Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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: 2.29, per 1000 atoms: 0.68 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: 0.74 Conformation dependent library (CDL) restraints added in 223.0 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.96: 898 0.96 - 1.24: 861 1.24 - 1.52: 928 1.52 - 1.79: 458 1.79 - 2.07: 8 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.237 1.020 0.217 1.09e-02 8.42e+03 3.96e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.233 0.226 1.23e-02 6.61e+03 3.37e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.27e-02 6.20e+03 3.36e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.050 0.187 1.13e-02 7.83e+03 2.73e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.728 -0.190 1.19e-02 7.06e+03 2.54e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3219 4.69 - 9.39: 1812 9.39 - 14.08: 621 14.08 - 18.77: 114 18.77 - 23.46: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 120.57 103.80 16.77 1.07e+00 8.73e-01 2.46e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 108.26 14.34 1.00e+00 1.00e+00 2.06e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.65 -12.45 9.00e-01 1.23e+00 1.91e+02 angle pdb=" CA ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 116.51 101.93 14.58 1.07e+00 8.73e-01 1.86e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 106.64 14.21 1.06e+00 8.90e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 914 15.39 - 30.78: 129 30.78 - 46.17: 45 46.17 - 61.56: 17 61.56 - 76.95: 6 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual 180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA BGLY A 65 " pdb=" C BGLY A 65 " pdb=" N BPRO A 66 " pdb=" CA BPRO A 66 " ideal model delta harmonic sigma weight residual 0.00 20.30 -20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 99 0.214 - 0.428: 78 0.428 - 0.642: 38 0.642 - 0.856: 20 0.856 - 1.070: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.63 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.63 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 9.57e-02 2.75e+02 pdb=" CG PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.126 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.173 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.160 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" CG PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.159 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.108 9.50e-02 1.11e+02 8.40e-02 1.31e+02 pdb=" NE ARG A 48 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.114 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.120 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 811 2.28 - 2.86: 7922 2.86 - 3.44: 10498 3.44 - 4.02: 15339 4.02 - 4.60: 22072 Nonbonded interactions: 56642 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.705 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.829 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.843 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.845 2.450 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.846 2.450 ... (remaining 56637 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_6113322_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= 0.2601 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784618 | | target function (ml) not normalized (work): 231975.423290 | | target function (ml) not normalized (free): 11783.235251 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2133 7.0292 4.9492| | 2: 3.57 - 2.84 1.00 2876 122 0.2455 0.1798 4.3553 4.3373| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1612 4.1314 4.1425| | 4: 2.47 - 2.25 1.00 2825 136 0.2308 0.1430 3.8326 3.8319| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1482 3.8028 3.8321| | 6: 2.09 - 1.97 1.00 2846 113 0.2517 0.1682 3.4563 3.587| | 7: 1.97 - 1.87 1.00 2787 165 0.2568 0.1965 3.1406 3.236| | 8: 1.87 - 1.79 1.00 2789 144 0.2442 0.1862 3.0601 3.148| | 9: 1.79 - 1.72 1.00 2745 138 0.2433 0.1996 2.8877 2.9522| | 10: 1.72 - 1.66 1.00 2789 158 0.2388 0.1860 2.7943 2.8408| | 11: 1.66 - 1.61 1.00 2740 147 0.2520 0.1616 2.7352 2.6754| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.2092 2.6543 2.7| | 13: 1.56 - 1.52 1.00 2745 130 0.2544 0.1934 2.5579 2.6257| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2016 2.4934 2.5645| | 15: 1.48 - 1.45 1.00 2738 128 0.2584 0.1756 2.4098 2.3288| | 16: 1.45 - 1.42 1.00 2756 161 0.2631 0.1981 2.3699 2.3892| | 17: 1.42 - 1.39 1.00 2785 139 0.2650 0.2057 2.3236 2.3755| | 18: 1.39 - 1.36 1.00 2741 179 0.2636 0.2292 2.253 2.3469| | 19: 1.36 - 1.34 1.00 2807 134 0.2651 0.2239 2.2418 2.2276| | 20: 1.34 - 1.32 1.00 2696 147 0.2630 0.2326 2.19 2.2238| | 21: 1.32 - 1.30 1.00 2785 112 0.2762 0.2074 2.1675 2.1446| | 22: 1.29 - 1.27 1.00 2704 152 0.2743 0.2501 2.1303 2.227| | 23: 1.27 - 1.26 1.00 2802 156 0.2700 0.2502 2.0817 2.1986| | 24: 1.26 - 1.24 1.00 2744 132 0.2749 0.2280 2.068 2.089| | 25: 1.24 - 1.22 1.00 2734 148 0.2800 0.2530 2.0428 2.0515| | 26: 1.22 - 1.21 1.00 2727 135 0.2837 0.2205 2.0085 2.0764| | 27: 1.21 - 1.19 1.00 2814 148 0.2958 0.2618 2.003 2.0258| | 28: 1.19 - 1.18 1.00 2671 147 0.2957 0.2782 1.982 2.0061| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2655 1.9507 1.9918| | 30: 1.16 - 1.15 1.00 2740 148 0.3069 0.2799 1.9292 1.9848| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.95 0.76 0.23 1497.13| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.28 0.23 1497.13| | 3: 2.84 - 2.48 2833 165 0.74 32.11 1.24 0.23 1241.81| | 4: 2.47 - 2.25 2825 136 0.81 25.71 1.25 0.25 579.20| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.27 0.25 579.20| | 6: 2.09 - 1.97 2846 113 0.83 22.92 1.29 0.25 317.36| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 94.04| | 8: 1.87 - 1.79 2789 144 0.86 21.32 1.24 0.26 94.04| | 9: 1.79 - 1.72 2745 138 0.88 18.73 1.24 0.25 56.04| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.22 0.25 48.43| | 11: 1.66 - 1.61 2740 147 0.85 21.63 1.25 0.25 46.65| | 12: 1.61 - 1.56 2787 146 0.89 18.30 1.23 0.25 28.61| | 13: 1.56 - 1.52 2745 130 0.87 20.07 1.24 0.25 28.61| | 14: 1.52 - 1.48 2803 134 0.87 20.34 1.24 0.25 25.37| | 15: 1.48 - 1.45 2738 128 0.87 19.73 1.23 0.25 19.43| | 16: 1.45 - 1.42 2756 161 0.86 21.09 1.23 0.25 19.43| | 17: 1.42 - 1.39 2785 139 0.87 20.12 1.23 0.25 16.69| | 18: 1.39 - 1.36 2741 179 0.87 20.59 1.23 0.25 15.10| | 19: 1.36 - 1.34 2807 134 0.86 21.41 1.21 0.25 15.10| | 20: 1.34 - 1.32 2696 147 0.88 20.13 1.20 0.25 12.42| | 21: 1.32 - 1.30 2785 112 0.86 21.31 1.21 0.25 12.23| | 22: 1.29 - 1.27 2704 152 0.86 21.95 1.21 0.24 11.98| | 23: 1.27 - 1.26 2802 156 0.86 21.63 1.21 0.24 10.73| | 24: 1.26 - 1.24 2744 132 0.86 22.25 1.20 0.24 10.73| | 25: 1.24 - 1.22 2734 148 0.85 23.15 1.19 0.24 10.27| | 26: 1.22 - 1.21 2727 135 0.84 23.73 1.19 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.83 24.72 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 25.42 1.18 0.23 9.42| | 29: 1.18 - 1.16 2800 134 0.82 26.09 1.17 0.23 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.16 0.23 9.30| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1497.13 mean = 217.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.47| |phase err.(test): min = 0.00 max = 89.66 mean = 22.37| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.276 1557 Z= 5.511 Angle : 5.139 16.891 2118 Z= 3.679 Chirality : 0.395 1.070 243 Planarity : 0.032 0.119 284 Dihedral : 13.647 76.946 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 25.95 % 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: -2.37 (0.49), residues: 224 helix: -2.22 (0.41), residues: 109 sheet: -0.66 (0.85), residues: 38 loop : -0.61 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.026 ARG A 98 TYR 0.083 0.041 TYR A 139 PHE 0.190 0.055 PHE A 164 HIS 0.069 0.042 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= 0.2601 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.784618 | | target function (ml) not normalized (work): 231975.423290 | | target function (ml) not normalized (free): 11783.235251 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2602 0.1925 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2602 0.1925 n_refl.: 87602 remove outliers: r(all,work,free)=0.1969 0.1973 0.1925 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1996 0.2001 0.1939 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1735 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1626 0.1735 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 0.3875 386.308 353.769 0.665 1.002 0.401 11.894-9.307 99.02 97 4 0.1814 613.631 594.186 0.924 1.003 0.375 9.237-7.194 100.00 213 7 0.2111 501.875 491.466 0.952 1.003 0.349 7.162-5.571 100.00 427 22 0.2187 376.629 364.364 0.930 1.003 0.330 5.546-4.326 100.00 867 58 0.1273 517.019 511.077 0.962 1.002 0.224 4.315-3.360 100.00 1859 96 0.1165 491.689 487.543 1.007 1.002 0.199 3.356-2.611 100.00 3867 181 0.1428 323.014 319.646 1.000 1.001 0.043 2.608-2.026 99.99 8198 413 0.1349 214.129 211.933 1.004 0.999 0.000 2.025-1.573 100.00 17313 902 0.1621 104.569 103.719 1.016 0.996 0.000 1.573-1.221 100.00 36679 1900 0.2046 46.370 45.116 1.008 0.991 0.000 1.221-1.150 99.97 13689 708 0.2571 29.217 26.979 0.987 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1626 r_free=0.1735 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1627 r_free=0.1737 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.383908 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1982.955643 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 0.1211 0.1459 0.0248 0.007 0.9 1.3 0.5 0.0 0 11.692 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.59 2.48 3.013 19.078 1982.956 0.017 12.42 15.30 2.87 3.336 19.657 1982.956 0.016 Individual atomic B min max mean iso aniso Overall: 8.73 118.79 21.20 2.90 0 1785 Protein: 8.73 118.79 18.05 2.90 0 1519 Water: 11.20 114.62 39.52 N/A 0 258 Other: 23.31 37.97 29.68 N/A 0 8 Chain A: 8.73 118.79 21.20 N/A 0 1785 Histogram: Values Number of atoms 8.73 - 19.74 1211 19.74 - 30.75 228 30.75 - 41.75 160 41.75 - 52.76 102 52.76 - 63.76 51 63.76 - 74.77 17 74.77 - 85.78 9 85.78 - 96.78 2 96.78 - 107.79 2 107.79 - 118.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1529 r_work=0.1246 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1534 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 = 0.1246 r_free = 0.1539 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1539 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015459 | | target function (ls_wunit_k1) not normalized (work): 1287.655451 | | target function (ls_wunit_k1) not normalized (free): 111.707148 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1246 0.1539 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1715 0.1714 0.1780 n_refl.: 87593 remove outliers: r(all,work,free)=0.1715 0.1714 0.1780 n_refl.: 87593 overall B=0.05 to atoms: r(all,work,free)=0.1724 0.1723 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1246 0.1531 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 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 0.3572 297.619 277.818 0.642 1.002 0.380 11.894-9.307 99.02 97 4 0.1617 476.769 465.670 0.914 1.003 0.368 9.237-7.194 100.00 213 7 0.1814 389.938 385.461 0.956 1.003 0.314 7.162-5.571 100.00 427 22 0.1689 292.627 287.781 0.936 1.003 0.290 5.546-4.326 100.00 867 58 0.0908 401.705 399.309 0.957 1.003 0.209 4.315-3.360 100.00 1859 96 0.0770 382.024 380.999 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1026 250.970 250.211 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.0988 166.370 165.724 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1217 81.247 81.407 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1647 36.028 35.481 1.013 0.998 0.000 1.221-1.150 99.97 13689 708 0.2360 22.700 21.197 0.975 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0769 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 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** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1247 r_free=0.1533 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1533 | n_water=258 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1257 r_free=0.1531 | n_water=252 | time (s): 26.000 (total time: 28.450) Filter (q & B) r_work=0.1259 r_free=0.1529 | n_water=249 | time (s): 3.800 (total time: 32.250) Compute maps r_work=0.1259 r_free=0.1529 | n_water=249 | time (s): 1.870 (total time: 34.120) Filter (map) r_work=0.1286 r_free=0.1546 | n_water=232 | time (s): 3.800 (total time: 37.920) Find peaks r_work=0.1286 r_free=0.1546 | n_water=232 | time (s): 0.720 (total time: 38.640) Add new water r_work=0.1439 r_free=0.1704 | n_water=446 | time (s): 3.740 (total time: 42.380) Refine new water occ: r_work=0.1339 r_free=0.1556 adp: r_work=0.1261 r_free=0.1505 occ: r_work=0.1273 r_free=0.1492 adp: r_work=0.1239 r_free=0.1477 occ: r_work=0.1242 r_free=0.1462 adp: r_work=0.1232 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1460 r_work=0.1232 r_free=0.1460 | n_water=446 | time (s): 92.770 (total time: 135.150) Filter (q & B) r_work=0.1237 r_free=0.1466 | n_water=428 | time (s): 3.840 (total time: 138.990) Filter (dist only) r_work=0.1237 r_free=0.1466 | n_water=428 | time (s): 39.880 (total time: 178.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.271911 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1606.624467 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 0.1229 0.1495 0.0265 0.007 0.9 1.9 0.5 0.0 0 13.136 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.95 2.65 3.825 23.240 1606.624 0.015 12.01 14.81 2.80 4.372 23.016 1606.624 0.015 Individual atomic B min max mean iso aniso Overall: 8.47 113.84 23.13 2.66 196 1759 Protein: 8.47 113.84 17.65 2.67 0 1519 Water: 11.08 74.99 42.46 N/A 196 232 Other: 24.01 34.86 28.50 N/A 0 8 Chain A: 8.47 113.84 20.37 N/A 0 1759 Chain S: 13.60 74.99 47.87 N/A 196 0 Histogram: Values Number of atoms 8.47 - 19.01 1201 19.01 - 29.55 254 29.55 - 40.08 187 40.08 - 50.62 135 50.62 - 61.16 115 61.16 - 71.69 46 71.69 - 82.23 10 82.23 - 92.77 3 92.77 - 103.31 2 103.31 - 113.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1481 r_work=0.1201 r_free=0.1481 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1481 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1473 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1201 r_free= 0.1473 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013954 | | target function (ls_wunit_k1) not normalized (work): 1162.291496 | | target function (ls_wunit_k1) not normalized (free): 98.417263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1201 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1605 0.1738 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1605 0.1738 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1617 0.1612 0.1743 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1470 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1198 0.1470 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 0.3274 290.349 273.851 0.581 1.002 0.350 11.894-9.307 99.02 97 4 0.1640 476.769 473.610 0.913 1.003 0.327 9.237-7.194 100.00 213 7 0.1674 389.938 389.997 0.979 1.003 0.260 7.162-5.571 100.00 427 22 0.1503 292.627 288.561 0.943 1.003 0.234 5.546-4.326 100.00 867 58 0.0811 401.705 399.148 0.956 1.003 0.205 4.315-3.360 100.00 1859 96 0.0707 382.024 381.062 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0955 250.970 250.462 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0962 166.370 166.069 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1184 81.247 81.451 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1619 36.028 35.524 1.015 0.998 0.000 1.221-1.150 99.97 13689 708 0.2343 22.700 21.232 0.974 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0770 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1470 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1470 | n_water=428 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1199 r_free=0.1471 | n_water=425 | time (s): 37.500 (total time: 39.860) Filter (q & B) r_work=0.1199 r_free=0.1471 | n_water=425 | time (s): 1.260 (total time: 41.120) Compute maps r_work=0.1199 r_free=0.1471 | n_water=425 | time (s): 1.500 (total time: 42.620) Filter (map) r_work=0.1244 r_free=0.1485 | n_water=294 | time (s): 3.270 (total time: 45.890) Find peaks r_work=0.1244 r_free=0.1485 | n_water=294 | time (s): 0.540 (total time: 46.430) Add new water r_work=0.1366 r_free=0.1597 | n_water=484 | time (s): 3.300 (total time: 49.730) Refine new water occ: r_work=0.1261 r_free=0.1510 adp: r_work=0.1261 r_free=0.1511 occ: r_work=0.1239 r_free=0.1494 adp: r_work=0.1235 r_free=0.1492 occ: r_work=0.1224 r_free=0.1480 adp: r_work=0.1216 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1477 r_work=0.1216 r_free=0.1477 | n_water=484 | time (s): 191.150 (total time: 240.880) Filter (q & B) r_work=0.1220 r_free=0.1478 | n_water=454 | time (s): 3.300 (total time: 244.180) Filter (dist only) r_work=0.1221 r_free=0.1476 | n_water=453 | time (s): 35.970 (total time: 280.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.033993 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.422103 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 0.1231 0.1441 0.0211 0.006 0.9 1.9 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.41 2.11 3.638 22.158 50.422 3.721 12.17 13.98 1.81 4.160 21.966 50.422 3.649 Individual atomic B min max mean iso aniso Overall: 9.14 108.89 21.78 2.35 224 1756 Protein: 9.14 108.89 17.21 2.35 0 1519 Water: 11.53 69.44 37.06 N/A 224 229 Other: 19.41 30.86 25.02 N/A 0 8 Chain A: 9.14 108.89 19.87 N/A 0 1756 Chain S: 15.76 68.42 36.80 N/A 224 0 Histogram: Values Number of atoms 9.14 - 19.12 1230 19.12 - 29.09 270 29.09 - 39.07 221 39.07 - 49.04 147 49.04 - 59.02 71 59.02 - 68.99 28 68.99 - 78.97 7 78.97 - 88.94 2 88.94 - 98.92 2 98.92 - 108.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1398 r_work=0.1218 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1398 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1212 r_free = 0.1400 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.16 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= 0.1212 r_free= 0.1400 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.647081 | | target function (ml) not normalized (work): 303772.661106 | | target function (ml) not normalized (free): 16046.646138 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1212 0.1400 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1539 0.1538 0.1600 n_refl.: 87588 remove outliers: r(all,work,free)=0.1539 0.1538 0.1600 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1537 0.1599 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1203 0.1391 n_refl.: 87588 remove outliers: r(all,work,free)=0.1209 0.1200 0.1391 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 89.58 81 5 0.3872 287.001 258.097 0.466 1.000 0.314 11.894-9.307 97.06 95 4 0.2460 470.186 459.135 0.856 1.001 0.310 9.237-7.194 98.18 209 7 0.2255 381.520 383.374 0.949 1.002 0.190 7.162-5.571 100.00 427 22 0.2018 292.627 283.337 0.914 1.002 0.166 5.546-4.326 100.00 867 58 0.1102 401.705 397.485 0.951 1.002 0.162 4.315-3.360 100.00 1859 96 0.0924 382.024 379.146 0.992 1.002 0.160 3.356-2.611 100.00 3867 181 0.1166 250.970 249.126 0.998 1.002 0.160 2.608-2.026 99.99 8198 413 0.1055 166.370 165.382 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.247 81.390 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1298 36.028 35.594 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2132 22.700 21.315 0.976 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1391 | n_water=453 | time (s): 1.920 (total time: 1.920) Filter (dist) r_work=0.1200 r_free=0.1392 | n_water=452 | time (s): 40.780 (total time: 42.700) Filter (q & B) r_work=0.1200 r_free=0.1391 | n_water=451 | time (s): 2.950 (total time: 45.650) Compute maps r_work=0.1200 r_free=0.1391 | n_water=451 | time (s): 1.790 (total time: 47.440) Filter (map) r_work=0.1224 r_free=0.1387 | n_water=308 | time (s): 2.860 (total time: 50.300) Find peaks r_work=0.1224 r_free=0.1387 | n_water=308 | time (s): 0.450 (total time: 50.750) Add new water r_work=0.1292 r_free=0.1442 | n_water=470 | time (s): 3.130 (total time: 53.880) Refine new water occ: r_work=0.1217 r_free=0.1368 adp: r_work=0.1218 r_free=0.1369 occ: r_work=0.1202 r_free=0.1359 adp: r_work=0.1200 r_free=0.1358 occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1187 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1349 r_work=0.1187 r_free=0.1349 | n_water=470 | time (s): 226.600 (total time: 280.480) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=431 | time (s): 2.650 (total time: 283.130) Filter (dist only) r_work=0.1194 r_free=0.1353 | n_water=430 | time (s): 38.680 (total time: 321.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.023951 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.310485 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 0.1200 0.1360 0.0160 0.006 1.0 1.9 0.5 0.0 0 1.012 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.60 1.60 3.430 21.437 40.310 3.634 11.92 13.60 1.69 3.682 21.359 40.310 3.624 Individual atomic B min max mean iso aniso Overall: 9.23 104.75 21.25 2.17 206 1751 Protein: 9.23 104.75 17.03 2.17 0 1519 Water: 11.55 68.87 36.08 N/A 206 224 Other: 18.83 28.08 23.88 N/A 0 8 Chain A: 9.23 104.75 19.55 N/A 0 1751 Chain S: 15.27 61.30 35.62 N/A 206 0 Histogram: Values Number of atoms 9.23 - 18.78 1221 18.78 - 28.33 277 28.33 - 37.89 201 37.89 - 47.44 149 47.44 - 56.99 68 56.99 - 66.54 28 66.54 - 76.10 8 76.10 - 85.65 1 85.65 - 95.20 2 95.20 - 104.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1360 r_work=0.1192 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1361 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1358 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.15 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= 0.1188 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622959 | | target function (ml) not normalized (work): 301734.556756 | | target function (ml) not normalized (free): 15942.579115 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1188 0.1358 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1520 0.1520 0.1564 n_refl.: 87580 remove outliers: r(all,work,free)=0.1520 0.1520 0.1564 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1518 0.1518 0.1563 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1187 0.1362 n_refl.: 87580 remove outliers: r(all,work,free)=0.1193 0.1184 0.1362 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3842 284.884 256.381 0.447 1.000 0.284 11.894-9.307 93.14 91 4 0.2135 472.345 447.455 0.835 1.002 0.265 9.237-7.194 97.73 208 7 0.2359 381.045 377.065 0.918 1.002 0.153 7.162-5.571 100.00 427 22 0.2152 292.627 282.776 0.906 1.002 0.141 5.546-4.326 100.00 867 58 0.1129 401.705 398.209 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0954 382.024 379.385 0.992 1.002 0.140 3.356-2.611 100.00 3867 181 0.1153 250.970 249.299 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1033 166.370 165.569 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0988 81.247 81.545 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.028 35.661 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2126 22.700 21.335 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0276 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1362 After: r_work=0.1185 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1361 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=0.1185 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1361 | n_water=430 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1185 r_free=0.1361 | n_water=430 | time (s): 34.260 (total time: 36.020) Filter (q & B) r_work=0.1186 r_free=0.1363 | n_water=426 | time (s): 3.340 (total time: 39.360) Compute maps r_work=0.1186 r_free=0.1363 | n_water=426 | time (s): 1.330 (total time: 40.690) Filter (map) r_work=0.1211 r_free=0.1372 | n_water=326 | time (s): 2.690 (total time: 43.380) Find peaks r_work=0.1211 r_free=0.1372 | n_water=326 | time (s): 0.670 (total time: 44.050) Add new water r_work=0.1268 r_free=0.1416 | n_water=490 | time (s): 3.160 (total time: 47.210) Refine new water occ: r_work=0.1200 r_free=0.1367 adp: r_work=0.1200 r_free=0.1368 occ: r_work=0.1188 r_free=0.1359 adp: r_work=0.1186 r_free=0.1359 occ: r_work=0.1178 r_free=0.1354 adp: r_work=0.1175 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1353 r_work=0.1175 r_free=0.1353 | n_water=490 | time (s): 142.670 (total time: 189.880) Filter (q & B) r_work=0.1182 r_free=0.1358 | n_water=448 | time (s): 2.840 (total time: 192.720) Filter (dist only) r_work=0.1182 r_free=0.1354 | n_water=446 | time (s): 37.750 (total time: 230.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.934516 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.216051 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 0.1205 0.1380 0.0175 0.007 1.0 3.5 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.80 1.75 3.315 21.275 47.216 3.632 12.06 13.76 1.70 3.895 21.109 47.216 3.620 Individual atomic B min max mean iso aniso Overall: 9.21 100.91 21.01 2.03 222 1751 Protein: 9.21 100.91 16.62 2.04 0 1519 Water: 11.47 67.01 35.96 N/A 222 224 Other: 18.41 25.32 21.68 N/A 0 8 Chain A: 9.21 100.91 19.12 N/A 0 1751 Chain S: 13.76 61.80 35.95 N/A 222 0 Histogram: Values Number of atoms 9.21 - 18.38 1218 18.38 - 27.55 278 27.55 - 36.72 202 36.72 - 45.89 160 45.89 - 55.06 73 55.06 - 64.23 27 64.23 - 73.40 10 73.40 - 82.57 2 82.57 - 91.74 1 91.74 - 100.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1376 r_work=0.1206 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1376 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1198 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617478 | | target function (ml) not normalized (work): 301252.749018 | | target function (ml) not normalized (free): 15932.210113 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1394 0.1400 5.6525 5.621| | 2: 3.57 - 2.84 1.00 2888 124 0.1132 0.1424 5.1903 5.2519| | 3: 2.83 - 2.48 1.00 2820 163 0.1242 0.1248 4.9997 5.0141| | 4: 2.47 - 2.25 1.00 2825 136 0.1034 0.1186 4.6999 4.7599| | 5: 2.25 - 2.09 1.00 2756 127 0.1005 0.1116 4.6399 4.704| | 6: 2.09 - 1.97 1.00 2846 113 0.0983 0.1213 4.3486 4.4781| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1224 4.0736 4.1759| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1238 3.9882 4.0727| | 9: 1.79 - 1.72 1.00 2745 138 0.0953 0.1263 3.7111 3.8868| | 10: 1.72 - 1.66 1.00 2831 160 0.0996 0.1230 3.6267 3.7547| | 11: 1.66 - 1.61 1.00 2712 147 0.0962 0.1109 3.5651 3.6131| | 12: 1.61 - 1.56 1.00 2773 144 0.0914 0.1203 3.3423 3.4993| | 13: 1.56 - 1.52 1.00 2745 130 0.0991 0.1096 3.3408 3.4518| | 14: 1.52 - 1.48 1.00 2803 134 0.0994 0.1132 3.2595 3.3534| | 15: 1.48 - 1.45 1.00 2738 128 0.1022 0.1326 3.1725 3.3115| | 16: 1.45 - 1.42 1.00 2756 161 0.1079 0.1264 3.1562 3.2413| | 17: 1.42 - 1.39 1.00 2785 139 0.1130 0.1330 3.1196 3.2525| | 18: 1.39 - 1.36 1.00 2741 179 0.1156 0.1372 3.0842 3.2603| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1604 3.0959 3.2667| | 20: 1.34 - 1.32 1.00 2696 147 0.1323 0.1446 3.0884 3.1298| | 21: 1.32 - 1.30 1.00 2785 112 0.1412 0.1655 3.0827 3.1753| | 22: 1.29 - 1.27 1.00 2704 152 0.1469 0.1914 3.0826 3.2827| | 23: 1.27 - 1.26 1.00 2802 156 0.1566 0.1880 3.0978 3.2239| | 24: 1.26 - 1.24 1.00 2744 132 0.1622 0.1828 3.0927 3.2096| | 25: 1.24 - 1.22 1.00 2733 148 0.1790 0.2310 3.1058 3.2886| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1770 3.118 3.1935| | 27: 1.21 - 1.19 1.00 2814 148 0.2009 0.2101 3.1337 3.1492| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2320 3.1345 3.1601| | 29: 1.18 - 1.16 1.00 2800 134 0.2212 0.2346 3.1201 3.2107| | 30: 1.16 - 1.15 1.00 2739 148 0.2372 0.2459 3.1123 3.1545| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.95 8.85 1.00 0.97 6006.81| | 2: 3.57 - 2.84 2888 124 0.92 12.98 1.01 0.97 6006.81| | 3: 2.83 - 2.48 2820 163 0.89 17.13 0.98 0.97 5040.80| | 4: 2.47 - 2.25 2825 136 0.91 14.36 1.00 0.98 2549.78| | 5: 2.25 - 2.09 2756 127 0.90 16.52 1.01 0.98 2549.78| | 6: 2.09 - 1.97 2846 113 0.92 13.51 1.02 0.97 1508.53| | 7: 1.97 - 1.87 2787 165 0.94 10.82 1.02 0.97 620.49| | 8: 1.87 - 1.79 2789 144 0.91 14.39 1.00 0.97 620.49| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.97 335.43| | 10: 1.72 - 1.66 2831 160 0.93 12.19 0.98 0.97 278.35| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 265.94| | 12: 1.61 - 1.56 2773 144 0.95 9.69 0.99 0.97 148.95| | 13: 1.56 - 1.52 2745 130 0.94 11.18 1.02 0.97 148.95| | 14: 1.52 - 1.48 2803 134 0.94 11.40 1.02 0.97 133.10| | 15: 1.48 - 1.45 2738 128 0.95 10.54 1.02 0.98 104.09| | 16: 1.45 - 1.42 2756 161 0.94 11.75 1.02 0.98 104.09| | 17: 1.42 - 1.39 2785 139 0.94 11.59 1.01 0.98 94.16| | 18: 1.39 - 1.36 2741 179 0.94 11.96 1.01 0.98 88.41| | 19: 1.36 - 1.34 2807 134 0.94 12.48 1.00 0.98 88.41| | 20: 1.34 - 1.32 2696 147 0.94 12.58 0.99 0.96 83.09| | 21: 1.32 - 1.30 2785 112 0.93 13.47 0.99 0.96 82.72| | 22: 1.29 - 1.27 2704 152 0.93 14.03 0.99 0.96 82.83| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.98 0.95 83.40| | 24: 1.26 - 1.24 2744 132 0.92 15.07 0.97 0.95 83.40| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.54| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.03 0.93 85.80| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 85.80| | 28: 1.19 - 1.18 2671 147 0.88 20.14 1.01 0.93 88.23| | 29: 1.18 - 1.16 2800 134 0.88 20.43 0.99 0.93 89.14| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.93 89.14| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.72 max = 6006.81 mean = 943.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.03| |phase err.(test): min = 0.00 max = 87.62 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1198 0.1365 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1517 0.1515 0.1582 n_refl.: 87573 remove outliers: r(all,work,free)=0.1517 0.1515 0.1582 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1512 0.1581 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1367 n_refl.: 87573 remove outliers: r(all,work,free)=0.1206 0.1198 0.1367 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4025 284.884 251.805 0.442 1.000 0.314 11.894-9.307 93.14 91 4 0.2316 472.345 454.663 0.855 1.002 0.221 9.237-7.194 97.73 208 7 0.2443 381.045 377.085 0.908 1.002 0.140 7.162-5.571 100.00 427 22 0.2213 292.627 281.933 0.900 1.002 0.129 5.546-4.326 100.00 867 58 0.1183 401.705 398.033 0.951 1.002 0.129 4.315-3.360 100.00 1859 96 0.0990 382.024 378.997 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1195 250.970 249.087 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1052 166.370 165.478 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0979 81.247 81.509 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1230 36.028 35.663 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2115 22.700 21.337 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0348 ================= 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 : 0.2601 0.1924 0.084 5.139 8.8 119.3 19.9 258 0.000 1_bss: 0.1626 0.1735 0.084 5.139 9.1 119.5 20.1 258 0.000 1_settarget: 0.1626 0.1735 0.084 5.139 9.1 119.5 20.1 258 0.000 1_nqh: 0.1627 0.1737 0.084 5.139 9.1 119.5 20.1 258 0.003 1_weight: 0.1627 0.1737 0.084 5.139 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1459 0.007 0.930 9.1 119.5 20.1 258 0.130 1_adp: 0.1242 0.1529 0.007 0.930 8.7 118.8 21.2 258 0.130 1_regHadp: 0.1246 0.1534 0.007 0.930 8.7 118.8 21.2 258 0.130 1_occ: 0.1246 0.1539 0.007 0.930 8.7 118.8 21.2 258 0.130 2_bss: 0.1245 0.1531 0.007 0.930 8.8 118.8 21.3 258 0.130 2_settarget: 0.1245 0.1531 0.007 0.930 8.8 118.8 21.3 258 0.130 2_updatecdl: 0.1245 0.1531 0.007 0.933 8.8 118.8 21.3 258 0.130 2_nqh: 0.1247 0.1533 0.007 0.933 8.8 118.8 21.3 258 0.130 2_sol: 0.1237 0.1466 0.007 0.933 8.8 118.8 23.5 428 n/a 2_weight: 0.1237 0.1466 0.007 0.933 8.8 118.8 23.5 428 n/a 2_xyzrec: 0.1229 0.1495 0.007 0.885 8.8 118.8 23.5 428 n/a 2_adp: 0.1201 0.1481 0.007 0.885 8.5 113.8 23.1 428 n/a 2_regHadp: 0.1201 0.1481 0.007 0.885 8.5 113.8 23.1 428 n/a 2_occ: 0.1201 0.1473 0.007 0.885 8.5 113.8 23.1 428 n/a 3_bss: 0.1198 0.1470 0.007 0.885 8.5 113.9 23.2 428 n/a 3_settarget: 0.1198 0.1470 0.007 0.885 8.5 113.9 23.2 428 n/a 3_updatecdl: 0.1198 0.1470 0.007 0.886 8.5 113.9 23.2 428 n/a 3_nqh: 0.1198 0.1470 0.007 0.886 8.5 113.9 23.2 428 n/a 3_sol: 0.1221 0.1476 0.007 0.886 8.5 113.9 22.1 453 n/a 3_weight: 0.1221 0.1476 0.007 0.886 8.5 113.9 22.1 453 n/a 3_xyzrec: 0.1231 0.1441 0.006 0.920 8.5 113.9 22.1 453 n/a 3_adp: 0.1217 0.1398 0.006 0.920 9.1 108.9 21.8 453 n/a 3_regHadp: 0.1218 0.1398 0.006 0.920 9.1 108.9 21.8 453 n/a 3_occ: 0.1212 0.1400 0.006 0.920 9.1 108.9 21.8 453 n/a 4_bss: 0.1200 0.1391 0.006 0.920 9.1 108.9 21.8 453 n/a 4_settarget: 0.1200 0.1391 0.006 0.920 9.1 108.9 21.8 453 n/a 4_updatecdl: 0.1200 0.1391 0.006 0.919 9.1 108.9 21.8 453 n/a 4_nqh: 0.1200 0.1391 0.006 0.919 9.1 108.9 21.8 453 n/a 4_sol: 0.1194 0.1353 0.006 0.919 9.1 108.9 21.4 430 n/a 4_weight: 0.1194 0.1353 0.006 0.919 9.1 108.9 21.4 430 n/a 4_xyzrec: 0.1200 0.1360 0.006 0.961 9.1 108.9 21.4 430 n/a 4_adp: 0.1192 0.1360 0.006 0.961 9.2 104.8 21.2 430 n/a 4_regHadp: 0.1192 0.1361 0.006 0.961 9.2 104.8 21.2 430 n/a 4_occ: 0.1188 0.1358 0.006 0.961 9.2 104.8 21.2 430 n/a 5_bss: 0.1184 0.1362 0.006 0.961 9.2 104.7 21.2 430 n/a 5_settarget: 0.1184 0.1362 0.006 0.961 9.2 104.7 21.2 430 n/a 5_updatecdl: 0.1184 0.1362 0.006 0.962 9.2 104.7 21.2 430 n/a 5_setrh: 0.1185 0.1361 0.006 0.962 9.2 104.7 21.2 430 n/a 5_nqh: 0.1185 0.1361 0.006 0.962 9.2 104.7 21.2 430 n/a 5_sol: 0.1182 0.1354 0.006 0.962 9.2 104.7 21.3 446 n/a 5_weight: 0.1182 0.1354 0.006 0.962 9.2 104.7 21.3 446 n/a 5_xyzrec: 0.1205 0.1380 0.007 1.027 9.2 104.7 21.3 446 n/a 5_adp: 0.1206 0.1376 0.007 1.027 9.2 100.9 21.0 446 n/a 5_regHadp: 0.1206 0.1376 0.007 1.027 9.2 100.9 21.0 446 n/a 5_occ: 0.1198 0.1365 0.007 1.027 9.2 100.9 21.0 446 n/a end: 0.1198 0.1367 0.007 1.027 9.2 100.9 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6113322_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6113322_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9500 Refinement macro-cycles (run) : 3550.3400 Write final files (write_after_run_outputs) : 65.6600 Total : 3620.9500 Total CPU time: 60.97 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:00 PST -0800 (1735452720.58 s) Start R-work = 0.1626, R-free = 0.1735 Final R-work = 0.1198, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3760.57 seconds wall clock time: 67 minutes 13.98 seconds (4033.98 seconds total)