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_9451893.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_9451893.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.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 =============================================================================== Symmetric amino acids flipped. Time to flip 1 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: 1.47, per 1000 atoms: 0.43 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: 0.43 Conformation dependent library (CDL) restraints added in 107.0 milliseconds Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 494 0.91 - 1.17: 1146 1.17 - 1.43: 671 1.43 - 1.69: 816 1.69 - 1.95: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 1.236 1.511 -0.275 1.24e-02 6.50e+03 4.91e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.495 -0.260 1.28e-02 6.10e+03 4.13e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.241 1.054 0.188 9.80e-03 1.04e+04 3.67e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.24e-02 6.50e+03 3.56e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.430 -0.193 1.07e-02 8.73e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 3262 4.80 - 9.61: 1836 9.61 - 14.41: 578 14.41 - 19.21: 94 19.21 - 24.02: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 105.49 15.36 1.06e+00 8.90e-01 2.10e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N BCYS A 53 " ideal model delta sigma weight residual 123.26 138.41 -15.15 1.08e+00 8.57e-01 1.97e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 135.44 -13.53 9.80e-01 1.04e+00 1.91e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.26 137.20 -13.94 1.08e+00 8.57e-01 1.67e+02 angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 107.10 13.29 1.05e+00 9.07e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 921 15.68 - 31.35: 121 31.35 - 47.03: 45 47.03 - 62.71: 20 62.71 - 78.38: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 110 0.234 - 0.469: 74 0.469 - 0.703: 40 0.703 - 0.937: 16 0.937 - 1.171: 3 Chirality restraints: 243 Sorted by residual: 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 1.34 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA ARG A 5 " pdb=" N ARG A 5 " pdb=" C ARG A 5 " pdb=" CB ARG A 5 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.030 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.080 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.097 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.015 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.105 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.095 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 897 2.29 - 2.87: 7938 2.87 - 3.45: 10599 3.45 - 4.02: 15296 4.02 - 4.60: 21855 Nonbonded interactions: 56585 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.718 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.798 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.798 1.850 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.815 1.850 x-y,-y,-z-4/3 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.843 1.850 ... (remaining 56580 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_9451893_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= 0.2604 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.782134 | | target function (ml) not normalized (work): 231768.419287 | | target function (ml) not normalized (free): 11786.273580 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2152 6.9426 4.9635| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1858 4.363 4.3625| | 3: 2.84 - 2.48 1.00 2833 165 0.2369 0.1720 4.1425 4.1787| | 4: 2.47 - 2.25 1.00 2825 136 0.2299 0.1465 3.8424 3.8381| | 5: 2.25 - 2.09 1.00 2756 127 0.2475 0.1537 3.811 3.8357| | 6: 2.09 - 1.97 1.00 2846 113 0.2544 0.1862 3.474 3.6029| | 7: 1.97 - 1.87 1.00 2787 165 0.2544 0.1768 3.1235 3.1816| | 8: 1.87 - 1.79 1.00 2789 144 0.2523 0.1815 3.0619 3.1334| | 9: 1.79 - 1.72 1.00 2745 138 0.2398 0.1925 2.886 2.9555| | 10: 1.72 - 1.66 1.00 2789 158 0.2363 0.2083 2.7859 2.9225| | 11: 1.66 - 1.61 1.00 2740 147 0.2507 0.1687 2.7492 2.7433| | 12: 1.61 - 1.56 1.00 2787 146 0.2528 0.1973 2.6269 2.6211| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.1948 2.5625 2.5966| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.1811 2.5078 2.5474| | 15: 1.48 - 1.45 1.00 2738 128 0.2584 0.2006 2.4048 2.4784| | 16: 1.45 - 1.42 1.00 2756 161 0.2635 0.2222 2.3792 2.4689| | 17: 1.42 - 1.39 1.00 2785 139 0.2687 0.2188 2.3203 2.3747| | 18: 1.39 - 1.36 1.00 2741 179 0.2663 0.2087 2.2597 2.2581| | 19: 1.36 - 1.34 1.00 2807 134 0.2650 0.2337 2.2318 2.2797| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2171 2.1885 2.2243| | 21: 1.32 - 1.30 1.00 2785 112 0.2688 0.2270 2.1456 2.1807| | 22: 1.29 - 1.27 1.00 2704 152 0.2749 0.2482 2.126 2.149| | 23: 1.27 - 1.26 1.00 2802 156 0.2727 0.2258 2.0902 2.1152| | 24: 1.26 - 1.24 1.00 2744 132 0.2778 0.2370 2.0744 2.1416| | 25: 1.24 - 1.22 1.00 2734 148 0.2838 0.2648 2.0383 2.0853| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2292 2.0098 2.0568| | 27: 1.21 - 1.19 1.00 2814 148 0.2966 0.2387 1.9916 1.9524| | 28: 1.19 - 1.18 1.00 2671 147 0.2980 0.2649 1.9779 2.0012| | 29: 1.18 - 1.16 1.00 2800 134 0.3000 0.2613 1.9665 1.9897| | 30: 1.16 - 1.15 1.00 2740 148 0.3033 0.2839 1.9289 1.9451| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.86 19.35 0.76 0.23 1544.06| | 2: 3.57 - 2.84 2876 122 0.80 26.62 1.27 0.23 1544.06| | 3: 2.84 - 2.48 2833 165 0.73 32.67 1.25 0.23 1278.95| | 4: 2.47 - 2.25 2825 136 0.81 25.86 1.25 0.25 590.96| | 5: 2.25 - 2.09 2756 127 0.77 29.67 1.28 0.25 590.96| | 6: 2.09 - 1.97 2846 113 0.83 22.71 1.29 0.25 320.49| | 7: 1.97 - 1.87 2787 165 0.90 16.42 1.29 0.26 89.80| | 8: 1.87 - 1.79 2789 144 0.86 21.04 1.25 0.26 89.80| | 9: 1.79 - 1.72 2745 138 0.88 18.62 1.23 0.25 55.02| | 10: 1.72 - 1.66 2789 158 0.86 20.33 1.22 0.25 48.05| | 11: 1.66 - 1.61 2740 147 0.86 21.37 1.24 0.25 46.35| | 12: 1.61 - 1.56 2787 146 0.89 18.28 1.24 0.25 29.11| | 13: 1.56 - 1.52 2745 130 0.87 20.36 1.25 0.25 29.11| | 14: 1.52 - 1.48 2803 134 0.86 20.68 1.24 0.25 26.08| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.53| | 16: 1.45 - 1.42 2756 161 0.86 21.59 1.23 0.25 20.53| | 17: 1.42 - 1.39 2785 139 0.87 20.66 1.24 0.25 17.33| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.24 15.47| | 19: 1.36 - 1.34 2807 134 0.85 22.07 1.22 0.24 15.47| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.21 0.24 12.73| | 21: 1.32 - 1.30 2785 112 0.86 21.71 1.20 0.24 12.53| | 22: 1.29 - 1.27 2704 152 0.86 22.14 1.21 0.24 12.24| | 23: 1.27 - 1.26 2802 156 0.86 21.81 1.21 0.24 10.74| | 24: 1.26 - 1.24 2744 132 0.85 22.44 1.21 0.24 10.74| | 25: 1.24 - 1.22 2734 148 0.85 23.18 1.20 0.24 10.18| | 26: 1.22 - 1.21 2727 135 0.84 23.56 1.21 0.23 9.55| | 27: 1.21 - 1.19 2814 148 0.83 24.47 1.21 0.23 9.55| | 28: 1.19 - 1.18 2671 147 0.83 24.79 1.19 0.23 8.82| | 29: 1.18 - 1.16 2800 134 0.83 24.72 1.17 0.23 8.55| | 30: 1.16 - 1.15 2740 148 0.82 26.04 1.15 0.23 8.55| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.55 max = 1544.06 mean = 222.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.51| |phase err.(test): min = 0.00 max = 89.83 mean = 22.35| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.275 1557 Z= 5.352 Angle : 5.186 17.364 2118 Z= 3.623 Chirality : 0.393 1.171 243 Planarity : 0.028 0.076 284 Dihedral : 13.704 78.382 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 29.73 % 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: -2.64 (0.46), residues: 224 helix: -2.29 (0.38), residues: 108 sheet: -1.39 (0.93), residues: 30 loop : -0.79 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.018 ARG A 28 TYR 0.097 0.044 TYR A 139 PHE 0.113 0.031 PHE A 162 HIS 0.065 0.027 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2604 r_free= 0.1950 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.782134 | | target function (ml) not normalized (work): 231768.419287 | | target function (ml) not normalized (free): 11786.273580 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1951 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1951 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1975 0.1951 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.1995 0.1999 0.1962 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1624 0.1775 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1624 0.1775 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 0.3811 386.365 357.072 0.735 0.914 0.407 11.894-9.307 99.02 97 4 0.1762 613.721 594.215 1.010 0.915 0.390 9.237-7.194 100.00 213 7 0.2135 501.948 490.260 1.053 0.915 0.344 7.162-5.571 100.00 427 22 0.2168 376.684 365.208 1.028 0.916 0.330 5.546-4.326 100.00 867 58 0.1293 517.095 511.215 1.054 0.917 0.226 4.315-3.360 100.00 1859 96 0.1139 491.761 487.788 1.095 0.918 0.199 3.356-2.611 100.00 3867 181 0.1433 323.061 319.585 1.088 0.920 0.052 2.608-2.026 99.99 8198 413 0.1329 214.160 212.267 1.090 0.923 0.000 2.025-1.573 100.00 17313 902 0.1642 104.585 103.994 1.089 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.377 45.152 1.065 0.939 0.000 1.221-1.150 99.97 13689 708 0.2576 29.221 26.992 1.026 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0429 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1775 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 Total number of N/Q/H flips: 2 r_work=0.1631 r_free=0.1788 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.238519 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2010.039321 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 0.1706 0.1827 0.0121 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1571 0.1716 0.0145 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1444 0.1618 0.0173 0.001 0.4 3.8 0.0 0.0 0 0.500 0.1397 0.1592 0.0195 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1352 0.1558 0.0206 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1352 0.1557 0.0205 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1298 0.1518 0.0220 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1265 0.1490 0.0224 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1486 0.0231 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1246 0.1478 0.0232 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1476 0.0233 0.004 0.7 3.2 0.5 0.0 0 6.000 0.1236 0.1470 0.0234 0.005 0.8 3.2 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 0.1233 0.1474 0.0240 0.006 0.8 3.2 0.5 0.0 0 9.000 0.1230 0.1472 0.0242 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1228 0.1479 0.0250 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1475 0.0248 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1225 0.1476 0.0251 0.007 0.9 3.5 0.5 0.6 0 13.119 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1236 0.1470 0.0234 0.005 0.8 3.2 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.70 2.34 3.013 19.046 2010.039 0.018 12.36 14.69 2.33 2.989 19.046 60.301 0.018 12.43 14.68 2.25 2.656 19.046 251.255 0.018 12.86 15.50 2.64 3.066 19.446 1005.020 0.017 12.61 15.50 2.90 3.282 19.600 2010.039 0.016 12.32 15.12 2.80 2.714 19.200 3015.059 0.016 12.39 15.46 3.07 3.395 19.661 4020.079 0.015 12.41 15.52 3.10 3.475 19.682 5025.098 0.015 12.31 15.45 3.14 3.455 19.670 6030.118 0.015 12.33 15.51 3.18 3.522 19.694 7035.138 0.015 12.31 15.56 3.24 3.571 19.707 8040.157 0.015 12.31 15.58 3.27 3.635 19.731 9045.177 0.015 12.29 15.58 3.30 3.565 19.681 10050.197 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: 251.255 Accepted refinement result: 12.43 14.68 2.25 2.656 19.046 251.255 0.018 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.07 3.29 0 1785 Protein: 9.05 114.86 16.98 3.29 0 1519 Water: 11.43 119.42 38.21 N/A 0 258 Other: 19.71 26.60 22.06 N/A 0 8 Chain A: 9.05 119.42 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.08 1271 20.08 - 31.12 228 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 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=0.1243 r_free=0.1468 r_work=0.1244 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1471 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1238 r_free = 0.1464 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= 0.1238 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017090 | | target function (ls_wunit_k1) not normalized (work): 1423.560617 | | target function (ls_wunit_k1) not normalized (free): 109.903208 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1249 0.1238 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1678 0.1680 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1678 0.1680 0.1689 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1685 0.1687 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1247 0.1236 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1247 0.1236 0.1458 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 96.88 88 5 0.3520 304.201 283.473 0.665 1.003 0.395 11.894-9.307 99.02 97 4 0.1629 483.208 470.262 0.924 1.003 0.385 9.237-7.194 100.00 213 7 0.1892 395.204 389.757 0.965 1.003 0.319 7.162-5.571 100.00 427 22 0.1839 296.579 290.843 0.938 1.003 0.263 5.546-4.326 100.00 867 58 0.1010 407.130 404.161 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0881 387.183 386.073 1.008 1.003 0.190 3.356-2.611 100.00 3867 181 0.1182 254.359 253.177 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1032 168.617 167.849 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1124 82.344 82.522 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1460 36.515 36.012 1.019 0.996 0.000 1.221-1.150 99.97 13689 708 0.2257 23.007 21.487 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0563 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1458 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 Total number of N/Q/H flips: 2 r_work=0.1238 r_free=0.1460 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1460 | n_water=258 | time (s): 1.880 (total time: 1.880) Filter (dist) r_work=0.1244 r_free=0.1459 | n_water=251 | time (s): 20.650 (total time: 22.530) Filter (q & B) r_work=0.1247 r_free=0.1458 | n_water=248 | time (s): 3.430 (total time: 25.960) Compute maps r_work=0.1247 r_free=0.1458 | n_water=248 | time (s): 1.550 (total time: 27.510) Filter (map) r_work=0.1267 r_free=0.1466 | n_water=225 | time (s): 2.960 (total time: 30.470) Find peaks r_work=0.1267 r_free=0.1466 | n_water=225 | time (s): 0.690 (total time: 31.160) Add new water r_work=0.1420 r_free=0.1642 | n_water=429 | time (s): 3.260 (total time: 34.420) Refine new water occ: r_work=0.1321 r_free=0.1509 adp: r_work=0.1241 r_free=0.1453 occ: r_work=0.1254 r_free=0.1444 adp: r_work=0.1220 r_free=0.1425 occ: r_work=0.1222 r_free=0.1421 adp: r_work=0.1213 r_free=0.1414 ADP+occupancy (water only), MIN, final r_work=0.1213 r_free=0.1414 r_work=0.1213 r_free=0.1414 | n_water=429 | time (s): 52.640 (total time: 87.060) Filter (q & B) r_work=0.1215 r_free=0.1414 | n_water=420 | time (s): 3.200 (total time: 90.260) Filter (dist only) r_work=0.1216 r_free=0.1414 | n_water=419 | time (s): 37.230 (total time: 127.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.554965 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1489.310095 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 0.1672 0.1785 0.0113 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1539 0.1670 0.0132 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1427 0.1580 0.0153 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1347 0.1511 0.0165 0.001 0.5 6.1 0.0 0.0 0 0.750 0.1299 0.1483 0.0184 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1311 0.1486 0.0175 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1256 0.1455 0.0199 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1227 0.1431 0.0203 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1215 0.1423 0.0208 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1206 0.1424 0.0218 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1200 0.1414 0.0214 0.005 0.7 4.5 0.5 0.0 0 6.000 0.1195 0.1418 0.0223 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1193 0.1412 0.0219 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1193 0.1413 0.0220 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1192 0.1413 0.0221 0.006 0.8 4.5 0.5 0.0 0 10.000 0.1192 0.1414 0.0222 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1190 0.1416 0.0226 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1186 0.1406 0.0220 0.008 0.9 5.1 0.5 0.0 0 13.777 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1186 0.1406 0.0220 0.008 0.9 5.1 0.5 0.0 0 13.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.86 14.06 2.20 3.764 21.799 1489.310 0.016 11.86 14.06 2.20 3.764 21.799 44.679 0.016 11.86 14.06 2.20 3.764 21.799 186.164 0.016 12.00 14.41 2.41 3.631 21.799 744.655 0.015 11.99 14.76 2.77 3.475 21.952 1489.310 0.015 11.80 14.60 2.80 3.444 22.153 2233.965 0.014 11.77 14.69 2.92 3.458 22.174 2978.620 0.014 11.66 14.65 2.99 3.536 21.921 3723.275 0.014 11.69 14.64 2.95 3.489 22.175 4467.930 0.014 11.66 14.67 3.01 3.509 22.176 5212.585 0.014 11.63 14.65 3.02 3.517 22.107 5957.240 0.014 11.58 14.62 3.04 3.530 22.052 6701.895 0.014 11.59 14.68 3.08 3.559 22.181 7446.550 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: 44.679 Accepted refinement result: 11.86 14.06 2.20 3.764 21.799 44.679 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 114.90 22.23 3.29 194 1752 Protein: 9.08 114.90 17.02 3.29 0 1519 Water: 11.47 76.66 41.14 N/A 194 225 Other: 19.75 26.64 22.09 N/A 0 8 Chain A: 9.08 114.90 19.43 N/A 0 1752 Chain S: 16.88 60.00 47.52 N/A 194 0 Histogram: Values Number of atoms 9.08 - 19.66 1259 19.66 - 30.25 245 30.25 - 40.83 162 40.83 - 51.41 130 51.41 - 61.99 127 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1406 r_work=0.1186 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1406 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1400 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1400 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014889 | | target function (ls_wunit_k1) not normalized (work): 1240.190210 | | target function (ls_wunit_k1) not normalized (free): 97.380248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1183 0.1400 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1588 0.1590 0.1609 n_refl.: 87593 remove outliers: r(all,work,free)=0.1588 0.1590 0.1609 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1592 0.1610 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1181 0.1396 n_refl.: 87593 remove outliers: r(all,work,free)=0.1189 0.1179 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 0.3435 297.539 275.473 0.607 1.003 0.370 11.894-9.307 99.02 97 4 0.1536 483.208 476.216 0.918 1.003 0.319 9.237-7.194 100.00 213 7 0.1727 395.204 396.736 0.985 1.003 0.254 7.162-5.571 100.00 427 22 0.1620 296.579 291.575 0.939 1.003 0.230 5.546-4.326 100.00 867 58 0.0877 407.130 404.169 0.961 1.003 0.220 4.315-3.360 100.00 1859 96 0.0774 387.183 386.609 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1068 254.359 253.348 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.1006 168.617 168.123 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1096 82.344 82.576 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.515 36.044 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 23.007 21.509 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1179 r_free=0.1396 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=0.1179 r_free=0.1396 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1396 | n_water=419 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1179 r_free=0.1395 | n_water=414 | time (s): 35.720 (total time: 37.800) Filter (q & B) r_work=0.1180 r_free=0.1396 | n_water=413 | time (s): 3.390 (total time: 41.190) Compute maps r_work=0.1180 r_free=0.1396 | n_water=413 | time (s): 1.540 (total time: 42.730) Filter (map) r_work=0.1216 r_free=0.1397 | n_water=290 | time (s): 2.620 (total time: 45.350) Find peaks r_work=0.1216 r_free=0.1397 | n_water=290 | time (s): 0.440 (total time: 45.790) Add new water r_work=0.1336 r_free=0.1519 | n_water=481 | time (s): 2.510 (total time: 48.300) Refine new water occ: r_work=0.1245 r_free=0.1438 adp: r_work=0.1246 r_free=0.1439 occ: r_work=0.1222 r_free=0.1411 adp: r_work=0.1221 r_free=0.1413 occ: r_work=0.1204 r_free=0.1386 adp: r_work=0.1199 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1387 r_work=0.1199 r_free=0.1387 | n_water=481 | time (s): 148.370 (total time: 196.670) Filter (q & B) r_work=0.1204 r_free=0.1391 | n_water=448 | time (s): 2.890 (total time: 199.560) Filter (dist only) r_work=0.1204 r_free=0.1390 | n_water=447 | time (s): 38.020 (total time: 237.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.668176 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.377514 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 0.1231 0.1360 0.0128 0.002 0.6 4.2 0.5 0.0 0 0.083 0.1193 0.1331 0.0138 0.003 0.7 3.2 0.5 0.0 0 0.250 0.1174 0.1319 0.0145 0.004 0.8 2.9 0.5 0.0 0 0.500 0.1168 0.1321 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.751 0.1162 0.1320 0.0157 0.006 1.0 2.9 0.5 0.0 0 1.001 0.1159 0.1319 0.0160 0.006 1.0 3.2 0.5 0.0 0 1.251 0.1158 0.1321 0.0162 0.007 1.0 3.2 0.5 0.0 0 1.501 0.1156 0.1318 0.0162 0.008 1.1 3.2 0.5 0.0 0 1.752 0.1166 0.1320 0.0155 0.005 0.9 3.2 0.5 0.0 0 0.834 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1318 0.0162 0.008 1.1 3.2 0.5 0.0 0 1.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.18 1.62 3.767 21.337 43.378 3.619 11.56 13.18 1.62 3.767 21.337 1.301 3.619 11.56 13.18 1.62 3.757 21.337 5.422 3.618 11.58 13.23 1.65 3.701 21.330 21.689 3.611 11.66 13.38 1.72 3.714 21.297 43.378 3.615 11.54 13.31 1.77 3.746 21.288 65.066 3.607 11.50 13.28 1.78 3.758 21.282 86.755 3.602 11.48 13.29 1.81 3.769 21.274 108.444 3.599 11.46 13.30 1.84 3.783 21.266 130.133 3.598 11.45 13.31 1.86 3.798 21.258 151.821 3.597 11.44 13.29 1.86 3.807 21.251 173.510 3.595 11.41 13.25 1.84 3.811 21.249 195.199 3.593 11.40 13.27 1.86 3.820 21.248 216.888 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.301 Accepted refinement result: 11.56 13.18 1.62 3.767 21.337 1.301 3.619 Individual atomic B min max mean iso aniso Overall: 9.10 114.91 21.38 3.29 223 1751 Protein: 9.10 114.91 17.03 3.29 0 1519 Water: 11.48 76.67 36.13 N/A 223 224 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.10 114.91 19.43 N/A 0 1751 Chain S: 15.69 60.01 36.69 N/A 223 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 293 30.26 - 40.84 207 40.84 - 51.42 127 51.42 - 62.00 62 62.00 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1318 r_work=0.1156 r_free=0.1318 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1318 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1311 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1146 r_free= 0.1311 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611849 | | target function (ml) not normalized (work): 300841.730250 | | target function (ml) not normalized (free): 15838.370390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1311 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1492 0.1491 0.1535 n_refl.: 87589 remove outliers: r(all,work,free)=0.1492 0.1491 0.1535 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1492 0.1491 0.1535 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1307 n_refl.: 87589 remove outliers: r(all,work,free)=0.1147 0.1139 0.1307 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3934 297.539 266.549 0.498 0.999 0.330 11.894-9.307 95.10 93 4 0.2259 470.338 459.887 0.875 1.001 0.258 9.237-7.194 99.09 211 7 0.2245 389.697 387.898 0.958 1.001 0.188 7.162-5.571 100.00 427 22 0.2092 296.579 286.101 0.919 1.001 0.181 5.546-4.326 100.00 867 58 0.1092 407.130 402.954 0.966 1.001 0.177 4.315-3.360 100.00 1859 96 0.0924 387.183 384.458 1.004 1.001 0.160 3.356-2.611 100.00 3867 181 0.1132 254.359 252.319 1.007 1.001 0.043 2.608-2.026 99.99 8198 413 0.0929 168.617 167.922 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.344 82.650 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.515 36.093 1.024 1.001 0.000 1.221-1.150 99.97 13689 708 0.2167 23.007 21.467 0.981 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0028 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1307 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=0.1139 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1307 | n_water=447 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1138 r_free=0.1304 | n_water=445 | time (s): 46.220 (total time: 48.720) Filter (q & B) r_work=0.1139 r_free=0.1306 | n_water=443 | time (s): 3.970 (total time: 52.690) Compute maps r_work=0.1139 r_free=0.1306 | n_water=443 | time (s): 1.880 (total time: 54.570) Filter (map) r_work=0.1166 r_free=0.1315 | n_water=326 | time (s): 3.740 (total time: 58.310) Find peaks r_work=0.1166 r_free=0.1315 | n_water=326 | time (s): 0.680 (total time: 58.990) Add new water r_work=0.1235 r_free=0.1394 | n_water=489 | time (s): 3.660 (total time: 62.650) Refine new water occ: r_work=0.1168 r_free=0.1336 adp: r_work=0.1169 r_free=0.1339 occ: r_work=0.1152 r_free=0.1318 adp: r_work=0.1151 r_free=0.1320 occ: r_work=0.1139 r_free=0.1304 adp: r_work=0.1136 r_free=0.1304 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1304 r_work=0.1136 r_free=0.1304 | n_water=489 | time (s): 233.970 (total time: 296.620) Filter (q & B) r_work=0.1143 r_free=0.1315 | n_water=447 | time (s): 3.970 (total time: 300.590) Filter (dist only) r_work=0.1150 r_free=0.1312 | n_water=445 | time (s): 46.010 (total time: 346.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.792827 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.332536 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 0.1209 0.1343 0.0134 0.002 0.6 3.5 0.5 0.0 0 0.090 0.1178 0.1325 0.0147 0.003 0.7 2.9 0.5 0.0 0 0.269 0.1163 0.1319 0.0156 0.005 0.9 2.9 0.5 0.0 0 0.538 0.1157 0.1318 0.0161 0.006 0.9 2.9 0.5 0.0 0 0.807 0.1154 0.1319 0.0165 0.006 1.0 2.6 0.5 0.0 0 1.076 0.1151 0.1318 0.0167 0.007 1.0 2.6 0.5 0.0 0 1.345 0.1149 0.1316 0.0167 0.008 1.1 2.6 0.5 0.0 0 1.614 0.1147 0.1317 0.0170 0.009 1.1 2.6 0.5 0.0 0 1.882 0.1156 0.1318 0.0162 0.006 1.0 2.9 0.5 0.0 0 0.896 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1149 0.1316 0.0167 0.008 1.1 2.6 0.5 0.0 0 1.614 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.49 13.16 1.67 3.768 21.247 39.333 3.613 11.49 13.16 1.67 3.768 21.247 1.180 3.613 11.49 13.16 1.67 3.768 21.247 4.917 3.613 11.51 13.18 1.67 3.702 21.242 19.666 3.607 11.61 13.34 1.73 3.718 21.212 39.333 3.613 11.52 13.30 1.78 3.743 21.200 58.999 3.607 11.46 13.28 1.81 3.757 21.194 78.665 3.601 11.45 13.29 1.83 3.768 21.191 98.331 3.599 11.40 13.23 1.84 3.775 21.193 117.998 3.595 11.41 13.30 1.89 3.793 21.177 137.664 3.595 11.41 13.30 1.89 3.804 21.169 157.330 3.595 11.39 13.28 1.89 3.813 21.169 176.996 3.593 11.37 13.27 1.89 3.819 21.168 196.663 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: 1.180 Accepted refinement result: 11.49 13.16 1.67 3.768 21.247 1.180 3.613 Individual atomic B min max mean iso aniso Overall: 9.09 114.91 21.21 3.29 224 1748 Protein: 9.09 114.91 17.03 3.29 0 1519 Water: 11.48 76.67 35.47 N/A 224 221 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.09 114.91 19.38 N/A 0 1748 Chain S: 16.37 60.01 35.48 N/A 224 0 Histogram: Values Number of atoms 9.09 - 19.68 1261 19.68 - 30.26 296 30.26 - 40.84 212 40.84 - 51.42 130 51.42 - 62.00 50 62.00 - 72.58 11 72.58 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1316 r_work=0.1149 r_free=0.1316 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1316 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1312 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1145 r_free= 0.1312 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.610989 | | target function (ml) not normalized (work): 300748.450019 | | target function (ml) not normalized (free): 15831.933861 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1145 0.1312 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1486 0.1485 0.1527 n_refl.: 87583 remove outliers: r(all,work,free)=0.1486 0.1485 0.1527 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1485 0.1484 0.1527 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1144 0.1314 n_refl.: 87583 remove outliers: r(all,work,free)=0.1149 0.1140 0.1314 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 88.54 80 5 0.4076 286.126 249.332 0.451 0.999 0.320 11.894-9.307 94.12 92 4 0.2433 472.247 450.798 0.839 1.001 0.238 9.237-7.194 98.18 209 7 0.2340 391.894 380.440 0.930 1.002 0.160 7.162-5.571 100.00 427 22 0.2205 296.579 285.014 0.906 1.002 0.155 5.546-4.326 100.00 867 58 0.1134 407.130 402.555 0.967 1.003 0.150 4.315-3.360 100.00 1859 96 0.0927 387.183 385.078 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1129 254.359 252.698 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0919 168.617 168.005 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.344 82.712 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.515 36.119 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2174 23.007 21.546 0.990 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0090 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1140 r_free=0.1314 After: r_work=0.1142 r_free=0.1315 ================================== NQH flips ================================== r_work=0.1142 r_free=0.1315 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=0.1142 r_free=0.1315 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1315 | n_water=445 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1142 r_free=0.1315 | n_water=445 | time (s): 42.190 (total time: 44.660) Filter (q & B) r_work=0.1142 r_free=0.1314 | n_water=444 | time (s): 3.980 (total time: 48.640) Compute maps r_work=0.1142 r_free=0.1314 | n_water=444 | time (s): 1.910 (total time: 50.550) Filter (map) r_work=0.1164 r_free=0.1317 | n_water=354 | time (s): 3.880 (total time: 54.430) Find peaks r_work=0.1164 r_free=0.1317 | n_water=354 | time (s): 0.690 (total time: 55.120) Add new water r_work=0.1211 r_free=0.1367 | n_water=499 | time (s): 3.750 (total time: 58.870) Refine new water occ: r_work=0.1156 r_free=0.1316 adp: r_work=0.1156 r_free=0.1318 occ: r_work=0.1146 r_free=0.1307 adp: r_work=0.1145 r_free=0.1308 occ: r_work=0.1140 r_free=0.1301 adp: r_work=0.1136 r_free=0.1301 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1301 r_work=0.1136 r_free=0.1301 | n_water=499 | time (s): 245.360 (total time: 304.230) Filter (q & B) r_work=0.1145 r_free=0.1314 | n_water=452 | time (s): 3.930 (total time: 308.160) Filter (dist only) r_work=0.1146 r_free=0.1313 | n_water=451 | time (s): 47.790 (total time: 355.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.778977 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.086337 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 0.1225 0.1358 0.0133 0.004 0.7 5.1 0.0 0.0 0 0.089 0.1179 0.1329 0.0150 0.004 0.8 4.8 0.0 0.0 0 0.267 0.1166 0.1321 0.0155 0.005 0.9 4.5 0.5 0.0 0 0.534 0.1156 0.1316 0.0160 0.006 1.0 4.5 0.5 0.0 0 0.801 0.1150 0.1313 0.0163 0.007 1.1 4.2 0.5 0.0 0 1.067 0.1147 0.1313 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.334 0.1146 0.1313 0.0167 0.008 1.1 3.8 0.5 0.0 0 1.601 0.1145 0.1313 0.0168 0.008 1.1 3.8 0.5 0.0 0 1.868 0.1154 0.1315 0.0161 0.006 1.0 4.2 0.5 0.0 0 0.889 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1313 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.334 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 13.13 1.66 3.768 21.219 44.086 3.611 11.47 13.13 1.66 3.768 21.219 1.323 3.611 11.47 13.13 1.66 3.761 21.219 5.511 3.611 11.48 13.16 1.67 3.704 21.213 22.043 3.605 11.54 13.31 1.77 3.730 21.181 44.086 3.608 11.46 13.28 1.81 3.752 21.171 66.130 3.602 11.41 13.24 1.83 3.766 21.169 88.173 3.597 11.38 13.22 1.84 3.774 21.168 110.216 3.594 11.36 13.22 1.86 3.786 21.164 132.259 3.593 11.36 13.25 1.89 3.802 21.155 154.302 3.592 11.36 13.26 1.90 3.816 21.148 176.345 3.592 11.34 13.26 1.91 3.823 21.147 198.389 3.590 11.33 13.25 1.91 3.828 21.148 220.432 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.323 Accepted refinement result: 11.47 13.13 1.66 3.768 21.219 1.323 3.611 Individual atomic B min max mean iso aniso Overall: 9.09 114.91 21.17 3.29 230 1748 Protein: 9.09 114.91 17.03 3.29 0 1519 Water: 11.47 76.67 35.09 N/A 230 221 Other: 19.75 26.65 22.10 N/A 0 8 Chain A: 9.09 114.91 19.38 N/A 0 1748 Chain S: 15.72 60.01 34.73 N/A 230 0 Histogram: Values Number of atoms 9.09 - 19.67 1261 19.67 - 30.25 304 30.25 - 40.84 211 40.84 - 51.42 134 51.42 - 62.00 45 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1313 r_work=0.1147 r_free=0.1313 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1313 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1310 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1144 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.610070 | | target function (ml) not normalized (work): 300646.631579 | | target function (ml) not normalized (free): 15832.594704 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1365 0.1397 5.6681 5.6277| | 2: 3.57 - 2.84 1.00 2888 124 0.1079 0.1466 5.185 5.2596| | 3: 2.83 - 2.48 1.00 2820 163 0.1121 0.1229 4.9688 4.9971| | 4: 2.47 - 2.25 1.00 2825 136 0.0907 0.1029 4.6468 4.6869| | 5: 2.25 - 2.09 1.00 2756 127 0.0876 0.0919 4.5954 4.6379| | 6: 2.09 - 1.97 1.00 2846 113 0.0861 0.0996 4.274 4.3639| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1075 3.9717 4.0701| | 8: 1.87 - 1.79 1.00 2789 144 0.0910 0.1107 3.8818 3.9756| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1203 3.6454 3.8349| | 10: 1.72 - 1.66 1.00 2831 160 0.0923 0.1228 3.5667 3.7361| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1041 3.4978 3.5728| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1176 3.3361 3.4751| | 13: 1.56 - 1.52 1.00 2745 130 0.0943 0.1058 3.3104 3.4167| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1026 3.2469 3.3107| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1243 3.1583 3.2718| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1248 3.14 3.241| | 17: 1.42 - 1.39 1.00 2785 139 0.1148 0.1316 3.1256 3.2432| | 18: 1.39 - 1.36 1.00 2741 179 0.1204 0.1320 3.1104 3.239| | 19: 1.36 - 1.34 1.00 2807 134 0.1265 0.1559 3.1179 3.264| | 20: 1.34 - 1.32 1.00 2696 147 0.1378 0.1444 3.1173 3.1517| | 21: 1.32 - 1.30 1.00 2785 112 0.1478 0.1537 3.1178 3.1181| | 22: 1.29 - 1.27 1.00 2704 152 0.1572 0.1995 3.1286 3.3001| | 23: 1.27 - 1.26 1.00 2802 156 0.1654 0.1795 3.1375 3.2021| | 24: 1.26 - 1.24 1.00 2744 132 0.1715 0.1826 3.1301 3.2241| | 25: 1.24 - 1.22 1.00 2733 148 0.1893 0.2154 3.1474 3.2584| | 26: 1.22 - 1.21 1.00 2727 135 0.1914 0.1774 3.1514 3.2016| | 27: 1.21 - 1.19 1.00 2814 148 0.2082 0.2186 3.1741 3.1659| | 28: 1.19 - 1.18 1.00 2671 147 0.2208 0.2301 3.1687 3.1747| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2393 3.1503 3.2299| | 30: 1.16 - 1.15 1.00 2739 148 0.2457 0.2466 3.1461 3.1705| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.92 1.00 0.97 6107.70| | 2: 3.57 - 2.84 2888 124 0.92 12.97 1.01 0.97 6107.70| | 3: 2.83 - 2.48 2820 163 0.89 16.91 0.99 0.97 5090.63| | 4: 2.47 - 2.25 2825 136 0.92 13.78 1.00 0.98 2467.93| | 5: 2.25 - 2.09 2756 127 0.90 16.01 1.01 0.98 2467.93| | 6: 2.09 - 1.97 2846 113 0.92 12.43 1.02 0.98 1405.62| | 7: 1.97 - 1.87 2787 165 0.95 9.19 1.02 0.98 499.61| | 8: 1.87 - 1.79 2789 144 0.93 12.42 1.00 0.98 499.61| | 9: 1.79 - 1.72 2745 138 0.94 10.03 0.98 0.98 287.85| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.98 245.44| | 11: 1.66 - 1.61 2712 147 0.93 11.75 0.98 0.98 235.31| | 12: 1.61 - 1.56 2773 144 0.95 8.97 0.99 0.97 139.75| | 13: 1.56 - 1.52 2745 130 0.95 10.52 1.02 0.97 139.75| | 14: 1.52 - 1.48 2803 134 0.94 10.87 1.02 0.98 125.31| | 15: 1.48 - 1.45 2738 128 0.95 10.00 1.02 0.99 98.87| | 16: 1.45 - 1.42 2756 161 0.94 11.15 1.02 0.99 98.87| | 17: 1.42 - 1.39 2785 139 0.95 10.99 1.01 0.99 89.96| | 18: 1.39 - 1.36 2741 179 0.94 11.60 1.01 0.98 84.81| | 19: 1.36 - 1.34 2807 134 0.94 11.93 0.99 0.98 84.81| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.97 80.48| | 21: 1.32 - 1.30 2785 112 0.94 13.13 0.98 0.97 80.18| | 22: 1.29 - 1.27 2704 152 0.93 13.69 0.98 0.96 80.59| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.95 82.67| | 24: 1.26 - 1.24 2744 132 0.92 14.90 0.96 0.95 82.67| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.66| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.02 0.93 86.86| | 27: 1.21 - 1.19 2814 148 0.89 18.85 1.02 0.93 86.86| | 28: 1.19 - 1.18 2671 147 0.88 20.50 1.01 0.93 90.70| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.92 92.14| | 30: 1.16 - 1.15 2739 148 0.86 22.14 0.98 0.92 92.14| |alpha: min = 0.92 max = 0.99 mean = 0.97| |beta: min = 80.18 max = 6107.70 mean = 930.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.55| |phase err.(test): min = 0.00 max = 89.35 mean = 13.57| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1310 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1462 0.1461 0.1506 n_refl.: 87576 remove outliers: r(all,work,free)=0.1462 0.1461 0.1506 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1461 0.1460 0.1505 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1144 0.1308 n_refl.: 87576 remove outliers: r(all,work,free)=0.1151 0.1143 0.1308 n_refl.: 87573 ======================== 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 0.4226 286.126 247.087 0.427 0.999 0.287 11.894-9.307 93.14 91 4 0.2580 468.377 452.321 0.842 1.001 0.225 9.237-7.194 97.27 207 7 0.2363 388.862 381.485 0.934 1.002 0.157 7.162-5.571 100.00 427 22 0.2171 296.579 285.019 0.903 1.002 0.133 5.546-4.326 100.00 867 58 0.1151 407.130 402.053 0.966 1.002 0.115 4.315-3.360 100.00 1859 96 0.0932 387.183 384.994 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1131 254.359 252.403 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0918 168.617 167.909 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.344 82.663 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.515 36.105 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 23.007 21.541 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=-0.0126 ================= 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 : 0.2604 0.1950 0.081 5.186 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1775 0.081 5.186 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1775 0.081 5.186 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1788 0.081 5.186 9.0 119.5 20.1 258 0.007 1_weight: 0.1631 0.1788 0.081 5.186 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1236 0.1470 0.005 0.784 9.0 119.5 20.1 258 0.137 1_adp: 0.1243 0.1468 0.005 0.784 9.0 119.4 20.1 258 0.137 1_regHadp: 0.1244 0.1471 0.005 0.784 9.0 119.4 20.1 258 0.137 1_occ: 0.1238 0.1464 0.005 0.784 9.0 119.4 20.1 258 0.137 2_bss: 0.1236 0.1458 0.005 0.784 9.1 119.5 20.1 258 0.137 2_settarget: 0.1236 0.1458 0.005 0.784 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1236 0.1458 0.005 0.797 9.1 119.5 20.1 258 0.137 2_nqh: 0.1238 0.1460 0.005 0.797 9.1 119.5 20.1 258 0.137 2_sol: 0.1216 0.1414 0.005 0.797 9.1 114.9 22.2 419 n/a 2_weight: 0.1216 0.1414 0.005 0.797 9.1 114.9 22.2 419 n/a 2_xyzrec: 0.1186 0.1406 0.008 0.925 9.1 114.9 22.2 419 n/a 2_adp: 0.1186 0.1406 0.008 0.925 9.1 114.9 22.2 419 n/a 2_regHadp: 0.1186 0.1406 0.008 0.925 9.1 114.9 22.2 419 n/a 2_occ: 0.1183 0.1400 0.008 0.925 9.1 114.9 22.2 419 n/a 3_bss: 0.1179 0.1396 0.008 0.925 9.1 114.9 22.2 419 n/a 3_settarget: 0.1179 0.1396 0.008 0.925 9.1 114.9 22.2 419 n/a 3_updatecdl: 0.1179 0.1396 0.008 0.927 9.1 114.9 22.2 419 n/a 3_nqh: 0.1179 0.1396 0.008 0.927 9.1 114.9 22.2 419 n/a 3_sol: 0.1204 0.1390 0.008 0.927 9.1 114.9 21.4 447 n/a 3_weight: 0.1204 0.1390 0.008 0.927 9.1 114.9 21.4 447 n/a 3_xyzrec: 0.1156 0.1318 0.008 1.075 9.1 114.9 21.4 447 n/a 3_adp: 0.1156 0.1318 0.008 1.075 9.1 114.9 21.4 447 n/a 3_regHadp: 0.1156 0.1318 0.008 1.075 9.1 114.9 21.4 447 n/a 3_occ: 0.1146 0.1311 0.008 1.075 9.1 114.9 21.4 447 n/a 4_bss: 0.1139 0.1307 0.008 1.075 9.1 114.9 21.4 447 n/a 4_settarget: 0.1139 0.1307 0.008 1.075 9.1 114.9 21.4 447 n/a 4_updatecdl: 0.1139 0.1307 0.008 1.075 9.1 114.9 21.4 447 n/a 4_nqh: 0.1139 0.1307 0.008 1.075 9.1 114.9 21.4 447 n/a 4_sol: 0.1150 0.1312 0.008 1.075 9.1 114.9 21.2 445 n/a 4_weight: 0.1150 0.1312 0.008 1.075 9.1 114.9 21.2 445 n/a 4_xyzrec: 0.1149 0.1316 0.008 1.086 9.1 114.9 21.2 445 n/a 4_adp: 0.1149 0.1316 0.008 1.086 9.1 114.9 21.2 445 n/a 4_regHadp: 0.1149 0.1316 0.008 1.086 9.1 114.9 21.2 445 n/a 4_occ: 0.1145 0.1312 0.008 1.086 9.1 114.9 21.2 445 n/a 5_bss: 0.1140 0.1314 0.008 1.086 9.1 114.9 21.2 445 n/a 5_settarget: 0.1140 0.1314 0.008 1.086 9.1 114.9 21.2 445 n/a 5_updatecdl: 0.1140 0.1314 0.008 1.087 9.1 114.9 21.2 445 n/a 5_setrh: 0.1142 0.1315 0.008 1.087 9.1 114.9 21.2 445 n/a 5_nqh: 0.1142 0.1315 0.008 1.087 9.1 114.9 21.2 445 n/a 5_sol: 0.1146 0.1313 0.008 1.087 9.1 114.9 21.2 451 n/a 5_weight: 0.1146 0.1313 0.008 1.087 9.1 114.9 21.2 451 n/a 5_xyzrec: 0.1147 0.1313 0.008 1.085 9.1 114.9 21.2 451 n/a 5_adp: 0.1147 0.1313 0.008 1.085 9.1 114.9 21.2 451 n/a 5_regHadp: 0.1147 0.1313 0.008 1.085 9.1 114.9 21.2 451 n/a 5_occ: 0.1144 0.1310 0.008 1.085 9.1 114.9 21.2 451 n/a end: 0.1143 0.1308 0.008 1.085 9.1 114.9 21.2 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9451893_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9451893_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.4400 Refinement macro-cycles (run) : 14122.2900 Write final files (write_after_run_outputs) : 77.5100 Total : 14203.2400 Total CPU time: 3.95 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:16:49 PST -0800 (1735366609.82 s) Start R-work = 0.1624, R-free = 0.1775 Final R-work = 0.1143, R-free = 0.1308 =============================================================================== Job complete usr+sys time: 14352.70 seconds wall clock time: 260 minutes 28.23 seconds (15628.23 seconds total)