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_2667343.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 2.17, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 248.1 milliseconds Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 716 0.94 - 1.20: 972 1.20 - 1.46: 762 1.46 - 1.72: 690 1.72 - 1.98: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.027 0.208 1.02e-02 9.61e+03 4.16e+02 bond pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 1.237 1.458 -0.221 1.10e-02 8.26e+03 4.03e+02 bond pdb=" CA CYS A 46 " pdb=" C CYS A 46 " ideal model delta sigma weight residual 1.528 1.279 0.250 1.38e-02 5.25e+03 3.27e+02 bond pdb=" C SER A 161 " pdb=" O SER A 161 " ideal model delta sigma weight residual 1.237 1.444 -0.207 1.17e-02 7.31e+03 3.14e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.148 0.173 1.00e-02 1.00e+04 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3450 5.14 - 10.28: 1734 10.28 - 15.42: 524 15.42 - 20.56: 62 20.56 - 25.70: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 135 " pdb=" CB ASN A 135 " pdb=" CG ASN A 135 " ideal model delta sigma weight residual 112.60 128.60 -16.00 1.00e+00 1.00e+00 2.56e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.41 -13.21 9.00e-01 1.23e+00 2.15e+02 angle pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 120.39 106.39 14.00 1.05e+00 9.07e-01 1.78e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.27 108.24 15.03 1.16e+00 7.43e-01 1.68e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 121.32 136.11 -14.79 1.15e+00 7.56e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.98: 934 16.98 - 33.94: 124 33.94 - 50.91: 39 50.91 - 67.88: 10 67.88 - 84.85: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " pdb=" HE1 HIS A 126 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+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 -157.52 -22.48 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.204: 80 0.204 - 0.406: 74 0.406 - 0.608: 53 0.608 - 0.809: 30 0.809 - 1.011: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" C2 ADTT A 201 " pdb=" C1 ADTT A 201 " pdb=" C3 ADTT A 201 " pdb=" O2 ADTT A 201 " both_signs ideal model delta sigma weight residual False -2.43 -1.42 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA GLU A 116 " pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CB GLU A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.053 2.00e-02 2.50e+03 7.44e-02 1.24e+02 pdb=" CG HIS A 138 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.122 9.50e-02 1.11e+02 8.35e-02 1.21e+02 pdb=" NE ARG A 5 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.070 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.070 2.00e-02 2.50e+03 5.82e-02 1.02e+02 pdb=" CG PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1255 2.35 - 2.91: 8223 2.91 - 3.47: 10470 3.47 - 4.04: 15282 4.04 - 4.60: 21441 Nonbonded interactions: 56671 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.786 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.821 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.862 2.450 x-y,-y,-z-4/3 ... (remaining 56666 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_2667343_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= 0.2611 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792063 | | target function (ml) not normalized (work): 232595.585086 | | target function (ml) not normalized (free): 11834.789719 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2128 7.009 4.9541| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1814 4.3525 4.341| | 3: 2.84 - 2.48 1.00 2833 165 0.2348 0.1578 4.1331 4.1579| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1429 3.8417 3.8364| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1609 3.8 3.831| | 6: 2.09 - 1.97 1.00 2846 113 0.2539 0.1767 3.4568 3.5187| | 7: 1.97 - 1.87 1.00 2787 165 0.2563 0.1855 3.1194 3.1967| | 8: 1.87 - 1.79 1.00 2789 144 0.2492 0.1815 3.0542 3.0771| | 9: 1.79 - 1.72 1.00 2745 138 0.2431 0.1777 2.9179 2.9212| | 10: 1.72 - 1.66 1.00 2789 158 0.2383 0.1852 2.7985 2.8106| | 11: 1.66 - 1.61 1.00 2740 147 0.2531 0.1860 2.7511 2.7863| | 12: 1.61 - 1.56 1.00 2787 146 0.2560 0.1848 2.6369 2.6134| | 13: 1.56 - 1.52 1.00 2745 130 0.2562 0.1968 2.5932 2.6103| | 14: 1.52 - 1.48 1.00 2803 134 0.2616 0.2050 2.491 2.5795| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.2278 2.4157 2.5554| | 16: 1.45 - 1.42 1.00 2756 161 0.2639 0.2175 2.3877 2.4458| | 17: 1.42 - 1.39 1.00 2785 139 0.2735 0.1961 2.3415 2.283| | 18: 1.39 - 1.36 1.00 2741 179 0.2656 0.2188 2.2766 2.3158| | 19: 1.36 - 1.34 1.00 2807 134 0.2628 0.2523 2.2517 2.3869| | 20: 1.34 - 1.32 1.00 2696 147 0.2721 0.2278 2.2263 2.2223| | 21: 1.32 - 1.30 1.00 2785 112 0.2711 0.2234 2.1774 2.1794| | 22: 1.29 - 1.27 1.00 2704 152 0.2738 0.2504 2.1352 2.191| | 23: 1.27 - 1.26 1.00 2802 156 0.2790 0.2460 2.1162 2.219| | 24: 1.26 - 1.24 1.00 2744 132 0.2763 0.2545 2.0739 2.1926| | 25: 1.24 - 1.22 1.00 2734 148 0.2819 0.2621 2.0448 2.0926| | 26: 1.22 - 1.21 1.00 2727 135 0.2845 0.2246 2.0204 2.0857| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2621 2.0028 1.9903| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2915 1.9918 2.0666| | 29: 1.18 - 1.16 1.00 2800 134 0.2983 0.2760 1.9649 2.0394| | 30: 1.16 - 1.15 1.00 2740 148 0.3023 0.3082 1.928 2.0089| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.13 0.76 0.23 1512.79| | 2: 3.57 - 2.84 2876 122 0.80 26.41 1.27 0.23 1512.79| | 3: 2.84 - 2.48 2833 165 0.74 32.25 1.24 0.24 1252.77| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 577.97| | 5: 2.25 - 2.09 2756 127 0.77 29.55 1.28 0.25 577.97| | 6: 2.09 - 1.97 2846 113 0.84 22.46 1.29 0.25 312.94| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.29 0.26 86.89| | 8: 1.87 - 1.79 2789 144 0.86 20.51 1.25 0.26 86.89| | 9: 1.79 - 1.72 2745 138 0.89 17.88 1.23 0.26 52.91| | 10: 1.72 - 1.66 2789 158 0.87 19.51 1.22 0.26 46.11| | 11: 1.66 - 1.61 2740 147 0.86 20.82 1.24 0.26 44.55| | 12: 1.61 - 1.56 2787 146 0.89 18.18 1.24 0.25 28.74| | 13: 1.56 - 1.52 2745 130 0.87 19.95 1.23 0.25 28.74| | 14: 1.52 - 1.48 2803 134 0.87 20.53 1.25 0.25 25.88| | 15: 1.48 - 1.45 2738 128 0.87 20.22 1.24 0.25 20.63| | 16: 1.45 - 1.42 2756 161 0.86 21.49 1.23 0.25 20.63| | 17: 1.42 - 1.39 2785 139 0.86 21.07 1.24 0.25 17.63| | 18: 1.39 - 1.36 2741 179 0.86 21.29 1.22 0.25 15.90| | 19: 1.36 - 1.34 2807 134 0.86 21.84 1.21 0.25 15.90| | 20: 1.34 - 1.32 2696 147 0.87 21.13 1.20 0.24 13.35| | 21: 1.32 - 1.30 2785 112 0.85 22.27 1.19 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.92 1.21 0.24 12.92| | 23: 1.27 - 1.26 2802 156 0.85 22.66 1.21 0.24 11.67| | 24: 1.26 - 1.24 2744 132 0.84 23.53 1.20 0.24 11.67| | 25: 1.24 - 1.22 2734 148 0.83 24.50 1.20 0.24 11.24| | 26: 1.22 - 1.21 2727 135 0.83 24.99 1.20 0.23 10.76| | 27: 1.21 - 1.19 2814 148 0.82 26.16 1.21 0.23 10.76| | 28: 1.19 - 1.18 2671 147 0.81 27.14 1.18 0.22 10.49| | 29: 1.18 - 1.16 2800 134 0.80 27.94 1.16 0.22 10.39| | 30: 1.16 - 1.15 2740 148 0.78 29.69 1.15 0.22 10.39| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.39 max = 1512.79 mean = 218.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.93| |phase err.(test): min = 0.00 max = 89.56 mean = 22.79| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.250 1557 Z= 5.477 Angle : 5.405 17.557 2118 Z= 3.813 Chirality : 0.414 1.011 243 Planarity : 0.030 0.104 284 Dihedral : 13.616 84.852 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % 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: -2.16 (0.48), residues: 224 helix: -2.44 (0.37), residues: 107 sheet: -0.79 (0.94), residues: 28 loop : 0.08 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.022 ARG A 145 TYR 0.086 0.039 TYR A 141 PHE 0.092 0.051 PHE A 162 HIS 0.109 0.043 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1943 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792063 | | target function (ml) not normalized (work): 232595.585086 | | target function (ml) not normalized (free): 11834.789719 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2612 0.1943 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2612 0.1943 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1987 0.1943 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2009 0.2013 0.1959 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1642 0.1760 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 0.3814 386.380 357.488 0.663 1.002 0.401 11.894-9.307 99.02 97 4 0.1829 613.747 594.993 0.925 1.003 0.375 9.237-7.194 100.00 213 7 0.2141 501.969 491.906 0.957 1.004 0.361 7.162-5.571 100.00 427 22 0.2249 376.700 364.266 0.930 1.004 0.289 5.546-4.326 100.00 867 58 0.1301 517.116 510.431 0.962 1.003 0.219 4.315-3.360 100.00 1859 96 0.1151 491.781 487.995 1.006 1.003 0.209 3.356-2.611 100.00 3867 181 0.1436 323.075 319.434 0.995 1.002 0.119 2.608-2.026 99.99 8198 413 0.1353 214.169 211.849 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1653 104.589 103.942 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.379 45.047 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2559 29.222 26.978 0.978 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1760 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.579905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2012.849949 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1463 0.0251 0.007 0.9 1.3 0.5 0.0 0 11.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.63 2.51 3.013 19.068 2012.850 0.017 12.41 15.39 2.98 3.140 19.507 2012.850 0.016 Individual atomic B min max mean iso aniso Overall: 8.46 118.40 20.93 2.88 0 1785 Protein: 8.46 118.40 17.82 2.88 0 1519 Water: 11.03 114.72 38.98 N/A 0 258 Other: 22.82 35.67 28.70 N/A 0 8 Chain A: 8.46 118.40 20.93 N/A 0 1785 Histogram: Values Number of atoms 8.46 - 19.46 1207 19.46 - 30.45 232 30.45 - 41.44 164 41.44 - 52.44 100 52.44 - 63.43 53 63.43 - 74.42 17 74.42 - 85.42 5 85.42 - 96.41 4 96.41 - 107.40 0 107.40 - 118.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1539 r_work=0.1246 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1246 r_free = 0.1543 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 = 0.1544 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= 0.1544 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015378 | | target function (ls_wunit_k1) not normalized (work): 1280.909462 | | target function (ls_wunit_k1) not normalized (free): 113.351308 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1259 0.1245 0.1544 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1695 0.1693 0.1762 n_refl.: 87593 remove outliers: r(all,work,free)=0.1695 0.1693 0.1762 n_refl.: 87593 overall B=0.17 to atoms: r(all,work,free)=0.1723 0.1723 0.1782 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1242 0.1538 n_refl.: 87593 remove outliers: r(all,work,free)=0.1256 0.1242 0.1538 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 0.3636 299.035 278.739 0.686 0.923 0.380 11.894-9.307 99.02 97 4 0.1618 479.037 467.253 0.982 0.924 0.380 9.237-7.194 100.00 213 7 0.1823 391.794 386.891 1.027 0.925 0.340 7.162-5.571 100.00 427 22 0.1742 294.019 288.489 0.995 0.925 0.253 5.546-4.326 100.00 867 58 0.0920 403.616 400.862 1.025 0.926 0.209 4.315-3.360 100.00 1859 96 0.0776 383.842 382.865 1.073 0.927 0.199 3.356-2.611 100.00 3867 181 0.1018 252.164 251.467 1.073 0.929 0.062 2.608-2.026 99.99 8198 413 0.0973 167.162 166.593 1.081 0.933 0.000 2.025-1.573 100.00 17313 902 0.1207 81.633 81.823 1.082 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1650 36.199 35.662 1.057 0.947 0.000 1.221-1.150 99.97 13689 708 0.2362 22.808 21.336 1.013 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0400 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1538 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=0.1243 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1243 r_free=0.1539 | n_water=258 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1252 r_free=0.1538 | n_water=252 | time (s): 26.520 (total time: 28.700) Filter (q & B) r_work=0.1256 r_free=0.1537 | n_water=249 | time (s): 3.820 (total time: 32.520) Compute maps r_work=0.1256 r_free=0.1537 | n_water=249 | time (s): 1.870 (total time: 34.390) Filter (map) r_work=0.1268 r_free=0.1548 | n_water=237 | time (s): 3.900 (total time: 38.290) Find peaks r_work=0.1268 r_free=0.1548 | n_water=237 | time (s): 0.740 (total time: 39.030) Add new water r_work=0.1423 r_free=0.1693 | n_water=452 | time (s): 3.870 (total time: 42.900) Refine new water occ: r_work=0.1330 r_free=0.1573 adp: r_work=0.1253 r_free=0.1525 occ: r_work=0.1265 r_free=0.1519 adp: r_work=0.1232 r_free=0.1505 occ: r_work=0.1235 r_free=0.1496 adp: r_work=0.1224 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1494 r_work=0.1224 r_free=0.1494 | n_water=452 | time (s): 84.210 (total time: 127.110) Filter (q & B) r_work=0.1231 r_free=0.1501 | n_water=431 | time (s): 3.910 (total time: 131.020) Filter (dist only) r_work=0.1231 r_free=0.1502 | n_water=430 | time (s): 45.070 (total time: 176.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.621990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1503.597801 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 0.1228 0.1516 0.0287 0.007 0.9 2.9 0.5 0.0 0 12.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 15.16 2.87 3.781 23.146 1503.598 0.015 12.02 14.88 2.86 4.172 22.943 1503.598 0.015 Individual atomic B min max mean iso aniso Overall: 8.67 114.61 23.10 2.59 193 1764 Protein: 8.67 114.61 17.62 2.59 0 1519 Water: 11.05 74.87 42.36 N/A 193 237 Other: 25.28 36.27 29.46 N/A 0 8 Chain A: 8.67 114.61 20.32 N/A 0 1764 Chain S: 15.25 74.87 48.53 N/A 193 0 Histogram: Values Number of atoms 8.67 - 19.26 1207 19.26 - 29.86 246 29.86 - 40.45 191 40.45 - 51.04 146 51.04 - 61.64 110 61.64 - 72.23 44 72.23 - 82.83 7 82.83 - 93.42 3 93.42 - 104.01 1 104.01 - 114.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1488 r_work=0.1202 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1488 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 = 0.1205 r_free = 0.1483 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= 0.1205 r_free= 0.1483 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014051 | | target function (ls_wunit_k1) not normalized (work): 1170.402939 | | target function (ls_wunit_k1) not normalized (free): 103.633807 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1205 0.1483 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1603 0.1704 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1603 0.1704 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1613 0.1609 0.1708 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1202 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1214 0.1200 0.1483 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3221 291.730 273.403 0.596 1.002 0.364 11.894-9.307 99.02 97 4 0.1497 479.037 474.865 0.918 1.003 0.360 9.237-7.194 100.00 213 7 0.1657 391.794 392.706 0.976 1.003 0.280 7.162-5.571 100.00 427 22 0.1501 294.019 290.384 0.939 1.003 0.235 5.546-4.326 100.00 867 58 0.0854 403.616 400.944 0.958 1.003 0.224 4.315-3.360 100.00 1859 96 0.0709 383.842 382.849 1.002 1.003 0.218 3.356-2.611 100.00 3867 181 0.0965 252.164 251.446 1.009 1.002 0.140 2.608-2.026 99.99 8198 413 0.0968 167.162 166.712 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1180 81.633 81.833 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1615 36.199 35.692 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2341 22.808 21.328 0.978 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0614 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1483 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1483 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1483 | n_water=430 | time (s): 2.050 (total time: 2.050) Filter (dist) r_work=0.1200 r_free=0.1483 | n_water=427 | time (s): 39.130 (total time: 41.180) Filter (q & B) r_work=0.1201 r_free=0.1484 | n_water=426 | time (s): 2.430 (total time: 43.610) Compute maps r_work=0.1201 r_free=0.1484 | n_water=426 | time (s): 1.630 (total time: 45.240) Filter (map) r_work=0.1239 r_free=0.1483 | n_water=290 | time (s): 2.660 (total time: 47.900) Find peaks r_work=0.1239 r_free=0.1483 | n_water=290 | time (s): 0.580 (total time: 48.480) Add new water r_work=0.1374 r_free=0.1628 | n_water=492 | time (s): 3.630 (total time: 52.110) Refine new water occ: r_work=0.1270 r_free=0.1518 adp: r_work=0.1272 r_free=0.1520 occ: r_work=0.1248 r_free=0.1499 adp: r_work=0.1247 r_free=0.1499 occ: r_work=0.1232 r_free=0.1482 adp: r_work=0.1226 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1479 r_work=0.1226 r_free=0.1479 | n_water=492 | time (s): 194.230 (total time: 246.340) Filter (q & B) r_work=0.1228 r_free=0.1481 | n_water=455 | time (s): 3.160 (total time: 249.500) Filter (dist only) r_work=0.1227 r_free=0.1480 | n_water=454 | time (s): 41.520 (total time: 291.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.064554 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.865256 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 0.1228 0.1454 0.0226 0.006 0.9 1.6 0.5 0.0 0 1.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.54 2.26 3.610 22.057 47.865 3.725 12.09 14.09 1.99 4.121 21.873 47.865 3.653 Individual atomic B min max mean iso aniso Overall: 9.25 109.96 21.62 2.31 220 1761 Protein: 9.25 109.96 17.19 2.31 0 1519 Water: 11.52 71.07 36.37 N/A 220 234 Other: 21.03 32.36 26.60 N/A 0 8 Chain A: 9.25 109.96 19.84 N/A 0 1761 Chain S: 16.55 64.67 35.87 N/A 220 0 Histogram: Values Number of atoms 9.25 - 19.32 1237 19.32 - 29.40 287 29.40 - 39.47 214 39.47 - 49.54 136 49.54 - 59.61 74 59.61 - 69.68 20 69.68 - 79.75 7 79.75 - 89.82 3 89.82 - 99.89 1 99.89 - 109.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1409 r_work=0.1210 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1410 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1408 target_work(ml) = 3.651 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651302 | | target function (ml) not normalized (work): 304124.282866 | | target function (ml) not normalized (free): 16061.297605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1205 0.1408 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1531 0.1530 0.1573 n_refl.: 87588 remove outliers: r(all,work,free)=0.1531 0.1530 0.1573 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1528 0.1528 0.1571 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1194 0.1372 n_refl.: 87588 remove outliers: r(all,work,free)=0.1199 0.1190 0.1372 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 88.54 80 5 0.3809 283.657 257.836 0.463 1.000 0.297 11.894-9.307 98.04 96 4 0.2457 475.495 464.283 0.855 1.001 0.280 9.237-7.194 98.18 209 7 0.2424 383.335 384.014 0.932 1.001 0.197 7.162-5.571 100.00 427 22 0.2086 294.019 282.571 0.906 1.002 0.163 5.546-4.326 100.00 867 58 0.1104 403.616 398.937 0.951 1.002 0.148 4.315-3.360 100.00 1859 96 0.0911 383.842 381.380 0.995 1.002 0.140 3.356-2.611 100.00 3867 181 0.1136 252.164 250.076 1.000 1.001 0.130 2.608-2.026 99.99 8198 413 0.1033 167.162 166.249 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1005 81.633 81.779 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1294 36.199 35.767 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.808 21.414 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0333 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 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=0.1190 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1372 | n_water=454 | time (s): 2.150 (total time: 2.150) Filter (dist) r_work=0.1190 r_free=0.1372 | n_water=454 | time (s): 36.400 (total time: 38.550) Filter (q & B) r_work=0.1190 r_free=0.1372 | n_water=454 | time (s): 1.210 (total time: 39.760) Compute maps r_work=0.1190 r_free=0.1372 | n_water=454 | time (s): 1.800 (total time: 41.560) Filter (map) r_work=0.1216 r_free=0.1396 | n_water=318 | time (s): 3.200 (total time: 44.760) Find peaks r_work=0.1216 r_free=0.1396 | n_water=318 | time (s): 0.510 (total time: 45.270) Add new water r_work=0.1281 r_free=0.1436 | n_water=479 | time (s): 2.920 (total time: 48.190) Refine new water occ: r_work=0.1213 r_free=0.1367 adp: r_work=0.1214 r_free=0.1370 occ: r_work=0.1197 r_free=0.1356 adp: r_work=0.1196 r_free=0.1358 occ: r_work=0.1186 r_free=0.1348 adp: r_work=0.1182 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1348 r_work=0.1182 r_free=0.1348 | n_water=479 | time (s): 176.420 (total time: 224.610) Filter (q & B) r_work=0.1189 r_free=0.1355 | n_water=446 | time (s): 2.720 (total time: 227.330) Filter (dist only) r_work=0.1189 r_free=0.1354 | n_water=445 | time (s): 37.450 (total time: 264.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.064611 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.820427 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 0.1189 0.1375 0.0186 0.006 1.0 1.6 0.5 0.0 0 1.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.75 1.86 3.415 21.465 48.820 3.635 11.80 13.70 1.90 3.823 21.336 48.820 3.620 Individual atomic B min max mean iso aniso Overall: 9.21 105.39 21.20 2.16 216 1756 Protein: 9.21 105.39 16.89 2.17 0 1519 Water: 11.57 69.50 35.84 N/A 216 229 Other: 20.75 29.55 25.12 N/A 0 8 Chain A: 9.21 105.39 19.41 N/A 0 1756 Chain S: 16.40 60.08 35.71 N/A 216 0 Histogram: Values Number of atoms 9.21 - 18.83 1230 18.83 - 28.45 281 28.45 - 38.07 212 38.07 - 47.69 141 47.69 - 57.30 70 57.30 - 66.92 25 66.92 - 76.54 8 76.54 - 86.16 2 86.16 - 95.77 1 95.77 - 105.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1180 r_free=0.1370 r_work=0.1181 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1370 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1176 r_free = 0.1368 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1176 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618447 | | target function (ml) not normalized (work): 301358.698459 | | target function (ml) not normalized (free): 15929.882866 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1176 0.1368 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1505 0.1503 0.1580 n_refl.: 87580 remove outliers: r(all,work,free)=0.1505 0.1503 0.1580 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1502 0.1499 0.1578 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1175 0.1372 n_refl.: 87580 remove outliers: r(all,work,free)=0.1182 0.1172 0.1372 n_refl.: 87573 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4006 283.657 253.607 0.429 1.000 0.281 11.894-9.307 92.16 90 4 0.2352 460.409 441.236 0.831 1.001 0.202 9.237-7.194 97.73 208 7 0.2377 383.870 377.248 0.909 1.002 0.139 7.162-5.571 100.00 427 22 0.2187 294.019 282.195 0.899 1.002 0.130 5.546-4.326 100.00 867 58 0.1132 403.616 399.281 0.952 1.002 0.130 4.315-3.360 100.00 1859 96 0.0938 383.842 381.902 0.996 1.002 0.130 3.356-2.611 100.00 3867 181 0.1156 252.164 250.288 1.002 1.001 0.053 2.608-2.026 99.99 8198 413 0.1017 167.162 166.324 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0956 81.633 81.925 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.199 35.840 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2122 22.808 21.447 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1172 r_free=0.1372 After: r_work=0.1173 r_free=0.1372 ================================== NQH flips ================================== r_work=0.1173 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=0.1173 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1173 r_free=0.1372 | n_water=445 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1173 r_free=0.1372 | n_water=445 | time (s): 34.000 (total time: 36.210) Filter (q & B) r_work=0.1173 r_free=0.1372 | n_water=445 | time (s): 0.890 (total time: 37.100) Compute maps r_work=0.1173 r_free=0.1372 | n_water=445 | time (s): 1.220 (total time: 38.320) Filter (map) r_work=0.1199 r_free=0.1386 | n_water=332 | time (s): 3.210 (total time: 41.530) Find peaks r_work=0.1199 r_free=0.1386 | n_water=332 | time (s): 0.530 (total time: 42.060) Add new water r_work=0.1245 r_free=0.1428 | n_water=484 | time (s): 3.220 (total time: 45.280) Refine new water occ: r_work=0.1187 r_free=0.1360 adp: r_work=0.1187 r_free=0.1364 occ: r_work=0.1175 r_free=0.1348 adp: r_work=0.1174 r_free=0.1351 occ: r_work=0.1167 r_free=0.1338 adp: r_work=0.1164 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1340 r_work=0.1164 r_free=0.1340 | n_water=484 | time (s): 196.450 (total time: 241.730) Filter (q & B) r_work=0.1171 r_free=0.1349 | n_water=445 | time (s): 3.400 (total time: 245.130) Filter (dist only) r_work=0.1171 r_free=0.1347 | n_water=443 | time (s): 38.330 (total time: 283.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.922509 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.635674 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 0.1364 0.0172 0.008 1.0 2.9 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.64 1.72 3.284 21.043 48.636 3.621 11.94 13.65 1.71 3.484 20.973 48.636 3.616 Individual atomic B min max mean iso aniso Overall: 9.28 101.39 20.90 2.03 215 1755 Protein: 9.28 101.39 16.71 2.03 0 1519 Water: 11.52 68.54 35.19 N/A 215 228 Other: 20.79 29.00 24.86 N/A 0 8 Chain A: 9.28 101.39 19.21 N/A 0 1755 Chain S: 15.89 58.87 34.72 N/A 215 0 Histogram: Values Number of atoms 9.28 - 18.49 1225 18.49 - 27.70 279 27.70 - 36.91 212 36.91 - 46.12 145 46.12 - 55.33 73 55.33 - 64.54 20 64.54 - 73.75 11 73.75 - 82.96 2 82.96 - 92.17 1 92.17 - 101.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1365 r_work=0.1194 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1360 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1192 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.614412 | | target function (ml) not normalized (work): 300997.364084 | | target function (ml) not normalized (free): 15903.973946 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1416 0.1416 5.6905 5.6213| | 2: 3.57 - 2.84 1.00 2888 124 0.1126 0.1443 5.1961 5.2697| | 3: 2.83 - 2.48 1.00 2820 163 0.1220 0.1269 4.9992 5.0117| | 4: 2.47 - 2.25 1.00 2825 136 0.1027 0.1208 4.6998 4.7704| | 5: 2.25 - 2.09 1.00 2756 127 0.0992 0.1094 4.6413 4.7035| | 6: 2.09 - 1.97 1.00 2846 113 0.0961 0.1131 4.3409 4.4342| | 7: 1.97 - 1.87 1.00 2787 165 0.0981 0.1214 4.067 4.1773| | 8: 1.87 - 1.79 1.00 2789 144 0.1012 0.1225 3.9809 4.0686| | 9: 1.79 - 1.72 1.00 2745 138 0.0934 0.1240 3.6982 3.8748| | 10: 1.72 - 1.66 1.00 2831 160 0.0986 0.1273 3.6173 3.7604| | 11: 1.66 - 1.61 1.00 2712 147 0.0959 0.1115 3.5567 3.6073| | 12: 1.61 - 1.56 1.00 2773 144 0.0908 0.1129 3.3364 3.4722| | 13: 1.56 - 1.52 1.00 2745 130 0.0964 0.1017 3.3266 3.4162| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1076 3.2498 3.3118| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1304 3.1524 3.3175| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1229 3.139 3.2317| | 17: 1.42 - 1.39 1.00 2785 139 0.1106 0.1268 3.103 3.2189| | 18: 1.39 - 1.36 1.00 2741 179 0.1141 0.1368 3.0757 3.2536| | 19: 1.36 - 1.34 1.00 2807 134 0.1206 0.1574 3.0837 3.264| | 20: 1.34 - 1.32 1.00 2696 147 0.1314 0.1477 3.0808 3.1311| | 21: 1.32 - 1.30 1.00 2785 112 0.1407 0.1577 3.0803 3.1436| | 22: 1.29 - 1.27 1.00 2704 152 0.1473 0.1900 3.0806 3.2779| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1843 3.099 3.203| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1758 3.0921 3.1931| | 25: 1.24 - 1.22 1.00 2733 148 0.1782 0.2270 3.1053 3.282| | 26: 1.22 - 1.21 1.00 2727 135 0.1857 0.1796 3.1215 3.2013| | 27: 1.21 - 1.19 1.00 2814 148 0.2008 0.2091 3.1411 3.1514| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2318 3.1417 3.1676| | 29: 1.18 - 1.16 1.00 2800 134 0.2211 0.2394 3.1268 3.2311| | 30: 1.16 - 1.15 1.00 2739 148 0.2376 0.2477 3.1168 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 2915 171 0.95 9.00 1.00 0.97 6132.01| | 2: 3.57 - 2.84 2888 124 0.92 13.10 1.01 0.97 6132.01| | 3: 2.83 - 2.48 2820 163 0.89 17.28 0.99 0.97 5140.81| | 4: 2.47 - 2.25 2825 136 0.91 14.39 1.00 0.98 2584.82| | 5: 2.25 - 2.09 2756 127 0.90 16.65 1.01 0.98 2584.82| | 6: 2.09 - 1.97 2846 113 0.92 13.44 1.02 0.97 1520.28| | 7: 1.97 - 1.87 2787 165 0.94 10.62 1.02 0.97 612.37| | 8: 1.87 - 1.79 2789 144 0.91 14.21 1.00 0.97 612.37| | 9: 1.79 - 1.72 2745 138 0.93 11.22 0.98 0.97 330.04| | 10: 1.72 - 1.66 2831 160 0.93 12.04 0.98 0.97 273.50| | 11: 1.66 - 1.61 2712 147 0.93 12.68 0.98 0.97 261.12| | 12: 1.61 - 1.56 2773 144 0.95 9.41 0.99 0.97 144.43| | 13: 1.56 - 1.52 2745 130 0.94 10.93 1.02 0.97 144.43| | 14: 1.52 - 1.48 2803 134 0.94 11.10 1.02 0.97 128.69| | 15: 1.48 - 1.45 2738 128 0.95 10.15 1.01 0.98 99.84| | 16: 1.45 - 1.42 2756 161 0.94 11.33 1.01 0.98 99.84| | 17: 1.42 - 1.39 2785 139 0.95 11.18 1.01 0.98 90.40| | 18: 1.39 - 1.36 2741 179 0.95 11.47 1.01 0.98 84.94| | 19: 1.36 - 1.34 2807 134 0.94 12.02 1.00 0.98 84.94| | 20: 1.34 - 1.32 2696 147 0.94 12.23 0.99 0.96 80.33| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.96 80.01| | 22: 1.29 - 1.27 2704 152 0.93 13.76 0.98 0.96 80.30| | 23: 1.27 - 1.26 2802 156 0.93 14.71 0.98 0.95 81.80| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.97 0.95 81.80| | 25: 1.24 - 1.22 2733 148 0.91 16.27 0.96 0.94 83.79| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.00| | 27: 1.21 - 1.19 2814 148 0.89 18.66 1.02 0.93 86.00| | 28: 1.19 - 1.18 2671 147 0.88 20.34 1.01 0.93 90.25| | 29: 1.18 - 1.16 2800 134 0.88 20.69 0.99 0.92 91.85| | 30: 1.16 - 1.15 2739 148 0.86 22.13 0.98 0.92 91.85| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 80.01 max = 6132.01 mean = 956.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.89| |phase err.(test): min = 0.00 max = 89.88 mean = 13.93| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1192 0.1360 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1509 0.1508 0.1553 n_refl.: 87573 remove outliers: r(all,work,free)=0.1509 0.1508 0.1553 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1507 0.1506 0.1551 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1193 0.1360 n_refl.: 87573 remove outliers: r(all,work,free)=0.1200 0.1191 0.1360 n_refl.: 87570 ======================== 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 0.4017 286.239 248.290 0.428 1.002 0.298 11.894-9.307 91.18 89 4 0.2373 464.325 441.085 0.833 1.002 0.290 9.237-7.194 97.27 207 7 0.2541 384.953 375.579 0.903 1.002 0.163 7.162-5.571 100.00 427 22 0.2270 294.019 281.709 0.893 1.003 0.144 5.546-4.326 100.00 867 58 0.1192 403.616 398.976 0.951 1.002 0.117 4.315-3.360 100.00 1859 96 0.0990 383.842 381.690 0.996 1.002 0.113 3.356-2.611 100.00 3867 181 0.1195 252.164 250.145 1.001 1.001 0.048 2.608-2.026 99.99 8198 413 0.1034 167.162 166.217 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0964 81.633 81.929 1.029 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1217 36.199 35.834 1.024 0.995 0.000 1.221-1.150 99.97 13689 708 0.2114 22.808 21.437 0.983 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0354 ================= 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 : 0.2611 0.1943 0.084 5.405 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_weight: 0.1642 0.1760 0.084 5.405 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1463 0.007 0.940 9.1 119.5 20.1 258 0.125 1_adp: 0.1241 0.1539 0.007 0.940 8.5 118.4 20.9 258 0.125 1_regHadp: 0.1246 0.1543 0.007 0.940 8.5 118.4 20.9 258 0.125 1_occ: 0.1245 0.1544 0.007 0.940 8.5 118.4 20.9 258 0.125 2_bss: 0.1242 0.1538 0.007 0.940 8.6 118.6 21.1 258 0.125 2_settarget: 0.1242 0.1538 0.007 0.940 8.6 118.6 21.1 258 0.125 2_updatecdl: 0.1242 0.1538 0.007 0.940 8.6 118.6 21.1 258 0.125 2_nqh: 0.1243 0.1539 0.007 0.940 8.6 118.6 21.1 258 0.128 2_sol: 0.1231 0.1502 0.007 0.940 8.6 118.6 23.5 430 n/a 2_weight: 0.1231 0.1502 0.007 0.940 8.6 118.6 23.5 430 n/a 2_xyzrec: 0.1228 0.1516 0.007 0.875 8.6 118.6 23.5 430 n/a 2_adp: 0.1202 0.1488 0.007 0.875 8.7 114.6 23.1 430 n/a 2_regHadp: 0.1202 0.1488 0.007 0.875 8.7 114.6 23.1 430 n/a 2_occ: 0.1205 0.1483 0.007 0.875 8.7 114.6 23.1 430 n/a 3_bss: 0.1200 0.1483 0.007 0.875 8.7 114.6 23.1 430 n/a 3_settarget: 0.1200 0.1483 0.007 0.875 8.7 114.6 23.1 430 n/a 3_updatecdl: 0.1200 0.1483 0.007 0.875 8.7 114.6 23.1 430 n/a 3_nqh: 0.1200 0.1483 0.007 0.875 8.7 114.6 23.1 430 n/a 3_sol: 0.1227 0.1480 0.007 0.875 8.7 114.6 22.0 454 n/a 3_weight: 0.1227 0.1480 0.007 0.875 8.7 114.6 22.0 454 n/a 3_xyzrec: 0.1228 0.1454 0.006 0.920 8.7 114.6 22.0 454 n/a 3_adp: 0.1209 0.1409 0.006 0.920 9.3 110.0 21.6 454 n/a 3_regHadp: 0.1210 0.1410 0.006 0.920 9.3 110.0 21.6 454 n/a 3_occ: 0.1205 0.1408 0.006 0.920 9.3 110.0 21.6 454 n/a 4_bss: 0.1190 0.1372 0.006 0.920 9.2 109.9 21.6 454 n/a 4_settarget: 0.1190 0.1372 0.006 0.920 9.2 109.9 21.6 454 n/a 4_updatecdl: 0.1190 0.1372 0.006 0.921 9.2 109.9 21.6 454 n/a 4_nqh: 0.1190 0.1372 0.006 0.921 9.2 109.9 21.6 454 n/a 4_sol: 0.1189 0.1354 0.006 0.921 9.2 109.9 21.4 445 n/a 4_weight: 0.1189 0.1354 0.006 0.921 9.2 109.9 21.4 445 n/a 4_xyzrec: 0.1189 0.1375 0.006 0.965 9.2 109.9 21.4 445 n/a 4_adp: 0.1180 0.1370 0.006 0.965 9.2 105.4 21.2 445 n/a 4_regHadp: 0.1181 0.1370 0.006 0.965 9.2 105.4 21.2 445 n/a 4_occ: 0.1176 0.1368 0.006 0.965 9.2 105.4 21.2 445 n/a 5_bss: 0.1172 0.1372 0.006 0.965 9.2 105.4 21.2 445 n/a 5_settarget: 0.1172 0.1372 0.006 0.965 9.2 105.4 21.2 445 n/a 5_updatecdl: 0.1172 0.1372 0.006 0.964 9.2 105.4 21.2 445 n/a 5_setrh: 0.1173 0.1372 0.006 0.964 9.2 105.4 21.2 445 n/a 5_nqh: 0.1173 0.1372 0.006 0.964 9.2 105.4 21.2 445 n/a 5_sol: 0.1171 0.1347 0.006 0.964 9.2 105.4 21.0 443 n/a 5_weight: 0.1171 0.1347 0.006 0.964 9.2 105.4 21.0 443 n/a 5_xyzrec: 0.1191 0.1364 0.008 1.038 9.2 105.4 21.0 443 n/a 5_adp: 0.1194 0.1365 0.008 1.038 9.3 101.4 20.9 443 n/a 5_regHadp: 0.1194 0.1365 0.008 1.038 9.3 101.4 20.9 443 n/a 5_occ: 0.1192 0.1360 0.008 1.038 9.3 101.4 20.9 443 n/a end: 0.1191 0.1360 0.008 1.038 9.3 101.4 20.9 443 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2667343_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2667343_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0300 Refinement macro-cycles (run) : 3515.8100 Write final files (write_after_run_outputs) : 71.3100 Total : 3592.1500 Total CPU time: 60.49 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.07 s) Start R-work = 0.1642, R-free = 0.1760 Final R-work = 0.1191, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 3731.23 seconds wall clock time: 66 minutes 58.20 seconds (4018.20 seconds total)