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_8498250.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 { 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_8498250.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.pdb" 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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.68, per 1000 atoms: 0.50 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 108.1 milliseconds Time building geometry restraints manager: 0.44 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: 524 0.91 - 1.17: 1127 1.17 - 1.42: 638 1.42 - 1.68: 824 1.68 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.948 0.289 1.16e-02 7.43e+03 6.19e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.65e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.331 1.522 -0.191 1.05e-02 9.07e+03 3.32e+02 bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.455 1.231 0.224 1.25e-02 6.40e+03 3.21e+02 bond pdb=" CA ALA A 165 " pdb=" C ALA A 165 " ideal model delta sigma weight residual 1.524 1.300 0.224 1.29e-02 6.01e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 3296 4.97 - 9.94: 1848 9.94 - 14.91: 558 14.91 - 19.88: 72 19.88 - 24.85: 3 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 95.86 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 122.27 138.23 -15.96 1.23e+00 6.61e-01 1.68e+02 angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 135.57 -12.97 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" N ALYS A 93 " ideal model delta sigma weight residual 117.39 101.55 15.84 1.24e+00 6.50e-01 1.63e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " ideal model delta sigma weight residual 115.61 102.52 13.09 1.03e+00 9.43e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 15.72: 910 15.72 - 31.43: 144 31.43 - 47.13: 31 47.13 - 62.84: 22 62.84 - 78.55: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 115 0.253 - 0.506: 72 0.506 - 0.759: 40 0.759 - 1.011: 12 1.011 - 1.264: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -3.85 1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" CA HIS A 138 " pdb=" N HIS A 138 " pdb=" C HIS A 138 " pdb=" CB HIS A 138 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.006 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.138 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.094 2.00e-02 2.50e+03 7.07e-02 1.12e+02 pdb=" CG HIS A 126 " -0.124 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.018 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.113 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 620 2.25 - 2.84: 7617 2.84 - 3.42: 10668 3.42 - 4.01: 15427 4.01 - 4.60: 22287 Nonbonded interactions: 56619 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" O GLY A 37 " pdb=" H LEU A 58 " model vdw 1.810 1.850 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.853 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 1.850 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.875 2.270 ... (remaining 56614 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_8498250_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= 0.2599 r_free= 0.1938 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790223 | | target function (ml) not normalized (work): 232442.341864 | | target function (ml) not normalized (free): 11821.779078 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3037 0.2094 7.1009 4.9491| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1797 4.3469 4.3353| | 3: 2.84 - 2.48 1.00 2833 165 0.2329 0.1532 4.1174 4.1375| | 4: 2.47 - 2.25 1.00 2825 136 0.2343 0.1403 3.8257 3.8112| | 5: 2.25 - 2.09 1.00 2756 127 0.2459 0.1777 3.7918 3.8313| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1638 3.4668 3.4897| | 7: 1.97 - 1.87 1.00 2787 165 0.2495 0.1730 3.1246 3.1603| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1835 3.0627 3.112| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.1939 2.8922 3.0102| | 10: 1.72 - 1.66 1.00 2789 158 0.2346 0.2081 2.7974 2.9316| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.2048 2.7485 2.8418| | 12: 1.61 - 1.56 1.00 2787 146 0.2549 0.2012 2.6593 2.6875| | 13: 1.56 - 1.52 1.00 2745 130 0.2527 0.1976 2.5863 2.6666| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2215 2.5195 2.6255| | 15: 1.48 - 1.45 1.00 2738 128 0.2572 0.2096 2.4135 2.4887| | 16: 1.45 - 1.42 1.00 2756 161 0.2665 0.2405 2.3923 2.5309| | 17: 1.42 - 1.39 1.00 2785 139 0.2716 0.2048 2.3369 2.3586| | 18: 1.39 - 1.36 1.00 2741 179 0.2698 0.2323 2.2787 2.3792| | 19: 1.36 - 1.34 1.00 2807 134 0.2598 0.2402 2.2454 2.3188| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2240 2.1899 2.2147| | 21: 1.32 - 1.30 1.00 2785 112 0.2744 0.2262 2.1703 2.1977| | 22: 1.29 - 1.27 1.00 2704 152 0.2737 0.2429 2.1286 2.1841| | 23: 1.27 - 1.26 1.00 2802 156 0.2705 0.2474 2.0963 2.1458| | 24: 1.26 - 1.24 1.00 2744 132 0.2786 0.2369 2.0767 2.1136| | 25: 1.24 - 1.22 1.00 2734 148 0.2811 0.2527 2.0168 2.0718| | 26: 1.22 - 1.21 1.00 2727 135 0.2903 0.2179 2.0127 2.0071| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2422 1.9924 1.9612| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2308 1.9757 1.9079| | 29: 1.18 - 1.16 1.00 2800 134 0.2960 0.2530 1.9518 1.985| | 30: 1.16 - 1.15 1.00 2740 148 0.3052 0.2776 1.9298 1.9304| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1454.69| | 2: 3.57 - 2.84 2876 122 0.81 25.77 1.27 0.23 1454.69| | 3: 2.84 - 2.48 2833 165 0.74 31.71 1.24 0.24 1205.87| | 4: 2.47 - 2.25 2825 136 0.81 25.25 1.25 0.25 560.14| | 5: 2.25 - 2.09 2756 127 0.78 28.98 1.28 0.25 560.14| | 6: 2.09 - 1.97 2846 113 0.84 22.41 1.29 0.25 306.47| | 7: 1.97 - 1.87 2787 165 0.90 16.34 1.27 0.26 90.12| | 8: 1.87 - 1.79 2789 144 0.86 21.00 1.25 0.26 90.12| | 9: 1.79 - 1.72 2745 138 0.88 18.99 1.23 0.25 57.21| | 10: 1.72 - 1.66 2789 158 0.86 20.57 1.22 0.25 50.61| | 11: 1.66 - 1.61 2740 147 0.85 22.08 1.24 0.25 48.96| | 12: 1.61 - 1.56 2787 146 0.87 19.62 1.23 0.25 32.20| | 13: 1.56 - 1.52 2745 130 0.86 21.30 1.23 0.25 32.20| | 14: 1.52 - 1.48 2803 134 0.85 21.93 1.24 0.25 28.88| | 15: 1.48 - 1.45 2738 128 0.86 21.47 1.24 0.25 22.80| | 16: 1.45 - 1.42 2756 161 0.84 23.03 1.24 0.25 22.80| | 17: 1.42 - 1.39 2785 139 0.85 22.06 1.24 0.25 19.18| | 18: 1.39 - 1.36 2741 179 0.85 22.19 1.24 0.25 17.08| | 19: 1.36 - 1.34 2807 134 0.84 23.00 1.21 0.25 17.08| | 20: 1.34 - 1.32 2696 147 0.86 21.44 1.21 0.24 13.43| | 21: 1.32 - 1.30 2785 112 0.85 22.40 1.21 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.64 1.21 0.24 12.75| | 23: 1.27 - 1.26 2802 156 0.87 21.25 1.20 0.24 10.62| | 24: 1.26 - 1.24 2744 132 0.86 22.03 1.20 0.24 10.62| | 25: 1.24 - 1.22 2734 148 0.85 22.46 1.21 0.24 9.78| | 26: 1.22 - 1.21 2727 135 0.86 22.26 1.21 0.24 8.86| | 27: 1.21 - 1.19 2814 148 0.85 23.12 1.21 0.24 8.86| | 28: 1.19 - 1.18 2671 147 0.85 22.94 1.19 0.23 7.89| | 29: 1.18 - 1.16 2800 134 0.85 22.86 1.17 0.23 7.52| | 30: 1.16 - 1.15 2740 148 0.84 24.19 1.16 0.23 7.52| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 7.52 max = 1454.69 mean = 211.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.47| |phase err.(test): min = 0.00 max = 89.77 mean = 22.27| |-----------------------------------------------------------------------------| ----------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 0.289 1557 Z= 5.583 Angle : 5.285 17.694 2118 Z= 3.771 Chirality : 0.415 1.264 243 Planarity : 0.033 0.111 284 Dihedral : 13.679 78.546 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % 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: -2.46 (0.44), residues: 224 helix: -2.54 (0.34), residues: 108 sheet: -0.48 (0.92), residues: 28 loop : -0.44 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.020 ARG A 5 TYR 0.091 0.043 TYR A 141 PHE 0.105 0.045 PHE A 162 HIS 0.081 0.050 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2599 r_free= 0.1938 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790223 | | target function (ml) not normalized (work): 232442.341864 | | target function (ml) not normalized (free): 11821.779078 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2599 0.1939 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2599 0.1939 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1972 0.1939 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1990 0.1994 0.1950 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1625 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1624 0.1785 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 0.3802 386.489 360.633 0.729 0.922 0.407 11.894-9.307 99.02 97 4 0.1803 613.919 593.469 1.014 0.923 0.390 9.237-7.194 100.00 213 7 0.2196 502.110 489.542 1.041 0.923 0.344 7.162-5.571 100.00 427 22 0.2223 376.806 364.554 1.013 0.923 0.330 5.546-4.326 100.00 867 58 0.1300 517.261 510.974 1.050 0.922 0.240 4.315-3.360 100.00 1859 96 0.1120 491.919 487.422 1.093 0.922 0.158 3.356-2.611 100.00 3867 181 0.1417 323.165 320.549 1.086 0.922 0.129 2.608-2.026 99.99 8198 413 0.1351 214.229 211.896 1.097 0.921 0.000 2.025-1.573 100.00 17313 902 0.1635 104.618 103.837 1.096 0.920 0.000 1.573-1.221 100.00 36679 1900 0.2042 46.392 45.119 1.089 0.918 0.000 1.221-1.150 99.97 13689 708 0.2559 29.230 27.080 1.066 0.916 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1624 r_free=0.1785 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.892841 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2041.846519 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 0.1694 0.1813 0.0119 0.002 0.4 5.4 0.0 0.0 0 0.125 0.1551 0.1691 0.0140 0.001 0.5 4.2 0.0 0.0 0 0.250 0.1431 0.1600 0.0169 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1360 0.1546 0.0186 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1339 0.1542 0.0203 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1348 0.1549 0.0200 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1294 0.1516 0.0222 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1273 0.1500 0.0227 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1488 0.0233 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1481 0.0234 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1237 0.1472 0.0235 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1234 0.1472 0.0237 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1231 0.1465 0.0234 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1226 0.1462 0.0235 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1227 0.1467 0.0240 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1223 0.1465 0.0242 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1223 0.1466 0.0243 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1219 0.1469 0.0250 0.008 1.0 4.2 0.5 0.6 0 13.446 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1462 0.0235 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.62 2.35 3.013 19.034 2041.847 0.017 12.27 14.61 2.35 2.989 19.034 61.255 0.017 12.33 14.59 2.26 2.675 19.033 255.231 0.017 12.68 15.24 2.56 2.748 19.204 1020.923 0.017 12.52 15.43 2.91 3.200 19.531 2041.847 0.016 12.40 15.38 2.98 3.299 19.611 3062.770 0.015 12.33 15.41 3.08 3.379 19.632 4083.693 0.015 12.29 15.40 3.11 3.387 19.621 5104.616 0.015 12.24 15.39 3.16 3.411 19.633 6125.540 0.015 12.19 15.43 3.24 3.444 19.636 7146.463 0.015 12.22 15.48 3.26 3.551 19.693 8167.386 0.015 12.21 15.53 3.31 3.635 19.720 9188.309 0.015 12.19 15.52 3.33 3.610 19.696 10209.233 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: 255.231 Accepted refinement result: 12.33 14.59 2.26 2.675 19.033 255.231 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.06 3.32 0 1785 Protein: 9.05 115.04 16.97 3.33 0 1519 Water: 11.46 119.42 38.20 N/A 0 258 Other: 19.68 26.58 22.03 N/A 0 8 Chain A: 9.05 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.08 1273 20.08 - 31.12 226 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.34 4 97.34 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1459 r_work=0.1234 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1462 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 = 0.1228 r_free = 0.1459 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1228 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016964 | | target function (ls_wunit_k1) not normalized (work): 1413.030784 | | target function (ls_wunit_k1) not normalized (free): 108.330185 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1459 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1671 0.1672 0.1692 n_refl.: 87593 remove outliers: r(all,work,free)=0.1671 0.1672 0.1692 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1679 0.1680 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1229 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1229 0.1453 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3518 304.846 283.092 0.664 1.003 0.393 11.894-9.307 99.02 97 4 0.1617 484.233 472.406 0.928 1.003 0.380 9.237-7.194 100.00 213 7 0.1906 396.043 390.426 0.963 1.003 0.323 7.162-5.571 100.00 427 22 0.1830 297.208 291.442 0.934 1.003 0.263 5.546-4.326 100.00 867 58 0.1003 407.994 405.066 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.0878 388.005 386.950 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1175 254.899 253.762 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1024 168.975 168.266 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.518 82.709 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.592 36.097 1.018 0.996 0.000 1.221-1.150 99.97 13689 708 0.2254 23.056 21.531 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0658 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1453 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** Total number of N/Q/H flips: 1 r_work=0.1230 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1455 | n_water=258 | time (s): 1.990 (total time: 1.990) Filter (dist) r_work=0.1239 r_free=0.1453 | n_water=250 | time (s): 21.590 (total time: 23.580) Filter (q & B) r_work=0.1241 r_free=0.1453 | n_water=247 | time (s): 2.950 (total time: 26.530) Compute maps r_work=0.1241 r_free=0.1453 | n_water=247 | time (s): 1.630 (total time: 28.160) Filter (map) r_work=0.1264 r_free=0.1460 | n_water=221 | time (s): 3.240 (total time: 31.400) Find peaks r_work=0.1264 r_free=0.1460 | n_water=221 | time (s): 0.490 (total time: 31.890) Add new water r_work=0.1421 r_free=0.1634 | n_water=427 | time (s): 3.280 (total time: 35.170) Refine new water occ: r_work=0.1323 r_free=0.1483 adp: r_work=0.1236 r_free=0.1430 occ: r_work=0.1248 r_free=0.1420 adp: r_work=0.1215 r_free=0.1409 occ: r_work=0.1217 r_free=0.1401 adp: r_work=0.1207 r_free=0.1401 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1401 r_work=0.1207 r_free=0.1401 | n_water=427 | time (s): 60.540 (total time: 95.710) Filter (q & B) r_work=0.1210 r_free=0.1404 | n_water=415 | time (s): 2.980 (total time: 98.690) Filter (dist only) r_work=0.1210 r_free=0.1403 | n_water=414 | time (s): 34.400 (total time: 133.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.438193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1500.119474 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 0.1677 0.1778 0.0100 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1525 0.1648 0.0123 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1425 0.1570 0.0145 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1353 0.1516 0.0163 0.002 0.5 6.1 0.0 0.0 0 0.750 0.1324 0.1497 0.0173 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1338 0.1510 0.0172 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1261 0.1457 0.0196 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1233 0.1437 0.0204 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1222 0.1431 0.0209 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1212 0.1422 0.0211 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1207 0.1427 0.0220 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1203 0.1424 0.0221 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1201 0.1429 0.0228 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1197 0.1426 0.0229 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1194 0.1420 0.0226 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1191 0.1414 0.0223 0.006 0.9 5.4 0.5 0.0 0 11.000 0.1188 0.1417 0.0228 0.007 0.9 5.4 0.5 0.6 0 12.000 0.1188 0.1416 0.0228 0.007 0.9 4.8 0.5 0.0 0 13.000 0.1185 0.1413 0.0227 0.008 1.0 5.8 0.5 0.6 0 14.219 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1185 0.1413 0.0227 0.008 1.0 5.8 0.5 0.6 0 14.219 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 14.13 2.27 3.779 21.755 1500.119 0.015 11.85 14.13 2.27 3.779 21.755 45.004 0.015 11.85 14.13 2.27 3.779 21.755 187.515 0.015 12.06 14.60 2.54 3.611 21.770 750.060 0.015 12.06 14.89 2.83 3.556 21.820 1500.119 0.015 11.93 14.95 3.02 3.458 22.020 2250.179 0.014 11.81 14.85 3.04 3.497 22.112 3000.239 0.014 11.75 14.87 3.12 3.496 22.124 3750.299 0.014 11.73 14.90 3.18 3.517 22.115 4500.358 0.014 11.61 14.76 3.15 3.517 22.071 5250.418 0.013 11.69 14.93 3.25 3.546 22.092 6000.478 0.013 11.64 14.93 3.29 3.573 22.120 6750.538 0.013 11.62 14.91 3.29 3.581 22.113 7500.597 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 187.515 Accepted refinement result: 11.85 14.13 2.27 3.779 21.755 187.515 0.015 Individual atomic B min max mean iso aniso Overall: 9.09 115.08 22.16 3.32 193 1748 Protein: 9.09 115.08 17.01 3.33 0 1519 Water: 11.50 76.68 41.07 N/A 193 221 Other: 19.72 26.62 22.07 N/A 0 8 Chain A: 9.09 115.08 19.35 N/A 0 1748 Chain S: 17.39 60.00 47.62 N/A 193 0 Histogram: Values Number of atoms 9.09 - 19.69 1257 19.69 - 30.29 246 30.29 - 40.89 160 40.89 - 51.49 132 51.49 - 62.09 123 62.09 - 72.68 12 72.68 - 83.28 5 83.28 - 93.88 4 93.88 - 104.48 0 104.48 - 115.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1413 r_work=0.1185 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1413 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1410 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1185 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014723 | | target function (ls_wunit_k1) not normalized (work): 1226.349703 | | target function (ls_wunit_k1) not normalized (free): 104.289549 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1185 0.1410 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1590 0.1589 0.1632 n_refl.: 87593 remove outliers: r(all,work,free)=0.1590 0.1589 0.1632 n_refl.: 87593 overall B=0.01 to atoms: r(all,work,free)=0.1592 0.1592 0.1634 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1183 0.1406 n_refl.: 87593 remove outliers: r(all,work,free)=0.1192 0.1181 0.1406 n_refl.: 87590 ======================== 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 93.75 85 5 0.3352 300.822 276.957 0.601 1.003 0.350 11.894-9.307 99.02 97 4 0.1611 484.233 476.809 0.925 1.003 0.330 9.237-7.194 100.00 213 7 0.1661 396.043 396.355 0.985 1.003 0.280 7.162-5.571 100.00 427 22 0.1538 297.208 293.210 0.942 1.003 0.250 5.546-4.326 100.00 867 58 0.0873 407.994 405.059 0.962 1.003 0.230 4.315-3.360 100.00 1859 96 0.0781 388.005 387.280 1.004 1.003 0.190 3.356-2.611 100.00 3867 181 0.1080 254.899 253.931 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1014 168.975 168.459 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1100 82.518 82.749 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.592 36.126 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2246 23.056 21.563 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0233 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1406 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=0.1181 r_free=0.1406 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1406 | n_water=414 | time (s): 1.690 (total time: 1.690) Filter (dist) r_work=0.1181 r_free=0.1404 | n_water=411 | time (s): 36.450 (total time: 38.140) Filter (q & B) r_work=0.1181 r_free=0.1404 | n_water=411 | time (s): 0.960 (total time: 39.100) Compute maps r_work=0.1181 r_free=0.1404 | n_water=411 | time (s): 1.240 (total time: 40.340) Filter (map) r_work=0.1220 r_free=0.1407 | n_water=279 | time (s): 3.030 (total time: 43.370) Find peaks r_work=0.1220 r_free=0.1407 | n_water=279 | time (s): 0.470 (total time: 43.840) Add new water r_work=0.1348 r_free=0.1574 | n_water=469 | time (s): 3.050 (total time: 46.890) Refine new water occ: r_work=0.1254 r_free=0.1473 adp: r_work=0.1255 r_free=0.1476 occ: r_work=0.1230 r_free=0.1441 adp: r_work=0.1230 r_free=0.1444 occ: r_work=0.1211 r_free=0.1409 adp: r_work=0.1206 r_free=0.1410 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1410 r_work=0.1206 r_free=0.1410 | n_water=469 | time (s): 198.390 (total time: 245.280) Filter (q & B) r_work=0.1211 r_free=0.1414 | n_water=440 | time (s): 2.840 (total time: 248.120) Filter (dist only) r_work=0.1211 r_free=0.1413 | n_water=438 | time (s): 37.210 (total time: 285.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.784838 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.324011 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 0.1245 0.1382 0.0137 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1202 0.1350 0.0148 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1184 0.1340 0.0156 0.004 0.8 2.9 0.5 0.0 0 0.535 0.1175 0.1333 0.0158 0.005 0.9 3.2 0.5 0.0 0 0.803 0.1169 0.1330 0.0161 0.006 1.0 3.5 0.5 0.0 0 1.071 0.1167 0.1331 0.0164 0.007 1.0 3.2 0.5 0.0 0 1.339 0.1164 0.1330 0.0165 0.007 1.1 3.2 0.5 0.6 0 1.606 0.1164 0.1330 0.0167 0.008 1.1 3.2 0.5 0.6 0 1.874 0.1172 0.1332 0.0160 0.005 0.9 3.2 0.5 0.0 0 0.892 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1330 0.0165 0.007 1.1 3.2 0.5 0.6 0 1.606 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 13.30 1.65 3.783 21.230 44.324 3.626 11.64 13.30 1.65 3.783 21.230 1.330 3.626 11.65 13.30 1.65 3.780 21.230 5.541 3.626 11.71 13.38 1.67 3.713 21.216 22.162 3.622 11.70 13.43 1.73 3.739 21.196 44.324 3.621 11.67 13.44 1.76 3.755 21.173 66.486 3.617 11.61 13.39 1.77 3.770 21.170 88.648 3.611 11.59 13.39 1.80 3.779 21.163 110.810 3.609 11.57 13.39 1.81 3.794 21.151 132.972 3.608 11.58 13.40 1.83 3.808 21.135 155.134 3.608 11.56 13.40 1.84 3.819 21.132 177.296 3.607 11.54 13.38 1.84 3.825 21.135 199.458 3.605 11.53 13.37 1.83 3.834 21.128 221.620 3.604 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.330 Accepted refinement result: 11.64 13.30 1.65 3.783 21.230 1.330 3.626 Individual atomic B min max mean iso aniso Overall: 9.11 115.09 21.19 3.32 217 1748 Protein: 9.11 115.09 17.03 3.33 0 1519 Water: 11.51 76.70 35.60 N/A 217 221 Other: 19.74 26.64 22.08 N/A 0 8 Chain A: 9.11 115.09 19.37 N/A 0 1748 Chain S: 16.34 60.01 35.84 N/A 217 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.30 289 30.30 - 40.90 208 40.90 - 51.50 133 51.50 - 62.10 50 62.10 - 72.70 12 72.70 - 83.30 5 83.30 - 93.90 4 93.90 - 104.50 0 104.50 - 115.09 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1330 r_work=0.1164 r_free=0.1330 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1330 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1322 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1154 r_free= 0.1322 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619148 | | target function (ml) not normalized (work): 301453.351294 | | target function (ml) not normalized (free): 15878.268216 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1322 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1490 0.1489 0.1539 n_refl.: 87590 remove outliers: r(all,work,free)=0.1490 0.1489 0.1539 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1489 0.1488 0.1539 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1156 0.1147 0.1313 n_refl.: 87590 remove outliers: r(all,work,free)=0.1153 0.1145 0.1313 n_refl.: 87584 ======================== 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 91.67 83 5 0.3851 292.705 268.601 0.503 1.001 0.330 11.894-9.307 98.04 96 4 0.2348 484.358 468.040 0.870 1.002 0.330 9.237-7.194 98.64 210 7 0.2356 388.503 386.767 0.955 1.003 0.187 7.162-5.571 100.00 427 22 0.2106 297.208 286.498 0.922 1.003 0.171 5.546-4.326 100.00 867 58 0.1110 407.994 403.355 0.964 1.003 0.160 4.315-3.360 100.00 1859 96 0.0934 388.005 385.507 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1147 254.899 252.804 1.007 1.002 0.038 2.608-2.026 99.99 8198 413 0.0935 168.975 168.091 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.518 82.809 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.592 36.167 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2164 23.056 21.583 0.989 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0060 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1313 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=0.1145 r_free=0.1313 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1313 | n_water=438 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1145 r_free=0.1313 | n_water=438 | time (s): 41.970 (total time: 44.510) Filter (q & B) r_work=0.1146 r_free=0.1313 | n_water=437 | time (s): 4.130 (total time: 48.640) Compute maps r_work=0.1146 r_free=0.1313 | n_water=437 | time (s): 1.920 (total time: 50.560) Filter (map) r_work=0.1172 r_free=0.1312 | n_water=329 | time (s): 3.890 (total time: 54.450) Find peaks r_work=0.1172 r_free=0.1312 | n_water=329 | time (s): 0.720 (total time: 55.170) Add new water r_work=0.1236 r_free=0.1378 | n_water=490 | time (s): 3.800 (total time: 58.970) Refine new water occ: r_work=0.1163 r_free=0.1316 adp: r_work=0.1163 r_free=0.1320 occ: r_work=0.1148 r_free=0.1301 adp: r_work=0.1146 r_free=0.1304 occ: r_work=0.1136 r_free=0.1292 adp: r_work=0.1132 r_free=0.1293 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1293 r_work=0.1132 r_free=0.1293 | n_water=490 | time (s): 210.650 (total time: 269.620) Filter (q & B) r_work=0.1138 r_free=0.1305 | n_water=452 | time (s): 3.960 (total time: 273.580) Filter (dist only) r_work=0.1141 r_free=0.1307 | n_water=449 | time (s): 46.960 (total time: 320.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.754495 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.581328 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 0.1205 0.1344 0.0139 0.002 0.6 3.5 0.5 0.0 0 0.088 0.1163 0.1315 0.0153 0.003 0.8 3.2 0.5 0.0 0 0.263 0.1152 0.1310 0.0158 0.004 0.9 2.9 0.5 0.0 0 0.526 0.1145 0.1307 0.0162 0.006 0.9 2.9 0.5 0.0 0 0.790 0.1141 0.1308 0.0167 0.006 1.0 2.6 0.5 0.0 0 1.053 0.1139 0.1308 0.0169 0.007 1.0 2.6 0.5 0.0 0 1.316 0.1137 0.1305 0.0167 0.008 1.1 2.6 0.5 0.0 0 1.579 0.1135 0.1304 0.0169 0.008 1.1 2.6 0.5 0.0 0 1.842 0.1144 0.1306 0.0162 0.006 1.0 2.6 0.5 0.0 0 0.877 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1135 0.1304 0.0169 0.008 1.1 2.6 0.5 0.0 0 1.842 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.35 13.04 1.69 3.785 21.237 44.581 3.609 11.35 13.04 1.69 3.785 21.237 1.337 3.609 11.35 13.04 1.69 3.784 21.237 5.573 3.609 11.38 13.08 1.69 3.718 21.230 22.291 3.605 11.41 13.17 1.75 3.741 21.206 44.581 3.606 11.39 13.18 1.79 3.759 21.189 66.872 3.603 11.35 13.18 1.83 3.772 21.183 89.163 3.599 11.31 13.15 1.84 3.785 21.178 111.453 3.596 11.28 13.11 1.83 3.792 21.177 133.744 3.593 11.28 13.13 1.85 3.807 21.170 156.035 3.593 11.29 13.15 1.86 3.822 21.160 178.325 3.593 11.25 13.11 1.86 3.823 21.167 200.616 3.590 11.25 13.11 1.86 3.835 21.162 222.907 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: 5.573 Accepted refinement result: 11.35 13.04 1.69 3.784 21.237 5.573 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 115.08 21.20 3.32 231 1745 Protein: 9.10 115.08 17.02 3.33 0 1519 Water: 11.51 76.70 35.31 N/A 231 218 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.10 115.08 19.34 N/A 0 1745 Chain S: 16.33 60.01 35.24 N/A 231 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.30 297 30.30 - 40.90 213 40.90 - 51.50 129 51.50 - 62.09 50 62.09 - 72.69 12 72.69 - 83.29 5 83.29 - 93.89 4 93.89 - 104.49 0 104.49 - 115.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1135 r_free=0.1304 r_work=0.1135 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1135 r_free = 0.1304 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1130 r_free = 0.1299 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1130 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606512 | | target function (ml) not normalized (work): 300379.161975 | | target function (ml) not normalized (free): 15832.299390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1130 0.1299 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1468 0.1467 0.1504 n_refl.: 87584 remove outliers: r(all,work,free)=0.1468 0.1467 0.1504 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1467 0.1466 0.1504 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1129 0.1297 n_refl.: 87584 remove outliers: r(all,work,free)=0.1135 0.1127 0.1297 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3971 297.530 247.966 0.461 1.000 0.320 11.894-9.307 95.10 93 4 0.2252 474.974 469.495 0.872 1.002 0.320 9.237-7.194 98.64 210 7 0.2331 388.503 382.379 0.936 1.002 0.170 7.162-5.571 100.00 427 22 0.2079 297.208 287.115 0.919 1.002 0.150 5.546-4.326 100.00 867 58 0.1120 407.994 403.476 0.963 1.002 0.124 4.315-3.360 100.00 1859 96 0.0918 388.005 385.799 1.005 1.002 0.110 3.356-2.611 100.00 3867 181 0.1106 254.899 252.962 1.008 1.002 0.029 2.608-2.026 99.99 8198 413 0.0912 168.975 168.258 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0880 82.518 82.881 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.592 36.209 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 23.056 21.608 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=-0.0125 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1127 r_free=0.1297 After: r_work=0.1128 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1128 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=0.1128 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1128 r_free=0.1297 | n_water=449 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1128 r_free=0.1297 | n_water=449 | time (s): 43.190 (total time: 45.640) Filter (q & B) r_work=0.1129 r_free=0.1297 | n_water=448 | time (s): 4.010 (total time: 49.650) Compute maps r_work=0.1129 r_free=0.1297 | n_water=448 | time (s): 1.890 (total time: 51.540) Filter (map) r_work=0.1159 r_free=0.1310 | n_water=353 | time (s): 3.990 (total time: 55.530) Find peaks r_work=0.1159 r_free=0.1310 | n_water=353 | time (s): 0.720 (total time: 56.250) Add new water r_work=0.1208 r_free=0.1363 | n_water=498 | time (s): 3.830 (total time: 60.080) Refine new water occ: r_work=0.1149 r_free=0.1298 adp: r_work=0.1149 r_free=0.1301 occ: r_work=0.1138 r_free=0.1284 adp: r_work=0.1137 r_free=0.1288 occ: r_work=0.1129 r_free=0.1274 adp: r_work=0.1126 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1276 r_work=0.1126 r_free=0.1276 | n_water=498 | time (s): 192.060 (total time: 252.140) Filter (q & B) r_work=0.1133 r_free=0.1283 | n_water=456 | time (s): 3.990 (total time: 256.130) Filter (dist only) r_work=0.1133 r_free=0.1282 | n_water=455 | time (s): 47.620 (total time: 303.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.746596 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.730598 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1344 0.0125 0.004 0.7 5.1 0.0 0.0 0 0.087 0.1174 0.1314 0.0139 0.004 0.8 4.2 0.0 0.0 0 0.262 0.1152 0.1298 0.0145 0.005 0.9 3.8 0.5 0.0 0 0.524 0.1146 0.1292 0.0146 0.005 1.0 4.2 0.5 0.0 0 0.786 0.1140 0.1287 0.0147 0.006 1.1 3.8 0.5 0.0 0 1.048 0.1136 0.1284 0.0148 0.007 1.1 3.8 0.5 0.0 0 1.310 0.1134 0.1283 0.0149 0.008 1.1 3.8 0.5 0.0 0 1.572 0.1133 0.1282 0.0149 0.008 1.1 3.8 0.5 0.0 0 1.834 0.1144 0.1291 0.0147 0.006 1.0 3.8 0.5 0.0 0 0.873 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1282 0.0149 0.008 1.1 3.8 0.5 0.0 0 1.834 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.82 1.49 3.784 21.207 34.731 3.605 11.33 12.82 1.49 3.784 21.207 1.042 3.605 11.33 12.82 1.49 3.784 21.207 4.341 3.605 11.38 12.88 1.50 3.710 21.200 17.365 3.602 11.42 12.98 1.56 3.730 21.181 34.731 3.604 11.38 12.99 1.61 3.748 21.166 52.096 3.601 11.36 13.00 1.64 3.756 21.158 69.461 3.598 11.31 12.95 1.64 3.772 21.156 86.826 3.594 11.28 12.94 1.66 3.779 21.155 104.192 3.592 11.26 12.92 1.66 3.787 21.154 121.557 3.590 11.24 12.91 1.67 3.793 21.149 138.922 3.588 11.24 12.94 1.69 3.807 21.143 156.288 3.589 11.25 12.96 1.71 3.819 21.136 173.653 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.042 Accepted refinement result: 11.33 12.82 1.49 3.784 21.207 1.042 3.605 Individual atomic B min max mean iso aniso Overall: 9.10 115.08 21.15 3.32 238 1744 Protein: 9.10 115.08 17.02 3.33 0 1519 Water: 11.51 76.69 34.92 N/A 238 217 Other: 19.73 26.63 22.08 N/A 0 8 Chain A: 9.10 115.08 19.32 N/A 0 1744 Chain S: 16.29 60.01 34.57 N/A 238 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.30 304 30.30 - 40.89 214 40.89 - 51.49 136 51.49 - 62.09 41 62.09 - 72.69 12 72.69 - 83.29 5 83.29 - 93.88 4 93.88 - 104.48 0 104.48 - 115.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1282 r_work=0.1133 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1282 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1277 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603020 | | target function (ml) not normalized (work): 300070.310352 | | target function (ml) not normalized (free): 15806.010542 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1342 0.1325 5.6639 5.5868| | 2: 3.57 - 2.84 1.00 2888 124 0.1054 0.1385 5.1547 5.2272| | 3: 2.83 - 2.48 1.00 2820 163 0.1101 0.1204 4.9412 4.9825| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.0949 4.6264 4.6411| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0943 4.5716 4.6279| | 6: 2.09 - 1.97 1.00 2846 113 0.0840 0.1014 4.259 4.3554| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1095 3.9709 4.073| | 8: 1.87 - 1.79 1.00 2789 144 0.0905 0.1037 3.8824 3.9665| | 9: 1.79 - 1.72 1.00 2745 138 0.0868 0.1205 3.6415 3.843| | 10: 1.72 - 1.66 1.00 2831 160 0.0902 0.1207 3.5558 3.7169| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1006 3.4922 3.5614| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1158 3.3269 3.4658| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1017 3.3056 3.3877| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1049 3.2386 3.3171| | 15: 1.48 - 1.45 1.00 2738 128 0.0993 0.1215 3.1508 3.2699| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1248 3.1347 3.2463| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1311 3.1208 3.2453| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1320 3.1057 3.2418| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1575 3.1134 3.2753| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1466 3.1135 3.1616| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1492 3.1149 3.101| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1984 3.1235 3.2952| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1783 3.1348 3.2001| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1842 3.1296 3.235| | 25: 1.24 - 1.22 1.00 2733 148 0.1882 0.2148 3.1447 3.2609| | 26: 1.22 - 1.21 1.00 2727 135 0.1904 0.1755 3.1506 3.205| | 27: 1.21 - 1.19 1.00 2814 148 0.2068 0.2155 3.1729 3.1638| | 28: 1.19 - 1.18 1.00 2671 147 0.2197 0.2299 3.1682 3.1772| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2382 3.1502 3.2328| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2447 3.1457 3.1695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.39 1.00 0.97 5675.91| | 2: 3.57 - 2.84 2888 124 0.93 12.32 1.01 0.97 5675.91| | 3: 2.83 - 2.48 2820 163 0.90 16.34 0.99 0.98 4740.79| | 4: 2.47 - 2.25 2825 136 0.92 13.33 1.00 0.98 2329.41| | 5: 2.25 - 2.09 2756 127 0.90 15.46 1.01 0.98 2329.41| | 6: 2.09 - 1.97 2846 113 0.93 12.24 1.02 0.98 1344.10| | 7: 1.97 - 1.87 2787 165 0.95 9.20 1.02 0.98 503.77| | 8: 1.87 - 1.79 2789 144 0.93 12.47 1.00 0.98 503.77| | 9: 1.79 - 1.72 2745 138 0.94 9.94 0.98 0.98 286.45| | 10: 1.72 - 1.66 2831 160 0.94 11.03 0.98 0.98 242.92| | 11: 1.66 - 1.61 2712 147 0.94 11.64 0.98 0.98 232.81| | 12: 1.61 - 1.56 2773 144 0.96 8.82 0.99 0.98 137.44| | 13: 1.56 - 1.52 2745 130 0.95 10.37 1.03 0.98 137.44| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 123.44| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.99 97.80| | 16: 1.45 - 1.42 2756 161 0.94 11.03 1.02 0.99 97.80| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.99 89.37| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.98 84.50| | 19: 1.36 - 1.34 2807 134 0.94 11.87 0.99 0.98 84.50| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 80.45| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.97 80.17| | 22: 1.29 - 1.27 2704 152 0.93 13.66 0.98 0.96 80.57| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.62| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.95 82.62| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.59| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 86.79| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.79| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.67| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 92.13| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.93 92.13| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.17 max = 5675.91 mean = 876.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.39| |phase err.(test): min = 0.00 max = 89.92 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1129 0.1277 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1447 0.1448 0.1460 n_refl.: 87579 remove outliers: r(all,work,free)=0.1447 0.1448 0.1460 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1447 0.1448 0.1460 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1129 0.1279 n_refl.: 87579 remove outliers: r(all,work,free)=0.1134 0.1127 0.1279 n_refl.: 87574 ======================== 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 0.3959 289.344 257.301 0.458 0.999 0.304 11.894-9.307 94.12 92 4 0.2442 468.640 459.618 0.858 1.002 0.244 9.237-7.194 97.73 208 7 0.2307 387.011 381.788 0.929 1.002 0.190 7.162-5.571 100.00 427 22 0.2136 297.208 286.822 0.914 1.002 0.135 5.546-4.326 100.00 867 58 0.1126 407.994 403.538 0.962 1.002 0.110 4.315-3.360 100.00 1859 96 0.0923 388.005 385.603 1.003 1.002 0.110 3.356-2.611 100.00 3867 181 0.1098 254.899 252.896 1.009 1.002 0.070 2.608-2.026 99.99 8198 413 0.0907 168.975 168.232 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.518 82.847 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.592 36.187 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.056 21.592 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0059 ================= 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 : 0.2599 0.1938 0.083 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_nqh: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_weight: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1226 0.1462 0.006 0.867 9.0 119.5 20.1 258 0.131 1_adp: 0.1233 0.1459 0.006 0.867 9.0 119.4 20.1 258 0.131 1_regHadp: 0.1234 0.1462 0.006 0.867 9.0 119.4 20.1 258 0.131 1_occ: 0.1228 0.1459 0.006 0.867 9.0 119.4 20.1 258 0.131 2_bss: 0.1229 0.1453 0.006 0.867 9.1 119.5 20.1 258 0.131 2_settarget: 0.1229 0.1453 0.006 0.867 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1229 0.1453 0.006 0.869 9.1 119.5 20.1 258 0.131 2_nqh: 0.1230 0.1455 0.006 0.869 9.1 119.5 20.1 258 0.134 2_sol: 0.1210 0.1403 0.006 0.869 9.1 115.1 22.2 414 n/a 2_weight: 0.1210 0.1403 0.006 0.869 9.1 115.1 22.2 414 n/a 2_xyzrec: 0.1185 0.1413 0.008 0.951 9.1 115.1 22.2 414 n/a 2_adp: 0.1185 0.1413 0.008 0.951 9.1 115.1 22.2 414 n/a 2_regHadp: 0.1185 0.1413 0.008 0.951 9.1 115.1 22.2 414 n/a 2_occ: 0.1185 0.1410 0.008 0.951 9.1 115.1 22.2 414 n/a 3_bss: 0.1181 0.1406 0.008 0.951 9.1 115.1 22.2 414 n/a 3_settarget: 0.1181 0.1406 0.008 0.951 9.1 115.1 22.2 414 n/a 3_updatecdl: 0.1181 0.1406 0.008 0.951 9.1 115.1 22.2 414 n/a 3_nqh: 0.1181 0.1406 0.008 0.951 9.1 115.1 22.2 414 n/a 3_sol: 0.1211 0.1413 0.008 0.951 9.1 115.1 21.2 438 n/a 3_weight: 0.1211 0.1413 0.008 0.951 9.1 115.1 21.2 438 n/a 3_xyzrec: 0.1164 0.1330 0.007 1.055 9.1 115.1 21.2 438 n/a 3_adp: 0.1164 0.1330 0.007 1.055 9.1 115.1 21.2 438 n/a 3_regHadp: 0.1164 0.1330 0.007 1.055 9.1 115.1 21.2 438 n/a 3_occ: 0.1154 0.1322 0.007 1.055 9.1 115.1 21.2 438 n/a 4_bss: 0.1145 0.1313 0.007 1.055 9.1 115.1 21.2 438 n/a 4_settarget: 0.1145 0.1313 0.007 1.055 9.1 115.1 21.2 438 n/a 4_updatecdl: 0.1145 0.1313 0.007 1.055 9.1 115.1 21.2 438 n/a 4_nqh: 0.1145 0.1313 0.007 1.055 9.1 115.1 21.2 438 n/a 4_sol: 0.1141 0.1307 0.007 1.055 9.1 115.1 21.2 449 n/a 4_weight: 0.1141 0.1307 0.007 1.055 9.1 115.1 21.2 449 n/a 4_xyzrec: 0.1135 0.1304 0.008 1.119 9.1 115.1 21.2 449 n/a 4_adp: 0.1135 0.1304 0.008 1.119 9.1 115.1 21.2 449 n/a 4_regHadp: 0.1135 0.1304 0.008 1.119 9.1 115.1 21.2 449 n/a 4_occ: 0.1130 0.1299 0.008 1.119 9.1 115.1 21.2 449 n/a 5_bss: 0.1127 0.1297 0.008 1.119 9.1 115.1 21.2 449 n/a 5_settarget: 0.1127 0.1297 0.008 1.119 9.1 115.1 21.2 449 n/a 5_updatecdl: 0.1127 0.1297 0.008 1.121 9.1 115.1 21.2 449 n/a 5_setrh: 0.1128 0.1297 0.008 1.121 9.1 115.1 21.2 449 n/a 5_nqh: 0.1128 0.1297 0.008 1.121 9.1 115.1 21.2 449 n/a 5_sol: 0.1133 0.1282 0.008 1.121 9.1 115.1 21.1 455 n/a 5_weight: 0.1133 0.1282 0.008 1.121 9.1 115.1 21.1 455 n/a 5_xyzrec: 0.1133 0.1282 0.008 1.136 9.1 115.1 21.1 455 n/a 5_adp: 0.1133 0.1282 0.008 1.136 9.1 115.1 21.1 455 n/a 5_regHadp: 0.1133 0.1282 0.008 1.136 9.1 115.1 21.1 455 n/a 5_occ: 0.1129 0.1277 0.008 1.136 9.1 115.1 21.1 455 n/a end: 0.1127 0.1279 0.008 1.136 9.1 115.1 21.1 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8498250_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8498250_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1600 Refinement macro-cycles (run) : 14196.3900 Write final files (write_after_run_outputs) : 81.7300 Total : 14281.2800 Total CPU time: 3.97 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:18:09 PST -0800 (1735366689.27 s) Start R-work = 0.1624, R-free = 0.1785 Final R-work = 0.1127, R-free = 0.1279 =============================================================================== Job complete usr+sys time: 14427.38 seconds wall clock time: 261 minutes 44.66 seconds (15704.66 seconds total)