Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.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 { 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_2514713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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: 2.47, per 1000 atoms: 0.73 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: 0.79 Conformation dependent library (CDL) restraints added in 264.9 milliseconds Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.42: 642 1.42 - 1.67: 817 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.444 1.695 -0.251 1.38e-02 5.25e+03 3.31e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.529 -0.193 1.11e-02 8.12e+03 3.01e+02 bond pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 1.459 1.235 0.224 1.32e-02 5.74e+03 2.88e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.17e-02 7.31e+03 2.65e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.652 -0.193 1.21e-02 6.83e+03 2.53e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 3049 4.68 - 9.35: 1933 9.35 - 14.03: 681 14.03 - 18.71: 104 18.71 - 23.38: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 120.55 138.65 -18.10 1.06e+00 8.90e-01 2.92e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.63 -14.51 1.06e+00 8.90e-01 1.87e+02 angle pdb=" O ALA A 61 " pdb=" C ALA A 61 " pdb=" N LYS A 62 " ideal model delta sigma weight residual 122.33 140.46 -18.13 1.34e+00 5.57e-01 1.83e+02 angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 117.30 102.08 15.22 1.16e+00 7.43e-01 1.72e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.55 106.79 13.76 1.06e+00 8.90e-01 1.68e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 918 16.43 - 32.87: 137 32.87 - 49.30: 40 49.30 - 65.73: 13 65.73 - 82.16: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+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 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.251: 103 0.251 - 0.500: 86 0.500 - 0.750: 42 0.750 - 0.999: 9 0.999 - 1.248: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 178 " pdb=" N ALA A 178 " pdb=" C ALA A 178 " pdb=" CB ALA A 178 " both_signs ideal model delta sigma weight residual False 2.48 3.73 -1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.095 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.147 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.001 2.00e-02 2.50e+03 5.66e-02 9.60e+01 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.071 2.00e-02 2.50e+03 5.58e-02 9.33e+01 pdb=" CG PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 782 2.28 - 2.86: 7820 2.86 - 3.44: 10665 3.44 - 4.02: 15303 4.02 - 4.60: 22068 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.700 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.806 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.822 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.833 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.839 2.100 ... (remaining 56633 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_2514713_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= 0.2613 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793216 | | target function (ml) not normalized (work): 232691.668698 | | target function (ml) not normalized (free): 11788.630217 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3028 0.2052 7.099 4.9369| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1769 4.3431 4.3477| | 3: 2.84 - 2.48 1.00 2833 165 0.2382 0.1711 4.1241 4.1616| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1463 3.8298 3.8312| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1719 3.7935 3.8161| | 6: 2.09 - 1.97 1.00 2846 113 0.2538 0.1728 3.4681 3.5016| | 7: 1.97 - 1.87 1.00 2787 165 0.2528 0.1881 3.1387 3.2411| | 8: 1.87 - 1.79 1.00 2789 144 0.2448 0.1895 3.0576 3.1572| | 9: 1.79 - 1.72 1.00 2745 138 0.2434 0.1715 2.9107 2.864| | 10: 1.72 - 1.66 1.00 2789 158 0.2415 0.1949 2.7981 2.8895| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1864 2.7379 2.7625| | 12: 1.61 - 1.56 1.00 2787 146 0.2524 0.1778 2.6319 2.5503| | 13: 1.56 - 1.52 1.00 2745 130 0.2557 0.1802 2.5834 2.5962| | 14: 1.52 - 1.48 1.00 2803 134 0.2596 0.2132 2.4957 2.5883| | 15: 1.48 - 1.45 1.00 2738 128 0.2575 0.2108 2.4387 2.5288| | 16: 1.45 - 1.42 1.00 2756 161 0.2712 0.2136 2.4137 2.4306| | 17: 1.42 - 1.39 1.00 2785 139 0.2687 0.2096 2.3306 2.3396| | 18: 1.39 - 1.36 1.00 2741 179 0.2739 0.2143 2.2817 2.3264| | 19: 1.36 - 1.34 1.00 2807 134 0.2690 0.2179 2.2469 2.2508| | 20: 1.34 - 1.32 1.00 2696 147 0.2678 0.2099 2.1958 2.1896| | 21: 1.32 - 1.30 1.00 2785 112 0.2735 0.2192 2.1623 2.1604| | 22: 1.29 - 1.27 1.00 2704 152 0.2780 0.2775 2.135 2.2447| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2433 2.0809 2.1748| | 24: 1.26 - 1.24 1.00 2744 132 0.2796 0.2591 2.0763 2.1499| | 25: 1.24 - 1.22 1.00 2734 148 0.2881 0.2492 2.0494 2.0459| | 26: 1.22 - 1.21 1.00 2727 135 0.2875 0.2239 2.017 2.0928| | 27: 1.21 - 1.19 1.00 2814 148 0.2997 0.2569 2.0135 1.9962| | 28: 1.19 - 1.18 1.00 2671 147 0.3012 0.2965 1.9924 2.0469| | 29: 1.18 - 1.16 1.00 2800 134 0.2932 0.2555 1.9538 2.0057| | 30: 1.16 - 1.15 1.00 2740 148 0.3130 0.2746 1.9401 1.9273| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.65 0.76 0.23 1466.21| | 2: 3.57 - 2.84 2876 122 0.80 25.98 1.27 0.23 1466.21| | 3: 2.84 - 2.48 2833 165 0.74 31.90 1.24 0.24 1216.55| | 4: 2.47 - 2.25 2825 136 0.81 25.41 1.26 0.25 568.64| | 5: 2.25 - 2.09 2756 127 0.77 29.23 1.28 0.25 568.64| | 6: 2.09 - 1.97 2846 113 0.83 22.63 1.29 0.25 311.98| | 7: 1.97 - 1.87 2787 165 0.90 16.71 1.28 0.26 93.09| | 8: 1.87 - 1.79 2789 144 0.85 21.39 1.24 0.26 93.09| | 9: 1.79 - 1.72 2745 138 0.88 18.42 1.23 0.25 55.32| | 10: 1.72 - 1.66 2789 158 0.87 20.06 1.22 0.25 47.75| | 11: 1.66 - 1.61 2740 147 0.86 21.32 1.24 0.25 46.04| | 12: 1.61 - 1.56 2787 146 0.88 18.40 1.23 0.25 28.73| | 13: 1.56 - 1.52 2745 130 0.87 19.93 1.24 0.25 28.73| | 14: 1.52 - 1.48 2803 134 0.86 20.62 1.24 0.25 25.81| | 15: 1.48 - 1.45 2738 128 0.87 19.98 1.22 0.25 20.46| | 16: 1.45 - 1.42 2756 161 0.86 21.34 1.24 0.25 20.46| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.24 0.25 17.25| | 18: 1.39 - 1.36 2741 179 0.87 21.01 1.24 0.25 15.39| | 19: 1.36 - 1.34 2807 134 0.86 21.86 1.22 0.25 15.39| | 20: 1.34 - 1.32 2696 147 0.87 20.79 1.21 0.25 12.72| | 21: 1.32 - 1.30 2785 112 0.86 21.60 1.21 0.25 12.53| | 22: 1.29 - 1.27 2704 152 0.86 22.19 1.22 0.24 12.25| | 23: 1.27 - 1.26 2802 156 0.86 22.07 1.23 0.24 10.82| | 24: 1.26 - 1.24 2744 132 0.85 22.40 1.21 0.24 10.82| | 25: 1.24 - 1.22 2734 148 0.85 23.36 1.21 0.24 10.31| | 26: 1.22 - 1.21 2727 135 0.85 23.50 1.20 0.23 9.75| | 27: 1.21 - 1.19 2814 148 0.83 24.63 1.20 0.23 9.75| | 28: 1.19 - 1.18 2671 147 0.83 24.96 1.19 0.23 9.11| | 29: 1.18 - 1.16 2800 134 0.83 24.95 1.16 0.23 8.87| | 30: 1.16 - 1.15 2740 148 0.81 26.98 1.16 0.23 8.87| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.87 max = 1466.21 mean = 213.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.43| |phase err.(test): min = 0.00 max = 89.90 mean = 22.31| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.251 1557 Z= 5.405 Angle : 5.461 18.127 2118 Z= 3.839 Chirality : 0.407 1.248 243 Planarity : 0.033 0.095 284 Dihedral : 13.777 82.164 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 37.84 % 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: -2.79 (0.46), residues: 224 helix: -2.69 (0.38), residues: 109 sheet: -1.93 (0.70), residues: 30 loop : -0.19 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.029 ARG A 5 TYR 0.078 0.038 TYR A 139 PHE 0.145 0.050 PHE A 119 HIS 0.079 0.041 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= 0.2613 r_free= 0.1934 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.793216 | | target function (ml) not normalized (work): 232691.668698 | | target function (ml) not normalized (free): 11788.630217 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2613 0.1933 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2613 0.1933 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1933 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2010 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1635 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1641 0.1635 0.1755 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 0.3857 386.469 359.071 0.737 0.914 0.408 11.894-9.307 99.02 97 4 0.1839 613.887 595.206 1.016 0.915 0.385 9.237-7.194 100.00 213 7 0.2166 502.084 490.718 1.037 0.916 0.349 7.162-5.571 100.00 427 22 0.2197 376.786 363.390 1.017 0.916 0.278 5.546-4.326 100.00 867 58 0.1253 517.234 511.251 1.052 0.917 0.239 4.315-3.360 100.00 1859 96 0.1133 491.894 487.873 1.101 0.918 0.209 3.356-2.611 100.00 3867 181 0.1436 323.149 319.487 1.086 0.919 0.089 2.608-2.026 99.99 8198 413 0.1350 214.218 211.984 1.094 0.922 0.000 2.025-1.573 100.00 17313 902 0.1637 104.613 103.939 1.091 0.925 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.390 45.098 1.074 0.932 0.000 1.221-1.150 99.97 13689 708 0.2606 29.229 27.002 1.036 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0456 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1637 r_free=0.1758 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.040282 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2009.992458 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 0.1461 0.0250 0.008 1.0 0.6 0.5 0.0 0 13.020 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.61 2.50 3.013 19.058 2009.992 0.017 12.41 15.42 3.00 3.205 19.544 2009.992 0.016 Individual atomic B min max mean iso aniso Overall: 8.52 118.48 21.01 2.88 0 1785 Protein: 8.52 118.48 17.88 2.88 0 1519 Water: 11.05 114.50 39.17 N/A 0 258 Other: 23.06 36.28 29.15 N/A 0 8 Chain A: 8.52 118.48 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.52 - 19.52 1210 19.52 - 30.51 227 30.51 - 41.51 162 41.51 - 52.51 102 52.51 - 63.50 55 63.50 - 74.50 15 74.50 - 85.49 7 85.49 - 96.49 4 96.49 - 107.48 0 107.48 - 118.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1242 r_free=0.1542 r_work=0.1246 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1547 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 = 0.1245 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1245 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015380 | | target function (ls_wunit_k1) not normalized (work): 1281.130323 | | target function (ls_wunit_k1) not normalized (free): 113.679225 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1245 0.1548 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1769 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1699 0.1769 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1723 0.1723 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1544 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1244 0.1544 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 0.3607 298.738 277.669 0.628 1.003 0.373 11.894-9.307 99.02 97 4 0.1612 478.562 467.275 0.906 1.003 0.368 9.237-7.194 100.00 213 7 0.1828 391.405 386.454 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1734 293.727 288.623 0.924 1.003 0.280 5.546-4.326 100.00 867 58 0.0927 403.215 400.367 0.949 1.003 0.209 4.315-3.360 100.00 1859 96 0.0776 383.461 382.527 0.996 1.003 0.199 3.356-2.611 100.00 3867 181 0.1016 251.914 251.252 0.998 1.002 0.110 2.608-2.026 99.99 8198 413 0.0974 166.996 166.410 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1213 81.552 81.734 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.164 35.623 1.007 0.997 0.000 1.221-1.150 99.97 13689 708 0.2362 22.786 21.291 0.970 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0546 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1544 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=0.1244 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1544 | n_water=258 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1254 r_free=0.1542 | n_water=252 | time (s): 26.090 (total time: 28.520) Filter (q & B) r_work=0.1257 r_free=0.1542 | n_water=249 | time (s): 3.810 (total time: 32.330) Compute maps r_work=0.1257 r_free=0.1542 | n_water=249 | time (s): 1.850 (total time: 34.180) Filter (map) r_work=0.1266 r_free=0.1547 | n_water=238 | time (s): 3.860 (total time: 38.040) Find peaks r_work=0.1266 r_free=0.1547 | n_water=238 | time (s): 0.700 (total time: 38.740) Add new water r_work=0.1415 r_free=0.1700 | n_water=449 | time (s): 3.520 (total time: 42.260) Refine new water occ: r_work=0.1324 r_free=0.1571 adp: r_work=0.1250 r_free=0.1526 occ: r_work=0.1265 r_free=0.1519 adp: r_work=0.1230 r_free=0.1505 occ: r_work=0.1235 r_free=0.1497 adp: r_work=0.1224 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1495 r_work=0.1224 r_free=0.1495 | n_water=449 | time (s): 102.250 (total time: 144.510) Filter (q & B) r_work=0.1230 r_free=0.1501 | n_water=429 | time (s): 4.070 (total time: 148.580) Filter (dist only) r_work=0.1230 r_free=0.1501 | n_water=429 | time (s): 40.370 (total time: 188.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.605132 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1514.418959 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 0.1520 0.0289 0.007 0.9 1.6 0.5 0.0 0 12.303 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 15.20 2.89 3.792 23.143 1514.419 0.015 12.02 14.86 2.84 4.214 22.950 1514.419 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 113.95 23.09 2.60 191 1765 Protein: 8.80 113.95 17.65 2.60 0 1519 Water: 11.15 72.96 42.25 N/A 191 238 Other: 24.99 36.60 29.68 N/A 0 8 Chain A: 8.80 113.95 20.39 N/A 0 1765 Chain S: 15.39 71.60 48.08 N/A 191 0 Histogram: Values Number of atoms 8.80 - 19.31 1206 19.31 - 29.83 250 29.83 - 40.34 189 40.34 - 50.86 143 50.86 - 61.37 104 61.37 - 71.89 52 71.89 - 82.40 6 82.40 - 92.92 3 92.92 - 103.43 1 103.43 - 113.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1486 r_work=0.1202 r_free=0.1486 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1486 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 = 0.1207 r_free = 0.1486 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= 0.1207 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014204 | | target function (ls_wunit_k1) not normalized (work): 1183.117219 | | target function (ls_wunit_k1) not normalized (free): 105.579908 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1207 0.1486 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1613 0.1609 0.1724 n_refl.: 87592 remove outliers: r(all,work,free)=0.1613 0.1609 0.1724 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1618 0.1614 0.1728 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1204 0.1484 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1203 0.1484 n_refl.: 87590 ======================== 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 93.75 85 5 0.3438 297.299 270.943 0.591 1.002 0.364 11.894-9.307 99.02 97 4 0.1524 478.562 476.330 0.921 1.003 0.360 9.237-7.194 100.00 213 7 0.1698 391.405 391.549 0.981 1.003 0.280 7.162-5.571 100.00 427 22 0.1566 293.727 290.115 0.936 1.003 0.235 5.546-4.326 100.00 867 58 0.0852 403.215 400.067 0.959 1.003 0.220 4.315-3.360 100.00 1859 96 0.0720 383.461 382.392 1.002 1.002 0.210 3.356-2.611 100.00 3867 181 0.0961 251.914 251.330 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0960 166.996 166.540 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1187 81.552 81.746 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1614 36.164 35.655 1.018 0.998 0.000 1.221-1.150 99.97 13689 708 0.2337 22.786 21.317 0.978 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0532 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1484 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1203 r_free=0.1486 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1486 | n_water=429 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1205 r_free=0.1486 | n_water=426 | time (s): 38.500 (total time: 40.160) Filter (q & B) r_work=0.1205 r_free=0.1486 | n_water=426 | time (s): 1.270 (total time: 41.430) Compute maps r_work=0.1205 r_free=0.1486 | n_water=426 | time (s): 1.820 (total time: 43.250) Filter (map) r_work=0.1242 r_free=0.1486 | n_water=292 | time (s): 3.290 (total time: 46.540) Find peaks r_work=0.1242 r_free=0.1486 | n_water=292 | time (s): 0.640 (total time: 47.180) Add new water r_work=0.1368 r_free=0.1612 | n_water=470 | time (s): 2.590 (total time: 49.770) Refine new water occ: r_work=0.1271 r_free=0.1532 adp: r_work=0.1272 r_free=0.1533 occ: r_work=0.1249 r_free=0.1511 adp: r_work=0.1247 r_free=0.1513 occ: r_work=0.1234 r_free=0.1492 adp: r_work=0.1227 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1493 r_work=0.1227 r_free=0.1493 | n_water=470 | time (s): 225.120 (total time: 274.890) Filter (q & B) r_work=0.1231 r_free=0.1494 | n_water=442 | time (s): 2.620 (total time: 277.510) Filter (dist only) r_work=0.1231 r_free=0.1494 | n_water=442 | time (s): 32.720 (total time: 310.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.009759 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.897289 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 0.1232 0.1456 0.0224 0.006 0.9 1.9 0.5 0.0 0 1.005 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.56 2.24 3.616 22.092 49.897 3.728 12.17 14.13 1.97 4.142 21.895 49.897 3.655 Individual atomic B min max mean iso aniso Overall: 9.29 109.39 21.64 2.32 208 1761 Protein: 9.29 109.39 17.19 2.32 0 1519 Water: 11.51 71.63 36.84 N/A 208 234 Other: 20.89 32.54 26.72 N/A 0 8 Chain A: 9.29 109.39 19.86 N/A 0 1761 Chain S: 14.62 68.25 36.68 N/A 208 0 Histogram: Values Number of atoms 9.29 - 19.30 1239 19.30 - 29.31 275 29.31 - 39.32 205 39.32 - 49.33 141 49.33 - 59.34 72 59.34 - 69.35 24 69.35 - 79.36 7 79.36 - 89.37 3 89.37 - 99.38 1 99.38 - 109.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1413 r_work=0.1218 r_free=0.1415 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1415 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1407 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651834 | | target function (ml) not normalized (work): 304175.841330 | | target function (ml) not normalized (free): 16064.298379 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1211 0.1407 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1548 0.1547 0.1600 n_refl.: 87590 remove outliers: r(all,work,free)=0.1548 0.1547 0.1600 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1546 0.1545 0.1598 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1203 0.1372 n_refl.: 87590 remove outliers: r(all,work,free)=0.1207 0.1198 0.1372 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3641 290.685 263.445 0.480 0.999 0.304 11.894-9.307 96.08 94 4 0.2284 475.175 457.564 0.858 1.001 0.287 9.237-7.194 98.18 209 7 0.2335 382.954 384.360 0.947 1.001 0.180 7.162-5.571 100.00 427 22 0.2097 293.727 284.934 0.912 1.002 0.175 5.546-4.326 100.00 867 58 0.1100 403.215 398.680 0.953 1.002 0.170 4.315-3.360 100.00 1859 96 0.0942 383.461 380.743 0.992 1.002 0.160 3.356-2.611 100.00 3867 181 0.1163 251.914 249.944 0.999 1.002 0.072 2.608-2.026 99.99 8198 413 0.1046 166.996 166.039 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1013 81.552 81.698 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.164 35.745 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2130 22.786 21.404 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0294 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1372 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=0.1198 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1372 | n_water=442 | time (s): 1.680 (total time: 1.680) Filter (dist) r_work=0.1198 r_free=0.1372 | n_water=441 | time (s): 36.620 (total time: 38.300) Filter (q & B) r_work=0.1198 r_free=0.1372 | n_water=441 | time (s): 1.040 (total time: 39.340) Compute maps r_work=0.1198 r_free=0.1372 | n_water=441 | time (s): 1.630 (total time: 40.970) Filter (map) r_work=0.1219 r_free=0.1381 | n_water=315 | time (s): 3.550 (total time: 44.520) Find peaks r_work=0.1219 r_free=0.1381 | n_water=315 | time (s): 0.640 (total time: 45.160) Add new water r_work=0.1291 r_free=0.1450 | n_water=481 | time (s): 3.470 (total time: 48.630) Refine new water occ: r_work=0.1219 r_free=0.1381 adp: r_work=0.1219 r_free=0.1383 occ: r_work=0.1202 r_free=0.1364 adp: r_work=0.1200 r_free=0.1366 occ: r_work=0.1190 r_free=0.1355 adp: r_work=0.1186 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1353 r_work=0.1186 r_free=0.1353 | n_water=481 | time (s): 206.910 (total time: 255.540) Filter (q & B) r_work=0.1192 r_free=0.1352 | n_water=449 | time (s): 2.840 (total time: 258.380) Filter (dist only) r_work=0.1192 r_free=0.1352 | n_water=448 | time (s): 38.560 (total time: 296.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.960414 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.124788 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 0.1191 0.1370 0.0180 0.006 1.0 1.6 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.70 1.80 3.418 21.506 43.125 3.635 11.84 13.66 1.82 3.655 21.422 43.125 3.624 Individual atomic B min max mean iso aniso Overall: 9.29 105.87 21.36 2.16 217 1758 Protein: 9.29 105.87 17.00 2.16 0 1519 Water: 11.53 70.88 36.07 N/A 217 231 Other: 21.10 30.28 25.95 N/A 0 8 Chain A: 9.29 105.87 19.59 N/A 0 1758 Chain S: 15.34 65.08 35.70 N/A 217 0 Histogram: Values Number of atoms 9.29 - 18.94 1235 18.94 - 28.60 277 28.60 - 38.26 207 38.26 - 47.92 147 47.92 - 57.58 68 57.58 - 67.24 27 67.24 - 76.89 9 76.89 - 86.55 2 86.55 - 96.21 1 96.21 - 105.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1366 r_work=0.1185 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1367 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1369 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1182 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623634 | | target function (ml) not normalized (work): 301783.456019 | | target function (ml) not normalized (free): 15954.255434 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1182 0.1369 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1500 0.1498 0.1570 n_refl.: 87578 remove outliers: r(all,work,free)=0.1500 0.1498 0.1570 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1495 0.1568 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1371 n_refl.: 87578 remove outliers: r(all,work,free)=0.1188 0.1179 0.1371 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 87.50 79 5 0.3813 285.955 256.149 0.463 0.999 0.328 11.894-9.307 94.12 92 4 0.2297 470.184 452.218 0.853 1.001 0.226 9.237-7.194 98.18 209 7 0.2472 382.954 376.873 0.915 1.001 0.137 7.162-5.571 100.00 427 22 0.2116 293.727 284.352 0.905 1.002 0.132 5.546-4.326 100.00 867 58 0.1129 403.215 398.763 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0941 383.461 380.914 0.993 1.002 0.127 3.356-2.611 100.00 3867 181 0.1148 251.914 250.098 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1032 166.996 166.056 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.552 81.797 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.164 35.791 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2118 22.786 21.421 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0406 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1371 After: r_work=0.1180 r_free=0.1371 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1371 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=0.1180 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1371 | n_water=448 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1180 r_free=0.1370 | n_water=447 | time (s): 36.920 (total time: 38.480) Filter (q & B) r_work=0.1180 r_free=0.1373 | n_water=445 | time (s): 2.760 (total time: 41.240) Compute maps r_work=0.1180 r_free=0.1373 | n_water=445 | time (s): 1.490 (total time: 42.730) Filter (map) r_work=0.1207 r_free=0.1383 | n_water=330 | time (s): 2.920 (total time: 45.650) Find peaks r_work=0.1207 r_free=0.1383 | n_water=330 | time (s): 0.480 (total time: 46.130) Add new water r_work=0.1260 r_free=0.1422 | n_water=500 | time (s): 3.010 (total time: 49.140) Refine new water occ: r_work=0.1197 r_free=0.1366 adp: r_work=0.1197 r_free=0.1368 occ: r_work=0.1184 r_free=0.1357 adp: r_work=0.1183 r_free=0.1357 occ: r_work=0.1175 r_free=0.1351 adp: r_work=0.1171 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1350 r_work=0.1171 r_free=0.1350 | n_water=500 | time (s): 110.110 (total time: 159.250) Filter (q & B) r_work=0.1180 r_free=0.1347 | n_water=453 | time (s): 3.570 (total time: 162.820) Filter (dist only) r_work=0.1180 r_free=0.1347 | n_water=451 | time (s): 39.940 (total time: 202.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.288017 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.809347 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 0.1192 0.1363 0.0171 0.007 1.1 4.5 0.5 0.0 0 1.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.63 1.71 3.313 21.263 51.809 3.626 11.89 13.60 1.71 3.729 21.123 51.809 3.616 Individual atomic B min max mean iso aniso Overall: 9.26 101.62 21.04 2.05 221 1757 Protein: 9.26 101.62 16.67 2.06 0 1519 Water: 11.53 69.27 35.66 N/A 221 230 Other: 21.96 30.08 25.87 N/A 0 8 Chain A: 9.26 101.62 19.22 N/A 0 1757 Chain S: 14.26 61.69 35.44 N/A 221 0 Histogram: Values Number of atoms 9.26 - 18.50 1231 18.50 - 27.73 270 27.73 - 36.97 208 36.97 - 46.21 156 46.21 - 55.44 74 55.44 - 64.68 23 64.68 - 73.91 11 73.91 - 83.15 2 83.15 - 92.39 1 92.39 - 101.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1360 r_work=0.1189 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1360 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1357 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1186 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614300 | | target function (ml) not normalized (work): 300995.297243 | | target function (ml) not normalized (free): 15927.064703 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1405 0.1403 5.6695 5.6422| | 2: 3.57 - 2.84 1.00 2888 124 0.1115 0.1390 5.1933 5.245| | 3: 2.83 - 2.48 1.00 2820 163 0.1224 0.1273 4.999 5.0274| | 4: 2.47 - 2.25 1.00 2825 136 0.1020 0.1114 4.7009 4.7458| | 5: 2.25 - 2.09 1.00 2756 127 0.0985 0.1100 4.6416 4.7084| | 6: 2.09 - 1.97 1.00 2846 113 0.0961 0.1221 4.3437 4.4509| | 7: 1.97 - 1.87 1.00 2787 165 0.0975 0.1222 4.0672 4.1915| | 8: 1.87 - 1.79 1.00 2789 144 0.1008 0.1283 3.9848 4.0898| | 9: 1.79 - 1.72 1.00 2745 138 0.0933 0.1269 3.7035 3.8846| | 10: 1.72 - 1.66 1.00 2831 160 0.0980 0.1217 3.6234 3.7572| | 11: 1.66 - 1.61 1.00 2712 147 0.0946 0.1126 3.5593 3.6177| | 12: 1.61 - 1.56 1.00 2773 144 0.0898 0.1150 3.3366 3.4863| | 13: 1.56 - 1.52 1.00 2745 130 0.0960 0.1056 3.3299 3.4371| | 14: 1.52 - 1.48 1.00 2803 134 0.0970 0.1126 3.2504 3.3446| | 15: 1.48 - 1.45 1.00 2738 128 0.0992 0.1321 3.1568 3.3129| | 16: 1.45 - 1.42 1.00 2756 161 0.1059 0.1260 3.145 3.2382| | 17: 1.42 - 1.39 1.00 2785 139 0.1108 0.1321 3.1095 3.232| | 18: 1.39 - 1.36 1.00 2741 179 0.1134 0.1365 3.0743 3.2557| | 19: 1.36 - 1.34 1.00 2807 134 0.1199 0.1581 3.0861 3.264| | 20: 1.34 - 1.32 1.00 2696 147 0.1319 0.1465 3.0825 3.1431| | 21: 1.32 - 1.30 1.00 2785 112 0.1401 0.1630 3.0787 3.1632| | 22: 1.29 - 1.27 1.00 2704 152 0.1462 0.1891 3.0784 3.2812| | 23: 1.27 - 1.26 1.00 2802 156 0.1558 0.1880 3.0974 3.2174| | 24: 1.26 - 1.24 1.00 2744 132 0.1618 0.1741 3.0916 3.1795| | 25: 1.24 - 1.22 1.00 2733 148 0.1783 0.2319 3.1037 3.2873| | 26: 1.22 - 1.21 1.00 2727 135 0.1850 0.1774 3.1182 3.1964| | 27: 1.21 - 1.19 1.00 2814 148 0.2000 0.2114 3.1367 3.1477| | 28: 1.19 - 1.18 1.00 2671 147 0.2141 0.2278 3.1368 3.1611| | 29: 1.18 - 1.16 1.00 2800 134 0.2214 0.2378 3.1236 3.2234| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2483 3.1144 3.1586| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 9.03 1.00 0.97 6156.74| | 2: 3.57 - 2.84 2888 124 0.92 13.28 1.01 0.97 6156.74| | 3: 2.83 - 2.48 2820 163 0.89 17.35 0.99 0.97 5164.18| | 4: 2.47 - 2.25 2825 136 0.91 14.50 1.00 0.97 2604.66| | 5: 2.25 - 2.09 2756 127 0.89 16.75 1.01 0.97 2604.66| | 6: 2.09 - 1.97 2846 113 0.92 13.64 1.02 0.97 1536.65| | 7: 1.97 - 1.87 2787 165 0.94 10.82 1.02 0.97 625.78| | 8: 1.87 - 1.79 2789 144 0.91 14.45 1.00 0.97 625.78| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.97 337.60| | 10: 1.72 - 1.66 2831 160 0.93 12.22 0.98 0.97 279.89| | 11: 1.66 - 1.61 2712 147 0.93 12.84 0.98 0.97 267.28| | 12: 1.61 - 1.56 2773 144 0.95 9.57 0.99 0.97 148.40| | 13: 1.56 - 1.52 2745 130 0.94 11.13 1.02 0.97 148.40| | 14: 1.52 - 1.48 2803 134 0.94 11.29 1.02 0.97 132.24| | 15: 1.48 - 1.45 2738 128 0.95 10.35 1.01 0.98 102.65| | 16: 1.45 - 1.42 2756 161 0.94 11.56 1.01 0.98 102.65| | 17: 1.42 - 1.39 2785 139 0.94 11.39 1.01 0.98 92.69| | 18: 1.39 - 1.36 2741 179 0.94 11.70 1.01 0.98 86.93| | 19: 1.36 - 1.34 2807 134 0.94 12.25 1.00 0.98 86.93| | 20: 1.34 - 1.32 2696 147 0.94 12.39 0.99 0.96 81.89| | 21: 1.32 - 1.30 2785 112 0.94 13.29 0.98 0.96 81.53| | 22: 1.29 - 1.27 2704 152 0.93 13.82 0.98 0.96 81.72| | 23: 1.27 - 1.26 2802 156 0.93 14.74 0.98 0.95 82.64| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 82.64| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.94 84.11| | 26: 1.22 - 1.21 2727 135 0.90 18.02 1.02 0.93 85.73| | 27: 1.21 - 1.19 2814 148 0.89 18.65 1.02 0.93 85.73| | 28: 1.19 - 1.18 2671 147 0.88 20.14 1.01 0.93 88.77| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.92 89.91| | 30: 1.16 - 1.15 2739 148 0.86 21.83 0.98 0.92 89.91| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.53 max = 6156.74 mean = 963.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.99| |phase err.(test): min = 0.00 max = 89.40 mean = 14.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1186 0.1357 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1500 0.1498 0.1559 n_refl.: 87575 remove outliers: r(all,work,free)=0.1500 0.1498 0.1559 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1496 0.1558 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1187 0.1357 n_refl.: 87575 remove outliers: r(all,work,free)=0.1194 0.1186 0.1357 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 87.50 79 5 0.3939 285.955 255.542 0.433 0.998 0.281 11.894-9.307 92.16 90 4 0.2361 470.316 454.697 0.851 1.000 0.196 9.237-7.194 97.73 208 7 0.2520 382.478 377.308 0.906 1.000 0.140 7.162-5.571 100.00 427 22 0.2231 293.727 282.907 0.896 1.001 0.122 5.546-4.326 100.00 867 58 0.1190 403.215 398.112 0.952 1.001 0.120 4.315-3.360 100.00 1859 96 0.0979 383.461 380.829 0.995 1.001 0.117 3.356-2.611 100.00 3867 181 0.1185 251.914 249.671 1.001 1.001 0.048 2.608-2.026 99.99 8198 413 0.1032 166.996 166.062 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0960 81.552 81.794 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1216 36.164 35.812 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2115 22.786 21.387 0.974 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0271 ================= 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 : 0.2613 0.1934 0.082 5.461 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1755 0.082 5.461 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1755 0.082 5.461 9.0 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1758 0.082 5.461 9.0 119.5 20.1 258 0.003 1_weight: 0.1637 0.1758 0.082 5.461 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1211 0.1461 0.008 0.976 9.0 119.5 20.1 258 0.124 1_adp: 0.1242 0.1542 0.008 0.976 8.5 118.5 21.0 258 0.124 1_regHadp: 0.1246 0.1547 0.008 0.976 8.5 118.5 21.0 258 0.124 1_occ: 0.1245 0.1548 0.008 0.976 8.5 118.5 21.0 258 0.124 2_bss: 0.1244 0.1544 0.008 0.976 8.7 118.6 21.1 258 0.124 2_settarget: 0.1244 0.1544 0.008 0.976 8.7 118.6 21.1 258 0.124 2_updatecdl: 0.1244 0.1544 0.008 0.974 8.7 118.6 21.1 258 0.124 2_nqh: 0.1244 0.1544 0.008 0.974 8.7 118.6 21.1 258 0.124 2_sol: 0.1230 0.1501 0.008 0.974 8.7 118.6 23.4 429 n/a 2_weight: 0.1230 0.1501 0.008 0.974 8.7 118.6 23.4 429 n/a 2_xyzrec: 0.1231 0.1520 0.007 0.866 8.7 118.6 23.4 429 n/a 2_adp: 0.1202 0.1486 0.007 0.866 8.8 113.9 23.1 429 n/a 2_regHadp: 0.1202 0.1486 0.007 0.866 8.8 113.9 23.1 429 n/a 2_occ: 0.1207 0.1486 0.007 0.866 8.8 113.9 23.1 429 n/a 3_bss: 0.1203 0.1484 0.007 0.866 8.8 114.0 23.1 429 n/a 3_settarget: 0.1203 0.1484 0.007 0.866 8.8 114.0 23.1 429 n/a 3_updatecdl: 0.1203 0.1484 0.007 0.867 8.8 114.0 23.1 429 n/a 3_nqh: 0.1203 0.1486 0.007 0.867 8.8 114.0 23.1 429 n/a 3_sol: 0.1231 0.1494 0.007 0.867 8.8 114.0 22.0 442 n/a 3_weight: 0.1231 0.1494 0.007 0.867 8.8 114.0 22.0 442 n/a 3_xyzrec: 0.1232 0.1456 0.006 0.918 8.8 114.0 22.0 442 n/a 3_adp: 0.1217 0.1413 0.006 0.918 9.3 109.4 21.6 442 n/a 3_regHadp: 0.1218 0.1415 0.006 0.918 9.3 109.4 21.6 442 n/a 3_occ: 0.1211 0.1407 0.006 0.918 9.3 109.4 21.6 442 n/a 4_bss: 0.1198 0.1372 0.006 0.918 9.3 109.4 21.6 442 n/a 4_settarget: 0.1198 0.1372 0.006 0.918 9.3 109.4 21.6 442 n/a 4_updatecdl: 0.1198 0.1372 0.006 0.916 9.3 109.4 21.6 442 n/a 4_nqh: 0.1198 0.1372 0.006 0.916 9.3 109.4 21.6 442 n/a 4_sol: 0.1192 0.1352 0.006 0.916 9.3 109.4 21.5 448 n/a 4_weight: 0.1192 0.1352 0.006 0.916 9.3 109.4 21.5 448 n/a 4_xyzrec: 0.1191 0.1370 0.006 0.953 9.3 109.4 21.5 448 n/a 4_adp: 0.1184 0.1366 0.006 0.953 9.3 105.9 21.4 448 n/a 4_regHadp: 0.1185 0.1367 0.006 0.953 9.3 105.9 21.4 448 n/a 4_occ: 0.1182 0.1369 0.006 0.953 9.3 105.9 21.4 448 n/a 5_bss: 0.1179 0.1371 0.006 0.953 9.3 105.9 21.3 448 n/a 5_settarget: 0.1179 0.1371 0.006 0.953 9.3 105.9 21.3 448 n/a 5_updatecdl: 0.1179 0.1371 0.006 0.955 9.3 105.9 21.3 448 n/a 5_setrh: 0.1180 0.1371 0.006 0.955 9.3 105.9 21.3 448 n/a 5_nqh: 0.1180 0.1371 0.006 0.955 9.3 105.9 21.3 448 n/a 5_sol: 0.1180 0.1347 0.006 0.955 9.3 105.9 21.3 451 n/a 5_weight: 0.1180 0.1347 0.006 0.955 9.3 105.9 21.3 451 n/a 5_xyzrec: 0.1192 0.1363 0.007 1.081 9.3 105.9 21.3 451 n/a 5_adp: 0.1189 0.1360 0.007 1.081 9.3 101.6 21.0 451 n/a 5_regHadp: 0.1189 0.1360 0.007 1.081 9.3 101.6 21.0 451 n/a 5_occ: 0.1186 0.1357 0.007 1.081 9.3 101.6 21.0 451 n/a end: 0.1186 0.1357 0.007 1.081 9.3 101.6 21.0 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2514713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2514713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8400 Refinement macro-cycles (run) : 3537.7800 Write final files (write_after_run_outputs) : 70.5200 Total : 3613.1400 Total CPU time: 60.85 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:28 PST -0800 (1735452688.93 s) Start R-work = 0.1635, R-free = 0.1755 Final R-work = 0.1186, R-free = 0.1357 =============================================================================== Job complete usr+sys time: 3758.17 seconds wall clock time: 66 minutes 48.18 seconds (4008.18 seconds total)