Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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_4813131.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.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 } 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 } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.18, per 1000 atoms: 0.64 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: 0.76 Conformation dependent library (CDL) restraints added in 286.5 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 406 0.89 - 1.15: 1203 1.15 - 1.41: 628 1.41 - 1.67: 881 1.67 - 1.93: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 11 " pdb=" N LYS A 12 " ideal model delta sigma weight residual 1.332 1.626 -0.295 1.35e-02 5.49e+03 4.76e+02 bond pdb=" CA ALA A 104 " pdb=" C ALA A 104 " ideal model delta sigma weight residual 1.520 1.294 0.227 1.22e-02 6.72e+03 3.46e+02 bond pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 1.456 1.214 0.242 1.32e-02 5.74e+03 3.36e+02 bond pdb=" N GLU A 163 " pdb=" CA GLU A 163 " ideal model delta sigma weight residual 1.459 1.671 -0.212 1.19e-02 7.06e+03 3.18e+02 bond pdb=" C ARG A 145 " pdb=" O ARG A 145 " ideal model delta sigma weight residual 1.237 1.441 -0.205 1.16e-02 7.43e+03 3.11e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3333 4.94 - 9.87: 1811 9.87 - 14.81: 548 14.81 - 19.74: 79 19.74 - 24.68: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA BLYS A 175 " pdb=" C BLYS A 175 " pdb=" O BLYS A 175 " ideal model delta sigma weight residual 120.55 136.26 -15.71 1.06e+00 8.90e-01 2.20e+02 angle pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " pdb=" O ATYR A 67 " ideal model delta sigma weight residual 120.71 135.51 -14.80 1.06e+00 8.90e-01 1.95e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 106.38 15.77 1.14e+00 7.69e-01 1.91e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.76 107.13 13.63 1.03e+00 9.43e-01 1.75e+02 angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.07 109.11 12.96 1.03e+00 9.43e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 938 17.33 - 34.66: 115 34.66 - 51.98: 40 51.98 - 69.31: 16 69.31 - 86.64: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+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 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.215: 103 0.215 - 0.427: 77 0.427 - 0.640: 41 0.640 - 0.852: 19 0.852 - 1.065: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 51 " pdb=" N VAL A 51 " pdb=" C VAL A 51 " pdb=" CB VAL A 51 " both_signs ideal model delta sigma weight residual False 2.44 3.51 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CG LEU A 187 " pdb=" CB LEU A 187 " pdb=" CD1 LEU A 187 " pdb=" CD2 LEU A 187 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.105 9.50e-02 1.11e+02 8.77e-02 1.47e+02 pdb=" NE ARG A 27 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " -0.131 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.069 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.073 2.00e-02 2.50e+03 6.18e-02 1.15e+02 pdb=" CG PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.042 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 869 2.29 - 2.87: 7884 2.87 - 3.44: 10567 3.44 - 4.02: 15298 4.02 - 4.60: 22023 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.710 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.805 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.870 2.100 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.895 2.450 ... (remaining 56636 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 } 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 } } output { prefix = "shake_4813131_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= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785229 | | target function (ml) not normalized (work): 232026.292978 | | target function (ml) not normalized (free): 11790.774630 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2105 7.0314 4.9449| | 2: 3.57 - 2.84 1.00 2876 122 0.2442 0.1826 4.3529 4.3434| | 3: 2.84 - 2.48 1.00 2833 165 0.2345 0.1737 4.131 4.1624| | 4: 2.47 - 2.25 1.00 2825 136 0.2305 0.1516 3.8313 3.8385| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1592 3.7983 3.812| | 6: 2.09 - 1.97 1.00 2846 113 0.2532 0.1622 3.4568 3.5318| | 7: 1.97 - 1.87 1.00 2787 165 0.2510 0.1761 3.1262 3.1778| | 8: 1.87 - 1.79 1.00 2789 144 0.2447 0.1980 3.0443 3.1744| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.1764 2.8805 2.873| | 10: 1.72 - 1.66 1.00 2789 158 0.2305 0.1847 2.7867 2.8348| | 11: 1.66 - 1.61 1.00 2740 147 0.2456 0.1833 2.7261 2.7774| | 12: 1.61 - 1.56 1.00 2787 146 0.2517 0.2161 2.6274 2.7102| | 13: 1.56 - 1.52 1.00 2745 130 0.2567 0.1914 2.5625 2.6066| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1815 2.5112 2.4832| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2195 2.4295 2.5005| | 16: 1.45 - 1.42 1.00 2756 161 0.2587 0.2175 2.3656 2.4316| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.2203 2.3358 2.4169| | 18: 1.39 - 1.36 1.00 2741 179 0.2653 0.2109 2.2658 2.3145| | 19: 1.36 - 1.34 1.00 2807 134 0.2658 0.2180 2.2415 2.2595| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2252 2.2042 2.1934| | 21: 1.32 - 1.30 1.00 2785 112 0.2767 0.2286 2.1699 2.1835| | 22: 1.29 - 1.27 1.00 2704 152 0.2713 0.2619 2.1235 2.2224| | 23: 1.27 - 1.26 1.00 2802 156 0.2811 0.2311 2.1032 2.1478| | 24: 1.26 - 1.24 1.00 2744 132 0.2787 0.2272 2.0746 2.0893| | 25: 1.24 - 1.22 1.00 2734 148 0.2821 0.2554 2.0443 2.094| | 26: 1.22 - 1.21 1.00 2727 135 0.2828 0.2175 2.0115 2.0508| | 27: 1.21 - 1.19 1.00 2814 148 0.2899 0.2731 1.9923 2.0343| | 28: 1.19 - 1.18 1.00 2671 147 0.2941 0.2819 1.9743 1.9624| | 29: 1.18 - 1.16 1.00 2800 134 0.2976 0.2895 1.9617 2.0665| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2724 1.9371 1.9489| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.99 0.76 0.23 1490.98| | 2: 3.57 - 2.84 2876 122 0.80 26.23 1.27 0.23 1490.98| | 3: 2.84 - 2.48 2833 165 0.74 31.99 1.24 0.23 1235.68| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.25 0.25 573.11| | 5: 2.25 - 2.09 2756 127 0.77 29.30 1.28 0.25 573.11| | 6: 2.09 - 1.97 2846 113 0.83 22.62 1.29 0.25 312.28| | 7: 1.97 - 1.87 2787 165 0.90 16.64 1.28 0.25 89.82| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.25 89.82| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.23 0.25 53.83| | 10: 1.72 - 1.66 2789 158 0.87 19.64 1.21 0.25 46.63| | 11: 1.66 - 1.61 2740 147 0.86 21.22 1.24 0.25 45.04| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.23 0.25 28.99| | 13: 1.56 - 1.52 2745 130 0.87 20.12 1.25 0.25 28.99| | 14: 1.52 - 1.48 2803 134 0.87 20.50 1.24 0.25 25.85| | 15: 1.48 - 1.45 2738 128 0.87 19.91 1.23 0.25 20.10| | 16: 1.45 - 1.42 2756 161 0.86 21.18 1.23 0.25 20.10| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.23 0.25 17.23| | 18: 1.39 - 1.36 2741 179 0.86 21.07 1.22 0.25 15.57| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.21 0.25 15.57| | 20: 1.34 - 1.32 2696 147 0.87 20.59 1.20 0.24 12.69| | 21: 1.32 - 1.30 2785 112 0.86 21.99 1.20 0.24 12.48| | 22: 1.29 - 1.27 2704 152 0.86 22.14 1.21 0.24 12.23| | 23: 1.27 - 1.26 2802 156 0.86 22.03 1.21 0.24 10.91| | 24: 1.26 - 1.24 2744 132 0.85 22.58 1.20 0.24 10.91| | 25: 1.24 - 1.22 2734 148 0.85 23.47 1.20 0.23 10.41| | 26: 1.22 - 1.21 2727 135 0.84 23.90 1.19 0.23 9.85| | 27: 1.21 - 1.19 2814 148 0.83 24.54 1.20 0.23 9.85| | 28: 1.19 - 1.18 2671 147 0.82 25.55 1.17 0.23 9.40| | 29: 1.18 - 1.16 2800 134 0.82 25.92 1.16 0.23 9.23| | 30: 1.16 - 1.15 2740 148 0.80 27.41 1.14 0.23 9.23| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.23 max = 1490.98 mean = 215.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.50| |phase err.(test): min = 0.00 max = 89.84 mean = 22.35| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.295 1557 Z= 5.317 Angle : 5.198 18.421 2118 Z= 3.650 Chirality : 0.370 1.065 243 Planarity : 0.032 0.132 284 Dihedral : 14.016 86.638 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.65 % 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: -2.38 (0.47), residues: 224 helix: -1.87 (0.39), residues: 109 sheet: -1.46 (0.77), residues: 38 loop : -0.76 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.125 0.030 ARG A 28 TYR 0.076 0.029 TYR A 139 PHE 0.121 0.037 PHE A 164 HIS 0.088 0.036 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2598 r_free= 0.1946 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.785229 | | target function (ml) not normalized (work): 232026.292978 | | target function (ml) not normalized (free): 11790.774630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1971 0.1946 n_refl.: 87594 overall B=0.24 to atoms: r(all,work,free)=0.1997 0.2001 0.1963 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1634 0.1627 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1626 0.1761 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 0.3816 386.100 356.779 0.717 0.931 0.402 11.894-9.307 99.02 97 4 0.1847 613.301 595.548 1.001 0.932 0.380 9.237-7.194 100.00 213 7 0.2164 501.605 490.120 1.031 0.932 0.344 7.162-5.571 100.00 427 22 0.2181 376.427 364.331 0.999 0.932 0.329 5.546-4.326 100.00 867 58 0.1284 516.741 511.288 1.033 0.932 0.218 4.315-3.360 100.00 1859 96 0.1147 491.424 487.517 1.079 0.932 0.189 3.356-2.611 100.00 3867 181 0.1445 322.840 319.707 1.074 0.931 0.043 2.608-2.026 99.99 8198 413 0.1336 214.014 212.001 1.082 0.930 0.000 2.025-1.573 100.00 17313 902 0.1616 104.513 103.823 1.086 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2058 46.345 45.040 1.079 0.927 0.000 1.221-1.150 99.97 13689 708 0.2572 29.201 26.911 1.046 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0542 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1626 r_free=0.1761 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.049008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2029.693997 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 0.1210 0.1458 0.0248 0.008 1.0 0.6 0.5 0.0 0 13.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.58 2.48 3.013 19.095 2029.694 0.017 12.41 15.27 2.86 3.167 19.548 2029.694 0.016 Individual atomic B min max mean iso aniso Overall: 8.66 118.73 20.98 2.88 0 1785 Protein: 8.66 118.73 17.85 2.88 0 1519 Water: 11.10 114.86 39.15 N/A 0 258 Other: 22.91 36.11 28.83 N/A 0 8 Chain A: 8.66 118.73 20.98 N/A 0 1785 Histogram: Values Number of atoms 8.66 - 19.67 1214 19.67 - 30.68 223 30.68 - 41.68 169 41.68 - 52.69 95 52.69 - 63.70 55 63.70 - 74.70 17 74.70 - 85.71 5 85.71 - 96.72 4 96.72 - 107.72 0 107.72 - 118.73 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1527 r_work=0.1246 r_free=0.1532 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1532 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1536 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1244 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015303 | | target function (ls_wunit_k1) not normalized (work): 1274.683190 | | target function (ls_wunit_k1) not normalized (free): 112.098523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1536 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1702 0.1701 0.1763 n_refl.: 87593 remove outliers: r(all,work,free)=0.1702 0.1701 0.1763 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1724 0.1723 0.1779 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1244 0.1531 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1243 0.1531 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 0.3625 298.471 277.504 0.636 1.002 0.380 11.894-9.307 99.02 97 4 0.1631 478.135 467.057 0.907 1.003 0.367 9.237-7.194 100.00 213 7 0.1793 391.055 386.484 0.948 1.003 0.319 7.162-5.571 100.00 427 22 0.1708 293.465 288.337 0.922 1.003 0.300 5.546-4.326 100.00 867 58 0.0921 402.855 400.323 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0775 383.118 382.153 0.994 1.003 0.190 3.356-2.611 100.00 3867 181 0.1015 251.689 250.999 1.000 1.002 0.052 2.608-2.026 99.99 8198 413 0.0971 166.847 166.272 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1211 81.479 81.663 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1661 36.131 35.590 1.007 0.997 0.000 1.221-1.150 99.97 13689 708 0.2367 22.765 21.266 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0510 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1533 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1533 | n_water=258 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1254 r_free=0.1530 | n_water=252 | time (s): 25.000 (total time: 27.300) Filter (q & B) r_work=0.1257 r_free=0.1529 | n_water=249 | time (s): 3.540 (total time: 30.840) Compute maps r_work=0.1257 r_free=0.1529 | n_water=249 | time (s): 1.780 (total time: 32.620) Filter (map) r_work=0.1269 r_free=0.1540 | n_water=237 | time (s): 3.750 (total time: 36.370) Find peaks r_work=0.1269 r_free=0.1540 | n_water=237 | time (s): 0.730 (total time: 37.100) Add new water r_work=0.1420 r_free=0.1678 | n_water=454 | time (s): 3.750 (total time: 40.850) Refine new water occ: r_work=0.1325 r_free=0.1538 adp: r_work=0.1250 r_free=0.1499 occ: r_work=0.1262 r_free=0.1489 adp: r_work=0.1228 r_free=0.1480 occ: r_work=0.1231 r_free=0.1470 adp: r_work=0.1221 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1472 r_work=0.1221 r_free=0.1472 | n_water=454 | time (s): 75.450 (total time: 116.300) Filter (q & B) r_work=0.1227 r_free=0.1475 | n_water=432 | time (s): 3.940 (total time: 120.240) Filter (dist only) r_work=0.1227 r_free=0.1475 | n_water=432 | time (s): 40.210 (total time: 160.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.207141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1544.311418 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 0.1227 0.1495 0.0268 0.007 0.9 1.9 0.5 0.0 0 12.604 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.95 2.68 3.785 23.093 1544.311 0.015 11.97 14.77 2.79 4.153 22.912 1544.311 0.015 Individual atomic B min max mean iso aniso Overall: 8.62 114.72 23.06 2.60 195 1764 Protein: 8.62 114.72 17.66 2.60 0 1519 Water: 11.01 72.67 41.92 N/A 195 237 Other: 24.54 35.46 29.54 N/A 0 8 Chain A: 8.62 114.72 20.37 N/A 0 1764 Chain S: 19.93 70.42 47.38 N/A 195 0 Histogram: Values Number of atoms 8.62 - 19.23 1201 19.23 - 29.84 259 29.84 - 40.45 193 40.45 - 51.06 145 51.06 - 61.67 106 61.67 - 72.28 44 72.28 - 82.89 5 82.89 - 93.50 3 93.50 - 104.11 1 104.11 - 114.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1477 r_work=0.1198 r_free=0.1477 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1477 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1471 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1199 r_free= 0.1471 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013857 | | target function (ls_wunit_k1) not normalized (work): 1154.206929 | | target function (ls_wunit_k1) not normalized (free): 98.211616 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1199 0.1471 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1611 0.1707 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1611 0.1707 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1618 0.1615 0.1710 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1472 n_refl.: 87592 remove outliers: r(all,work,free)=0.1208 0.1195 0.1472 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3270 293.864 273.793 0.600 1.002 0.370 11.894-9.307 99.02 97 4 0.1456 478.135 476.239 0.926 1.003 0.360 9.237-7.194 100.00 213 7 0.1651 391.055 392.814 0.979 1.003 0.270 7.162-5.571 100.00 427 22 0.1485 293.465 289.963 0.938 1.003 0.260 5.546-4.326 100.00 867 58 0.0835 402.855 400.557 0.958 1.003 0.205 4.315-3.360 100.00 1859 96 0.0707 383.118 382.183 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0958 251.689 250.853 1.010 1.002 0.072 2.608-2.026 99.99 8198 413 0.0952 166.847 166.403 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1179 81.479 81.660 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1618 36.131 35.627 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2340 22.765 21.309 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0394 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1472 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1472 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1472 | n_water=432 | time (s): 1.550 (total time: 1.550) Filter (dist) r_work=0.1195 r_free=0.1472 | n_water=430 | time (s): 37.680 (total time: 39.230) Filter (q & B) r_work=0.1195 r_free=0.1472 | n_water=430 | time (s): 1.050 (total time: 40.280) Compute maps r_work=0.1195 r_free=0.1472 | n_water=430 | time (s): 1.140 (total time: 41.420) Filter (map) r_work=0.1245 r_free=0.1490 | n_water=300 | time (s): 2.580 (total time: 44.000) Find peaks r_work=0.1245 r_free=0.1490 | n_water=300 | time (s): 0.690 (total time: 44.690) Add new water r_work=0.1372 r_free=0.1605 | n_water=486 | time (s): 3.390 (total time: 48.080) Refine new water occ: r_work=0.1264 r_free=0.1516 adp: r_work=0.1265 r_free=0.1517 occ: r_work=0.1242 r_free=0.1490 adp: r_work=0.1239 r_free=0.1491 occ: r_work=0.1226 r_free=0.1467 adp: r_work=0.1218 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1218 r_free=0.1466 r_work=0.1218 r_free=0.1466 | n_water=486 | time (s): 203.190 (total time: 251.270) Filter (q & B) r_work=0.1223 r_free=0.1468 | n_water=455 | time (s): 3.000 (total time: 254.270) Filter (dist only) r_work=0.1223 r_free=0.1468 | n_water=455 | time (s): 36.970 (total time: 291.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.990488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.653442 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 0.1227 0.1443 0.0215 0.006 0.9 1.9 0.5 0.0 0 0.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.43 2.15 3.619 22.210 48.653 3.723 12.11 13.90 1.80 4.167 22.015 48.653 3.650 Individual atomic B min max mean iso aniso Overall: 9.21 109.74 21.84 2.31 220 1762 Protein: 9.21 109.74 17.19 2.31 0 1519 Water: 11.50 71.37 37.30 N/A 220 235 Other: 20.33 31.47 26.08 N/A 0 8 Chain A: 9.21 109.74 19.90 N/A 0 1762 Chain S: 16.34 66.98 37.38 N/A 220 0 Histogram: Values Number of atoms 9.21 - 19.26 1235 19.26 - 29.31 272 29.31 - 39.37 215 39.37 - 49.42 144 49.42 - 59.47 78 59.47 - 69.53 24 69.53 - 79.58 8 79.58 - 89.63 3 89.63 - 99.69 1 99.69 - 109.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1390 r_work=0.1212 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1391 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1383 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646614 | | target function (ml) not normalized (work): 303737.417293 | | target function (ml) not normalized (free): 16032.294044 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1205 0.1383 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1536 0.1536 0.1576 n_refl.: 87589 remove outliers: r(all,work,free)=0.1536 0.1536 0.1576 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1534 0.1533 0.1575 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1195 0.1355 n_refl.: 87589 remove outliers: r(all,work,free)=0.1199 0.1191 0.1355 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 0.3851 283.122 257.890 0.478 1.000 0.303 11.894-9.307 96.08 94 4 0.2324 475.364 462.928 0.856 1.001 0.283 9.237-7.194 98.18 209 7 0.2174 385.700 387.358 0.951 1.002 0.160 7.162-5.571 100.00 427 22 0.2009 293.465 283.857 0.909 1.002 0.160 5.546-4.326 100.00 867 58 0.1087 402.855 398.486 0.953 1.002 0.158 4.315-3.360 100.00 1859 96 0.0912 383.118 380.734 0.992 1.002 0.157 3.356-2.611 100.00 3867 181 0.1145 251.689 249.891 1.000 1.002 0.140 2.608-2.026 99.99 8198 413 0.1049 166.847 165.825 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1012 81.479 81.639 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1294 36.131 35.699 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2137 22.765 21.374 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0369 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1359 | n_water=455 | time (s): 1.840 (total time: 1.840) Filter (dist) r_work=0.1191 r_free=0.1359 | n_water=455 | time (s): 39.510 (total time: 41.350) Filter (q & B) r_work=0.1191 r_free=0.1359 | n_water=455 | time (s): 1.070 (total time: 42.420) Compute maps r_work=0.1191 r_free=0.1359 | n_water=455 | time (s): 1.240 (total time: 43.660) Filter (map) r_work=0.1220 r_free=0.1393 | n_water=314 | time (s): 2.780 (total time: 46.440) Find peaks r_work=0.1220 r_free=0.1393 | n_water=314 | time (s): 0.550 (total time: 46.990) Add new water r_work=0.1287 r_free=0.1461 | n_water=483 | time (s): 2.490 (total time: 49.480) Refine new water occ: r_work=0.1214 r_free=0.1377 adp: r_work=0.1215 r_free=0.1384 occ: r_work=0.1199 r_free=0.1357 adp: r_work=0.1198 r_free=0.1364 occ: r_work=0.1188 r_free=0.1345 adp: r_work=0.1184 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1348 r_work=0.1184 r_free=0.1348 | n_water=483 | time (s): 191.900 (total time: 241.380) Filter (q & B) r_work=0.1191 r_free=0.1358 | n_water=447 | time (s): 3.690 (total time: 245.070) Filter (dist only) r_work=0.1191 r_free=0.1356 | n_water=446 | time (s): 37.750 (total time: 282.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.082057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.524732 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 0.1194 0.1365 0.0171 0.006 1.0 1.6 0.5 0.0 0 1.041 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.65 1.71 3.413 21.460 42.525 3.636 11.87 13.59 1.72 3.733 21.366 42.525 3.623 Individual atomic B min max mean iso aniso Overall: 9.29 105.73 21.26 2.14 214 1759 Protein: 9.29 105.73 16.96 2.14 0 1519 Water: 11.47 70.20 35.83 N/A 214 232 Other: 20.49 28.79 24.93 N/A 0 8 Chain A: 9.29 105.73 19.58 N/A 0 1759 Chain S: 15.84 66.74 35.07 N/A 214 0 Histogram: Values Number of atoms 9.29 - 18.93 1232 18.93 - 28.57 287 28.57 - 38.22 209 38.22 - 47.86 135 47.86 - 57.51 72 57.51 - 67.15 25 67.15 - 76.79 8 76.79 - 86.44 2 86.44 - 96.08 1 96.08 - 105.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1359 r_work=0.1188 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1360 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1359 target_work(ml) = 3.621 | | 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.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1184 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621448 | | target function (ml) not normalized (work): 301601.393455 | | target function (ml) not normalized (free): 15935.280066 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1184 0.1359 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1505 0.1505 0.1537 n_refl.: 87578 remove outliers: r(all,work,free)=0.1505 0.1505 0.1537 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1501 0.1501 0.1535 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1183 0.1355 n_refl.: 87578 remove outliers: r(all,work,free)=0.1190 0.1182 0.1355 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4122 283.122 246.643 0.443 1.000 0.324 11.894-9.307 95.10 93 4 0.2332 477.336 452.851 0.830 1.002 0.320 9.237-7.194 97.73 208 7 0.2454 383.686 377.154 0.917 1.002 0.167 7.162-5.571 100.00 427 22 0.2187 293.465 282.962 0.902 1.002 0.137 5.546-4.326 100.00 867 58 0.1154 402.855 397.713 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0945 383.118 380.545 0.994 1.002 0.123 3.356-2.611 100.00 3867 181 0.1153 251.689 249.945 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1024 166.847 165.974 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0972 81.479 81.757 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.131 35.763 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2125 22.765 21.403 0.984 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0579 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1355 After: r_work=0.1182 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1182 r_free=0.1355 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=0.1182 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1355 | n_water=446 | time (s): 1.700 (total time: 1.700) Filter (dist) r_work=0.1182 r_free=0.1355 | n_water=446 | time (s): 34.690 (total time: 36.390) Filter (q & B) r_work=0.1183 r_free=0.1354 | n_water=444 | time (s): 3.240 (total time: 39.630) Compute maps r_work=0.1183 r_free=0.1354 | n_water=444 | time (s): 1.190 (total time: 40.820) Filter (map) r_work=0.1204 r_free=0.1386 | n_water=338 | time (s): 3.110 (total time: 43.930) Find peaks r_work=0.1204 r_free=0.1386 | n_water=338 | time (s): 0.660 (total time: 44.590) Add new water r_work=0.1255 r_free=0.1414 | n_water=497 | time (s): 3.120 (total time: 47.710) Refine new water occ: r_work=0.1192 r_free=0.1353 adp: r_work=0.1192 r_free=0.1355 occ: r_work=0.1179 r_free=0.1343 adp: r_work=0.1177 r_free=0.1345 occ: r_work=0.1169 r_free=0.1337 adp: r_work=0.1166 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1166 r_free=0.1338 r_work=0.1166 r_free=0.1338 | n_water=497 | time (s): 194.970 (total time: 242.680) Filter (q & B) r_work=0.1172 r_free=0.1349 | n_water=461 | time (s): 3.000 (total time: 245.680) Filter (dist only) r_work=0.1172 r_free=0.1346 | n_water=460 | time (s): 38.560 (total time: 284.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.259773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.215063 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 0.1204 0.1365 0.0161 0.007 1.1 6.1 0.5 0.0 0 1.130 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.65 1.61 3.288 21.229 38.215 3.628 12.07 13.68 1.61 3.512 21.155 38.215 3.623 Individual atomic B min max mean iso aniso Overall: 9.32 101.53 21.15 2.00 229 1758 Protein: 9.32 101.53 16.76 2.00 0 1519 Water: 11.55 69.36 35.60 N/A 229 231 Other: 20.34 28.71 24.81 N/A 0 8 Chain A: 9.32 101.53 19.36 N/A 0 1758 Chain S: 15.28 66.87 34.96 N/A 229 0 Histogram: Values Number of atoms 9.32 - 18.54 1222 18.54 - 27.76 285 27.76 - 36.98 215 36.98 - 46.20 146 46.20 - 55.42 77 55.42 - 64.64 25 64.64 - 73.87 12 73.87 - 83.09 2 83.09 - 92.31 1 92.31 - 101.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1368 r_work=0.1207 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1368 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1364 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622212 | | target function (ml) not normalized (work): 301657.806654 | | target function (ml) not normalized (free): 15934.159369 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1418 0.1401 5.6804 5.6213| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1448 5.2035 5.2714| | 3: 2.83 - 2.48 1.00 2820 163 0.1241 0.1301 5.0053 5.0277| | 4: 2.47 - 2.25 1.00 2825 136 0.1045 0.1079 4.7092 4.7315| | 5: 2.25 - 2.09 1.00 2756 127 0.1001 0.1109 4.6448 4.7185| | 6: 2.09 - 1.97 1.00 2846 113 0.0990 0.1191 4.3592 4.4779| | 7: 1.97 - 1.87 1.00 2787 165 0.1012 0.1238 4.0869 4.1868| | 8: 1.87 - 1.79 1.00 2789 144 0.1028 0.1246 3.9925 4.0896| | 9: 1.79 - 1.72 1.00 2745 138 0.0967 0.1355 3.7205 3.9327| | 10: 1.72 - 1.66 1.00 2831 160 0.1016 0.1253 3.6384 3.7584| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1075 3.5674 3.6034| | 12: 1.61 - 1.56 1.00 2773 144 0.0921 0.1172 3.3476 3.486| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1066 3.3385 3.4323| | 14: 1.52 - 1.48 1.00 2803 134 0.0989 0.1093 3.2603 3.3221| | 15: 1.48 - 1.45 1.00 2738 128 0.1013 0.1346 3.1651 3.3288| | 16: 1.45 - 1.42 1.00 2756 161 0.1074 0.1243 3.1486 3.2313| | 17: 1.42 - 1.39 1.00 2785 139 0.1114 0.1280 3.1082 3.2272| | 18: 1.39 - 1.36 1.00 2741 179 0.1155 0.1379 3.0846 3.257| | 19: 1.36 - 1.34 1.00 2807 134 0.1227 0.1607 3.0935 3.2717| | 20: 1.34 - 1.32 1.00 2696 147 0.1330 0.1507 3.0916 3.1361| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1617 3.0861 3.1536| | 22: 1.29 - 1.27 1.00 2704 152 0.1490 0.1931 3.0891 3.2834| | 23: 1.27 - 1.26 1.00 2802 156 0.1579 0.1859 3.1028 3.2101| | 24: 1.26 - 1.24 1.00 2744 132 0.1631 0.1756 3.0949 3.2008| | 25: 1.24 - 1.22 1.00 2733 148 0.1795 0.2282 3.1088 3.2844| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1804 3.1232 3.1995| | 27: 1.21 - 1.19 1.00 2814 148 0.2017 0.2069 3.1415 3.1521| | 28: 1.19 - 1.18 1.00 2671 147 0.2150 0.2346 3.1404 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2211 0.2342 3.125 3.2182| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2504 3.1145 3.1696| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.97 1.00 0.97 6160.71| | 2: 3.57 - 2.84 2888 124 0.92 13.21 1.01 0.97 6160.71| | 3: 2.83 - 2.48 2820 163 0.89 17.40 0.98 0.97 5169.28| | 4: 2.47 - 2.25 2825 136 0.91 14.53 1.00 0.98 2612.70| | 5: 2.25 - 2.09 2756 127 0.89 16.81 1.01 0.98 2612.70| | 6: 2.09 - 1.97 2846 113 0.92 13.61 1.02 0.97 1543.24| | 7: 1.97 - 1.87 2787 165 0.94 10.86 1.02 0.97 631.13| | 8: 1.87 - 1.79 2789 144 0.91 14.53 1.00 0.97 631.13| | 9: 1.79 - 1.72 2745 138 0.93 11.52 0.98 0.97 341.65| | 10: 1.72 - 1.66 2831 160 0.93 12.35 0.98 0.97 283.68| | 11: 1.66 - 1.61 2712 147 0.93 12.98 0.98 0.97 270.50| | 12: 1.61 - 1.56 2773 144 0.95 9.47 0.99 0.97 146.23| | 13: 1.56 - 1.52 2745 130 0.94 11.08 1.02 0.97 146.23| | 14: 1.52 - 1.48 2803 134 0.94 11.17 1.02 0.97 130.56| | 15: 1.48 - 1.45 2738 128 0.95 10.30 1.01 0.98 101.87| | 16: 1.45 - 1.42 2756 161 0.94 11.52 1.02 0.98 101.87| | 17: 1.42 - 1.39 2785 139 0.94 11.37 1.01 0.98 92.00| | 18: 1.39 - 1.36 2741 179 0.94 11.65 1.01 0.98 86.28| | 19: 1.36 - 1.34 2807 134 0.94 12.18 1.00 0.98 86.28| | 20: 1.34 - 1.32 2696 147 0.94 12.42 0.99 0.97 81.74| | 21: 1.32 - 1.30 2785 112 0.94 13.31 0.99 0.96 81.42| | 22: 1.29 - 1.27 2704 152 0.93 13.96 0.98 0.96 81.63| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.98 0.95 82.68| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 82.68| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.46| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 86.44| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.44| | 28: 1.19 - 1.18 2671 147 0.88 20.37 1.01 0.93 90.16| | 29: 1.18 - 1.16 2800 134 0.88 20.66 0.99 0.92 91.56| | 30: 1.16 - 1.15 2739 148 0.86 22.10 0.98 0.92 91.56| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.42 max = 6160.71 mean = 965.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.03| |phase err.(test): min = 0.00 max = 88.27 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1206 0.1364 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1556 n_refl.: 87576 remove outliers: r(all,work,free)=0.1522 0.1521 0.1556 n_refl.: 87576 overall B=-0.02 to atoms: r(all,work,free)=0.1518 0.1518 0.1554 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1368 n_refl.: 87576 remove outliers: r(all,work,free)=0.1213 0.1205 0.1368 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4265 283.122 244.369 0.442 1.000 0.324 11.894-9.307 94.12 92 4 0.2224 477.428 459.011 0.847 1.002 0.221 9.237-7.194 97.27 207 7 0.2472 384.228 375.524 0.908 1.001 0.130 7.162-5.571 100.00 427 22 0.2205 293.465 283.308 0.901 1.002 0.130 5.546-4.326 100.00 867 58 0.1193 402.855 397.910 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.1007 383.118 380.282 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1205 251.689 249.906 1.000 1.001 0.057 2.608-2.026 99.99 8198 413 0.1054 166.847 165.848 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0988 81.479 81.781 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.131 35.769 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2117 22.765 21.375 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0482 ================= 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 : 0.2598 0.1946 0.080 5.198 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_nqh: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_weight: 0.1626 0.1761 0.080 5.198 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1210 0.1458 0.008 0.958 9.1 119.5 20.1 258 0.123 1_adp: 0.1242 0.1527 0.008 0.958 8.7 118.7 21.0 258 0.123 1_regHadp: 0.1246 0.1532 0.008 0.958 8.7 118.7 21.0 258 0.123 1_occ: 0.1244 0.1536 0.008 0.958 8.7 118.7 21.0 258 0.123 2_bss: 0.1243 0.1531 0.008 0.958 8.8 118.9 21.1 258 0.123 2_settarget: 0.1243 0.1531 0.008 0.958 8.8 118.9 21.1 258 0.123 2_updatecdl: 0.1243 0.1531 0.008 0.971 8.8 118.9 21.1 258 0.123 2_nqh: 0.1245 0.1533 0.008 0.971 8.8 118.9 21.1 258 0.126 2_sol: 0.1227 0.1475 0.008 0.971 8.8 118.9 23.4 432 n/a 2_weight: 0.1227 0.1475 0.008 0.971 8.8 118.9 23.4 432 n/a 2_xyzrec: 0.1227 0.1495 0.007 0.887 8.8 118.9 23.4 432 n/a 2_adp: 0.1198 0.1477 0.007 0.887 8.6 114.7 23.1 432 n/a 2_regHadp: 0.1198 0.1477 0.007 0.887 8.6 114.7 23.1 432 n/a 2_occ: 0.1199 0.1471 0.007 0.887 8.6 114.7 23.1 432 n/a 3_bss: 0.1195 0.1472 0.007 0.887 8.6 114.7 23.1 432 n/a 3_settarget: 0.1195 0.1472 0.007 0.887 8.6 114.7 23.1 432 n/a 3_updatecdl: 0.1195 0.1472 0.007 0.886 8.6 114.7 23.1 432 n/a 3_nqh: 0.1195 0.1472 0.007 0.886 8.6 114.7 23.1 432 n/a 3_sol: 0.1223 0.1468 0.007 0.886 8.6 114.7 22.2 455 n/a 3_weight: 0.1223 0.1468 0.007 0.886 8.6 114.7 22.2 455 n/a 3_xyzrec: 0.1227 0.1443 0.006 0.920 8.6 114.7 22.2 455 n/a 3_adp: 0.1211 0.1390 0.006 0.920 9.2 109.7 21.8 455 n/a 3_regHadp: 0.1212 0.1391 0.006 0.920 9.2 109.7 21.8 455 n/a 3_occ: 0.1205 0.1383 0.006 0.920 9.2 109.7 21.8 455 n/a 4_bss: 0.1191 0.1355 0.006 0.920 9.2 109.7 21.8 455 n/a 4_settarget: 0.1191 0.1355 0.006 0.920 9.2 109.7 21.8 455 n/a 4_updatecdl: 0.1191 0.1355 0.006 0.919 9.2 109.7 21.8 455 n/a 4_nqh: 0.1191 0.1359 0.006 0.919 9.2 109.7 21.8 455 n/a 4_sol: 0.1191 0.1356 0.006 0.919 9.2 109.7 21.4 446 n/a 4_weight: 0.1191 0.1356 0.006 0.919 9.2 109.7 21.4 446 n/a 4_xyzrec: 0.1194 0.1365 0.006 0.963 9.2 109.7 21.4 446 n/a 4_adp: 0.1187 0.1359 0.006 0.963 9.3 105.7 21.3 446 n/a 4_regHadp: 0.1188 0.1360 0.006 0.963 9.3 105.7 21.3 446 n/a 4_occ: 0.1184 0.1359 0.006 0.963 9.3 105.7 21.3 446 n/a 5_bss: 0.1182 0.1355 0.006 0.963 9.3 105.7 21.2 446 n/a 5_settarget: 0.1182 0.1355 0.006 0.963 9.3 105.7 21.2 446 n/a 5_updatecdl: 0.1182 0.1355 0.006 0.962 9.3 105.7 21.2 446 n/a 5_setrh: 0.1182 0.1355 0.006 0.962 9.3 105.7 21.2 446 n/a 5_nqh: 0.1182 0.1355 0.006 0.962 9.3 105.7 21.2 446 n/a 5_sol: 0.1172 0.1346 0.006 0.962 9.3 105.7 21.3 460 n/a 5_weight: 0.1172 0.1346 0.006 0.962 9.3 105.7 21.3 460 n/a 5_xyzrec: 0.1204 0.1365 0.007 1.098 9.3 105.7 21.3 460 n/a 5_adp: 0.1207 0.1368 0.007 1.098 9.3 101.5 21.2 460 n/a 5_regHadp: 0.1207 0.1368 0.007 1.098 9.3 101.5 21.2 460 n/a 5_occ: 0.1206 0.1364 0.007 1.098 9.3 101.5 21.2 460 n/a end: 0.1205 0.1368 0.007 1.098 9.3 101.5 21.1 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4813131_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4813131_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9700 Refinement macro-cycles (run) : 3385.0700 Write final files (write_after_run_outputs) : 68.8000 Total : 3458.8400 Total CPU time: 58.24 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:59 PST -0800 (1735452599.97 s) Start R-work = 0.1626, R-free = 0.1761 Final R-work = 0.1205, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 3606.63 seconds wall clock time: 65 minutes 24.96 seconds (3924.96 seconds total)