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_3473948.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3473948.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.84, per 1000 atoms: 0.54 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: 0.50 Conformation dependent library (CDL) restraints added in 204.8 milliseconds Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 405 0.89 - 1.15: 1221 1.15 - 1.42: 638 1.42 - 1.69: 852 1.69 - 1.95: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.701 -0.166 6.80e-03 2.16e+04 5.97e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.683 -0.225 1.19e-02 7.06e+03 3.58e+02 bond pdb=" C THR A 154 " pdb=" O THR A 154 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.28e-02 6.10e+03 2.84e+02 bond pdb=" CA GLU A 16 " pdb=" C GLU A 16 " ideal model delta sigma weight residual 1.523 1.750 -0.227 1.35e-02 5.49e+03 2.83e+02 bond pdb=" CA VAL A 50 " pdb=" CB VAL A 50 " ideal model delta sigma weight residual 1.538 1.727 -0.189 1.13e-02 7.83e+03 2.79e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3216 4.82 - 9.63: 1845 9.63 - 14.45: 610 14.45 - 19.26: 99 19.26 - 24.08: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " ideal model delta sigma weight residual 121.77 106.84 14.93 1.00e+00 1.00e+00 2.23e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.52 -14.72 1.00e+00 1.00e+00 2.17e+02 angle pdb=" CA AGLU A 90 " pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 120.82 135.89 -15.07 1.05e+00 9.07e-01 2.06e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 119.76 105.07 14.69 1.03e+00 9.43e-01 2.03e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.62 -12.42 9.00e-01 1.23e+00 1.90e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 924 15.61 - 31.21: 123 31.21 - 46.81: 37 46.81 - 62.42: 21 62.42 - 78.02: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+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 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 91 0.217 - 0.433: 82 0.433 - 0.649: 46 0.649 - 0.866: 18 0.866 - 1.082: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CA LEU A 7 " pdb=" N LEU A 7 " pdb=" C LEU A 7 " pdb=" CB LEU A 7 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA GLN A 180 " pdb=" N GLN A 180 " pdb=" C GLN A 180 " pdb=" CB GLN A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.003 2.00e-02 2.50e+03 7.23e-02 1.57e+02 pdb=" CG PHE A 164 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.075 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.084 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.109 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.097 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.035 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.042 2.00e-02 2.50e+03 5.38e-02 8.68e+01 pdb=" CG PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.039 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.017 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1126 2.33 - 2.90: 8225 2.90 - 3.47: 10447 3.47 - 4.03: 15200 4.03 - 4.60: 21578 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.766 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 1.850 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.835 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.847 1.850 ... (remaining 56571 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_3473948_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795734 | | target function (ml) not normalized (work): 232901.437821 | | target function (ml) not normalized (free): 11833.313609 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2003 7.1008 4.9264| | 2: 3.57 - 2.84 1.00 2876 122 0.2416 0.1757 4.3428 4.3396| | 3: 2.84 - 2.48 1.00 2833 165 0.2366 0.1789 4.1227 4.1514| | 4: 2.47 - 2.25 1.00 2825 136 0.2328 0.1380 3.8273 3.8266| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1716 3.7933 3.8162| | 6: 2.09 - 1.97 1.00 2846 113 0.2551 0.1610 3.4712 3.5574| | 7: 1.97 - 1.87 1.00 2787 165 0.2513 0.1854 3.1448 3.2081| | 8: 1.87 - 1.79 1.00 2789 144 0.2472 0.2096 3.0941 3.1943| | 9: 1.79 - 1.72 1.00 2745 138 0.2437 0.2146 2.9088 3.0194| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.2056 2.8204 2.924| | 11: 1.66 - 1.61 1.00 2740 147 0.2486 0.1997 2.7644 2.7924| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.1954 2.6467 2.6549| | 13: 1.56 - 1.52 1.00 2745 130 0.2617 0.2049 2.585 2.6502| | 14: 1.52 - 1.48 1.00 2803 134 0.2607 0.1982 2.5037 2.5547| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.2281 2.4207 2.5137| | 16: 1.45 - 1.42 1.00 2756 161 0.2619 0.2141 2.3629 2.3884| | 17: 1.42 - 1.39 1.00 2785 139 0.2647 0.1924 2.3274 2.2936| | 18: 1.39 - 1.36 1.00 2741 179 0.2641 0.2248 2.2666 2.3374| | 19: 1.36 - 1.34 1.00 2807 134 0.2721 0.2229 2.248 2.2905| | 20: 1.34 - 1.32 1.00 2696 147 0.2749 0.2317 2.1979 2.1832| | 21: 1.32 - 1.30 1.00 2785 112 0.2718 0.2401 2.1726 2.2033| | 22: 1.29 - 1.27 1.00 2704 152 0.2739 0.2599 2.1248 2.2347| | 23: 1.27 - 1.26 1.00 2802 156 0.2782 0.2477 2.1007 2.1543| | 24: 1.26 - 1.24 1.00 2744 132 0.2771 0.2259 2.0805 2.0658| | 25: 1.24 - 1.22 1.00 2734 148 0.2922 0.2364 2.0799 2.0615| | 26: 1.22 - 1.21 1.00 2727 135 0.2860 0.2307 2.0092 2.0767| | 27: 1.21 - 1.19 1.00 2814 148 0.2982 0.2606 2.0154 2.0287| | 28: 1.19 - 1.18 1.00 2671 147 0.2949 0.2933 1.9816 2.0022| | 29: 1.18 - 1.16 1.00 2800 134 0.2954 0.2977 1.964 2.1028| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2688 1.9354 1.9469| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.58 0.76 0.23 1444.95| | 2: 3.57 - 2.84 2876 122 0.81 25.72 1.27 0.23 1444.95| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.23 1200.93| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 567.67| | 5: 2.25 - 2.09 2756 127 0.77 29.16 1.28 0.25 567.67| | 6: 2.09 - 1.97 2846 113 0.83 23.09 1.29 0.25 315.85| | 7: 1.97 - 1.87 2787 165 0.89 17.63 1.28 0.26 101.08| | 8: 1.87 - 1.79 2789 144 0.85 22.13 1.24 0.26 101.08| | 9: 1.79 - 1.72 2745 138 0.87 19.48 1.24 0.25 61.07| | 10: 1.72 - 1.66 2789 158 0.86 21.20 1.22 0.25 53.06| | 11: 1.66 - 1.61 2740 147 0.84 22.56 1.24 0.25 51.08| | 12: 1.61 - 1.56 2787 146 0.88 18.80 1.23 0.25 31.01| | 13: 1.56 - 1.52 2745 130 0.86 21.21 1.25 0.25 31.01| | 14: 1.52 - 1.48 2803 134 0.86 21.14 1.25 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.87 20.35 1.23 0.25 20.86| | 16: 1.45 - 1.42 2756 161 0.85 21.89 1.24 0.25 20.86| | 17: 1.42 - 1.39 2785 139 0.86 20.98 1.22 0.25 17.62| | 18: 1.39 - 1.36 2741 179 0.86 21.14 1.23 0.25 15.75| | 19: 1.36 - 1.34 2807 134 0.86 21.94 1.23 0.25 15.75| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.22 0.25 12.94| | 21: 1.32 - 1.30 2785 112 0.86 21.88 1.20 0.25 12.74| | 22: 1.29 - 1.27 2704 152 0.86 22.25 1.22 0.24 12.48| | 23: 1.27 - 1.26 2802 156 0.86 22.16 1.21 0.24 11.15| | 24: 1.26 - 1.24 2744 132 0.85 22.57 1.20 0.24 11.15| | 25: 1.24 - 1.22 2734 148 0.84 23.61 1.20 0.24 10.68| | 26: 1.22 - 1.21 2727 135 0.83 24.46 1.20 0.23 10.15| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.21 0.23 10.15| | 28: 1.19 - 1.18 2671 147 0.82 26.30 1.18 0.23 9.78| | 29: 1.18 - 1.16 2800 134 0.81 26.69 1.16 0.22 9.64| | 30: 1.16 - 1.15 2740 148 0.80 28.16 1.15 0.22 9.64| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.64 max = 1444.95 mean = 212.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.94| |phase err.(test): min = 0.00 max = 89.62 mean = 22.91| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.246 1557 Z= 5.496 Angle : 5.302 19.071 2118 Z= 3.752 Chirality : 0.400 1.082 243 Planarity : 0.033 0.096 284 Dihedral : 13.800 78.020 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 32.97 % 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: -3.15 (0.45), residues: 224 helix: -2.90 (0.38), residues: 102 sheet: -0.55 (0.68), residues: 38 loop : -1.43 (0.56), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.012 ARG A 5 TYR 0.088 0.042 TYR A 141 PHE 0.108 0.043 PHE A 164 HIS 0.104 0.029 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795734 | | target function (ml) not normalized (work): 232901.437821 | | target function (ml) not normalized (free): 11833.313609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1958 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1958 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1981 0.1958 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2003 0.2007 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1638 0.1780 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1637 0.1780 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 97.87 87 5 0.3703 389.766 370.079 0.760 0.918 0.401 11.894-9.307 99.02 97 4 0.1881 613.927 592.064 1.005 0.919 0.380 9.237-7.194 100.00 213 7 0.2217 502.117 488.953 1.039 0.919 0.354 7.162-5.571 100.00 427 22 0.2202 376.811 364.115 1.007 0.920 0.288 5.546-4.326 100.00 867 58 0.1269 517.268 510.758 1.045 0.920 0.229 4.315-3.360 100.00 1859 96 0.1148 491.925 488.902 1.092 0.921 0.209 3.356-2.611 100.00 3867 181 0.1439 323.170 319.932 1.083 0.922 0.038 2.608-2.026 99.99 8198 413 0.1346 214.232 212.104 1.089 0.924 0.000 2.025-1.573 100.00 17313 902 0.1648 104.620 104.018 1.089 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2067 46.393 45.106 1.074 0.933 0.000 1.221-1.150 99.97 13689 708 0.2602 29.231 26.897 1.030 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0479 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1639 r_free=0.1784 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.214098 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.473208 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 0.1726 0.1839 0.0113 0.002 0.4 5.1 0.0 0.0 0 0.125 0.1561 0.1700 0.0139 0.001 0.5 4.5 0.0 0.0 0 0.250 0.1428 0.1593 0.0165 0.002 0.5 4.5 0.0 0.0 0 0.500 0.1374 0.1560 0.0186 0.002 0.5 4.2 0.0 0.0 0 0.750 0.1332 0.1528 0.0196 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1355 0.1555 0.0201 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1297 0.1514 0.0217 0.002 0.6 4.2 0.5 0.0 0 2.000 0.1270 0.1490 0.0221 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1254 0.1479 0.0224 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1250 0.1479 0.0229 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1243 0.1474 0.0231 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1234 0.1465 0.0230 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1469 0.0235 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1230 0.1467 0.0237 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1228 0.1468 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1465 0.0240 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1222 0.1465 0.0243 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1220 0.1469 0.0249 0.008 1.0 3.8 0.5 0.0 0 13.607 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1234 0.1465 0.0230 0.005 0.8 3.8 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.65 2.30 3.013 19.067 2007.473 0.018 12.34 14.64 2.30 2.989 19.067 60.224 0.018 12.41 14.62 2.21 2.666 19.067 250.934 0.017 12.77 15.32 2.55 2.742 19.243 1003.737 0.017 12.62 15.49 2.87 3.248 19.605 2007.473 0.016 12.54 15.54 3.00 3.326 19.654 3011.210 0.016 12.46 15.53 3.07 3.469 19.721 4014.946 0.015 12.41 15.54 3.13 3.418 19.685 5018.683 0.015 12.31 15.46 3.15 3.369 19.659 6022.420 0.015 12.29 15.47 3.18 3.346 19.632 7026.156 0.015 12.29 15.53 3.24 3.388 19.647 8029.893 0.015 12.27 15.50 3.24 3.499 19.701 9033.629 0.015 12.28 15.58 3.31 3.696 19.788 10037.366 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: 250.934 Accepted refinement result: 12.41 14.62 2.21 2.666 19.067 250.934 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.09 3.31 0 1785 Protein: 9.08 114.99 17.00 3.31 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.74 26.62 22.07 N/A 0 8 Chain A: 9.08 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1462 r_work=0.1243 r_free=0.1465 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1465 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 = 0.1237 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1237 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017025 | | target function (ls_wunit_k1) not normalized (work): 1418.108955 | | target function (ls_wunit_k1) not normalized (free): 109.972865 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1248 0.1237 0.1461 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1680 0.1681 0.1695 n_refl.: 87592 remove outliers: r(all,work,free)=0.1680 0.1681 0.1695 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1685 0.1686 0.1699 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1248 0.1237 0.1460 n_refl.: 87592 remove outliers: r(all,work,free)=0.1247 0.1236 0.1460 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3408 303.496 281.750 0.658 1.003 0.380 11.894-9.307 99.02 97 4 0.1631 482.068 469.279 0.926 1.003 0.380 9.237-7.194 100.00 213 7 0.1880 394.272 388.270 0.965 1.003 0.348 7.162-5.571 100.00 427 22 0.1856 295.879 290.134 0.934 1.003 0.259 5.546-4.326 100.00 867 58 0.1017 406.169 402.981 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0888 386.270 385.092 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1178 253.759 252.573 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1030 168.219 167.459 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1123 82.149 82.328 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1461 36.428 35.923 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2260 22.952 21.433 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0451 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1460 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1237 r_free=0.1462 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1462 | n_water=258 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1245 r_free=0.1458 | n_water=251 | time (s): 21.370 (total time: 22.930) Filter (q & B) r_work=0.1247 r_free=0.1459 | n_water=248 | time (s): 2.890 (total time: 25.820) Compute maps r_work=0.1247 r_free=0.1459 | n_water=248 | time (s): 1.280 (total time: 27.100) Filter (map) r_work=0.1264 r_free=0.1463 | n_water=228 | time (s): 2.500 (total time: 29.600) Find peaks r_work=0.1264 r_free=0.1463 | n_water=228 | time (s): 0.480 (total time: 30.080) Add new water r_work=0.1411 r_free=0.1628 | n_water=439 | time (s): 2.610 (total time: 32.690) Refine new water occ: r_work=0.1315 r_free=0.1498 adp: r_work=0.1234 r_free=0.1445 occ: r_work=0.1247 r_free=0.1435 adp: r_work=0.1214 r_free=0.1421 occ: r_work=0.1217 r_free=0.1415 adp: r_work=0.1206 r_free=0.1411 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1411 r_work=0.1206 r_free=0.1411 | n_water=439 | time (s): 53.950 (total time: 86.640) Filter (q & B) r_work=0.1209 r_free=0.1415 | n_water=424 | time (s): 3.060 (total time: 89.700) Filter (dist only) r_work=0.1209 r_free=0.1413 | n_water=423 | time (s): 36.020 (total time: 125.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.641983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1469.486831 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1674 0.1787 0.0114 0.001 0.4 8.6 0.0 0.0 0 0.125 0.1522 0.1659 0.0137 0.001 0.4 8.0 0.0 0.0 0 0.250 0.1403 0.1565 0.0162 0.001 0.4 7.0 0.0 0.0 0 0.500 0.1360 0.1531 0.0171 0.001 0.4 6.4 0.0 0.0 0 0.750 0.1305 0.1488 0.0183 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1315 0.1501 0.0186 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1255 0.1461 0.0206 0.002 0.5 5.4 0.5 0.0 0 2.000 0.1228 0.1446 0.0218 0.003 0.6 5.4 0.5 0.0 0 3.000 0.1212 0.1429 0.0217 0.003 0.6 5.8 0.5 0.0 0 4.000 0.1207 0.1429 0.0222 0.004 0.7 6.1 0.5 0.0 0 5.000 0.1200 0.1426 0.0227 0.004 0.7 5.4 0.5 0.0 0 6.000 0.1200 0.1421 0.0221 0.005 0.8 6.1 0.5 0.0 0 7.000 0.1199 0.1428 0.0229 0.005 0.8 6.1 0.5 0.0 0 8.000 0.1196 0.1423 0.0227 0.006 0.8 5.8 0.5 0.0 0 9.000 0.1192 0.1416 0.0224 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1189 0.1410 0.0221 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1188 0.1418 0.0231 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1189 0.1414 0.0226 0.007 0.9 5.1 0.5 0.0 0 13.000 0.1184 0.1417 0.0233 0.008 0.9 5.4 0.5 0.0 0 14.321 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1410 0.0221 0.007 0.9 5.4 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 14.10 2.21 3.774 21.800 1469.487 0.016 11.89 14.10 2.21 3.774 21.800 44.085 0.016 11.89 14.10 2.21 3.774 21.800 183.686 0.016 12.15 14.65 2.50 3.581 21.834 734.743 0.016 12.09 14.86 2.76 3.557 21.862 1469.487 0.015 11.91 14.75 2.84 3.471 21.987 2204.230 0.015 11.84 14.64 2.80 3.499 22.063 2938.974 0.014 11.74 14.60 2.86 3.483 22.022 3673.717 0.014 11.80 14.82 3.01 3.526 22.167 4408.460 0.014 11.77 14.80 3.03 3.543 22.182 5143.204 0.014 11.75 14.86 3.10 3.553 22.157 5877.947 0.014 11.72 14.89 3.17 3.587 22.216 6612.691 0.014 11.71 14.86 3.15 3.593 22.176 7347.434 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: 44.085 Accepted refinement result: 11.89 14.10 2.21 3.774 21.800 44.085 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 22.22 3.31 195 1755 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 11.50 76.69 40.85 N/A 195 228 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.02 19.49 N/A 0 1755 Chain S: 16.69 60.00 46.79 N/A 195 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.29 246 30.29 - 40.88 166 40.88 - 51.47 134 51.47 - 62.06 121 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1410 r_work=0.1189 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1404 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1191 r_free= 0.1404 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015213 | | target function (ls_wunit_k1) not normalized (work): 1267.168132 | | target function (ls_wunit_k1) not normalized (free): 102.107962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1191 0.1404 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1589 0.1589 0.1620 n_refl.: 87591 remove outliers: r(all,work,free)=0.1589 0.1589 0.1620 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1591 0.1621 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1188 0.1401 n_refl.: 87591 remove outliers: r(all,work,free)=0.1197 0.1187 0.1401 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3282 299.448 278.112 0.601 1.002 0.360 11.894-9.307 99.02 97 4 0.1616 482.068 474.580 0.916 1.003 0.352 9.237-7.194 100.00 213 7 0.1740 394.272 394.885 0.979 1.003 0.290 7.162-5.571 100.00 427 22 0.1609 295.879 290.895 0.932 1.003 0.240 5.546-4.326 100.00 867 58 0.0892 406.169 402.667 0.959 1.003 0.205 4.315-3.360 100.00 1859 96 0.0796 386.270 385.735 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1088 253.759 253.040 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1008 168.219 167.582 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.149 82.376 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1440 36.428 35.964 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.952 21.460 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0123 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1401 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1401 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1401 | n_water=423 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1186 r_free=0.1403 | n_water=417 | time (s): 37.850 (total time: 39.660) Filter (q & B) r_work=0.1186 r_free=0.1403 | n_water=417 | time (s): 0.890 (total time: 40.550) Compute maps r_work=0.1186 r_free=0.1403 | n_water=417 | time (s): 1.820 (total time: 42.370) Filter (map) r_work=0.1220 r_free=0.1389 | n_water=287 | time (s): 3.290 (total time: 45.660) Find peaks r_work=0.1220 r_free=0.1389 | n_water=287 | time (s): 0.690 (total time: 46.350) Add new water r_work=0.1339 r_free=0.1511 | n_water=467 | time (s): 3.090 (total time: 49.440) Refine new water occ: r_work=0.1252 r_free=0.1435 adp: r_work=0.1253 r_free=0.1435 occ: r_work=0.1230 r_free=0.1416 adp: r_work=0.1229 r_free=0.1414 occ: r_work=0.1212 r_free=0.1401 adp: r_work=0.1207 r_free=0.1395 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1395 r_work=0.1207 r_free=0.1395 | n_water=467 | time (s): 192.070 (total time: 241.510) Filter (q & B) r_work=0.1211 r_free=0.1395 | n_water=435 | time (s): 3.460 (total time: 244.970) Filter (dist only) r_work=0.1211 r_free=0.1395 | n_water=435 | time (s): 36.200 (total time: 281.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.737077 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.249297 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 0.1240 0.1379 0.0139 0.002 0.6 4.5 0.5 0.0 0 0.087 0.1199 0.1344 0.0145 0.003 0.7 3.5 0.5 0.0 0 0.261 0.1180 0.1331 0.0151 0.004 0.8 3.5 0.5 0.0 0 0.521 0.1173 0.1327 0.0154 0.005 0.9 3.2 0.5 0.0 0 0.782 0.1169 0.1326 0.0158 0.006 1.0 3.8 0.5 0.0 0 1.042 0.1166 0.1327 0.0160 0.007 1.0 3.8 0.5 0.0 0 1.303 0.1163 0.1327 0.0164 0.007 1.0 4.2 0.5 0.0 0 1.563 0.1162 0.1328 0.0165 0.008 1.1 4.2 0.5 0.0 0 1.824 0.1172 0.1328 0.0156 0.005 0.9 3.2 0.5 0.0 0 0.869 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1169 0.1326 0.0158 0.006 1.0 3.8 0.5 0.0 0 1.042 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 13.26 1.58 3.777 21.222 39.249 3.630 11.69 13.26 1.58 3.777 21.222 1.177 3.630 11.69 13.26 1.57 3.775 21.222 4.906 3.630 11.71 13.29 1.58 3.706 21.215 19.625 3.622 11.80 13.45 1.66 3.723 21.184 39.249 3.625 11.69 13.41 1.72 3.752 21.171 58.874 3.618 11.64 13.40 1.76 3.767 21.164 78.499 3.614 11.60 13.38 1.78 3.779 21.160 98.123 3.610 11.58 13.38 1.80 3.790 21.152 117.748 3.608 11.57 13.38 1.82 3.803 21.147 137.373 3.607 11.56 13.39 1.83 3.817 21.135 156.997 3.606 11.55 13.39 1.84 3.826 21.133 176.622 3.605 11.54 13.38 1.84 3.834 21.129 196.246 3.604 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.177 Accepted refinement result: 11.69 13.26 1.58 3.777 21.222 1.177 3.630 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.16 3.31 212 1750 Protein: 9.11 115.02 17.04 3.31 0 1519 Water: 11.51 76.69 35.52 N/A 212 223 Other: 19.77 26.65 22.11 N/A 0 8 Chain A: 9.11 115.02 19.40 N/A 0 1750 Chain S: 16.70 60.01 35.65 N/A 212 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.30 288 30.30 - 40.89 213 40.89 - 51.48 123 51.48 - 62.07 52 62.07 - 72.66 12 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=0.1169 r_free=0.1326 r_work=0.1169 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1169 r_free = 0.1326 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1323 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1155 r_free= 0.1323 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.619911 | | target function (ml) not normalized (work): 301509.600231 | | target function (ml) not normalized (free): 15874.538135 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1155 0.1323 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1489 0.1489 0.1528 n_refl.: 87588 remove outliers: r(all,work,free)=0.1489 0.1489 0.1528 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1488 0.1487 0.1527 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1309 n_refl.: 87588 remove outliers: r(all,work,free)=0.1154 0.1146 0.1309 n_refl.: 87582 ======================== 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 0.3922 299.448 270.027 0.500 1.000 0.318 11.894-9.307 97.06 95 4 0.2302 475.412 458.938 0.877 1.002 0.264 9.237-7.194 98.18 209 7 0.2217 385.760 387.369 0.954 1.002 0.220 7.162-5.571 100.00 427 22 0.1998 295.879 286.686 0.921 1.002 0.184 5.546-4.326 100.00 867 58 0.1130 406.169 400.617 0.963 1.002 0.154 4.315-3.360 100.00 1859 96 0.0931 386.270 384.022 1.006 1.002 0.140 3.356-2.611 100.00 3867 181 0.1145 253.759 251.786 1.008 1.002 0.053 2.608-2.026 99.99 8198 413 0.0935 168.219 167.361 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0906 82.149 82.399 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1263 36.428 36.000 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.952 21.487 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=-0.0195 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1309 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=0.1146 r_free=0.1309 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1309 | n_water=435 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1146 r_free=0.1309 | n_water=435 | time (s): 42.940 (total time: 45.440) Filter (q & B) r_work=0.1146 r_free=0.1309 | n_water=434 | time (s): 4.380 (total time: 49.820) Compute maps r_work=0.1146 r_free=0.1309 | n_water=434 | time (s): 1.880 (total time: 51.700) Filter (map) r_work=0.1165 r_free=0.1285 | n_water=331 | time (s): 3.990 (total time: 55.690) Find peaks r_work=0.1165 r_free=0.1285 | n_water=331 | time (s): 0.700 (total time: 56.390) Add new water r_work=0.1231 r_free=0.1355 | n_water=485 | time (s): 3.750 (total time: 60.140) Refine new water occ: r_work=0.1164 r_free=0.1292 adp: r_work=0.1165 r_free=0.1295 occ: r_work=0.1150 r_free=0.1281 adp: r_work=0.1148 r_free=0.1282 occ: r_work=0.1138 r_free=0.1273 adp: r_work=0.1134 r_free=0.1272 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1272 r_work=0.1134 r_free=0.1272 | n_water=485 | time (s): 246.980 (total time: 307.120) Filter (q & B) r_work=0.1139 r_free=0.1281 | n_water=458 | time (s): 3.960 (total time: 311.080) Filter (dist only) r_work=0.1139 r_free=0.1281 | n_water=457 | time (s): 47.240 (total time: 358.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.780201 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 34.500932 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 0.1193 0.1314 0.0121 0.002 0.6 4.2 0.5 0.0 0 0.089 0.1156 0.1291 0.0134 0.003 0.7 2.9 0.5 0.0 0 0.267 0.1141 0.1284 0.0144 0.005 0.9 3.8 0.5 0.0 0 0.534 0.1135 0.1281 0.0146 0.006 0.9 3.5 0.5 0.0 0 0.801 0.1131 0.1280 0.0150 0.006 1.0 3.2 0.5 0.0 0 1.068 0.1127 0.1282 0.0155 0.007 1.0 4.2 0.5 0.0 0 1.335 0.1126 0.1281 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.602 0.1124 0.1281 0.0158 0.008 1.1 4.2 0.5 0.0 0 1.869 0.1133 0.1285 0.0152 0.006 1.0 4.2 0.5 0.0 0 0.890 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1280 0.0150 0.006 1.0 3.2 0.5 0.0 0 1.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.80 1.50 3.778 21.251 34.501 3.604 11.31 12.80 1.50 3.778 21.251 1.035 3.604 11.31 12.80 1.50 3.778 21.251 4.313 3.604 11.36 12.85 1.49 3.704 21.247 17.250 3.600 11.39 12.95 1.56 3.724 21.232 34.501 3.601 11.37 12.99 1.61 3.736 21.213 51.751 3.597 11.32 12.95 1.63 3.757 21.209 69.002 3.594 11.29 12.94 1.65 3.768 21.204 86.252 3.591 11.26 12.92 1.66 3.774 21.203 103.503 3.588 11.24 12.90 1.67 3.783 21.202 120.753 3.586 11.25 12.96 1.71 3.799 21.188 138.004 3.586 11.23 12.95 1.72 3.806 21.188 155.254 3.585 11.22 12.94 1.72 3.813 21.187 172.505 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.035 Accepted refinement result: 11.31 12.80 1.50 3.778 21.251 1.035 3.604 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.22 3.31 235 1749 Protein: 9.11 115.02 17.03 3.31 0 1519 Water: 11.50 76.69 35.10 N/A 235 222 Other: 19.77 26.65 22.10 N/A 0 8 Chain A: 9.11 115.02 19.38 N/A 0 1749 Chain S: 16.18 60.00 34.90 N/A 235 0 Histogram: Values Number of atoms 9.11 - 19.70 1267 19.70 - 30.29 297 30.29 - 40.88 224 40.88 - 51.47 125 51.47 - 62.06 48 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.84 4 93.84 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1280 r_work=0.1131 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1280 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 = 0.1276 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1276 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601802 | | target function (ml) not normalized (work): 299979.683013 | | target function (ml) not normalized (free): 15793.785523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1126 0.1276 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1463 0.1463 0.1499 n_refl.: 87582 remove outliers: r(all,work,free)=0.1463 0.1463 0.1499 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1462 0.1462 0.1499 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1125 0.1280 n_refl.: 87582 remove outliers: r(all,work,free)=0.1131 0.1123 0.1280 n_refl.: 87578 ======================== 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 0.3877 292.815 260.140 0.470 1.000 0.320 11.894-9.307 97.06 95 4 0.2412 475.412 460.619 0.858 1.002 0.272 9.237-7.194 97.73 208 7 0.2265 386.842 380.795 0.927 1.002 0.192 7.162-5.571 100.00 427 22 0.2053 295.879 287.000 0.917 1.003 0.160 5.546-4.326 100.00 867 58 0.1105 406.169 401.699 0.963 1.002 0.121 4.315-3.360 100.00 1859 96 0.0905 386.270 384.327 1.003 1.002 0.100 3.356-2.611 100.00 3867 181 0.1085 253.759 252.077 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0908 168.219 167.558 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.149 82.482 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.428 36.027 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.952 21.494 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=-0.0136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1123 r_free=0.1280 After: r_work=0.1124 r_free=0.1280 ================================== NQH flips ================================== r_work=0.1124 r_free=0.1280 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1124 r_free=0.1280 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1124 r_free=0.1280 | n_water=457 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1124 r_free=0.1280 | n_water=457 | time (s): 43.810 (total time: 46.270) Filter (q & B) r_work=0.1124 r_free=0.1279 | n_water=456 | time (s): 3.970 (total time: 50.240) Compute maps r_work=0.1124 r_free=0.1279 | n_water=456 | time (s): 1.900 (total time: 52.140) Filter (map) r_work=0.1148 r_free=0.1287 | n_water=368 | time (s): 3.880 (total time: 56.020) Find peaks r_work=0.1148 r_free=0.1287 | n_water=368 | time (s): 0.740 (total time: 56.760) Add new water r_work=0.1193 r_free=0.1341 | n_water=498 | time (s): 3.690 (total time: 60.450) Refine new water occ: r_work=0.1142 r_free=0.1302 adp: r_work=0.1143 r_free=0.1303 occ: r_work=0.1132 r_free=0.1292 adp: r_work=0.1131 r_free=0.1292 occ: r_work=0.1124 r_free=0.1286 adp: r_work=0.1122 r_free=0.1283 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1283 r_work=0.1122 r_free=0.1283 | n_water=498 | time (s): 230.010 (total time: 290.460) Filter (q & B) r_work=0.1128 r_free=0.1284 | n_water=466 | time (s): 4.030 (total time: 294.490) Filter (dist only) r_work=0.1128 r_free=0.1283 | n_water=465 | time (s): 49.270 (total time: 343.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.742544 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.802995 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 0.1207 0.1331 0.0125 0.003 0.7 6.1 0.0 0.0 0 0.087 0.1164 0.1304 0.0141 0.004 0.8 5.8 0.0 0.0 0 0.261 0.1143 0.1291 0.0148 0.005 0.9 5.1 0.5 0.0 0 0.523 0.1133 0.1285 0.0151 0.006 1.0 5.1 0.5 0.0 0 0.784 0.1129 0.1282 0.0154 0.006 1.0 4.8 0.5 0.0 0 1.046 0.1128 0.1282 0.0154 0.007 1.0 4.8 0.5 0.0 0 1.307 0.1127 0.1282 0.0155 0.007 1.0 4.8 0.5 0.0 0 1.568 0.1126 0.1281 0.0156 0.008 1.1 4.8 0.5 0.0 0 1.830 0.1130 0.1283 0.0153 0.006 1.0 4.8 0.5 0.0 0 0.871 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1281 0.0156 0.008 1.1 4.8 0.5 0.0 0 1.830 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.81 1.56 3.777 21.255 40.803 3.603 11.26 12.81 1.56 3.777 21.255 1.224 3.603 11.26 12.81 1.56 3.777 21.255 5.100 3.603 11.29 12.87 1.58 3.710 21.250 20.401 3.598 11.39 13.04 1.65 3.729 21.220 40.803 3.603 11.30 13.00 1.70 3.753 21.210 61.204 3.596 11.26 12.99 1.73 3.768 21.205 81.606 3.593 11.22 12.96 1.74 3.779 21.203 102.007 3.589 11.19 12.94 1.75 3.788 21.201 122.409 3.587 11.17 12.92 1.75 3.796 21.200 142.810 3.585 11.20 12.99 1.79 3.817 21.183 163.212 3.586 11.18 12.97 1.80 3.825 21.185 183.613 3.585 11.15 12.94 1.79 3.829 21.184 204.015 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.100 Accepted refinement result: 11.26 12.81 1.56 3.777 21.255 5.100 3.603 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 21.23 3.30 244 1748 Protein: 9.10 115.01 17.03 3.31 0 1519 Water: 11.50 76.68 34.93 N/A 244 221 Other: 19.76 26.64 22.09 N/A 0 8 Chain A: 9.10 115.01 19.35 N/A 0 1748 Chain S: 16.18 60.00 34.64 N/A 244 0 Histogram: Values Number of atoms 9.10 - 19.69 1266 19.69 - 30.28 307 30.28 - 40.87 227 40.87 - 51.46 118 51.46 - 62.06 51 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1126 r_free=0.1281 r_work=0.1126 r_free=0.1281 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1281 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1278 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1278 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601801 | | target function (ml) not normalized (work): 299965.180125 | | target function (ml) not normalized (free): 15806.824049 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1315 0.1307 5.6242 5.6309| | 2: 3.57 - 2.84 1.00 2888 124 0.1051 0.1403 5.1662 5.2354| | 3: 2.83 - 2.48 1.00 2820 163 0.1082 0.1217 4.9521 4.9859| | 4: 2.47 - 2.25 1.00 2825 136 0.0886 0.0981 4.6355 4.6692| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0947 4.5883 4.6402| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.0998 4.2658 4.3643| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1125 3.9777 4.0929| | 8: 1.87 - 1.79 1.00 2789 144 0.0902 0.1091 3.8848 3.9877| | 9: 1.79 - 1.72 1.00 2745 138 0.0866 0.1151 3.6437 3.807| | 10: 1.72 - 1.66 1.00 2831 160 0.0918 0.1179 3.5623 3.7209| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1043 3.4944 3.576| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1115 3.3272 3.4413| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1031 3.3041 3.3879| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1055 3.2323 3.3206| | 15: 1.48 - 1.45 1.00 2738 128 0.0998 0.1208 3.1466 3.2559| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1227 3.1313 3.2293| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1295 3.1141 3.2231| | 18: 1.39 - 1.36 1.00 2741 179 0.1198 0.1328 3.1016 3.2361| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1577 3.1092 3.2725| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1454 3.1084 3.1573| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1498 3.1116 3.0989| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.1980 3.1224 3.2934| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1797 3.1319 3.2| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1831 3.1253 3.2273| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2128 3.1412 3.2559| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1768 3.1464 3.1997| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2174 3.1687 3.1636| | 28: 1.19 - 1.18 1.00 2671 147 0.2198 0.2275 3.164 3.1682| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2372 3.1462 3.2265| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2440 3.1417 3.1631| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.86 1.00 0.96 5969.48| | 2: 3.57 - 2.84 2888 124 0.92 12.90 1.01 0.96 5969.48| | 3: 2.83 - 2.48 2820 163 0.89 16.86 0.99 0.97 4982.29| | 4: 2.47 - 2.25 2825 136 0.92 13.74 1.00 0.98 2436.65| | 5: 2.25 - 2.09 2756 127 0.90 15.92 1.01 0.98 2436.65| | 6: 2.09 - 1.97 2846 113 0.92 12.55 1.02 0.98 1398.66| | 7: 1.97 - 1.87 2787 165 0.95 9.34 1.02 0.98 513.40| | 8: 1.87 - 1.79 2789 144 0.93 12.64 1.00 0.98 513.40| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.97 289.16| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.97 244.25| | 11: 1.66 - 1.61 2712 147 0.94 11.70 0.98 0.97 233.95| | 12: 1.61 - 1.56 2773 144 0.95 8.87 0.99 0.97 136.83| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.97 136.83| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.02 0.98 122.59| | 15: 1.48 - 1.45 2738 128 0.95 9.83 1.02 0.98 96.51| | 16: 1.45 - 1.42 2756 161 0.94 11.02 1.02 0.98 96.51| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.10| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.98 83.22| | 19: 1.36 - 1.34 2807 134 0.94 11.83 1.00 0.98 83.22| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.96 79.56| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.96 79.30| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 79.73| | 23: 1.27 - 1.26 2802 156 0.92 14.79 0.97 0.94 81.92| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 81.92| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 83.79| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.93 85.87| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 85.87| | 28: 1.19 - 1.18 2671 147 0.88 20.34 1.01 0.93 89.28| | 29: 1.18 - 1.16 2800 134 0.88 20.41 0.99 0.92 90.57| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.92 90.57| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.30 max = 5969.48 mean = 914.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.49| |phase err.(test): min = 0.00 max = 89.23 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1123 0.1278 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1493 n_refl.: 87578 remove outliers: r(all,work,free)=0.1449 0.1448 0.1493 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1448 0.1447 0.1492 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1123 0.1280 n_refl.: 87578 remove outliers: r(all,work,free)=0.1129 0.1121 0.1280 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3924 288.050 258.888 0.449 1.000 0.285 11.894-9.307 93.14 91 4 0.2443 470.757 460.716 0.853 1.001 0.268 9.237-7.194 97.73 208 7 0.2329 386.842 380.506 0.926 1.002 0.173 7.162-5.571 100.00 427 22 0.2100 295.879 286.613 0.912 1.002 0.140 5.546-4.326 100.00 867 58 0.1109 406.169 401.438 0.962 1.002 0.096 4.315-3.360 100.00 1859 96 0.0898 386.270 384.232 1.004 1.002 0.080 3.356-2.611 100.00 3867 181 0.1087 253.759 251.921 1.011 1.002 0.040 2.608-2.026 99.99 8198 413 0.0902 168.219 167.535 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0883 82.149 82.460 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.428 36.022 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.952 21.499 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=-0.0165 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1957 0.082 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1780 0.082 5.302 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1780 0.082 5.302 9.1 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1784 0.082 5.302 9.1 119.5 20.1 258 0.006 1_weight: 0.1639 0.1784 0.082 5.302 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1234 0.1465 0.005 0.791 9.1 119.5 20.1 258 0.133 1_adp: 0.1241 0.1462 0.005 0.791 9.1 119.4 20.1 258 0.133 1_regHadp: 0.1243 0.1465 0.005 0.791 9.1 119.4 20.1 258 0.133 1_occ: 0.1237 0.1461 0.005 0.791 9.1 119.4 20.1 258 0.133 2_bss: 0.1236 0.1460 0.005 0.791 9.1 119.5 20.1 258 0.133 2_settarget: 0.1236 0.1460 0.005 0.791 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1236 0.1460 0.005 0.808 9.1 119.5 20.1 258 0.133 2_nqh: 0.1237 0.1462 0.005 0.808 9.1 119.5 20.1 258 0.133 2_sol: 0.1209 0.1413 0.005 0.808 9.1 115.0 22.2 423 n/a 2_weight: 0.1209 0.1413 0.005 0.808 9.1 115.0 22.2 423 n/a 2_xyzrec: 0.1189 0.1410 0.007 0.868 9.1 115.0 22.2 423 n/a 2_adp: 0.1189 0.1410 0.007 0.868 9.1 115.0 22.2 423 n/a 2_regHadp: 0.1189 0.1410 0.007 0.868 9.1 115.0 22.2 423 n/a 2_occ: 0.1191 0.1404 0.007 0.868 9.1 115.0 22.2 423 n/a 3_bss: 0.1187 0.1401 0.007 0.868 9.1 115.0 22.2 423 n/a 3_settarget: 0.1187 0.1401 0.007 0.868 9.1 115.0 22.2 423 n/a 3_updatecdl: 0.1187 0.1401 0.007 0.869 9.1 115.0 22.2 423 n/a 3_nqh: 0.1187 0.1401 0.007 0.869 9.1 115.0 22.2 423 n/a 3_sol: 0.1211 0.1395 0.007 0.869 9.1 115.0 21.2 435 n/a 3_weight: 0.1211 0.1395 0.007 0.869 9.1 115.0 21.2 435 n/a 3_xyzrec: 0.1169 0.1326 0.006 0.953 9.1 115.0 21.2 435 n/a 3_adp: 0.1169 0.1326 0.006 0.953 9.1 115.0 21.2 435 n/a 3_regHadp: 0.1169 0.1326 0.006 0.953 9.1 115.0 21.2 435 n/a 3_occ: 0.1155 0.1323 0.006 0.953 9.1 115.0 21.2 435 n/a 4_bss: 0.1146 0.1309 0.006 0.953 9.1 115.0 21.2 435 n/a 4_settarget: 0.1146 0.1309 0.006 0.953 9.1 115.0 21.2 435 n/a 4_updatecdl: 0.1146 0.1309 0.006 0.955 9.1 115.0 21.2 435 n/a 4_nqh: 0.1146 0.1309 0.006 0.955 9.1 115.0 21.2 435 n/a 4_sol: 0.1139 0.1281 0.006 0.955 9.1 115.0 21.2 457 n/a 4_weight: 0.1139 0.1281 0.006 0.955 9.1 115.0 21.2 457 n/a 4_xyzrec: 0.1131 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 4_adp: 0.1131 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 4_regHadp: 0.1131 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 4_occ: 0.1126 0.1276 0.006 0.999 9.1 115.0 21.2 457 n/a 5_bss: 0.1123 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 5_settarget: 0.1123 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 5_updatecdl: 0.1123 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 5_setrh: 0.1124 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 5_nqh: 0.1124 0.1280 0.006 0.999 9.1 115.0 21.2 457 n/a 5_sol: 0.1128 0.1283 0.006 0.999 9.1 115.0 21.2 465 n/a 5_weight: 0.1128 0.1283 0.006 0.999 9.1 115.0 21.2 465 n/a 5_xyzrec: 0.1126 0.1281 0.008 1.075 9.1 115.0 21.2 465 n/a 5_adp: 0.1126 0.1281 0.008 1.075 9.1 115.0 21.2 465 n/a 5_regHadp: 0.1126 0.1281 0.008 1.075 9.1 115.0 21.2 465 n/a 5_occ: 0.1123 0.1278 0.008 1.075 9.1 115.0 21.2 465 n/a end: 0.1121 0.1280 0.008 1.075 9.1 115.0 21.2 465 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3473948_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3473948_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5800 Refinement macro-cycles (run) : 13852.4300 Write final files (write_after_run_outputs) : 92.8500 Total : 13948.8600 Total CPU time: 3.88 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:12:13 PST -0800 (1735366333.18 s) Start R-work = 0.1637, R-free = 0.1780 Final R-work = 0.1121, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 14128.91 seconds wall clock time: 256 minutes 20.51 seconds (15380.51 seconds total)