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_2353655.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_2353655.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2353655.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 =============================================================================== 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: 2.14, per 1000 atoms: 0.63 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 353.6 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 532 0.91 - 1.16: 1109 1.16 - 1.42: 624 1.42 - 1.67: 838 1.67 - 1.92: 50 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 0.974 0.262 1.19e-02 7.06e+03 4.84e+02 bond pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 1.523 1.699 -0.176 9.20e-03 1.18e+04 3.64e+02 bond pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 1.237 1.011 0.226 1.19e-02 7.06e+03 3.59e+02 bond pdb=" ND1 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 1.321 1.132 0.189 1.00e-02 1.00e+04 3.57e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.639 -0.100 5.40e-03 3.43e+04 3.41e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 3034 4.38 - 8.76: 1829 8.76 - 13.13: 729 13.13 - 17.51: 159 17.51 - 21.89: 26 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 134.62 -13.12 1.00e+00 1.00e+00 1.72e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.15 137.09 -14.94 1.14e+00 7.69e-01 1.72e+02 angle pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " pdb=" CG PHE A 119 " ideal model delta sigma weight residual 113.80 126.88 -13.08 1.00e+00 1.00e+00 1.71e+02 angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.19 109.67 11.52 9.40e-01 1.13e+00 1.50e+02 angle pdb=" O PRO A 158 " pdb=" C PRO A 158 " pdb=" N GLY A 159 " ideal model delta sigma weight residual 122.23 136.92 -14.69 1.20e+00 6.94e-01 1.50e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 924 16.75 - 33.50: 127 33.50 - 50.25: 43 50.25 - 67.00: 15 67.00 - 83.75: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 105 0.225 - 0.449: 85 0.449 - 0.673: 38 0.673 - 0.897: 8 0.897 - 1.122: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 14 " pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CB ALA A 14 " both_signs ideal model delta sigma weight residual False 2.48 3.61 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.58 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.090 9.50e-02 1.11e+02 7.28e-02 1.00e+02 pdb=" NE ARG A 156 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " 0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " -0.077 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.034 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " -0.066 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.67e-02 9.65e+01 pdb=" CG BTYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.070 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.048 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.114 2.00e-02 2.50e+03 6.49e-02 9.46e+01 pdb=" CG HIS A 138 " -0.112 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 984 2.31 - 2.88: 8064 2.88 - 3.46: 10527 3.46 - 4.03: 15145 4.03 - 4.60: 21916 Nonbonded interactions: 56636 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.738 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.766 2.100 nonbonded pdb=" HE3ALYS A 132 " pdb=" HO2ADTT A 201 " model vdw 1.792 2.270 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.808 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.832 2.450 ... (remaining 56631 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_2353655_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= 0.2594 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.780728 | | target function (ml) not normalized (work): 231651.315679 | | target function (ml) not normalized (free): 11805.514883 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3026 0.2092 7.0432 4.9518| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1746 4.3497 4.3356| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1634 4.1285 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2322 0.1559 3.8378 3.8479| | 5: 2.25 - 2.09 1.00 2756 127 0.2504 0.1553 3.7977 3.8116| | 6: 2.09 - 1.97 1.00 2846 113 0.2494 0.1680 3.4535 3.5476| | 7: 1.97 - 1.87 1.00 2787 165 0.2520 0.1820 3.1252 3.1758| | 8: 1.87 - 1.79 1.00 2789 144 0.2423 0.1840 3.037 3.1328| | 9: 1.79 - 1.72 1.00 2745 138 0.2374 0.1946 2.8905 2.9844| | 10: 1.72 - 1.66 1.00 2789 158 0.2368 0.1940 2.7972 2.884| | 11: 1.66 - 1.61 1.00 2740 147 0.2466 0.1964 2.7246 2.7751| | 12: 1.61 - 1.56 1.00 2787 146 0.2517 0.2007 2.594 2.5956| | 13: 1.56 - 1.52 1.00 2745 130 0.2549 0.1881 2.5565 2.5924| | 14: 1.52 - 1.48 1.00 2803 134 0.2576 0.2005 2.5203 2.5338| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.2299 2.4169 2.5561| | 16: 1.45 - 1.42 1.00 2756 161 0.2658 0.2065 2.3807 2.3974| | 17: 1.42 - 1.39 1.00 2785 139 0.2688 0.2074 2.321 2.3753| | 18: 1.39 - 1.36 1.00 2741 179 0.2673 0.2273 2.2538 2.3778| | 19: 1.36 - 1.34 1.00 2807 134 0.2617 0.2523 2.2223 2.3968| | 20: 1.34 - 1.32 1.00 2696 147 0.2637 0.2348 2.1852 2.254| | 21: 1.32 - 1.30 1.00 2785 112 0.2654 0.2189 2.1684 2.1299| | 22: 1.29 - 1.27 1.00 2704 152 0.2687 0.2645 2.1209 2.2453| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2285 2.0994 2.1076| | 24: 1.26 - 1.24 1.00 2744 132 0.2773 0.2330 2.0673 2.1016| | 25: 1.24 - 1.22 1.00 2734 148 0.2824 0.2512 2.0332 2.0254| | 26: 1.22 - 1.21 1.00 2727 135 0.2883 0.2233 2.0029 2.0798| | 27: 1.21 - 1.19 1.00 2814 148 0.2918 0.2435 1.9849 1.9532| | 28: 1.19 - 1.18 1.00 2671 147 0.2976 0.2800 1.9698 1.9874| | 29: 1.18 - 1.16 1.00 2800 134 0.2970 0.2779 1.955 2.0481| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.2824 1.9277 1.9306| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.77 0.76 0.23 1495.94| | 2: 3.57 - 2.84 2876 122 0.80 26.15 1.27 0.23 1495.94| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.25 0.24 1239.86| | 4: 2.47 - 2.25 2825 136 0.81 25.63 1.25 0.25 575.28| | 5: 2.25 - 2.09 2756 127 0.77 29.48 1.29 0.25 575.28| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.29 0.25 313.50| | 7: 1.97 - 1.87 2787 165 0.90 16.55 1.28 0.25 90.24| | 8: 1.87 - 1.79 2789 144 0.86 21.11 1.25 0.25 90.24| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.23 0.25 55.01| | 10: 1.72 - 1.66 2789 158 0.87 20.09 1.22 0.25 47.95| | 11: 1.66 - 1.61 2740 147 0.86 21.39 1.24 0.25 46.28| | 12: 1.61 - 1.56 2787 146 0.88 18.65 1.24 0.25 29.32| | 13: 1.56 - 1.52 2745 130 0.87 20.35 1.24 0.25 29.32| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.23 0.25 26.39| | 15: 1.48 - 1.45 2738 128 0.87 20.33 1.24 0.25 21.02| | 16: 1.45 - 1.42 2756 161 0.85 21.82 1.24 0.25 21.02| | 17: 1.42 - 1.39 2785 139 0.86 20.99 1.24 0.25 17.90| | 18: 1.39 - 1.36 2741 179 0.86 21.43 1.24 0.25 16.09| | 19: 1.36 - 1.34 2807 134 0.85 22.27 1.22 0.25 16.09| | 20: 1.34 - 1.32 2696 147 0.86 21.12 1.20 0.25 13.25| | 21: 1.32 - 1.30 2785 112 0.86 22.00 1.19 0.25 13.05| | 22: 1.29 - 1.27 2704 152 0.85 22.53 1.21 0.24 12.69| | 23: 1.27 - 1.26 2802 156 0.86 21.81 1.20 0.24 10.83| | 24: 1.26 - 1.24 2744 132 0.85 22.61 1.20 0.24 10.83| | 25: 1.24 - 1.22 2734 148 0.85 23.30 1.21 0.24 10.23| | 26: 1.22 - 1.21 2727 135 0.84 23.67 1.21 0.23 9.57| | 27: 1.21 - 1.19 2814 148 0.83 24.49 1.21 0.23 9.57| | 28: 1.19 - 1.18 2671 147 0.83 24.88 1.19 0.23 9.03| | 29: 1.18 - 1.16 2800 134 0.83 25.11 1.17 0.23 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.85 1.15 0.23 8.83| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.83 max = 1495.94 mean = 216.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.59| |phase err.(test): min = 0.00 max = 89.79 mean = 22.40| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.262 1557 Z= 5.579 Angle : 5.302 19.172 2118 Z= 3.691 Chirality : 0.374 1.122 243 Planarity : 0.033 0.109 284 Dihedral : 13.894 83.747 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -1.96 (0.51), residues: 224 helix: -2.43 (0.37), residues: 108 sheet: 0.13 (0.94), residues: 28 loop : 0.11 (0.67), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.027 ARG A 145 TYR 0.086 0.035 TYR A 141 PHE 0.103 0.033 PHE A 119 HIS 0.053 0.028 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2594 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.780728 | | target function (ml) not normalized (work): 231651.315679 | | target function (ml) not normalized (free): 11805.514883 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2552 0.2594 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2552 0.2594 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1965 0.1968 0.1941 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1987 0.1991 0.1952 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1626 0.1619 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1626 0.1619 0.1765 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 0.3863 386.290 358.196 0.675 1.003 0.414 11.894-9.307 99.02 97 4 0.1842 613.603 592.725 0.931 1.004 0.400 9.237-7.194 100.00 213 7 0.2167 501.852 492.504 0.963 1.004 0.354 7.162-5.571 100.00 427 22 0.2183 376.612 364.362 0.930 1.004 0.293 5.546-4.326 100.00 867 58 0.1290 516.995 511.330 0.962 1.004 0.224 4.315-3.360 100.00 1859 96 0.1145 491.666 487.807 1.006 1.004 0.199 3.356-2.611 100.00 3867 181 0.1429 322.999 319.976 0.997 1.003 0.048 2.608-2.026 99.99 8198 413 0.1337 214.119 212.058 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1608 104.565 103.935 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2041 46.368 45.133 1.004 0.995 0.000 1.221-1.150 99.97 13689 708 0.2555 29.215 26.984 0.980 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0416 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1623 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.400603 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.566442 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1209 0.1465 0.0257 0.008 1.0 1.3 0.5 0.0 0 14.700 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.65 2.57 3.013 19.040 2014.566 0.017 12.43 15.38 2.96 3.308 19.590 2014.566 0.016 Individual atomic B min max mean iso aniso Overall: 8.59 118.78 21.11 2.89 0 1785 Protein: 8.59 118.78 17.96 2.89 0 1519 Water: 11.15 114.51 39.39 N/A 0 258 Other: 23.53 37.10 29.73 N/A 0 8 Chain A: 8.59 118.78 21.11 N/A 0 1785 Histogram: Values Number of atoms 8.59 - 19.60 1207 19.60 - 30.62 230 30.62 - 41.64 159 41.64 - 52.66 105 52.66 - 63.68 51 63.68 - 74.70 17 74.70 - 85.72 9 85.72 - 96.74 2 96.74 - 107.76 2 107.76 - 118.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1538 r_work=0.1247 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1247 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 = 0.1248 r_free = 0.1545 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1248 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015386 | | target function (ls_wunit_k1) not normalized (work): 1281.627507 | | target function (ls_wunit_k1) not normalized (free): 115.423485 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1248 0.1545 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1704 0.1770 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1729 0.1728 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1245 0.1536 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1245 0.1536 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3621 298.972 278.964 0.688 0.921 0.380 11.894-9.307 99.02 97 4 0.1596 478.936 466.725 0.985 0.922 0.380 9.237-7.194 100.00 213 7 0.1820 391.711 386.473 1.032 0.923 0.340 7.162-5.571 100.00 427 22 0.1711 293.957 288.672 1.001 0.923 0.253 5.546-4.326 100.00 867 58 0.0910 403.531 400.946 1.028 0.924 0.204 4.315-3.360 100.00 1859 96 0.0773 383.761 382.778 1.078 0.925 0.190 3.356-2.611 100.00 3867 181 0.1021 252.111 251.347 1.078 0.928 0.048 2.608-2.026 99.99 8198 413 0.0980 167.126 166.482 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1217 81.616 81.778 1.085 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1653 36.192 35.652 1.059 0.947 0.000 1.221-1.150 99.97 13689 708 0.2363 22.803 21.335 1.013 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0554 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1247 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1538 | n_water=258 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1256 r_free=0.1537 | n_water=252 | time (s): 26.650 (total time: 29.260) Filter (q & B) r_work=0.1259 r_free=0.1536 | n_water=249 | time (s): 3.850 (total time: 33.110) Compute maps r_work=0.1259 r_free=0.1536 | n_water=249 | time (s): 1.850 (total time: 34.960) Filter (map) r_work=0.1276 r_free=0.1540 | n_water=235 | time (s): 3.760 (total time: 38.720) Find peaks r_work=0.1276 r_free=0.1540 | n_water=235 | time (s): 0.720 (total time: 39.440) Add new water r_work=0.1436 r_free=0.1709 | n_water=462 | time (s): 3.770 (total time: 43.210) Refine new water occ: r_work=0.1340 r_free=0.1585 adp: r_work=0.1257 r_free=0.1522 occ: r_work=0.1270 r_free=0.1524 adp: r_work=0.1234 r_free=0.1498 occ: r_work=0.1238 r_free=0.1489 adp: r_work=0.1228 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1488 r_work=0.1228 r_free=0.1488 | n_water=462 | time (s): 81.600 (total time: 124.810) Filter (q & B) r_work=0.1234 r_free=0.1493 | n_water=439 | time (s): 3.920 (total time: 128.730) Filter (dist only) r_work=0.1234 r_free=0.1493 | n_water=439 | time (s): 42.200 (total time: 170.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.031683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1553.352983 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 0.1238 0.1529 0.0291 0.007 0.9 1.9 0.5 0.0 0 12.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 15.29 2.91 3.811 23.316 1553.353 0.015 12.06 15.06 3.00 4.305 23.102 1553.353 0.015 Individual atomic B min max mean iso aniso Overall: 8.75 113.92 23.29 2.64 204 1762 Protein: 8.75 113.92 17.68 2.64 0 1519 Water: 11.06 73.73 42.63 N/A 204 235 Other: 21.85 33.53 26.87 N/A 0 8 Chain A: 8.75 113.92 20.39 N/A 0 1762 Chain S: 17.01 73.73 48.30 N/A 204 0 Histogram: Values Number of atoms 8.75 - 19.27 1208 19.27 - 29.79 245 29.79 - 40.30 203 40.30 - 50.82 127 50.82 - 61.34 113 61.34 - 71.86 55 71.86 - 82.37 9 82.37 - 92.89 2 92.89 - 103.41 2 103.41 - 113.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1506 r_work=0.1206 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1507 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 = 0.1205 r_free = 0.1506 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= 0.1506 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014058 | | target function (ls_wunit_k1) not normalized (work): 1170.952390 | | target function (ls_wunit_k1) not normalized (free): 111.259733 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1205 0.1506 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1598 0.1735 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1598 0.1735 n_refl.: 87592 overall B=0.09 to atoms: r(all,work,free)=0.1616 0.1611 0.1743 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1202 0.1502 n_refl.: 87592 remove outliers: r(all,work,free)=0.1216 0.1201 0.1502 n_refl.: 87590 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3375 297.532 274.417 0.586 1.002 0.370 11.894-9.307 99.02 97 4 0.1563 478.936 475.285 0.898 1.003 0.360 9.237-7.194 100.00 213 7 0.1695 391.711 391.711 0.971 1.003 0.280 7.162-5.571 100.00 427 22 0.1518 293.957 289.726 0.924 1.003 0.209 5.546-4.326 100.00 867 58 0.0835 403.531 400.972 0.946 1.003 0.200 4.315-3.360 100.00 1859 96 0.0707 383.761 382.592 0.992 1.002 0.190 3.356-2.611 100.00 3867 181 0.0954 252.111 251.470 1.001 1.002 0.067 2.608-2.026 99.99 8198 413 0.0964 167.126 166.690 1.009 1.001 0.000 2.025-1.573 100.00 17313 902 0.1187 81.616 81.816 1.019 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1622 36.192 35.683 1.009 0.998 0.000 1.221-1.150 99.97 13689 708 0.2340 22.803 21.329 0.971 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0338 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1502 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1502 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1502 | n_water=439 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1201 r_free=0.1502 | n_water=438 | time (s): 38.790 (total time: 41.090) Filter (q & B) r_work=0.1201 r_free=0.1502 | n_water=438 | time (s): 1.050 (total time: 42.140) Compute maps r_work=0.1201 r_free=0.1502 | n_water=438 | time (s): 1.540 (total time: 43.680) Filter (map) r_work=0.1242 r_free=0.1480 | n_water=296 | time (s): 2.610 (total time: 46.290) Find peaks r_work=0.1242 r_free=0.1480 | n_water=296 | time (s): 0.640 (total time: 46.930) Add new water r_work=0.1368 r_free=0.1597 | n_water=499 | time (s): 3.260 (total time: 50.190) Refine new water occ: r_work=0.1266 r_free=0.1513 adp: r_work=0.1267 r_free=0.1514 occ: r_work=0.1243 r_free=0.1496 adp: r_work=0.1241 r_free=0.1495 occ: r_work=0.1227 r_free=0.1485 adp: r_work=0.1221 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1482 r_work=0.1221 r_free=0.1482 | n_water=499 | time (s): 155.250 (total time: 205.440) Filter (q & B) r_work=0.1224 r_free=0.1485 | n_water=457 | time (s): 3.100 (total time: 208.540) Filter (dist only) r_work=0.1224 r_free=0.1483 | n_water=456 | time (s): 39.320 (total time: 247.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.082840 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.794675 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1449 0.0220 0.006 0.9 3.2 0.5 0.0 0 1.041 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.49 2.20 3.637 22.216 41.795 3.729 12.18 14.01 1.84 4.101 22.029 41.795 3.659 Individual atomic B min max mean iso aniso Overall: 9.22 109.23 21.83 2.32 222 1761 Protein: 9.22 109.23 17.30 2.32 0 1519 Water: 11.63 71.02 36.84 N/A 222 234 Other: 18.78 30.10 24.55 N/A 0 8 Chain A: 9.22 109.23 20.01 N/A 0 1761 Chain S: 15.90 67.07 36.23 N/A 222 0 Histogram: Values Number of atoms 9.22 - 19.23 1232 19.23 - 29.23 276 29.23 - 39.23 216 39.23 - 49.23 148 49.23 - 59.23 76 59.23 - 69.23 22 69.23 - 79.23 7 79.23 - 89.23 3 89.23 - 99.23 1 99.23 - 109.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1401 r_work=0.1219 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1403 target_work(ml) = 3.660 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1213 r_free = 0.1402 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1213 r_free= 0.1402 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.657673 | | target function (ml) not normalized (work): 304662.201034 | | target function (ml) not normalized (free): 16082.284348 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1213 0.1402 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1542 0.1541 0.1594 n_refl.: 87590 remove outliers: r(all,work,free)=0.1542 0.1541 0.1594 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1541 0.1539 0.1593 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1381 n_refl.: 87590 remove outliers: r(all,work,free)=0.1211 0.1202 0.1381 n_refl.: 87582 ======================== 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 0.3748 294.275 262.531 0.484 0.998 0.330 11.894-9.307 97.06 95 4 0.2384 472.324 454.337 0.849 1.000 0.253 9.237-7.194 99.09 211 7 0.2321 386.252 385.824 0.950 1.001 0.180 7.162-5.571 100.00 427 22 0.2032 293.957 284.224 0.912 1.001 0.163 5.546-4.326 100.00 867 58 0.1099 403.531 398.655 0.952 1.001 0.162 4.315-3.360 100.00 1859 96 0.0911 383.761 381.143 0.993 1.002 0.161 3.356-2.611 100.00 3867 181 0.1150 252.111 250.278 0.998 1.002 0.077 2.608-2.026 99.99 8198 413 0.1061 167.126 166.200 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1029 81.616 81.794 1.024 1.003 0.000 1.573-1.221 100.00 36679 1900 0.1303 36.192 35.724 1.014 1.003 0.000 1.221-1.150 99.97 13689 708 0.2136 22.803 21.288 0.969 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0221 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1381 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=0.1202 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1381 | n_water=456 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1203 r_free=0.1382 | n_water=455 | time (s): 40.900 (total time: 43.260) Filter (q & B) r_work=0.1203 r_free=0.1382 | n_water=454 | time (s): 3.000 (total time: 46.260) Compute maps r_work=0.1203 r_free=0.1382 | n_water=454 | time (s): 1.570 (total time: 47.830) Filter (map) r_work=0.1231 r_free=0.1395 | n_water=322 | time (s): 2.730 (total time: 50.560) Find peaks r_work=0.1231 r_free=0.1395 | n_water=322 | time (s): 0.470 (total time: 51.030) Add new water r_work=0.1299 r_free=0.1440 | n_water=486 | time (s): 2.770 (total time: 53.800) Refine new water occ: r_work=0.1227 r_free=0.1376 adp: r_work=0.1227 r_free=0.1378 occ: r_work=0.1211 r_free=0.1370 adp: r_work=0.1209 r_free=0.1369 occ: r_work=0.1200 r_free=0.1368 adp: r_work=0.1196 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1364 r_work=0.1196 r_free=0.1364 | n_water=486 | time (s): 267.640 (total time: 321.440) Filter (q & B) r_work=0.1203 r_free=0.1371 | n_water=455 | time (s): 3.170 (total time: 324.610) Filter (dist only) r_work=0.1203 r_free=0.1370 | n_water=454 | time (s): 39.660 (total time: 364.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.060120 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.457319 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 0.1207 0.1382 0.0175 0.006 1.0 5.8 0.5 0.0 0 1.030 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.82 1.75 3.441 21.639 39.457 3.646 11.92 13.78 1.86 3.823 21.518 39.457 3.633 Individual atomic B min max mean iso aniso Overall: 9.28 105.71 21.41 2.15 223 1758 Protein: 9.28 105.71 17.03 2.16 0 1519 Water: 11.32 69.89 36.05 N/A 223 231 Other: 18.74 27.13 22.94 N/A 0 8 Chain A: 9.28 105.71 19.64 N/A 0 1758 Chain S: 15.93 58.03 35.39 N/A 223 0 Histogram: Values Number of atoms 9.28 - 18.93 1231 18.93 - 28.57 280 28.57 - 38.21 211 38.21 - 47.85 143 47.85 - 57.50 76 57.50 - 67.14 26 67.14 - 76.78 9 76.78 - 86.42 2 86.42 - 96.06 1 96.06 - 105.71 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1378 r_work=0.1193 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1378 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1377 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.632064 | | target function (ml) not normalized (work): 302500.043336 | | target function (ml) not normalized (free): 15980.289368 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1188 0.1377 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1505 0.1503 0.1583 n_refl.: 87582 remove outliers: r(all,work,free)=0.1505 0.1503 0.1583 n_refl.: 87582 overall B=-0.02 to atoms: r(all,work,free)=0.1502 0.1500 0.1581 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1187 0.1378 n_refl.: 87582 remove outliers: r(all,work,free)=0.1196 0.1186 0.1378 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 0.4069 289.637 253.148 0.457 0.999 0.324 11.894-9.307 96.08 94 4 0.2468 476.161 455.199 0.836 1.001 0.255 9.237-7.194 99.09 211 7 0.2507 386.252 380.711 0.928 1.002 0.166 7.162-5.571 100.00 427 22 0.2148 293.957 283.696 0.908 1.002 0.140 5.546-4.326 100.00 867 58 0.1134 403.531 399.253 0.953 1.002 0.140 4.315-3.360 100.00 1859 96 0.0921 383.761 380.976 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1145 252.111 250.459 1.001 1.002 0.120 2.608-2.026 99.99 8198 413 0.1031 167.126 166.234 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0986 81.616 81.871 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.192 35.804 1.022 0.999 0.000 1.221-1.150 99.97 13689 708 0.2135 22.803 21.420 0.981 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0483 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1378 After: r_work=0.1187 r_free=0.1378 ================================== NQH flips ================================== r_work=0.1187 r_free=0.1378 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=0.1187 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1378 | n_water=454 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1187 r_free=0.1378 | n_water=454 | time (s): 34.850 (total time: 36.450) Filter (q & B) r_work=0.1187 r_free=0.1380 | n_water=452 | time (s): 2.600 (total time: 39.050) Compute maps r_work=0.1187 r_free=0.1380 | n_water=452 | time (s): 1.440 (total time: 40.490) Filter (map) r_work=0.1222 r_free=0.1383 | n_water=332 | time (s): 3.020 (total time: 43.510) Find peaks r_work=0.1222 r_free=0.1383 | n_water=332 | time (s): 0.610 (total time: 44.120) Add new water r_work=0.1278 r_free=0.1431 | n_water=490 | time (s): 3.090 (total time: 47.210) Refine new water occ: r_work=0.1203 r_free=0.1369 adp: r_work=0.1203 r_free=0.1370 occ: r_work=0.1190 r_free=0.1364 adp: r_work=0.1188 r_free=0.1363 occ: r_work=0.1181 r_free=0.1360 adp: r_work=0.1177 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1177 r_free=0.1358 r_work=0.1177 r_free=0.1358 | n_water=490 | time (s): 142.850 (total time: 190.060) Filter (q & B) r_work=0.1185 r_free=0.1368 | n_water=454 | time (s): 3.120 (total time: 193.180) Filter (dist only) r_work=0.1185 r_free=0.1368 | n_water=453 | time (s): 39.210 (total time: 232.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.074066 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.565883 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 0.1206 0.1378 0.0172 0.007 1.1 4.2 0.5 0.0 0 1.037 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.78 1.72 3.309 21.255 46.566 3.636 12.07 13.77 1.70 3.719 21.135 46.566 3.624 Individual atomic B min max mean iso aniso Overall: 9.27 101.92 21.06 2.03 226 1754 Protein: 9.27 101.92 16.71 2.03 0 1519 Water: 11.33 68.36 35.63 N/A 226 227 Other: 18.16 24.83 21.38 N/A 0 8 Chain A: 9.27 101.92 19.24 N/A 0 1754 Chain S: 13.58 60.84 35.20 N/A 226 0 Histogram: Values Number of atoms 9.27 - 18.53 1232 18.53 - 27.80 272 27.80 - 37.06 204 37.06 - 46.33 160 46.33 - 55.59 70 55.59 - 64.86 26 64.86 - 74.12 11 74.12 - 83.39 2 83.39 - 92.65 1 92.65 - 101.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1377 r_work=0.1208 r_free=0.1377 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1377 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1374 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622409 | | target function (ml) not normalized (work): 301688.679319 | | target function (ml) not normalized (free): 15948.797726 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1425 0.1419 5.682 5.6399| | 2: 3.57 - 2.84 1.00 2888 124 0.1125 0.1479 5.2057 5.2635| | 3: 2.83 - 2.48 1.00 2820 163 0.1247 0.1377 5.0151 5.0527| | 4: 2.47 - 2.25 1.00 2825 136 0.1034 0.1086 4.7125 4.7442| | 5: 2.25 - 2.09 1.00 2756 127 0.1015 0.1105 4.6569 4.72| | 6: 2.09 - 1.97 1.00 2846 113 0.0983 0.1204 4.3586 4.4937| | 7: 1.97 - 1.87 1.00 2787 165 0.0993 0.1201 4.0763 4.175| | 8: 1.87 - 1.79 1.00 2789 144 0.1027 0.1215 3.9905 4.0692| | 9: 1.79 - 1.72 1.00 2745 138 0.0963 0.1310 3.7166 3.9286| | 10: 1.72 - 1.66 1.00 2831 160 0.0997 0.1185 3.6286 3.7243| | 11: 1.66 - 1.61 1.00 2712 147 0.0963 0.1056 3.5657 3.5936| | 12: 1.61 - 1.56 1.00 2773 144 0.0916 0.1189 3.345 3.5006| | 13: 1.56 - 1.52 1.00 2745 130 0.0976 0.1108 3.3362 3.456| | 14: 1.52 - 1.48 1.00 2803 134 0.0989 0.1138 3.2607 3.3565| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1356 3.1661 3.3276| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1197 3.1526 3.2091| | 17: 1.42 - 1.39 1.00 2785 139 0.1124 0.1332 3.1168 3.2405| | 18: 1.39 - 1.36 1.00 2741 179 0.1139 0.1367 3.0817 3.2759| | 19: 1.36 - 1.34 1.00 2807 134 0.1217 0.1609 3.0969 3.2823| | 20: 1.34 - 1.32 1.00 2696 147 0.1325 0.1505 3.0907 3.1466| | 21: 1.32 - 1.30 1.00 2785 112 0.1415 0.1629 3.0876 3.161| | 22: 1.29 - 1.27 1.00 2704 152 0.1465 0.1901 3.0847 3.2942| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1824 3.1027 3.2128| | 24: 1.26 - 1.24 1.00 2744 132 0.1614 0.1780 3.0929 3.21| | 25: 1.24 - 1.22 1.00 2733 148 0.1791 0.2296 3.1102 3.2816| | 26: 1.22 - 1.21 1.00 2727 135 0.1849 0.1767 3.1212 3.197| | 27: 1.21 - 1.19 1.00 2814 148 0.1996 0.2094 3.1375 3.1523| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2318 3.1403 3.1651| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2370 3.1275 3.2247| | 30: 1.16 - 1.15 1.00 2739 148 0.2371 0.2512 3.1154 3.1676| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2922 171 0.94 9.21 1.00 0.97 6350.40| | 2: 3.57 - 2.84 2888 124 0.92 13.42 1.01 0.97 6350.40| | 3: 2.83 - 2.48 2820 163 0.88 17.66 0.99 0.97 5321.70| | 4: 2.47 - 2.25 2825 136 0.91 14.72 1.00 0.98 2669.01| | 5: 2.25 - 2.09 2756 127 0.89 16.97 1.01 0.98 2669.01| | 6: 2.09 - 1.97 2846 113 0.92 13.67 1.02 0.98 1565.39| | 7: 1.97 - 1.87 2787 165 0.94 10.77 1.02 0.97 624.15| | 8: 1.87 - 1.79 2789 144 0.91 14.34 1.00 0.97 624.15| | 9: 1.79 - 1.72 2745 138 0.93 11.38 0.98 0.97 336.44| | 10: 1.72 - 1.66 2831 160 0.93 12.20 0.98 0.97 278.83| | 11: 1.66 - 1.61 2712 147 0.93 12.82 0.98 0.97 266.24| | 12: 1.61 - 1.56 2773 144 0.95 9.61 0.99 0.97 147.53| | 13: 1.56 - 1.52 2745 130 0.94 11.11 1.02 0.97 147.53| | 14: 1.52 - 1.48 2803 134 0.94 11.24 1.02 0.98 132.07| | 15: 1.48 - 1.45 2738 128 0.95 10.43 1.01 0.98 103.75| | 16: 1.45 - 1.42 2756 161 0.94 11.60 1.02 0.98 103.75| | 17: 1.42 - 1.39 2785 139 0.94 11.52 1.01 0.98 93.87| | 18: 1.39 - 1.36 2741 179 0.94 11.84 1.01 0.98 88.15| | 19: 1.36 - 1.34 2807 134 0.94 12.37 1.00 0.98 88.15| | 20: 1.34 - 1.32 2696 147 0.94 12.53 0.99 0.97 83.21| | 21: 1.32 - 1.30 2785 112 0.93 13.47 0.99 0.97 82.87| | 22: 1.29 - 1.27 2704 152 0.93 13.95 0.98 0.96 83.02| | 23: 1.27 - 1.26 2802 156 0.92 14.90 0.98 0.95 83.82| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.82| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 85.33| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 87.01| | 27: 1.21 - 1.19 2814 148 0.89 18.82 1.02 0.93 87.01| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.93 90.28| | 29: 1.18 - 1.16 2800 134 0.88 20.68 0.99 0.93 91.51| | 30: 1.16 - 1.15 2739 148 0.86 22.02 0.98 0.93 91.51| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.87 max = 6350.40 mean = 987.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.87 mean = 14.09| |phase err.(test): min = 0.00 max = 89.41 mean = 14.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1203 0.1374 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1567 n_refl.: 87580 remove outliers: r(all,work,free)=0.1514 0.1512 0.1567 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1510 0.1565 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1203 0.1374 n_refl.: 87580 remove outliers: r(all,work,free)=0.1211 0.1203 0.1374 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4172 289.637 247.260 0.445 0.999 0.320 11.894-9.307 96.08 94 4 0.2445 476.161 459.413 0.842 1.001 0.255 9.237-7.194 98.64 210 7 0.2560 384.253 377.648 0.921 1.001 0.160 7.162-5.571 100.00 427 22 0.2254 293.957 283.332 0.899 1.001 0.130 5.546-4.326 100.00 867 58 0.1212 403.531 398.078 0.951 1.001 0.130 4.315-3.360 100.00 1859 96 0.0977 383.761 380.907 0.995 1.001 0.110 3.356-2.611 100.00 3867 181 0.1202 252.111 250.205 1.000 1.001 0.043 2.608-2.026 99.99 8198 413 0.1052 167.126 166.142 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0980 81.616 81.866 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.192 35.805 1.019 1.000 0.000 1.221-1.150 99.97 13689 708 0.2113 22.803 21.356 0.973 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0298 ================= 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 : 0.2594 0.1940 0.083 5.302 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1765 0.083 5.302 9.0 119.5 20.1 258 0.000 1_settarget: 0.1619 0.1765 0.083 5.302 9.0 119.5 20.1 258 0.000 1_nqh: 0.1623 0.1770 0.083 5.302 9.0 119.5 20.1 258 0.006 1_weight: 0.1623 0.1770 0.083 5.302 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1209 0.1465 0.008 1.002 9.0 119.5 20.1 258 0.130 1_adp: 0.1243 0.1538 0.008 1.002 8.6 118.8 21.1 258 0.130 1_regHadp: 0.1247 0.1543 0.008 1.002 8.6 118.8 21.1 258 0.130 1_occ: 0.1248 0.1545 0.008 1.002 8.6 118.8 21.1 258 0.130 2_bss: 0.1245 0.1536 0.008 1.002 8.7 118.9 21.3 258 0.130 2_settarget: 0.1245 0.1536 0.008 1.002 8.7 118.9 21.3 258 0.130 2_updatecdl: 0.1245 0.1536 0.008 1.005 8.7 118.9 21.3 258 0.130 2_nqh: 0.1247 0.1538 0.008 1.005 8.7 118.9 21.3 258 0.130 2_sol: 0.1234 0.1493 0.008 1.005 8.7 118.9 23.7 439 n/a 2_weight: 0.1234 0.1493 0.008 1.005 8.7 118.9 23.7 439 n/a 2_xyzrec: 0.1238 0.1529 0.007 0.874 8.7 118.9 23.7 439 n/a 2_adp: 0.1206 0.1506 0.007 0.874 8.8 113.9 23.3 439 n/a 2_regHadp: 0.1206 0.1507 0.007 0.874 8.8 113.9 23.3 439 n/a 2_occ: 0.1205 0.1506 0.007 0.874 8.8 113.9 23.3 439 n/a 3_bss: 0.1201 0.1502 0.007 0.874 8.8 114.0 23.4 439 n/a 3_settarget: 0.1201 0.1502 0.007 0.874 8.8 114.0 23.4 439 n/a 3_updatecdl: 0.1201 0.1502 0.007 0.874 8.8 114.0 23.4 439 n/a 3_nqh: 0.1201 0.1502 0.007 0.874 8.8 114.0 23.4 439 n/a 3_sol: 0.1224 0.1483 0.007 0.874 8.8 114.0 22.2 456 n/a 3_weight: 0.1224 0.1483 0.007 0.874 8.8 114.0 22.2 456 n/a 3_xyzrec: 0.1229 0.1449 0.006 0.921 8.8 114.0 22.2 456 n/a 3_adp: 0.1218 0.1401 0.006 0.921 9.2 109.2 21.8 456 n/a 3_regHadp: 0.1219 0.1403 0.006 0.921 9.2 109.2 21.8 456 n/a 3_occ: 0.1213 0.1402 0.006 0.921 9.2 109.2 21.8 456 n/a 4_bss: 0.1202 0.1381 0.006 0.921 9.2 109.2 21.8 456 n/a 4_settarget: 0.1202 0.1381 0.006 0.921 9.2 109.2 21.8 456 n/a 4_updatecdl: 0.1202 0.1381 0.006 0.921 9.2 109.2 21.8 456 n/a 4_nqh: 0.1202 0.1381 0.006 0.921 9.2 109.2 21.8 456 n/a 4_sol: 0.1203 0.1370 0.006 0.921 9.2 109.2 21.6 454 n/a 4_weight: 0.1203 0.1370 0.006 0.921 9.2 109.2 21.6 454 n/a 4_xyzrec: 0.1207 0.1382 0.006 0.966 9.2 109.2 21.6 454 n/a 4_adp: 0.1192 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 4_regHadp: 0.1193 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 4_occ: 0.1188 0.1377 0.006 0.966 9.3 105.7 21.4 454 n/a 5_bss: 0.1186 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 5_settarget: 0.1186 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 5_updatecdl: 0.1186 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 5_setrh: 0.1187 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 5_nqh: 0.1187 0.1378 0.006 0.966 9.3 105.7 21.4 454 n/a 5_sol: 0.1185 0.1368 0.006 0.966 9.3 105.7 21.3 453 n/a 5_weight: 0.1185 0.1368 0.006 0.966 9.3 105.7 21.3 453 n/a 5_xyzrec: 0.1206 0.1378 0.007 1.081 9.3 105.7 21.3 453 n/a 5_adp: 0.1207 0.1377 0.007 1.081 9.3 101.9 21.1 453 n/a 5_regHadp: 0.1208 0.1377 0.007 1.081 9.3 101.9 21.1 453 n/a 5_occ: 0.1203 0.1374 0.007 1.081 9.3 101.9 21.1 453 n/a end: 0.1203 0.1374 0.007 1.081 9.3 101.9 21.1 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2353655_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2353655_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0600 Refinement macro-cycles (run) : 3525.4100 Write final files (write_after_run_outputs) : 68.8100 Total : 3599.2800 Total CPU time: 60.59 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:38 PST -0800 (1735452698.56 s) Start R-work = 0.1619, R-free = 0.1765 Final R-work = 0.1203, R-free = 0.1374 =============================================================================== Job complete usr+sys time: 3736.61 seconds wall clock time: 66 minutes 52.15 seconds (4012.15 seconds total)