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_4023827.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.35, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 179.9 milliseconds Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 502 0.91 - 1.16: 1128 1.16 - 1.41: 621 1.41 - 1.66: 847 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.10e-02 8.26e+03 3.83e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.531 -0.201 1.13e-02 7.83e+03 3.18e+02 bond pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 1.237 1.443 -0.207 1.16e-02 7.43e+03 3.17e+02 bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.446 1.598 -0.151 8.70e-03 1.32e+04 3.02e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.662 -0.201 1.17e-02 7.31e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 3028 4.41 - 8.81: 1860 8.81 - 13.22: 705 13.22 - 17.62: 166 17.62 - 22.03: 18 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 113.50 132.47 -18.97 1.23e+00 6.61e-01 2.38e+02 angle pdb=" O BGLU A 90 " pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" CA MET A 134 " pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 119.28 134.81 -15.53 1.21e+00 6.83e-01 1.65e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.15 136.24 -14.09 1.14e+00 7.69e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.43: 940 17.43 - 34.86: 122 34.86 - 52.28: 30 52.28 - 69.71: 15 69.71 - 87.14: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.235: 122 0.235 - 0.465: 71 0.465 - 0.695: 36 0.695 - 0.925: 12 0.925 - 1.155: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.67 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.45 -0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.012 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG BTYR A 67 " -0.037 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.117 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.094 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.108 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.066 2.00e-02 2.50e+03 6.94e-02 1.09e+02 pdb=" CG HIS A 126 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.097 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.044 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.022 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.139 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1259 2.35 - 2.91: 8260 2.91 - 3.48: 10522 3.48 - 4.04: 15154 4.04 - 4.60: 21363 Nonbonded interactions: 56558 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.791 1.850 x-y,-y,-z-4/3 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.812 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.825 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.845 1.850 ... (remaining 56553 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_4023827_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= 0.2606 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791791 | | target function (ml) not normalized (work): 232572.916545 | | target function (ml) not normalized (free): 11841.897127 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2086 7.1006 4.9525| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1733 4.3449 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2335 0.1740 4.1277 4.1603| | 4: 2.47 - 2.25 1.00 2825 136 0.2315 0.1322 3.826 3.8089| | 5: 2.25 - 2.09 1.00 2756 127 0.2433 0.1533 3.7894 3.7979| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1642 3.4617 3.5133| | 7: 1.97 - 1.87 1.00 2787 165 0.2620 0.1767 3.1338 3.1646| | 8: 1.87 - 1.79 1.00 2789 144 0.2495 0.1914 3.059 3.1598| | 9: 1.79 - 1.72 1.00 2745 138 0.2436 0.1825 2.889 2.9071| | 10: 1.72 - 1.66 1.00 2789 158 0.2468 0.2049 2.8012 2.8851| | 11: 1.66 - 1.61 1.00 2740 147 0.2428 0.1805 2.7349 2.7393| | 12: 1.61 - 1.56 1.00 2787 146 0.2489 0.1926 2.6127 2.6457| | 13: 1.56 - 1.52 1.00 2745 130 0.2513 0.1964 2.5695 2.636| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.2117 2.5122 2.5984| | 15: 1.48 - 1.45 1.00 2738 128 0.2623 0.2168 2.4477 2.5408| | 16: 1.45 - 1.42 1.00 2756 161 0.2682 0.2103 2.4092 2.4674| | 17: 1.42 - 1.39 1.00 2785 139 0.2653 0.1965 2.3497 2.3627| | 18: 1.39 - 1.36 1.00 2741 179 0.2707 0.2294 2.2855 2.3433| | 19: 1.36 - 1.34 1.00 2807 134 0.2653 0.2395 2.2461 2.3107| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2317 2.2037 2.2586| | 21: 1.32 - 1.30 1.00 2785 112 0.2699 0.2319 2.1673 2.182| | 22: 1.29 - 1.27 1.00 2704 152 0.2734 0.2678 2.1403 2.2123| | 23: 1.27 - 1.26 1.00 2802 156 0.2791 0.2567 2.1033 2.2082| | 24: 1.26 - 1.24 1.00 2744 132 0.2742 0.2590 2.0684 2.1776| | 25: 1.24 - 1.22 1.00 2734 148 0.2844 0.2665 2.0464 2.1082| | 26: 1.22 - 1.21 1.00 2727 135 0.2835 0.2321 2.0059 2.0747| | 27: 1.21 - 1.19 1.00 2814 148 0.2967 0.2771 2.007 2.0305| | 28: 1.19 - 1.18 1.00 2671 147 0.2955 0.2633 1.9742 1.9785| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2778 1.9435 2.0243| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2749 1.9351 1.9525| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1474.93| | 2: 3.57 - 2.84 2876 122 0.81 25.90 1.27 0.23 1474.93| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.24 1222.23| | 4: 2.47 - 2.25 2825 136 0.81 25.45 1.25 0.25 566.44| | 5: 2.25 - 2.09 2756 127 0.77 29.12 1.28 0.25 566.44| | 6: 2.09 - 1.97 2846 113 0.83 22.60 1.30 0.25 308.39| | 7: 1.97 - 1.87 2787 165 0.90 16.59 1.30 0.26 88.31| | 8: 1.87 - 1.79 2789 144 0.86 20.76 1.25 0.26 88.31| | 9: 1.79 - 1.72 2745 138 0.88 18.53 1.23 0.25 54.49| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.23 0.25 47.72| | 11: 1.66 - 1.61 2740 147 0.86 21.17 1.24 0.25 46.07| | 12: 1.61 - 1.56 2787 146 0.88 18.43 1.23 0.25 29.35| | 13: 1.56 - 1.52 2745 130 0.87 20.45 1.23 0.25 29.35| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.22 0.25 26.43| | 15: 1.48 - 1.45 2738 128 0.87 20.22 1.23 0.25 21.06| | 16: 1.45 - 1.42 2756 161 0.85 22.01 1.23 0.25 21.06| | 17: 1.42 - 1.39 2785 139 0.87 20.89 1.21 0.25 18.01| | 18: 1.39 - 1.36 2741 179 0.86 21.57 1.23 0.25 16.24| | 19: 1.36 - 1.34 2807 134 0.85 22.37 1.21 0.25 16.24| | 20: 1.34 - 1.32 2696 147 0.86 21.48 1.21 0.25 13.65| | 21: 1.32 - 1.30 2785 112 0.85 22.36 1.21 0.25 13.47| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.25 13.17| | 23: 1.27 - 1.26 2802 156 0.85 22.63 1.22 0.24 11.66| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.66| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.99| | 26: 1.22 - 1.21 2727 135 0.84 24.25 1.21 0.24 10.23| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.20 0.24 10.23| | 28: 1.19 - 1.18 2671 147 0.83 25.16 1.19 0.23 9.22| | 29: 1.18 - 1.16 2800 134 0.83 25.04 1.17 0.23 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.76 1.15 0.23 8.83| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.83 max = 1474.93 mean = 213.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.66| |phase err.(test): min = 0.00 max = 89.07 mean = 22.59| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.240 1557 Z= 5.502 Angle : 5.255 18.971 2118 Z= 3.703 Chirality : 0.369 1.155 243 Planarity : 0.033 0.120 284 Dihedral : 14.232 87.135 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % 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: -2.63 (0.47), residues: 224 helix: -2.43 (0.40), residues: 108 sheet: -0.87 (0.81), residues: 38 loop : -0.73 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.020 ARG A 28 TYR 0.121 0.038 TYR A 139 PHE 0.103 0.040 PHE A 162 HIS 0.071 0.039 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= 0.2606 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791791 | | target function (ml) not normalized (work): 232572.916545 | | target function (ml) not normalized (free): 11841.897127 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2564 0.2606 0.1933 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2564 0.2606 0.1933 n_refl.: 87602 remove outliers: r(all,work,free)=0.1974 0.1978 0.1933 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1998 0.2003 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1631 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1630 0.1756 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3804 386.249 357.177 0.664 1.002 0.401 11.894-9.307 98.04 96 4 0.1735 616.027 589.963 0.923 1.003 0.380 9.237-7.194 100.00 213 7 0.2168 501.798 491.721 0.955 1.003 0.370 7.162-5.571 100.00 427 22 0.2244 376.572 363.709 0.931 1.003 0.310 5.546-4.326 100.00 867 58 0.1281 516.940 512.015 0.963 1.003 0.228 4.315-3.360 100.00 1859 96 0.1145 491.613 487.823 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1437 322.965 319.831 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1326 214.096 211.719 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.553 104.093 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2071 46.363 45.078 1.001 0.997 0.000 1.221-1.150 99.97 13689 708 0.2555 29.212 27.012 0.978 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1637 r_free=0.1764 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.737947 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1994.625816 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 0.1718 0.1834 0.0116 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1565 0.1705 0.0140 0.002 0.4 4.5 0.0 0.0 0 0.250 0.1460 0.1623 0.0163 0.002 0.4 3.8 0.0 0.0 0 0.500 0.1401 0.1587 0.0186 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1369 0.1563 0.0194 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1343 0.1539 0.0196 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1289 0.1499 0.0210 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1276 0.1496 0.0220 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1476 0.0222 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1479 0.0231 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1245 0.1474 0.0229 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1239 0.1470 0.0231 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1237 0.1470 0.0233 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1234 0.1471 0.0237 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1231 0.1472 0.0241 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1229 0.1467 0.0238 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1228 0.1470 0.0243 0.007 0.9 3.5 0.5 0.6 0 12.000 0.1225 0.1471 0.0246 0.008 1.0 3.8 0.5 0.6 0 13.369 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1467 0.0238 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.67 2.38 3.012 19.061 1994.626 0.017 12.30 14.67 2.37 2.988 19.061 59.839 0.017 12.37 14.63 2.26 2.656 19.061 249.328 0.017 12.70 15.35 2.65 2.820 19.295 997.313 0.016 12.59 15.49 2.90 3.371 19.673 1994.626 0.016 12.40 15.40 2.99 3.279 19.627 2991.939 0.015 12.25 15.25 3.00 2.786 19.258 3989.252 0.015 12.30 15.46 3.16 3.472 19.716 4986.565 0.015 12.22 15.37 3.15 3.351 19.642 5983.877 0.015 12.20 15.38 3.18 3.345 19.631 6981.190 0.015 12.21 15.43 3.22 3.316 19.607 7978.503 0.015 12.19 15.44 3.25 3.379 19.636 8975.816 0.015 12.17 15.44 3.28 3.430 19.656 9973.129 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 249.328 Accepted refinement result: 12.37 14.63 2.26 2.656 19.061 249.328 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.09 3.29 0 1785 Protein: 9.06 114.88 17.00 3.29 0 1519 Water: 11.45 119.44 38.23 N/A 0 258 Other: 19.74 26.60 22.07 N/A 0 8 Chain A: 9.06 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.10 1271 20.10 - 31.14 228 31.14 - 42.18 125 42.18 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1463 r_work=0.1239 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016809 | | target function (ls_wunit_k1) not normalized (work): 1400.083647 | | target function (ls_wunit_k1) not normalized (free): 108.565417 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1463 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1672 0.1673 0.1693 n_refl.: 87592 remove outliers: r(all,work,free)=0.1672 0.1673 0.1693 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1678 0.1679 0.1697 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1451 n_refl.: 87592 remove outliers: r(all,work,free)=0.1238 0.1228 0.1451 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3573 301.226 280.885 0.649 1.003 0.380 11.894-9.307 98.04 96 4 0.1566 484.505 473.188 0.932 1.003 0.364 9.237-7.194 100.00 213 7 0.1918 394.664 388.853 0.962 1.003 0.318 7.162-5.571 100.00 427 22 0.1830 296.173 290.169 0.936 1.003 0.253 5.546-4.326 100.00 867 58 0.1007 406.573 403.406 0.963 1.003 0.199 4.315-3.360 100.00 1859 96 0.0869 386.654 385.614 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1177 254.011 252.848 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1025 168.386 167.628 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.231 82.421 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.465 35.965 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.975 21.462 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0496 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1451 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 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1225 r_free=0.1448 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1448 | n_water=258 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1233 r_free=0.1446 | n_water=252 | time (s): 20.410 (total time: 22.170) Filter (q & B) r_work=0.1236 r_free=0.1445 | n_water=249 | time (s): 3.120 (total time: 25.290) Compute maps r_work=0.1236 r_free=0.1445 | n_water=249 | time (s): 1.260 (total time: 26.550) Filter (map) r_work=0.1251 r_free=0.1454 | n_water=227 | time (s): 2.720 (total time: 29.270) Find peaks r_work=0.1251 r_free=0.1454 | n_water=227 | time (s): 0.660 (total time: 29.930) Add new water r_work=0.1388 r_free=0.1620 | n_water=429 | time (s): 3.030 (total time: 32.960) Refine new water occ: r_work=0.1296 r_free=0.1477 adp: r_work=0.1220 r_free=0.1424 occ: r_work=0.1232 r_free=0.1418 adp: r_work=0.1200 r_free=0.1397 occ: r_work=0.1202 r_free=0.1391 adp: r_work=0.1194 r_free=0.1388 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1388 r_work=0.1194 r_free=0.1388 | n_water=429 | time (s): 56.990 (total time: 89.950) Filter (q & B) r_work=0.1198 r_free=0.1390 | n_water=410 | time (s): 3.380 (total time: 93.330) Filter (dist only) r_work=0.1198 r_free=0.1390 | n_water=409 | time (s): 34.640 (total time: 127.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.017214 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1482.901304 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 0.1674 0.1777 0.0103 0.001 0.4 6.7 0.0 0.0 0 0.125 0.1587 0.1696 0.0109 0.001 0.4 6.1 0.0 0.0 0 0.250 0.1391 0.1533 0.0142 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1359 0.1508 0.0149 0.002 0.4 4.5 0.0 0.0 0 0.750 0.1322 0.1480 0.0158 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1322 0.1481 0.0159 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1260 0.1444 0.0184 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1225 0.1415 0.0190 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1216 0.1414 0.0199 0.003 0.7 5.1 0.5 0.0 0 4.000 0.1207 0.1411 0.0205 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1202 0.1404 0.0202 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1197 0.1404 0.0207 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1196 0.1399 0.0203 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1192 0.1401 0.0209 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1189 0.1399 0.0210 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1187 0.1397 0.0210 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1186 0.1395 0.0209 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1187 0.1404 0.0217 0.007 0.9 5.4 0.5 0.0 0 13.000 0.1184 0.1399 0.0215 0.008 1.0 4.8 0.5 0.0 0 14.509 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1186 0.1395 0.0209 0.007 0.9 4.5 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.86 13.95 2.09 3.765 21.714 1482.901 0.016 11.86 13.95 2.09 3.765 21.714 44.487 0.016 11.86 13.95 2.09 3.765 21.714 185.363 0.016 12.06 14.38 2.32 3.626 21.714 741.451 0.015 12.04 14.71 2.66 3.560 21.769 1482.901 0.015 11.90 14.63 2.73 3.485 22.087 2224.352 0.014 11.80 14.64 2.84 3.521 21.843 2965.803 0.014 11.78 14.64 2.85 3.483 22.052 3707.253 0.014 11.77 14.71 2.95 3.517 22.110 4448.704 0.014 11.74 14.74 3.00 3.537 22.105 5190.155 0.014 11.69 14.70 3.01 3.544 22.077 5931.605 0.014 11.66 14.71 3.05 3.564 22.089 6673.056 0.014 11.65 14.74 3.09 3.583 22.074 7414.507 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: 185.363 Accepted refinement result: 11.86 13.95 2.09 3.765 21.714 185.363 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 114.90 22.07 3.29 182 1754 Protein: 9.09 114.90 17.03 3.29 0 1519 Water: 11.48 76.68 40.79 N/A 182 227 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.09 114.90 19.49 N/A 0 1754 Chain S: 13.12 60.00 46.96 N/A 182 0 Histogram: Values Number of atoms 9.09 - 19.67 1257 19.67 - 30.26 253 30.26 - 40.84 156 40.84 - 51.42 126 51.42 - 62.00 121 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1186 r_free=0.1395 r_work=0.1186 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1395 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 = 0.1387 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014908 | | target function (ls_wunit_k1) not normalized (work): 1241.771601 | | target function (ls_wunit_k1) not normalized (free): 97.964638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1183 0.1387 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1566 0.1565 0.1613 n_refl.: 87591 remove outliers: r(all,work,free)=0.1566 0.1565 0.1613 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1567 0.1567 0.1614 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1381 n_refl.: 87591 remove outliers: r(all,work,free)=0.1189 0.1179 0.1381 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3399 297.132 274.840 0.597 1.003 0.362 11.894-9.307 98.04 96 4 0.1583 484.505 476.981 0.922 1.003 0.350 9.237-7.194 100.00 213 7 0.1731 394.664 394.089 0.980 1.003 0.249 7.162-5.571 100.00 427 22 0.1545 296.173 291.561 0.937 1.003 0.214 5.546-4.326 100.00 867 58 0.0883 406.573 403.792 0.962 1.003 0.195 4.315-3.360 100.00 1859 96 0.0777 386.654 385.813 1.005 1.002 0.190 3.356-2.611 100.00 3867 181 0.1079 254.011 253.046 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1003 168.386 167.819 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.231 82.445 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.465 35.997 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.975 21.494 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0122 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1179 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1179 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1381 | n_water=409 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1180 r_free=0.1381 | n_water=404 | time (s): 34.630 (total time: 36.830) Filter (q & B) r_work=0.1180 r_free=0.1381 | n_water=404 | time (s): 1.270 (total time: 38.100) Compute maps r_work=0.1180 r_free=0.1381 | n_water=404 | time (s): 1.460 (total time: 39.560) Filter (map) r_work=0.1225 r_free=0.1389 | n_water=283 | time (s): 2.480 (total time: 42.040) Find peaks r_work=0.1225 r_free=0.1389 | n_water=283 | time (s): 0.550 (total time: 42.590) Add new water r_work=0.1336 r_free=0.1499 | n_water=471 | time (s): 3.270 (total time: 45.860) Refine new water occ: r_work=0.1241 r_free=0.1410 adp: r_work=0.1243 r_free=0.1413 occ: r_work=0.1218 r_free=0.1385 adp: r_work=0.1217 r_free=0.1387 occ: r_work=0.1202 r_free=0.1369 adp: r_work=0.1198 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1368 r_work=0.1198 r_free=0.1368 | n_water=471 | time (s): 212.840 (total time: 258.700) Filter (q & B) r_work=0.1202 r_free=0.1379 | n_water=439 | time (s): 3.240 (total time: 261.940) Filter (dist only) r_work=0.1202 r_free=0.1379 | n_water=438 | time (s): 35.310 (total time: 297.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.757296 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.885490 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 0.1230 0.1352 0.0122 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1189 0.1325 0.0136 0.003 0.7 3.5 0.5 0.0 0 0.264 0.1173 0.1314 0.0141 0.004 0.8 3.2 0.5 0.0 0 0.527 0.1166 0.1311 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.791 0.1161 0.1310 0.0149 0.006 1.0 3.2 0.5 0.0 0 1.054 0.1158 0.1309 0.0151 0.007 1.0 3.5 0.5 0.0 0 1.318 0.1155 0.1308 0.0153 0.007 1.1 3.5 0.5 0.0 0 1.582 0.1153 0.1306 0.0153 0.008 1.1 4.5 0.5 0.0 0 1.845 0.1163 0.1311 0.0148 0.005 0.9 3.2 0.5 0.0 0 0.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1306 0.0153 0.008 1.1 4.5 0.5 0.0 0 1.845 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 13.06 1.53 3.768 21.213 45.885 3.616 11.53 13.06 1.53 3.768 21.213 1.377 3.616 11.54 13.06 1.52 3.758 21.213 5.736 3.616 11.55 13.12 1.57 3.706 21.205 22.943 3.609 11.62 13.28 1.67 3.726 21.167 45.885 3.610 11.52 13.23 1.71 3.753 21.159 68.828 3.604 11.49 13.22 1.72 3.766 21.152 91.771 3.600 11.46 13.20 1.75 3.779 21.146 114.714 3.598 11.44 13.20 1.76 3.795 21.133 137.656 3.596 11.44 13.24 1.80 3.811 21.126 160.599 3.596 11.41 13.18 1.77 3.815 21.122 183.542 3.593 11.41 13.19 1.78 3.824 21.119 206.485 3.593 11.37 13.15 1.78 3.823 21.125 229.427 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: 1.377 Accepted refinement result: 11.53 13.06 1.53 3.768 21.213 1.377 3.616 Individual atomic B min max mean iso aniso Overall: 9.10 114.91 21.15 3.29 217 1748 Protein: 9.10 114.91 17.04 3.29 0 1519 Water: 11.49 76.69 35.38 N/A 217 221 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.10 114.91 19.39 N/A 0 1748 Chain S: 13.12 60.01 35.27 N/A 217 0 Histogram: Values Number of atoms 9.10 - 19.68 1261 19.68 - 30.26 293 30.26 - 40.84 215 40.84 - 51.42 124 51.42 - 62.01 49 62.01 - 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=0.1153 r_free=0.1306 r_work=0.1153 r_free=0.1306 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1306 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1306 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1145 r_free= 0.1306 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.609794 | | target function (ml) not normalized (work): 300666.986760 | | target function (ml) not normalized (free): 15821.810426 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1145 0.1306 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1486 0.1486 0.1520 n_refl.: 87588 remove outliers: r(all,work,free)=0.1486 0.1486 0.1520 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1485 0.1485 0.1520 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1150 0.1142 0.1297 n_refl.: 87588 remove outliers: r(all,work,free)=0.1147 0.1139 0.1297 n_refl.: 87580 ======================== 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 0.3808 283.606 266.526 0.486 1.002 0.293 11.894-9.307 96.08 94 4 0.2213 484.771 462.825 0.876 1.002 0.273 9.237-7.194 98.64 210 7 0.2292 387.150 388.275 0.955 1.002 0.170 7.162-5.571 100.00 427 22 0.2112 296.173 285.263 0.917 1.002 0.165 5.546-4.326 100.00 867 58 0.1102 406.573 402.272 0.964 1.002 0.150 4.315-3.360 100.00 1859 96 0.0922 386.654 384.142 1.005 1.002 0.140 3.356-2.611 100.00 3867 181 0.1134 254.011 252.046 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.0930 168.386 167.619 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.231 82.516 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.465 36.048 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 22.975 21.520 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0145 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1139 r_free=0.1297 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1139 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1297 | n_water=438 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1139 r_free=0.1298 | n_water=435 | time (s): 46.010 (total time: 48.440) Filter (q & B) r_work=0.1140 r_free=0.1300 | n_water=432 | time (s): 3.800 (total time: 52.240) Compute maps r_work=0.1140 r_free=0.1300 | n_water=432 | time (s): 1.860 (total time: 54.100) Filter (map) r_work=0.1165 r_free=0.1298 | n_water=337 | time (s): 3.930 (total time: 58.030) Find peaks r_work=0.1165 r_free=0.1298 | n_water=337 | time (s): 0.730 (total time: 58.760) Add new water r_work=0.1225 r_free=0.1356 | n_water=498 | time (s): 3.720 (total time: 62.480) Refine new water occ: r_work=0.1155 r_free=0.1312 adp: r_work=0.1155 r_free=0.1313 occ: r_work=0.1141 r_free=0.1301 adp: r_work=0.1140 r_free=0.1300 occ: r_work=0.1131 r_free=0.1293 adp: r_work=0.1128 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1290 r_work=0.1128 r_free=0.1290 | n_water=498 | time (s): 326.010 (total time: 388.490) Filter (q & B) r_work=0.1135 r_free=0.1298 | n_water=460 | time (s): 3.880 (total time: 392.370) Filter (dist only) r_work=0.1135 r_free=0.1297 | n_water=459 | time (s): 46.880 (total time: 439.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.848281 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.006424 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 0.1196 0.1325 0.0129 0.002 0.6 4.5 0.5 0.0 0 0.092 0.1159 0.1308 0.0149 0.003 0.8 3.2 0.5 0.0 0 0.277 0.1144 0.1299 0.0155 0.005 0.9 3.5 0.5 0.0 0 0.554 0.1138 0.1297 0.0160 0.006 1.0 3.2 0.5 0.0 0 0.832 0.1135 0.1298 0.0163 0.007 1.0 3.2 0.5 0.0 0 1.109 0.1133 0.1297 0.0164 0.007 1.1 3.2 0.5 0.0 0 1.386 0.1129 0.1295 0.0166 0.008 1.1 3.2 0.5 0.0 0 1.663 0.1128 0.1296 0.0168 0.009 1.1 3.2 0.5 0.0 0 1.941 0.1136 0.1297 0.0160 0.006 1.0 3.2 0.5 0.0 0 0.924 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1129 0.1295 0.0166 0.008 1.1 3.2 0.5 0.0 0 1.663 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 12.95 1.66 3.768 21.259 37.006 3.602 11.29 12.95 1.66 3.768 21.259 1.110 3.602 11.29 12.95 1.66 3.768 21.259 4.626 3.602 11.33 13.01 1.67 3.701 21.251 18.503 3.599 11.35 13.10 1.76 3.723 21.234 37.006 3.598 11.36 13.17 1.81 3.740 21.212 55.510 3.598 11.28 13.12 1.83 3.756 21.208 74.013 3.592 11.24 13.08 1.84 3.766 21.208 92.516 3.588 11.23 13.08 1.85 3.776 21.204 111.019 3.587 11.22 13.09 1.87 3.786 21.200 129.522 3.586 11.21 13.10 1.89 3.801 21.191 148.026 3.586 11.21 13.11 1.90 3.812 21.184 166.529 3.585 11.19 13.08 1.90 3.817 21.184 185.032 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.626 Accepted refinement result: 11.29 12.95 1.66 3.768 21.259 4.626 3.602 Individual atomic B min max mean iso aniso Overall: 9.10 114.90 21.23 3.28 239 1747 Protein: 9.10 114.90 17.03 3.29 0 1519 Water: 11.48 76.68 35.12 N/A 239 220 Other: 19.77 26.63 22.11 N/A 0 8 Chain A: 9.10 114.90 19.39 N/A 0 1747 Chain S: 13.12 60.00 34.72 N/A 239 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 307 30.26 - 40.84 220 40.84 - 51.42 127 51.42 - 62.00 47 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1129 r_free=0.1295 r_work=0.1129 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1129 r_free = 0.1295 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1294 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600838 | | target function (ml) not normalized (work): 299892.211416 | | target function (ml) not normalized (free): 15803.100295 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1294 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1450 0.1450 0.1484 n_refl.: 87580 remove outliers: r(all,work,free)=0.1450 0.1450 0.1484 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1449 0.1449 0.1483 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1125 0.1294 n_refl.: 87580 remove outliers: r(all,work,free)=0.1131 0.1123 0.1294 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4065 285.735 245.747 0.424 1.001 0.281 11.894-9.307 93.14 91 4 0.2285 492.203 470.042 0.874 1.002 0.260 9.237-7.194 98.18 209 7 0.2338 386.143 381.278 0.932 1.002 0.150 7.162-5.571 100.00 427 22 0.2087 296.173 285.897 0.914 1.002 0.140 5.546-4.326 100.00 867 58 0.1093 406.573 402.323 0.966 1.002 0.135 4.315-3.360 100.00 1859 96 0.0904 386.654 384.642 1.005 1.002 0.130 3.356-2.611 100.00 3867 181 0.1094 254.011 252.273 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0910 168.386 167.840 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0882 82.231 82.595 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.465 36.085 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 22.975 21.536 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0171 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1294 After: r_work=0.1124 r_free=0.1294 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1294 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1124 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1294 | n_water=459 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1124 r_free=0.1294 | n_water=459 | time (s): 45.470 (total time: 47.910) Filter (q & B) r_work=0.1125 r_free=0.1294 | n_water=456 | time (s): 3.990 (total time: 51.900) Compute maps r_work=0.1125 r_free=0.1294 | n_water=456 | time (s): 1.860 (total time: 53.760) Filter (map) r_work=0.1151 r_free=0.1299 | n_water=359 | time (s): 3.880 (total time: 57.640) Find peaks r_work=0.1151 r_free=0.1299 | n_water=359 | time (s): 0.700 (total time: 58.340) Add new water r_work=0.1194 r_free=0.1344 | n_water=496 | time (s): 3.670 (total time: 62.010) Refine new water occ: r_work=0.1142 r_free=0.1298 adp: r_work=0.1142 r_free=0.1300 occ: r_work=0.1131 r_free=0.1286 adp: r_work=0.1130 r_free=0.1288 occ: r_work=0.1123 r_free=0.1279 adp: r_work=0.1120 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1279 r_work=0.1120 r_free=0.1279 | n_water=496 | time (s): 202.630 (total time: 264.640) Filter (q & B) r_work=0.1128 r_free=0.1288 | n_water=458 | time (s): 3.750 (total time: 268.390) Filter (dist only) r_work=0.1128 r_free=0.1288 | n_water=457 | time (s): 47.400 (total time: 315.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.751909 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.452400 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 6.4 0.0 0.0 0 0.088 0.1175 0.1315 0.0140 0.004 0.8 5.4 0.0 0.0 0 0.263 0.1152 0.1300 0.0149 0.005 0.9 5.1 0.5 0.0 0 0.526 0.1145 0.1296 0.0152 0.006 1.0 5.1 0.5 0.0 0 0.788 0.1137 0.1291 0.0155 0.006 1.0 4.8 0.5 0.0 0 1.051 0.1132 0.1288 0.0157 0.007 1.1 4.8 0.5 0.0 0 1.314 0.1129 0.1288 0.0159 0.008 1.1 4.5 0.5 0.0 0 1.577 0.1128 0.1288 0.0160 0.008 1.1 4.5 0.5 0.0 0 1.840 0.1142 0.1295 0.0152 0.006 1.0 5.1 0.5 0.0 0 0.876 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1288 0.0160 0.008 1.1 4.5 0.5 0.0 0 1.840 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.88 1.60 3.767 21.228 42.452 3.601 11.28 12.88 1.60 3.767 21.228 1.274 3.601 11.28 12.88 1.60 3.767 21.228 5.307 3.601 11.31 12.91 1.60 3.704 21.219 21.226 3.596 11.38 13.07 1.70 3.726 21.188 42.452 3.599 11.30 13.05 1.75 3.749 21.178 63.679 3.593 11.24 13.02 1.77 3.764 21.175 84.905 3.589 11.20 12.98 1.78 3.771 21.176 106.131 3.585 11.19 13.00 1.81 3.785 21.169 127.357 3.584 11.18 13.01 1.83 3.797 21.165 148.583 3.583 11.18 13.02 1.85 3.813 21.156 169.810 3.583 11.16 13.01 1.85 3.820 21.156 191.036 3.582 11.15 13.00 1.85 3.825 21.156 212.262 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.307 Accepted refinement result: 11.28 12.88 1.60 3.767 21.228 5.307 3.601 Individual atomic B min max mean iso aniso Overall: 9.09 114.89 21.18 3.28 237 1747 Protein: 9.09 114.89 17.02 3.29 0 1519 Water: 11.48 76.68 34.98 N/A 237 220 Other: 19.76 26.63 22.10 N/A 0 8 Chain A: 9.09 114.89 19.38 N/A 0 1747 Chain S: 13.11 60.00 34.46 N/A 237 0 Histogram: Values Number of atoms 9.09 - 19.67 1262 19.67 - 30.25 306 30.25 - 40.83 220 40.83 - 51.41 132 51.41 - 61.99 41 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1128 r_free=0.1288 r_work=0.1128 r_free=0.1288 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1288 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1288 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1288 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599855 | | target function (ml) not normalized (work): 299792.354693 | | target function (ml) not normalized (free): 15792.076134 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1312 0.1322 5.6406 5.5641| | 2: 3.57 - 2.84 1.00 2888 124 0.1055 0.1369 5.143 5.2211| | 3: 2.83 - 2.48 1.00 2820 163 0.1094 0.1239 4.9302 4.9677| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.1025 4.6125 4.6645| | 5: 2.25 - 2.09 1.00 2756 127 0.0860 0.1001 4.5598 4.6257| | 6: 2.09 - 1.97 1.00 2846 113 0.0844 0.0975 4.2533 4.3519| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1097 3.9757 4.0794| | 8: 1.87 - 1.79 1.00 2789 144 0.0914 0.1115 3.8855 3.9947| | 9: 1.79 - 1.72 1.00 2745 138 0.0873 0.1196 3.6447 3.8369| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1168 3.5629 3.6918| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1033 3.4929 3.5606| | 12: 1.61 - 1.56 1.00 2773 144 0.0898 0.1164 3.3255 3.4619| | 13: 1.56 - 1.52 1.00 2745 130 0.0942 0.1055 3.305 3.4073| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1047 3.2393 3.3278| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1216 3.1533 3.2576| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1246 3.1332 3.2435| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1281 3.1172 3.2216| | 18: 1.39 - 1.36 1.00 2741 179 0.1199 0.1336 3.1042 3.2402| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1541 3.1102 3.2573| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1455 3.1106 3.147| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1507 3.1125 3.1063| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1986 3.1224 3.2958| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1801 3.1333 3.2012| | 24: 1.26 - 1.24 1.00 2744 132 0.1712 0.1839 3.1272 3.2303| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2173 3.1428 3.2627| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1745 3.1484 3.1949| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2163 3.1711 3.1581| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2302 3.1659 3.1769| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2396 3.1477 3.2306| | 30: 1.16 - 1.15 1.00 2739 148 0.2454 0.2435 3.1437 3.1648| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.20 1.00 0.97 5459.28| | 2: 3.57 - 2.84 2888 124 0.93 12.14 1.01 0.97 5459.28| | 3: 2.83 - 2.48 2820 163 0.90 16.00 0.99 0.97 4566.32| | 4: 2.47 - 2.25 2825 136 0.92 13.15 1.00 0.98 2263.66| | 5: 2.25 - 2.09 2756 127 0.91 15.24 1.01 0.98 2263.66| | 6: 2.09 - 1.97 2846 113 0.93 12.24 1.02 0.98 1317.30| | 7: 1.97 - 1.87 2787 165 0.95 9.30 1.02 0.97 510.18| | 8: 1.87 - 1.79 2789 144 0.93 12.66 1.00 0.97 510.18| | 9: 1.79 - 1.72 2745 138 0.94 10.11 0.98 0.97 289.51| | 10: 1.72 - 1.66 2831 160 0.94 11.16 0.98 0.97 245.32| | 11: 1.66 - 1.61 2712 147 0.94 11.71 0.98 0.97 234.97| | 12: 1.61 - 1.56 2773 144 0.95 8.89 0.99 0.97 137.39| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.02 0.97 137.39| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 123.32| | 15: 1.48 - 1.45 2738 128 0.95 9.89 1.02 0.98 97.56| | 16: 1.45 - 1.42 2756 161 0.94 11.07 1.02 0.98 97.56| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.77| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.69| | 19: 1.36 - 1.34 2807 134 0.94 11.84 0.99 0.98 83.69| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.74| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.96 79.47| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 79.90| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 82.09| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.94 82.09| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.16| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.45| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.45| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.92 90.24| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.98 0.92 91.67| | 30: 1.16 - 1.15 2739 148 0.86 22.12 0.97 0.92 91.67| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.47 max = 5459.28 mean = 850.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.38| |phase err.(test): min = 0.00 max = 89.97 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1125 0.1288 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1441 0.1441 0.1478 n_refl.: 87575 remove outliers: r(all,work,free)=0.1441 0.1441 0.1478 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1440 0.1440 0.1478 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1289 n_refl.: 87575 remove outliers: r(all,work,free)=0.1131 0.1123 0.1289 n_refl.: 87571 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4010 288.336 243.354 0.436 1.002 0.304 11.894-9.307 92.16 90 4 0.2245 485.752 467.299 0.885 1.003 0.300 9.237-7.194 97.27 207 7 0.2302 387.773 378.344 0.923 1.003 0.134 7.162-5.571 100.00 427 22 0.2116 296.173 285.856 0.907 1.003 0.124 5.546-4.326 100.00 867 58 0.1099 406.573 401.942 0.965 1.003 0.121 4.315-3.360 100.00 1859 96 0.0904 386.654 384.681 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1101 254.011 252.364 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0903 168.386 167.858 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.231 82.617 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.465 36.095 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 22.975 21.542 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0138 ================= 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 : 0.2606 0.1933 0.083 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1756 0.083 5.255 9.0 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1756 0.083 5.255 9.0 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1764 0.083 5.255 9.0 119.5 20.1 258 0.010 1_weight: 0.1637 0.1764 0.083 5.255 9.0 119.5 20.1 258 0.010 1_xyzrec: 0.1229 0.1467 0.007 0.899 9.0 119.5 20.1 258 0.141 1_adp: 0.1237 0.1463 0.007 0.899 9.1 119.4 20.1 258 0.141 1_regHadp: 0.1239 0.1467 0.007 0.899 9.1 119.4 20.1 258 0.141 1_occ: 0.1232 0.1463 0.007 0.899 9.1 119.4 20.1 258 0.141 2_bss: 0.1228 0.1451 0.007 0.899 9.1 119.5 20.1 258 0.141 2_settarget: 0.1228 0.1451 0.007 0.899 9.1 119.5 20.1 258 0.141 2_updatecdl: 0.1228 0.1451 0.007 0.912 9.1 119.5 20.1 258 0.141 2_nqh: 0.1225 0.1448 0.007 0.912 9.1 119.5 20.1 258 0.135 2_sol: 0.1198 0.1390 0.007 0.912 9.1 114.9 22.1 409 n/a 2_weight: 0.1198 0.1390 0.007 0.912 9.1 114.9 22.1 409 n/a 2_xyzrec: 0.1186 0.1395 0.007 0.907 9.1 114.9 22.1 409 n/a 2_adp: 0.1186 0.1395 0.007 0.907 9.1 114.9 22.1 409 n/a 2_regHadp: 0.1186 0.1395 0.007 0.907 9.1 114.9 22.1 409 n/a 2_occ: 0.1183 0.1387 0.007 0.907 9.1 114.9 22.1 409 n/a 3_bss: 0.1179 0.1381 0.007 0.907 9.1 114.9 22.1 409 n/a 3_settarget: 0.1179 0.1381 0.007 0.907 9.1 114.9 22.1 409 n/a 3_updatecdl: 0.1179 0.1381 0.007 0.906 9.1 114.9 22.1 409 n/a 3_nqh: 0.1179 0.1381 0.007 0.906 9.1 114.9 22.1 409 n/a 3_sol: 0.1202 0.1379 0.007 0.906 9.1 114.9 21.1 438 n/a 3_weight: 0.1202 0.1379 0.007 0.906 9.1 114.9 21.1 438 n/a 3_xyzrec: 0.1153 0.1306 0.008 1.087 9.1 114.9 21.1 438 n/a 3_adp: 0.1153 0.1306 0.008 1.087 9.1 114.9 21.1 438 n/a 3_regHadp: 0.1153 0.1306 0.008 1.087 9.1 114.9 21.1 438 n/a 3_occ: 0.1145 0.1306 0.008 1.087 9.1 114.9 21.1 438 n/a 4_bss: 0.1139 0.1297 0.008 1.087 9.1 114.9 21.1 438 n/a 4_settarget: 0.1139 0.1297 0.008 1.087 9.1 114.9 21.1 438 n/a 4_updatecdl: 0.1139 0.1297 0.008 1.090 9.1 114.9 21.1 438 n/a 4_nqh: 0.1139 0.1297 0.008 1.090 9.1 114.9 21.1 438 n/a 4_sol: 0.1135 0.1297 0.008 1.090 9.1 114.9 21.2 459 n/a 4_weight: 0.1135 0.1297 0.008 1.090 9.1 114.9 21.2 459 n/a 4_xyzrec: 0.1129 0.1295 0.008 1.099 9.1 114.9 21.2 459 n/a 4_adp: 0.1129 0.1295 0.008 1.099 9.1 114.9 21.2 459 n/a 4_regHadp: 0.1129 0.1295 0.008 1.099 9.1 114.9 21.2 459 n/a 4_occ: 0.1126 0.1294 0.008 1.099 9.1 114.9 21.2 459 n/a 5_bss: 0.1123 0.1294 0.008 1.099 9.1 114.9 21.2 459 n/a 5_settarget: 0.1123 0.1294 0.008 1.099 9.1 114.9 21.2 459 n/a 5_updatecdl: 0.1123 0.1294 0.008 1.101 9.1 114.9 21.2 459 n/a 5_setrh: 0.1124 0.1294 0.008 1.101 9.1 114.9 21.2 459 n/a 5_nqh: 0.1124 0.1294 0.008 1.101 9.1 114.9 21.2 459 n/a 5_sol: 0.1128 0.1288 0.008 1.101 9.1 114.9 21.2 457 n/a 5_weight: 0.1128 0.1288 0.008 1.101 9.1 114.9 21.2 457 n/a 5_xyzrec: 0.1128 0.1288 0.008 1.123 9.1 114.9 21.2 457 n/a 5_adp: 0.1128 0.1288 0.008 1.123 9.1 114.9 21.2 457 n/a 5_regHadp: 0.1128 0.1288 0.008 1.123 9.1 114.9 21.2 457 n/a 5_occ: 0.1125 0.1288 0.008 1.123 9.1 114.9 21.2 457 n/a end: 0.1123 0.1289 0.008 1.123 9.1 114.9 21.2 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4023827_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4023827_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8400 Refinement macro-cycles (run) : 13683.9800 Write final files (write_after_run_outputs) : 97.2300 Total : 13785.0500 Total CPU time: 3.84 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:08:22 PST -0800 (1735366102.26 s) Start R-work = 0.1630, R-free = 0.1756 Final R-work = 0.1123, R-free = 0.1289 =============================================================================== Job complete usr+sys time: 13965.65 seconds wall clock time: 252 minutes 33.33 seconds (15153.33 seconds total)