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_9291273.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_9291273.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9291273.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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.30, per 1000 atoms: 0.38 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: 0.35 Conformation dependent library (CDL) restraints added in 112.7 milliseconds Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 454 0.90 - 1.17: 1203 1.17 - 1.44: 682 1.44 - 1.70: 798 1.70 - 1.97: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.121 0.208 1.00e-02 1.00e+04 4.32e+02 bond pdb=" N PRO A 127 " pdb=" CD PRO A 127 " ideal model delta sigma weight residual 1.473 1.198 0.275 1.40e-02 5.10e+03 3.85e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.017 0.216 1.22e-02 6.72e+03 3.15e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.189 0.189 1.10e-02 8.26e+03 2.95e+02 bond pdb=" C BTYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 1.333 1.584 -0.251 1.49e-02 4.50e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2960 4.24 - 8.48: 1845 8.48 - 12.72: 762 12.72 - 16.96: 180 16.96 - 21.20: 30 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 108.45 11.62 7.10e-01 1.98e+00 2.68e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 137.39 -14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.48 12.72 9.00e-01 1.23e+00 2.00e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 122.93 108.17 14.76 1.06e+00 8.90e-01 1.94e+02 angle pdb=" O LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " ideal model delta sigma weight residual 120.85 134.61 -13.76 1.01e+00 9.80e-01 1.86e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.66: 916 15.66 - 31.32: 128 31.32 - 46.97: 46 46.97 - 62.63: 19 62.63 - 78.28: 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 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.244: 104 0.244 - 0.485: 83 0.485 - 0.725: 39 0.725 - 0.966: 15 0.966 - 1.206: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" CA ALA A 6 " pdb=" N ALA A 6 " pdb=" C ALA A 6 " pdb=" CB ALA A 6 " both_signs ideal model delta sigma weight residual False 2.48 3.44 -0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.049 2.00e-02 2.50e+03 7.54e-02 1.71e+02 pdb=" CG PHE A 119 " -0.127 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.053 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" CG ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.132 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.056 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.031 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.072 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.055 2.00e-02 2.50e+03 5.97e-02 1.07e+02 pdb=" CG TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.086 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.093 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.068 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 911 2.30 - 2.87: 7913 2.87 - 3.45: 10588 3.45 - 4.02: 15323 4.02 - 4.60: 21834 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.719 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.823 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.830 1.850 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.844 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56564 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_9291273_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= 0.2612 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792439 | | target function (ml) not normalized (work): 232626.927135 | | target function (ml) not normalized (free): 11831.385904 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3036 0.2090 7.1262 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2440 0.1644 4.341 4.3228| | 3: 2.84 - 2.48 1.00 2833 165 0.2364 0.1863 4.1214 4.1635| | 4: 2.47 - 2.25 1.00 2825 136 0.2369 0.1438 3.826 3.8255| | 5: 2.25 - 2.09 1.00 2756 127 0.2525 0.1622 3.7917 3.8399| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1774 3.4715 3.5246| | 7: 1.97 - 1.87 1.00 2787 165 0.2520 0.1752 3.1403 3.1589| | 8: 1.87 - 1.79 1.00 2789 144 0.2438 0.1766 3.06 3.0925| | 9: 1.79 - 1.72 1.00 2745 138 0.2422 0.1735 2.8941 2.9325| | 10: 1.72 - 1.66 1.00 2789 158 0.2424 0.2040 2.8178 2.9543| | 11: 1.66 - 1.61 1.00 2740 147 0.2436 0.1800 2.7563 2.7458| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2139 2.6248 2.6839| | 13: 1.56 - 1.52 1.00 2745 130 0.2583 0.1976 2.5723 2.6184| | 14: 1.52 - 1.48 1.00 2803 134 0.2600 0.2028 2.4909 2.5498| | 15: 1.48 - 1.45 1.00 2738 128 0.2595 0.1951 2.4457 2.4232| | 16: 1.45 - 1.42 1.00 2756 161 0.2643 0.2026 2.3791 2.3895| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.2153 2.3182 2.3851| | 18: 1.39 - 1.36 1.00 2741 179 0.2668 0.2399 2.2589 2.448| | 19: 1.36 - 1.34 1.00 2807 134 0.2678 0.2438 2.2447 2.3404| | 20: 1.34 - 1.32 1.00 2696 147 0.2709 0.2237 2.2062 2.1863| | 21: 1.32 - 1.30 1.00 2785 112 0.2709 0.2272 2.1597 2.1788| | 22: 1.29 - 1.27 1.00 2704 152 0.2787 0.2477 2.1338 2.212| | 23: 1.27 - 1.26 1.00 2802 156 0.2788 0.2537 2.1021 2.1933| | 24: 1.26 - 1.24 1.00 2744 132 0.2748 0.2344 2.0727 2.0888| | 25: 1.24 - 1.22 1.00 2734 148 0.2848 0.2553 2.0511 2.0724| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2231 2.0081 2.0755| | 27: 1.21 - 1.19 1.00 2814 148 0.2959 0.2636 2.0162 2.0139| | 28: 1.19 - 1.18 1.00 2671 147 0.2928 0.2865 1.9814 2.0253| | 29: 1.18 - 1.16 1.00 2800 134 0.3030 0.2847 1.9691 2.0339| | 30: 1.16 - 1.15 1.00 2740 148 0.3079 0.3095 1.9325 2.0017| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.61 0.76 0.23 1454.08| | 2: 3.57 - 2.84 2876 122 0.81 25.81 1.27 0.23 1454.08| | 3: 2.84 - 2.48 2833 165 0.74 31.73 1.24 0.24 1206.10| | 4: 2.47 - 2.25 2825 136 0.81 25.44 1.26 0.25 562.56| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.29 0.25 562.56| | 6: 2.09 - 1.97 2846 113 0.84 22.58 1.29 0.25 308.53| | 7: 1.97 - 1.87 2787 165 0.90 16.67 1.28 0.25 91.88| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.24 0.25 91.88| | 9: 1.79 - 1.72 2745 138 0.88 18.75 1.24 0.25 55.63| | 10: 1.72 - 1.66 2789 158 0.87 20.11 1.22 0.25 48.37| | 11: 1.66 - 1.61 2740 147 0.86 21.22 1.22 0.25 46.67| | 12: 1.61 - 1.56 2787 146 0.88 18.70 1.23 0.25 29.37| | 13: 1.56 - 1.52 2745 130 0.87 20.28 1.25 0.25 29.37| | 14: 1.52 - 1.48 2803 134 0.86 20.77 1.25 0.25 26.19| | 15: 1.48 - 1.45 2738 128 0.88 19.64 1.23 0.25 20.38| | 16: 1.45 - 1.42 2756 161 0.86 21.53 1.24 0.25 20.38| | 17: 1.42 - 1.39 2785 139 0.87 20.60 1.23 0.25 17.69| | 18: 1.39 - 1.36 2741 179 0.86 21.54 1.24 0.25 16.14| | 19: 1.36 - 1.34 2807 134 0.85 22.49 1.22 0.25 16.14| | 20: 1.34 - 1.32 2696 147 0.87 21.10 1.21 0.25 13.34| | 21: 1.32 - 1.30 2785 112 0.86 22.15 1.21 0.25 13.15| | 22: 1.29 - 1.27 2704 152 0.85 22.89 1.22 0.24 12.88| | 23: 1.27 - 1.26 2802 156 0.85 22.95 1.21 0.24 11.52| | 24: 1.26 - 1.24 2744 132 0.84 23.31 1.20 0.24 11.52| | 25: 1.24 - 1.22 2734 148 0.84 24.02 1.21 0.24 10.97| | 26: 1.22 - 1.21 2727 135 0.83 24.73 1.19 0.23 10.35| | 27: 1.21 - 1.19 2814 148 0.82 25.65 1.20 0.23 10.35| | 28: 1.19 - 1.18 2671 147 0.81 26.61 1.18 0.22 9.93| | 29: 1.18 - 1.16 2800 134 0.80 27.61 1.17 0.22 9.77| | 30: 1.16 - 1.15 2740 148 0.79 29.02 1.16 0.22 9.77| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.77 max = 1454.08 mean = 211.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.89| |phase err.(test): min = 0.00 max = 89.19 mean = 22.71| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.463 Angle : 5.274 19.994 2118 Z= 3.722 Chirality : 0.402 1.206 243 Planarity : 0.031 0.090 284 Dihedral : 13.567 78.285 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -3.03 (0.45), residues: 224 helix: -2.85 (0.34), residues: 108 sheet: -2.04 (0.68), residues: 30 loop : -0.39 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.019 ARG A 5 TYR 0.076 0.045 TYR A 141 PHE 0.119 0.031 PHE A 119 HIS 0.069 0.020 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792439 | | target function (ml) not normalized (work): 232626.927135 | | target function (ml) not normalized (free): 11831.385904 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2613 0.1947 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2613 0.1947 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1947 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2007 0.2011 0.1960 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1638 0.1779 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1779 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 0.3831 386.444 357.272 0.679 1.003 0.420 11.894-9.307 99.02 97 4 0.1817 613.847 589.971 0.925 1.003 0.388 9.237-7.194 100.00 213 7 0.2215 502.052 490.702 0.960 1.004 0.369 7.162-5.571 100.00 427 22 0.2169 376.762 366.367 0.925 1.004 0.288 5.546-4.326 100.00 867 58 0.1252 517.201 512.224 0.963 1.004 0.238 4.315-3.360 100.00 1859 96 0.1144 491.862 488.463 1.005 1.003 0.222 3.356-2.611 100.00 3867 181 0.1459 323.128 319.658 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.1349 214.204 212.039 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1652 104.606 103.949 1.009 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.387 45.084 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2583 29.227 26.926 0.974 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0450 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1779 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=0.1640 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.083605 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1999.648476 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 0.1651 0.1776 0.0124 0.001 0.5 3.8 0.0 0.0 0 0.125 0.1548 0.1684 0.0136 0.002 0.5 3.5 0.0 0.0 0 0.250 0.1462 0.1623 0.0161 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1407 0.1589 0.0182 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1366 0.1561 0.0196 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1358 0.1556 0.0198 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1291 0.1505 0.0214 0.002 0.6 2.6 0.5 0.0 0 2.000 0.1276 0.1501 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1264 0.1495 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1255 0.1491 0.0236 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1247 0.1485 0.0239 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1242 0.1483 0.0241 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1241 0.1480 0.0238 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1239 0.1481 0.0241 0.006 0.9 2.9 0.5 0.0 0 9.000 0.1233 0.1474 0.0242 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1232 0.1475 0.0242 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1229 0.1471 0.0242 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1227 0.1476 0.0250 0.008 1.0 3.5 0.5 0.6 0 13.542 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1471 0.0242 0.007 0.9 3.8 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.71 2.42 3.013 19.055 1999.648 0.017 12.29 14.70 2.41 2.989 19.055 59.989 0.017 12.35 14.68 2.33 2.669 19.055 249.956 0.017 12.73 15.41 2.68 2.900 19.348 999.824 0.016 12.56 15.46 2.91 3.361 19.655 1999.648 0.016 12.42 15.48 3.06 3.329 19.637 2999.473 0.015 12.33 15.44 3.11 3.302 19.615 3999.297 0.015 12.31 15.48 3.17 3.410 19.653 4999.121 0.015 12.15 15.35 3.20 3.255 19.578 5998.945 0.015 12.13 15.34 3.21 3.277 19.576 6998.770 0.015 12.15 15.39 3.24 3.368 19.613 7998.594 0.015 12.18 15.45 3.26 3.299 19.566 8998.418 0.015 12.18 15.48 3.30 3.413 19.616 9998.242 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: 249.956 Accepted refinement result: 12.35 14.68 2.33 2.669 19.055 249.956 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.44 20.08 3.31 0 1785 Protein: 9.07 115.00 16.99 3.32 0 1519 Water: 11.45 119.44 38.22 N/A 0 258 Other: 19.71 26.59 22.05 N/A 0 8 Chain A: 9.07 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.14 227 31.14 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1468 r_work=0.1237 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1472 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 = 0.1230 r_free = 0.1465 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1230 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016866 | | target function (ls_wunit_k1) not normalized (work): 1404.883144 | | target function (ls_wunit_k1) not normalized (free): 111.204340 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1241 0.1230 0.1465 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1696 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1700 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1227 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1454 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 0.3510 301.387 281.562 0.650 1.003 0.374 11.894-9.307 99.02 97 4 0.1666 482.806 471.097 0.923 1.003 0.370 9.237-7.194 100.00 213 7 0.1912 394.876 388.673 0.965 1.003 0.349 7.162-5.571 100.00 427 22 0.1801 296.332 290.507 0.937 1.003 0.259 5.546-4.326 100.00 867 58 0.0993 406.791 403.947 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0871 386.861 385.779 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1173 254.148 253.030 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1024 168.477 167.756 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.275 82.454 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.484 35.989 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.988 21.471 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0502 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1454 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=0.1227 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1454 | n_water=258 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1235 r_free=0.1451 | n_water=252 | time (s): 25.330 (total time: 27.000) Filter (q & B) r_work=0.1237 r_free=0.1451 | n_water=249 | time (s): 2.410 (total time: 29.410) Compute maps r_work=0.1237 r_free=0.1451 | n_water=249 | time (s): 1.430 (total time: 30.840) Filter (map) r_work=0.1250 r_free=0.1449 | n_water=225 | time (s): 3.290 (total time: 34.130) Find peaks r_work=0.1250 r_free=0.1449 | n_water=225 | time (s): 0.470 (total time: 34.600) Add new water r_work=0.1399 r_free=0.1639 | n_water=440 | time (s): 2.490 (total time: 37.090) Refine new water occ: r_work=0.1301 r_free=0.1492 adp: r_work=0.1218 r_free=0.1441 occ: r_work=0.1232 r_free=0.1427 adp: r_work=0.1198 r_free=0.1413 occ: r_work=0.1203 r_free=0.1403 adp: r_work=0.1191 r_free=0.1401 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1401 r_work=0.1191 r_free=0.1401 | n_water=440 | time (s): 50.270 (total time: 87.360) Filter (q & B) r_work=0.1195 r_free=0.1407 | n_water=423 | time (s): 2.540 (total time: 89.900) Filter (dist only) r_work=0.1195 r_free=0.1406 | n_water=422 | time (s): 36.130 (total time: 126.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.746896 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1502.902473 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 0.1634 0.1767 0.0134 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1536 0.1678 0.0142 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1413 0.1571 0.0158 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1358 0.1530 0.0171 0.002 0.4 5.1 0.0 0.0 0 0.750 0.1315 0.1496 0.0181 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1314 0.1494 0.0181 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1250 0.1447 0.0197 0.002 0.5 5.1 0.5 0.0 0 2.000 0.1220 0.1427 0.0207 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1210 0.1423 0.0214 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1204 0.1424 0.0220 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1200 0.1423 0.0224 0.005 0.8 5.1 0.5 0.0 0 6.000 0.1197 0.1423 0.0226 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1192 0.1424 0.0232 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1191 0.1420 0.0230 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1189 0.1423 0.0234 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1186 0.1422 0.0236 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1184 0.1417 0.0233 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1181 0.1425 0.0244 0.008 0.9 4.5 0.5 0.6 0 13.873 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1184 0.1417 0.0233 0.007 0.9 4.2 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 14.17 2.33 3.775 21.806 1502.902 0.016 11.84 14.17 2.33 3.775 21.806 45.087 0.016 11.84 14.17 2.33 3.775 21.806 187.863 0.016 12.06 14.59 2.53 3.632 21.804 751.451 0.015 12.03 14.85 2.82 3.558 21.862 1502.902 0.015 11.88 14.82 2.94 3.457 22.008 2254.354 0.014 11.81 14.87 3.06 3.491 21.980 3005.805 0.014 11.72 14.71 2.99 3.476 22.090 3757.256 0.014 11.71 14.79 3.07 3.488 22.152 4508.707 0.014 11.66 14.76 3.09 3.511 22.170 5260.159 0.014 11.62 14.73 3.11 3.519 22.162 6011.610 0.014 11.62 14.78 3.15 3.545 22.203 6763.061 0.014 11.62 14.82 3.20 3.556 22.152 7514.512 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: 45.087 Accepted refinement result: 11.84 14.17 2.33 3.775 21.806 45.087 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 22.24 3.31 197 1752 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.49 76.69 41.02 N/A 197 225 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.10 115.03 19.44 N/A 0 1752 Chain S: 12.65 60.00 47.14 N/A 197 0 Histogram: Values Number of atoms 9.10 - 19.70 1260 19.70 - 30.29 244 30.29 - 40.88 166 40.88 - 51.47 132 51.47 - 62.07 125 62.07 - 72.66 11 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1417 r_work=0.1184 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1417 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 = 0.1186 r_free = 0.1421 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1186 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015115 | | target function (ls_wunit_k1) not normalized (work): 1259.036513 | | target function (ls_wunit_k1) not normalized (free): 106.150741 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1186 0.1421 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1583 0.1581 0.1646 n_refl.: 87592 remove outliers: r(all,work,free)=0.1583 0.1581 0.1646 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1585 0.1583 0.1647 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1183 0.1413 n_refl.: 87592 remove outliers: r(all,work,free)=0.1193 0.1182 0.1413 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 0.3450 299.936 274.117 0.586 1.002 0.350 11.894-9.307 99.02 97 4 0.1774 482.806 474.885 0.915 1.003 0.330 9.237-7.194 100.00 213 7 0.1621 394.876 395.873 0.986 1.003 0.264 7.162-5.571 100.00 427 22 0.1607 296.332 292.205 0.937 1.003 0.250 5.546-4.326 100.00 867 58 0.0876 406.791 403.715 0.959 1.003 0.196 4.315-3.360 100.00 1859 96 0.0787 386.861 385.814 1.004 1.003 0.177 3.356-2.611 100.00 3867 181 0.1075 254.148 253.258 1.009 1.002 0.130 2.608-2.026 99.99 8198 413 0.1004 168.477 167.962 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1093 82.275 82.500 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.484 36.012 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.988 21.492 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0150 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1413 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1413 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1413 | n_water=422 | time (s): 1.950 (total time: 1.950) Filter (dist) r_work=0.1181 r_free=0.1413 | n_water=420 | time (s): 35.010 (total time: 36.960) Filter (q & B) r_work=0.1181 r_free=0.1413 | n_water=419 | time (s): 2.680 (total time: 39.640) Compute maps r_work=0.1181 r_free=0.1413 | n_water=419 | time (s): 1.250 (total time: 40.890) Filter (map) r_work=0.1219 r_free=0.1407 | n_water=289 | time (s): 2.390 (total time: 43.280) Find peaks r_work=0.1219 r_free=0.1407 | n_water=289 | time (s): 0.620 (total time: 43.900) Add new water r_work=0.1333 r_free=0.1539 | n_water=482 | time (s): 3.360 (total time: 47.260) Refine new water occ: r_work=0.1240 r_free=0.1445 adp: r_work=0.1242 r_free=0.1446 occ: r_work=0.1219 r_free=0.1422 adp: r_work=0.1219 r_free=0.1422 occ: r_work=0.1202 r_free=0.1405 adp: r_work=0.1198 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1402 r_work=0.1198 r_free=0.1402 | n_water=482 | time (s): 165.960 (total time: 213.220) Filter (q & B) r_work=0.1203 r_free=0.1407 | n_water=444 | time (s): 3.370 (total time: 216.590) Filter (dist only) r_work=0.1203 r_free=0.1405 | n_water=443 | time (s): 36.480 (total time: 253.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767147 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.724993 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 0.1236 0.1379 0.0143 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1188 0.1345 0.0157 0.003 0.7 3.2 0.5 0.0 0 0.265 0.1172 0.1333 0.0161 0.004 0.8 3.2 0.5 0.0 0 0.530 0.1164 0.1331 0.0168 0.005 0.9 2.9 0.5 0.0 0 0.795 0.1159 0.1330 0.0171 0.006 1.0 2.9 0.5 0.0 0 1.060 0.1157 0.1331 0.0174 0.007 1.0 2.9 0.5 0.0 0 1.325 0.1156 0.1327 0.0172 0.007 1.1 3.2 0.5 0.0 0 1.590 0.1153 0.1328 0.0175 0.008 1.1 3.8 0.5 0.0 0 1.856 0.1162 0.1332 0.0170 0.005 0.9 2.9 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1327 0.0172 0.007 1.1 3.2 0.5 0.0 0 1.590 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.27 1.72 3.779 21.231 42.725 3.622 11.56 13.27 1.72 3.779 21.231 1.282 3.622 11.56 13.27 1.72 3.779 21.231 5.341 3.622 11.58 13.32 1.74 3.707 21.224 21.362 3.614 11.63 13.43 1.81 3.728 21.193 42.725 3.617 11.53 13.38 1.86 3.753 21.182 64.087 3.609 11.51 13.40 1.88 3.764 21.171 85.450 3.606 11.47 13.37 1.90 3.779 21.163 106.812 3.602 11.43 13.34 1.91 3.787 21.168 128.175 3.600 11.46 13.39 1.93 3.811 21.143 149.537 3.600 11.44 13.36 1.92 3.818 21.139 170.900 3.598 11.41 13.33 1.91 3.825 21.137 192.262 3.596 11.40 13.33 1.94 3.833 21.138 213.625 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.341 Accepted refinement result: 11.56 13.27 1.72 3.779 21.231 5.341 3.622 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.18 3.31 221 1749 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 35.40 N/A 221 222 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.11 115.04 19.39 N/A 0 1749 Chain S: 12.66 60.01 35.33 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.30 298 30.30 - 40.89 213 40.89 - 51.48 120 51.48 - 62.07 54 62.07 - 72.67 11 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1327 r_work=0.1156 r_free=0.1328 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1328 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1320 target_work(ml) = 3.613 | | 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= 0.1143 r_free= 0.1320 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612534 | | target function (ml) not normalized (work): 300902.427049 | | target function (ml) not normalized (free): 15843.514770 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1143 0.1320 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1487 0.1485 0.1551 n_refl.: 87590 remove outliers: r(all,work,free)=0.1487 0.1485 0.1551 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1486 0.1484 0.1551 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1315 n_refl.: 87590 remove outliers: r(all,work,free)=0.1145 0.1137 0.1315 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3853 291.842 270.283 0.492 0.999 0.320 11.894-9.307 97.06 95 4 0.2349 476.140 459.361 0.876 1.001 0.283 9.237-7.194 98.64 210 7 0.2215 388.380 389.171 0.962 1.002 0.195 7.162-5.571 100.00 427 22 0.2060 296.332 286.144 0.922 1.002 0.180 5.546-4.326 100.00 867 58 0.1123 406.791 401.930 0.966 1.002 0.154 4.315-3.360 100.00 1859 96 0.0927 386.861 384.403 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1124 254.148 252.121 1.007 1.002 0.100 2.608-2.026 99.99 8198 413 0.0923 168.477 167.708 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.275 82.531 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.484 36.057 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.988 21.522 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0166 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1315 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1137 r_free=0.1315 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1315 | n_water=443 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1137 r_free=0.1317 | n_water=442 | time (s): 46.930 (total time: 49.200) Filter (q & B) r_work=0.1138 r_free=0.1315 | n_water=441 | time (s): 3.920 (total time: 53.120) Compute maps r_work=0.1138 r_free=0.1315 | n_water=441 | time (s): 1.710 (total time: 54.830) Filter (map) r_work=0.1167 r_free=0.1297 | n_water=340 | time (s): 3.870 (total time: 58.700) Find peaks r_work=0.1167 r_free=0.1297 | n_water=340 | time (s): 0.720 (total time: 59.420) Add new water r_work=0.1231 r_free=0.1354 | n_water=493 | time (s): 3.710 (total time: 63.130) Refine new water occ: r_work=0.1164 r_free=0.1321 adp: r_work=0.1164 r_free=0.1322 occ: r_work=0.1148 r_free=0.1312 adp: r_work=0.1147 r_free=0.1311 occ: r_work=0.1136 r_free=0.1304 adp: r_work=0.1132 r_free=0.1303 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1303 r_work=0.1132 r_free=0.1303 | n_water=493 | time (s): 244.840 (total time: 307.970) Filter (q & B) r_work=0.1137 r_free=0.1307 | n_water=458 | time (s): 3.940 (total time: 311.910) Filter (dist only) r_work=0.1137 r_free=0.1307 | n_water=457 | time (s): 47.700 (total time: 359.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.799365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.702210 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 0.1199 0.1346 0.0147 0.002 0.6 3.8 0.5 0.0 0 0.090 0.1161 0.1322 0.0161 0.003 0.8 2.9 0.5 0.0 0 0.270 0.1147 0.1315 0.0167 0.005 0.9 3.5 0.5 0.0 0 0.540 0.1141 0.1314 0.0173 0.006 0.9 3.5 0.5 0.0 0 0.810 0.1137 0.1311 0.0175 0.007 1.0 3.5 0.5 0.0 0 1.080 0.1134 0.1311 0.0177 0.007 1.1 3.5 0.5 0.0 0 1.350 0.1132 0.1311 0.0179 0.008 1.1 3.5 0.5 0.0 0 1.619 0.1131 0.1310 0.0180 0.009 1.1 3.5 0.5 0.0 0 1.889 0.1139 0.1313 0.0174 0.006 1.0 3.5 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1310 0.0180 0.009 1.1 3.5 0.5 0.0 0 1.889 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 13.10 1.80 3.779 21.280 33.702 3.606 11.31 13.10 1.80 3.779 21.280 1.011 3.606 11.31 13.10 1.80 3.779 21.280 4.213 3.606 11.34 13.14 1.80 3.708 21.274 16.851 3.602 11.36 13.21 1.85 3.722 21.263 33.702 3.602 11.33 13.23 1.90 3.741 21.249 50.553 3.600 11.34 13.25 1.91 3.750 21.234 67.404 3.597 11.29 13.22 1.93 3.766 21.232 84.256 3.594 11.25 13.19 1.94 3.772 21.233 101.107 3.591 11.24 13.19 1.94 3.782 21.229 117.958 3.590 11.22 13.18 1.96 3.789 21.227 134.809 3.588 11.23 13.22 1.99 3.805 21.216 151.660 3.589 11.23 13.22 1.99 3.814 21.213 168.511 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: 1.011 Accepted refinement result: 11.31 13.10 1.80 3.779 21.280 1.011 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.27 3.31 238 1746 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 35.38 N/A 238 219 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.11 115.03 19.34 N/A 0 1746 Chain S: 12.65 60.00 35.48 N/A 238 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.29 300 30.29 - 40.88 226 40.88 - 51.48 121 51.48 - 62.07 53 62.07 - 72.66 10 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1310 r_work=0.1131 r_free=0.1310 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1310 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1309 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1309 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604021 | | target function (ml) not normalized (work): 300168.077788 | | target function (ml) not normalized (free): 15825.491625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1126 0.1309 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1466 0.1464 0.1533 n_refl.: 87583 remove outliers: r(all,work,free)=0.1466 0.1464 0.1533 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1466 0.1464 0.1533 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1125 0.1311 n_refl.: 87583 remove outliers: r(all,work,free)=0.1133 0.1124 0.1311 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 88.54 80 5 0.3883 291.977 249.534 0.448 0.998 0.308 11.894-9.307 96.08 94 4 0.2362 476.171 456.382 0.857 1.000 0.300 9.237-7.194 98.64 210 7 0.2360 388.380 383.525 0.937 1.001 0.170 7.162-5.571 100.00 427 22 0.2128 296.332 286.497 0.916 1.001 0.149 5.546-4.326 100.00 867 58 0.1106 406.791 401.678 0.963 1.001 0.130 4.315-3.360 100.00 1859 96 0.0897 386.861 384.873 1.005 1.001 0.130 3.356-2.611 100.00 3867 181 0.1101 254.148 252.409 1.008 1.002 0.024 2.608-2.026 99.99 8198 413 0.0905 168.477 167.971 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0878 82.275 82.655 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.484 36.082 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2167 22.988 21.451 0.980 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0012 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1124 r_free=0.1311 After: r_work=0.1125 r_free=0.1311 ================================== NQH flips ================================== r_work=0.1125 r_free=0.1311 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=0.1125 r_free=0.1311 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1125 r_free=0.1311 | n_water=457 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1125 r_free=0.1311 | n_water=457 | time (s): 44.730 (total time: 47.060) Filter (q & B) r_work=0.1126 r_free=0.1311 | n_water=455 | time (s): 3.800 (total time: 50.860) Compute maps r_work=0.1126 r_free=0.1311 | n_water=455 | time (s): 1.820 (total time: 52.680) Filter (map) r_work=0.1151 r_free=0.1307 | n_water=363 | time (s): 4.180 (total time: 56.860) Find peaks r_work=0.1151 r_free=0.1307 | n_water=363 | time (s): 0.640 (total time: 57.500) Add new water r_work=0.1200 r_free=0.1360 | n_water=502 | time (s): 3.330 (total time: 60.830) Refine new water occ: r_work=0.1147 r_free=0.1316 adp: r_work=0.1147 r_free=0.1319 occ: r_work=0.1135 r_free=0.1303 adp: r_work=0.1134 r_free=0.1305 occ: r_work=0.1125 r_free=0.1295 adp: r_work=0.1122 r_free=0.1294 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1294 r_work=0.1122 r_free=0.1294 | n_water=502 | time (s): 282.850 (total time: 343.680) Filter (q & B) r_work=0.1128 r_free=0.1297 | n_water=464 | time (s): 3.590 (total time: 347.270) Filter (dist only) r_work=0.1128 r_free=0.1295 | n_water=462 | time (s): 46.900 (total time: 394.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.794203 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.277948 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 0.1215 0.1350 0.0135 0.004 0.7 9.0 0.0 0.0 0 0.090 0.1166 0.1318 0.0151 0.004 0.8 9.3 0.0 0.0 0 0.269 0.1152 0.1308 0.0156 0.005 0.9 8.3 0.5 0.0 0 0.538 0.1143 0.1303 0.0160 0.006 1.0 8.6 0.5 0.0 0 0.807 0.1136 0.1299 0.0163 0.006 1.1 8.6 0.5 0.0 0 1.077 0.1133 0.1296 0.0164 0.007 1.1 8.6 0.5 0.0 0 1.346 0.1129 0.1295 0.0165 0.008 1.1 8.6 0.5 0.0 0 1.615 0.1128 0.1295 0.0166 0.009 1.1 8.6 0.5 0.0 0 1.884 0.1141 0.1302 0.0161 0.006 1.0 8.3 0.5 0.0 0 0.897 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1295 0.0166 0.009 1.1 8.6 0.5 0.0 0 1.884 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 12.95 1.66 3.779 21.303 41.278 3.604 11.28 12.95 1.66 3.779 21.303 1.238 3.604 11.28 12.95 1.66 3.778 21.303 5.160 3.604 11.30 12.99 1.68 3.712 21.297 20.639 3.599 11.42 13.17 1.75 3.720 21.268 41.278 3.604 11.32 13.11 1.79 3.753 21.257 61.917 3.597 11.27 13.08 1.81 3.768 21.253 82.556 3.593 11.24 13.04 1.81 3.776 21.253 103.195 3.590 11.20 13.03 1.82 3.786 21.251 123.834 3.587 11.21 13.07 1.86 3.804 21.240 144.473 3.587 11.21 13.08 1.87 3.817 21.233 165.112 3.587 11.19 13.06 1.87 3.822 21.235 185.751 3.585 11.18 13.05 1.87 3.829 21.233 206.390 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.160 Accepted refinement result: 11.28 12.95 1.66 3.778 21.303 5.160 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.32 3.31 244 1745 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 11.49 76.69 35.41 N/A 244 218 Other: 19.74 26.62 22.09 N/A 0 8 Chain A: 9.11 115.02 19.32 N/A 0 1745 Chain S: 12.65 60.00 35.61 N/A 244 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 295 30.29 - 40.88 229 40.88 - 51.47 124 51.47 - 62.06 56 62.06 - 72.66 10 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1128 r_free=0.1295 r_work=0.1128 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1128 r_free = 0.1295 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1293 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= 0.1126 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603228 | | target function (ml) not normalized (work): 300087.603293 | | target function (ml) not normalized (free): 15809.815834 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1334 0.1376 5.6427 5.6288| | 2: 3.57 - 2.84 1.00 2888 124 0.1059 0.1373 5.1661 5.2272| | 3: 2.83 - 2.48 1.00 2820 163 0.1069 0.1253 4.9453 4.9949| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.0940 4.6344 4.6571| | 5: 2.25 - 2.09 1.00 2756 127 0.0861 0.0986 4.5837 4.6452| | 6: 2.09 - 1.97 1.00 2846 113 0.0839 0.0984 4.2672 4.3633| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1110 3.9787 4.0801| | 8: 1.87 - 1.79 1.00 2789 144 0.0907 0.1086 3.8865 3.9905| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1198 3.6439 3.832| | 10: 1.72 - 1.66 1.00 2831 160 0.0912 0.1198 3.5612 3.7159| | 11: 1.66 - 1.61 1.00 2712 147 0.0863 0.1015 3.4932 3.5595| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1135 3.3266 3.4554| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1041 3.3059 3.3975| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1046 3.2351 3.3141| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1229 3.1503 3.2656| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1221 3.1318 3.2281| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1315 3.1151 3.2359| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1314 3.1025 3.2269| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1566 3.1113 3.2771| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1458 3.1125 3.1489| | 21: 1.32 - 1.30 1.00 2785 112 0.1467 0.1499 3.1111 3.1042| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1973 3.1223 3.2894| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1782 3.132 3.1964| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1840 3.1277 3.2303| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2146 3.1435 3.2639| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1780 3.1504 3.2039| | 27: 1.21 - 1.19 1.00 2814 148 0.2078 0.2166 3.1731 3.163| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2294 3.1658 3.1723| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2378 3.148 3.2289| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2435 3.1434 3.1637| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.67 1.00 0.97 5898.22| | 2: 3.57 - 2.84 2888 124 0.92 12.74 1.01 0.97 5898.22| | 3: 2.83 - 2.48 2820 163 0.89 16.72 0.99 0.97 4924.71| | 4: 2.47 - 2.25 2825 136 0.92 13.61 1.00 0.98 2414.34| | 5: 2.25 - 2.09 2756 127 0.90 15.85 1.01 0.98 2414.34| | 6: 2.09 - 1.97 2846 113 0.92 12.45 1.02 0.98 1388.81| | 7: 1.97 - 1.87 2787 165 0.95 9.34 1.02 0.98 514.17| | 8: 1.87 - 1.79 2789 144 0.93 12.70 0.99 0.98 514.17| | 9: 1.79 - 1.72 2745 138 0.94 10.05 0.98 0.98 289.82| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.98 244.89| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.98 234.46| | 12: 1.61 - 1.56 2773 144 0.96 8.79 0.99 0.98 136.14| | 13: 1.56 - 1.52 2745 130 0.95 10.36 1.03 0.98 136.14| | 14: 1.52 - 1.48 2803 134 0.94 10.70 1.02 0.98 122.17| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.99 96.58| | 16: 1.45 - 1.42 2756 161 0.94 10.98 1.02 0.99 96.58| | 17: 1.42 - 1.39 2785 139 0.95 10.82 1.01 0.99 88.10| | 18: 1.39 - 1.36 2741 179 0.94 11.48 1.01 0.98 83.19| | 19: 1.36 - 1.34 2807 134 0.94 11.78 0.99 0.98 83.19| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 79.65| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.40| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 79.84| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.06| | 24: 1.26 - 1.24 2744 132 0.92 14.83 0.96 0.95 82.06| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.04| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.03 0.93 86.24| | 27: 1.21 - 1.19 2814 148 0.89 18.79 1.03 0.93 86.24| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.93 89.76| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 91.09| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 91.09| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.40 max = 5898.22 mean = 906.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.45| |phase err.(test): min = 0.00 max = 89.80 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1293 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1449 0.1447 0.1516 n_refl.: 87579 remove outliers: r(all,work,free)=0.1449 0.1447 0.1516 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1449 0.1446 0.1516 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1125 0.1294 n_refl.: 87579 remove outliers: r(all,work,free)=0.1132 0.1123 0.1294 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3964 288.491 253.651 0.455 0.998 0.297 11.894-9.307 95.10 93 4 0.2432 469.947 457.929 0.865 1.001 0.219 9.237-7.194 97.73 208 7 0.2326 388.073 382.338 0.927 1.002 0.160 7.162-5.571 100.00 427 22 0.2092 296.332 286.860 0.912 1.002 0.143 5.546-4.326 100.00 867 58 0.1111 406.791 401.573 0.961 1.002 0.106 4.315-3.360 100.00 1859 96 0.0923 386.861 384.713 1.004 1.002 0.087 3.356-2.611 100.00 3867 181 0.1094 254.148 252.289 1.009 1.002 0.019 2.608-2.026 99.99 8198 413 0.0898 168.477 167.861 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.275 82.610 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.484 36.075 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2168 22.988 21.526 0.990 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0114 ================= 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 : 0.2612 0.1947 0.083 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1779 0.083 5.274 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1779 0.083 5.274 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1786 0.083 5.274 9.0 119.5 20.1 258 0.003 1_weight: 0.1640 0.1786 0.083 5.274 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1229 0.1471 0.007 0.940 9.0 119.5 20.1 258 0.139 1_adp: 0.1235 0.1468 0.007 0.940 9.1 119.4 20.1 258 0.139 1_regHadp: 0.1237 0.1472 0.007 0.940 9.1 119.4 20.1 258 0.139 1_occ: 0.1230 0.1465 0.007 0.940 9.1 119.4 20.1 258 0.139 2_bss: 0.1227 0.1454 0.007 0.940 9.1 119.5 20.1 258 0.139 2_settarget: 0.1227 0.1454 0.007 0.940 9.1 119.5 20.1 258 0.139 2_updatecdl: 0.1227 0.1454 0.007 0.932 9.1 119.5 20.1 258 0.139 2_nqh: 0.1227 0.1454 0.007 0.932 9.1 119.5 20.1 258 0.139 2_sol: 0.1195 0.1406 0.007 0.932 9.1 115.0 22.2 422 n/a 2_weight: 0.1195 0.1406 0.007 0.932 9.1 115.0 22.2 422 n/a 2_xyzrec: 0.1184 0.1417 0.007 0.911 9.1 115.0 22.2 422 n/a 2_adp: 0.1184 0.1417 0.007 0.911 9.1 115.0 22.2 422 n/a 2_regHadp: 0.1184 0.1417 0.007 0.911 9.1 115.0 22.2 422 n/a 2_occ: 0.1186 0.1421 0.007 0.911 9.1 115.0 22.2 422 n/a 3_bss: 0.1182 0.1413 0.007 0.911 9.1 115.0 22.2 422 n/a 3_settarget: 0.1182 0.1413 0.007 0.911 9.1 115.0 22.2 422 n/a 3_updatecdl: 0.1182 0.1413 0.007 0.912 9.1 115.0 22.2 422 n/a 3_nqh: 0.1182 0.1413 0.007 0.912 9.1 115.0 22.2 422 n/a 3_sol: 0.1203 0.1405 0.007 0.912 9.1 115.0 21.2 443 n/a 3_weight: 0.1203 0.1405 0.007 0.912 9.1 115.0 21.2 443 n/a 3_xyzrec: 0.1156 0.1327 0.007 1.051 9.1 115.0 21.2 443 n/a 3_adp: 0.1156 0.1327 0.007 1.051 9.1 115.0 21.2 443 n/a 3_regHadp: 0.1156 0.1328 0.007 1.051 9.1 115.0 21.2 443 n/a 3_occ: 0.1143 0.1320 0.007 1.051 9.1 115.0 21.2 443 n/a 4_bss: 0.1137 0.1315 0.007 1.051 9.1 115.0 21.2 443 n/a 4_settarget: 0.1137 0.1315 0.007 1.051 9.1 115.0 21.2 443 n/a 4_updatecdl: 0.1137 0.1315 0.007 1.051 9.1 115.0 21.2 443 n/a 4_nqh: 0.1137 0.1315 0.007 1.051 9.1 115.0 21.2 443 n/a 4_sol: 0.1137 0.1307 0.007 1.051 9.1 115.0 21.3 457 n/a 4_weight: 0.1137 0.1307 0.007 1.051 9.1 115.0 21.3 457 n/a 4_xyzrec: 0.1131 0.1310 0.009 1.130 9.1 115.0 21.3 457 n/a 4_adp: 0.1131 0.1310 0.009 1.130 9.1 115.0 21.3 457 n/a 4_regHadp: 0.1131 0.1310 0.009 1.130 9.1 115.0 21.3 457 n/a 4_occ: 0.1126 0.1309 0.009 1.130 9.1 115.0 21.3 457 n/a 5_bss: 0.1124 0.1311 0.009 1.130 9.1 115.0 21.3 457 n/a 5_settarget: 0.1124 0.1311 0.009 1.130 9.1 115.0 21.3 457 n/a 5_updatecdl: 0.1124 0.1311 0.009 1.132 9.1 115.0 21.3 457 n/a 5_setrh: 0.1125 0.1311 0.009 1.132 9.1 115.0 21.3 457 n/a 5_nqh: 0.1125 0.1311 0.009 1.132 9.1 115.0 21.3 457 n/a 5_sol: 0.1128 0.1295 0.009 1.132 9.1 115.0 21.3 462 n/a 5_weight: 0.1128 0.1295 0.009 1.132 9.1 115.0 21.3 462 n/a 5_xyzrec: 0.1128 0.1295 0.009 1.140 9.1 115.0 21.3 462 n/a 5_adp: 0.1128 0.1295 0.009 1.140 9.1 115.0 21.3 462 n/a 5_regHadp: 0.1128 0.1295 0.009 1.140 9.1 115.0 21.3 462 n/a 5_occ: 0.1126 0.1293 0.009 1.140 9.1 115.0 21.3 462 n/a end: 0.1123 0.1294 0.009 1.140 9.1 115.0 21.3 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9291273_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_9291273_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5700 Refinement macro-cycles (run) : 13363.2400 Write final files (write_after_run_outputs) : 91.8000 Total : 13458.6100 Total CPU time: 3.75 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:03:04 PST -0800 (1735365784.89 s) Start R-work = 0.1638, R-free = 0.1779 Final R-work = 0.1123, R-free = 0.1294 =============================================================================== Job complete usr+sys time: 13637.82 seconds wall clock time: 247 minutes 26.92 seconds (14846.92 seconds total)