Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.22, per 1000 atoms: 0.66 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 305.1 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1164 1.17 - 1.43: 688 1.43 - 1.70: 803 1.70 - 1.96: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.158 0.181 7.50e-03 1.78e+04 5.81e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.292 0.234 1.01e-02 9.80e+03 5.37e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.227 0.230 1.14e-02 7.69e+03 4.08e+02 bond pdb=" CA MET A 133 " pdb=" C MET A 133 " ideal model delta sigma weight residual 1.524 1.752 -0.229 1.29e-02 6.01e+03 3.14e+02 bond pdb=" C PRO A 109 " pdb=" O PRO A 109 " ideal model delta sigma weight residual 1.237 1.006 0.231 1.32e-02 5.74e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 3311 4.92 - 9.84: 1823 9.84 - 14.77: 555 14.77 - 19.69: 80 19.69 - 24.61: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 134.66 -13.43 8.10e-01 1.52e+00 2.75e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 109.32 9.97 6.50e-01 2.37e+00 2.35e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 125.38 -14.76 1.02e+00 9.61e-01 2.09e+02 angle pdb=" O THR A 34 " pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 123.27 140.32 -17.05 1.18e+00 7.18e-01 2.09e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.42 135.34 -14.92 1.06e+00 8.90e-01 1.98e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.32: 955 17.32 - 34.64: 103 34.64 - 51.96: 37 51.96 - 69.28: 13 69.28 - 86.59: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -158.17 -21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.171: 72 0.171 - 0.341: 69 0.341 - 0.511: 55 0.511 - 0.681: 33 0.681 - 0.851: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 125 " pdb=" CA THR A 125 " pdb=" OG1 THR A 125 " pdb=" CG2 THR A 125 " both_signs ideal model delta sigma weight residual False 2.55 1.70 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.040 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.095 2.00e-02 2.50e+03 7.14e-02 1.15e+02 pdb=" CG HIS A 126 " -0.113 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.048 9.50e-02 1.11e+02 6.84e-02 9.97e+01 pdb=" NE ARG A 48 " 0.104 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.096 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.052 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.056 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.099 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1368 2.36 - 2.92: 8316 2.92 - 3.48: 10404 3.48 - 4.04: 15058 4.04 - 4.60: 21501 Nonbonded interactions: 56647 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.804 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.808 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.821 2.450 nonbonded pdb=" O MET A 134 " pdb=" H GLY A 137 " model vdw 1.848 2.450 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.864 2.450 ... (remaining 56642 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_1498316_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= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792382 | | target function (ml) not normalized (work): 232622.140756 | | target function (ml) not normalized (free): 11868.708597 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3021 0.2065 7.0497 4.9419| | 2: 3.57 - 2.84 1.00 2876 122 0.2436 0.1822 4.3523 4.3338| | 3: 2.84 - 2.48 1.00 2833 165 0.2371 0.1637 4.1272 4.1455| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1460 3.8324 3.8359| | 5: 2.25 - 2.09 1.00 2756 127 0.2470 0.1515 3.7982 3.807| | 6: 2.09 - 1.97 1.00 2846 113 0.2566 0.1843 3.4631 3.5367| | 7: 1.97 - 1.87 1.00 2787 165 0.2569 0.1797 3.1239 3.1741| | 8: 1.87 - 1.79 1.00 2789 144 0.2467 0.1940 3.0547 3.1115| | 9: 1.79 - 1.72 1.00 2745 138 0.2339 0.1971 2.8974 2.9742| | 10: 1.72 - 1.66 1.00 2789 158 0.2363 0.1967 2.8118 2.8886| | 11: 1.66 - 1.61 1.00 2740 147 0.2458 0.2166 2.7466 2.8612| | 12: 1.61 - 1.56 1.00 2787 146 0.2540 0.2013 2.6413 2.6683| | 13: 1.56 - 1.52 1.00 2745 130 0.2592 0.2003 2.5756 2.5886| | 14: 1.52 - 1.48 1.00 2803 134 0.2609 0.1896 2.5103 2.5119| | 15: 1.48 - 1.45 1.00 2738 128 0.2591 0.1919 2.4259 2.4502| | 16: 1.45 - 1.42 1.00 2756 161 0.2655 0.2248 2.3875 2.5238| | 17: 1.42 - 1.39 1.00 2785 139 0.2652 0.2237 2.3135 2.378| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.2344 2.2676 2.3717| | 19: 1.36 - 1.34 1.00 2807 134 0.2657 0.2444 2.2565 2.3359| | 20: 1.34 - 1.32 1.00 2696 147 0.2647 0.2176 2.2091 2.2112| | 21: 1.32 - 1.30 1.00 2785 112 0.2685 0.2274 2.1488 2.1704| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2434 2.1447 2.1586| | 23: 1.27 - 1.26 1.00 2802 156 0.2827 0.2559 2.1192 2.206| | 24: 1.26 - 1.24 1.00 2744 132 0.2828 0.2519 2.0905 2.1872| | 25: 1.24 - 1.22 1.00 2734 148 0.2861 0.2741 2.0591 2.1339| | 26: 1.22 - 1.21 1.00 2727 135 0.2920 0.2427 2.0264 2.1405| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2678 2.0138 2.0129| | 28: 1.19 - 1.18 1.00 2671 147 0.2929 0.3088 1.9765 2.0354| | 29: 1.18 - 1.16 1.00 2800 134 0.2955 0.2621 1.9561 2.0116| | 30: 1.16 - 1.15 1.00 2740 148 0.3105 0.2943 1.9368 1.9974| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.85 0.76 0.23 1480.65| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1480.65| | 3: 2.84 - 2.48 2833 165 0.74 32.04 1.24 0.23 1226.74| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 567.80| | 5: 2.25 - 2.09 2756 127 0.77 29.07 1.28 0.25 567.80| | 6: 2.09 - 1.97 2846 113 0.84 22.49 1.30 0.25 309.30| | 7: 1.97 - 1.87 2787 165 0.90 16.41 1.29 0.26 88.82| | 8: 1.87 - 1.79 2789 144 0.86 20.58 1.25 0.26 88.82| | 9: 1.79 - 1.72 2745 138 0.88 18.29 1.22 0.26 55.34| | 10: 1.72 - 1.66 2789 158 0.87 20.13 1.22 0.26 48.63| | 11: 1.66 - 1.61 2740 147 0.86 21.44 1.24 0.26 47.03| | 12: 1.61 - 1.56 2787 146 0.88 18.82 1.24 0.25 30.77| | 13: 1.56 - 1.52 2745 130 0.86 20.89 1.25 0.25 30.77| | 14: 1.52 - 1.48 2803 134 0.86 21.22 1.24 0.25 27.46| | 15: 1.48 - 1.45 2738 128 0.87 20.33 1.23 0.25 21.39| | 16: 1.45 - 1.42 2756 161 0.85 22.21 1.23 0.25 21.39| | 17: 1.42 - 1.39 2785 139 0.86 21.37 1.23 0.25 18.16| | 18: 1.39 - 1.36 2741 179 0.86 21.43 1.24 0.25 16.30| | 19: 1.36 - 1.34 2807 134 0.85 22.34 1.22 0.25 16.30| | 20: 1.34 - 1.32 2696 147 0.87 21.02 1.20 0.25 13.52| | 21: 1.32 - 1.30 2785 112 0.85 22.46 1.21 0.25 13.33| | 22: 1.29 - 1.27 2704 152 0.85 22.96 1.21 0.24 13.04| | 23: 1.27 - 1.26 2802 156 0.85 22.99 1.22 0.24 11.60| | 24: 1.26 - 1.24 2744 132 0.84 23.53 1.20 0.24 11.60| | 25: 1.24 - 1.22 2734 148 0.84 24.27 1.20 0.24 11.08| | 26: 1.22 - 1.21 2727 135 0.83 25.06 1.21 0.23 10.50| | 27: 1.21 - 1.19 2814 148 0.82 25.48 1.20 0.23 10.50| | 28: 1.19 - 1.18 2671 147 0.82 26.10 1.17 0.23 9.77| | 29: 1.18 - 1.16 2800 134 0.82 26.37 1.17 0.22 9.50| | 30: 1.16 - 1.15 2740 148 0.79 28.34 1.16 0.22 9.50| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.50 max = 1480.65 mean = 214.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.94| |phase err.(test): min = 0.00 max = 88.69 mean = 22.72| |-----------------------------------------------------------------------------| ----------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 0.234 1557 Z= 5.492 Angle : 5.277 17.058 2118 Z= 3.714 Chirality : 0.374 0.851 243 Planarity : 0.031 0.102 284 Dihedral : 13.681 86.594 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.48), residues: 224 helix: -2.89 (0.33), residues: 103 sheet: -0.37 (0.95), residues: 28 loop : -0.02 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.020 ARG A 98 TYR 0.106 0.042 TYR A 139 PHE 0.076 0.036 PHE A 164 HIS 0.047 0.022 HIS A 126 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= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792382 | | target function (ml) not normalized (work): 232622.140756 | | target function (ml) not normalized (free): 11868.708597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1986 0.1962 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2007 0.2011 0.1975 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1636 0.1792 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1792 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3816 386.562 359.643 0.669 1.004 0.407 11.894-9.307 99.02 97 4 0.1812 614.034 593.195 0.929 1.004 0.390 9.237-7.194 100.00 213 7 0.2136 502.204 491.907 0.960 1.004 0.370 7.162-5.571 100.00 427 22 0.2202 376.876 365.483 0.936 1.004 0.288 5.546-4.326 100.00 867 58 0.1305 517.358 511.895 0.963 1.004 0.259 4.315-3.360 100.00 1859 96 0.1137 492.011 488.752 1.001 1.004 0.203 3.356-2.611 100.00 3867 181 0.1433 323.226 319.821 1.000 1.003 0.057 2.608-2.026 99.99 8198 413 0.1359 214.269 212.130 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1639 104.638 104.033 1.011 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2065 46.401 45.096 1.008 0.994 0.000 1.221-1.150 99.97 13689 708 0.2586 29.236 26.960 0.978 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0447 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1792 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1797 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.588747 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.813676 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 0.1216 0.1468 0.0253 0.007 0.9 1.6 0.5 0.0 0 12.294 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 14.68 2.53 3.013 19.054 2026.814 0.017 12.40 15.40 3.00 3.138 19.495 2026.814 0.016 Individual atomic B min max mean iso aniso Overall: 8.41 118.44 20.92 2.88 0 1785 Protein: 8.41 118.44 17.81 2.88 0 1519 Water: 11.09 114.93 38.95 N/A 0 258 Other: 22.63 35.42 28.77 N/A 0 8 Chain A: 8.41 118.44 20.92 N/A 0 1785 Histogram: Values Number of atoms 8.41 - 19.42 1211 19.42 - 30.42 224 30.42 - 41.42 168 41.42 - 52.43 99 52.43 - 63.43 54 63.43 - 74.43 18 74.43 - 85.43 4 85.43 - 96.44 4 96.44 - 107.44 0 107.44 - 118.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1540 r_work=0.1245 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1544 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 = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.29 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= 0.1546 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015441 | | target function (ls_wunit_k1) not normalized (work): 1286.215999 | | target function (ls_wunit_k1) not normalized (free): 115.123606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1244 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1696 0.1695 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1696 0.1695 0.1765 n_refl.: 87593 overall B=0.16 to atoms: r(all,work,free)=0.1723 0.1722 0.1784 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1242 0.1539 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1242 0.1539 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 0.3614 299.155 278.156 0.637 1.003 0.380 11.894-9.307 99.02 97 4 0.1622 479.230 467.887 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1818 391.951 386.795 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1724 294.138 289.006 0.920 1.003 0.258 5.546-4.326 100.00 867 58 0.0935 403.779 400.934 0.949 1.003 0.230 4.315-3.360 100.00 1859 96 0.0782 383.996 383.012 0.991 1.003 0.189 3.356-2.611 100.00 3867 181 0.1022 252.266 251.586 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.0975 167.229 166.655 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1205 81.666 81.857 1.016 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1643 36.214 35.678 1.006 0.997 0.000 1.221-1.150 99.97 13689 708 0.2356 22.817 21.325 0.971 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0370 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1245 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1541 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1254 r_free=0.1538 | n_water=252 | time (s): 27.720 (total time: 30.120) Filter (q & B) r_work=0.1257 r_free=0.1537 | n_water=249 | time (s): 3.570 (total time: 33.690) Compute maps r_work=0.1257 r_free=0.1537 | n_water=249 | time (s): 1.800 (total time: 35.490) Filter (map) r_work=0.1269 r_free=0.1546 | n_water=236 | time (s): 3.520 (total time: 39.010) Find peaks r_work=0.1269 r_free=0.1546 | n_water=236 | time (s): 0.710 (total time: 39.720) Add new water r_work=0.1430 r_free=0.1704 | n_water=458 | time (s): 3.610 (total time: 43.330) Refine new water occ: r_work=0.1343 r_free=0.1584 adp: r_work=0.1258 r_free=0.1532 occ: r_work=0.1273 r_free=0.1518 adp: r_work=0.1235 r_free=0.1505 occ: r_work=0.1239 r_free=0.1497 adp: r_work=0.1229 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1498 r_work=0.1229 r_free=0.1498 | n_water=458 | time (s): 74.950 (total time: 118.280) Filter (q & B) r_work=0.1234 r_free=0.1502 | n_water=436 | time (s): 4.090 (total time: 122.370) Filter (dist only) r_work=0.1234 r_free=0.1502 | n_water=436 | time (s): 41.700 (total time: 164.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.535672 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1513.762876 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 0.1230 0.1515 0.0285 0.006 0.9 1.9 0.5 0.0 0 12.268 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.15 2.85 3.779 23.162 1513.763 0.015 12.06 14.90 2.84 4.175 22.996 1513.763 0.015 Individual atomic B min max mean iso aniso Overall: 8.89 114.25 23.22 2.59 200 1763 Protein: 8.89 114.25 17.62 2.59 0 1519 Water: 11.08 72.52 42.60 N/A 200 236 Other: 26.76 38.01 31.51 N/A 0 8 Chain A: 8.89 114.25 20.33 N/A 0 1763 Chain S: 13.62 72.19 48.75 N/A 200 0 Histogram: Values Number of atoms 8.89 - 19.43 1213 19.43 - 29.96 244 29.96 - 40.50 196 40.50 - 51.03 140 51.03 - 61.57 104 61.57 - 72.11 53 72.11 - 82.64 7 82.64 - 93.18 3 93.18 - 103.72 1 103.72 - 114.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1490 r_work=0.1206 r_free=0.1490 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1490 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1485 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 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= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014153 | | target function (ls_wunit_k1) not normalized (work): 1178.889585 | | target function (ls_wunit_k1) not normalized (free): 102.071951 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1207 0.1485 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1605 0.1723 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1605 0.1723 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1615 0.1611 0.1726 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1204 0.1481 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1203 0.1481 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 0.3193 294.538 272.813 0.596 1.002 0.364 11.894-9.307 99.02 97 4 0.1528 479.230 475.320 0.915 1.003 0.329 9.237-7.194 100.00 213 7 0.1740 391.951 392.379 0.976 1.003 0.300 7.162-5.571 100.00 427 22 0.1534 294.138 290.487 0.937 1.003 0.230 5.546-4.326 100.00 867 58 0.0838 403.779 401.079 0.958 1.002 0.219 4.315-3.360 100.00 1859 96 0.0716 383.996 382.848 1.001 1.002 0.208 3.356-2.611 100.00 3867 181 0.0969 252.266 251.606 1.010 1.002 0.140 2.608-2.026 99.99 8198 413 0.0965 167.229 166.787 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.666 81.843 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1615 36.214 35.705 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2338 22.817 21.348 0.978 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0587 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1481 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1481 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1481 | n_water=436 | time (s): 1.630 (total time: 1.630) Filter (dist) r_work=0.1202 r_free=0.1480 | n_water=434 | time (s): 37.950 (total time: 39.580) Filter (q & B) r_work=0.1203 r_free=0.1481 | n_water=433 | time (s): 2.940 (total time: 42.520) Compute maps r_work=0.1203 r_free=0.1481 | n_water=433 | time (s): 1.500 (total time: 44.020) Filter (map) r_work=0.1243 r_free=0.1486 | n_water=292 | time (s): 2.840 (total time: 46.860) Find peaks r_work=0.1243 r_free=0.1486 | n_water=292 | time (s): 0.490 (total time: 47.350) Add new water r_work=0.1375 r_free=0.1624 | n_water=482 | time (s): 3.170 (total time: 50.520) Refine new water occ: r_work=0.1272 r_free=0.1536 adp: r_work=0.1274 r_free=0.1538 occ: r_work=0.1250 r_free=0.1513 adp: r_work=0.1248 r_free=0.1513 occ: r_work=0.1235 r_free=0.1502 adp: r_work=0.1228 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1497 r_work=0.1228 r_free=0.1497 | n_water=482 | time (s): 132.980 (total time: 183.500) Filter (q & B) r_work=0.1231 r_free=0.1497 | n_water=447 | time (s): 3.360 (total time: 186.860) Filter (dist only) r_work=0.1231 r_free=0.1497 | n_water=447 | time (s): 35.240 (total time: 222.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.280331 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 57.859583 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 0.1461 0.0229 0.006 0.9 1.6 0.5 0.0 0 1.140 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.61 2.29 3.608 22.074 57.860 3.726 12.12 14.15 2.03 4.099 21.879 57.860 3.650 Individual atomic B min max mean iso aniso Overall: 9.26 110.00 21.63 2.36 214 1760 Protein: 9.26 110.00 17.19 2.36 0 1519 Water: 11.48 71.36 36.62 N/A 214 233 Other: 21.98 33.72 28.02 N/A 0 8 Chain A: 9.26 110.00 19.84 N/A 0 1760 Chain S: 16.42 65.03 36.38 N/A 214 0 Histogram: Values Number of atoms 9.26 - 19.33 1234 19.33 - 29.41 273 29.41 - 39.48 229 39.48 - 49.56 132 49.56 - 59.63 71 59.63 - 69.71 22 69.71 - 79.78 7 79.78 - 89.85 3 89.85 - 99.93 1 99.93 - 110.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1212 r_free=0.1415 r_work=0.1213 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1213 r_free = 0.1416 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1415 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.647446 | | target function (ml) not normalized (work): 303806.744894 | | target function (ml) not normalized (free): 16063.486792 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1206 0.1415 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1534 0.1533 0.1591 n_refl.: 87589 remove outliers: r(all,work,free)=0.1534 0.1533 0.1591 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1532 0.1531 0.1589 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1196 0.1383 n_refl.: 87589 remove outliers: r(all,work,free)=0.1201 0.1192 0.1383 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3876 288.482 260.578 0.470 1.000 0.298 11.894-9.307 97.06 95 4 0.2385 475.776 460.555 0.853 1.001 0.283 9.237-7.194 98.18 209 7 0.2353 383.489 384.661 0.949 1.002 0.180 7.162-5.571 100.00 427 22 0.2028 294.138 284.263 0.910 1.002 0.160 5.546-4.326 100.00 867 58 0.1090 403.779 398.936 0.951 1.002 0.157 4.315-3.360 100.00 1859 96 0.0927 383.996 381.273 0.992 1.002 0.155 3.356-2.611 100.00 3867 181 0.1179 252.266 250.079 1.000 1.002 0.150 2.608-2.026 99.99 8198 413 0.1042 167.229 166.227 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.0998 81.666 81.802 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1276 36.214 35.797 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2119 22.817 21.441 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=-0.0270 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1383 | n_water=447 | time (s): 1.870 (total time: 1.870) Filter (dist) r_work=0.1192 r_free=0.1383 | n_water=447 | time (s): 32.910 (total time: 34.780) Filter (q & B) r_work=0.1192 r_free=0.1383 | n_water=447 | time (s): 0.870 (total time: 35.650) Compute maps r_work=0.1192 r_free=0.1383 | n_water=447 | time (s): 1.240 (total time: 36.890) Filter (map) r_work=0.1216 r_free=0.1384 | n_water=317 | time (s): 2.800 (total time: 39.690) Find peaks r_work=0.1216 r_free=0.1384 | n_water=317 | time (s): 0.450 (total time: 40.140) Add new water r_work=0.1284 r_free=0.1442 | n_water=491 | time (s): 2.750 (total time: 42.890) Refine new water occ: r_work=0.1212 r_free=0.1369 adp: r_work=0.1213 r_free=0.1372 occ: r_work=0.1197 r_free=0.1357 adp: r_work=0.1195 r_free=0.1359 occ: r_work=0.1185 r_free=0.1354 adp: r_work=0.1181 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1354 r_work=0.1181 r_free=0.1354 | n_water=491 | time (s): 150.710 (total time: 193.600) Filter (q & B) r_work=0.1188 r_free=0.1356 | n_water=451 | time (s): 3.140 (total time: 196.740) Filter (dist only) r_work=0.1188 r_free=0.1355 | n_water=450 | time (s): 38.980 (total time: 235.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.801610 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.306947 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1371 0.0178 0.006 0.9 1.9 0.5 0.0 0 0.901 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.71 1.78 3.435 21.538 48.307 3.633 11.87 13.68 1.81 3.634 21.463 48.307 3.624 Individual atomic B min max mean iso aniso Overall: 9.24 106.27 21.41 2.20 219 1758 Protein: 9.24 106.27 17.02 2.21 0 1519 Water: 11.31 70.73 36.15 N/A 219 231 Other: 21.16 31.50 27.01 N/A 0 8 Chain A: 9.24 106.27 19.61 N/A 0 1758 Chain S: 16.29 63.74 35.91 N/A 219 0 Histogram: Values Number of atoms 9.24 - 18.94 1233 18.94 - 28.64 269 28.64 - 38.35 229 38.35 - 48.05 133 48.05 - 57.75 75 57.75 - 67.46 25 67.46 - 77.16 8 77.16 - 86.86 2 86.86 - 96.57 1 96.57 - 106.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1368 r_work=0.1187 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1368 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1370 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623343 | | target function (ml) not normalized (work): 301766.538047 | | target function (ml) not normalized (free): 15949.440502 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1370 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1495 0.1493 0.1566 n_refl.: 87580 remove outliers: r(all,work,free)=0.1495 0.1493 0.1566 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1491 0.1565 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1184 0.1371 n_refl.: 87580 remove outliers: r(all,work,free)=0.1190 0.1181 0.1371 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4121 283.771 252.115 0.431 1.001 0.292 11.894-9.307 93.14 91 4 0.2313 484.435 453.263 0.840 1.002 0.286 9.237-7.194 97.73 208 7 0.2388 384.565 377.642 0.913 1.002 0.130 7.162-5.571 100.00 427 22 0.2143 294.138 282.732 0.898 1.002 0.130 5.546-4.326 100.00 867 58 0.1143 403.779 398.937 0.953 1.002 0.131 4.315-3.360 100.00 1859 96 0.0944 383.996 381.766 0.993 1.002 0.124 3.356-2.611 100.00 3867 181 0.1165 252.266 250.469 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1027 167.229 166.415 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0972 81.666 81.981 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.214 35.865 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.817 21.460 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0256 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1181 r_free=0.1371 After: r_work=0.1182 r_free=0.1371 ================================== NQH flips ================================== r_work=0.1182 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=0.1182 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1371 | n_water=450 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1182 r_free=0.1371 | n_water=450 | time (s): 35.220 (total time: 36.970) Filter (q & B) r_work=0.1182 r_free=0.1371 | n_water=448 | time (s): 2.740 (total time: 39.710) Compute maps r_work=0.1182 r_free=0.1371 | n_water=448 | time (s): 1.390 (total time: 41.100) Filter (map) r_work=0.1204 r_free=0.1391 | n_water=341 | time (s): 2.350 (total time: 43.450) Find peaks r_work=0.1204 r_free=0.1391 | n_water=341 | time (s): 0.600 (total time: 44.050) Add new water r_work=0.1250 r_free=0.1432 | n_water=496 | time (s): 3.150 (total time: 47.200) Refine new water occ: r_work=0.1191 r_free=0.1371 adp: r_work=0.1191 r_free=0.1373 occ: r_work=0.1180 r_free=0.1361 adp: r_work=0.1179 r_free=0.1363 occ: r_work=0.1172 r_free=0.1352 adp: r_work=0.1169 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1169 r_free=0.1354 r_work=0.1169 r_free=0.1354 | n_water=496 | time (s): 192.780 (total time: 239.980) Filter (q & B) r_work=0.1178 r_free=0.1357 | n_water=454 | time (s): 2.680 (total time: 242.660) Filter (dist only) r_work=0.1178 r_free=0.1355 | n_water=453 | time (s): 39.570 (total time: 282.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.929070 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.414326 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 0.1203 0.1376 0.0172 0.006 1.0 2.2 0.5 0.0 0 0.965 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.76 1.72 3.337 21.308 45.414 3.631 12.11 13.81 1.70 3.813 21.162 45.414 3.626 Individual atomic B min max mean iso aniso Overall: 9.25 101.26 21.06 2.02 223 1757 Protein: 9.25 101.26 16.66 2.02 0 1519 Water: 11.51 69.10 35.72 N/A 223 230 Other: 21.77 29.76 26.17 N/A 0 8 Chain A: 9.25 101.26 19.22 N/A 0 1757 Chain S: 14.79 64.22 35.54 N/A 223 0 Histogram: Values Number of atoms 9.25 - 18.45 1229 18.45 - 27.65 267 27.65 - 36.85 226 36.85 - 46.05 135 46.05 - 55.25 77 55.25 - 64.46 30 64.46 - 73.66 11 73.66 - 82.86 2 82.86 - 92.06 1 92.06 - 101.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1381 r_work=0.1211 r_free=0.1381 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1381 target_work(ml) = 3.626 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1376 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1208 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.624982 | | target function (ml) not normalized (work): 301881.217403 | | target function (ml) not normalized (free): 15954.111520 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1451 0.1454 5.7098 5.6614| | 2: 3.57 - 2.84 1.00 2888 124 0.1140 0.1460 5.2196 5.2725| | 3: 2.83 - 2.48 1.00 2820 163 0.1244 0.1260 5.0181 5.0284| | 4: 2.47 - 2.25 1.00 2825 136 0.1039 0.1153 4.7172 4.7671| | 5: 2.25 - 2.09 1.00 2756 127 0.1003 0.1135 4.6584 4.7226| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1169 4.3568 4.4784| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1180 4.0741 4.1713| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1303 3.9884 4.0912| | 9: 1.79 - 1.72 1.00 2745 138 0.0951 0.1247 3.7112 3.8703| | 10: 1.72 - 1.66 1.00 2831 160 0.0999 0.1242 3.6311 3.7622| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1096 3.5664 3.612| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1197 3.3482 3.5023| | 13: 1.56 - 1.52 1.00 2745 130 0.0975 0.1047 3.3406 3.4364| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1137 3.2611 3.3491| | 15: 1.48 - 1.45 1.00 2738 128 0.1011 0.1354 3.1703 3.332| | 16: 1.45 - 1.42 1.00 2756 161 0.1066 0.1249 3.1544 3.2441| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1288 3.1208 3.2296| | 18: 1.39 - 1.36 1.00 2741 179 0.1149 0.1372 3.0871 3.2707| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1603 3.0961 3.2652| | 20: 1.34 - 1.32 1.00 2696 147 0.1328 0.1526 3.092 3.1561| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1627 3.0859 3.1646| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1915 3.0844 3.2949| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1857 3.1033 3.2069| | 24: 1.26 - 1.24 1.00 2744 132 0.1630 0.1741 3.0963 3.1825| | 25: 1.24 - 1.22 1.00 2733 148 0.1804 0.2302 3.1129 3.2896| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1789 3.1242 3.21| | 27: 1.21 - 1.19 1.00 2814 148 0.2009 0.2111 3.1406 3.1501| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2306 3.1415 3.1656| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2392 3.1268 3.2346| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2484 3.1172 3.167| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.94 9.40 1.00 0.97 6466.17| | 2: 3.57 - 2.84 2888 124 0.92 13.63 1.01 0.97 6466.17| | 3: 2.83 - 2.48 2820 163 0.88 17.83 0.99 0.97 5413.67| | 4: 2.47 - 2.25 2825 136 0.91 14.79 1.00 0.97 2699.61| | 5: 2.25 - 2.09 2756 127 0.89 17.06 1.01 0.97 2699.61| | 6: 2.09 - 1.97 2846 113 0.92 13.67 1.02 0.97 1576.08| | 7: 1.97 - 1.87 2787 165 0.94 10.66 1.02 0.97 617.85| | 8: 1.87 - 1.79 2789 144 0.91 14.29 1.00 0.97 617.85| | 9: 1.79 - 1.72 2745 138 0.93 11.37 0.98 0.97 336.72| | 10: 1.72 - 1.66 2831 160 0.93 12.21 0.98 0.97 280.42| | 11: 1.66 - 1.61 2712 147 0.93 12.84 0.98 0.97 267.88| | 12: 1.61 - 1.56 2773 144 0.95 9.64 0.99 0.97 149.61| | 13: 1.56 - 1.52 2745 130 0.94 11.19 1.02 0.97 149.61| | 14: 1.52 - 1.48 2803 134 0.94 11.36 1.02 0.97 133.56| | 15: 1.48 - 1.45 2738 128 0.95 10.49 1.01 0.98 104.16| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.02 0.98 104.16| | 17: 1.42 - 1.39 2785 139 0.94 11.48 1.01 0.98 94.18| | 18: 1.39 - 1.36 2741 179 0.94 11.86 1.01 0.98 88.41| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.98 88.41| | 20: 1.34 - 1.32 2696 147 0.94 12.51 0.99 0.96 83.21| | 21: 1.32 - 1.30 2785 112 0.93 13.43 0.98 0.96 82.84| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.96 82.98| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 83.71| | 24: 1.26 - 1.24 2744 132 0.92 15.03 0.97 0.95 83.71| | 25: 1.24 - 1.22 2733 148 0.91 16.44 0.96 0.94 85.29| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.93 87.05| | 27: 1.21 - 1.19 2814 148 0.89 18.88 1.02 0.93 87.05| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.92 90.58| | 29: 1.18 - 1.16 2800 134 0.88 20.76 0.99 0.92 91.91| | 30: 1.16 - 1.15 2739 148 0.86 22.11 0.98 0.92 91.91| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.84 max = 6466.17 mean = 1001.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.13| |phase err.(test): min = 0.00 max = 89.45 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1208 0.1376 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1512 0.1510 0.1571 n_refl.: 87574 remove outliers: r(all,work,free)=0.1512 0.1510 0.1571 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1511 0.1509 0.1570 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1208 0.1379 n_refl.: 87574 remove outliers: r(all,work,free)=0.1215 0.1207 0.1379 n_refl.: 87571 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4033 283.771 252.859 0.429 0.999 0.291 11.894-9.307 91.18 89 4 0.2360 470.997 460.546 0.863 1.000 0.192 9.237-7.194 97.27 207 7 0.2488 384.091 377.989 0.906 1.001 0.115 7.162-5.571 100.00 427 22 0.2308 294.138 281.022 0.889 1.001 0.110 5.546-4.326 100.00 867 58 0.1245 403.779 398.063 0.953 1.001 0.110 4.315-3.360 100.00 1859 96 0.1007 383.996 381.360 0.995 1.001 0.110 3.356-2.611 100.00 3867 181 0.1211 252.266 249.835 1.001 1.001 0.090 2.608-2.026 99.99 8198 413 0.1051 167.229 166.105 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.666 81.880 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1228 36.214 35.850 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2117 22.817 21.420 0.974 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0248 ================= 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 0.1961 0.082 5.277 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1792 0.082 5.277 9.0 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1792 0.082 5.277 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1797 0.082 5.277 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1797 0.082 5.277 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1216 0.1468 0.007 0.942 9.0 119.5 20.1 258 0.128 1_adp: 0.1240 0.1540 0.007 0.942 8.4 118.4 20.9 258 0.128 1_regHadp: 0.1245 0.1544 0.007 0.942 8.4 118.4 20.9 258 0.128 1_occ: 0.1244 0.1546 0.007 0.942 8.4 118.4 20.9 258 0.128 2_bss: 0.1242 0.1539 0.007 0.942 8.6 118.6 21.1 258 0.128 2_settarget: 0.1242 0.1539 0.007 0.942 8.6 118.6 21.1 258 0.128 2_updatecdl: 0.1242 0.1539 0.007 0.950 8.6 118.6 21.1 258 0.128 2_nqh: 0.1245 0.1541 0.007 0.950 8.6 118.6 21.1 258 0.128 2_sol: 0.1234 0.1502 0.007 0.950 8.6 118.6 23.5 436 n/a 2_weight: 0.1234 0.1502 0.007 0.950 8.6 118.6 23.5 436 n/a 2_xyzrec: 0.1230 0.1515 0.006 0.869 8.6 118.6 23.5 436 n/a 2_adp: 0.1207 0.1490 0.006 0.869 8.9 114.3 23.2 436 n/a 2_regHadp: 0.1206 0.1490 0.006 0.869 8.9 114.3 23.2 436 n/a 2_occ: 0.1207 0.1485 0.006 0.869 8.9 114.3 23.2 436 n/a 3_bss: 0.1203 0.1481 0.006 0.869 8.9 114.3 23.3 436 n/a 3_settarget: 0.1203 0.1481 0.006 0.869 8.9 114.3 23.3 436 n/a 3_updatecdl: 0.1203 0.1481 0.006 0.872 8.9 114.3 23.3 436 n/a 3_nqh: 0.1203 0.1481 0.006 0.872 8.9 114.3 23.3 436 n/a 3_sol: 0.1231 0.1497 0.006 0.872 8.9 114.3 22.0 447 n/a 3_weight: 0.1231 0.1497 0.006 0.872 8.9 114.3 22.0 447 n/a 3_xyzrec: 0.1232 0.1461 0.006 0.940 8.9 114.3 22.0 447 n/a 3_adp: 0.1212 0.1415 0.006 0.940 9.3 110.0 21.6 447 n/a 3_regHadp: 0.1213 0.1416 0.006 0.940 9.3 110.0 21.6 447 n/a 3_occ: 0.1206 0.1415 0.006 0.940 9.3 110.0 21.6 447 n/a 4_bss: 0.1192 0.1383 0.006 0.940 9.2 110.0 21.6 447 n/a 4_settarget: 0.1192 0.1383 0.006 0.940 9.2 110.0 21.6 447 n/a 4_updatecdl: 0.1192 0.1383 0.006 0.940 9.2 110.0 21.6 447 n/a 4_nqh: 0.1192 0.1383 0.006 0.940 9.2 110.0 21.6 447 n/a 4_sol: 0.1188 0.1355 0.006 0.940 9.2 110.0 21.5 450 n/a 4_weight: 0.1188 0.1355 0.006 0.940 9.2 110.0 21.5 450 n/a 4_xyzrec: 0.1194 0.1371 0.006 0.937 9.2 110.0 21.5 450 n/a 4_adp: 0.1187 0.1368 0.006 0.937 9.2 106.3 21.4 450 n/a 4_regHadp: 0.1187 0.1368 0.006 0.937 9.2 106.3 21.4 450 n/a 4_occ: 0.1185 0.1370 0.006 0.937 9.2 106.3 21.4 450 n/a 5_bss: 0.1181 0.1371 0.006 0.937 9.2 106.3 21.4 450 n/a 5_settarget: 0.1181 0.1371 0.006 0.937 9.2 106.3 21.4 450 n/a 5_updatecdl: 0.1181 0.1371 0.006 0.939 9.2 106.3 21.4 450 n/a 5_setrh: 0.1182 0.1371 0.006 0.939 9.2 106.3 21.4 450 n/a 5_nqh: 0.1182 0.1371 0.006 0.939 9.2 106.3 21.4 450 n/a 5_sol: 0.1178 0.1355 0.006 0.939 9.2 106.3 21.3 453 n/a 5_weight: 0.1178 0.1355 0.006 0.939 9.2 106.3 21.3 453 n/a 5_xyzrec: 0.1203 0.1376 0.006 1.015 9.2 106.3 21.3 453 n/a 5_adp: 0.1211 0.1381 0.006 1.015 9.2 101.3 21.1 453 n/a 5_regHadp: 0.1211 0.1381 0.006 1.015 9.2 101.3 21.1 453 n/a 5_occ: 0.1208 0.1376 0.006 1.015 9.2 101.3 21.1 453 n/a end: 0.1207 0.1379 0.006 1.015 9.2 101.3 21.0 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1498316_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1498316_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8100 Refinement macro-cycles (run) : 3332.3200 Write final files (write_after_run_outputs) : 75.5100 Total : 3412.6400 Total CPU time: 57.49 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:33 PST -0800 (1735452513.07 s) Start R-work = 0.1636, R-free = 0.1792 Final R-work = 0.1207, R-free = 0.1379 =============================================================================== Job complete usr+sys time: 3565.83 seconds wall clock time: 64 minutes 2.01 seconds (3842.01 seconds total)