Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" 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_2655235.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.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 } 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: 1.36, per 1000 atoms: 0.40 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 118.7 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.90: 478 0.90 - 1.15: 1138 1.15 - 1.40: 568 1.40 - 1.64: 894 1.64 - 1.89: 75 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.301 0.239 1.11e-02 8.12e+03 4.63e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.093 0.233 1.10e-02 8.26e+03 4.47e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.111 0.210 1.00e-02 1.00e+04 4.40e+02 bond pdb=" CA ALA A 167 " pdb=" C ALA A 167 " ideal model delta sigma weight residual 1.523 1.260 0.263 1.30e-02 5.92e+03 4.11e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.422 -0.186 1.07e-02 8.73e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2865 4.17 - 8.34: 1869 8.34 - 12.51: 804 12.51 - 16.68: 215 16.68 - 20.85: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.16 -16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 109.64 13.42 9.50e-01 1.11e+00 1.99e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.15 106.60 15.55 1.14e+00 7.69e-01 1.86e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 107.57 15.05 1.17e+00 7.31e-01 1.66e+02 angle pdb=" O SER A 142 " pdb=" C SER A 142 " pdb=" N GLU A 143 " ideal model delta sigma weight residual 123.27 138.96 -15.69 1.22e+00 6.72e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.91: 955 17.91 - 35.80: 106 35.80 - 53.69: 34 53.69 - 71.58: 14 71.58 - 89.48: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+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 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.188: 91 0.188 - 0.373: 75 0.373 - 0.558: 47 0.558 - 0.742: 20 0.742 - 0.927: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR A 140 " pdb=" N THR A 140 " pdb=" C THR A 140 " pdb=" CB THR A 140 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 62 " pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CB LYS A 62 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.093 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG PHE A 164 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.019 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.014 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 97 " -0.003 2.00e-02 2.50e+03 8.06e-02 9.74e+01 pdb=" CG BASN A 97 " 0.098 2.00e-02 2.50e+03 pdb=" OD1BASN A 97 " -0.037 2.00e-02 2.50e+03 pdb=" ND2BASN A 97 " -0.151 2.00e-02 2.50e+03 pdb="HD21BASN A 97 " 0.066 2.00e-02 2.50e+03 pdb="HD22BASN A 97 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1400 2.37 - 2.93: 8341 2.93 - 3.48: 10427 3.48 - 4.04: 15040 4.04 - 4.60: 21376 Nonbonded interactions: 56584 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.810 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.823 1.850 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.847 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O PHE A 162 " pdb=" H LEU A 166 " model vdw 1.848 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.856 2.100 ... (remaining 56579 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_2655235_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= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791181 | | target function (ml) not normalized (work): 232522.092267 | | target function (ml) not normalized (free): 11809.165722 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3051 0.2107 7.0682 4.947| | 2: 3.57 - 2.84 1.00 2876 122 0.2418 0.1822 4.3427 4.339| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1778 4.1301 4.1605| | 4: 2.47 - 2.25 1.00 2825 136 0.2320 0.1392 3.8288 3.8208| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1524 3.7959 3.8089| | 6: 2.09 - 1.97 1.00 2846 113 0.2551 0.1838 3.4625 3.568| | 7: 1.97 - 1.87 1.00 2787 165 0.2540 0.1831 3.1451 3.1497| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.2116 3.0643 3.1736| | 9: 1.79 - 1.72 1.00 2745 138 0.2452 0.1810 2.9085 2.9412| | 10: 1.72 - 1.66 1.00 2789 158 0.2435 0.1951 2.7941 2.9394| | 11: 1.66 - 1.61 1.00 2740 147 0.2519 0.2037 2.7692 2.8466| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.1837 2.6247 2.6108| | 13: 1.56 - 1.52 1.00 2745 130 0.2585 0.1713 2.5855 2.5411| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.2032 2.5301 2.5733| | 15: 1.48 - 1.45 1.00 2738 128 0.2616 0.2089 2.4207 2.4657| | 16: 1.45 - 1.42 1.00 2756 161 0.2621 0.2063 2.3862 2.4212| | 17: 1.42 - 1.39 1.00 2785 139 0.2613 0.1964 2.3325 2.3348| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2249 2.2566 2.3177| | 19: 1.36 - 1.34 1.00 2807 134 0.2637 0.2136 2.2295 2.2712| | 20: 1.34 - 1.32 1.00 2696 147 0.2704 0.2119 2.2148 2.1851| | 21: 1.32 - 1.30 1.00 2785 112 0.2674 0.2282 2.1515 2.1882| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2468 2.124 2.156| | 23: 1.27 - 1.26 1.00 2802 156 0.2799 0.2626 2.1048 2.2252| | 24: 1.26 - 1.24 1.00 2744 132 0.2755 0.2527 2.0635 2.1776| | 25: 1.24 - 1.22 1.00 2734 148 0.2866 0.2533 2.0474 2.1046| | 26: 1.22 - 1.21 1.00 2727 135 0.2822 0.2197 2.0165 2.056| | 27: 1.21 - 1.19 1.00 2814 148 0.2959 0.2694 2.0122 2.0249| | 28: 1.19 - 1.18 1.00 2671 147 0.2930 0.2630 1.9799 1.9678| | 29: 1.18 - 1.16 1.00 2800 134 0.2935 0.2929 1.9523 2.0599| | 30: 1.16 - 1.15 1.00 2740 148 0.3069 0.2720 1.9375 1.9411| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.85 0.76 0.23 1473.86| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1473.86| | 3: 2.84 - 2.48 2833 165 0.74 31.83 1.24 0.24 1222.52| | 4: 2.47 - 2.25 2825 136 0.81 25.50 1.25 0.25 570.24| | 5: 2.25 - 2.09 2756 127 0.77 29.20 1.28 0.25 570.24| | 6: 2.09 - 1.97 2846 113 0.83 22.69 1.29 0.25 312.92| | 7: 1.97 - 1.87 2787 165 0.90 16.81 1.28 0.26 93.46| | 8: 1.87 - 1.79 2789 144 0.86 21.25 1.25 0.26 93.46| | 9: 1.79 - 1.72 2745 138 0.88 18.87 1.24 0.26 57.50| | 10: 1.72 - 1.66 2789 158 0.86 20.62 1.23 0.25 50.30| | 11: 1.66 - 1.61 2740 147 0.85 21.87 1.24 0.25 48.49| | 12: 1.61 - 1.56 2787 146 0.88 18.91 1.24 0.25 30.15| | 13: 1.56 - 1.52 2745 130 0.86 20.87 1.24 0.25 30.15| | 14: 1.52 - 1.48 2803 134 0.87 20.68 1.23 0.25 26.77| | 15: 1.48 - 1.45 2738 128 0.87 20.34 1.24 0.25 20.59| | 16: 1.45 - 1.42 2756 161 0.85 21.74 1.23 0.25 20.59| | 17: 1.42 - 1.39 2785 139 0.87 20.60 1.22 0.25 17.35| | 18: 1.39 - 1.36 2741 179 0.86 21.08 1.23 0.25 15.47| | 19: 1.36 - 1.34 2807 134 0.86 21.93 1.22 0.25 15.47| | 20: 1.34 - 1.32 2696 147 0.87 20.93 1.21 0.24 13.04| | 21: 1.32 - 1.30 2785 112 0.86 22.03 1.20 0.24 12.87| | 22: 1.29 - 1.27 2704 152 0.85 22.65 1.21 0.24 12.61| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.22 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 23.05 1.20 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 24.04 1.20 0.24 10.75| | 26: 1.22 - 1.21 2727 135 0.84 24.16 1.20 0.23 10.18| | 27: 1.21 - 1.19 2814 148 0.83 25.22 1.20 0.23 10.18| | 28: 1.19 - 1.18 2671 147 0.83 25.44 1.17 0.23 9.53| | 29: 1.18 - 1.16 2800 134 0.82 26.07 1.16 0.22 9.29| | 30: 1.16 - 1.15 2740 148 0.81 27.43 1.15 0.22 9.29| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.29 max = 1473.86 mean = 214.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.78| |phase err.(test): min = 0.00 max = 89.90 mean = 22.67| |-----------------------------------------------------------------------------| ----------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 0.263 1557 Z= 5.670 Angle : 5.286 17.753 2118 Z= 3.726 Chirality : 0.365 0.927 243 Planarity : 0.033 0.083 284 Dihedral : 14.241 89.475 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.84 (0.47), residues: 224 helix: -2.55 (0.37), residues: 107 sheet: -0.26 (0.83), residues: 38 loop : -1.38 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 5 TYR 0.058 0.025 TYR A 139 PHE 0.058 0.025 PHE A 164 HIS 0.053 0.025 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= 0.1952 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791181 | | target function (ml) not normalized (work): 232522.092267 | | target function (ml) not normalized (free): 11809.165722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1953 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1953 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1953 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2007 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1632 0.1768 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1631 0.1768 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 0.3889 386.398 355.070 0.670 1.002 0.408 11.894-9.307 99.02 97 4 0.1855 613.774 595.879 0.929 1.003 0.390 9.237-7.194 100.00 213 7 0.2148 501.992 490.684 0.964 1.003 0.370 7.162-5.571 100.00 427 22 0.2207 376.717 364.066 0.928 1.003 0.297 5.546-4.326 100.00 867 58 0.1264 517.139 511.300 0.960 1.003 0.229 4.315-3.360 100.00 1859 96 0.1147 491.803 487.388 1.008 1.003 0.209 3.356-2.611 100.00 3867 181 0.1407 323.089 319.899 0.996 1.002 0.099 2.608-2.026 99.99 8198 413 0.1353 214.179 211.996 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1646 104.594 103.852 1.014 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.381 45.105 1.003 0.997 0.000 1.221-1.150 99.97 13689 708 0.2581 29.223 27.000 0.973 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0478 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1768 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1631 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.015196 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.225757 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 0.1744 0.1867 0.0123 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1586 0.1729 0.0143 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1468 0.1640 0.0172 0.002 0.4 3.8 0.0 0.0 0 0.500 0.1392 0.1586 0.0194 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1364 0.1569 0.0205 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1368 0.1575 0.0207 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1296 0.1517 0.0221 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1271 0.1504 0.0233 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1256 0.1489 0.0233 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1252 0.1490 0.0239 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1242 0.1479 0.0236 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1237 0.1475 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1233 0.1475 0.0241 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1231 0.1474 0.0243 0.006 0.8 2.9 0.5 0.0 0 9.000 0.1231 0.1475 0.0244 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1475 0.0247 0.007 0.9 3.8 0.5 0.6 0 11.000 0.1226 0.1479 0.0253 0.007 0.9 3.8 0.5 0.6 0 12.000 0.1225 0.1480 0.0255 0.008 1.0 3.5 0.5 0.6 0 13.508 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1474 0.0243 0.006 0.8 2.9 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.74 2.43 3.013 19.068 1996.226 0.017 12.31 14.74 2.43 3.011 19.067 59.887 0.017 12.38 14.71 2.33 2.669 19.066 249.528 0.017 12.72 15.31 2.59 2.728 19.218 998.113 0.017 12.55 15.44 2.90 3.225 19.572 1996.226 0.016 12.47 15.48 3.01 3.298 19.616 2994.339 0.015 12.31 15.34 3.04 3.181 19.540 3992.452 0.015 12.31 15.45 3.15 3.311 19.612 4990.564 0.015 12.26 15.44 3.17 3.347 19.613 5988.677 0.015 12.26 15.45 3.19 3.169 19.511 6986.790 0.015 12.21 15.40 3.18 3.353 19.594 7984.903 0.015 12.18 15.47 3.28 3.412 19.621 8983.016 0.015 12.27 15.64 3.37 3.561 19.676 9981.129 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 249.528 Accepted refinement result: 12.38 14.71 2.33 2.669 19.066 249.528 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.45 20.09 3.31 0 1785 Protein: 9.09 115.01 17.00 3.32 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.70 26.61 22.06 N/A 0 8 Chain A: 9.09 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1471 r_work=0.1240 r_free=0.1475 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1475 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 = 0.1236 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1236 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017045 | | target function (ls_wunit_k1) not normalized (work): 1419.777532 | | target function (ls_wunit_k1) not normalized (free): 113.214575 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1247 0.1236 0.1468 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1681 0.1683 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1681 0.1683 0.1693 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1687 0.1688 0.1697 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1233 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1233 0.1458 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3622 301.096 281.848 0.640 1.002 0.376 11.894-9.307 99.02 97 4 0.1712 482.339 468.512 0.919 1.003 0.373 9.237-7.194 100.00 213 7 0.1904 394.494 388.299 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1843 296.046 289.872 0.935 1.003 0.263 5.546-4.326 100.00 867 58 0.1015 406.398 403.214 0.961 1.003 0.209 4.315-3.360 100.00 1859 96 0.0872 386.487 385.379 1.010 1.002 0.190 3.356-2.611 100.00 3867 181 0.1182 253.902 252.749 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1026 168.314 167.591 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1114 82.196 82.375 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1455 36.449 35.954 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.965 21.451 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1458 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1234 r_free=0.1459 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1459 | n_water=258 | time (s): 1.510 (total time: 1.510) Filter (dist) r_work=0.1243 r_free=0.1459 | n_water=251 | time (s): 20.860 (total time: 22.370) Filter (q & B) r_work=0.1245 r_free=0.1458 | n_water=248 | time (s): 3.050 (total time: 25.420) Compute maps r_work=0.1245 r_free=0.1458 | n_water=248 | time (s): 1.480 (total time: 26.900) Filter (map) r_work=0.1264 r_free=0.1460 | n_water=223 | time (s): 2.640 (total time: 29.540) Find peaks r_work=0.1264 r_free=0.1460 | n_water=223 | time (s): 0.520 (total time: 30.060) Add new water r_work=0.1413 r_free=0.1640 | n_water=429 | time (s): 2.540 (total time: 32.600) Refine new water occ: r_work=0.1318 r_free=0.1497 adp: r_work=0.1234 r_free=0.1438 occ: r_work=0.1247 r_free=0.1425 adp: r_work=0.1213 r_free=0.1408 occ: r_work=0.1217 r_free=0.1405 adp: r_work=0.1206 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1402 r_work=0.1206 r_free=0.1402 | n_water=429 | time (s): 60.670 (total time: 93.270) Filter (q & B) r_work=0.1210 r_free=0.1404 | n_water=415 | time (s): 2.770 (total time: 96.040) Filter (dist only) r_work=0.1211 r_free=0.1402 | n_water=414 | time (s): 34.360 (total time: 130.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.858242 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.706234 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 0.1680 0.1790 0.0109 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1542 0.1667 0.0125 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1407 0.1562 0.0154 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1362 0.1532 0.0170 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1324 0.1504 0.0180 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1319 0.1498 0.0179 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1265 0.1463 0.0198 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1235 0.1442 0.0207 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1223 0.1436 0.0213 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1216 0.1432 0.0217 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1211 0.1431 0.0220 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1208 0.1429 0.0221 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1203 0.1423 0.0220 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1198 0.1419 0.0221 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1194 0.1419 0.0225 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1195 0.1426 0.0231 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1194 0.1426 0.0232 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1190 0.1426 0.0235 0.008 0.9 5.8 0.5 0.0 0 13.929 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1419 0.0221 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 14.19 2.21 3.777 21.747 1487.706 0.016 11.98 14.19 2.21 3.777 21.747 44.631 0.016 11.98 14.19 2.21 3.777 21.747 185.963 0.016 12.24 14.85 2.61 3.579 21.792 743.853 0.016 12.19 15.11 2.92 3.511 22.156 1487.706 0.015 11.95 14.87 2.92 3.462 22.074 2231.559 0.015 11.92 14.96 3.04 3.477 22.073 2975.412 0.014 11.81 14.91 3.11 3.527 21.906 3719.266 0.014 11.80 14.87 3.08 3.514 22.034 4463.119 0.014 11.81 15.08 3.26 3.533 22.019 5206.972 0.014 11.78 15.03 3.25 3.552 22.062 5950.825 0.014 11.73 14.94 3.21 3.569 22.081 6694.678 0.014 11.71 14.94 3.23 3.577 22.037 7438.531 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.963 Accepted refinement result: 11.98 14.19 2.21 3.777 21.747 185.963 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 22.13 3.31 191 1750 Protein: 9.12 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 40.82 N/A 191 223 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.12 115.04 19.41 N/A 0 1750 Chain S: 14.69 60.00 46.96 N/A 191 0 Histogram: Values Number of atoms 9.12 - 19.71 1260 19.71 - 30.30 244 30.30 - 40.89 167 40.89 - 51.49 130 51.49 - 62.08 117 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1419 r_work=0.1198 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1419 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1419 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1195 r_free= 0.1419 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015340 | | target function (ls_wunit_k1) not normalized (work): 1277.761590 | | target function (ls_wunit_k1) not normalized (free): 105.441220 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1195 0.1419 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1589 0.1589 0.1628 n_refl.: 87592 remove outliers: r(all,work,free)=0.1589 0.1589 0.1628 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1590 0.1590 0.1629 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1192 0.1414 n_refl.: 87592 remove outliers: r(all,work,free)=0.1202 0.1191 0.1414 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 0.3416 297.004 275.357 0.582 1.002 0.350 11.894-9.307 99.02 97 4 0.1691 482.339 474.939 0.911 1.003 0.333 9.237-7.194 100.00 213 7 0.1764 394.494 392.989 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1600 296.046 291.245 0.938 1.003 0.220 5.546-4.326 100.00 867 58 0.0903 406.398 403.132 0.958 1.003 0.194 4.315-3.360 100.00 1859 96 0.0780 386.487 385.543 1.007 1.002 0.180 3.356-2.611 100.00 3867 181 0.1088 253.902 253.132 1.011 1.002 0.120 2.608-2.026 99.99 8198 413 0.1012 168.314 167.801 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.196 82.400 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.449 35.985 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 22.965 21.482 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=0.0108 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1414 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1414 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1414 | n_water=414 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1192 r_free=0.1417 | n_water=412 | time (s): 33.220 (total time: 34.900) Filter (q & B) r_work=0.1192 r_free=0.1417 | n_water=412 | time (s): 0.930 (total time: 35.830) Compute maps r_work=0.1192 r_free=0.1417 | n_water=412 | time (s): 1.420 (total time: 37.250) Filter (map) r_work=0.1231 r_free=0.1393 | n_water=285 | time (s): 2.490 (total time: 39.740) Find peaks r_work=0.1231 r_free=0.1393 | n_water=285 | time (s): 0.630 (total time: 40.370) Add new water r_work=0.1347 r_free=0.1506 | n_water=462 | time (s): 2.830 (total time: 43.200) Refine new water occ: r_work=0.1256 r_free=0.1428 adp: r_work=0.1257 r_free=0.1428 occ: r_work=0.1234 r_free=0.1407 adp: r_work=0.1233 r_free=0.1406 occ: r_work=0.1218 r_free=0.1388 adp: r_work=0.1212 r_free=0.1384 ADP+occupancy (water only), MIN, final r_work=0.1212 r_free=0.1384 r_work=0.1212 r_free=0.1384 | n_water=462 | time (s): 168.550 (total time: 211.750) Filter (q & B) r_work=0.1217 r_free=0.1386 | n_water=433 | time (s): 3.030 (total time: 214.780) Filter (dist only) r_work=0.1217 r_free=0.1385 | n_water=431 | time (s): 36.590 (total time: 251.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.713953 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.566968 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 0.1247 0.1353 0.0106 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1196 0.1323 0.0126 0.003 0.7 3.5 0.5 0.0 0 0.257 0.1179 0.1315 0.0136 0.004 0.8 3.5 0.5 0.0 0 0.514 0.1170 0.1313 0.0143 0.005 0.9 3.5 0.5 0.0 0 0.771 0.1166 0.1308 0.0142 0.006 1.0 3.2 0.5 0.0 0 1.028 0.1163 0.1311 0.0148 0.007 1.0 3.8 0.5 0.0 0 1.285 0.1161 0.1309 0.0148 0.007 1.0 3.8 0.5 0.0 0 1.543 0.1160 0.1311 0.0151 0.008 1.1 4.2 0.5 0.0 0 1.800 0.1169 0.1310 0.0141 0.005 0.9 3.2 0.5 0.0 0 0.857 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1308 0.0142 0.006 1.0 3.2 0.5 0.0 0 1.028 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 13.08 1.42 3.779 21.252 51.567 3.623 11.66 13.08 1.42 3.779 21.252 1.547 3.623 11.67 13.08 1.41 3.769 21.252 6.446 3.623 11.71 13.19 1.48 3.715 21.236 25.783 3.616 11.68 13.25 1.57 3.743 21.207 51.567 3.614 11.60 13.20 1.60 3.764 21.198 77.350 3.607 11.57 13.18 1.61 3.777 21.190 103.134 3.603 11.53 13.15 1.62 3.788 21.191 128.917 3.601 11.54 13.19 1.65 3.811 21.170 154.701 3.601 11.52 13.16 1.65 3.820 21.167 180.484 3.599 11.52 13.18 1.67 3.831 21.165 206.268 3.599 11.49 13.15 1.66 3.834 21.169 232.051 3.597 11.49 13.15 1.67 3.845 21.163 257.835 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.446 Accepted refinement result: 11.67 13.08 1.41 3.769 21.252 6.446 3.623 Individual atomic B min max mean iso aniso Overall: 9.13 114.93 21.21 3.28 212 1746 Protein: 9.13 114.93 17.04 3.28 0 1519 Water: 11.51 76.70 35.90 N/A 212 219 Other: 19.67 26.59 22.08 N/A 0 8 Chain A: 9.13 114.93 19.36 N/A 0 1746 Chain S: 14.68 60.01 36.48 N/A 212 0 Histogram: Values Number of atoms 9.13 - 19.71 1262 19.71 - 30.29 283 30.29 - 40.87 211 40.87 - 51.45 121 51.45 - 62.03 58 62.03 - 72.61 11 72.61 - 83.19 6 83.19 - 93.77 4 93.77 - 104.35 0 104.35 - 114.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1308 r_work=0.1167 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1308 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1158 r_free = 0.1308 target_work(ml) = 3.615 | | 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1158 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615011 | | target function (ml) not normalized (work): 301105.071592 | | target function (ml) not normalized (free): 15829.511971 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1158 0.1308 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1497 0.1496 0.1536 n_refl.: 87589 remove outliers: r(all,work,free)=0.1497 0.1496 0.1536 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1496 0.1495 0.1535 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1155 0.1304 n_refl.: 87589 remove outliers: r(all,work,free)=0.1160 0.1153 0.1304 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 92.71 84 5 0.3901 297.004 269.380 0.498 1.000 0.306 11.894-9.307 98.04 96 4 0.2325 482.464 466.921 0.881 1.002 0.290 9.237-7.194 98.18 209 7 0.2271 385.977 385.635 0.959 1.002 0.200 7.162-5.571 100.00 427 22 0.2114 296.046 285.404 0.920 1.002 0.183 5.546-4.326 100.00 867 58 0.1093 406.398 401.666 0.965 1.002 0.180 4.315-3.360 100.00 1859 96 0.0924 386.487 383.862 1.006 1.002 0.180 3.356-2.611 100.00 3867 181 0.1151 253.902 251.888 1.008 1.002 0.110 2.608-2.026 99.99 8198 413 0.0951 168.314 167.541 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0914 82.196 82.472 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1266 36.449 36.029 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.965 21.504 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1153 r_free=0.1304 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=0.1153 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1153 r_free=0.1304 | n_water=431 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1153 r_free=0.1302 | n_water=430 | time (s): 45.330 (total time: 47.960) Filter (q & B) r_work=0.1154 r_free=0.1305 | n_water=428 | time (s): 4.090 (total time: 52.050) Compute maps r_work=0.1154 r_free=0.1305 | n_water=428 | time (s): 1.930 (total time: 53.980) Filter (map) r_work=0.1178 r_free=0.1305 | n_water=317 | time (s): 3.870 (total time: 57.850) Find peaks r_work=0.1178 r_free=0.1305 | n_water=317 | time (s): 0.700 (total time: 58.550) Add new water r_work=0.1249 r_free=0.1381 | n_water=461 | time (s): 3.560 (total time: 62.110) Refine new water occ: r_work=0.1179 r_free=0.1319 adp: r_work=0.1179 r_free=0.1322 occ: r_work=0.1164 r_free=0.1306 adp: r_work=0.1163 r_free=0.1307 occ: r_work=0.1152 r_free=0.1296 adp: r_work=0.1149 r_free=0.1295 ADP+occupancy (water only), MIN, final r_work=0.1149 r_free=0.1295 r_work=0.1149 r_free=0.1295 | n_water=461 | time (s): 213.310 (total time: 275.420) Filter (q & B) r_work=0.1153 r_free=0.1300 | n_water=433 | time (s): 4.100 (total time: 279.520) Filter (dist only) r_work=0.1160 r_free=0.1301 | n_water=430 | time (s): 46.090 (total time: 325.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.762487 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.855445 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 0.1339 0.0120 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1181 0.1315 0.0134 0.003 0.7 3.8 0.5 0.0 0 0.264 0.1167 0.1308 0.0141 0.005 0.9 3.8 0.5 0.0 0 0.529 0.1160 0.1304 0.0144 0.006 0.9 3.5 0.5 0.0 0 0.793 0.1156 0.1302 0.0146 0.006 1.0 3.5 0.5 0.0 0 1.057 0.1152 0.1300 0.0147 0.007 1.1 3.8 0.5 0.0 0 1.322 0.1150 0.1299 0.0149 0.008 1.1 3.8 0.5 0.0 0 1.586 0.1148 0.1298 0.0150 0.008 1.1 3.8 0.5 0.0 0 1.851 0.1158 0.1303 0.0145 0.006 1.0 3.5 0.5 0.0 0 0.881 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1148 0.1298 0.0150 0.008 1.1 3.8 0.5 0.0 0 1.851 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.48 12.98 1.50 3.765 21.114 41.855 3.608 11.48 12.98 1.50 3.765 21.114 1.256 3.608 11.48 12.98 1.50 3.765 21.114 5.232 3.608 11.52 13.05 1.53 3.700 21.106 20.928 3.603 11.51 13.13 1.61 3.723 21.089 41.855 3.602 11.53 13.19 1.66 3.742 21.064 62.783 3.601 11.46 13.13 1.68 3.761 21.061 83.711 3.596 11.43 13.13 1.70 3.770 21.059 104.639 3.594 11.40 13.12 1.71 3.782 21.054 125.566 3.592 11.39 13.13 1.74 3.794 21.049 146.494 3.591 11.39 13.14 1.75 3.810 21.038 167.422 3.590 11.37 13.12 1.75 3.816 21.036 188.350 3.588 11.37 13.12 1.76 3.825 21.035 209.277 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.232 Accepted refinement result: 11.48 12.98 1.50 3.765 21.114 5.232 3.608 Individual atomic B min max mean iso aniso Overall: 9.12 114.92 20.97 3.28 215 1742 Protein: 9.12 114.92 17.03 3.28 0 1519 Water: 11.51 76.69 34.85 N/A 215 215 Other: 19.66 26.58 22.08 N/A 0 8 Chain A: 9.12 114.92 19.31 N/A 0 1742 Chain S: 14.67 60.00 34.42 N/A 215 0 Histogram: Values Number of atoms 9.12 - 19.70 1265 19.70 - 30.28 290 30.28 - 40.86 214 40.86 - 51.44 121 51.44 - 62.02 44 62.02 - 72.60 11 72.60 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1298 r_work=0.1148 r_free=0.1298 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1298 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1295 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605638 | | target function (ml) not normalized (work): 300306.406725 | | target function (ml) not normalized (free): 15814.376314 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1143 0.1295 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1487 0.1488 0.1512 n_refl.: 87584 remove outliers: r(all,work,free)=0.1487 0.1488 0.1512 n_refl.: 87584 overall B=-0.01 to atoms: r(all,work,free)=0.1486 0.1486 0.1511 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1299 n_refl.: 87584 remove outliers: r(all,work,free)=0.1148 0.1140 0.1299 n_refl.: 87581 ======================== 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 90.62 82 5 0.4061 293.732 255.355 0.465 1.000 0.310 11.894-9.307 97.06 95 4 0.2432 475.680 466.213 0.869 1.002 0.262 9.237-7.194 98.18 209 7 0.2390 385.977 378.288 0.930 1.002 0.189 7.162-5.571 100.00 427 22 0.2111 296.046 285.735 0.913 1.002 0.156 5.546-4.326 100.00 867 58 0.1122 406.398 401.767 0.965 1.002 0.145 4.315-3.360 100.00 1859 96 0.0923 386.487 384.200 1.005 1.002 0.140 3.356-2.611 100.00 3867 181 0.1138 253.902 252.000 1.010 1.002 0.034 2.608-2.026 99.99 8198 413 0.0929 168.314 167.673 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.196 82.523 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1247 36.449 36.050 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 22.965 21.514 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0191 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1140 r_free=0.1299 After: r_work=0.1142 r_free=0.1298 ================================== NQH flips ================================== r_work=0.1142 r_free=0.1298 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1142 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1298 | n_water=430 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1142 r_free=0.1298 | n_water=430 | time (s): 41.100 (total time: 43.600) Filter (q & B) r_work=0.1142 r_free=0.1299 | n_water=428 | time (s): 3.670 (total time: 47.270) Compute maps r_work=0.1142 r_free=0.1299 | n_water=428 | time (s): 1.770 (total time: 49.040) Filter (map) r_work=0.1177 r_free=0.1314 | n_water=340 | time (s): 3.880 (total time: 52.920) Find peaks r_work=0.1177 r_free=0.1314 | n_water=340 | time (s): 0.670 (total time: 53.590) Add new water r_work=0.1231 r_free=0.1360 | n_water=485 | time (s): 3.780 (total time: 57.370) Refine new water occ: r_work=0.1164 r_free=0.1314 adp: r_work=0.1164 r_free=0.1313 occ: r_work=0.1154 r_free=0.1307 adp: r_work=0.1152 r_free=0.1306 occ: r_work=0.1145 r_free=0.1300 adp: r_work=0.1141 r_free=0.1298 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1298 r_work=0.1141 r_free=0.1298 | n_water=485 | time (s): 238.900 (total time: 296.270) Filter (q & B) r_work=0.1146 r_free=0.1305 | n_water=447 | time (s): 3.930 (total time: 300.200) Filter (dist only) r_work=0.1146 r_free=0.1303 | n_water=445 | time (s): 47.010 (total time: 347.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.817345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.104458 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 0.1232 0.1353 0.0122 0.004 0.7 6.7 0.0 0.0 0 0.091 0.1192 0.1330 0.0138 0.004 0.8 6.7 0.0 0.0 0 0.273 0.1170 0.1318 0.0148 0.005 0.9 7.0 0.5 0.0 0 0.545 0.1163 0.1314 0.0151 0.006 1.0 7.0 0.5 0.0 0 0.818 0.1156 0.1309 0.0153 0.006 1.1 7.7 0.5 0.0 0 1.090 0.1151 0.1304 0.0153 0.007 1.1 7.7 0.5 0.0 0 1.363 0.1148 0.1302 0.0154 0.008 1.1 7.4 0.5 0.0 0 1.636 0.1146 0.1302 0.0155 0.009 1.2 7.4 0.5 0.0 0 1.908 0.1160 0.1312 0.0152 0.006 1.0 7.0 0.5 0.0 0 0.909 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1302 0.0155 0.009 1.2 7.4 0.5 0.0 0 1.908 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 13.02 1.55 3.765 21.133 41.104 3.608 11.46 13.02 1.55 3.765 21.133 1.233 3.608 11.46 13.02 1.55 3.765 21.133 5.138 3.608 11.49 13.06 1.57 3.700 21.125 20.552 3.604 11.49 13.14 1.65 3.723 21.108 41.104 3.602 11.50 13.22 1.72 3.745 21.082 61.657 3.602 11.42 13.16 1.74 3.763 21.080 82.209 3.596 11.38 13.13 1.75 3.770 21.080 102.761 3.593 11.40 13.16 1.76 3.787 21.067 123.313 3.593 11.36 13.12 1.76 3.791 21.073 143.866 3.591 11.37 13.15 1.79 3.812 21.059 164.418 3.591 11.35 13.14 1.79 3.819 21.057 184.970 3.589 11.34 13.13 1.79 3.827 21.055 205.522 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.138 Accepted refinement result: 11.46 13.02 1.55 3.765 21.133 5.138 3.608 Individual atomic B min max mean iso aniso Overall: 9.12 114.91 21.01 3.28 231 1741 Protein: 9.12 114.91 17.03 3.28 0 1519 Water: 11.50 76.69 34.59 N/A 231 214 Other: 19.66 26.58 22.07 N/A 0 8 Chain A: 9.12 114.91 19.30 N/A 0 1741 Chain S: 14.67 59.99 33.88 N/A 231 0 Histogram: Values Number of atoms 9.12 - 19.70 1266 19.70 - 30.28 297 30.28 - 40.86 223 40.86 - 51.44 120 51.44 - 62.01 43 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1302 r_work=0.1146 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1302 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1298 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1298 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605619 | | target function (ml) not normalized (work): 300293.952686 | | target function (ml) not normalized (free): 15813.589344 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2923 171 0.1360 0.1358 5.6683 5.622| | 2: 3.57 - 2.84 1.00 2888 124 0.1070 0.1413 5.1738 5.2449| | 3: 2.83 - 2.48 1.00 2820 163 0.1119 0.1284 4.9609 4.9991| | 4: 2.47 - 2.25 1.00 2825 136 0.0921 0.0999 4.6459 4.6642| | 5: 2.25 - 2.09 1.00 2756 127 0.0885 0.0937 4.5907 4.6318| | 6: 2.09 - 1.97 1.00 2846 113 0.0867 0.0984 4.2723 4.377| | 7: 1.97 - 1.87 1.00 2787 165 0.0889 0.1092 3.9782 4.0798| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1097 3.8877 3.9861| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1212 3.6477 3.8391| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1208 3.5639 3.722| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1050 3.497 3.5718| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1166 3.3274 3.4689| | 13: 1.56 - 1.52 1.00 2745 130 0.0947 0.1030 3.3076 3.3854| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1029 3.2399 3.321| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1210 3.1512 3.2512| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1263 3.1338 3.2465| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1287 3.1174 3.2232| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1301 3.1013 3.2328| | 19: 1.36 - 1.34 1.00 2807 134 0.1254 0.1552 3.1079 3.2634| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1461 3.1101 3.1491| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1511 3.1105 3.1046| | 22: 1.29 - 1.27 1.00 2704 152 0.1557 0.1975 3.1193 3.2889| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1792 3.1315 3.1974| | 24: 1.26 - 1.24 1.00 2744 132 0.1702 0.1835 3.1247 3.226| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2157 3.1399 3.2626| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1782 3.1466 3.2034| | 27: 1.21 - 1.19 1.00 2814 148 0.2073 0.2176 3.1689 3.1624| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2294 3.1656 3.1691| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2379 3.1467 3.2235| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2440 3.1423 3.1656| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2923 171 0.95 8.85 1.00 0.97 5975.29| | 2: 3.57 - 2.84 2888 124 0.92 12.83 1.01 0.97 5975.29| | 3: 2.83 - 2.48 2820 163 0.89 16.83 0.99 0.97 4984.30| | 4: 2.47 - 2.25 2825 136 0.92 13.67 1.00 0.98 2428.84| | 5: 2.25 - 2.09 2756 127 0.90 15.88 1.01 0.98 2428.84| | 6: 2.09 - 1.97 2846 113 0.92 12.43 1.02 0.98 1390.10| | 7: 1.97 - 1.87 2787 165 0.95 9.18 1.02 0.97 504.20| | 8: 1.87 - 1.79 2789 144 0.93 12.47 1.00 0.97 504.20| | 9: 1.79 - 1.72 2745 138 0.94 10.10 0.98 0.97 289.48| | 10: 1.72 - 1.66 2831 160 0.94 11.23 0.98 0.97 246.48| | 11: 1.66 - 1.61 2712 147 0.93 11.82 0.98 0.97 236.13| | 12: 1.61 - 1.56 2773 144 0.95 8.95 0.99 0.97 138.55| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.03 0.97 138.55| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.02 0.98 124.14| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 97.77| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.98 97.77| | 17: 1.42 - 1.39 2785 139 0.95 10.92 1.01 0.98 88.74| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.52| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.98 83.52| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.96 79.54| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.26| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 79.69| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.94 81.84| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 81.84| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 83.79| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.93 85.94| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.93 85.94| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.93 89.40| | 29: 1.18 - 1.16 2800 134 0.88 20.42 0.99 0.92 90.70| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.92 90.70| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.26 max = 5975.29 mean = 914.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.48| |phase err.(test): min = 0.00 max = 89.84 mean = 13.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1143 0.1298 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1473 0.1473 0.1497 n_refl.: 87581 remove outliers: r(all,work,free)=0.1473 0.1473 0.1497 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1472 0.1472 0.1496 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1143 0.1298 n_refl.: 87581 remove outliers: r(all,work,free)=0.1149 0.1141 0.1298 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4109 291.164 246.215 0.447 0.999 0.310 11.894-9.307 95.10 93 4 0.2343 479.615 457.596 0.851 1.002 0.257 9.237-7.194 97.73 208 7 0.2440 387.060 377.772 0.923 1.002 0.175 7.162-5.571 100.00 427 22 0.2191 296.046 284.994 0.909 1.002 0.147 5.546-4.326 100.00 867 58 0.1139 406.398 401.457 0.963 1.002 0.128 4.315-3.360 100.00 1859 96 0.0920 386.487 384.502 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1119 253.902 252.197 1.011 1.002 0.060 2.608-2.026 99.99 8198 413 0.0931 168.314 167.744 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0891 82.196 82.567 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.449 36.070 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.965 21.521 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0163 ================= 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 0.1952 0.083 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_weight: 0.1631 0.1768 0.083 5.286 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1231 0.1474 0.006 0.845 9.1 119.5 20.1 258 0.133 1_adp: 0.1238 0.1471 0.006 0.845 9.1 119.5 20.1 258 0.133 1_regHadp: 0.1240 0.1475 0.006 0.845 9.1 119.5 20.1 258 0.133 1_occ: 0.1236 0.1468 0.006 0.845 9.1 119.5 20.1 258 0.133 2_bss: 0.1233 0.1458 0.006 0.845 9.1 119.5 20.1 258 0.133 2_settarget: 0.1233 0.1458 0.006 0.845 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1233 0.1458 0.006 0.862 9.1 119.5 20.1 258 0.133 2_nqh: 0.1234 0.1459 0.006 0.862 9.1 119.5 20.1 258 0.136 2_sol: 0.1211 0.1402 0.006 0.862 9.1 115.0 22.1 414 n/a 2_weight: 0.1211 0.1402 0.006 0.862 9.1 115.0 22.1 414 n/a 2_xyzrec: 0.1198 0.1419 0.006 0.817 9.1 115.0 22.1 414 n/a 2_adp: 0.1198 0.1419 0.006 0.817 9.1 115.0 22.1 414 n/a 2_regHadp: 0.1198 0.1419 0.006 0.817 9.1 115.0 22.1 414 n/a 2_occ: 0.1195 0.1419 0.006 0.817 9.1 115.0 22.1 414 n/a 3_bss: 0.1191 0.1414 0.006 0.817 9.1 115.0 22.1 414 n/a 3_settarget: 0.1191 0.1414 0.006 0.817 9.1 115.0 22.1 414 n/a 3_updatecdl: 0.1191 0.1414 0.006 0.819 9.1 115.0 22.1 414 n/a 3_nqh: 0.1191 0.1414 0.006 0.819 9.1 115.0 22.1 414 n/a 3_sol: 0.1217 0.1385 0.006 0.819 9.1 115.0 21.2 431 n/a 3_weight: 0.1217 0.1385 0.006 0.819 9.1 115.0 21.2 431 n/a 3_xyzrec: 0.1166 0.1308 0.006 0.961 9.1 115.0 21.2 431 n/a 3_adp: 0.1167 0.1308 0.006 0.961 9.1 114.9 21.2 431 n/a 3_regHadp: 0.1167 0.1308 0.006 0.961 9.1 114.9 21.2 431 n/a 3_occ: 0.1158 0.1308 0.006 0.961 9.1 114.9 21.2 431 n/a 4_bss: 0.1153 0.1304 0.006 0.961 9.1 114.9 21.2 431 n/a 4_settarget: 0.1153 0.1304 0.006 0.961 9.1 114.9 21.2 431 n/a 4_updatecdl: 0.1153 0.1304 0.006 0.961 9.1 114.9 21.2 431 n/a 4_nqh: 0.1153 0.1304 0.006 0.961 9.1 114.9 21.2 431 n/a 4_sol: 0.1160 0.1301 0.006 0.961 9.1 114.9 21.0 430 n/a 4_weight: 0.1160 0.1301 0.006 0.961 9.1 114.9 21.0 430 n/a 4_xyzrec: 0.1148 0.1298 0.008 1.129 9.1 114.9 21.0 430 n/a 4_adp: 0.1148 0.1298 0.008 1.129 9.1 114.9 21.0 430 n/a 4_regHadp: 0.1148 0.1298 0.008 1.129 9.1 114.9 21.0 430 n/a 4_occ: 0.1143 0.1295 0.008 1.129 9.1 114.9 21.0 430 n/a 5_bss: 0.1140 0.1299 0.008 1.129 9.1 114.9 21.0 430 n/a 5_settarget: 0.1140 0.1299 0.008 1.129 9.1 114.9 21.0 430 n/a 5_updatecdl: 0.1140 0.1299 0.009 1.132 9.1 114.9 21.0 430 n/a 5_setrh: 0.1142 0.1298 0.009 1.132 9.1 114.9 21.0 430 n/a 5_nqh: 0.1142 0.1298 0.009 1.132 9.1 114.9 21.0 430 n/a 5_sol: 0.1146 0.1303 0.009 1.132 9.1 114.9 21.0 445 n/a 5_weight: 0.1146 0.1303 0.009 1.132 9.1 114.9 21.0 445 n/a 5_xyzrec: 0.1146 0.1302 0.009 1.161 9.1 114.9 21.0 445 n/a 5_adp: 0.1146 0.1302 0.009 1.161 9.1 114.9 21.0 445 n/a 5_regHadp: 0.1146 0.1302 0.009 1.161 9.1 114.9 21.0 445 n/a 5_occ: 0.1143 0.1298 0.009 1.161 9.1 114.9 21.0 445 n/a end: 0.1141 0.1298 0.009 1.161 9.1 114.9 21.0 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2655235_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2655235_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1700 Refinement macro-cycles (run) : 13678.5500 Write final files (write_after_run_outputs) : 96.5900 Total : 13778.3100 Total CPU time: 3.83 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:10:38 PST -0800 (1735366238.52 s) Start R-work = 0.1631, R-free = 0.1768 Final R-work = 0.1141, R-free = 0.1298 =============================================================================== Job complete usr+sys time: 13966.28 seconds wall clock time: 254 minutes 58.05 seconds (15298.05 seconds total)