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_4426565.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_4426565.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4426565.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 3 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: 2.30, 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: 0.56 Conformation dependent library (CDL) restraints added in 217.4 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.86: 293 0.86 - 1.12: 1283 1.12 - 1.38: 539 1.38 - 1.64: 957 1.64 - 1.90: 81 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 1.331 1.591 -0.260 1.34e-02 5.57e+03 3.77e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.334 1.104 0.230 1.25e-02 6.40e+03 3.38e+02 bond pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " ideal model delta sigma weight residual 1.326 1.130 0.196 1.10e-02 8.26e+03 3.16e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.183 0.195 1.10e-02 8.26e+03 3.15e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.034 0.202 1.15e-02 7.56e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 2974 4.40 - 8.80: 1886 8.80 - 13.20: 737 13.20 - 17.60: 160 17.60 - 22.00: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.02 14.18 9.00e-01 1.23e+00 2.48e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 137.48 -15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" O SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " ideal model delta sigma weight residual 122.96 105.96 17.00 1.13e+00 7.83e-01 2.26e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.07 106.73 15.34 1.03e+00 9.43e-01 2.22e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.32 135.38 -16.06 1.12e+00 7.97e-01 2.06e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.43: 947 17.43 - 34.84: 110 34.84 - 52.25: 36 52.25 - 69.65: 16 69.65 - 87.06: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -156.63 -23.37 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.193: 92 0.193 - 0.385: 70 0.385 - 0.577: 51 0.577 - 0.769: 23 0.769 - 0.961: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA BLYS A 93 " pdb=" N BLYS A 93 " pdb=" C BLYS A 93 " pdb=" CB BLYS A 93 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.12e+01 chirality pdb=" CA ALA A 2 " pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CB ALA A 2 " both_signs ideal model delta sigma weight residual False 2.48 3.40 -0.92 2.00e-01 2.50e+01 2.10e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.053 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.117 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.108 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.029 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG BTYR A 67 " -0.097 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.142 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.107 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.98e-02 1.10e+02 pdb=" CG HIS A 126 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.044 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.121 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1105 2.33 - 2.90: 8231 2.90 - 3.47: 10484 3.47 - 4.03: 15091 4.03 - 4.60: 21643 Nonbonded interactions: 56554 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.767 2.100 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.802 2.270 -y,x-y-1,z+1/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.828 2.100 ... (remaining 56549 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_4426565_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= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792806 | | target function (ml) not normalized (work): 232657.475660 | | target function (ml) not normalized (free): 11842.586551 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3043 0.2101 6.9975 4.9503| | 2: 3.57 - 2.84 1.00 2876 122 0.2430 0.1876 4.3575 4.352| | 3: 2.84 - 2.48 1.00 2833 165 0.2379 0.1741 4.138 4.1772| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1333 3.8441 3.8206| | 5: 2.25 - 2.09 1.00 2756 127 0.2447 0.1621 3.8105 3.8272| | 6: 2.09 - 1.97 1.00 2846 113 0.2507 0.1800 3.4887 3.5444| | 7: 1.97 - 1.87 1.00 2787 165 0.2549 0.1829 3.1513 3.271| | 8: 1.87 - 1.79 1.00 2789 144 0.2464 0.1929 3.0805 3.1881| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.1844 2.9085 2.9308| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2172 2.8183 2.9595| | 11: 1.66 - 1.61 1.00 2740 147 0.2489 0.1648 2.778 2.7036| | 12: 1.61 - 1.56 1.00 2787 146 0.2533 0.2003 2.6336 2.6385| | 13: 1.56 - 1.52 1.00 2745 130 0.2641 0.1965 2.5734 2.6186| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.1910 2.5249 2.5572| | 15: 1.48 - 1.45 1.00 2738 128 0.2614 0.2158 2.4336 2.5122| | 16: 1.45 - 1.42 1.00 2756 161 0.2665 0.2262 2.3937 2.4986| | 17: 1.42 - 1.39 1.00 2785 139 0.2608 0.2004 2.3064 2.367| | 18: 1.39 - 1.36 1.00 2741 179 0.2653 0.2220 2.2712 2.3358| | 19: 1.36 - 1.34 1.00 2807 134 0.2649 0.2542 2.2556 2.3704| | 20: 1.34 - 1.32 1.00 2696 147 0.2615 0.2004 2.1949 2.158| | 21: 1.32 - 1.30 1.00 2785 112 0.2749 0.2418 2.1464 2.2028| | 22: 1.29 - 1.27 1.00 2704 152 0.2750 0.2447 2.1239 2.1595| | 23: 1.27 - 1.26 1.00 2802 156 0.2780 0.2136 2.1027 2.0747| | 24: 1.26 - 1.24 1.00 2744 132 0.2722 0.2424 2.0583 2.1034| | 25: 1.24 - 1.22 1.00 2734 148 0.2829 0.2366 2.0452 2.0582| | 26: 1.22 - 1.21 1.00 2727 135 0.2913 0.2350 2.0189 2.0789| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2507 2.0061 1.9711| | 28: 1.19 - 1.18 1.00 2671 147 0.2967 0.2710 1.9853 2.023| | 29: 1.18 - 1.16 1.00 2800 134 0.2912 0.2855 1.9565 2.0719| | 30: 1.16 - 1.15 1.00 2740 148 0.3052 0.2972 1.9271 2.0208| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.10 0.76 0.23 1518.32| | 2: 3.57 - 2.84 2876 122 0.80 26.40 1.27 0.23 1518.32| | 3: 2.84 - 2.48 2833 165 0.74 32.38 1.25 0.23 1260.10| | 4: 2.47 - 2.25 2825 136 0.81 26.07 1.26 0.25 589.98| | 5: 2.25 - 2.09 2756 127 0.77 29.66 1.28 0.25 589.98| | 6: 2.09 - 1.97 2846 113 0.83 23.20 1.28 0.25 324.13| | 7: 1.97 - 1.87 2787 165 0.90 17.09 1.28 0.26 97.40| | 8: 1.87 - 1.79 2789 144 0.85 21.88 1.25 0.26 97.40| | 9: 1.79 - 1.72 2745 138 0.88 18.86 1.23 0.25 57.98| | 10: 1.72 - 1.66 2789 158 0.86 20.41 1.22 0.25 50.09| | 11: 1.66 - 1.61 2740 147 0.85 21.67 1.23 0.25 48.23| | 12: 1.61 - 1.56 2787 146 0.89 18.39 1.24 0.25 29.31| | 13: 1.56 - 1.52 2745 130 0.86 20.61 1.25 0.25 29.31| | 14: 1.52 - 1.48 2803 134 0.86 20.82 1.24 0.25 26.38| | 15: 1.48 - 1.45 2738 128 0.87 20.42 1.23 0.25 21.01| | 16: 1.45 - 1.42 2756 161 0.85 21.80 1.23 0.25 21.01| | 17: 1.42 - 1.39 2785 139 0.86 20.87 1.23 0.25 17.72| | 18: 1.39 - 1.36 2741 179 0.86 21.15 1.23 0.25 15.81| | 19: 1.36 - 1.34 2807 134 0.86 21.70 1.22 0.25 15.81| | 20: 1.34 - 1.32 2696 147 0.87 20.44 1.19 0.25 12.81| | 21: 1.32 - 1.30 2785 112 0.86 22.00 1.21 0.25 12.60| | 22: 1.29 - 1.27 2704 152 0.86 22.10 1.22 0.25 12.25| | 23: 1.27 - 1.26 2802 156 0.86 21.40 1.21 0.24 10.47| | 24: 1.26 - 1.24 2744 132 0.86 21.99 1.19 0.24 10.47| | 25: 1.24 - 1.22 2734 148 0.85 22.97 1.21 0.24 10.13| | 26: 1.22 - 1.21 2727 135 0.84 23.97 1.20 0.23 9.76| | 27: 1.21 - 1.19 2814 148 0.83 24.62 1.20 0.23 9.76| | 28: 1.19 - 1.18 2671 147 0.82 26.16 1.18 0.23 9.81| | 29: 1.18 - 1.16 2800 134 0.81 26.95 1.16 0.22 9.83| | 30: 1.16 - 1.15 2740 148 0.79 28.61 1.16 0.22 9.83| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.76 max = 1518.32 mean = 220.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.79| |phase err.(test): min = 0.00 max = 89.87 mean = 22.64| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.260 1557 Z= 5.645 Angle : 5.327 18.348 2118 Z= 3.706 Chirality : 0.379 0.961 243 Planarity : 0.029 0.128 284 Dihedral : 13.731 87.063 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 25.41 % 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: -2.74 (0.46), residues: 224 helix: -2.53 (0.34), residues: 109 sheet: -0.74 (0.77), residues: 40 loop : -0.85 (0.65), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.025 ARG A 28 TYR 0.079 0.025 TYR A 139 PHE 0.093 0.035 PHE A 119 HIS 0.067 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1953 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792806 | | target function (ml) not normalized (work): 232657.475660 | | target function (ml) not normalized (free): 11842.586551 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2608 0.1953 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2608 0.1953 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1953 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2006 0.2010 0.1967 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1761 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1642 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 0.3904 386.357 358.262 0.677 1.003 0.407 11.894-9.307 99.02 97 4 0.1864 613.709 596.170 0.932 1.004 0.390 9.237-7.194 100.00 213 7 0.2126 501.938 491.493 0.963 1.004 0.354 7.162-5.571 100.00 427 22 0.2210 376.677 362.536 0.933 1.004 0.320 5.546-4.326 100.00 867 58 0.1282 517.084 511.874 0.959 1.004 0.209 4.315-3.360 100.00 1859 96 0.1155 491.751 487.557 1.008 1.003 0.179 3.356-2.611 100.00 3867 181 0.1439 323.055 319.714 0.998 1.002 0.089 2.608-2.026 99.99 8198 413 0.1347 214.156 212.070 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1666 104.583 103.827 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2067 46.376 45.073 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2583 29.220 26.951 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1761 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1644 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.445880 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.195538 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1463 0.0251 0.007 0.9 1.0 0.5 0.0 0 12.223 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.63 2.51 3.013 19.051 2011.196 0.017 12.39 15.35 2.96 3.054 19.436 2011.196 0.016 Individual atomic B min max mean iso aniso Overall: 8.39 118.34 20.81 2.89 0 1785 Protein: 8.39 118.34 17.71 2.89 0 1519 Water: 11.05 114.93 38.83 N/A 0 258 Other: 22.35 34.91 28.15 N/A 0 8 Chain A: 8.39 118.34 20.81 N/A 0 1785 Histogram: Values Number of atoms 8.39 - 19.39 1211 19.39 - 30.38 234 30.38 - 41.38 161 41.38 - 52.37 97 52.37 - 63.36 53 63.36 - 74.36 18 74.36 - 85.35 4 85.35 - 96.35 4 96.35 - 107.34 0 107.34 - 118.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1535 r_work=0.1244 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1244 r_free = 0.1539 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 = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 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= 0.1542 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015433 | | target function (ls_wunit_k1) not normalized (work): 1285.534183 | | target function (ls_wunit_k1) not normalized (free): 113.612751 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1542 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1690 0.1689 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1690 0.1689 0.1765 n_refl.: 87593 overall B=0.18 to atoms: r(all,work,free)=0.1719 0.1718 0.1785 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1242 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1242 0.1536 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 0.3566 300.143 279.200 0.629 1.002 0.372 11.894-9.307 99.02 97 4 0.1625 480.813 469.858 0.906 1.003 0.367 9.237-7.194 100.00 213 7 0.1830 393.246 388.054 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1741 295.109 290.011 0.921 1.003 0.290 5.546-4.326 100.00 867 58 0.0931 405.112 402.421 0.947 1.003 0.204 4.315-3.360 100.00 1859 96 0.0781 385.264 384.369 0.994 1.003 0.189 3.356-2.611 100.00 3867 181 0.1022 253.099 252.412 0.996 1.002 0.052 2.608-2.026 99.99 8198 413 0.0970 167.781 167.233 1.007 1.002 0.000 2.025-1.573 100.00 17313 902 0.1204 81.936 82.130 1.015 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1647 36.334 35.793 1.004 0.998 0.000 1.221-1.150 99.97 13689 708 0.2363 22.893 21.393 0.968 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0414 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1242 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1242 r_free=0.1537 | n_water=258 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1251 r_free=0.1533 | n_water=252 | time (s): 25.430 (total time: 27.700) Filter (q & B) r_work=0.1254 r_free=0.1533 | n_water=249 | time (s): 3.540 (total time: 31.240) Compute maps r_work=0.1254 r_free=0.1533 | n_water=249 | time (s): 1.790 (total time: 33.030) Filter (map) r_work=0.1272 r_free=0.1538 | n_water=235 | time (s): 3.640 (total time: 36.670) Find peaks r_work=0.1272 r_free=0.1538 | n_water=235 | time (s): 0.720 (total time: 37.390) Add new water r_work=0.1427 r_free=0.1705 | n_water=454 | time (s): 3.590 (total time: 40.980) Refine new water occ: r_work=0.1333 r_free=0.1564 adp: r_work=0.1251 r_free=0.1515 occ: r_work=0.1264 r_free=0.1509 adp: r_work=0.1227 r_free=0.1495 occ: r_work=0.1231 r_free=0.1482 adp: r_work=0.1221 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1485 r_work=0.1221 r_free=0.1485 | n_water=454 | time (s): 72.000 (total time: 112.980) Filter (q & B) r_work=0.1227 r_free=0.1490 | n_water=433 | time (s): 4.050 (total time: 117.030) Filter (dist only) r_work=0.1227 r_free=0.1490 | n_water=433 | time (s): 41.200 (total time: 158.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.559088 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1544.039847 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 0.1516 0.0289 0.007 0.9 2.6 0.5 0.0 0 12.280 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.16 2.89 3.765 22.987 1544.040 0.015 12.00 14.87 2.87 4.072 22.840 1544.040 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.76 23.04 2.59 198 1762 Protein: 8.70 114.76 17.58 2.59 0 1519 Water: 10.89 73.76 42.03 N/A 198 235 Other: 25.07 37.18 30.38 N/A 0 8 Chain A: 8.70 114.76 20.26 N/A 0 1762 Chain S: 15.00 69.74 47.74 N/A 198 0 Histogram: Values Number of atoms 8.70 - 19.31 1211 19.31 - 29.91 248 29.91 - 40.52 197 40.52 - 51.13 143 51.13 - 61.73 97 61.73 - 72.34 53 72.34 - 82.95 5 82.95 - 93.55 3 93.55 - 104.16 1 104.16 - 114.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1488 r_work=0.1200 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1487 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 = 0.18 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): 0.014208 | | target function (ls_wunit_k1) not normalized (work): 1183.436860 | | target function (ls_wunit_k1) not normalized (free): 103.169428 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1201 0.1473 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1601 0.1731 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1601 0.1731 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1613 0.1608 0.1736 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1197 0.1474 n_refl.: 87592 remove outliers: r(all,work,free)=0.1209 0.1196 0.1474 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 0.3384 296.065 270.917 0.628 0.938 0.364 11.894-9.307 99.02 97 4 0.1542 480.813 478.033 0.971 0.939 0.360 9.237-7.194 100.00 213 7 0.1732 393.246 393.823 1.047 0.939 0.290 7.162-5.571 100.00 427 22 0.1531 295.109 290.912 0.999 0.939 0.240 5.546-4.326 100.00 867 58 0.0845 405.112 402.242 1.020 0.940 0.215 4.315-3.360 100.00 1859 96 0.0721 385.264 384.340 1.068 0.940 0.210 3.356-2.611 100.00 3867 181 0.0973 253.099 252.371 1.074 0.941 0.067 2.608-2.026 99.99 8198 413 0.0951 167.781 167.340 1.080 0.943 0.000 2.025-1.573 100.00 17313 902 0.1168 81.936 82.156 1.086 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1602 36.334 35.851 1.068 0.949 0.000 1.221-1.150 99.97 13689 708 0.2338 22.893 21.439 1.021 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0660 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1474 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=0.1196 r_free=0.1474 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1474 | n_water=433 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1195 r_free=0.1471 | n_water=431 | time (s): 41.320 (total time: 43.210) Filter (q & B) r_work=0.1196 r_free=0.1473 | n_water=430 | time (s): 2.530 (total time: 45.740) Compute maps r_work=0.1196 r_free=0.1473 | n_water=430 | time (s): 1.280 (total time: 47.020) Filter (map) r_work=0.1235 r_free=0.1486 | n_water=299 | time (s): 2.430 (total time: 49.450) Find peaks r_work=0.1235 r_free=0.1486 | n_water=299 | time (s): 0.530 (total time: 49.980) Add new water r_work=0.1355 r_free=0.1591 | n_water=483 | time (s): 2.300 (total time: 52.280) Refine new water occ: r_work=0.1256 r_free=0.1497 adp: r_work=0.1258 r_free=0.1498 occ: r_work=0.1236 r_free=0.1481 adp: r_work=0.1234 r_free=0.1481 occ: r_work=0.1222 r_free=0.1467 adp: r_work=0.1215 r_free=0.1465 ADP+occupancy (water only), MIN, final r_work=0.1215 r_free=0.1465 r_work=0.1215 r_free=0.1465 | n_water=483 | time (s): 169.400 (total time: 221.680) Filter (q & B) r_work=0.1220 r_free=0.1469 | n_water=447 | time (s): 2.600 (total time: 224.280) Filter (dist only) r_work=0.1220 r_free=0.1469 | n_water=447 | time (s): 35.520 (total time: 259.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.949461 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.747761 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 0.1225 0.1447 0.0223 0.006 0.9 2.6 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.47 2.23 3.605 22.062 51.748 3.723 12.10 14.10 1.99 4.139 21.865 51.748 3.653 Individual atomic B min max mean iso aniso Overall: 9.21 110.25 21.62 2.33 215 1759 Protein: 9.21 110.25 17.14 2.33 0 1519 Water: 11.40 72.54 36.77 N/A 215 232 Other: 20.89 33.30 27.05 N/A 0 8 Chain A: 9.21 110.25 19.76 N/A 0 1759 Chain S: 15.99 63.82 36.83 N/A 215 0 Histogram: Values Number of atoms 9.21 - 19.32 1238 19.32 - 29.42 271 29.42 - 39.53 216 39.53 - 49.63 137 49.63 - 59.73 79 59.73 - 69.84 22 69.84 - 79.94 5 79.94 - 90.05 3 90.05 - 100.15 1 100.15 - 110.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1410 r_work=0.1212 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1411 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1407 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.18 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= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650489 | | target function (ml) not normalized (work): 304060.161138 | | target function (ml) not normalized (free): 16058.664967 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1205 0.1407 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1535 0.1533 0.1599 n_refl.: 87589 remove outliers: r(all,work,free)=0.1535 0.1533 0.1599 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1533 0.1531 0.1597 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1376 n_refl.: 87589 remove outliers: r(all,work,free)=0.1202 0.1193 0.1376 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3829 295.428 258.940 0.478 0.999 0.320 11.894-9.307 96.08 94 4 0.2174 479.865 462.322 0.861 1.001 0.320 9.237-7.194 98.18 209 7 0.2313 384.756 387.346 0.943 1.002 0.200 7.162-5.571 100.00 427 22 0.2079 295.109 284.715 0.910 1.002 0.190 5.546-4.326 100.00 867 58 0.1103 405.112 400.624 0.952 1.002 0.168 4.315-3.360 100.00 1859 96 0.0938 385.264 382.863 0.993 1.002 0.157 3.356-2.611 100.00 3867 181 0.1154 253.099 251.345 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1051 167.781 166.805 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1000 81.936 82.117 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1284 36.334 35.922 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2127 22.893 21.507 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=-0.0284 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1376 | n_water=447 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1194 r_free=0.1377 | n_water=445 | time (s): 40.280 (total time: 41.940) Filter (q & B) r_work=0.1194 r_free=0.1377 | n_water=445 | time (s): 0.760 (total time: 42.700) Compute maps r_work=0.1194 r_free=0.1377 | n_water=445 | time (s): 1.390 (total time: 44.090) Filter (map) r_work=0.1221 r_free=0.1390 | n_water=305 | time (s): 2.590 (total time: 46.680) Find peaks r_work=0.1221 r_free=0.1390 | n_water=305 | time (s): 0.430 (total time: 47.110) Add new water r_work=0.1295 r_free=0.1468 | n_water=467 | time (s): 2.730 (total time: 49.840) Refine new water occ: r_work=0.1217 r_free=0.1394 adp: r_work=0.1218 r_free=0.1396 occ: r_work=0.1201 r_free=0.1373 adp: r_work=0.1199 r_free=0.1376 occ: r_work=0.1189 r_free=0.1365 adp: r_work=0.1185 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1364 r_work=0.1185 r_free=0.1364 | n_water=467 | time (s): 159.460 (total time: 209.300) Filter (q & B) r_work=0.1192 r_free=0.1366 | n_water=432 | time (s): 2.670 (total time: 211.970) Filter (dist only) r_work=0.1192 r_free=0.1366 | n_water=432 | time (s): 33.760 (total time: 245.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.001365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.530642 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 0.1197 0.1367 0.0170 0.006 1.0 1.6 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.67 1.70 3.414 21.326 38.531 3.639 11.96 13.66 1.70 3.595 21.263 38.531 3.633 Individual atomic B min max mean iso aniso Overall: 9.24 106.16 21.11 2.15 204 1755 Protein: 9.24 106.16 17.00 2.16 0 1519 Water: 11.42 72.02 35.46 N/A 204 228 Other: 21.29 31.09 26.57 N/A 0 8 Chain A: 9.24 106.16 19.52 N/A 0 1755 Chain S: 15.66 64.01 34.74 N/A 204 0 Histogram: Values Number of atoms 9.24 - 18.94 1230 18.94 - 28.63 282 28.63 - 38.32 215 38.32 - 48.01 126 48.01 - 57.70 67 57.70 - 67.39 26 67.39 - 77.09 8 77.09 - 86.78 2 86.78 - 96.47 1 96.47 - 106.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1366 r_work=0.1197 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1366 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1371 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.632028 | | target function (ml) not normalized (work): 302486.218342 | | target function (ml) not normalized (free): 15987.906423 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1193 0.1371 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1514 0.1513 0.1573 n_refl.: 87579 remove outliers: r(all,work,free)=0.1514 0.1513 0.1573 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1511 0.1571 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1191 0.1376 n_refl.: 87579 remove outliers: r(all,work,free)=0.1198 0.1189 0.1376 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3971 295.428 260.285 0.465 1.001 0.308 11.894-9.307 92.16 90 4 0.2011 480.931 459.990 0.856 1.002 0.300 9.237-7.194 98.18 209 7 0.2476 384.756 379.882 0.916 1.002 0.140 7.162-5.571 100.00 427 22 0.2143 295.109 284.953 0.902 1.002 0.140 5.546-4.326 100.00 867 58 0.1147 405.112 400.535 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0959 385.264 382.930 0.993 1.002 0.132 3.356-2.611 100.00 3867 181 0.1179 253.099 251.322 1.001 1.002 0.053 2.608-2.026 99.99 8198 413 0.1044 167.781 166.884 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.936 82.234 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.334 35.960 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2120 22.893 21.515 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0332 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1376 After: r_work=0.1190 r_free=0.1376 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1376 | n_water=432 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1190 r_free=0.1376 | n_water=432 | time (s): 34.260 (total time: 36.090) Filter (q & B) r_work=0.1191 r_free=0.1378 | n_water=428 | time (s): 2.600 (total time: 38.690) Compute maps r_work=0.1191 r_free=0.1378 | n_water=428 | time (s): 1.070 (total time: 39.760) Filter (map) r_work=0.1215 r_free=0.1385 | n_water=326 | time (s): 2.470 (total time: 42.230) Find peaks r_work=0.1215 r_free=0.1385 | n_water=326 | time (s): 0.440 (total time: 42.670) Add new water r_work=0.1272 r_free=0.1452 | n_water=493 | time (s): 2.370 (total time: 45.040) Refine new water occ: r_work=0.1204 r_free=0.1377 adp: r_work=0.1204 r_free=0.1379 occ: r_work=0.1191 r_free=0.1362 adp: r_work=0.1191 r_free=0.1364 occ: r_work=0.1181 r_free=0.1351 adp: r_work=0.1179 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1352 r_work=0.1179 r_free=0.1352 | n_water=493 | time (s): 164.200 (total time: 209.240) Filter (q & B) r_work=0.1187 r_free=0.1358 | n_water=444 | time (s): 3.170 (total time: 212.410) Filter (dist only) r_work=0.1187 r_free=0.1356 | n_water=443 | time (s): 38.430 (total time: 250.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.200545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.185468 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 0.1209 0.1380 0.0171 0.007 1.1 4.8 0.5 0.0 0 1.100 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.80 1.71 3.313 21.145 36.185 3.637 12.14 13.87 1.74 3.683 21.032 36.185 3.633 Individual atomic B min max mean iso aniso Overall: 9.25 101.20 20.85 1.99 216 1754 Protein: 9.25 101.20 16.72 1.99 0 1519 Water: 11.37 71.02 34.94 N/A 216 227 Other: 21.12 29.80 26.03 N/A 0 8 Chain A: 9.25 101.20 19.21 N/A 0 1754 Chain S: 15.24 64.64 34.18 N/A 216 0 Histogram: Values Number of atoms 9.25 - 18.44 1219 18.44 - 27.64 282 27.64 - 36.83 223 36.83 - 46.03 142 46.03 - 55.22 63 55.22 - 64.42 25 64.42 - 73.61 12 73.61 - 82.81 1 82.81 - 92.00 1 92.00 - 101.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1387 r_work=0.1214 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1214 r_free = 0.1388 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1383 target_work(ml) = 3.631 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1210 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.631309 | | target function (ml) not normalized (work): 302411.771035 | | target function (ml) not normalized (free): 15974.235618 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1446 0.1445 5.705 5.6707| | 2: 3.57 - 2.84 1.00 2888 124 0.1139 0.1506 5.2261 5.3| | 3: 2.83 - 2.48 1.00 2820 163 0.1231 0.1291 5.0303 5.0428| | 4: 2.47 - 2.25 1.00 2825 136 0.1047 0.1147 4.7322 4.7737| | 5: 2.25 - 2.09 1.00 2756 127 0.1010 0.1106 4.673 4.739| | 6: 2.09 - 1.97 1.00 2846 113 0.0986 0.1196 4.369 4.4956| | 7: 1.97 - 1.87 1.00 2787 165 0.0989 0.1261 4.0775 4.2024| | 8: 1.87 - 1.79 1.00 2789 144 0.1032 0.1243 3.9964 4.0716| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1263 3.7214 3.877| | 10: 1.72 - 1.66 1.00 2831 160 0.1001 0.1271 3.6365 3.7841| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1090 3.5722 3.6078| | 12: 1.61 - 1.56 1.00 2773 144 0.0924 0.1147 3.3564 3.4642| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1078 3.3401 3.4391| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1160 3.2636 3.3643| | 15: 1.48 - 1.45 1.00 2738 128 0.1024 0.1324 3.1775 3.3227| | 16: 1.45 - 1.42 1.00 2756 161 0.1080 0.1258 3.1589 3.2498| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1282 3.1217 3.2308| | 18: 1.39 - 1.36 1.00 2741 179 0.1163 0.1385 3.0948 3.2622| | 19: 1.36 - 1.34 1.00 2807 134 0.1231 0.1623 3.1035 3.2836| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1461 3.0972 3.1388| | 21: 1.32 - 1.30 1.00 2785 112 0.1422 0.1638 3.0954 3.1767| | 22: 1.29 - 1.27 1.00 2704 152 0.1484 0.1934 3.0931 3.2895| | 23: 1.27 - 1.26 1.00 2802 156 0.1584 0.1891 3.1102 3.2211| | 24: 1.26 - 1.24 1.00 2744 132 0.1622 0.1767 3.1002 3.1975| | 25: 1.24 - 1.22 1.00 2733 148 0.1797 0.2309 3.1167 3.2859| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1781 3.1283 3.2076| | 27: 1.21 - 1.19 1.00 2814 148 0.2017 0.2089 3.1454 3.1545| | 28: 1.19 - 1.18 1.00 2671 147 0.2152 0.2282 3.1456 3.1669| | 29: 1.18 - 1.16 1.00 2800 134 0.2221 0.2404 3.1336 3.2385| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2512 3.1226 3.1756| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.94 9.52 1.00 0.97 6710.26| | 2: 3.57 - 2.84 2888 124 0.92 13.94 1.01 0.97 6710.26| | 3: 2.83 - 2.48 2820 163 0.88 18.02 0.99 0.97 5616.22| | 4: 2.47 - 2.25 2825 136 0.91 15.09 1.00 0.98 2795.01| | 5: 2.25 - 2.09 2756 127 0.89 17.29 1.01 0.98 2795.01| | 6: 2.09 - 1.97 2846 113 0.91 13.84 1.02 0.98 1626.77| | 7: 1.97 - 1.87 2787 165 0.94 10.74 1.02 0.98 630.41| | 8: 1.87 - 1.79 2789 144 0.91 14.40 1.00 0.98 630.41| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.98 339.88| | 10: 1.72 - 1.66 2831 160 0.93 12.18 0.98 0.98 281.70| | 11: 1.66 - 1.61 2712 147 0.93 12.81 0.98 0.98 268.87| | 12: 1.61 - 1.56 2773 144 0.95 9.43 0.99 0.98 147.82| | 13: 1.56 - 1.52 2745 130 0.94 11.07 1.02 0.98 147.82| | 14: 1.52 - 1.48 2803 134 0.94 11.21 1.02 0.98 132.31| | 15: 1.48 - 1.45 2738 128 0.95 10.40 1.02 0.99 103.92| | 16: 1.45 - 1.42 2756 161 0.94 11.57 1.02 0.99 103.92| | 17: 1.42 - 1.39 2785 139 0.94 11.42 1.01 0.99 94.05| | 18: 1.39 - 1.36 2741 179 0.94 11.79 1.01 0.99 88.33| | 19: 1.36 - 1.34 2807 134 0.94 12.33 1.00 0.99 88.33| | 20: 1.34 - 1.32 2696 147 0.94 12.46 0.99 0.97 83.52| | 21: 1.32 - 1.30 2785 112 0.93 13.40 0.98 0.97 83.18| | 22: 1.29 - 1.27 2704 152 0.93 13.93 0.98 0.97 83.36| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 84.28| | 24: 1.26 - 1.24 2744 132 0.92 15.03 0.97 0.95 84.28| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.96 0.94 85.98| | 26: 1.22 - 1.21 2727 135 0.90 18.20 1.02 0.94 87.87| | 27: 1.21 - 1.19 2814 148 0.89 18.87 1.02 0.94 87.87| | 28: 1.19 - 1.18 2671 147 0.88 20.43 1.01 0.93 91.52| | 29: 1.18 - 1.16 2800 134 0.88 20.77 0.99 0.93 92.90| | 30: 1.16 - 1.15 2739 148 0.86 22.16 0.98 0.93 92.90| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 83.18 max = 6710.26 mean = 1034.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.15| |phase err.(test): min = 0.00 max = 88.47 mean = 14.28| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1210 0.1383 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1525 0.1525 0.1561 n_refl.: 87575 remove outliers: r(all,work,free)=0.1525 0.1525 0.1561 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1522 0.1522 0.1559 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1210 0.1384 n_refl.: 87575 remove outliers: r(all,work,free)=0.1217 0.1209 0.1384 n_refl.: 87572 ======================== 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 0.4309 295.428 253.443 0.437 1.002 0.320 11.894-9.307 91.18 89 4 0.2282 474.332 450.698 0.850 1.003 0.320 9.237-7.194 97.27 207 7 0.2542 385.359 378.174 0.900 1.003 0.120 7.162-5.571 100.00 427 22 0.2340 295.109 283.008 0.889 1.003 0.120 5.546-4.326 100.00 867 58 0.1225 405.112 400.281 0.952 1.003 0.120 4.315-3.360 100.00 1859 96 0.1002 385.264 382.606 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1202 253.099 250.988 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1055 167.781 166.779 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0980 81.936 82.206 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.334 35.962 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.893 21.505 0.980 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 : 0.2608 0.1953 0.083 5.327 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1761 0.083 5.327 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1761 0.083 5.327 9.0 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1768 0.083 5.327 9.0 119.5 20.1 258 0.006 1_weight: 0.1644 0.1768 0.083 5.327 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1212 0.1463 0.007 0.939 9.0 119.5 20.1 258 0.129 1_adp: 0.1240 0.1535 0.007 0.939 8.4 118.3 20.8 258 0.129 1_regHadp: 0.1244 0.1539 0.007 0.939 8.4 118.3 20.8 258 0.129 1_occ: 0.1244 0.1542 0.007 0.939 8.4 118.3 20.8 258 0.129 2_bss: 0.1242 0.1536 0.007 0.939 8.6 118.5 21.0 258 0.129 2_settarget: 0.1242 0.1536 0.007 0.939 8.6 118.5 21.0 258 0.129 2_updatecdl: 0.1242 0.1536 0.007 0.955 8.6 118.5 21.0 258 0.129 2_nqh: 0.1242 0.1537 0.007 0.955 8.6 118.5 21.0 258 0.127 2_sol: 0.1227 0.1490 0.007 0.955 8.6 118.5 23.3 433 n/a 2_weight: 0.1227 0.1490 0.007 0.955 8.6 118.5 23.3 433 n/a 2_xyzrec: 0.1227 0.1516 0.007 0.876 8.6 118.5 23.3 433 n/a 2_adp: 0.1200 0.1488 0.007 0.876 8.7 114.8 23.0 433 n/a 2_regHadp: 0.1200 0.1487 0.007 0.876 8.7 114.8 23.0 433 n/a 2_occ: 0.1201 0.1473 0.007 0.876 8.7 114.8 23.0 433 n/a 3_bss: 0.1196 0.1474 0.007 0.876 8.7 114.8 23.1 433 n/a 3_settarget: 0.1196 0.1474 0.007 0.876 8.7 114.8 23.1 433 n/a 3_updatecdl: 0.1196 0.1474 0.007 0.876 8.7 114.8 23.1 433 n/a 3_nqh: 0.1196 0.1474 0.007 0.876 8.7 114.8 23.1 433 n/a 3_sol: 0.1220 0.1469 0.007 0.876 8.7 114.8 22.0 447 n/a 3_weight: 0.1220 0.1469 0.007 0.876 8.7 114.8 22.0 447 n/a 3_xyzrec: 0.1225 0.1447 0.006 0.916 8.7 114.8 22.0 447 n/a 3_adp: 0.1211 0.1410 0.006 0.916 9.2 110.3 21.6 447 n/a 3_regHadp: 0.1212 0.1411 0.006 0.916 9.2 110.3 21.6 447 n/a 3_occ: 0.1205 0.1407 0.006 0.916 9.2 110.3 21.6 447 n/a 4_bss: 0.1193 0.1376 0.006 0.916 9.2 110.2 21.6 447 n/a 4_settarget: 0.1193 0.1376 0.006 0.916 9.2 110.2 21.6 447 n/a 4_updatecdl: 0.1193 0.1376 0.006 0.914 9.2 110.2 21.6 447 n/a 4_nqh: 0.1193 0.1376 0.006 0.914 9.2 110.2 21.6 447 n/a 4_sol: 0.1192 0.1366 0.006 0.914 9.2 110.2 21.2 432 n/a 4_weight: 0.1192 0.1366 0.006 0.914 9.2 110.2 21.2 432 n/a 4_xyzrec: 0.1197 0.1367 0.006 0.952 9.2 110.2 21.2 432 n/a 4_adp: 0.1196 0.1366 0.006 0.952 9.2 106.2 21.1 432 n/a 4_regHadp: 0.1197 0.1366 0.006 0.952 9.2 106.2 21.1 432 n/a 4_occ: 0.1193 0.1371 0.006 0.952 9.2 106.2 21.1 432 n/a 5_bss: 0.1189 0.1376 0.006 0.952 9.2 106.1 21.1 432 n/a 5_settarget: 0.1189 0.1376 0.006 0.952 9.2 106.1 21.1 432 n/a 5_updatecdl: 0.1189 0.1376 0.006 0.953 9.2 106.1 21.1 432 n/a 5_setrh: 0.1190 0.1376 0.006 0.953 9.2 106.1 21.1 432 n/a 5_nqh: 0.1190 0.1376 0.006 0.953 9.2 106.1 21.1 432 n/a 5_sol: 0.1187 0.1356 0.006 0.953 9.2 106.1 21.1 443 n/a 5_weight: 0.1187 0.1356 0.006 0.953 9.2 106.1 21.1 443 n/a 5_xyzrec: 0.1209 0.1380 0.007 1.114 9.2 106.1 21.1 443 n/a 5_adp: 0.1214 0.1387 0.007 1.114 9.2 101.2 20.9 443 n/a 5_regHadp: 0.1214 0.1388 0.007 1.114 9.2 101.2 20.9 443 n/a 5_occ: 0.1210 0.1383 0.007 1.114 9.2 101.2 20.9 443 n/a end: 0.1209 0.1384 0.007 1.114 9.2 101.2 20.8 443 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4426565_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4426565_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8000 Refinement macro-cycles (run) : 3295.5600 Write final files (write_after_run_outputs) : 73.2100 Total : 3373.5700 Total CPU time: 56.84 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:37 PST -0800 (1735452517.29 s) Start R-work = 0.1642, R-free = 0.1761 Final R-work = 0.1209, R-free = 0.1384 =============================================================================== Job complete usr+sys time: 3531.56 seconds wall clock time: 64 minutes 9.74 seconds (3849.74 seconds total)