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_6712476.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_6712476.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.46, per 1000 atoms: 0.43 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: 0.31 Conformation dependent library (CDL) restraints added in 111.5 milliseconds Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 595 0.92 - 1.18: 1069 1.18 - 1.43: 675 1.43 - 1.69: 783 1.69 - 1.95: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.235 1.007 0.228 1.28e-02 6.10e+03 3.18e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.457 1.674 -0.217 1.23e-02 6.61e+03 3.11e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.060 0.175 1.01e-02 9.80e+03 3.01e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.654 -0.197 1.20e-02 6.94e+03 2.70e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.520 1.329 0.191 1.21e-02 6.83e+03 2.50e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3221 4.82 - 9.65: 1857 9.65 - 14.47: 594 14.47 - 19.29: 94 19.29 - 24.11: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.69 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 136.72 -14.60 1.06e+00 8.90e-01 1.90e+02 angle pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 113.80 100.71 13.09 1.00e+00 1.00e+00 1.71e+02 angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.02 131.02 -14.00 1.11e+00 8.12e-01 1.59e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 108.87 13.25 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 939 17.49 - 34.97: 118 34.97 - 52.46: 37 52.46 - 69.94: 14 69.94 - 87.43: 3 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 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+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 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.213: 100 0.213 - 0.421: 63 0.421 - 0.629: 50 0.629 - 0.838: 24 0.838 - 1.046: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALA A 11 " pdb=" N ALA A 11 " pdb=" C ALA A 11 " pdb=" CB ALA A 11 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA LYS A 12 " pdb=" N LYS A 12 " pdb=" C LYS A 12 " pdb=" CB LYS A 12 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.047 2.00e-02 2.50e+03 5.85e-02 1.03e+02 pdb=" CG PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.122 2.00e-02 2.50e+03 5.38e-02 8.69e+01 pdb=" CG PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.059 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 95 " -0.036 2.00e-02 2.50e+03 7.41e-02 8.23e+01 pdb=" CD GLN A 95 " -0.068 2.00e-02 2.50e+03 pdb=" OE1 GLN A 95 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 GLN A 95 " 0.085 2.00e-02 2.50e+03 pdb="HE21 GLN A 95 " 0.055 2.00e-02 2.50e+03 pdb="HE22 GLN A 95 " -0.107 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1115 2.33 - 2.90: 8135 2.90 - 3.46: 10501 3.46 - 4.03: 15194 4.03 - 4.60: 21730 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.760 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 1.850 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.826 2.270 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.849 1.850 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.852 2.100 ... (remaining 56670 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_6712476_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787811 | | target function (ml) not normalized (work): 232241.375283 | | target function (ml) not normalized (free): 11789.328695 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2103 7.0998 4.9458| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1799 4.3435 4.3313| | 3: 2.84 - 2.48 1.00 2833 165 0.2389 0.1714 4.1291 4.1584| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1363 3.8271 3.8139| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1679 3.7945 3.8377| | 6: 2.09 - 1.97 1.00 2846 113 0.2526 0.1731 3.4738 3.5343| | 7: 1.97 - 1.87 1.00 2787 165 0.2532 0.1787 3.1499 3.2116| | 8: 1.87 - 1.79 1.00 2789 144 0.2489 0.1987 3.0734 3.1287| | 9: 1.79 - 1.72 1.00 2745 138 0.2397 0.1897 2.8902 2.971| | 10: 1.72 - 1.66 1.00 2789 158 0.2446 0.2076 2.7982 2.9192| | 11: 1.66 - 1.61 1.00 2740 147 0.2515 0.1781 2.7594 2.7292| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.1797 2.6275 2.5956| | 13: 1.56 - 1.52 1.00 2745 130 0.2486 0.1774 2.5519 2.5472| | 14: 1.52 - 1.48 1.00 2803 134 0.2517 0.1778 2.4852 2.4964| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2205 2.4137 2.518| | 16: 1.45 - 1.42 1.00 2756 161 0.2655 0.2187 2.3701 2.449| | 17: 1.42 - 1.39 1.00 2785 139 0.2726 0.2095 2.3399 2.3493| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2389 2.2799 2.4135| | 19: 1.36 - 1.34 1.00 2807 134 0.2640 0.2370 2.2392 2.2745| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2262 2.1882 2.2188| | 21: 1.32 - 1.30 1.00 2785 112 0.2750 0.2276 2.1671 2.1487| | 22: 1.29 - 1.27 1.00 2704 152 0.2700 0.2531 2.127 2.1993| | 23: 1.27 - 1.26 1.00 2802 156 0.2715 0.2492 2.0867 2.1712| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2500 2.0638 2.1551| | 25: 1.24 - 1.22 1.00 2734 148 0.2802 0.2337 2.0307 2.0564| | 26: 1.22 - 1.21 1.00 2727 135 0.2868 0.2315 2.0073 2.0886| | 27: 1.21 - 1.19 1.00 2814 148 0.2931 0.2379 1.9994 1.9619| | 28: 1.19 - 1.18 1.00 2671 147 0.3005 0.2544 1.9848 1.9667| | 29: 1.18 - 1.16 1.00 2800 134 0.2917 0.2607 1.9501 1.9702| | 30: 1.16 - 1.15 1.00 2740 148 0.3081 0.2888 1.9236 1.9736| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.68 0.76 0.23 1460.06| | 2: 3.57 - 2.84 2876 122 0.81 25.84 1.27 0.23 1460.06| | 3: 2.84 - 2.48 2833 165 0.74 31.72 1.25 0.24 1211.88| | 4: 2.47 - 2.25 2825 136 0.81 25.59 1.26 0.25 567.81| | 5: 2.25 - 2.09 2756 127 0.77 29.31 1.28 0.25 567.81| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 312.48| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 94.73| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.26 94.73| | 9: 1.79 - 1.72 2745 138 0.88 18.80 1.23 0.25 56.61| | 10: 1.72 - 1.66 2789 158 0.87 20.24 1.23 0.25 48.97| | 11: 1.66 - 1.61 2740 147 0.86 21.44 1.24 0.25 47.14| | 12: 1.61 - 1.56 2787 146 0.89 18.21 1.24 0.25 28.63| | 13: 1.56 - 1.52 2745 130 0.87 20.00 1.23 0.25 28.63| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.23 0.25 25.60| | 15: 1.48 - 1.45 2738 128 0.87 19.81 1.23 0.25 20.06| | 16: 1.45 - 1.42 2756 161 0.86 21.51 1.24 0.25 20.06| | 17: 1.42 - 1.39 2785 139 0.87 20.64 1.24 0.25 17.31| | 18: 1.39 - 1.36 2741 179 0.86 21.11 1.23 0.25 15.72| | 19: 1.36 - 1.34 2807 134 0.86 21.72 1.23 0.25 15.72| | 20: 1.34 - 1.32 2696 147 0.87 20.61 1.22 0.25 13.07| | 21: 1.32 - 1.30 2785 112 0.86 21.82 1.21 0.25 12.88| | 22: 1.29 - 1.27 2704 152 0.86 21.92 1.21 0.25 12.57| | 23: 1.27 - 1.26 2802 156 0.86 21.59 1.21 0.24 10.95| | 24: 1.26 - 1.24 2744 132 0.85 22.51 1.20 0.24 10.95| | 25: 1.24 - 1.22 2734 148 0.85 23.22 1.21 0.24 10.23| | 26: 1.22 - 1.21 2727 135 0.85 23.28 1.20 0.23 9.44| | 27: 1.21 - 1.19 2814 148 0.84 23.91 1.20 0.23 9.44| | 28: 1.19 - 1.18 2671 147 0.84 24.20 1.19 0.23 8.71| | 29: 1.18 - 1.16 2800 134 0.84 24.13 1.16 0.23 8.44| | 30: 1.16 - 1.15 2740 148 0.81 26.46 1.15 0.23 8.44| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.44 max = 1460.06 mean = 212.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.33| |phase err.(test): min = 0.00 max = 89.68 mean = 22.21| |-----------------------------------------------------------------------------| ----------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 0.237 1557 Z= 5.394 Angle : 5.266 18.400 2118 Z= 3.699 Chirality : 0.406 1.046 243 Planarity : 0.031 0.102 284 Dihedral : 14.221 87.429 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 28.11 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.50), residues: 224 helix: -2.80 (0.36), residues: 103 sheet: -1.52 (0.78), residues: 38 loop : 0.39 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.035 ARG A 28 TYR 0.087 0.033 TYR A 141 PHE 0.091 0.041 PHE A 119 HIS 0.081 0.037 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= 0.2605 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787811 | | target function (ml) not normalized (work): 232241.375283 | | target function (ml) not normalized (free): 11789.328695 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1974 0.1978 0.1941 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1999 0.2004 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1638 0.1631 0.1764 n_refl.: 87594 remove outliers: r(all,work,free)=0.1637 0.1630 0.1764 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 0.3842 386.339 355.645 0.731 0.916 0.401 11.894-9.307 99.02 97 4 0.1808 613.680 594.500 1.011 0.917 0.380 9.237-7.194 100.00 213 7 0.2092 501.915 491.755 1.045 0.917 0.360 7.162-5.571 100.00 427 22 0.2210 376.659 364.272 1.014 0.918 0.340 5.546-4.326 100.00 867 58 0.1271 517.060 510.511 1.049 0.919 0.219 4.315-3.360 100.00 1859 96 0.1154 491.728 487.828 1.095 0.920 0.199 3.356-2.611 100.00 3867 181 0.1438 323.040 320.049 1.084 0.921 0.048 2.608-2.026 99.99 8198 413 0.1352 214.146 212.123 1.093 0.924 0.000 2.025-1.573 100.00 17313 902 0.1645 104.578 103.898 1.087 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2038 46.374 45.071 1.069 0.936 0.000 1.221-1.150 99.97 13689 708 0.2572 29.219 26.998 1.030 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1638 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.430280 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.759041 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1744 0.1859 0.0115 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1580 0.1718 0.0138 0.002 0.4 4.8 0.0 0.0 0 0.250 0.1448 0.1614 0.0167 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1390 0.1580 0.0190 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1357 0.1555 0.0198 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1343 0.1541 0.0198 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1297 0.1513 0.0216 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1270 0.1493 0.0223 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1256 0.1481 0.0225 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1247 0.1474 0.0228 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1474 0.0231 0.004 0.8 3.8 0.5 0.0 0 6.000 0.1238 0.1470 0.0232 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1235 0.1474 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1468 0.0237 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1229 0.1471 0.0241 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1228 0.1473 0.0246 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1226 0.1475 0.0249 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1224 0.1476 0.0252 0.007 1.0 3.8 0.5 0.6 0 13.215 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1468 0.0237 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.68 2.37 3.013 19.065 2004.759 0.018 12.31 14.68 2.37 3.013 19.065 60.143 0.018 12.38 14.65 2.28 2.669 19.064 250.595 0.018 12.76 15.41 2.64 2.907 19.368 1002.380 0.017 12.61 15.48 2.87 3.336 19.657 2004.759 0.016 12.47 15.48 3.01 3.321 19.651 3007.139 0.016 12.42 15.50 3.08 3.404 19.677 4009.518 0.015 12.34 15.45 3.11 3.347 19.637 5011.898 0.015 12.26 15.40 3.14 3.380 19.662 6014.277 0.015 12.25 15.44 3.19 3.352 19.628 7016.657 0.015 12.22 15.44 3.22 3.394 19.647 8019.036 0.015 12.15 15.34 3.18 3.299 19.574 9021.416 0.015 12.13 15.34 3.21 3.331 19.582 10023.795 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: 250.595 Accepted refinement result: 12.38 14.65 2.28 2.669 19.064 250.595 0.018 Individual atomic B min max mean iso aniso Overall: 9.08 119.45 20.09 3.31 0 1785 Protein: 9.08 115.01 17.00 3.32 0 1519 Water: 11.48 119.45 38.23 N/A 0 258 Other: 19.70 26.60 22.06 N/A 0 8 Chain A: 9.08 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 227 31.15 - 42.19 125 42.19 - 53.23 94 53.23 - 64.26 42 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1465 r_work=0.1239 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1469 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 = 0.1232 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1232 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017023 | | target function (ls_wunit_k1) not normalized (work): 1417.995378 | | target function (ls_wunit_k1) not normalized (free): 107.306925 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1677 0.1678 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1677 0.1678 0.1690 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1684 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1231 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1230 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 0.3533 301.196 281.204 0.650 1.003 0.380 11.894-9.307 99.02 97 4 0.1674 482.499 470.853 0.922 1.003 0.370 9.237-7.194 100.00 213 7 0.1933 394.625 387.865 0.963 1.003 0.346 7.162-5.571 100.00 427 22 0.1838 296.144 290.621 0.938 1.003 0.310 5.546-4.326 100.00 867 58 0.1008 406.533 403.650 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0872 386.615 385.577 1.009 1.003 0.190 3.356-2.611 100.00 3867 181 0.1174 253.986 252.838 1.009 1.002 0.048 2.608-2.026 99.99 8198 413 0.1025 168.370 167.614 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1118 82.223 82.411 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.461 35.964 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2255 22.973 21.453 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 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** A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1230 r_free=0.1451 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1451 | n_water=258 | time (s): 1.520 (total time: 1.520) Filter (dist) r_work=0.1240 r_free=0.1450 | n_water=249 | time (s): 22.590 (total time: 24.110) Filter (q & B) r_work=0.1242 r_free=0.1451 | n_water=246 | time (s): 3.030 (total time: 27.140) Compute maps r_work=0.1242 r_free=0.1451 | n_water=246 | time (s): 1.420 (total time: 28.560) Filter (map) r_work=0.1257 r_free=0.1450 | n_water=225 | time (s): 2.950 (total time: 31.510) Find peaks r_work=0.1257 r_free=0.1450 | n_water=225 | time (s): 0.510 (total time: 32.020) Add new water r_work=0.1402 r_free=0.1616 | n_water=422 | time (s): 2.330 (total time: 34.350) Refine new water occ: r_work=0.1309 r_free=0.1477 adp: r_work=0.1232 r_free=0.1429 occ: r_work=0.1245 r_free=0.1415 adp: r_work=0.1211 r_free=0.1401 occ: r_work=0.1214 r_free=0.1392 adp: r_work=0.1203 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1390 r_work=0.1203 r_free=0.1390 | n_water=422 | time (s): 84.010 (total time: 118.360) Filter (q & B) r_work=0.1207 r_free=0.1388 | n_water=409 | time (s): 2.950 (total time: 121.310) Filter (dist only) r_work=0.1207 r_free=0.1387 | n_water=408 | time (s): 33.510 (total time: 154.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.461717 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1487.252262 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 0.1610 0.1725 0.0115 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1515 0.1644 0.0130 0.001 0.4 5.8 0.0 0.0 0 0.250 0.1418 0.1564 0.0147 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1335 0.1500 0.0165 0.001 0.5 5.1 0.0 0.0 0 0.750 0.1316 0.1487 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1332 0.1500 0.0168 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1248 0.1438 0.0190 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1231 0.1427 0.0197 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1217 0.1422 0.0205 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1210 0.1418 0.0207 0.004 0.7 5.1 0.5 0.0 0 5.000 0.1204 0.1418 0.0213 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1202 0.1416 0.0214 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1200 0.1416 0.0217 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1195 0.1413 0.0218 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1194 0.1417 0.0223 0.006 0.8 4.8 0.5 0.0 0 10.000 0.1192 0.1421 0.0229 0.006 0.9 4.8 0.5 0.0 0 11.000 0.1192 0.1421 0.0229 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1190 0.1419 0.0228 0.007 0.9 4.5 0.5 0.0 0 13.000 0.1187 0.1422 0.0235 0.008 0.9 5.8 0.5 0.0 0 14.231 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1413 0.0218 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 14.13 2.18 3.777 21.721 1487.252 0.016 11.95 14.13 2.18 3.777 21.721 44.618 0.016 11.95 14.13 2.18 3.776 21.721 185.907 0.016 12.16 14.59 2.42 3.633 21.721 743.626 0.016 12.18 14.98 2.80 3.478 22.079 1487.252 0.015 11.97 14.83 2.85 3.457 22.069 2230.878 0.015 11.87 14.82 2.95 3.479 21.917 2974.505 0.014 11.82 14.86 3.04 3.522 21.874 3718.131 0.014 11.74 14.79 3.05 3.519 21.899 4461.757 0.014 11.76 14.88 3.12 3.517 21.979 5205.383 0.014 11.78 14.93 3.15 3.564 22.107 5949.009 0.014 11.74 14.88 3.14 3.557 22.042 6692.635 0.014 11.66 14.78 3.13 3.570 22.047 7436.261 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.907 Accepted refinement result: 11.95 14.13 2.18 3.776 21.721 185.907 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 22.08 3.31 183 1752 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.51 76.69 40.88 N/A 183 225 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.11 115.03 19.45 N/A 0 1752 Chain S: 15.32 60.00 47.27 N/A 183 0 Histogram: Values Number of atoms 9.11 - 19.70 1259 19.70 - 30.29 242 30.29 - 40.89 166 40.89 - 51.48 127 51.48 - 62.07 118 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1413 r_work=0.1195 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1413 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1408 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 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= 0.1196 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015501 | | target function (ls_wunit_k1) not normalized (work): 1291.210580 | | target function (ls_wunit_k1) not normalized (free): 97.078581 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1196 0.1408 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1600 0.1600 0.1636 n_refl.: 87592 remove outliers: r(all,work,free)=0.1600 0.1600 0.1636 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1601 0.1601 0.1637 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1192 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1200 0.1190 0.1402 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 0.3255 293.838 278.023 0.587 1.002 0.344 11.894-9.307 99.02 97 4 0.1682 482.499 476.206 0.915 1.003 0.340 9.237-7.194 100.00 213 7 0.1748 394.625 393.148 0.978 1.003 0.300 7.162-5.571 100.00 427 22 0.1632 296.144 291.273 0.934 1.003 0.240 5.546-4.326 100.00 867 58 0.0883 406.533 403.571 0.958 1.003 0.200 4.315-3.360 100.00 1859 96 0.0802 386.615 385.198 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1088 253.986 252.969 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1013 168.370 167.823 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1104 82.223 82.460 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.461 36.006 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.973 21.498 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0097 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1402 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=0.1190 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1402 | n_water=408 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1189 r_free=0.1403 | n_water=405 | time (s): 36.790 (total time: 38.990) Filter (q & B) r_work=0.1189 r_free=0.1403 | n_water=405 | time (s): 1.070 (total time: 40.060) Compute maps r_work=0.1189 r_free=0.1403 | n_water=405 | time (s): 1.140 (total time: 41.200) Filter (map) r_work=0.1228 r_free=0.1408 | n_water=279 | time (s): 2.700 (total time: 43.900) Find peaks r_work=0.1228 r_free=0.1408 | n_water=279 | time (s): 0.500 (total time: 44.400) Add new water r_work=0.1337 r_free=0.1530 | n_water=460 | time (s): 2.820 (total time: 47.220) Refine new water occ: r_work=0.1248 r_free=0.1435 adp: r_work=0.1250 r_free=0.1437 occ: r_work=0.1227 r_free=0.1412 adp: r_work=0.1227 r_free=0.1412 occ: r_work=0.1213 r_free=0.1395 adp: r_work=0.1209 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1391 r_work=0.1209 r_free=0.1391 | n_water=460 | time (s): 182.110 (total time: 229.330) Filter (q & B) r_work=0.1213 r_free=0.1390 | n_water=426 | time (s): 2.710 (total time: 232.040) Filter (dist only) r_work=0.1213 r_free=0.1389 | n_water=425 | time (s): 34.070 (total time: 266.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.782152 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.606535 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 0.1237 0.1361 0.0124 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1194 0.1328 0.0134 0.003 0.7 3.5 0.5 0.0 0 0.267 0.1175 0.1315 0.0139 0.004 0.8 3.2 0.5 0.0 0 0.535 0.1167 0.1310 0.0143 0.005 0.9 3.2 0.5 0.0 0 0.802 0.1164 0.1309 0.0145 0.006 1.0 2.9 0.5 0.0 0 1.069 0.1161 0.1307 0.0146 0.007 1.0 3.5 0.5 0.0 0 1.337 0.1158 0.1306 0.0148 0.007 1.0 3.5 0.5 0.0 0 1.604 0.1157 0.1307 0.0150 0.008 1.1 3.5 0.5 0.0 0 1.871 0.1167 0.1309 0.0142 0.005 0.9 3.2 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1306 0.0148 0.007 1.0 3.5 0.5 0.0 0 1.604 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.06 1.48 3.779 21.158 42.607 3.620 11.58 13.06 1.48 3.779 21.158 1.278 3.620 11.59 13.06 1.47 3.769 21.158 5.326 3.620 11.60 13.10 1.50 3.708 21.150 21.303 3.612 11.66 13.22 1.57 3.726 21.121 42.607 3.614 11.56 13.19 1.62 3.751 21.110 63.910 3.608 11.50 13.15 1.65 3.765 21.107 85.213 3.603 11.50 13.15 1.65 3.775 21.094 106.516 3.600 11.48 13.16 1.68 3.791 21.086 127.820 3.599 11.46 13.15 1.69 3.804 21.080 149.123 3.598 11.45 13.14 1.69 3.814 21.073 170.426 3.596 11.44 13.13 1.69 3.822 21.072 191.729 3.595 11.43 13.12 1.69 3.827 21.071 213.033 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.278 Accepted refinement result: 11.58 13.06 1.48 3.779 21.158 1.278 3.620 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.04 3.31 201 1751 Protein: 9.12 115.04 17.04 3.32 0 1519 Water: 11.51 76.70 35.35 N/A 201 224 Other: 19.74 26.63 22.10 N/A 0 8 Chain A: 9.12 115.04 19.44 N/A 0 1751 Chain S: 15.32 60.01 35.04 N/A 201 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.30 281 30.30 - 40.89 219 40.89 - 51.48 117 51.48 - 62.08 49 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1306 r_work=0.1158 r_free=0.1306 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1306 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1303 target_work(ml) = 3.612 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1151 r_free= 0.1303 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612398 | | target function (ml) not normalized (work): 300883.876207 | | target function (ml) not normalized (free): 15840.450419 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1151 0.1303 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1496 0.1496 0.1523 n_refl.: 87588 remove outliers: r(all,work,free)=0.1496 0.1496 0.1523 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1495 0.1495 0.1523 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1298 n_refl.: 87588 remove outliers: r(all,work,free)=0.1151 0.1144 0.1298 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3928 288.292 263.563 0.480 1.000 0.300 11.894-9.307 96.08 94 4 0.2404 476.377 462.634 0.870 1.002 0.286 9.237-7.194 98.18 209 7 0.2310 386.105 385.677 0.951 1.002 0.200 7.162-5.571 100.00 427 22 0.2082 296.144 285.363 0.918 1.002 0.184 5.546-4.326 100.00 867 58 0.1108 406.533 402.081 0.964 1.002 0.165 4.315-3.360 100.00 1859 96 0.0931 386.615 384.001 1.006 1.002 0.160 3.356-2.611 100.00 3867 181 0.1155 253.986 251.840 1.008 1.002 0.038 2.608-2.026 99.99 8198 413 0.0930 168.370 167.572 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0896 82.223 82.484 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.461 36.036 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.973 21.506 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0181 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1298 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1148 r_free=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1300 | n_water=425 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1148 r_free=0.1300 | n_water=423 | time (s): 47.440 (total time: 49.950) Filter (q & B) r_work=0.1149 r_free=0.1302 | n_water=420 | time (s): 3.730 (total time: 53.680) Compute maps r_work=0.1149 r_free=0.1302 | n_water=420 | time (s): 1.880 (total time: 55.560) Filter (map) r_work=0.1165 r_free=0.1302 | n_water=321 | time (s): 3.810 (total time: 59.370) Find peaks r_work=0.1165 r_free=0.1302 | n_water=321 | time (s): 0.720 (total time: 60.090) Add new water r_work=0.1237 r_free=0.1399 | n_water=485 | time (s): 3.940 (total time: 64.030) Refine new water occ: r_work=0.1171 r_free=0.1327 adp: r_work=0.1171 r_free=0.1331 occ: r_work=0.1155 r_free=0.1310 adp: r_work=0.1155 r_free=0.1313 occ: r_work=0.1143 r_free=0.1296 adp: r_work=0.1139 r_free=0.1298 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1298 r_work=0.1139 r_free=0.1298 | n_water=485 | time (s): 286.700 (total time: 350.730) Filter (q & B) r_work=0.1148 r_free=0.1297 | n_water=440 | time (s): 3.850 (total time: 354.580) Filter (dist only) r_work=0.1148 r_free=0.1296 | n_water=439 | time (s): 46.650 (total time: 401.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.758718 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.451741 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 0.1206 0.1338 0.0131 0.002 0.6 3.8 0.5 0.0 0 0.088 0.1169 0.1312 0.0144 0.003 0.7 2.9 0.5 0.0 0 0.264 0.1154 0.1307 0.0152 0.005 0.9 3.2 0.5 0.0 0 0.528 0.1148 0.1301 0.0153 0.006 0.9 3.5 0.5 0.0 0 0.791 0.1145 0.1302 0.0157 0.006 1.0 3.2 0.5 0.0 0 1.055 0.1142 0.1302 0.0160 0.007 1.0 2.9 0.5 0.0 0 1.319 0.1140 0.1303 0.0163 0.008 1.1 2.9 0.5 0.0 0 1.583 0.1138 0.1302 0.0164 0.009 1.1 2.9 0.5 0.0 0 1.847 0.1147 0.1304 0.0157 0.006 1.0 3.2 0.5 0.0 0 0.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1148 0.1301 0.0153 0.006 0.9 3.5 0.5 0.0 0 0.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.48 13.01 1.53 3.779 21.218 41.452 3.612 11.48 13.01 1.53 3.779 21.218 1.244 3.612 11.48 13.01 1.53 3.779 21.218 5.181 3.612 11.51 13.03 1.52 3.710 21.212 20.726 3.606 11.60 13.17 1.57 3.719 21.187 41.452 3.611 11.51 13.14 1.63 3.743 21.177 62.178 3.604 11.46 13.12 1.66 3.756 21.171 82.903 3.599 11.42 13.09 1.67 3.767 21.171 103.629 3.596 11.40 13.11 1.71 3.778 21.164 124.355 3.595 11.39 13.12 1.73 3.789 21.160 145.081 3.594 11.39 13.14 1.75 3.803 21.149 165.807 3.594 11.38 13.11 1.73 3.809 21.147 186.533 3.593 11.36 13.09 1.74 3.814 21.148 207.259 3.591 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.244 Accepted refinement result: 11.48 13.01 1.53 3.779 21.218 1.244 3.612 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.16 3.31 215 1751 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.51 76.69 35.42 N/A 215 224 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.11 115.03 19.43 N/A 0 1751 Chain S: 15.32 60.00 35.22 N/A 215 0 Histogram: Values Number of atoms 9.11 - 19.70 1262 19.70 - 30.29 299 30.29 - 40.89 204 40.89 - 51.48 127 51.48 - 62.07 51 62.07 - 72.66 12 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=0.1148 r_free=0.1301 r_work=0.1148 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1301 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1296 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1296 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608019 | | target function (ml) not normalized (work): 300490.226501 | | target function (ml) not normalized (free): 15814.867735 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1140 0.1296 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1479 0.1479 0.1510 n_refl.: 87580 remove outliers: r(all,work,free)=0.1479 0.1479 0.1510 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1478 0.1478 0.1509 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1139 0.1299 n_refl.: 87580 remove outliers: r(all,work,free)=0.1145 0.1137 0.1299 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 88.54 80 5 0.3955 283.052 257.990 0.454 1.000 0.293 11.894-9.307 94.12 92 4 0.2351 475.006 461.603 0.856 1.002 0.273 9.237-7.194 97.73 208 7 0.2330 385.625 380.033 0.927 1.002 0.170 7.162-5.571 100.00 427 22 0.2134 296.144 285.210 0.907 1.002 0.150 5.546-4.326 100.00 867 58 0.1116 406.533 401.650 0.965 1.002 0.121 4.315-3.360 100.00 1859 96 0.0928 386.615 384.459 1.003 1.002 0.107 3.356-2.611 100.00 3867 181 0.1114 253.986 252.092 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0915 168.370 167.767 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.223 82.565 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.461 36.060 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2174 22.973 21.510 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1299 After: r_work=0.1138 r_free=0.1299 ================================== NQH flips ================================== r_work=0.1138 r_free=0.1299 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=0.1138 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1299 | n_water=439 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1138 r_free=0.1299 | n_water=438 | time (s): 48.660 (total time: 51.120) Filter (q & B) r_work=0.1139 r_free=0.1300 | n_water=437 | time (s): 3.860 (total time: 54.980) Compute maps r_work=0.1139 r_free=0.1300 | n_water=437 | time (s): 1.850 (total time: 56.830) Filter (map) r_work=0.1174 r_free=0.1319 | n_water=346 | time (s): 3.850 (total time: 60.680) Find peaks r_work=0.1174 r_free=0.1319 | n_water=346 | time (s): 0.720 (total time: 61.400) Add new water r_work=0.1224 r_free=0.1380 | n_water=502 | time (s): 3.580 (total time: 64.980) Refine new water occ: r_work=0.1155 r_free=0.1308 adp: r_work=0.1155 r_free=0.1309 occ: r_work=0.1144 r_free=0.1299 adp: r_work=0.1143 r_free=0.1298 occ: r_work=0.1136 r_free=0.1293 adp: r_work=0.1133 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1291 r_work=0.1133 r_free=0.1291 | n_water=502 | time (s): 237.160 (total time: 302.140) Filter (q & B) r_work=0.1141 r_free=0.1293 | n_water=455 | time (s): 3.990 (total time: 306.130) Filter (dist only) r_work=0.1141 r_free=0.1292 | n_water=454 | time (s): 48.710 (total time: 354.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765458 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.533964 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 0.1212 0.1337 0.0125 0.003 0.7 5.8 0.0 0.0 0 0.088 0.1170 0.1310 0.0140 0.004 0.8 5.8 0.0 0.0 0 0.265 0.1149 0.1295 0.0146 0.005 0.9 5.4 0.5 0.0 0 0.530 0.1141 0.1291 0.0150 0.006 1.0 5.4 0.5 0.0 0 0.794 0.1139 0.1290 0.0151 0.006 1.0 5.4 0.5 0.0 0 1.059 0.1137 0.1288 0.0151 0.007 1.0 5.8 0.5 0.0 0 1.324 0.1135 0.1288 0.0152 0.008 1.1 5.4 0.5 0.0 0 1.589 0.1134 0.1287 0.0153 0.009 1.1 5.4 0.5 0.0 0 1.854 0.1140 0.1291 0.0151 0.006 1.0 5.4 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1134 0.1287 0.0153 0.009 1.1 5.4 0.5 0.0 0 1.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.34 12.87 1.53 3.779 21.233 42.534 3.603 11.34 12.87 1.53 3.779 21.233 1.276 3.603 11.34 12.87 1.53 3.779 21.233 5.317 3.603 11.37 12.92 1.54 3.710 21.226 21.267 3.598 11.46 13.06 1.60 3.723 21.198 42.534 3.602 11.37 13.03 1.66 3.749 21.189 63.801 3.595 11.29 12.97 1.68 3.761 21.189 85.068 3.590 11.29 12.98 1.69 3.773 21.183 106.335 3.588 11.26 12.98 1.72 3.784 21.181 127.602 3.586 11.28 13.04 1.76 3.801 21.167 148.869 3.587 11.25 13.01 1.76 3.810 21.168 170.136 3.585 11.24 12.99 1.75 3.817 21.166 191.403 3.584 11.23 12.98 1.75 3.823 21.165 212.670 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: 1.276 Accepted refinement result: 11.34 12.87 1.53 3.779 21.233 1.276 3.603 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.19 3.31 231 1750 Protein: 9.10 115.03 17.03 3.32 0 1519 Water: 11.50 76.69 35.11 N/A 231 223 Other: 19.73 26.62 22.08 N/A 0 8 Chain A: 9.10 115.03 19.43 N/A 0 1750 Chain S: 15.22 59.99 34.54 N/A 231 0 Histogram: Values Number of atoms 9.10 - 19.70 1264 19.70 - 30.29 303 30.29 - 40.88 212 40.88 - 51.47 131 51.47 - 62.07 48 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1134 r_free=0.1287 r_work=0.1134 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1134 r_free = 0.1287 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1131 r_free = 0.1285 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.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1131 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601702 | | target function (ml) not normalized (work): 299946.163725 | | target function (ml) not normalized (free): 15798.943168 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1327 0.1318 5.6502 5.586| | 2: 3.57 - 2.84 1.00 2888 124 0.1071 0.1341 5.1509 5.1912| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1289 4.93 4.9823| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0995 4.6154 4.6516| | 5: 2.25 - 2.09 1.00 2756 127 0.0861 0.0959 4.564 4.6104| | 6: 2.09 - 1.97 1.00 2846 113 0.0851 0.1029 4.2607 4.3695| | 7: 1.97 - 1.87 1.00 2787 165 0.0899 0.1118 3.9883 4.0909| | 8: 1.87 - 1.79 1.00 2789 144 0.0921 0.1102 3.8945 4.0038| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1164 3.6476 3.8126| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1174 3.5659 3.7027| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1009 3.4961 3.5702| | 12: 1.61 - 1.56 1.00 2773 144 0.0903 0.1130 3.3299 3.4643| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1036 3.307 3.4004| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1061 3.237 3.3252| | 15: 1.48 - 1.45 1.00 2738 128 0.0998 0.1213 3.1507 3.2597| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1225 3.1308 3.237| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1316 3.1181 3.2382| | 18: 1.39 - 1.36 1.00 2741 179 0.1193 0.1333 3.1022 3.242| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1571 3.1108 3.2717| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1447 3.1113 3.1526| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1518 3.1121 3.1065| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1983 3.1221 3.2922| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1790 3.1314 3.1966| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1834 3.1266 3.2247| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2145 3.1418 3.2629| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1770 3.148 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2157 3.1695 3.1614| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2295 3.1658 3.1722| | 29: 1.18 - 1.16 1.00 2800 134 0.2270 0.2392 3.1482 3.2322| | 30: 1.16 - 1.15 1.00 2739 148 0.2443 0.2452 3.1418 3.1689| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 8.31 1.00 0.97 5480.24| | 2: 3.57 - 2.84 2888 124 0.93 12.16 1.01 0.97 5480.24| | 3: 2.83 - 2.48 2820 163 0.90 16.12 0.99 0.97 4585.75| | 4: 2.47 - 2.25 2825 136 0.92 13.18 1.00 0.98 2279.16| | 5: 2.25 - 2.09 2756 127 0.91 15.35 1.01 0.98 2279.16| | 6: 2.09 - 1.97 2846 113 0.93 12.22 1.02 0.98 1329.24| | 7: 1.97 - 1.87 2787 165 0.95 9.42 1.02 0.97 519.08| | 8: 1.87 - 1.79 2789 144 0.92 12.75 1.00 0.97 519.08| | 9: 1.79 - 1.72 2745 138 0.94 10.08 0.98 0.97 291.95| | 10: 1.72 - 1.66 2831 160 0.94 11.19 0.98 0.97 246.46| | 11: 1.66 - 1.61 2712 147 0.93 11.81 0.98 0.97 236.04| | 12: 1.61 - 1.56 2773 144 0.95 8.90 0.99 0.97 137.76| | 13: 1.56 - 1.52 2745 130 0.95 10.43 1.03 0.97 137.76| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 123.60| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.98 97.66| | 16: 1.45 - 1.42 2756 161 0.94 11.09 1.02 0.98 97.66| | 17: 1.42 - 1.39 2785 139 0.95 10.92 1.01 0.98 89.08| | 18: 1.39 - 1.36 2741 179 0.94 11.55 1.01 0.98 84.12| | 19: 1.36 - 1.34 2807 134 0.94 11.91 1.00 0.98 84.12| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.98 0.96 80.04| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 79.75| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.14| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.13| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 82.13| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.14| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.03 0.93 86.38| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.38| | 28: 1.19 - 1.18 2671 147 0.88 20.46 1.01 0.93 90.36| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.92 91.85| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 91.85| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.75 max = 5480.24 mean = 855.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.42| |phase err.(test): min = 0.00 max = 89.70 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1138 0.1131 0.1285 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1463 0.1463 0.1489 n_refl.: 87575 remove outliers: r(all,work,free)=0.1463 0.1463 0.1489 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1462 0.1462 0.1488 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1288 n_refl.: 87575 remove outliers: r(all,work,free)=0.1137 0.1129 0.1288 n_refl.: 87571 ======================== 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 0.4003 285.622 247.863 0.434 1.000 0.308 11.894-9.307 92.16 90 4 0.2346 469.762 456.874 0.853 1.002 0.234 9.237-7.194 97.27 207 7 0.2326 386.711 379.022 0.920 1.002 0.170 7.162-5.571 100.00 427 22 0.2096 296.144 286.106 0.907 1.003 0.130 5.546-4.326 100.00 867 58 0.1118 406.533 401.721 0.962 1.003 0.103 4.315-3.360 100.00 1859 96 0.0926 386.615 384.560 1.003 1.002 0.090 3.356-2.611 100.00 3867 181 0.1109 253.986 252.076 1.011 1.002 0.050 2.608-2.026 99.99 8198 413 0.0904 168.370 167.754 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.223 82.573 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.461 36.068 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.973 21.517 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0151 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2605 0.1941 0.082 5.266 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1764 0.082 5.266 9.1 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1764 0.082 5.266 9.1 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1768 0.082 5.266 9.1 119.5 20.1 258 0.009 1_weight: 0.1638 0.1768 0.082 5.266 9.1 119.5 20.1 258 0.009 1_xyzrec: 0.1231 0.1468 0.006 0.858 9.1 119.5 20.1 258 0.141 1_adp: 0.1238 0.1465 0.006 0.858 9.1 119.4 20.1 258 0.141 1_regHadp: 0.1239 0.1469 0.006 0.858 9.1 119.4 20.1 258 0.141 1_occ: 0.1232 0.1462 0.006 0.858 9.1 119.4 20.1 258 0.141 2_bss: 0.1230 0.1454 0.006 0.858 9.1 119.5 20.1 258 0.141 2_settarget: 0.1230 0.1454 0.006 0.858 9.1 119.5 20.1 258 0.141 2_updatecdl: 0.1230 0.1454 0.006 0.864 9.1 119.5 20.1 258 0.141 2_nqh: 0.1230 0.1451 0.006 0.864 9.1 119.5 20.1 258 0.138 2_sol: 0.1207 0.1387 0.006 0.864 9.1 115.0 22.1 408 n/a 2_weight: 0.1207 0.1387 0.006 0.864 9.1 115.0 22.1 408 n/a 2_xyzrec: 0.1195 0.1413 0.006 0.820 9.1 115.0 22.1 408 n/a 2_adp: 0.1195 0.1413 0.006 0.820 9.1 115.0 22.1 408 n/a 2_regHadp: 0.1195 0.1413 0.006 0.820 9.1 115.0 22.1 408 n/a 2_occ: 0.1196 0.1408 0.006 0.820 9.1 115.0 22.1 408 n/a 3_bss: 0.1190 0.1402 0.006 0.820 9.1 115.0 22.1 408 n/a 3_settarget: 0.1190 0.1402 0.006 0.820 9.1 115.0 22.1 408 n/a 3_updatecdl: 0.1190 0.1402 0.006 0.820 9.1 115.0 22.1 408 n/a 3_nqh: 0.1190 0.1402 0.006 0.820 9.1 115.0 22.1 408 n/a 3_sol: 0.1213 0.1389 0.006 0.820 9.1 115.0 21.0 425 n/a 3_weight: 0.1213 0.1389 0.006 0.820 9.1 115.0 21.0 425 n/a 3_xyzrec: 0.1158 0.1306 0.007 1.049 9.1 115.0 21.0 425 n/a 3_adp: 0.1158 0.1306 0.007 1.049 9.1 115.0 21.0 425 n/a 3_regHadp: 0.1158 0.1306 0.007 1.049 9.1 115.0 21.0 425 n/a 3_occ: 0.1151 0.1303 0.007 1.049 9.1 115.0 21.0 425 n/a 4_bss: 0.1144 0.1298 0.007 1.049 9.1 115.0 21.0 425 n/a 4_settarget: 0.1144 0.1298 0.007 1.049 9.1 115.0 21.0 425 n/a 4_updatecdl: 0.1144 0.1298 0.007 1.052 9.1 115.0 21.0 425 n/a 4_nqh: 0.1148 0.1300 0.007 1.052 9.1 115.0 21.0 425 n/a 4_sol: 0.1148 0.1296 0.007 1.052 9.1 115.0 21.2 439 n/a 4_weight: 0.1148 0.1296 0.007 1.052 9.1 115.0 21.2 439 n/a 4_xyzrec: 0.1148 0.1301 0.006 0.950 9.1 115.0 21.2 439 n/a 4_adp: 0.1148 0.1301 0.006 0.950 9.1 115.0 21.2 439 n/a 4_regHadp: 0.1148 0.1301 0.006 0.950 9.1 115.0 21.2 439 n/a 4_occ: 0.1140 0.1296 0.006 0.950 9.1 115.0 21.2 439 n/a 5_bss: 0.1137 0.1299 0.006 0.950 9.1 115.0 21.2 439 n/a 5_settarget: 0.1137 0.1299 0.006 0.950 9.1 115.0 21.2 439 n/a 5_updatecdl: 0.1137 0.1299 0.006 0.949 9.1 115.0 21.2 439 n/a 5_setrh: 0.1138 0.1299 0.006 0.949 9.1 115.0 21.2 439 n/a 5_nqh: 0.1138 0.1299 0.006 0.949 9.1 115.0 21.2 439 n/a 5_sol: 0.1141 0.1292 0.006 0.949 9.1 115.0 21.2 454 n/a 5_weight: 0.1141 0.1292 0.006 0.949 9.1 115.0 21.2 454 n/a 5_xyzrec: 0.1134 0.1287 0.009 1.124 9.1 115.0 21.2 454 n/a 5_adp: 0.1134 0.1287 0.009 1.124 9.1 115.0 21.2 454 n/a 5_regHadp: 0.1134 0.1287 0.009 1.124 9.1 115.0 21.2 454 n/a 5_occ: 0.1131 0.1285 0.009 1.124 9.1 115.0 21.2 454 n/a end: 0.1129 0.1288 0.009 1.124 9.1 115.0 21.2 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6712476_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6712476_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 13857.7800 Write final files (write_after_run_outputs) : 85.3600 Total : 13946.2900 Total CPU time: 3.88 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:48 PST -0800 (1735366308.70 s) Start R-work = 0.1630, R-free = 0.1764 Final R-work = 0.1129, R-free = 0.1288 =============================================================================== Job complete usr+sys time: 14120.13 seconds wall clock time: 255 minutes 54.03 seconds (15354.03 seconds total)