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_9171019.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.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" } 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 =============================================================================== 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: 1.19, per 1000 atoms: 0.35 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: 0.30 Conformation dependent library (CDL) restraints added in 173.9 milliseconds Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 574 0.93 - 1.20: 1102 1.20 - 1.46: 785 1.46 - 1.73: 677 1.73 - 2.00: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" CA BLYS A 93 " pdb=" C BLYS A 93 " ideal model delta sigma weight residual 1.524 1.760 -0.236 1.27e-02 6.20e+03 3.45e+02 bond pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta sigma weight residual 1.470 1.246 0.224 1.22e-02 6.72e+03 3.36e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.140 0.181 1.00e-02 1.00e+04 3.27e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.411 -0.175 9.90e-03 1.02e+04 3.12e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.31e-02 5.83e+03 2.97e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 3445 5.15 - 10.29: 1760 10.29 - 15.44: 505 15.44 - 20.58: 60 20.58 - 25.73: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 119.32 137.03 -17.71 1.19e+00 7.06e-01 2.21e+02 angle pdb=" O VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 121.91 107.67 14.24 9.80e-01 1.04e+00 2.11e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.20 137.97 -14.77 1.06e+00 8.90e-01 1.94e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 109.16 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C BCYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 119.85 133.37 -13.52 1.01e+00 9.80e-01 1.79e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.89: 938 17.89 - 35.77: 128 35.77 - 53.65: 33 53.65 - 71.53: 11 71.53 - 89.41: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 155.06 24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.192: 98 0.192 - 0.383: 67 0.383 - 0.573: 45 0.573 - 0.764: 23 0.764 - 0.954: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 3.48 -0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.55 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.113 2.00e-02 2.50e+03 6.52e-02 1.28e+02 pdb=" CG PHE A 119 " -0.179 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.071 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE A 164 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 95 " -0.043 2.00e-02 2.50e+03 9.32e-02 8.69e+01 pdb=" C GLN A 95 " 0.161 2.00e-02 2.50e+03 pdb=" O GLN A 95 " -0.060 2.00e-02 2.50e+03 pdb=" N AGLU A 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 841 2.29 - 2.87: 7976 2.87 - 3.44: 10512 3.44 - 4.02: 15324 4.02 - 4.60: 21971 Nonbonded interactions: 56624 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.712 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.765 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.795 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 1.850 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.855 1.850 ... (remaining 56619 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_9171019_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= 0.2611 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790705 | | target function (ml) not normalized (work): 232482.467318 | | target function (ml) not normalized (free): 11795.170184 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2106 7.0416 4.9513| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1781 4.3519 4.3346| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1752 4.1331 4.1646| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1433 3.8305 3.8236| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1552 3.7978 3.8101| | 6: 2.09 - 1.97 1.00 2846 113 0.2581 0.1808 3.473 3.5955| | 7: 1.97 - 1.87 1.00 2787 165 0.2557 0.1748 3.1298 3.1583| | 8: 1.87 - 1.79 1.00 2789 144 0.2545 0.1937 3.0713 3.1452| | 9: 1.79 - 1.72 1.00 2745 138 0.2389 0.1949 2.89 2.9624| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1997 2.8115 2.903| | 11: 1.66 - 1.61 1.00 2740 147 0.2493 0.1780 2.7495 2.7399| | 12: 1.61 - 1.56 1.00 2787 146 0.2541 0.2047 2.6375 2.6759| | 13: 1.56 - 1.52 1.00 2745 130 0.2524 0.1800 2.566 2.5474| | 14: 1.52 - 1.48 1.00 2803 134 0.2631 0.1846 2.5359 2.5143| | 15: 1.48 - 1.45 1.00 2738 128 0.2551 0.2147 2.411 2.4851| | 16: 1.45 - 1.42 1.00 2756 161 0.2636 0.2298 2.3795 2.4631| | 17: 1.42 - 1.39 1.00 2785 139 0.2690 0.2040 2.3324 2.3162| | 18: 1.39 - 1.36 1.00 2741 179 0.2685 0.1990 2.2668 2.244| | 19: 1.36 - 1.34 1.00 2807 134 0.2695 0.2313 2.2429 2.2502| | 20: 1.34 - 1.32 1.00 2696 147 0.2713 0.2259 2.1934 2.2088| | 21: 1.32 - 1.30 1.00 2785 112 0.2762 0.2320 2.1665 2.163| | 22: 1.29 - 1.27 1.00 2704 152 0.2772 0.2399 2.1311 2.19| | 23: 1.27 - 1.26 1.00 2802 156 0.2751 0.2352 2.1044 2.1419| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2925 2.0671 2.2806| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2432 2.0438 2.0371| | 26: 1.22 - 1.21 1.00 2727 135 0.2882 0.2360 2.0112 2.0887| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2684 2.016 2.0026| | 28: 1.19 - 1.18 1.00 2671 147 0.3005 0.2922 1.9941 2.0057| | 29: 1.18 - 1.16 1.00 2800 134 0.2944 0.2783 1.9583 2.0682| | 30: 1.16 - 1.15 1.00 2740 148 0.3056 0.2863 1.927 1.9774| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.85 0.76 0.23 1488.08| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1488.08| | 3: 2.84 - 2.48 2833 165 0.74 32.01 1.24 0.24 1233.36| | 4: 2.47 - 2.25 2825 136 0.81 25.61 1.25 0.25 572.32| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 572.32| | 6: 2.09 - 1.97 2846 113 0.83 22.57 1.30 0.25 312.06| | 7: 1.97 - 1.87 2787 165 0.90 16.45 1.29 0.26 90.09| | 8: 1.87 - 1.79 2789 144 0.86 20.97 1.26 0.26 90.09| | 9: 1.79 - 1.72 2745 138 0.88 18.66 1.23 0.26 55.50| | 10: 1.72 - 1.66 2789 158 0.87 20.08 1.22 0.26 48.57| | 11: 1.66 - 1.61 2740 147 0.85 21.45 1.24 0.25 46.79| | 12: 1.61 - 1.56 2787 146 0.89 18.15 1.24 0.25 28.68| | 13: 1.56 - 1.52 2745 130 0.87 19.84 1.23 0.25 28.68| | 14: 1.52 - 1.48 2803 134 0.87 20.07 1.23 0.25 25.47| | 15: 1.48 - 1.45 2738 128 0.88 19.56 1.23 0.25 19.59| | 16: 1.45 - 1.42 2756 161 0.86 20.84 1.23 0.25 19.59| | 17: 1.42 - 1.39 2785 139 0.87 20.05 1.23 0.25 16.52| | 18: 1.39 - 1.36 2741 179 0.87 20.28 1.24 0.25 14.75| | 19: 1.36 - 1.34 2807 134 0.86 21.16 1.22 0.25 14.75| | 20: 1.34 - 1.32 2696 147 0.87 20.50 1.22 0.25 12.52| | 21: 1.32 - 1.30 2785 112 0.86 21.65 1.21 0.25 12.36| | 22: 1.29 - 1.27 2704 152 0.86 21.91 1.22 0.25 12.15| | 23: 1.27 - 1.26 2802 156 0.86 22.06 1.21 0.24 11.08| | 24: 1.26 - 1.24 2744 132 0.85 22.66 1.20 0.24 11.08| | 25: 1.24 - 1.22 2734 148 0.84 24.25 1.21 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.83 24.76 1.20 0.23 10.27| | 27: 1.21 - 1.19 2814 148 0.83 25.24 1.20 0.23 10.27| | 28: 1.19 - 1.18 2671 147 0.82 26.29 1.19 0.22 9.82| | 29: 1.18 - 1.16 2800 134 0.81 26.91 1.17 0.22 9.65| | 30: 1.16 - 1.15 2740 148 0.79 28.63 1.16 0.22 9.65| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.65 max = 1488.08 mean = 215.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.57| |phase err.(test): min = 0.00 max = 89.40 mean = 22.45| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.236 1557 Z= 5.337 Angle : 5.264 22.096 2118 Z= 3.767 Chirality : 0.373 0.954 243 Planarity : 0.033 0.166 284 Dihedral : 13.785 89.406 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 26.49 % 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: -2.56 (0.49), residues: 224 helix: -2.67 (0.40), residues: 102 sheet: -0.50 (0.82), residues: 38 loop : -0.62 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.023 ARG A 28 TYR 0.090 0.032 TYR A 141 PHE 0.185 0.046 PHE A 119 HIS 0.090 0.040 HIS A 126 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= 0.2611 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790705 | | target function (ml) not normalized (work): 232482.467318 | | target function (ml) not normalized (free): 11795.170184 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2612 0.1949 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2612 0.1949 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1949 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2006 0.2011 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1649 0.1643 0.1764 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1643 0.1764 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 0.3916 386.423 357.323 0.671 1.002 0.407 11.894-9.307 99.02 97 4 0.1796 613.815 596.005 0.927 1.003 0.390 9.237-7.194 100.00 213 7 0.2132 502.025 493.398 0.953 1.003 0.349 7.162-5.571 100.00 427 22 0.2205 376.742 364.802 0.922 1.003 0.283 5.546-4.326 100.00 867 58 0.1286 517.173 511.067 0.967 1.003 0.214 4.315-3.360 100.00 1859 96 0.1169 491.835 487.601 1.002 1.002 0.153 3.356-2.611 100.00 3867 181 0.1434 323.110 319.835 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1356 214.193 212.115 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1657 104.601 104.028 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.384 45.023 1.002 0.997 0.000 1.221-1.150 99.97 13689 708 0.2574 29.225 26.997 0.977 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0431 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1654 r_free=0.1787 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.198002 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.986186 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 0.1707 0.1821 0.0114 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1575 0.1716 0.0141 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1463 0.1636 0.0173 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1386 0.1576 0.0190 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1361 0.1570 0.0209 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1345 0.1548 0.0203 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1292 0.1513 0.0221 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1278 0.1510 0.0232 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1259 0.1493 0.0234 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1254 0.1495 0.0241 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1238 0.1472 0.0234 0.004 0.8 2.9 0.5 0.0 0 6.000 0.1240 0.1481 0.0241 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1236 0.1475 0.0239 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1234 0.1477 0.0244 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1234 0.1478 0.0243 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1233 0.1476 0.0243 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1229 0.1472 0.0243 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1227 0.1476 0.0249 0.007 0.9 3.5 0.5 0.0 0 13.099 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1472 0.0234 0.004 0.8 2.9 0.5 0.0 0 6.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.72 2.34 3.013 19.047 2014.986 0.018 12.38 14.72 2.34 3.008 19.047 60.450 0.018 12.44 14.70 2.25 2.651 19.048 251.873 0.018 12.79 15.45 2.67 2.894 19.353 1007.493 0.017 12.51 15.38 2.88 3.021 19.460 2014.986 0.016 12.52 15.56 3.04 3.475 19.734 3022.479 0.016 12.45 15.53 3.08 3.459 19.708 4029.972 0.015 12.39 15.54 3.15 3.512 19.724 5037.465 0.015 12.33 15.51 3.18 3.285 19.596 6044.959 0.015 12.28 15.44 3.16 3.298 19.592 7052.452 0.015 12.26 15.48 3.22 3.523 19.713 8059.945 0.015 12.27 15.55 3.28 3.521 19.699 9067.438 0.015 12.27 15.57 3.30 3.613 19.735 10074.931 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: 251.873 Accepted refinement result: 12.44 14.70 2.25 2.651 19.048 251.873 0.018 Individual atomic B min max mean iso aniso Overall: 9.06 119.41 20.08 3.28 0 1785 Protein: 9.06 114.81 16.98 3.28 0 1519 Water: 11.44 119.41 38.21 N/A 0 258 Other: 19.72 26.60 22.06 N/A 0 8 Chain A: 9.06 119.41 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1270 20.10 - 31.13 229 31.13 - 42.17 125 42.17 - 53.20 94 53.20 - 64.24 42 64.24 - 75.27 11 75.27 - 86.31 7 86.31 - 97.34 4 97.34 - 108.38 1 108.38 - 119.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1470 r_work=0.1246 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1472 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1239 r_free = 0.1465 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1239 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017213 | | target function (ls_wunit_k1) not normalized (work): 1433.791339 | | target function (ls_wunit_k1) not normalized (free): 111.287099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1250 0.1239 0.1465 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1681 0.1682 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1681 0.1682 0.1692 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1687 0.1689 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1249 0.1238 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1248 0.1237 0.1458 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3580 301.514 281.582 0.644 1.003 0.380 11.894-9.307 99.02 97 4 0.1659 483.009 470.231 0.921 1.003 0.375 9.237-7.194 100.00 213 7 0.1912 395.042 388.112 0.961 1.004 0.360 7.162-5.571 100.00 427 22 0.1880 296.457 290.051 0.933 1.004 0.263 5.546-4.326 100.00 867 58 0.1029 406.962 403.608 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.0884 387.024 385.729 1.007 1.003 0.170 3.356-2.611 100.00 3867 181 0.1180 254.255 253.029 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1026 168.548 167.780 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1123 82.310 82.497 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1460 36.500 36.001 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2258 22.997 21.484 0.982 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0562 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1458 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1234 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1454 | n_water=258 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1247 r_free=0.1452 | n_water=251 | time (s): 22.600 (total time: 24.180) Filter (q & B) r_work=0.1250 r_free=0.1453 | n_water=248 | time (s): 3.210 (total time: 27.390) Compute maps r_work=0.1250 r_free=0.1453 | n_water=248 | time (s): 1.160 (total time: 28.550) Filter (map) r_work=0.1268 r_free=0.1454 | n_water=228 | time (s): 2.760 (total time: 31.310) Find peaks r_work=0.1268 r_free=0.1454 | n_water=228 | time (s): 0.470 (total time: 31.780) Add new water r_work=0.1413 r_free=0.1604 | n_water=438 | time (s): 2.480 (total time: 34.260) Refine new water occ: r_work=0.1320 r_free=0.1484 adp: r_work=0.1238 r_free=0.1420 occ: r_work=0.1251 r_free=0.1421 adp: r_work=0.1216 r_free=0.1399 occ: r_work=0.1219 r_free=0.1397 adp: r_work=0.1210 r_free=0.1392 ADP+occupancy (water only), MIN, final r_work=0.1210 r_free=0.1392 r_work=0.1210 r_free=0.1392 | n_water=438 | time (s): 53.830 (total time: 88.090) Filter (q & B) r_work=0.1213 r_free=0.1397 | n_water=422 | time (s): 3.190 (total time: 91.280) Filter (dist only) r_work=0.1214 r_free=0.1396 | n_water=421 | time (s): 34.510 (total time: 125.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.053816 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1503.465720 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 0.1695 0.1808 0.0113 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1577 0.1702 0.0125 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1381 0.1531 0.0149 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1360 0.1520 0.0159 0.001 0.4 5.1 0.0 0.0 0 0.750 0.1326 0.1496 0.0169 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1306 0.1470 0.0164 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1262 0.1454 0.0192 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1233 0.1435 0.0202 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1218 0.1422 0.0204 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1213 0.1421 0.0208 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1210 0.1417 0.0208 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1207 0.1414 0.0208 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1203 0.1417 0.0213 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1198 0.1412 0.0214 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1197 0.1413 0.0216 0.006 0.8 4.5 0.5 0.0 0 10.000 0.1195 0.1418 0.0223 0.006 0.9 5.1 0.5 0.0 0 11.000 0.1195 0.1421 0.0226 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1195 0.1424 0.0230 0.007 0.9 5.1 0.5 0.0 0 13.000 0.1194 0.1427 0.0234 0.008 0.9 5.4 0.5 0.0 0 14.027 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1412 0.0214 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 14.12 2.14 3.759 21.822 1503.466 0.016 11.98 14.12 2.14 3.759 21.822 45.104 0.016 11.98 14.12 2.14 3.759 21.822 187.933 0.016 12.21 14.63 2.42 3.598 21.839 751.733 0.016 12.13 14.82 2.69 3.521 21.906 1503.466 0.015 12.03 14.96 2.93 3.505 21.953 2255.199 0.015 11.91 14.83 2.91 3.453 22.218 3006.931 0.015 11.92 14.97 3.05 3.488 22.229 3758.664 0.014 11.84 14.99 3.15 3.499 22.071 4510.397 0.014 11.80 14.87 3.06 3.521 22.204 5262.130 0.014 11.78 14.91 3.13 3.535 22.177 6013.863 0.014 11.77 14.93 3.16 3.566 22.242 6765.596 0.014 11.75 14.90 3.15 3.604 22.318 7517.329 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: 45.104 Accepted refinement result: 11.98 14.12 2.14 3.759 21.822 45.104 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.84 22.27 3.28 193 1755 Protein: 9.10 114.84 17.02 3.28 0 1519 Water: 11.48 76.67 41.23 N/A 193 228 Other: 19.75 26.64 22.10 N/A 0 8 Chain A: 9.10 114.84 19.52 N/A 0 1755 Chain S: 12.64 60.00 47.31 N/A 193 0 Histogram: Values Number of atoms 9.10 - 19.67 1258 19.67 - 30.25 245 30.25 - 40.82 161 40.82 - 51.40 132 51.40 - 61.97 128 61.97 - 72.55 12 72.55 - 83.12 6 83.12 - 93.70 4 93.70 - 104.27 0 104.27 - 114.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1412 r_work=0.1198 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1412 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 = 0.1200 r_free = 0.1413 target_work(ls_wunit_k1) = 0.016 | | 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1413 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015681 | | target function (ls_wunit_k1) not normalized (work): 1306.132450 | | target function (ls_wunit_k1) not normalized (free): 102.655892 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1200 0.1413 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1594 0.1591 0.1660 n_refl.: 87592 remove outliers: r(all,work,free)=0.1594 0.1591 0.1660 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1595 0.1593 0.1661 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1196 0.1404 n_refl.: 87592 remove outliers: r(all,work,free)=0.1205 0.1195 0.1404 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 0.3319 297.417 275.145 0.586 1.002 0.350 11.894-9.307 99.02 97 4 0.1635 483.009 475.812 0.917 1.003 0.333 9.237-7.194 100.00 213 7 0.1782 395.042 393.488 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1645 296.457 292.328 0.933 1.003 0.236 5.546-4.326 100.00 867 58 0.0915 406.962 403.588 0.963 1.003 0.220 4.315-3.360 100.00 1859 96 0.0810 387.024 385.744 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1097 254.255 253.244 1.011 1.002 0.090 2.608-2.026 99.99 8198 413 0.1015 168.548 167.962 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.310 82.497 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1446 36.500 36.027 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2253 22.997 21.507 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0171 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1404 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1407 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1407 | n_water=421 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1196 r_free=0.1411 | n_water=419 | time (s): 35.550 (total time: 37.220) Filter (q & B) r_work=0.1196 r_free=0.1411 | n_water=419 | time (s): 1.290 (total time: 38.510) Compute maps r_work=0.1196 r_free=0.1411 | n_water=419 | time (s): 1.490 (total time: 40.000) Filter (map) r_work=0.1228 r_free=0.1399 | n_water=291 | time (s): 3.030 (total time: 43.030) Find peaks r_work=0.1228 r_free=0.1399 | n_water=291 | time (s): 0.550 (total time: 43.580) Add new water r_work=0.1337 r_free=0.1505 | n_water=467 | time (s): 3.030 (total time: 46.610) Refine new water occ: r_work=0.1254 r_free=0.1437 adp: r_work=0.1255 r_free=0.1437 occ: r_work=0.1234 r_free=0.1418 adp: r_work=0.1234 r_free=0.1418 occ: r_work=0.1219 r_free=0.1401 adp: r_work=0.1214 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1399 r_work=0.1214 r_free=0.1399 | n_water=467 | time (s): 172.060 (total time: 218.670) Filter (q & B) r_work=0.1218 r_free=0.1402 | n_water=434 | time (s): 2.550 (total time: 221.220) Filter (dist only) r_work=0.1218 r_free=0.1401 | n_water=432 | time (s): 35.710 (total time: 256.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.729757 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.944423 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 0.1242 0.1373 0.0131 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1199 0.1344 0.0144 0.003 0.7 3.2 0.5 0.0 0 0.259 0.1182 0.1334 0.0152 0.004 0.8 3.2 0.5 0.0 0 0.519 0.1175 0.1332 0.0157 0.005 0.9 3.2 0.5 0.0 0 0.778 0.1170 0.1330 0.0160 0.006 1.0 2.9 0.5 0.0 0 1.038 0.1167 0.1329 0.0163 0.006 1.0 3.2 0.5 0.0 0 1.297 0.1165 0.1327 0.0162 0.007 1.0 3.5 0.5 0.0 0 1.557 0.1163 0.1328 0.0165 0.008 1.1 3.5 0.5 0.0 0 1.816 0.1172 0.1330 0.0158 0.005 0.9 2.9 0.5 0.0 0 0.865 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1165 0.1327 0.0162 0.007 1.0 3.5 0.5 0.0 0 1.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 13.27 1.62 3.762 21.271 46.944 3.625 11.65 13.27 1.62 3.762 21.271 1.408 3.625 11.66 13.28 1.62 3.752 21.271 5.868 3.625 11.69 13.34 1.66 3.697 21.263 23.472 3.617 11.76 13.51 1.75 3.712 21.227 46.944 3.621 11.63 13.43 1.80 3.744 21.219 70.417 3.612 11.61 13.41 1.81 3.754 21.211 93.889 3.608 11.56 13.38 1.82 3.767 21.207 117.361 3.605 11.57 13.42 1.85 3.787 21.186 140.833 3.605 11.56 13.40 1.85 3.798 21.180 164.305 3.603 11.53 13.38 1.86 3.805 21.181 187.778 3.601 11.51 13.37 1.86 3.811 21.182 211.250 3.600 11.51 13.36 1.85 3.819 21.175 234.722 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.408 Accepted refinement result: 11.65 13.27 1.62 3.762 21.271 1.408 3.625 Individual atomic B min max mean iso aniso Overall: 9.11 114.86 21.26 3.28 205 1754 Protein: 9.11 114.86 17.03 3.28 0 1519 Water: 11.49 76.68 36.10 N/A 205 227 Other: 19.76 26.65 22.11 N/A 0 8 Chain A: 9.11 114.86 19.51 N/A 0 1754 Chain S: 12.65 60.01 36.16 N/A 205 0 Histogram: Values Number of atoms 9.11 - 19.69 1262 19.69 - 30.26 283 30.26 - 40.83 209 40.83 - 51.41 124 51.41 - 61.98 57 61.98 - 72.56 12 72.56 - 83.13 6 83.13 - 93.71 4 93.71 - 104.28 0 104.28 - 114.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1165 r_free=0.1327 r_work=0.1165 r_free=0.1327 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1165 r_free = 0.1327 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1317 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.18 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= 0.1154 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.617277 | | target function (ml) not normalized (work): 301293.826675 | | target function (ml) not normalized (free): 15857.925662 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1317 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1498 0.1496 0.1557 n_refl.: 87589 remove outliers: r(all,work,free)=0.1498 0.1496 0.1557 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1497 0.1495 0.1557 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1311 n_refl.: 87589 remove outliers: r(all,work,free)=0.1156 0.1148 0.1311 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3971 297.417 268.967 0.497 1.000 0.320 11.894-9.307 98.04 96 4 0.2494 483.134 461.393 0.866 1.002 0.320 9.237-7.194 98.64 210 7 0.2307 387.520 387.549 0.952 1.002 0.210 7.162-5.571 100.00 427 22 0.2191 296.457 284.733 0.913 1.002 0.200 5.546-4.326 100.00 867 58 0.1125 406.962 402.180 0.964 1.002 0.155 4.315-3.360 100.00 1859 96 0.0937 387.024 384.750 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1131 254.255 252.143 1.008 1.002 0.090 2.608-2.026 99.99 8198 413 0.0929 168.548 167.759 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0900 82.310 82.612 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.500 36.082 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2167 22.997 21.536 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0122 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1311 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=0.1152 r_free=0.1314 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1314 | n_water=432 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1154 r_free=0.1313 | n_water=430 | time (s): 43.460 (total time: 45.760) Filter (q & B) r_work=0.1155 r_free=0.1313 | n_water=426 | time (s): 3.760 (total time: 49.520) Compute maps r_work=0.1155 r_free=0.1313 | n_water=426 | time (s): 1.780 (total time: 51.300) Filter (map) r_work=0.1183 r_free=0.1304 | n_water=320 | time (s): 3.670 (total time: 54.970) Find peaks r_work=0.1183 r_free=0.1304 | n_water=320 | time (s): 0.670 (total time: 55.640) Add new water r_work=0.1255 r_free=0.1387 | n_water=476 | time (s): 3.680 (total time: 59.320) Refine new water occ: r_work=0.1182 r_free=0.1323 adp: r_work=0.1183 r_free=0.1325 occ: r_work=0.1168 r_free=0.1313 adp: r_work=0.1167 r_free=0.1314 occ: r_work=0.1156 r_free=0.1306 adp: r_work=0.1153 r_free=0.1305 ADP+occupancy (water only), MIN, final r_work=0.1153 r_free=0.1305 r_work=0.1153 r_free=0.1305 | n_water=476 | time (s): 323.130 (total time: 382.450) Filter (q & B) r_work=0.1158 r_free=0.1310 | n_water=447 | time (s): 3.850 (total time: 386.300) Filter (dist only) r_work=0.1158 r_free=0.1308 | n_water=446 | time (s): 45.580 (total time: 431.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.729015 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.456837 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 0.1220 0.1355 0.0135 0.002 0.6 4.2 0.5 0.0 0 0.086 0.1181 0.1326 0.0146 0.003 0.7 2.9 0.5 0.0 0 0.259 0.1168 0.1318 0.0150 0.004 0.9 3.2 0.5 0.0 0 0.519 0.1161 0.1314 0.0153 0.006 0.9 3.2 0.5 0.0 0 0.778 0.1158 0.1312 0.0154 0.006 1.0 2.9 0.5 0.0 0 1.037 0.1155 0.1311 0.0156 0.007 1.0 3.2 0.5 0.0 0 1.297 0.1153 0.1311 0.0158 0.008 1.1 3.5 0.5 0.0 0 1.556 0.1151 0.1310 0.0159 0.008 1.1 3.5 0.5 0.0 0 1.815 0.1160 0.1313 0.0153 0.006 1.0 3.2 0.5 0.0 0 0.865 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1310 0.0159 0.008 1.1 3.5 0.5 0.0 0 1.815 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.10 1.59 3.763 21.237 35.457 3.613 11.51 13.10 1.59 3.763 21.237 1.064 3.613 11.51 13.10 1.59 3.763 21.237 4.432 3.613 11.54 13.13 1.59 3.697 21.232 17.728 3.607 11.58 13.23 1.65 3.715 21.216 35.457 3.609 11.54 13.26 1.71 3.737 21.192 53.185 3.605 11.50 13.24 1.74 3.751 21.187 70.914 3.601 11.46 13.21 1.75 3.760 21.184 88.642 3.598 11.47 13.25 1.78 3.771 21.173 106.371 3.597 11.44 13.22 1.78 3.781 21.172 124.099 3.595 11.45 13.26 1.81 3.796 21.156 141.827 3.596 11.42 13.23 1.81 3.803 21.159 159.556 3.594 11.41 13.22 1.81 3.811 21.154 177.284 3.592 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.432 Accepted refinement result: 11.51 13.10 1.59 3.763 21.237 4.432 3.613 Individual atomic B min max mean iso aniso Overall: 9.11 114.85 21.20 3.28 221 1752 Protein: 9.11 114.85 17.03 3.28 0 1519 Water: 11.49 76.67 35.38 N/A 221 225 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.11 114.85 19.51 N/A 0 1752 Chain S: 12.65 60.01 34.61 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.68 1262 19.68 - 30.26 294 30.26 - 40.83 215 40.83 - 51.40 131 51.40 - 61.98 47 61.98 - 72.55 12 72.55 - 83.13 6 83.13 - 93.70 4 93.70 - 104.28 0 104.28 - 114.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1310 r_work=0.1151 r_free=0.1310 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1310 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1307 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1146 r_free= 0.1307 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.610243 | | target function (ml) not normalized (work): 300693.567865 | | target function (ml) not normalized (free): 15835.799850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1307 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1479 0.1478 0.1530 n_refl.: 87585 remove outliers: r(all,work,free)=0.1479 0.1478 0.1530 n_refl.: 87585 overall B=-0.00 to atoms: r(all,work,free)=0.1478 0.1477 0.1530 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1144 0.1309 n_refl.: 87585 remove outliers: r(all,work,free)=0.1149 0.1141 0.1309 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3919 296.777 255.068 0.462 1.000 0.308 11.894-9.307 95.10 93 4 0.2530 473.774 462.808 0.854 1.002 0.300 9.237-7.194 98.18 209 7 0.2454 386.513 379.621 0.922 1.002 0.190 7.162-5.571 100.00 427 22 0.2226 296.457 285.071 0.906 1.003 0.150 5.546-4.326 100.00 867 58 0.1139 406.962 401.845 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0942 387.024 384.766 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1114 254.255 252.332 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0919 168.548 167.852 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.310 82.634 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.500 36.088 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2171 22.997 21.528 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0102 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1141 r_free=0.1309 After: r_work=0.1143 r_free=0.1310 ================================== NQH flips ================================== r_work=0.1143 r_free=0.1310 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=0.1143 r_free=0.1310 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1310 | n_water=446 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1143 r_free=0.1310 | n_water=446 | time (s): 42.290 (total time: 44.680) Filter (q & B) r_work=0.1143 r_free=0.1310 | n_water=443 | time (s): 3.800 (total time: 48.480) Compute maps r_work=0.1143 r_free=0.1310 | n_water=443 | time (s): 1.810 (total time: 50.290) Filter (map) r_work=0.1167 r_free=0.1313 | n_water=343 | time (s): 3.860 (total time: 54.150) Find peaks r_work=0.1167 r_free=0.1313 | n_water=343 | time (s): 0.700 (total time: 54.850) Add new water r_work=0.1221 r_free=0.1381 | n_water=497 | time (s): 3.640 (total time: 58.490) Refine new water occ: r_work=0.1161 r_free=0.1313 adp: r_work=0.1161 r_free=0.1315 occ: r_work=0.1149 r_free=0.1301 adp: r_work=0.1149 r_free=0.1303 occ: r_work=0.1140 r_free=0.1288 adp: r_work=0.1137 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1290 r_work=0.1137 r_free=0.1290 | n_water=497 | time (s): 281.740 (total time: 340.230) Filter (q & B) r_work=0.1145 r_free=0.1300 | n_water=452 | time (s): 3.930 (total time: 344.160) Filter (dist only) r_work=0.1145 r_free=0.1298 | n_water=451 | time (s): 46.990 (total time: 391.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.798944 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.015311 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 0.1229 0.1352 0.0123 0.004 0.7 5.1 0.0 0.0 0 0.090 0.1175 0.1316 0.0141 0.004 0.8 4.2 0.0 0.0 0 0.270 0.1162 0.1307 0.0145 0.005 0.9 3.8 0.5 0.0 0 0.540 0.1152 0.1301 0.0149 0.006 1.0 3.5 0.5 0.0 0 0.810 0.1149 0.1299 0.0150 0.007 1.1 3.8 0.5 0.0 0 1.079 0.1147 0.1298 0.0151 0.008 1.1 3.8 0.5 0.0 0 1.349 0.1145 0.1298 0.0153 0.008 1.1 3.8 0.5 0.0 0 1.619 0.1145 0.1298 0.0153 0.008 1.1 3.8 0.5 0.0 0 1.889 0.1151 0.1300 0.0149 0.006 1.1 3.8 0.5 0.0 0 0.899 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1298 0.0151 0.008 1.1 3.8 0.5 0.0 0 1.349 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 12.98 1.51 3.763 21.246 38.015 3.609 11.47 12.98 1.51 3.763 21.246 1.140 3.609 11.47 12.98 1.51 3.763 21.246 4.752 3.609 11.50 13.01 1.51 3.696 21.241 19.008 3.604 11.51 13.08 1.57 3.717 21.224 38.015 3.604 11.51 13.15 1.63 3.738 21.197 57.023 3.603 11.43 13.09 1.66 3.753 21.197 76.031 3.596 11.40 13.06 1.66 3.763 21.194 95.038 3.594 11.39 13.05 1.67 3.773 21.188 114.046 3.591 11.37 13.06 1.69 3.782 21.187 133.054 3.590 11.38 13.09 1.72 3.799 21.173 152.061 3.590 11.38 13.11 1.73 3.812 21.167 171.069 3.590 11.35 13.06 1.71 3.815 21.167 190.077 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: 1.140 Accepted refinement result: 11.47 12.98 1.51 3.763 21.246 1.140 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 114.85 21.22 3.28 228 1750 Protein: 9.10 114.85 17.02 3.28 0 1519 Water: 11.48 76.67 35.32 N/A 228 223 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.10 114.85 19.46 N/A 0 1750 Chain S: 12.64 60.00 34.67 N/A 228 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.25 296 30.25 - 40.83 218 40.83 - 51.40 129 51.40 - 61.98 49 61.98 - 72.55 12 72.55 - 83.12 6 83.12 - 93.70 4 93.70 - 104.27 0 104.27 - 114.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1298 r_work=0.1147 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1298 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1295 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607532 | | target function (ml) not normalized (work): 300442.494042 | | target function (ml) not normalized (free): 15817.145491 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1372 0.1389 5.6658 5.6397| | 2: 3.57 - 2.84 1.00 2888 124 0.1083 0.1415 5.1811 5.239| | 3: 2.83 - 2.48 1.00 2820 163 0.1094 0.1204 4.959 4.9895| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.0982 4.6406 4.6688| | 5: 2.25 - 2.09 1.00 2756 127 0.0876 0.0920 4.5898 4.6262| | 6: 2.09 - 1.97 1.00 2846 113 0.0852 0.0970 4.2686 4.3392| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1115 3.9718 4.0866| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1088 3.8766 3.9783| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1201 3.639 3.8413| | 10: 1.72 - 1.66 1.00 2831 160 0.0926 0.1194 3.5637 3.7236| | 11: 1.66 - 1.61 1.00 2712 147 0.0877 0.0990 3.4963 3.5478| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1163 3.3349 3.4757| | 13: 1.56 - 1.52 1.00 2745 130 0.0951 0.1036 3.3076 3.3896| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1043 3.2397 3.3177| | 15: 1.48 - 1.45 1.00 2738 128 0.1012 0.1249 3.1571 3.2706| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1253 3.1384 3.237| | 17: 1.42 - 1.39 1.00 2785 139 0.1149 0.1309 3.1239 3.2368| | 18: 1.39 - 1.36 1.00 2741 179 0.1206 0.1336 3.1095 3.2426| | 19: 1.36 - 1.34 1.00 2807 134 0.1268 0.1548 3.1174 3.2605| | 20: 1.34 - 1.32 1.00 2696 147 0.1378 0.1451 3.117 3.153| | 21: 1.32 - 1.30 1.00 2785 112 0.1479 0.1499 3.1173 3.1011| | 22: 1.29 - 1.27 1.00 2704 152 0.1567 0.1984 3.126 3.2984| | 23: 1.27 - 1.26 1.00 2802 156 0.1656 0.1787 3.1374 3.2032| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1846 3.1289 3.2301| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2160 3.1443 3.2592| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1781 3.1504 3.2039| | 27: 1.21 - 1.19 1.00 2814 148 0.2081 0.2180 3.1742 3.1636| | 28: 1.19 - 1.18 1.00 2671 147 0.2206 0.2287 3.1679 3.174| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2389 3.1501 3.231| | 30: 1.16 - 1.15 1.00 2739 148 0.2451 0.2449 3.145 3.1678| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2920 171 0.95 8.90 1.00 0.97 6026.04| | 2: 3.57 - 2.84 2888 124 0.92 12.93 1.01 0.97 6026.04| | 3: 2.83 - 2.48 2820 163 0.89 16.85 0.99 0.97 5022.17| | 4: 2.47 - 2.25 2825 136 0.92 13.69 1.00 0.98 2433.51| | 5: 2.25 - 2.09 2756 127 0.90 15.91 1.01 0.98 2433.51| | 6: 2.09 - 1.97 2846 113 0.93 12.31 1.02 0.98 1384.81| | 7: 1.97 - 1.87 2787 165 0.95 9.04 1.02 0.98 490.42| | 8: 1.87 - 1.79 2789 144 0.93 12.32 1.00 0.98 490.42| | 9: 1.79 - 1.72 2745 138 0.94 9.93 0.98 0.98 282.80| | 10: 1.72 - 1.66 2831 160 0.94 11.01 0.98 0.97 241.22| | 11: 1.66 - 1.61 2712 147 0.94 11.60 0.98 0.97 231.18| | 12: 1.61 - 1.56 2773 144 0.95 8.88 0.99 0.97 136.52| | 13: 1.56 - 1.52 2745 130 0.95 10.33 1.03 0.97 136.52| | 14: 1.52 - 1.48 2803 134 0.94 10.71 1.02 0.98 122.72| | 15: 1.48 - 1.45 2738 128 0.95 9.88 1.02 0.98 97.44| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.98 97.44| | 17: 1.42 - 1.39 2785 139 0.95 10.88 1.01 0.98 88.95| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.98 84.03| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.98 84.03| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 80.09| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 79.81| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.25| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.94 82.47| | 24: 1.26 - 1.24 2744 132 0.92 14.89 0.96 0.94 82.47| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.47| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.69| | 27: 1.21 - 1.19 2814 148 0.89 18.82 1.02 0.93 86.69| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.93 90.43| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.92 91.84| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 91.84| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.81 max = 6026.04 mean = 917.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.47| |phase err.(test): min = 0.00 max = 89.96 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1143 0.1295 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1461 0.1459 0.1510 n_refl.: 87578 remove outliers: r(all,work,free)=0.1461 0.1459 0.1510 n_refl.: 87578 overall B=-0.00 to atoms: r(all,work,free)=0.1460 0.1459 0.1509 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1142 0.1298 n_refl.: 87578 remove outliers: r(all,work,free)=0.1149 0.1141 0.1298 n_refl.: 87576 ======================== 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 89.58 81 5 0.4094 296.777 255.653 0.477 1.000 0.350 11.894-9.307 93.14 91 4 0.2449 476.282 462.380 0.845 1.002 0.330 9.237-7.194 98.18 209 7 0.2425 386.513 379.583 0.920 1.002 0.155 7.162-5.571 100.00 427 22 0.2227 296.457 284.790 0.901 1.003 0.152 5.546-4.326 100.00 867 58 0.1148 406.962 401.655 0.962 1.003 0.104 4.315-3.360 100.00 1859 96 0.0940 387.024 384.478 1.002 1.002 0.087 3.356-2.611 100.00 3867 181 0.1116 254.255 252.482 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0912 168.548 167.897 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.310 82.633 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.500 36.092 1.028 0.996 0.000 1.221-1.150 99.97 13689 708 0.2171 22.997 21.533 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0096 ================= 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 : 0.2611 0.1950 0.079 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1764 0.079 5.264 9.0 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1764 0.079 5.264 9.0 119.5 20.1 258 0.000 1_nqh: 0.1654 0.1787 0.079 5.264 9.0 119.5 20.1 258 0.013 1_weight: 0.1654 0.1787 0.079 5.264 9.0 119.5 20.1 258 0.013 1_xyzrec: 0.1238 0.1472 0.004 0.761 9.0 119.5 20.1 258 0.136 1_adp: 0.1244 0.1470 0.004 0.761 9.1 119.4 20.1 258 0.136 1_regHadp: 0.1246 0.1472 0.004 0.761 9.1 119.4 20.1 258 0.136 1_occ: 0.1239 0.1465 0.004 0.761 9.1 119.4 20.1 258 0.136 2_bss: 0.1237 0.1458 0.004 0.761 9.1 119.5 20.1 258 0.136 2_settarget: 0.1237 0.1458 0.004 0.761 9.1 119.5 20.1 258 0.136 2_updatecdl: 0.1237 0.1458 0.004 0.780 9.1 119.5 20.1 258 0.136 2_nqh: 0.1234 0.1454 0.004 0.780 9.1 119.5 20.1 258 0.127 2_sol: 0.1214 0.1396 0.004 0.780 9.1 114.8 22.3 421 n/a 2_weight: 0.1214 0.1396 0.004 0.780 9.1 114.8 22.3 421 n/a 2_xyzrec: 0.1198 0.1412 0.006 0.817 9.1 114.8 22.3 421 n/a 2_adp: 0.1198 0.1412 0.006 0.817 9.1 114.8 22.3 421 n/a 2_regHadp: 0.1198 0.1412 0.006 0.817 9.1 114.8 22.3 421 n/a 2_occ: 0.1200 0.1413 0.006 0.817 9.1 114.8 22.3 421 n/a 3_bss: 0.1195 0.1404 0.006 0.817 9.1 114.9 22.3 421 n/a 3_settarget: 0.1195 0.1404 0.006 0.817 9.1 114.9 22.3 421 n/a 3_updatecdl: 0.1195 0.1404 0.006 0.819 9.1 114.9 22.3 421 n/a 3_nqh: 0.1196 0.1407 0.006 0.819 9.1 114.9 22.3 421 n/a 3_sol: 0.1218 0.1401 0.006 0.819 9.1 114.9 21.3 432 n/a 3_weight: 0.1218 0.1401 0.006 0.819 9.1 114.9 21.3 432 n/a 3_xyzrec: 0.1165 0.1327 0.007 1.048 9.1 114.9 21.3 432 n/a 3_adp: 0.1165 0.1327 0.007 1.048 9.1 114.9 21.3 432 n/a 3_regHadp: 0.1165 0.1327 0.007 1.048 9.1 114.9 21.3 432 n/a 3_occ: 0.1154 0.1317 0.007 1.048 9.1 114.9 21.3 432 n/a 4_bss: 0.1148 0.1311 0.007 1.048 9.1 114.9 21.3 432 n/a 4_settarget: 0.1148 0.1311 0.007 1.048 9.1 114.9 21.3 432 n/a 4_updatecdl: 0.1148 0.1311 0.007 1.050 9.1 114.9 21.3 432 n/a 4_nqh: 0.1152 0.1314 0.007 1.050 9.1 114.9 21.3 432 n/a 4_sol: 0.1158 0.1308 0.007 1.050 9.1 114.9 21.2 446 n/a 4_weight: 0.1158 0.1308 0.007 1.050 9.1 114.9 21.2 446 n/a 4_xyzrec: 0.1151 0.1310 0.008 1.111 9.1 114.9 21.2 446 n/a 4_adp: 0.1151 0.1310 0.008 1.111 9.1 114.9 21.2 446 n/a 4_regHadp: 0.1151 0.1310 0.008 1.111 9.1 114.9 21.2 446 n/a 4_occ: 0.1146 0.1307 0.008 1.111 9.1 114.9 21.2 446 n/a 5_bss: 0.1141 0.1309 0.008 1.111 9.1 114.8 21.2 446 n/a 5_settarget: 0.1141 0.1309 0.008 1.111 9.1 114.8 21.2 446 n/a 5_updatecdl: 0.1141 0.1309 0.008 1.112 9.1 114.8 21.2 446 n/a 5_setrh: 0.1143 0.1310 0.008 1.112 9.1 114.8 21.2 446 n/a 5_nqh: 0.1143 0.1310 0.008 1.112 9.1 114.8 21.2 446 n/a 5_sol: 0.1145 0.1298 0.008 1.112 9.1 114.8 21.2 451 n/a 5_weight: 0.1145 0.1298 0.008 1.112 9.1 114.8 21.2 451 n/a 5_xyzrec: 0.1147 0.1298 0.008 1.104 9.1 114.8 21.2 451 n/a 5_adp: 0.1147 0.1298 0.008 1.104 9.1 114.8 21.2 451 n/a 5_regHadp: 0.1147 0.1298 0.008 1.104 9.1 114.8 21.2 451 n/a 5_occ: 0.1143 0.1295 0.008 1.104 9.1 114.8 21.2 451 n/a end: 0.1141 0.1298 0.008 1.104 9.1 114.8 21.2 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9171019_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9171019_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8400 Refinement macro-cycles (run) : 13402.5500 Write final files (write_after_run_outputs) : 88.9600 Total : 13494.3500 Total CPU time: 3.76 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:03:34 PST -0800 (1735365814.91 s) Start R-work = 0.1643, R-free = 0.1764 Final R-work = 0.1141, R-free = 0.1298 =============================================================================== Job complete usr+sys time: 13662.07 seconds wall clock time: 247 minutes 46.45 seconds (14866.45 seconds total)