Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8530786.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.34, per 1000 atoms: 0.69 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: 0.73 Conformation dependent library (CDL) restraints added in 312.4 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.14: 1213 1.14 - 1.39: 566 1.39 - 1.64: 903 1.64 - 1.89: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 1.234 0.998 0.235 1.17e-02 7.31e+03 4.05e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.522 -0.201 1.00e-02 1.00e+04 4.04e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.455 -0.218 1.17e-02 7.31e+03 3.49e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.144 0.182 1.10e-02 8.26e+03 2.75e+02 bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.261 0.194 1.17e-02 7.31e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3259 4.94 - 9.87: 1874 9.87 - 14.81: 580 14.81 - 19.74: 60 19.74 - 24.67: 4 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 124.34 -15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.27 139.65 -16.38 1.16e+00 7.43e-01 1.99e+02 angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 116.39 102.10 14.29 1.17e+00 7.31e-01 1.49e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 109.28 12.84 1.06e+00 8.90e-01 1.47e+02 angle pdb=" CA ASP A 60 " pdb=" C ASP A 60 " pdb=" O ASP A 60 " ideal model delta sigma weight residual 120.70 132.95 -12.25 1.03e+00 9.43e-01 1.41e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.23: 947 17.23 - 34.46: 108 34.46 - 51.68: 33 51.68 - 68.91: 20 68.91 - 86.13: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.214: 105 0.214 - 0.426: 61 0.426 - 0.638: 49 0.638 - 0.850: 21 0.850 - 1.062: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.53 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.67 0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA AGLN A 80 " pdb=" N AGLN A 80 " pdb=" C AGLN A 80 " pdb=" CB AGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.31e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.028 2.00e-02 2.50e+03 5.93e-02 1.05e+02 pdb=" CG PHE A 162 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.095 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.052 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.106 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.030 2.00e-02 2.50e+03 5.32e-02 8.50e+01 pdb=" CG PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.39: 1575 2.39 - 2.94: 8485 2.94 - 3.50: 10405 3.50 - 4.05: 15006 4.05 - 4.60: 21120 Nonbonded interactions: 56591 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.851 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.865 2.270 nonbonded pdb=" H BTYR A 67 " pdb=" O HOH A 324 " model vdw 1.870 2.450 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.874 1.816 ... (remaining 56586 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 } 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 } } output { prefix = "shake_8530786_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= 0.2605 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792489 | | target function (ml) not normalized (work): 232631.077968 | | target function (ml) not normalized (free): 11838.554933 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2112 6.9744 4.9452| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1883 4.3591 4.3519| | 3: 2.84 - 2.48 1.00 2833 165 0.2380 0.1704 4.1398 4.1678| | 4: 2.47 - 2.25 1.00 2825 136 0.2300 0.1412 3.8382 3.8352| | 5: 2.25 - 2.09 1.00 2756 127 0.2440 0.1691 3.809 3.849| | 6: 2.09 - 1.97 1.00 2846 113 0.2543 0.1700 3.4664 3.5676| | 7: 1.97 - 1.87 1.00 2787 165 0.2582 0.1841 3.1507 3.2216| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.2014 3.0639 3.145| | 9: 1.79 - 1.72 1.00 2745 138 0.2418 0.2061 2.931 2.9874| | 10: 1.72 - 1.66 1.00 2789 158 0.2468 0.1906 2.8198 2.8355| | 11: 1.66 - 1.61 1.00 2740 147 0.2480 0.1926 2.7517 2.7895| | 12: 1.61 - 1.56 1.00 2787 146 0.2541 0.1962 2.6267 2.6846| | 13: 1.56 - 1.52 1.00 2745 130 0.2480 0.1787 2.5632 2.5835| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1972 2.5267 2.5815| | 15: 1.48 - 1.45 1.00 2738 128 0.2605 0.2195 2.407 2.5604| | 16: 1.45 - 1.42 1.00 2756 161 0.2647 0.2106 2.3819 2.3876| | 17: 1.42 - 1.39 1.00 2785 139 0.2631 0.1996 2.3365 2.3702| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.1900 2.2724 2.2583| | 19: 1.36 - 1.34 1.00 2807 134 0.2653 0.2534 2.2469 2.3165| | 20: 1.34 - 1.32 1.00 2696 147 0.2656 0.2220 2.201 2.1857| | 21: 1.32 - 1.30 1.00 2785 112 0.2759 0.2313 2.1861 2.2195| | 22: 1.29 - 1.27 1.00 2704 152 0.2798 0.2738 2.1362 2.2564| | 23: 1.27 - 1.26 1.00 2802 156 0.2765 0.2385 2.0971 2.1433| | 24: 1.26 - 1.24 1.00 2744 132 0.2784 0.2572 2.0807 2.1602| | 25: 1.24 - 1.22 1.00 2734 148 0.2852 0.2460 2.0572 2.0924| | 26: 1.22 - 1.21 1.00 2727 135 0.2879 0.2331 2.0145 2.1041| | 27: 1.21 - 1.19 1.00 2814 148 0.2983 0.2727 2.0003 2.026| | 28: 1.19 - 1.18 1.00 2671 147 0.3008 0.2617 2.0001 1.9909| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2653 1.9671 2.023| | 30: 1.16 - 1.15 1.00 2740 148 0.3031 0.2806 1.9181 1.9345| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.09 0.76 0.23 1517.63| | 2: 3.57 - 2.84 2876 122 0.80 26.45 1.27 0.23 1517.63| | 3: 2.84 - 2.48 2833 165 0.73 32.46 1.25 0.23 1258.54| | 4: 2.47 - 2.25 2825 136 0.81 25.91 1.26 0.25 586.14| | 5: 2.25 - 2.09 2756 127 0.77 29.54 1.28 0.25 586.14| | 6: 2.09 - 1.97 2846 113 0.83 22.95 1.29 0.25 320.72| | 7: 1.97 - 1.87 2787 165 0.90 16.93 1.29 0.26 94.36| | 8: 1.87 - 1.79 2789 144 0.85 21.48 1.24 0.26 94.36| | 9: 1.79 - 1.72 2745 138 0.88 18.81 1.22 0.25 57.23| | 10: 1.72 - 1.66 2789 158 0.86 20.64 1.23 0.25 49.79| | 11: 1.66 - 1.61 2740 147 0.85 21.78 1.24 0.25 47.99| | 12: 1.61 - 1.56 2787 146 0.88 18.59 1.24 0.25 29.75| | 13: 1.56 - 1.52 2745 130 0.87 20.25 1.23 0.25 29.75| | 14: 1.52 - 1.48 2803 134 0.86 20.75 1.23 0.25 26.58| | 15: 1.48 - 1.45 2738 128 0.87 20.23 1.24 0.25 20.78| | 16: 1.45 - 1.42 2756 161 0.85 21.73 1.23 0.25 20.78| | 17: 1.42 - 1.39 2785 139 0.87 20.56 1.22 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.23 1.23 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.85 22.02 1.22 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.86 21.24 1.19 0.24 13.47| | 21: 1.32 - 1.30 2785 112 0.85 22.37 1.20 0.24 13.30| | 22: 1.29 - 1.27 2704 152 0.85 23.04 1.22 0.24 13.00| | 23: 1.27 - 1.26 2802 156 0.85 22.56 1.22 0.24 11.48| | 24: 1.26 - 1.24 2744 132 0.85 23.19 1.20 0.24 11.48| | 25: 1.24 - 1.22 2734 148 0.84 23.91 1.20 0.24 10.78| | 26: 1.22 - 1.21 2727 135 0.84 24.03 1.20 0.24 10.01| | 27: 1.21 - 1.19 2814 148 0.83 24.86 1.21 0.24 10.01| | 28: 1.19 - 1.18 2671 147 0.84 24.59 1.19 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.84 24.47 1.16 0.23 8.58| | 30: 1.16 - 1.15 2740 148 0.82 26.32 1.16 0.23 8.58| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.58 max = 1517.63 mean = 220.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.74| |phase err.(test): min = 0.00 max = 89.81 mean = 22.68| |-----------------------------------------------------------------------------| ----------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 0.254 1557 Z= 5.582 Angle : 5.191 16.376 2118 Z= 3.628 Chirality : 0.397 1.062 243 Planarity : 0.029 0.101 284 Dihedral : 13.965 86.132 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 27.03 % 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: -2.07 (0.48), residues: 224 helix: -2.12 (0.37), residues: 109 sheet: -0.42 (0.91), residues: 28 loop : -0.32 (0.63), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.014 ARG A 5 TYR 0.083 0.032 TYR A 139 PHE 0.088 0.041 PHE A 162 HIS 0.033 0.013 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= 0.2605 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792489 | | target function (ml) not normalized (work): 232631.077968 | | target function (ml) not normalized (free): 11838.554933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2606 0.1965 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2606 0.1965 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1982 0.1965 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2002 0.2005 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1643 0.1781 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1643 0.1781 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 0.3767 386.538 372.391 0.692 1.000 0.401 11.894-9.307 99.02 97 4 0.1791 613.997 594.724 0.930 1.000 0.375 9.237-7.194 100.00 213 7 0.2125 502.174 491.497 0.958 1.001 0.349 7.162-5.571 100.00 427 22 0.2232 376.854 364.539 0.927 1.001 0.283 5.546-4.326 100.00 867 58 0.1283 517.327 512.296 0.967 1.001 0.214 4.315-3.360 100.00 1859 96 0.1132 491.982 487.967 1.007 1.001 0.153 3.356-2.611 100.00 3867 181 0.1457 323.206 319.192 0.998 1.001 0.057 2.608-2.026 99.99 8198 413 0.1356 214.256 212.123 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1663 104.632 103.950 1.012 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2068 46.398 45.109 0.997 1.003 0.000 1.221-1.150 99.97 13689 708 0.2588 29.234 26.893 0.967 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0432 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1643 r_free=0.1781 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 Total number of N/Q/H flips: 1 r_work=0.1645 r_free=0.1782 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.610314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.530473 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 0.1213 0.1465 0.0251 0.007 0.9 0.6 0.5 0.0 0 11.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.65 2.51 3.012 19.047 2026.530 0.017 12.34 15.32 2.98 2.996 19.413 2026.530 0.016 Individual atomic B min max mean iso aniso Overall: 8.41 117.94 20.77 2.90 0 1785 Protein: 8.41 117.94 17.67 2.90 0 1519 Water: 10.98 114.98 38.81 N/A 0 258 Other: 22.13 34.19 27.57 N/A 0 8 Chain A: 8.41 117.94 20.77 N/A 0 1785 Histogram: Values Number of atoms 8.41 - 19.36 1211 19.36 - 30.31 233 30.31 - 41.27 163 41.27 - 52.22 96 52.22 - 63.17 52 63.17 - 74.13 19 74.13 - 85.08 4 85.08 - 96.03 4 96.03 - 106.99 0 106.99 - 117.94 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1532 r_work=0.1239 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1536 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1238 r_free = 0.1541 target_work(ls_wunit_k1) = 0.015 | | 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= 0.1541 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015408 | | target function (ls_wunit_k1) not normalized (work): 1283.454617 | | target function (ls_wunit_k1) not normalized (free): 113.348172 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1252 0.1238 0.1541 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1683 0.1682 0.1760 n_refl.: 87593 remove outliers: r(all,work,free)=0.1683 0.1682 0.1760 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1707 0.1705 0.1776 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1251 0.1236 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1250 0.1236 0.1536 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3595 300.018 278.984 0.631 1.002 0.373 11.894-9.307 99.02 97 4 0.1639 480.613 468.963 0.908 1.003 0.369 9.237-7.194 100.00 213 7 0.1848 393.082 387.534 0.950 1.003 0.340 7.162-5.571 100.00 427 22 0.1747 294.986 289.462 0.924 1.003 0.280 5.546-4.326 100.00 867 58 0.0924 404.944 402.319 0.951 1.003 0.199 4.315-3.360 100.00 1859 96 0.0784 385.104 384.077 0.996 1.002 0.180 3.356-2.611 100.00 3867 181 0.1026 252.993 252.291 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.0969 167.712 167.169 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1190 81.902 82.102 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1630 36.319 35.780 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2353 22.883 21.385 0.969 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0552 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1237 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1538 | n_water=258 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1248 r_free=0.1536 | n_water=251 | time (s): 25.850 (total time: 28.320) Filter (q & B) r_work=0.1251 r_free=0.1535 | n_water=248 | time (s): 3.700 (total time: 32.020) Compute maps r_work=0.1251 r_free=0.1535 | n_water=248 | time (s): 1.880 (total time: 33.900) Filter (map) r_work=0.1266 r_free=0.1539 | n_water=236 | time (s): 3.820 (total time: 37.720) Find peaks r_work=0.1266 r_free=0.1539 | n_water=236 | time (s): 0.750 (total time: 38.470) Add new water r_work=0.1421 r_free=0.1682 | n_water=461 | time (s): 3.820 (total time: 42.290) Refine new water occ: r_work=0.1331 r_free=0.1568 adp: r_work=0.1245 r_free=0.1510 occ: r_work=0.1259 r_free=0.1507 adp: r_work=0.1224 r_free=0.1491 occ: r_work=0.1226 r_free=0.1482 adp: r_work=0.1217 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1483 r_work=0.1217 r_free=0.1483 | n_water=461 | time (s): 147.150 (total time: 189.440) Filter (q & B) r_work=0.1223 r_free=0.1487 | n_water=439 | time (s): 3.960 (total time: 193.400) Filter (dist only) r_work=0.1223 r_free=0.1486 | n_water=438 | time (s): 45.190 (total time: 238.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.113259 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1546.764121 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 0.1221 0.1517 0.0296 0.007 0.9 2.2 0.5 0.0 0 12.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 15.17 2.96 3.757 22.986 1546.764 0.015 11.96 14.87 2.91 4.016 22.857 1546.764 0.015 Individual atomic B min max mean iso aniso Overall: 8.89 113.81 23.14 2.59 202 1763 Protein: 8.89 113.81 17.55 2.59 0 1519 Water: 11.06 73.88 42.38 N/A 202 236 Other: 24.85 36.31 29.88 N/A 0 8 Chain A: 8.89 113.81 20.24 N/A 0 1763 Chain S: 16.27 68.92 48.44 N/A 202 0 Histogram: Values Number of atoms 8.89 - 19.38 1212 19.38 - 29.87 252 29.87 - 40.37 191 40.37 - 50.86 134 50.86 - 61.35 115 61.35 - 71.84 50 71.84 - 82.34 5 82.34 - 92.83 3 92.83 - 103.32 1 103.32 - 113.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1488 r_work=0.1196 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1487 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1480 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1480 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014050 | | target function (ls_wunit_k1) not normalized (work): 1170.345006 | | target function (ls_wunit_k1) not normalized (free): 109.520122 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1197 0.1480 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1598 0.1594 0.1719 n_refl.: 87592 remove outliers: r(all,work,free)=0.1598 0.1594 0.1719 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1605 0.1600 0.1723 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1193 0.1477 n_refl.: 87592 remove outliers: r(all,work,free)=0.1206 0.1192 0.1477 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 0.3486 295.942 271.296 0.626 0.939 0.370 11.894-9.307 99.02 97 4 0.1406 480.613 480.473 0.978 0.939 0.370 9.237-7.194 100.00 213 7 0.1716 393.082 395.072 1.042 0.939 0.290 7.162-5.571 100.00 427 22 0.1487 294.986 291.273 1.001 0.939 0.250 5.546-4.326 100.00 867 58 0.0845 404.944 401.774 1.019 0.940 0.205 4.315-3.360 100.00 1859 96 0.0714 385.104 384.050 1.067 0.940 0.200 3.356-2.611 100.00 3867 181 0.0962 252.993 252.318 1.073 0.941 0.130 2.608-2.026 99.99 8198 413 0.0959 167.712 167.289 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1167 81.902 82.111 1.087 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1596 36.319 35.829 1.070 0.948 0.000 1.221-1.150 99.97 13689 708 0.2336 22.883 21.419 1.023 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0643 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1477 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1192 r_free=0.1477 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1477 | n_water=438 | time (s): 2.020 (total time: 2.020) Filter (dist) r_work=0.1192 r_free=0.1478 | n_water=436 | time (s): 41.840 (total time: 43.860) Filter (q & B) r_work=0.1192 r_free=0.1478 | n_water=436 | time (s): 1.280 (total time: 45.140) Compute maps r_work=0.1192 r_free=0.1478 | n_water=436 | time (s): 1.800 (total time: 46.940) Filter (map) r_work=0.1233 r_free=0.1475 | n_water=297 | time (s): 2.890 (total time: 49.830) Find peaks r_work=0.1233 r_free=0.1475 | n_water=297 | time (s): 0.590 (total time: 50.420) Add new water r_work=0.1352 r_free=0.1587 | n_water=485 | time (s): 3.430 (total time: 53.850) Refine new water occ: r_work=0.1255 r_free=0.1502 adp: r_work=0.1256 r_free=0.1504 occ: r_work=0.1235 r_free=0.1482 adp: r_work=0.1233 r_free=0.1483 occ: r_work=0.1221 r_free=0.1470 adp: r_work=0.1215 r_free=0.1469 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1469 r_work=0.1215 r_free=0.1469 | n_water=485 | time (s): 209.140 (total time: 262.990) Filter (q & B) r_work=0.1218 r_free=0.1469 | n_water=456 | time (s): 2.610 (total time: 265.600) Filter (dist only) r_work=0.1217 r_free=0.1468 | n_water=455 | time (s): 38.810 (total time: 304.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.016609 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.906572 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 0.1228 0.1442 0.0214 0.006 0.9 2.2 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.42 2.14 3.598 22.032 53.907 3.723 12.14 14.04 1.90 4.118 21.840 53.907 3.651 Individual atomic B min max mean iso aniso Overall: 9.21 109.61 21.61 2.33 221 1761 Protein: 9.21 109.61 17.12 2.34 0 1519 Water: 11.45 72.83 36.48 N/A 221 234 Other: 21.03 32.63 26.80 N/A 0 8 Chain A: 9.21 109.61 19.78 N/A 0 1761 Chain S: 15.74 64.20 36.20 N/A 221 0 Histogram: Values Number of atoms 9.21 - 19.25 1233 19.25 - 29.29 283 29.29 - 39.33 229 39.33 - 49.37 128 49.37 - 59.41 71 59.41 - 69.45 27 69.45 - 79.49 5 79.49 - 89.53 3 89.53 - 99.57 1 99.57 - 109.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1404 r_work=0.1215 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1405 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1399 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.17 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= 0.1208 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.648752 | | target function (ml) not normalized (work): 303915.514294 | | target function (ml) not normalized (free): 16056.336644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1208 0.1399 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1534 0.1533 0.1573 n_refl.: 87589 remove outliers: r(all,work,free)=0.1534 0.1533 0.1573 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1531 0.1531 0.1571 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1197 0.1368 n_refl.: 87589 remove outliers: r(all,work,free)=0.1200 0.1191 0.1368 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3796 295.305 259.877 0.475 1.000 0.320 11.894-9.307 93.14 91 4 0.2362 467.844 450.774 0.846 1.002 0.220 9.237-7.194 98.18 209 7 0.2341 384.596 388.101 0.940 1.002 0.170 7.162-5.571 100.00 427 22 0.2116 294.986 283.985 0.909 1.002 0.150 5.546-4.326 100.00 867 58 0.1100 404.944 399.994 0.951 1.002 0.148 4.315-3.360 100.00 1859 96 0.0926 385.104 382.427 0.993 1.002 0.147 3.356-2.611 100.00 3867 181 0.1161 252.993 250.913 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1050 167.712 166.766 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.0996 81.902 82.058 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1274 36.319 35.901 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2127 22.883 21.495 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0361 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1368 | n_water=455 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1191 r_free=0.1369 | n_water=454 | time (s): 40.020 (total time: 41.810) Filter (q & B) r_work=0.1191 r_free=0.1367 | n_water=452 | time (s): 2.830 (total time: 44.640) Compute maps r_work=0.1191 r_free=0.1367 | n_water=452 | time (s): 1.630 (total time: 46.270) Filter (map) r_work=0.1218 r_free=0.1398 | n_water=311 | time (s): 3.470 (total time: 49.740) Find peaks r_work=0.1218 r_free=0.1398 | n_water=311 | time (s): 0.590 (total time: 50.330) Add new water r_work=0.1280 r_free=0.1451 | n_water=487 | time (s): 2.550 (total time: 52.880) Refine new water occ: r_work=0.1208 r_free=0.1381 adp: r_work=0.1208 r_free=0.1384 occ: r_work=0.1193 r_free=0.1369 adp: r_work=0.1192 r_free=0.1370 occ: r_work=0.1182 r_free=0.1363 adp: r_work=0.1179 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1362 r_work=0.1179 r_free=0.1362 | n_water=487 | time (s): 208.540 (total time: 261.420) Filter (q & B) r_work=0.1189 r_free=0.1365 | n_water=444 | time (s): 2.660 (total time: 264.080) Filter (dist only) r_work=0.1189 r_free=0.1364 | n_water=443 | time (s): 37.550 (total time: 301.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.997141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.180848 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 0.1191 0.1381 0.0190 0.006 1.0 1.6 0.5 0.0 0 0.999 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.81 1.90 3.411 21.353 50.181 3.635 11.85 13.75 1.91 3.691 21.265 50.181 3.624 Individual atomic B min max mean iso aniso Overall: 9.30 105.07 21.12 2.17 212 1758 Protein: 9.30 105.07 16.92 2.17 0 1519 Water: 11.50 71.91 35.45 N/A 212 231 Other: 21.10 30.21 25.63 N/A 0 8 Chain A: 9.30 105.07 19.49 N/A 0 1758 Chain S: 15.41 61.64 34.68 N/A 212 0 Histogram: Values Number of atoms 9.30 - 18.88 1232 18.88 - 28.46 276 28.46 - 38.03 220 38.03 - 47.61 137 47.61 - 57.18 68 57.18 - 66.76 23 66.76 - 76.34 9 76.34 - 85.91 2 85.91 - 95.49 1 95.49 - 105.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1375 r_work=0.1185 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1376 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1374 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623623 | | target function (ml) not normalized (work): 301775.295859 | | target function (ml) not normalized (free): 15958.127734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1374 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1502 0.1500 0.1574 n_refl.: 87576 remove outliers: r(all,work,free)=0.1502 0.1500 0.1574 n_refl.: 87576 overall B=-0.02 to atoms: r(all,work,free)=0.1499 0.1497 0.1572 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1377 n_refl.: 87576 remove outliers: r(all,work,free)=0.1188 0.1179 0.1377 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 0.4082 290.651 253.152 0.458 0.953 0.298 11.894-9.307 92.16 90 4 0.2386 470.369 444.819 0.860 0.956 0.212 9.237-7.194 97.73 208 7 0.2485 385.674 377.105 0.949 0.956 0.140 7.162-5.571 100.00 427 22 0.2235 294.986 283.982 0.940 0.956 0.110 5.546-4.326 100.00 867 58 0.1149 404.944 400.400 0.996 0.957 0.110 4.315-3.360 100.00 1859 96 0.0959 385.104 382.703 1.041 0.956 0.110 3.356-2.611 100.00 3867 181 0.1154 252.993 251.031 1.049 0.956 0.080 2.608-2.026 99.99 8198 413 0.1023 167.712 166.903 1.062 0.955 0.000 2.025-1.573 100.00 17313 902 0.0954 81.902 82.189 1.078 0.954 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.319 35.946 1.073 0.951 0.000 1.221-1.150 99.97 13689 708 0.2120 22.883 21.506 1.029 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0450 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1377 After: r_work=0.1179 r_free=0.1377 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1377 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=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1377 | n_water=443 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1179 r_free=0.1377 | n_water=443 | time (s): 33.490 (total time: 35.840) Filter (q & B) r_work=0.1180 r_free=0.1376 | n_water=442 | time (s): 3.450 (total time: 39.290) Compute maps r_work=0.1180 r_free=0.1376 | n_water=442 | time (s): 1.600 (total time: 40.890) Filter (map) r_work=0.1209 r_free=0.1393 | n_water=322 | time (s): 2.620 (total time: 43.510) Find peaks r_work=0.1209 r_free=0.1393 | n_water=322 | time (s): 0.610 (total time: 44.120) Add new water r_work=0.1253 r_free=0.1432 | n_water=500 | time (s): 3.200 (total time: 47.320) Refine new water occ: r_work=0.1185 r_free=0.1373 adp: r_work=0.1185 r_free=0.1376 occ: r_work=0.1172 r_free=0.1362 adp: r_work=0.1172 r_free=0.1364 occ: r_work=0.1163 r_free=0.1355 adp: r_work=0.1161 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1356 r_work=0.1161 r_free=0.1356 | n_water=500 | time (s): 195.920 (total time: 243.240) Filter (q & B) r_work=0.1171 r_free=0.1367 | n_water=446 | time (s): 3.420 (total time: 246.660) Filter (dist only) r_work=0.1171 r_free=0.1366 | n_water=445 | time (s): 38.470 (total time: 285.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.195815 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.549015 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 0.1195 0.1383 0.0188 0.007 1.1 5.8 0.5 0.0 0 1.098 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.83 1.88 3.294 21.091 45.549 3.632 12.03 13.88 1.85 3.575 20.994 45.549 3.628 Individual atomic B min max mean iso aniso Overall: 9.28 100.65 20.88 2.01 214 1758 Protein: 9.28 100.65 16.69 2.01 0 1519 Water: 11.57 70.96 35.10 N/A 214 231 Other: 20.89 29.01 25.04 N/A 0 8 Chain A: 9.28 100.65 19.25 N/A 0 1758 Chain S: 14.25 61.70 34.23 N/A 214 0 Histogram: Values Number of atoms 9.28 - 18.41 1222 18.41 - 27.55 279 27.55 - 36.69 220 36.69 - 45.83 133 45.83 - 54.96 73 54.96 - 64.10 30 64.10 - 73.24 11 73.24 - 82.38 1 82.38 - 91.51 1 91.51 - 100.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1388 r_work=0.1203 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1388 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1383 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1200 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626854 | | target function (ml) not normalized (work): 302033.526820 | | target function (ml) not normalized (free): 15972.359711 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1428 0.1470 5.6801 5.681| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1474 5.2296 5.2925| | 3: 2.83 - 2.48 1.00 2820 163 0.1233 0.1230 5.0314 5.0311| | 4: 2.47 - 2.25 1.00 2825 136 0.1038 0.1169 4.7332 4.782| | 5: 2.25 - 2.09 1.00 2756 127 0.1001 0.1130 4.6751 4.7496| | 6: 2.09 - 1.97 1.00 2846 113 0.0978 0.1226 4.3687 4.492| | 7: 1.97 - 1.87 1.00 2787 165 0.0983 0.1266 4.0815 4.2038| | 8: 1.87 - 1.79 1.00 2789 144 0.1020 0.1250 3.9988 4.0928| | 9: 1.79 - 1.72 1.00 2745 138 0.0943 0.1259 3.7131 3.8918| | 10: 1.72 - 1.66 1.00 2831 160 0.0990 0.1247 3.6328 3.7724| | 11: 1.66 - 1.61 1.00 2712 147 0.0955 0.1115 3.57 3.6204| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1172 3.3469 3.4822| | 13: 1.56 - 1.52 1.00 2745 130 0.0969 0.1074 3.3364 3.4371| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1112 3.2578 3.3359| | 15: 1.48 - 1.45 1.00 2738 128 0.1007 0.1360 3.1673 3.339| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1233 3.1505 3.2348| | 17: 1.42 - 1.39 1.00 2785 139 0.1118 0.1305 3.1165 3.2338| | 18: 1.39 - 1.36 1.00 2741 179 0.1142 0.1374 3.0858 3.2638| | 19: 1.36 - 1.34 1.00 2807 134 0.1211 0.1630 3.0941 3.2754| | 20: 1.34 - 1.32 1.00 2696 147 0.1322 0.1442 3.0918 3.1222| | 21: 1.32 - 1.30 1.00 2785 112 0.1406 0.1617 3.0877 3.1718| | 22: 1.29 - 1.27 1.00 2704 152 0.1471 0.1956 3.0866 3.2962| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1857 3.104 3.2083| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1769 3.0984 3.1983| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2300 3.1119 3.2907| | 26: 1.22 - 1.21 1.00 2727 135 0.1856 0.1804 3.1249 3.2018| | 27: 1.21 - 1.19 1.00 2814 148 0.2008 0.2073 3.1435 3.1495| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2272 3.1435 3.1647| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2401 3.13 3.236| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2508 3.1207 3.1715| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.94 9.58 1.00 0.97 6769.77| | 2: 3.57 - 2.84 2888 124 0.92 13.97 1.01 0.97 6769.77| | 3: 2.83 - 2.48 2820 163 0.88 18.13 0.99 0.97 5667.64| | 4: 2.47 - 2.25 2825 136 0.91 15.17 1.00 0.98 2825.60| | 5: 2.25 - 2.09 2756 127 0.89 17.39 1.01 0.98 2825.60| | 6: 2.09 - 1.97 2846 113 0.91 13.98 1.02 0.98 1647.42| | 7: 1.97 - 1.87 2787 165 0.94 10.93 1.02 0.98 642.60| | 8: 1.87 - 1.79 2789 144 0.91 14.58 0.99 0.98 642.60| | 9: 1.79 - 1.72 2745 138 0.93 11.51 0.98 0.97 345.36| | 10: 1.72 - 1.66 2831 160 0.93 12.32 0.98 0.97 285.84| | 11: 1.66 - 1.61 2712 147 0.93 12.95 0.98 0.97 272.75| | 12: 1.61 - 1.56 2773 144 0.95 9.57 0.99 0.97 149.34| | 13: 1.56 - 1.52 2745 130 0.94 11.13 1.02 0.97 149.34| | 14: 1.52 - 1.48 2803 134 0.94 11.26 1.02 0.98 133.22| | 15: 1.48 - 1.45 2738 128 0.95 10.39 1.01 0.99 103.70| | 16: 1.45 - 1.42 2756 161 0.94 11.59 1.02 0.99 103.70| | 17: 1.42 - 1.39 2785 139 0.94 11.43 1.01 0.99 93.55| | 18: 1.39 - 1.36 2741 179 0.94 11.71 1.01 0.99 87.67| | 19: 1.36 - 1.34 2807 134 0.94 12.26 1.00 0.99 87.67| | 20: 1.34 - 1.32 2696 147 0.94 12.38 0.99 0.97 82.63| | 21: 1.32 - 1.30 2785 112 0.94 13.28 0.98 0.97 82.28| | 22: 1.29 - 1.27 2704 152 0.93 13.83 0.98 0.96 82.47| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 83.44| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 83.44| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 85.20| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.94 87.16| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 87.16| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.93 90.97| | 29: 1.18 - 1.16 2800 134 0.88 20.70 0.99 0.93 92.40| | 30: 1.16 - 1.15 2739 148 0.86 22.09 0.98 0.93 92.40| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.28 max = 6769.77 mean = 1043.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.17| |phase err.(test): min = 0.00 max = 88.01 mean = 14.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1200 0.1383 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1509 0.1507 0.1579 n_refl.: 87573 remove outliers: r(all,work,free)=0.1509 0.1507 0.1579 n_refl.: 87573 overall B=-0.02 to atoms: r(all,work,free)=0.1507 0.1504 0.1577 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1200 0.1386 n_refl.: 87573 remove outliers: r(all,work,free)=0.1209 0.1200 0.1386 n_refl.: 87572 ======================== 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 0.3973 290.651 256.401 0.440 0.955 0.250 11.894-9.307 91.18 89 4 0.2442 466.444 447.836 0.858 0.957 0.151 9.237-7.194 97.73 208 7 0.2559 385.674 378.181 0.943 0.957 0.106 7.162-5.571 100.00 427 22 0.2249 294.986 284.999 0.939 0.958 0.103 5.546-4.326 100.00 867 58 0.1204 404.944 400.399 0.997 0.958 0.102 4.315-3.360 100.00 1859 96 0.1012 385.104 382.257 1.040 0.957 0.100 3.356-2.611 100.00 3867 181 0.1198 252.993 250.772 1.047 0.957 0.090 2.608-2.026 99.99 8198 413 0.1047 167.712 166.701 1.062 0.956 0.000 2.025-1.573 100.00 17313 902 0.0969 81.902 82.135 1.076 0.955 0.000 1.573-1.221 100.00 36679 1900 0.1222 36.319 35.937 1.071 0.953 0.000 1.221-1.150 99.97 13689 708 0.2113 22.883 21.503 1.027 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0432 ================= 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 : 0.2605 0.1964 0.083 5.191 8.8 119.3 19.9 258 0.000 1_bss: 0.1643 0.1781 0.083 5.191 9.0 119.5 20.1 258 0.000 1_settarget: 0.1643 0.1781 0.083 5.191 9.0 119.5 20.1 258 0.000 1_nqh: 0.1645 0.1782 0.083 5.191 9.0 119.5 20.1 258 0.003 1_weight: 0.1645 0.1782 0.083 5.191 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1465 0.007 0.933 9.0 119.5 20.1 258 0.128 1_adp: 0.1235 0.1532 0.007 0.933 8.4 117.9 20.8 258 0.128 1_regHadp: 0.1239 0.1536 0.007 0.933 8.4 117.9 20.8 258 0.128 1_occ: 0.1238 0.1541 0.007 0.933 8.4 117.9 20.8 258 0.128 2_bss: 0.1236 0.1536 0.007 0.933 8.5 118.1 20.9 258 0.128 2_settarget: 0.1236 0.1536 0.007 0.933 8.5 118.1 20.9 258 0.128 2_updatecdl: 0.1236 0.1536 0.007 0.938 8.5 118.1 20.9 258 0.128 2_nqh: 0.1237 0.1538 0.007 0.938 8.5 118.1 20.9 258 0.131 2_sol: 0.1223 0.1486 0.007 0.938 8.5 118.1 23.4 438 n/a 2_weight: 0.1223 0.1486 0.007 0.938 8.5 118.1 23.4 438 n/a 2_xyzrec: 0.1221 0.1517 0.007 0.878 8.5 118.1 23.4 438 n/a 2_adp: 0.1196 0.1488 0.007 0.878 8.9 113.8 23.1 438 n/a 2_regHadp: 0.1196 0.1487 0.007 0.878 8.9 113.8 23.1 438 n/a 2_occ: 0.1197 0.1480 0.007 0.878 8.9 113.8 23.1 438 n/a 3_bss: 0.1192 0.1477 0.007 0.878 8.9 113.9 23.2 438 n/a 3_settarget: 0.1192 0.1477 0.007 0.878 8.9 113.9 23.2 438 n/a 3_updatecdl: 0.1192 0.1477 0.007 0.878 8.9 113.9 23.2 438 n/a 3_nqh: 0.1192 0.1477 0.007 0.878 8.9 113.9 23.2 438 n/a 3_sol: 0.1217 0.1468 0.007 0.878 8.9 113.9 22.0 455 n/a 3_weight: 0.1217 0.1468 0.007 0.878 8.9 113.9 22.0 455 n/a 3_xyzrec: 0.1228 0.1442 0.006 0.923 8.9 113.9 22.0 455 n/a 3_adp: 0.1214 0.1404 0.006 0.923 9.2 109.6 21.6 455 n/a 3_regHadp: 0.1215 0.1405 0.006 0.923 9.2 109.6 21.6 455 n/a 3_occ: 0.1208 0.1399 0.006 0.923 9.2 109.6 21.6 455 n/a 4_bss: 0.1192 0.1368 0.006 0.923 9.2 109.6 21.6 455 n/a 4_settarget: 0.1192 0.1368 0.006 0.923 9.2 109.6 21.6 455 n/a 4_updatecdl: 0.1192 0.1368 0.006 0.923 9.2 109.6 21.6 455 n/a 4_nqh: 0.1192 0.1368 0.006 0.923 9.2 109.6 21.6 455 n/a 4_sol: 0.1189 0.1364 0.006 0.923 9.2 109.6 21.3 443 n/a 4_weight: 0.1189 0.1364 0.006 0.923 9.2 109.6 21.3 443 n/a 4_xyzrec: 0.1191 0.1381 0.006 0.957 9.2 109.6 21.3 443 n/a 4_adp: 0.1185 0.1375 0.006 0.957 9.3 105.1 21.1 443 n/a 4_regHadp: 0.1185 0.1376 0.006 0.957 9.3 105.1 21.1 443 n/a 4_occ: 0.1182 0.1374 0.006 0.957 9.3 105.1 21.1 443 n/a 5_bss: 0.1179 0.1377 0.006 0.957 9.3 105.0 21.1 443 n/a 5_settarget: 0.1179 0.1377 0.006 0.957 9.3 105.0 21.1 443 n/a 5_updatecdl: 0.1179 0.1377 0.006 0.958 9.3 105.0 21.1 443 n/a 5_setrh: 0.1179 0.1377 0.006 0.958 9.3 105.0 21.1 443 n/a 5_nqh: 0.1179 0.1377 0.006 0.958 9.3 105.0 21.1 443 n/a 5_sol: 0.1171 0.1366 0.006 0.958 9.3 105.0 21.0 445 n/a 5_weight: 0.1171 0.1366 0.006 0.958 9.3 105.0 21.0 445 n/a 5_xyzrec: 0.1195 0.1383 0.007 1.084 9.3 105.0 21.0 445 n/a 5_adp: 0.1203 0.1388 0.007 1.084 9.3 100.7 20.9 445 n/a 5_regHadp: 0.1203 0.1388 0.007 1.084 9.3 100.7 20.9 445 n/a 5_occ: 0.1200 0.1383 0.007 1.084 9.3 100.7 20.9 445 n/a end: 0.1200 0.1386 0.007 1.084 9.3 100.6 20.9 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8530786_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8530786_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9900 Refinement macro-cycles (run) : 3622.9800 Write final files (write_after_run_outputs) : 57.6300 Total : 3685.6000 Total CPU time: 62.05 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:06 PST -0800 (1735452786.03 s) Start R-work = 0.1643, R-free = 0.1781 Final R-work = 0.1200, R-free = 0.1386 =============================================================================== Job complete usr+sys time: 3817.08 seconds wall clock time: 68 minutes 12.54 seconds (4092.54 seconds total)