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_8315495.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8315495.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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: 2.12, 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: 0.95 Conformation dependent library (CDL) restraints added in 315.4 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 547 0.91 - 1.17: 1097 1.17 - 1.42: 632 1.42 - 1.68: 839 1.68 - 1.94: 38 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 3 " pdb=" CA SER A 3 " ideal model delta sigma weight residual 1.454 1.725 -0.271 1.18e-02 7.18e+03 5.28e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.277 0.246 1.19e-02 7.06e+03 4.27e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.545 -0.219 1.10e-02 8.26e+03 3.97e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.236 1.056 0.181 1.02e-02 9.61e+03 3.14e+02 bond pdb=" C SER A 57 " pdb=" O SER A 57 " ideal model delta sigma weight residual 1.234 1.447 -0.213 1.23e-02 6.61e+03 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3263 4.85 - 9.70: 1816 9.70 - 14.55: 612 14.55 - 19.40: 79 19.40 - 24.25: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.32 -9.90 6.40e-01 2.44e+00 2.39e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 120.55 105.90 14.65 9.50e-01 1.11e+00 2.38e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 107.07 15.05 1.06e+00 8.90e-01 2.02e+02 angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.77 135.47 -13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 108.48 13.29 1.00e+00 1.00e+00 1.77e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 949 17.65 - 35.30: 108 35.30 - 52.95: 40 52.95 - 70.61: 12 70.61 - 88.26: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 159.84 20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 105 0.216 - 0.431: 72 0.431 - 0.646: 41 0.646 - 0.862: 22 0.862 - 1.077: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 3.32 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.100 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.014 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.067 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.125 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.011 9.50e-02 1.11e+02 6.69e-02 1.00e+02 pdb=" NE ARG A 28 " -0.106 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.082 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1025 2.31 - 2.88: 8054 2.88 - 3.46: 10574 3.46 - 4.03: 15124 4.03 - 4.60: 21875 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.741 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.743 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.770 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.787 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.788 2.100 ... (remaining 56647 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_8315495_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= 0.1937 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797706 | | target function (ml) not normalized (work): 233065.657431 | | target function (ml) not normalized (free): 11838.006266 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2101 7.1545 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2450 0.1661 4.3381 4.3078| | 3: 2.84 - 2.48 1.00 2833 165 0.2333 0.1723 4.1195 4.1382| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1445 3.8259 3.8277| | 5: 2.25 - 2.09 1.00 2756 127 0.2484 0.1612 3.7907 3.8144| | 6: 2.09 - 1.97 1.00 2846 113 0.2530 0.1767 3.4628 3.5538| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1822 3.1444 3.2132| | 8: 1.87 - 1.79 1.00 2789 144 0.2498 0.1756 3.0661 3.1126| | 9: 1.79 - 1.72 1.00 2745 138 0.2410 0.2035 2.8917 3.0375| | 10: 1.72 - 1.66 1.00 2789 158 0.2405 0.1899 2.8052 2.8841| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1914 2.7461 2.8037| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2148 2.6345 2.6988| | 13: 1.56 - 1.52 1.00 2745 130 0.2577 0.1750 2.5932 2.595| | 14: 1.52 - 1.48 1.00 2803 134 0.2633 0.1924 2.5198 2.5528| | 15: 1.48 - 1.45 1.00 2738 128 0.2641 0.2050 2.4525 2.4721| | 16: 1.45 - 1.42 1.00 2756 161 0.2660 0.2049 2.3961 2.4267| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.1992 2.331 2.3006| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2146 2.2653 2.3283| | 19: 1.36 - 1.34 1.00 2807 134 0.2615 0.2320 2.2375 2.3035| | 20: 1.34 - 1.32 1.00 2696 147 0.2719 0.2127 2.2167 2.1868| | 21: 1.32 - 1.30 1.00 2785 112 0.2703 0.2223 2.1703 2.1857| | 22: 1.29 - 1.27 1.00 2704 152 0.2706 0.2764 2.129 2.2638| | 23: 1.27 - 1.26 1.00 2802 156 0.2815 0.2513 2.1161 2.1343| | 24: 1.26 - 1.24 1.00 2744 132 0.2789 0.2554 2.0877 2.1727| | 25: 1.24 - 1.22 1.00 2734 148 0.2933 0.2721 2.0469 2.1316| | 26: 1.22 - 1.21 1.00 2727 135 0.2915 0.2374 2.0282 2.0656| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2695 2.0082 2.0295| | 28: 1.19 - 1.18 1.00 2671 147 0.3041 0.2740 1.9927 1.9933| | 29: 1.18 - 1.16 1.00 2800 134 0.3030 0.2588 1.9667 2.0255| | 30: 1.16 - 1.15 1.00 2740 148 0.3110 0.3020 1.9345 2.0038| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.46 0.76 0.23 1435.35| | 2: 3.57 - 2.84 2876 122 0.81 25.68 1.27 0.23 1435.35| | 3: 2.84 - 2.48 2833 165 0.75 31.35 1.24 0.24 1191.38| | 4: 2.47 - 2.25 2825 136 0.81 25.34 1.25 0.25 558.24| | 5: 2.25 - 2.09 2756 127 0.78 28.98 1.28 0.25 558.24| | 6: 2.09 - 1.97 2846 113 0.83 22.65 1.29 0.25 307.77| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.28 0.25 94.16| | 8: 1.87 - 1.79 2789 144 0.85 21.63 1.25 0.25 94.16| | 9: 1.79 - 1.72 2745 138 0.88 18.98 1.23 0.25 57.44| | 10: 1.72 - 1.66 2789 158 0.86 20.67 1.22 0.25 50.09| | 11: 1.66 - 1.61 2740 147 0.85 21.88 1.24 0.25 48.25| | 12: 1.61 - 1.56 2787 146 0.88 18.60 1.23 0.25 29.67| | 13: 1.56 - 1.52 2745 130 0.87 20.36 1.24 0.25 29.67| | 14: 1.52 - 1.48 2803 134 0.87 20.59 1.24 0.25 26.30| | 15: 1.48 - 1.45 2738 128 0.87 19.78 1.23 0.25 20.13| | 16: 1.45 - 1.42 2756 161 0.86 21.46 1.23 0.25 20.13| | 17: 1.42 - 1.39 2785 139 0.87 20.26 1.23 0.25 17.01| | 18: 1.39 - 1.36 2741 179 0.87 20.94 1.23 0.25 15.20| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.21 0.25 15.20| | 20: 1.34 - 1.32 2696 147 0.87 20.79 1.21 0.24 12.93| | 21: 1.32 - 1.30 2785 112 0.86 21.75 1.20 0.24 12.77| | 22: 1.29 - 1.27 2704 152 0.85 22.52 1.20 0.24 12.55| | 23: 1.27 - 1.26 2802 156 0.85 22.78 1.21 0.24 11.45| | 24: 1.26 - 1.24 2744 132 0.84 23.27 1.20 0.24 11.45| | 25: 1.24 - 1.22 2734 148 0.83 24.51 1.22 0.24 11.00| | 26: 1.22 - 1.21 2727 135 0.83 24.78 1.20 0.23 10.50| | 27: 1.21 - 1.19 2814 148 0.83 25.41 1.21 0.23 10.50| | 28: 1.19 - 1.18 2671 147 0.82 26.22 1.19 0.23 9.83| | 29: 1.18 - 1.16 2800 134 0.81 26.53 1.17 0.23 9.57| | 30: 1.16 - 1.15 2740 148 0.80 27.96 1.16 0.23 9.57| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.57 max = 1435.35 mean = 209.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.75| |phase err.(test): min = 0.00 max = 89.49 mean = 22.55| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.271 1557 Z= 5.557 Angle : 5.380 22.608 2118 Z= 3.810 Chirality : 0.381 1.077 243 Planarity : 0.033 0.126 284 Dihedral : 13.949 88.257 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 24.86 % 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: -1.85 (0.47), residues: 224 helix: -2.24 (0.40), residues: 102 sheet: -0.68 (0.82), residues: 28 loop : 0.15 (0.55), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.018 ARG A 28 TYR 0.116 0.041 TYR A 141 PHE 0.113 0.040 PHE A 119 HIS 0.067 0.033 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1937 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.797706 | | target function (ml) not normalized (work): 233065.657431 | | target function (ml) not normalized (free): 11838.006266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2569 0.2612 0.1937 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2569 0.2612 0.1937 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1990 0.1937 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2006 0.2012 0.1947 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1642 0.1755 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1755 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 98.94 88 5 0.3833 386.610 359.778 0.675 1.002 0.411 11.894-9.307 98.04 96 4 0.1724 616.604 592.192 0.929 1.003 0.379 9.237-7.194 100.00 213 7 0.2139 502.268 492.781 0.966 1.003 0.363 7.162-5.571 100.00 427 22 0.2218 376.924 366.425 0.935 1.003 0.330 5.546-4.326 100.00 867 58 0.1289 517.424 511.342 0.964 1.003 0.222 4.315-3.360 100.00 1859 96 0.1144 492.073 488.377 1.007 1.003 0.189 3.356-2.611 100.00 3867 181 0.1434 323.267 320.107 1.002 1.002 0.099 2.608-2.026 99.99 8198 413 0.1360 214.296 212.214 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.651 104.035 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2087 46.407 45.107 1.003 0.996 0.000 1.221-1.150 99.97 13689 708 0.2614 29.239 26.977 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1755 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1640 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.659829 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.782406 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 0.1208 0.1462 0.0254 0.008 1.0 1.6 0.5 0.0 0 13.330 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.62 2.54 3.013 19.034 2011.782 0.017 12.43 15.41 2.98 3.215 19.531 2011.782 0.015 Individual atomic B min max mean iso aniso Overall: 8.64 118.81 21.00 2.87 0 1785 Protein: 8.64 118.81 17.88 2.87 0 1519 Water: 11.04 114.47 39.15 N/A 0 258 Other: 22.75 36.33 28.95 N/A 0 8 Chain A: 8.64 118.81 21.00 N/A 0 1785 Histogram: Values Number of atoms 8.64 - 19.66 1208 19.66 - 30.68 229 30.68 - 41.69 168 41.69 - 52.71 99 52.71 - 63.73 52 63.73 - 74.74 16 74.74 - 85.76 6 85.76 - 96.77 4 96.77 - 107.79 0 107.79 - 118.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1541 r_work=0.1248 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1547 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1550 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015276 | | target function (ls_wunit_k1) not normalized (work): 1272.427052 | | target function (ls_wunit_k1) not normalized (free): 114.545113 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1550 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1702 0.1700 0.1771 n_refl.: 87592 remove outliers: r(all,work,free)=0.1702 0.1700 0.1771 n_refl.: 87592 overall B=0.15 to atoms: r(all,work,free)=0.1726 0.1725 0.1787 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1244 0.1541 n_refl.: 87592 remove outliers: r(all,work,free)=0.1258 0.1244 0.1541 n_refl.: 87591 ======================== 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 0.3570 299.352 279.804 0.691 0.924 0.380 11.894-9.307 98.04 96 4 0.1504 481.491 469.955 0.998 0.924 0.380 9.237-7.194 100.00 213 7 0.1815 392.209 387.826 1.030 0.925 0.319 7.162-5.571 100.00 427 22 0.1733 294.331 288.880 1.001 0.925 0.300 5.546-4.326 100.00 867 58 0.0926 404.044 401.216 1.026 0.926 0.199 4.315-3.360 100.00 1859 96 0.0774 384.249 383.195 1.075 0.927 0.180 3.356-2.611 100.00 3867 181 0.1015 252.431 251.697 1.078 0.929 0.052 2.608-2.026 99.99 8198 413 0.0975 167.339 166.745 1.083 0.932 0.000 2.025-1.573 100.00 17313 902 0.1214 81.720 81.900 1.084 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1656 36.238 35.699 1.058 0.948 0.000 1.221-1.150 99.97 13689 708 0.2369 22.832 21.359 1.012 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0571 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1541 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** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1542 | n_water=258 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1254 r_free=0.1540 | n_water=252 | time (s): 25.370 (total time: 27.710) Filter (q & B) r_work=0.1258 r_free=0.1539 | n_water=249 | time (s): 3.700 (total time: 31.410) Compute maps r_work=0.1258 r_free=0.1539 | n_water=249 | time (s): 1.840 (total time: 33.250) Filter (map) r_work=0.1273 r_free=0.1542 | n_water=236 | time (s): 3.650 (total time: 36.900) Find peaks r_work=0.1273 r_free=0.1542 | n_water=236 | time (s): 0.660 (total time: 37.560) Add new water r_work=0.1425 r_free=0.1687 | n_water=451 | time (s): 3.460 (total time: 41.020) Refine new water occ: r_work=0.1329 r_free=0.1573 adp: r_work=0.1254 r_free=0.1523 occ: r_work=0.1268 r_free=0.1517 adp: r_work=0.1232 r_free=0.1502 occ: r_work=0.1236 r_free=0.1489 adp: r_work=0.1226 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1488 r_work=0.1226 r_free=0.1488 | n_water=451 | time (s): 93.590 (total time: 134.610) Filter (q & B) r_work=0.1231 r_free=0.1491 | n_water=431 | time (s): 3.920 (total time: 138.530) Filter (dist only) r_work=0.1231 r_free=0.1491 | n_water=431 | time (s): 40.340 (total time: 178.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.870817 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1547.545553 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 0.1516 0.0287 0.007 0.9 2.2 0.5 0.0 0 12.435 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.16 2.87 3.790 23.227 1547.546 0.015 11.98 14.90 2.91 4.243 23.020 1547.546 0.015 Individual atomic B min max mean iso aniso Overall: 8.75 114.59 23.21 2.62 195 1763 Protein: 8.75 114.59 17.64 2.63 0 1519 Water: 11.01 72.62 42.76 N/A 195 236 Other: 23.13 33.24 27.49 N/A 0 8 Chain A: 8.75 114.59 20.35 N/A 0 1763 Chain S: 19.99 72.34 49.03 N/A 195 0 Histogram: Values Number of atoms 8.75 - 19.33 1205 19.33 - 29.91 260 29.91 - 40.50 176 40.50 - 51.08 141 51.08 - 61.67 115 61.67 - 72.25 48 72.25 - 82.83 7 82.83 - 93.42 3 93.42 - 104.00 1 104.00 - 114.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1490 r_work=0.1198 r_free=0.1489 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1489 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1474 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1474 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013886 | | target function (ls_wunit_k1) not normalized (work): 1156.675988 | | target function (ls_wunit_k1) not normalized (free): 104.160090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1200 0.1474 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1611 0.1609 0.1706 n_refl.: 87591 remove outliers: r(all,work,free)=0.1611 0.1609 0.1706 n_refl.: 87591 overall B=0.05 to atoms: r(all,work,free)=0.1619 0.1616 0.1710 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1468 n_refl.: 87591 remove outliers: r(all,work,free)=0.1211 0.1198 0.1468 n_refl.: 87587 ======================== 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 0.3323 292.039 273.066 0.571 1.003 0.340 11.894-9.307 98.04 96 4 0.1578 481.491 478.052 0.920 1.003 0.333 9.237-7.194 100.00 213 7 0.1666 392.209 392.896 0.974 1.003 0.280 7.162-5.571 100.00 427 22 0.1520 294.331 290.877 0.942 1.003 0.270 5.546-4.326 100.00 867 58 0.0833 404.044 401.277 0.957 1.003 0.212 4.315-3.360 100.00 1859 96 0.0709 384.249 383.429 1.001 1.003 0.200 3.356-2.611 100.00 3867 181 0.0957 252.431 251.778 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0962 167.339 166.976 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1181 81.720 81.919 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1614 36.238 35.729 1.015 0.998 0.000 1.221-1.150 99.97 13689 708 0.2342 22.832 21.343 0.974 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0733 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1468 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1198 r_free=0.1468 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1468 | n_water=431 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1198 r_free=0.1468 | n_water=431 | time (s): 36.650 (total time: 38.560) Filter (q & B) r_work=0.1198 r_free=0.1468 | n_water=430 | time (s): 3.450 (total time: 42.010) Compute maps r_work=0.1198 r_free=0.1468 | n_water=430 | time (s): 1.700 (total time: 43.710) Filter (map) r_work=0.1241 r_free=0.1480 | n_water=288 | time (s): 2.910 (total time: 46.620) Find peaks r_work=0.1241 r_free=0.1480 | n_water=288 | time (s): 0.500 (total time: 47.120) Add new water r_work=0.1371 r_free=0.1577 | n_water=484 | time (s): 3.550 (total time: 50.670) Refine new water occ: r_work=0.1265 r_free=0.1492 adp: r_work=0.1266 r_free=0.1492 occ: r_work=0.1243 r_free=0.1475 adp: r_work=0.1240 r_free=0.1473 occ: r_work=0.1226 r_free=0.1464 adp: r_work=0.1219 r_free=0.1460 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1460 r_work=0.1219 r_free=0.1460 | n_water=484 | time (s): 248.340 (total time: 299.010) Filter (q & B) r_work=0.1222 r_free=0.1468 | n_water=451 | time (s): 3.240 (total time: 302.250) Filter (dist only) r_work=0.1222 r_free=0.1467 | n_water=450 | time (s): 38.950 (total time: 341.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.983740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.695677 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 0.1432 0.0204 0.006 0.9 2.2 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.32 2.04 3.623 22.088 47.696 3.723 12.11 13.86 1.75 4.135 21.903 47.696 3.653 Individual atomic B min max mean iso aniso Overall: 9.22 110.23 21.66 2.32 217 1760 Protein: 9.22 110.23 17.21 2.32 0 1519 Water: 11.51 71.50 36.66 N/A 217 233 Other: 18.26 28.75 23.62 N/A 0 8 Chain A: 9.22 110.23 19.87 N/A 0 1760 Chain S: 16.21 68.85 36.23 N/A 217 0 Histogram: Values Number of atoms 9.22 - 19.32 1238 19.32 - 29.42 284 29.42 - 39.52 211 39.52 - 49.62 139 49.62 - 59.73 71 59.73 - 69.83 21 69.83 - 79.93 7 79.93 - 90.03 3 90.03 - 100.13 1 100.13 - 110.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1386 r_work=0.1212 r_free=0.1386 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1386 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1382 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1206 r_free= 0.1382 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650903 | | target function (ml) not normalized (work): 304087.358881 | | target function (ml) not normalized (free): 16058.327671 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1382 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1540 0.1539 0.1576 n_refl.: 87587 remove outliers: r(all,work,free)=0.1540 0.1539 0.1576 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1538 0.1575 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1198 0.1362 n_refl.: 87587 remove outliers: r(all,work,free)=0.1202 0.1194 0.1362 n_refl.: 87577 ======================== 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 0.3813 283.958 259.526 0.461 1.001 0.299 11.894-9.307 95.10 93 4 0.2333 478.745 463.387 0.860 1.002 0.283 9.237-7.194 98.18 209 7 0.2343 386.838 386.172 0.939 1.002 0.200 7.162-5.571 100.00 427 22 0.2021 294.331 284.275 0.914 1.002 0.175 5.546-4.326 100.00 867 58 0.1087 404.044 399.536 0.953 1.002 0.170 4.315-3.360 100.00 1859 96 0.0921 384.249 381.596 0.994 1.002 0.170 3.356-2.611 100.00 3867 181 0.1144 252.431 250.835 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1048 167.339 166.428 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.720 81.886 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.238 35.812 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2136 22.832 21.438 0.975 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0207 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 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=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=450 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1194 r_free=0.1363 | n_water=449 | time (s): 40.580 (total time: 42.920) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=448 | time (s): 3.570 (total time: 46.490) Compute maps r_work=0.1195 r_free=0.1363 | n_water=448 | time (s): 1.470 (total time: 47.960) Filter (map) r_work=0.1221 r_free=0.1385 | n_water=311 | time (s): 3.500 (total time: 51.460) Find peaks r_work=0.1221 r_free=0.1385 | n_water=311 | time (s): 0.470 (total time: 51.930) Add new water r_work=0.1290 r_free=0.1454 | n_water=473 | time (s): 2.690 (total time: 54.620) Refine new water occ: r_work=0.1218 r_free=0.1383 adp: r_work=0.1218 r_free=0.1385 occ: r_work=0.1201 r_free=0.1368 adp: r_work=0.1200 r_free=0.1369 occ: r_work=0.1190 r_free=0.1358 adp: r_work=0.1186 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1357 r_work=0.1186 r_free=0.1357 | n_water=473 | time (s): 159.160 (total time: 213.780) Filter (q & B) r_work=0.1191 r_free=0.1361 | n_water=443 | time (s): 3.370 (total time: 217.150) Filter (dist only) r_work=0.1191 r_free=0.1360 | n_water=442 | time (s): 36.560 (total time: 253.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.999714 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.192787 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1376 0.0178 0.006 1.0 2.2 0.5 0.0 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.76 1.78 3.420 21.445 38.193 3.641 11.96 13.74 1.78 3.630 21.375 38.193 3.632 Individual atomic B min max mean iso aniso Overall: 9.26 106.35 21.26 2.16 214 1755 Protein: 9.26 106.35 17.05 2.16 0 1519 Water: 11.54 70.88 35.71 N/A 214 228 Other: 17.31 26.10 22.43 N/A 0 8 Chain A: 9.26 106.35 19.59 N/A 0 1755 Chain S: 16.23 59.95 35.00 N/A 214 0 Histogram: Values Number of atoms 9.26 - 18.97 1233 18.97 - 28.68 282 28.68 - 38.39 206 38.39 - 48.09 139 48.09 - 57.80 71 57.80 - 67.51 24 67.51 - 77.22 9 77.22 - 86.93 2 86.93 - 96.64 1 96.64 - 106.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1374 r_work=0.1196 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1374 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1372 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1191 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629251 | | target function (ml) not normalized (work): 302247.693134 | | target function (ml) not normalized (free): 15971.414476 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1191 0.1372 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1521 0.1519 0.1569 n_refl.: 87577 remove outliers: r(all,work,free)=0.1521 0.1519 0.1569 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1519 0.1517 0.1567 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1190 0.1372 n_refl.: 87577 remove outliers: r(all,work,free)=0.1198 0.1189 0.1372 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3996 283.958 252.058 0.434 1.000 0.298 11.894-9.307 94.12 92 4 0.2286 472.559 457.229 0.842 1.002 0.218 9.237-7.194 97.73 208 7 0.2447 384.818 381.008 0.922 1.002 0.150 7.162-5.571 100.00 427 22 0.2187 294.331 282.523 0.904 1.002 0.150 5.546-4.326 100.00 867 58 0.1145 404.044 399.230 0.953 1.002 0.145 4.315-3.360 100.00 1859 96 0.0946 384.249 381.795 0.995 1.002 0.140 3.356-2.611 100.00 3867 181 0.1157 252.431 250.660 1.001 1.002 0.048 2.608-2.026 99.99 8198 413 0.1036 167.339 166.403 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0991 81.720 81.947 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.238 35.838 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.832 21.437 0.978 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0304 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1372 After: r_work=0.1190 r_free=0.1372 ================================== 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=442 | time (s): 1.860 (total time: 1.860) Filter (dist) r_work=0.1190 r_free=0.1372 | n_water=442 | time (s): 35.760 (total time: 37.620) Filter (q & B) r_work=0.1190 r_free=0.1371 | n_water=440 | time (s): 3.410 (total time: 41.030) Compute maps r_work=0.1190 r_free=0.1371 | n_water=440 | time (s): 1.470 (total time: 42.500) Filter (map) r_work=0.1226 r_free=0.1394 | n_water=335 | time (s): 3.220 (total time: 45.720) Find peaks r_work=0.1226 r_free=0.1394 | n_water=335 | time (s): 0.460 (total time: 46.180) Add new water r_work=0.1278 r_free=0.1439 | n_water=489 | time (s): 2.380 (total time: 48.560) Refine new water occ: r_work=0.1201 r_free=0.1372 adp: r_work=0.1201 r_free=0.1371 occ: r_work=0.1188 r_free=0.1363 adp: r_work=0.1187 r_free=0.1363 occ: r_work=0.1179 r_free=0.1359 adp: r_work=0.1176 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1357 r_work=0.1176 r_free=0.1357 | n_water=489 | time (s): 188.980 (total time: 237.540) Filter (q & B) r_work=0.1184 r_free=0.1361 | n_water=450 | time (s): 2.860 (total time: 240.400) Filter (dist only) r_work=0.1184 r_free=0.1357 | n_water=448 | time (s): 37.710 (total time: 278.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.893148 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.020090 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 0.1208 0.1381 0.0173 0.006 1.0 5.4 0.5 0.0 0 0.947 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.81 1.73 3.320 21.218 48.020 3.639 12.02 13.79 1.77 3.851 21.071 48.020 3.627 Individual atomic B min max mean iso aniso Overall: 9.28 101.34 20.91 2.04 222 1753 Protein: 9.28 101.34 16.66 2.04 0 1519 Water: 11.49 68.94 35.32 N/A 222 226 Other: 18.08 24.22 20.93 N/A 0 8 Chain A: 9.28 101.34 19.15 N/A 0 1753 Chain S: 14.50 55.33 34.76 N/A 222 0 Histogram: Values Number of atoms 9.28 - 18.48 1229 18.48 - 27.69 277 27.69 - 36.90 216 36.90 - 46.10 143 46.10 - 55.31 71 55.31 - 64.52 23 64.52 - 73.72 11 73.72 - 82.93 2 82.93 - 92.13 1 92.13 - 101.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1379 r_work=0.1202 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1378 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1376 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624801 | | target function (ml) not normalized (work): 301869.771115 | | target function (ml) not normalized (free): 15971.841991 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1407 0.1416 5.6582 5.6317| | 2: 3.57 - 2.84 1.00 2888 124 0.1120 0.1478 5.2052 5.2822| | 3: 2.83 - 2.48 1.00 2820 163 0.1220 0.1315 5.017 5.0471| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1105 4.7178 4.7611| | 5: 2.25 - 2.09 1.00 2756 127 0.0992 0.1127 4.6592 4.7403| | 6: 2.09 - 1.97 1.00 2846 113 0.0984 0.1229 4.3667 4.4921| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1234 4.0858 4.1985| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1251 4.0067 4.0935| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1293 3.7259 3.9222| | 10: 1.72 - 1.66 1.00 2831 160 0.1005 0.1241 3.6424 3.7653| | 11: 1.66 - 1.61 1.00 2712 147 0.0953 0.1079 3.5743 3.6038| | 12: 1.61 - 1.56 1.00 2773 144 0.0915 0.1165 3.3469 3.4963| | 13: 1.56 - 1.52 1.00 2745 130 0.0976 0.1138 3.3411 3.4735| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1111 3.2632 3.355| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1312 3.1724 3.3106| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1245 3.1539 3.2353| | 17: 1.42 - 1.39 1.00 2785 139 0.1118 0.1344 3.1165 3.2512| | 18: 1.39 - 1.36 1.00 2741 179 0.1140 0.1387 3.0833 3.2686| | 19: 1.36 - 1.34 1.00 2807 134 0.1208 0.1569 3.094 3.2742| | 20: 1.34 - 1.32 1.00 2696 147 0.1330 0.1487 3.0929 3.1453| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1617 3.0878 3.1684| | 22: 1.29 - 1.27 1.00 2704 152 0.1464 0.1876 3.0817 3.2814| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1860 3.1033 3.2208| | 24: 1.26 - 1.24 1.00 2744 132 0.1614 0.1790 3.095 3.1992| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2329 3.1095 3.2961| | 26: 1.22 - 1.21 1.00 2727 135 0.1861 0.1783 3.1241 3.1973| | 27: 1.21 - 1.19 1.00 2814 148 0.2003 0.2110 3.1401 3.155| | 28: 1.19 - 1.18 1.00 2671 147 0.2140 0.2327 3.1406 3.168| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2356 3.1285 3.2244| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2499 3.1179 3.1652| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 9.22 1.00 0.97 6399.95| | 2: 3.57 - 2.84 2888 124 0.92 13.49 1.01 0.97 6399.95| | 3: 2.83 - 2.48 2820 163 0.89 17.58 0.99 0.98 5368.83| | 4: 2.47 - 2.25 2825 136 0.91 14.73 1.00 0.98 2709.91| | 5: 2.25 - 2.09 2756 127 0.89 16.95 1.01 0.98 2709.91| | 6: 2.09 - 1.97 2846 113 0.91 13.89 1.02 0.98 1598.55| | 7: 1.97 - 1.87 2787 165 0.94 11.06 1.02 0.97 650.71| | 8: 1.87 - 1.79 2789 144 0.91 14.69 0.99 0.97 650.71| | 9: 1.79 - 1.72 2745 138 0.93 11.61 0.98 0.97 349.77| | 10: 1.72 - 1.66 2831 160 0.93 12.44 0.98 0.97 289.50| | 11: 1.66 - 1.61 2712 147 0.93 13.02 0.98 0.97 276.14| | 12: 1.61 - 1.56 2773 144 0.95 9.68 0.99 0.97 150.15| | 13: 1.56 - 1.52 2745 130 0.94 11.22 1.02 0.97 150.15| | 14: 1.52 - 1.48 2803 134 0.94 11.33 1.02 0.98 133.94| | 15: 1.48 - 1.45 2738 128 0.95 10.52 1.01 0.98 104.25| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.02 0.98 104.25| | 17: 1.42 - 1.39 2785 139 0.94 11.53 1.01 0.98 94.22| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.99 88.41| | 19: 1.36 - 1.34 2807 134 0.94 12.35 1.00 0.99 88.41| | 20: 1.34 - 1.32 2696 147 0.94 12.47 0.99 0.97 83.18| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.97 82.81| | 22: 1.29 - 1.27 2704 152 0.93 13.91 0.98 0.96 82.95| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.98 0.95 83.70| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.97 0.95 83.70| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 85.20| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.94 86.86| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 86.86| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 90.14| | 29: 1.18 - 1.16 2800 134 0.88 20.61 0.99 0.93 91.37| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.93 91.37| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 82.81 max = 6399.95 mean = 999.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.14| |phase err.(test): min = 0.00 max = 88.10 mean = 14.28| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1196 0.1376 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1515 0.1513 0.1580 n_refl.: 87575 remove outliers: r(all,work,free)=0.1515 0.1513 0.1580 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1512 0.1579 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1377 n_refl.: 87575 remove outliers: r(all,work,free)=0.1206 0.1197 0.1377 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4105 283.958 251.169 0.422 1.001 0.292 11.894-9.307 94.12 92 4 0.2361 472.559 452.816 0.839 1.002 0.234 9.237-7.194 97.73 208 7 0.2469 384.818 377.729 0.909 1.002 0.172 7.162-5.571 100.00 427 22 0.2242 294.331 282.744 0.900 1.002 0.155 5.546-4.326 100.00 867 58 0.1188 404.044 399.041 0.953 1.002 0.128 4.315-3.360 100.00 1859 96 0.0996 384.249 381.637 0.995 1.002 0.123 3.356-2.611 100.00 3867 181 0.1184 252.431 250.498 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1041 167.339 166.475 1.012 1.000 0.000 2.025-1.573 100.00 17313 902 0.0982 81.720 81.972 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.238 35.867 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2118 22.832 21.445 0.978 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0218 ================= 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 0.1937 0.082 5.380 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_nqh: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_weight: 0.1640 0.1755 0.082 5.380 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1208 0.1462 0.008 0.963 9.0 119.5 20.1 258 0.120 1_adp: 0.1243 0.1541 0.008 0.963 8.6 118.8 21.0 258 0.120 1_regHadp: 0.1248 0.1547 0.008 0.963 8.6 118.8 21.0 258 0.120 1_occ: 0.1247 0.1550 0.008 0.963 8.6 118.8 21.0 258 0.120 2_bss: 0.1244 0.1541 0.008 0.963 8.8 119.0 21.1 258 0.120 2_settarget: 0.1244 0.1541 0.008 0.963 8.8 119.0 21.1 258 0.120 2_updatecdl: 0.1244 0.1541 0.008 0.975 8.8 119.0 21.1 258 0.120 2_nqh: 0.1245 0.1542 0.008 0.975 8.8 119.0 21.1 258 0.123 2_sol: 0.1231 0.1491 0.008 0.975 8.8 119.0 23.6 431 n/a 2_weight: 0.1231 0.1491 0.008 0.975 8.8 119.0 23.6 431 n/a 2_xyzrec: 0.1229 0.1516 0.007 0.872 8.8 119.0 23.6 431 n/a 2_adp: 0.1198 0.1490 0.007 0.872 8.7 114.6 23.2 431 n/a 2_regHadp: 0.1198 0.1489 0.007 0.872 8.7 114.6 23.2 431 n/a 2_occ: 0.1200 0.1474 0.007 0.872 8.7 114.6 23.2 431 n/a 3_bss: 0.1198 0.1468 0.007 0.872 8.8 114.6 23.3 431 n/a 3_settarget: 0.1198 0.1468 0.007 0.872 8.8 114.6 23.3 431 n/a 3_updatecdl: 0.1198 0.1468 0.007 0.874 8.8 114.6 23.3 431 n/a 3_nqh: 0.1198 0.1468 0.007 0.874 8.8 114.6 23.3 431 n/a 3_sol: 0.1222 0.1467 0.007 0.874 8.8 114.6 22.0 450 n/a 3_weight: 0.1222 0.1467 0.007 0.874 8.8 114.6 22.0 450 n/a 3_xyzrec: 0.1228 0.1432 0.006 0.923 8.8 114.6 22.0 450 n/a 3_adp: 0.1211 0.1386 0.006 0.923 9.2 110.2 21.7 450 n/a 3_regHadp: 0.1212 0.1386 0.006 0.923 9.2 110.2 21.7 450 n/a 3_occ: 0.1206 0.1382 0.006 0.923 9.2 110.2 21.7 450 n/a 4_bss: 0.1194 0.1362 0.006 0.923 9.2 110.2 21.7 450 n/a 4_settarget: 0.1194 0.1362 0.006 0.923 9.2 110.2 21.7 450 n/a 4_updatecdl: 0.1194 0.1362 0.006 0.921 9.2 110.2 21.7 450 n/a 4_nqh: 0.1194 0.1362 0.006 0.921 9.2 110.2 21.7 450 n/a 4_sol: 0.1191 0.1360 0.006 0.921 9.2 110.2 21.4 442 n/a 4_weight: 0.1191 0.1360 0.006 0.921 9.2 110.2 21.4 442 n/a 4_xyzrec: 0.1197 0.1376 0.006 0.961 9.2 110.2 21.4 442 n/a 4_adp: 0.1196 0.1374 0.006 0.961 9.3 106.4 21.3 442 n/a 4_regHadp: 0.1196 0.1374 0.006 0.961 9.3 106.4 21.3 442 n/a 4_occ: 0.1191 0.1372 0.006 0.961 9.3 106.4 21.3 442 n/a 5_bss: 0.1189 0.1372 0.006 0.961 9.2 106.3 21.3 442 n/a 5_settarget: 0.1189 0.1372 0.006 0.961 9.2 106.3 21.3 442 n/a 5_updatecdl: 0.1189 0.1372 0.006 0.961 9.2 106.3 21.3 442 n/a 5_setrh: 0.1190 0.1372 0.006 0.961 9.2 106.3 21.3 442 n/a 5_nqh: 0.1190 0.1372 0.006 0.961 9.2 106.3 21.3 442 n/a 5_sol: 0.1184 0.1357 0.006 0.961 9.2 106.3 21.2 448 n/a 5_weight: 0.1184 0.1357 0.006 0.961 9.2 106.3 21.2 448 n/a 5_xyzrec: 0.1208 0.1381 0.006 1.047 9.2 106.3 21.2 448 n/a 5_adp: 0.1202 0.1379 0.006 1.047 9.3 101.3 20.9 448 n/a 5_regHadp: 0.1202 0.1378 0.006 1.047 9.3 101.3 20.9 448 n/a 5_occ: 0.1196 0.1376 0.006 1.047 9.3 101.3 20.9 448 n/a end: 0.1197 0.1377 0.006 1.047 9.3 101.3 20.9 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8315495_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8315495_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3397.0600 Write final files (write_after_run_outputs) : 69.2600 Total : 3471.1400 Total CPU time: 58.46 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:10:07 PST -0800 (1735452607.18 s) Start R-work = 0.1640, R-free = 0.1755 Final R-work = 0.1197, R-free = 0.1377 =============================================================================== Job complete usr+sys time: 3616.32 seconds wall clock time: 65 minutes 28.86 seconds (3928.86 seconds total)