.36 1.81 3.814 21.207 209.079 3.605 11.53 13.32 1.79 3.817 21.206 232.310 3.603 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.394 Accepted refinement result: 11.70 13.24 1.53 3.776 21.282 1.394 3.629 Individual atomic B min max mean iso aniso Overall: 9.09 115.00 21.28 3.31 212 1751 Protein: 9.09 115.00 17.03 3.31 0 1519 Water: 11.10 76.69 36.05 N/A 212 224 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.09 115.00 19.44 N/A 0 1751 Chain S: 11.10 60.01 36.40 N/A 212 0 Histogram: Values Number of atoms 9.09 - 19.68 1261 19.68 - 30.27 287 30.27 - 40.86 206 40.86 - 51.45 130 51.45 - 62.05 55 62.05 - 72.64 13 72.64 - 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=0.1170 r_free=0.1324 r_work=0.1170 r_free=0.1324 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1170 r_free = 0.1324 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1164 r_free = 0.1320 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1164 r_free= 0.1320 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.623880 | | target function (ml) not normalized (work): 301843.877281 | | target function (ml) not normalized (free): 15864.365257 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1172 0.1164 0.1320 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1495 0.1494 0.1545 n_refl.: 87589 remove outliers: r(all,work,free)=0.1495 0.1494 0.1545 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1494 0.1493 0.1545 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1160 0.1320 n_refl.: 87589 remove outliers: r(all,work,free)=0.1167 0.1159 0.1320 n_refl.: 87587 ======================== 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 0.3800 297.436 270.263 0.510 1.000 0.330 11.894-9.307 99.02 97 4 0.2326 483.039 471.272 0.876 1.002 0.320 9.237-7.194 99.09 211 7 0.2296 389.561 388.856 0.956 1.002 0.200 7.162-5.571 100.00 427 22 0.2171 296.476 284.277 0.916 1.002 0.178 5.546-4.326 100.00 867 58 0.1104 406.988 402.597 0.963 1.002 0.148 4.315-3.360 100.00 1859 96 0.0942 387.048 384.366 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1141 254.271 252.416 1.009 1.002 0.038 2.608-2.026 99.99 8198 413 0.0947 168.558 167.817 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0923 82.315 82.607 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1280 36.502 36.079 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2177 22.999 21.525 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0077 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1159 r_free=0.1320 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=0.1159 r_free=0.1320 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1159 r_free=0.1320 | n_water=436 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1159 r_free=0.1320 | n_water=436 | time (s): 40.250 (total time: 42.730) Filter (q & B) r_work=0.1161 r_free=0.1321 | n_water=433 | time (s): 3.860 (total time: 46.590) Compute maps r_work=0.1161 r_free=0.1321 | n_water=433 | time (s): 1.760 (total time: 48.350) Filter (map) r_work=0.1184 r_free=0.1315 | n_water=323 | time (s): 4.000 (total time: 52.350) Find peaks r_work=0.1184 r_free=0.1315 | n_water=323 | time (s): 0.700 (total time: 53.050) Add new water r_work=0.1250 r_free=0.1389 | n_water=490 | time (s): 3.710 (total time: 56.760) Refine new water occ: r_work=0.1181 r_free=0.1322 adp: r_work=0.1182 r_free=0.1325 occ: r_work=0.1165 r_free=0.1306 adp: r_work=0.1165 r_free=0.1308 occ: r_work=0.1154 r_free=0.1292 adp: r_work=0.1151 r_free=0.1294 ADP+occupancy (water only), MIN, final r_work=0.1151 r_free=0.1294 r_work=0.1151 r_free=0.1294 | n_water=490 | time (s): 256.670 (total time: 313.430) Filter (q & B) r_work=0.1158 r_free=0.1298 | n_water=453 | time (s): 3.980 (total time: 317.410) Filter (dist only) r_work=0.1158 r_free=0.1296 | n_water=452 | time (s): 47.480 (total time: 364.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.786518 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.977265 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1336 0.0132 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1167 0.1313 0.0146 0.003 0.7 3.2 0.5 0.0 0 0.268 0.1152 0.1301 0.0148 0.005 0.9 3.5 0.5 0.0 0 0.536 0.1145 0.1301 0.0155 0.006 1.0 3.5 0.5 0.0 0 0.804 0.1142 0.1303 0.0161 0.007 1.0 3.5 0.5 0.0 0 1.072 0.1139 0.1297 0.0158 0.007 1.1 4.2 0.5 0.0 0 1.340 0.1138 0.1300 0.0163 0.008 1.1 4.2 0.5 0.0 0 1.608 0.1136 0.1300 0.0164 0.009 1.1 4.2 0.5 0.0 0 1.876 0.1144 0.1298 0.0154 0.006 1.0 3.5 0.5 0.0 0 0.893 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1297 0.0158 0.007 1.1 4.2 0.5 0.0 0 1.340 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 12.97 1.58 3.777 21.254 37.977 3.608 11.39 12.97 1.58 3.777 21.254 1.139 3.608 11.39 12.97 1.58 3.777 21.254 4.747 3.608 11.42 13.00 1.58 3.706 21.250 18.989 3.604 11.51 13.18 1.67 3.720 21.225 37.977 3.609 11.43 13.15 1.72 3.741 21.211 56.966 3.602 11.36 13.10 1.74 3.758 21.208 75.955 3.597 11.36 13.11 1.75 3.763 21.204 94.943 3.595 11.30 13.04 1.74 3.773 21.205 113.932 3.591 11.30 13.07 1.77 3.785 21.198 132.920 3.590 11.30 13.11 1.81 3.800 21.185 151.909 3.590 11.29 13.10 1.81 3.810 21.183 170.898 3.589 11.27 13.07 1.81 3.815 21.181 189.886 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.139 Accepted refinement result: 11.39 12.97 1.58 3.777 21.254 1.139 3.608 Individual atomic B min max mean iso aniso Overall: 9.08 115.00 21.22 3.31 228 1751 Protein: 9.08 115.00 17.03 3.31 0 1519 Water: 11.10 76.69 35.31 N/A 228 224 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.08 115.00 19.44 N/A 0 1751 Chain S: 11.10 60.01 34.91 N/A 228 0 Histogram: Values Number of atoms 9.08 - 19.68 1260 19.68 - 30.27 298 30.27 - 40.86 218 40.86 - 51.45 132 51.45 - 62.04 47 62.04 - 72.64 13 72.64 - 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=0.1139 r_free=0.1297 r_work=0.1139 r_free=0.1297 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1297 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1294 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1133 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605093 | | target function (ml) not normalized (work): 300271.831465 | | target function (ml) not normalized (free): 15811.793836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1133 0.1294 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1469 0.1469 0.1511 n_refl.: 87587 remove outliers: r(all,work,free)=0.1469 0.1469 0.1511 n_refl.: 87587 overall B=-0.00 to atoms: r(all,work,free)=0.1468 0.1468 0.1510 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1132 0.1297 n_refl.: 87587 remove outliers: r(all,work,free)=0.1137 0.1129 0.1297 n_refl.: 87579 ======================== 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 0.4079 294.566 258.873 0.476 0.999 0.320 11.894-9.307 95.10 93 4 0.2362 478.880 467.948 0.860 1.002 0.320 9.237-7.194 98.18 209 7 0.2360 386.537 383.234 0.933 1.002 0.180 7.162-5.571 100.00 427 22 0.2113 296.476 285.767 0.913 1.002 0.150 5.546-4.326 100.00 867 58 0.1086 406.988 402.843 0.964 1.002 0.125 4.315-3.360 100.00 1859 96 0.0919 387.048 384.756 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1108 254.271 252.665 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0911 168.558 167.927 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.315 82.645 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.502 36.098 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.999 21.543 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0119 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1129 r_free=0.1297 After: r_work=0.1130 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1130 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=0.1130 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1130 r_free=0.1297 | n_water=452 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1130 r_free=0.1297 | n_water=452 | time (s): 43.640 (total time: 46.020) Filter (q & B) r_work=0.1131 r_free=0.1297 | n_water=449 | time (s): 4.030 (total time: 50.050) Compute maps r_work=0.1131 r_free=0.1297 | n_water=449 | time (s): 1.900 (total time: 51.950) Filter (map) r_work=0.1157 r_free=0.1312 | n_water=349 | time (s): 4.080 (total time: 56.030) Find peaks r_work=0.1157 r_free=0.1312 | n_water=349 | time (s): 0.690 (total time: 56.720) Add new water r_work=0.1209 r_free=0.1369 | n_water=508 | time (s): 3.720 (total time: 60.440) Refine new water occ: r_work=0.1149 r_free=0.1319 adp: r_work=0.1150 r_free=0.1321 occ: r_work=0.1137 r_free=0.1311 adp: r_work=0.1136 r_free=0.1311 occ: r_work=0.1127 r_free=0.1303 adp: r_work=0.1124 r_free=0.1302 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1302 r_work=0.1124 r_free=0.1302 | n_water=508 | time (s): 181.410 (total time: 241.850) Filter (q & B) r_work=0.1132 r_free=0.1311 | n_water=462 | time (s): 4.070 (total time: 245.920) Filter (dist only) r_work=0.1133 r_free=0.1309 | n_water=461 | time (s): 49.620 (total time: 295.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.760283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.324432 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 0.1219 0.1363 0.0144 0.003 0.7 5.8 0.0 0.0 0 0.088 0.1171 0.1330 0.0160 0.004 0.8 5.4 0.0 0.0 0 0.264 0.1152 0.1319 0.0167 0.005 0.9 4.8 0.5 0.0 0 0.528 0.1140 0.1311 0.0171 0.006 1.0 4.8 0.5 0.0 0 0.792 0.1134 0.1309 0.0174 0.007 1.1 4.5 0.5 0.0 0 1.056 0.1133 0.1308 0.0175 0.007 1.1 4.5 0.5 0.0 0 1.320 0.1132 0.1308 0.0176 0.007 1.1 4.5 0.5 0.0 0 1.584 0.1131 0.1308 0.0176 0.008 1.1 4.5 0.5 0.0 0 1.848 0.1139 0.1310 0.0171 0.006 1.0 4.8 0.5 0.0 0 0.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1308 0.0176 0.008 1.1 4.5 0.5 0.0 0 1.848 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 13.08 1.76 3.776 21.286 33.324 3.606 11.31 13.08 1.76 3.776 21.286 1.000 3.606 11.31 13.08 1.76 3.776 21.286 4.166 3.606 11.37 13.13 1.76 3.703 21.281 16.662 3.604 11.37 13.21 1.84 3.720 21.267 33.324 3.602 11.36 13.26 1.90 3.740 21.247 49.987 3.600 11.32 13.25 1.93 3.754 21.240 66.649 3.597 11.32 13.26 1.94 3.763 21.235 83.311 3.596 11.26 13.20 1.94 3.773 21.236 99.973 3.592 11.24 13.19 1.95 3.781 21.235 116.636 3.590 11.24 13.22 1.98 3.793 21.227 133.298 3.589 11.24 13.25 2.01 3.807 21.218 149.960 3.590 11.23 13.23 2.00 3.814 21.217 166.622 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.000 Accepted refinement result: 11.31 13.08 1.76 3.776 21.286 1.000 3.606 Individual atomic B min max mean iso aniso Overall: 9.08 115.00 21.29 3.31 239 1749 Protein: 9.08 115.00 17.02 3.31 0 1519 Water: 11.09 76.69 35.32 N/A 239 222 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.08 115.00 19.40 N/A 0 1749 Chain S: 11.09 60.00 35.08 N/A 239 0 Histogram: Values Number of atoms 9.08 - 19.67 1260 19.67 - 30.26 304 30.26 - 40.86 219 40.86 - 51.45 131 51.45 - 62.04 50 62.04 - 72.63 13 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1308 r_work=0.1131 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1308 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1306 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603840 | | target function (ml) not normalized (work): 300138.608932 | | target function (ml) not normalized (free): 15818.723662 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1316 0.1386 5.6192 5.6252| | 2: 3.57 - 2.84 1.00 2888 124 0.1058 0.1442 5.1719 5.2436| | 3: 2.83 - 2.48 1.00 2820 163 0.1092 0.1255 4.9544 4.9911| | 4: 2.47 - 2.25 1.00 2825 136 0.0888 0.1008 4.6364 4.6688| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0918 4.5862 4.6278| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.1028 4.2714 4.3627| | 7: 1.97 - 1.87 1.00 2787 165 0.0886 0.1099 3.9769 4.0799| | 8: 1.87 - 1.79 1.00 2789 144 0.0901 0.1137 3.881 4.0067| | 9: 1.79 - 1.72 1.00 2745 138 0.0857 0.1188 3.639 3.8333| | 10: 1.72 - 1.66 1.00 2831 160 0.0919 0.1204 3.5661 3.7165| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1022 3.4977 3.5567| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1120 3.3285 3.446| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1039 3.305 3.3902| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1050 3.2364 3.3205| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1227 3.1519 3.2667| | 16: 1.45 - 1.42 1.00 2756 161 0.1061 0.1238 3.1351 3.2364| | 17: 1.42 - 1.39 1.00 2785 139 0.1136 0.1310 3.117 3.2397| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1330 3.105 3.2411| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1569 3.1151 3.2703| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1474 3.1136 3.1587| | 21: 1.32 - 1.30 1.00 2785 112 0.1467 0.1533 3.1151 3.117| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1989 3.1234 3.2967| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1800 3.1332 3.2019| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1822 3.1278 3.2222| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2149 3.1436 3.2588| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1773 3.1494 3.2042| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2176 3.1714 3.1662| | 28: 1.19 - 1.18 1.00 2671 147 0.2199 0.2299 3.1662 3.1761| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2382 3.1484 3.2295| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2442 3.1439 3.1658| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.66 1.00 0.97 5966.47| | 2: 3.57 - 2.84 2888 124 0.92 12.79 1.01 0.97 5966.47| | 3: 2.83 - 2.48 2820 163 0.89 16.76 0.99 0.97 4978.20| | 4: 2.47 - 2.25 2825 136 0.92 13.59 1.00 0.98 2429.76| | 5: 2.25 - 2.09 2756 127 0.90 15.91 1.01 0.98 2429.76| | 6: 2.09 - 1.97 2846 113 0.92 12.48 1.02 0.98 1392.13| | 7: 1.97 - 1.87 2787 165 0.95 9.17 1.02 0.98 507.17| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.98 507.17| | 9: 1.79 - 1.72 2745 138 0.94 9.99 0.98 0.97 289.24| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.97 245.60| | 11: 1.66 - 1.61 2712 147 0.94 11.71 0.98 0.97 235.19| | 12: 1.61 - 1.56 2773 144 0.95 8.89 0.99 0.97 136.97| | 13: 1.56 - 1.52 2745 130 0.95 10.36 1.03 0.97 136.97| | 14: 1.52 - 1.48 2803 134 0.94 10.72 1.02 0.98 122.98| | 15: 1.48 - 1.45 2738 128 0.95 9.87 1.02 0.98 97.37| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.37| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.98 88.97| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 84.11| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 84.11| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.44| | 21: 1.32 - 1.30 2785 112 0.94 13.13 0.98 0.96 80.18| | 22: 1.29 - 1.27 2704 152 0.93 13.70 0.98 0.96 80.59| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.94 82.64| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.96 0.94 82.64| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.53| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.03 0.93 86.63| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.63| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 90.21| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 91.56| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.92 91.56| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.18 max = 5966.47 mean = 913.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.48| |phase err.(test): min = 0.00 max = 89.19 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1126 0.1306 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1461 0.1461 0.1495 n_refl.: 87579 remove outliers: r(all,work,free)=0.1461 0.1461 0.1495 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1460 0.1495 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1126 0.1305 n_refl.: 87579 remove outliers: r(all,work,free)=0.1133 0.1124 0.1305 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 88.54 80 5 0.4023 286.444 258.590 0.450 1.000 0.289 11.894-9.307 93.14 91 4 0.2415 475.141 459.868 0.849 1.002 0.267 9.237-7.194 98.18 209 7 0.2292 386.537 381.472 0.924 1.002 0.150 7.162-5.571 100.00 427 22 0.2094 296.476 286.098 0.909 1.003 0.140 5.546-4.326 100.00 867 58 0.1090 406.988 402.651 0.963 1.003 0.110 4.315-3.360 100.00 1859 96 0.0916 387.048 385.003 1.002 1.003 0.100 3.356-2.611 100.00 3867 181 0.1097 254.271 252.763 1.011 1.002 0.030 2.608-2.026 99.99 8198 413 0.0903 168.558 167.931 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.315 82.672 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.502 36.104 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.999 21.546 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=-0.0106 ================= 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 : 0.2601 0.1962 0.082 5.272 8.8 119.3 19.9 258 0.000 1_bss: 0.1625 0.1782 0.082 5.272 9.0 119.5 20.1 258 0.000 1_settarget: 0.1625 0.1782 0.082 5.272 9.0 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1797 0.082 5.272 9.0 119.5 20.1 258 0.010 1_weight: 0.1636 0.1797 0.082 5.272 9.0 119.5 20.1 258 0.010 1_xyzrec: 0.1229 0.1470 0.006 0.874 9.0 119.5 20.1 258 0.134 1_adp: 0.1236 0.1467 0.006 0.874 9.0 119.4 20.1 258 0.134 1_regHadp: 0.1237 0.1469 0.006 0.874 9.0 119.4 20.1 258 0.134 1_occ: 0.1230 0.1461 0.006 0.874 9.0 119.4 20.1 258 0.134 2_bss: 0.1228 0.1454 0.006 0.874 9.1 119.5 20.1 258 0.134 2_settarget: 0.1228 0.1454 0.006 0.874 9.1 119.5 20.1 258 0.134 2_updatecdl: 0.1228 0.1454 0.006 0.894 9.1 119.5 20.1 258 0.134 2_nqh: 0.1229 0.1455 0.006 0.894 9.1 119.5 20.1 258 0.132 2_sol: 0.1202 0.1392 0.006 0.894 9.1 115.0 22.2 422 n/a 2_weight: 0.1202 0.1392 0.006 0.894 9.1 115.0 22.2 422 n/a 2_xyzrec: 0.1182 0.1404 0.008 0.922 9.1 115.0 22.2 422 n/a 2_adp: 0.1182 0.1404 0.008 0.922 9.1 115.0 22.2 422 n/a 2_regHadp: 0.1182 0.1404 0.008 0.922 9.1 115.0 22.2 422 n/a 2_occ: 0.1182 0.1399 0.008 0.922 9.1 115.0 22.2 422 n/a 3_bss: 0.1178 0.1396 0.008 0.922 9.1 115.0 22.2 422 n/a 3_settarget: 0.1178 0.1396 0.008 0.922 9.1 115.0 22.2 422 n/a 3_updatecdl: 0.1178 0.1396 0.008 0.924 9.1 115.0 22.2 422 n/a 3_nqh: 0.1178 0.1396 0.008 0.924 9.1 115.0 22.2 422 n/a 3_sol: 0.1200 0.1395 0.008 0.924 9.1 115.0 21.3 436 n/a 3_weight: 0.1200 0.1395 0.008 0.924 9.1 115.0 21.3 436 n/a 3_xyzrec: 0.1170 0.1324 0.004 0.848 9.1 115.0 21.3 436 n/a 3_adp: 0.1170 0.1324 0.004 0.848 9.1 115.0 21.3 436 n/a 3_regHadp: 0.1170 0.1324 0.004 0.848 9.1 115.0 21.3 436 n/a 3_occ: 0.1164 0.1320 0.004 0.848 9.1 115.0 21.3 436 n/a 4_bss: 0.1159 0.1320 0.004 0.848 9.1 115.0 21.3 436 n/a 4_settarget: 0.1159 0.1320 0.004 0.848 9.1 115.0 21.3 436 n/a 4_updatecdl: 0.1159 0.1320 0.004 0.847 9.1 115.0 21.3 436 n/a 4_nqh: 0.1159 0.1320 0.004 0.847 9.1 115.0 21.3 436 n/a 4_sol: 0.1158 0.1296 0.004 0.847 9.1 115.0 21.2 452 n/a 4_weight: 0.1158 0.1296 0.004 0.847 9.1 115.0 21.2 452 n/a 4_xyzrec: 0.1139 0.1297 0.007 1.064 9.1 115.0 21.2 452 n/a 4_adp: 0.1139 0.1297 0.007 1.064 9.1 115.0 21.2 452 n/a 4_regHadp: 0.1139 0.1297 0.007 1.064 9.1 115.0 21.2 452 n/a 4_occ: 0.1133 0.1294 0.007 1.064 9.1 115.0 21.2 452 n/a 5_bss: 0.1129 0.1297 0.007 1.064 9.1 115.0 21.2 452 n/a 5_settarget: 0.1129 0.1297 0.007 1.064 9.1 115.0 21.2 452 n/a 5_updatecdl: 0.1129 0.1297 0.007 1.067 9.1 115.0 21.2 452 n/a 5_setrh: 0.1130 0.1297 0.007 1.067 9.1 115.0 21.2 452 n/a 5_nqh: 0.1130 0.1297 0.007 1.067 9.1 115.0 21.2 452 n/a 5_sol: 0.1133 0.1309 0.007 1.067 9.1 115.0 21.3 461 n/a 5_weight: 0.1133 0.1309 0.007 1.067 9.1 115.0 21.3 461 n/a 5_xyzrec: 0.1131 0.1308 0.008 1.101 9.1 115.0 21.3 461 n/a 5_adp: 0.1131 0.1308 0.008 1.101 9.1 115.0 21.3 461 n/a 5_regHadp: 0.1131 0.1308 0.008 1.101 9.1 115.0 21.3 461 n/a 5_occ: 0.1126 0.1306 0.008 1.101 9.1 115.0 21.3 461 n/a end: 0.1124 0.1305 0.008 1.101 9.1 115.0 21.3 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9049096_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9049096_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6900 Refinement macro-cycles (run) : 14206.6700 Write final files (write_after_run_outputs) : 77.8400 Total : 14288.2000 Total CPU time: 3.98 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:18:27 PST -0800 (1735366707.72 s) Start R-work = 0.1625, R-free = 0.1782 Final R-work = 0.1124, R-free = 0.1305 =============================================================================== Job complete usr+sys time: 14435.81 seconds wall clock time: 262 minutes 4.71 seconds (15724.71 seconds total)