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_2348261.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_2348261.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2348261.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.32, per 1000 atoms: 0.69 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 224.5 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 609 0.93 - 1.19: 1053 1.19 - 1.45: 737 1.45 - 1.72: 738 1.72 - 1.98: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALYS A 175 " pdb=" CA ALYS A 175 " ideal model delta sigma weight residual 1.459 1.219 0.240 1.23e-02 6.61e+03 3.80e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.19e-02 7.06e+03 3.67e+02 bond pdb=" N ILE A 152 " pdb=" CA ILE A 152 " ideal model delta sigma weight residual 1.459 1.695 -0.236 1.27e-02 6.20e+03 3.46e+02 bond pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 1.237 1.440 -0.203 1.19e-02 7.06e+03 2.91e+02 bond pdb=" CA SER A 121 " pdb=" C SER A 121 " ideal model delta sigma weight residual 1.524 1.305 0.218 1.30e-02 5.92e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 3308 4.89 - 9.78: 1855 9.78 - 14.67: 527 14.67 - 19.56: 82 19.56 - 24.45: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.50 132.51 -18.01 1.16e+00 7.43e-01 2.41e+02 angle pdb=" O AASN A 76 " pdb=" C AASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.12 105.97 16.15 1.06e+00 8.90e-01 2.32e+02 angle pdb=" O PRO A 54 " pdb=" C PRO A 54 " pdb=" N ASP A 55 " ideal model delta sigma weight residual 123.00 105.52 17.48 1.22e+00 6.72e-01 2.05e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 109.37 13.23 1.00e+00 1.00e+00 1.75e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.24: 927 16.24 - 32.48: 119 32.48 - 48.72: 43 48.72 - 64.95: 18 64.95 - 81.19: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+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 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 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 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 104 0.207 - 0.414: 74 0.414 - 0.620: 38 0.620 - 0.827: 23 0.827 - 1.034: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.49 -1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.058 9.50e-02 1.11e+02 7.06e-02 1.04e+02 pdb=" NE ARG A 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.107 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.053 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.115 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.014 2.00e-02 2.50e+03 5.76e-02 9.94e+01 pdb=" CG TYR A 141 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.091 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.007 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 664 2.26 - 2.84: 7701 2.84 - 3.43: 10651 3.43 - 4.01: 15373 4.01 - 4.60: 22153 Nonbonded interactions: 56542 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.670 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.756 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.809 2.450 nonbonded pdb="HD22BASN A 76 " pdb=" HB2 PHE A 119 " model vdw sym.op. 1.845 2.270 -y,x-y-1,z+1/3 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.847 2.450 ... (remaining 56537 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_2348261_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= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.800356 | | target function (ml) not normalized (work): 233286.478146 | | target function (ml) not normalized (free): 11851.840274 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3040 0.2038 7.0933 4.9424| | 2: 3.57 - 2.84 1.00 2876 122 0.2422 0.1719 4.3459 4.3358| | 3: 2.84 - 2.48 1.00 2833 165 0.2390 0.1630 4.123 4.1593| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1532 3.83 3.8326| | 5: 2.25 - 2.09 1.00 2756 127 0.2443 0.1518 3.7948 3.8165| | 6: 2.09 - 1.97 1.00 2846 113 0.2563 0.1847 3.4719 3.6129| | 7: 1.97 - 1.87 1.00 2787 165 0.2539 0.1773 3.1457 3.1964| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1798 3.076 3.1244| | 9: 1.79 - 1.72 1.00 2745 138 0.2406 0.1943 2.906 2.9608| | 10: 1.72 - 1.66 1.00 2789 158 0.2428 0.2164 2.8104 2.9544| | 11: 1.66 - 1.61 1.00 2740 147 0.2536 0.2003 2.7685 2.818| | 12: 1.61 - 1.56 1.00 2787 146 0.2519 0.1922 2.6538 2.6543| | 13: 1.56 - 1.52 1.00 2745 130 0.2567 0.1986 2.5933 2.6528| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.2107 2.5212 2.5854| | 15: 1.48 - 1.45 1.00 2738 128 0.2565 0.2050 2.4364 2.474| | 16: 1.45 - 1.42 1.00 2756 161 0.2625 0.2037 2.3839 2.4323| | 17: 1.42 - 1.39 1.00 2785 139 0.2657 0.2299 2.3394 2.4508| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2270 2.2919 2.363| | 19: 1.36 - 1.34 1.00 2807 134 0.2603 0.2178 2.2606 2.2397| | 20: 1.34 - 1.32 1.00 2696 147 0.2716 0.2078 2.2065 2.1603| | 21: 1.32 - 1.30 1.00 2785 112 0.2689 0.2319 2.1732 2.196| | 22: 1.29 - 1.27 1.00 2704 152 0.2812 0.2596 2.167 2.1942| | 23: 1.27 - 1.26 1.00 2802 156 0.2819 0.2426 2.1136 2.1663| | 24: 1.26 - 1.24 1.00 2744 132 0.2812 0.2676 2.09 2.2197| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2237 2.0495 1.9864| | 26: 1.22 - 1.21 1.00 2727 135 0.2907 0.2065 2.0122 2.0294| | 27: 1.21 - 1.19 1.00 2814 148 0.3007 0.2744 2.0185 2.0119| | 28: 1.19 - 1.18 1.00 2671 147 0.2978 0.2777 1.9922 1.9958| | 29: 1.18 - 1.16 1.00 2800 134 0.2921 0.2802 1.9533 2.0707| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.3048 1.9324 1.9926| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1460.83| | 2: 3.57 - 2.84 2876 122 0.81 25.82 1.27 0.23 1460.83| | 3: 2.84 - 2.48 2833 165 0.74 32.03 1.25 0.24 1212.28| | 4: 2.47 - 2.25 2825 136 0.81 25.38 1.26 0.25 567.26| | 5: 2.25 - 2.09 2756 127 0.77 29.13 1.28 0.25 567.26| | 6: 2.09 - 1.97 2846 113 0.83 22.81 1.29 0.25 312.52| | 7: 1.97 - 1.87 2787 165 0.90 17.04 1.28 0.26 95.27| | 8: 1.87 - 1.79 2789 144 0.85 21.46 1.24 0.26 95.27| | 9: 1.79 - 1.72 2745 138 0.88 19.01 1.23 0.25 58.36| | 10: 1.72 - 1.66 2789 158 0.86 21.16 1.23 0.25 50.97| | 11: 1.66 - 1.61 2740 147 0.85 22.10 1.24 0.25 49.22| | 12: 1.61 - 1.56 2787 146 0.88 19.18 1.23 0.25 31.39| | 13: 1.56 - 1.52 2745 130 0.86 21.45 1.24 0.25 31.39| | 14: 1.52 - 1.48 2803 134 0.86 21.46 1.24 0.25 27.86| | 15: 1.48 - 1.45 2738 128 0.86 20.69 1.23 0.25 21.39| | 16: 1.45 - 1.42 2756 161 0.85 22.16 1.24 0.25 21.39| | 17: 1.42 - 1.39 2785 139 0.86 21.18 1.22 0.25 18.10| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.22 0.25 16.20| | 19: 1.36 - 1.34 2807 134 0.85 22.06 1.20 0.25 16.20| | 20: 1.34 - 1.32 2696 147 0.86 21.15 1.21 0.24 12.89| | 21: 1.32 - 1.30 2785 112 0.86 21.67 1.20 0.24 12.66| | 22: 1.29 - 1.27 2704 152 0.85 22.36 1.21 0.24 12.38| | 23: 1.27 - 1.26 2802 156 0.86 21.87 1.22 0.24 10.96| | 24: 1.26 - 1.24 2744 132 0.85 22.38 1.21 0.24 10.96| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.21 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.84 24.09 1.21 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.68 1.20 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.82 25.70 1.18 0.23 9.60| | 29: 1.18 - 1.16 2800 134 0.82 26.30 1.15 0.22 9.49| | 30: 1.16 - 1.15 2740 148 0.80 27.94 1.15 0.22 9.49| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.49 max = 1460.83 mean = 213.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.89| |phase err.(test): min = 0.00 max = 89.40 mean = 22.66| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.258 1557 Z= 5.390 Angle : 5.224 18.008 2118 Z= 3.706 Chirality : 0.371 1.034 243 Planarity : 0.032 0.089 284 Dihedral : 13.767 81.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 29.19 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.49), residues: 224 helix: -2.33 (0.41), residues: 102 sheet: -1.05 (0.91), residues: 28 loop : -0.30 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.028 ARG A 27 TYR 0.107 0.036 TYR A 141 PHE 0.121 0.037 PHE A 164 HIS 0.065 0.033 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.800356 | | target function (ml) not normalized (work): 233286.478146 | | target function (ml) not normalized (free): 11851.840274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2611 0.1934 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2611 0.1934 n_refl.: 87602 remove outliers: r(all,work,free)=0.1984 0.1989 0.1934 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2009 0.2015 0.1944 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1653 0.1647 0.1766 n_refl.: 87594 remove outliers: r(all,work,free)=0.1652 0.1646 0.1766 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 97.87 87 5 0.3776 389.396 355.160 0.671 1.004 0.411 11.894-9.307 99.02 97 4 0.1913 613.345 590.540 0.924 1.004 0.376 9.237-7.194 100.00 213 7 0.2121 501.641 490.186 0.953 1.004 0.356 7.162-5.571 100.00 427 22 0.2200 376.454 364.667 0.932 1.004 0.310 5.546-4.326 100.00 867 58 0.1303 516.778 511.207 0.963 1.004 0.233 4.315-3.360 100.00 1859 96 0.1144 491.459 487.162 1.005 1.003 0.217 3.356-2.611 100.00 3867 181 0.1436 322.863 319.756 0.997 1.002 0.033 2.608-2.026 99.99 8198 413 0.1338 214.029 211.903 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1666 104.521 103.844 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2099 46.349 45.044 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2604 29.203 26.946 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0496 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1766 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1651 r_free=0.1769 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.192259 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.147206 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 0.1215 0.1463 0.0248 0.007 0.9 1.3 0.5 0.0 0 12.096 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.15 14.63 2.48 3.013 19.074 1992.147 0.017 12.44 15.36 2.92 3.205 19.555 1992.147 0.016 Individual atomic B min max mean iso aniso Overall: 8.59 118.90 21.01 2.88 0 1785 Protein: 8.59 118.90 17.91 2.88 0 1519 Water: 11.02 114.93 39.05 N/A 0 258 Other: 22.78 36.12 29.01 N/A 0 8 Chain A: 8.59 118.90 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.59 - 19.62 1211 19.62 - 30.65 227 30.65 - 41.68 168 41.68 - 52.71 99 52.71 - 63.74 51 63.74 - 74.77 16 74.77 - 85.81 6 85.81 - 96.84 4 96.84 - 107.87 0 107.87 - 118.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1536 r_work=0.1248 r_free=0.1538 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1538 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 = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 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= 0.1542 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015421 | | target function (ls_wunit_k1) not normalized (work): 1284.491030 | | target function (ls_wunit_k1) not normalized (free): 113.794938 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1261 0.1247 0.1542 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1769 n_refl.: 87592 remove outliers: r(all,work,free)=0.1704 0.1703 0.1769 n_refl.: 87592 overall B=0.13 to atoms: r(all,work,free)=0.1725 0.1724 0.1784 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1243 0.1533 n_refl.: 87592 remove outliers: r(all,work,free)=0.1257 0.1243 0.1533 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 94.79 86 5 0.3533 300.961 279.795 0.695 0.924 0.380 11.894-9.307 99.02 97 4 0.1616 478.041 466.458 0.985 0.924 0.380 9.237-7.194 100.00 213 7 0.1813 390.979 385.241 1.027 0.925 0.340 7.162-5.571 100.00 427 22 0.1723 293.408 287.792 0.999 0.925 0.290 5.546-4.326 100.00 867 58 0.0920 402.776 400.075 1.029 0.926 0.209 4.315-3.360 100.00 1859 96 0.0779 383.043 381.960 1.076 0.927 0.200 3.356-2.611 100.00 3867 181 0.1021 251.640 250.896 1.077 0.929 0.052 2.608-2.026 99.99 8198 413 0.0976 166.814 166.243 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1210 81.463 81.641 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1649 36.124 35.586 1.063 0.945 0.000 1.221-1.150 99.97 13689 708 0.2363 22.761 21.295 1.018 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1533 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 180 GLN Total number of N/Q/H flips: 2 r_work=0.1246 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1534 | n_water=258 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1256 r_free=0.1534 | n_water=252 | time (s): 26.530 (total time: 29.060) Filter (q & B) r_work=0.1258 r_free=0.1533 | n_water=249 | time (s): 3.710 (total time: 32.770) Compute maps r_work=0.1258 r_free=0.1533 | n_water=249 | time (s): 1.900 (total time: 34.670) Filter (map) r_work=0.1270 r_free=0.1540 | n_water=237 | time (s): 3.730 (total time: 38.400) Find peaks r_work=0.1270 r_free=0.1540 | n_water=237 | time (s): 0.790 (total time: 39.190) Add new water r_work=0.1432 r_free=0.1691 | n_water=457 | time (s): 3.890 (total time: 43.080) Refine new water occ: r_work=0.1342 r_free=0.1557 adp: r_work=0.1259 r_free=0.1513 occ: r_work=0.1272 r_free=0.1499 adp: r_work=0.1235 r_free=0.1490 occ: r_work=0.1238 r_free=0.1475 adp: r_work=0.1228 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1480 r_work=0.1228 r_free=0.1480 | n_water=457 | time (s): 84.520 (total time: 127.600) Filter (q & B) r_work=0.1234 r_free=0.1486 | n_water=434 | time (s): 4.030 (total time: 131.630) Filter (dist only) r_work=0.1234 r_free=0.1486 | n_water=434 | time (s): 41.540 (total time: 173.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.791281 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1530.144485 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1514 0.0283 0.007 0.9 1.6 0.5 0.0 0 12.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.14 2.83 3.792 23.241 1530.144 0.015 12.00 14.84 2.84 4.282 23.035 1530.144 0.015 Individual atomic B min max mean iso aniso Overall: 8.68 114.02 23.23 2.63 197 1764 Protein: 8.68 114.02 17.61 2.63 0 1519 Water: 10.99 73.38 42.76 N/A 197 237 Other: 24.77 35.39 29.97 N/A 0 8 Chain A: 8.68 114.02 20.36 N/A 0 1764 Chain S: 17.06 73.38 48.88 N/A 197 0 Histogram: Values Number of atoms 8.68 - 19.21 1211 19.21 - 29.75 242 29.75 - 40.28 195 40.28 - 50.81 134 50.81 - 61.35 111 61.35 - 71.88 54 71.88 - 82.42 8 82.42 - 92.95 3 92.95 - 103.49 1 103.49 - 114.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1485 r_work=0.1200 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1484 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1480 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1202 r_free= 0.1480 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014085 | | target function (ls_wunit_k1) not normalized (work): 1173.250716 | | target function (ls_wunit_k1) not normalized (free): 101.624879 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1480 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1607 0.1602 0.1733 n_refl.: 87591 remove outliers: r(all,work,free)=0.1607 0.1602 0.1733 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1614 0.1609 0.1738 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1480 n_refl.: 87591 remove outliers: r(all,work,free)=0.1210 0.1197 0.1480 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 90.62 82 5 0.3183 293.704 273.592 0.640 0.936 0.359 11.894-9.307 99.02 97 4 0.1501 478.041 475.988 0.979 0.937 0.351 9.237-7.194 100.00 213 7 0.1694 390.979 392.305 1.043 0.937 0.310 7.162-5.571 100.00 427 22 0.1507 293.408 289.086 1.001 0.938 0.229 5.546-4.326 100.00 867 58 0.0865 402.776 399.966 1.022 0.938 0.215 4.315-3.360 100.00 1859 96 0.0714 383.043 382.047 1.068 0.939 0.210 3.356-2.611 100.00 3867 181 0.0975 251.640 250.766 1.075 0.940 0.067 2.608-2.026 99.99 8198 413 0.0956 166.814 166.349 1.082 0.941 0.000 2.025-1.573 100.00 17313 902 0.1177 81.463 81.650 1.087 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1601 36.124 35.624 1.069 0.948 0.000 1.221-1.150 99.97 13689 708 0.2327 22.761 21.317 1.022 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0677 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1480 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1480 | n_water=434 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1197 r_free=0.1480 | n_water=433 | time (s): 39.510 (total time: 41.730) Filter (q & B) r_work=0.1197 r_free=0.1480 | n_water=433 | time (s): 0.880 (total time: 42.610) Compute maps r_work=0.1197 r_free=0.1480 | n_water=433 | time (s): 1.390 (total time: 44.000) Filter (map) r_work=0.1232 r_free=0.1493 | n_water=291 | time (s): 3.020 (total time: 47.020) Find peaks r_work=0.1232 r_free=0.1493 | n_water=291 | time (s): 0.710 (total time: 47.730) Add new water r_work=0.1359 r_free=0.1633 | n_water=479 | time (s): 3.420 (total time: 51.150) Refine new water occ: r_work=0.1257 r_free=0.1532 adp: r_work=0.1259 r_free=0.1534 occ: r_work=0.1234 r_free=0.1508 adp: r_work=0.1233 r_free=0.1510 occ: r_work=0.1218 r_free=0.1491 adp: r_work=0.1213 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1213 r_free=0.1490 r_work=0.1213 r_free=0.1490 | n_water=479 | time (s): 173.460 (total time: 224.610) Filter (q & B) r_work=0.1217 r_free=0.1497 | n_water=442 | time (s): 2.940 (total time: 227.550) Filter (dist only) r_work=0.1217 r_free=0.1497 | n_water=442 | time (s): 36.320 (total time: 263.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.059581 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.316149 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 0.1470 0.0241 0.006 0.9 1.9 0.5 0.0 0 1.030 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.70 2.41 3.621 21.996 42.316 3.723 12.21 14.33 2.12 4.067 21.818 42.316 3.658 Individual atomic B min max mean iso aniso Overall: 9.21 110.11 21.55 2.29 207 1762 Protein: 9.21 110.11 17.22 2.29 0 1519 Water: 11.50 69.81 36.33 N/A 207 235 Other: 20.37 31.15 26.37 N/A 0 8 Chain A: 9.21 110.11 19.93 N/A 0 1762 Chain S: 15.90 65.16 35.29 N/A 207 0 Histogram: Values Number of atoms 9.21 - 19.30 1236 19.30 - 29.39 287 29.39 - 39.48 211 39.48 - 49.57 135 49.57 - 59.66 69 59.66 - 69.75 18 69.75 - 79.84 7 79.84 - 89.93 3 89.93 - 100.02 1 100.02 - 110.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1433 r_work=0.1222 r_free=0.1434 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1222 r_free = 0.1434 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1433 target_work(ml) = 3.656 | | 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= 0.1217 r_free= 0.1433 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655959 | | target function (ml) not normalized (work): 304508.464321 | | target function (ml) not normalized (free): 16075.315847 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1217 0.1433 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1551 0.1549 0.1600 n_refl.: 87587 remove outliers: r(all,work,free)=0.1551 0.1549 0.1600 n_refl.: 87587 overall B=-0.01 to atoms: r(all,work,free)=0.1548 0.1547 0.1599 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1207 0.1395 n_refl.: 87587 remove outliers: r(all,work,free)=0.1212 0.1203 0.1395 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 0.3719 290.369 260.807 0.485 0.999 0.324 11.894-9.307 96.08 94 4 0.2276 475.271 458.952 0.855 1.001 0.258 9.237-7.194 97.73 208 7 0.2367 383.611 384.017 0.943 1.002 0.200 7.162-5.571 100.00 427 22 0.2062 293.408 282.510 0.911 1.002 0.165 5.546-4.326 100.00 867 58 0.1122 402.776 397.775 0.951 1.002 0.155 4.315-3.360 100.00 1859 96 0.0944 383.043 380.373 0.993 1.002 0.150 3.356-2.611 100.00 3867 181 0.1161 251.640 249.602 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1051 166.814 165.806 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1016 81.463 81.622 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1299 36.124 35.694 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2132 22.761 21.377 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0335 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1395 | n_water=442 | time (s): 1.740 (total time: 1.740) Filter (dist) r_work=0.1203 r_free=0.1395 | n_water=441 | time (s): 39.090 (total time: 40.830) Filter (q & B) r_work=0.1203 r_free=0.1393 | n_water=440 | time (s): 2.820 (total time: 43.650) Compute maps r_work=0.1203 r_free=0.1393 | n_water=440 | time (s): 1.320 (total time: 44.970) Filter (map) r_work=0.1227 r_free=0.1390 | n_water=317 | time (s): 2.740 (total time: 47.710) Find peaks r_work=0.1227 r_free=0.1390 | n_water=317 | time (s): 0.580 (total time: 48.290) Add new water r_work=0.1295 r_free=0.1437 | n_water=485 | time (s): 3.420 (total time: 51.710) Refine new water occ: r_work=0.1221 r_free=0.1373 adp: r_work=0.1221 r_free=0.1374 occ: r_work=0.1206 r_free=0.1364 adp: r_work=0.1204 r_free=0.1365 occ: r_work=0.1195 r_free=0.1362 adp: r_work=0.1191 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1361 r_work=0.1191 r_free=0.1361 | n_water=485 | time (s): 245.440 (total time: 297.150) Filter (q & B) r_work=0.1197 r_free=0.1365 | n_water=453 | time (s): 3.360 (total time: 300.510) Filter (dist only) r_work=0.1197 r_free=0.1365 | n_water=452 | time (s): 39.710 (total time: 340.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.008905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.889568 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 0.1199 0.1389 0.0189 0.006 1.0 1.9 0.5 0.0 0 1.004 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.89 1.89 3.417 21.540 50.890 3.639 11.78 13.73 1.95 3.896 21.391 50.890 3.616 Individual atomic B min max mean iso aniso Overall: 9.17 106.61 21.27 2.19 220 1759 Protein: 9.17 106.61 16.87 2.19 0 1519 Water: 11.45 67.98 36.01 N/A 220 232 Other: 20.70 29.52 24.89 N/A 0 8 Chain A: 9.17 106.61 19.48 N/A 0 1759 Chain S: 16.00 65.39 35.63 N/A 220 0 Histogram: Values Number of atoms 9.17 - 18.91 1231 18.91 - 28.66 285 28.66 - 38.40 217 38.40 - 48.15 144 48.15 - 57.89 68 57.89 - 67.64 22 67.64 - 77.38 7 77.38 - 87.12 2 87.12 - 96.87 1 96.87 - 106.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1374 r_work=0.1179 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1374 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1375 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1177 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.615680 | | target function (ml) not normalized (work): 301117.457358 | | target function (ml) not normalized (free): 15914.491781 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1177 0.1375 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1495 0.1492 0.1572 n_refl.: 87577 remove outliers: r(all,work,free)=0.1495 0.1492 0.1572 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1492 0.1490 0.1570 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1185 0.1175 0.1377 n_refl.: 87577 remove outliers: r(all,work,free)=0.1183 0.1173 0.1377 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3911 285.644 255.457 0.446 0.999 0.309 11.894-9.307 92.16 90 4 0.2234 467.276 447.309 0.833 1.001 0.206 9.237-7.194 97.73 208 7 0.2423 383.611 378.265 0.914 1.002 0.129 7.162-5.571 100.00 427 22 0.2187 293.408 282.364 0.900 1.002 0.120 5.546-4.326 100.00 867 58 0.1166 402.776 398.121 0.951 1.002 0.117 4.315-3.360 100.00 1859 96 0.0944 383.043 380.776 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1155 251.640 249.707 1.001 1.002 0.043 2.608-2.026 99.99 8198 413 0.1015 166.814 165.991 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0952 81.463 81.740 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.124 35.752 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2124 22.761 21.395 0.979 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0348 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1173 r_free=0.1377 After: r_work=0.1174 r_free=0.1378 ================================== NQH flips ================================== r_work=0.1174 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=0.1174 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1378 | n_water=452 | time (s): 1.640 (total time: 1.640) Filter (dist) r_work=0.1174 r_free=0.1378 | n_water=452 | time (s): 35.390 (total time: 37.030) Filter (q & B) r_work=0.1174 r_free=0.1378 | n_water=452 | time (s): 1.150 (total time: 38.180) Compute maps r_work=0.1174 r_free=0.1378 | n_water=452 | time (s): 1.420 (total time: 39.600) Filter (map) r_work=0.1210 r_free=0.1392 | n_water=336 | time (s): 3.080 (total time: 42.680) Find peaks r_work=0.1210 r_free=0.1392 | n_water=336 | time (s): 0.570 (total time: 43.250) Add new water r_work=0.1254 r_free=0.1432 | n_water=490 | time (s): 3.350 (total time: 46.600) Refine new water occ: r_work=0.1185 r_free=0.1376 adp: r_work=0.1186 r_free=0.1379 occ: r_work=0.1175 r_free=0.1367 adp: r_work=0.1174 r_free=0.1369 occ: r_work=0.1167 r_free=0.1360 adp: r_work=0.1164 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1164 r_free=0.1361 r_work=0.1164 r_free=0.1361 | n_water=490 | time (s): 248.680 (total time: 295.280) Filter (q & B) r_work=0.1174 r_free=0.1372 | n_water=447 | time (s): 2.890 (total time: 298.170) Filter (dist only) r_work=0.1174 r_free=0.1371 | n_water=446 | time (s): 37.410 (total time: 335.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.898003 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.393947 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 0.1198 0.1389 0.0191 0.006 1.0 2.2 0.5 0.0 0 0.949 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.89 1.91 3.290 21.087 47.394 3.625 12.01 13.89 1.88 3.381 21.044 47.394 3.621 Individual atomic B min max mean iso aniso Overall: 9.24 103.52 21.06 2.07 217 1756 Protein: 9.24 103.52 16.76 2.07 0 1519 Water: 11.50 67.55 35.63 N/A 217 229 Other: 20.99 29.33 25.01 N/A 0 8 Chain A: 9.24 103.52 19.33 N/A 0 1756 Chain S: 15.46 65.46 35.07 N/A 217 0 Histogram: Values Number of atoms 9.24 - 18.67 1227 18.67 - 28.10 289 28.10 - 37.53 201 37.53 - 46.95 143 46.95 - 56.38 74 56.38 - 65.81 25 65.81 - 75.24 9 75.24 - 84.67 2 84.67 - 94.10 1 94.10 - 103.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1389 r_work=0.1201 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1389 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1385 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87572 (all), 4.91 % free)------------| | | | r_work= 0.1198 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.619263 | | target function (ml) not normalized (work): 301397.704788 | | target function (ml) not normalized (free): 15936.663161 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2914 171 0.1421 0.1468 5.6719 5.6573| | 2: 3.57 - 2.84 1.00 2888 124 0.1133 0.1454 5.2103 5.2656| | 3: 2.83 - 2.48 1.00 2820 163 0.1222 0.1294 5.0102 5.0282| | 4: 2.47 - 2.25 1.00 2825 136 0.1028 0.1213 4.7132 4.7785| | 5: 2.25 - 2.09 1.00 2756 127 0.0996 0.1136 4.6559 4.7318| | 6: 2.09 - 1.97 1.00 2846 113 0.0977 0.1188 4.3588 4.479| | 7: 1.97 - 1.87 1.00 2787 165 0.0988 0.1190 4.0743 4.1631| | 8: 1.87 - 1.79 1.00 2789 144 0.1022 0.1251 3.9874 4.0807| | 9: 1.79 - 1.72 1.00 2745 138 0.0948 0.1311 3.7051 3.9017| | 10: 1.72 - 1.66 1.00 2831 160 0.0999 0.1228 3.6232 3.7468| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1106 3.5629 3.6063| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1167 3.338 3.4759| | 13: 1.56 - 1.52 1.00 2745 130 0.0968 0.1045 3.331 3.4209| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1121 3.2556 3.3411| | 15: 1.48 - 1.45 1.00 2738 128 0.1000 0.1348 3.1602 3.3291| | 16: 1.45 - 1.42 1.00 2756 161 0.1062 0.1252 3.1474 3.2411| | 17: 1.42 - 1.39 1.00 2785 139 0.1115 0.1296 3.1128 3.2225| | 18: 1.39 - 1.36 1.00 2741 179 0.1156 0.1369 3.0854 3.262| | 19: 1.36 - 1.34 1.00 2807 134 0.1207 0.1614 3.0883 3.2725| | 20: 1.34 - 1.32 1.00 2696 147 0.1313 0.1494 3.0834 3.1468| | 21: 1.32 - 1.30 1.00 2785 112 0.1410 0.1626 3.0828 3.1656| | 22: 1.29 - 1.27 1.00 2704 152 0.1468 0.1889 3.0806 3.2744| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1837 3.1006 3.2018| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1779 3.0954 3.1916| | 25: 1.24 - 1.22 1.00 2733 148 0.1804 0.2334 3.1097 3.2959| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1778 3.1221 3.1998| | 27: 1.21 - 1.19 1.00 2814 148 0.2006 0.2098 3.1373 3.1476| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2317 3.1405 3.1574| | 29: 1.18 - 1.16 1.00 2800 134 0.2220 0.2372 3.1262 3.2233| | 30: 1.16 - 1.15 1.00 2739 148 0.2379 0.2514 3.1164 3.1671| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2914 171 0.94 9.35 1.00 0.97 6450.53| | 2: 3.57 - 2.84 2888 124 0.92 13.54 1.01 0.97 6450.53| | 3: 2.83 - 2.48 2820 163 0.88 17.82 0.99 0.97 5402.52| | 4: 2.47 - 2.25 2825 136 0.91 14.80 1.00 0.97 2700.02| | 5: 2.25 - 2.09 2756 127 0.89 17.08 1.01 0.97 2700.02| | 6: 2.09 - 1.97 2846 113 0.92 13.75 1.02 0.97 1578.18| | 7: 1.97 - 1.87 2787 165 0.94 10.75 1.02 0.97 621.40| | 8: 1.87 - 1.79 2789 144 0.91 14.41 1.00 0.97 621.40| | 9: 1.79 - 1.72 2745 138 0.93 11.31 0.98 0.97 334.31| | 10: 1.72 - 1.66 2831 160 0.93 12.16 0.98 0.97 276.81| | 11: 1.66 - 1.61 2712 147 0.93 12.76 0.98 0.97 264.30| | 12: 1.61 - 1.56 2773 144 0.95 9.47 0.99 0.97 146.26| | 13: 1.56 - 1.52 2745 130 0.94 11.07 1.02 0.97 146.26| | 14: 1.52 - 1.48 2803 134 0.94 11.22 1.02 0.97 130.83| | 15: 1.48 - 1.45 2738 128 0.95 10.45 1.01 0.98 102.57| | 16: 1.45 - 1.42 2756 161 0.94 11.57 1.01 0.98 102.57| | 17: 1.42 - 1.39 2785 139 0.94 11.37 1.01 0.98 92.77| | 18: 1.39 - 1.36 2741 179 0.94 11.80 1.01 0.98 87.09| | 19: 1.36 - 1.34 2807 134 0.94 12.30 1.00 0.98 87.09| | 20: 1.34 - 1.32 2696 147 0.94 12.46 0.99 0.96 82.18| | 21: 1.32 - 1.30 2785 112 0.94 13.34 0.98 0.96 81.83| | 22: 1.29 - 1.27 2704 152 0.93 13.87 0.98 0.96 81.98| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.97 0.94 82.71| | 24: 1.26 - 1.24 2744 132 0.92 14.97 0.96 0.94 82.71| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 84.30| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.05| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.05| | 28: 1.19 - 1.18 2671 147 0.88 20.25 1.01 0.92 89.36| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.92 90.60| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.60| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.83 max = 6450.53 mean = 998.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.07| |phase err.(test): min = 0.00 max = 89.53 mean = 14.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1198 0.1385 n_refl.: 87572 re-set all scales: r(all,work,free)=0.1507 0.1505 0.1573 n_refl.: 87572 remove outliers: r(all,work,free)=0.1507 0.1505 0.1573 n_refl.: 87572 overall B=-0.01 to atoms: r(all,work,free)=0.1506 0.1504 0.1572 n_refl.: 87572 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1198 0.1388 n_refl.: 87572 remove outliers: r(all,work,free)=0.1208 0.1198 0.1388 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4105 285.644 245.808 0.431 1.001 0.310 11.894-9.307 92.16 90 4 0.2344 467.276 446.997 0.833 1.002 0.211 9.237-7.194 97.73 208 7 0.2554 383.611 376.249 0.904 1.002 0.120 7.162-5.571 100.00 427 22 0.2300 293.408 281.305 0.891 1.002 0.108 5.546-4.326 100.00 867 58 0.1214 402.776 398.152 0.950 1.002 0.098 4.315-3.360 100.00 1859 96 0.0992 383.043 380.762 0.995 1.002 0.097 3.356-2.611 100.00 3867 181 0.1194 251.640 249.525 1.001 1.001 0.080 2.608-2.026 99.99 8198 413 0.1039 166.814 165.867 1.013 1.000 0.000 2.025-1.573 100.00 17313 902 0.0975 81.463 81.703 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1224 36.124 35.747 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2119 22.761 21.374 0.979 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0208 ================= 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 0.1933 0.081 5.224 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1766 0.081 5.224 9.1 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1766 0.081 5.224 9.1 119.5 20.1 258 0.000 1_nqh: 0.1651 0.1769 0.081 5.224 9.1 119.5 20.1 258 0.006 1_weight: 0.1651 0.1769 0.081 5.224 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1215 0.1463 0.007 0.946 9.1 119.5 20.1 258 0.130 1_adp: 0.1244 0.1536 0.007 0.946 8.6 118.9 21.0 258 0.130 1_regHadp: 0.1248 0.1538 0.007 0.946 8.6 118.9 21.0 258 0.130 1_occ: 0.1247 0.1542 0.007 0.946 8.6 118.9 21.0 258 0.130 2_bss: 0.1243 0.1533 0.007 0.946 8.7 119.0 21.1 258 0.130 2_settarget: 0.1243 0.1533 0.007 0.946 8.7 119.0 21.1 258 0.130 2_updatecdl: 0.1243 0.1533 0.007 0.953 8.7 119.0 21.1 258 0.130 2_nqh: 0.1246 0.1534 0.007 0.953 8.7 119.0 21.1 258 0.130 2_sol: 0.1234 0.1486 0.007 0.953 8.7 119.0 23.6 434 n/a 2_weight: 0.1234 0.1486 0.007 0.953 8.7 119.0 23.6 434 n/a 2_xyzrec: 0.1230 0.1514 0.007 0.885 8.7 119.0 23.6 434 n/a 2_adp: 0.1201 0.1485 0.007 0.885 8.7 114.0 23.2 434 n/a 2_regHadp: 0.1200 0.1484 0.007 0.885 8.7 114.0 23.2 434 n/a 2_occ: 0.1202 0.1480 0.007 0.885 8.7 114.0 23.2 434 n/a 3_bss: 0.1197 0.1480 0.007 0.885 8.7 114.1 23.3 434 n/a 3_settarget: 0.1197 0.1480 0.007 0.885 8.7 114.1 23.3 434 n/a 3_updatecdl: 0.1197 0.1480 0.007 0.885 8.7 114.1 23.3 434 n/a 3_nqh: 0.1197 0.1480 0.007 0.885 8.7 114.1 23.3 434 n/a 3_sol: 0.1217 0.1497 0.007 0.885 8.7 114.1 21.9 442 n/a 3_weight: 0.1217 0.1497 0.007 0.885 8.7 114.1 21.9 442 n/a 3_xyzrec: 0.1229 0.1470 0.006 0.916 8.7 114.1 21.9 442 n/a 3_adp: 0.1221 0.1433 0.006 0.916 9.2 110.1 21.5 442 n/a 3_regHadp: 0.1222 0.1434 0.006 0.916 9.2 110.1 21.5 442 n/a 3_occ: 0.1217 0.1433 0.006 0.916 9.2 110.1 21.5 442 n/a 4_bss: 0.1203 0.1395 0.006 0.916 9.2 110.1 21.5 442 n/a 4_settarget: 0.1203 0.1395 0.006 0.916 9.2 110.1 21.5 442 n/a 4_updatecdl: 0.1203 0.1395 0.006 0.916 9.2 110.1 21.5 442 n/a 4_nqh: 0.1203 0.1395 0.006 0.916 9.2 110.1 21.5 442 n/a 4_sol: 0.1197 0.1365 0.006 0.916 9.2 110.1 21.5 452 n/a 4_weight: 0.1197 0.1365 0.006 0.916 9.2 110.1 21.5 452 n/a 4_xyzrec: 0.1199 0.1389 0.006 0.963 9.2 110.1 21.5 452 n/a 4_adp: 0.1179 0.1374 0.006 0.963 9.2 106.6 21.3 452 n/a 4_regHadp: 0.1179 0.1374 0.006 0.963 9.2 106.6 21.3 452 n/a 4_occ: 0.1177 0.1375 0.006 0.963 9.2 106.6 21.3 452 n/a 5_bss: 0.1173 0.1377 0.006 0.963 9.2 106.6 21.3 452 n/a 5_settarget: 0.1173 0.1377 0.006 0.963 9.2 106.6 21.3 452 n/a 5_updatecdl: 0.1173 0.1377 0.006 0.961 9.2 106.6 21.3 452 n/a 5_setrh: 0.1174 0.1378 0.006 0.961 9.2 106.6 21.3 452 n/a 5_nqh: 0.1174 0.1378 0.006 0.961 9.2 106.6 21.3 452 n/a 5_sol: 0.1174 0.1371 0.006 0.961 9.2 106.6 21.1 446 n/a 5_weight: 0.1174 0.1371 0.006 0.961 9.2 106.6 21.1 446 n/a 5_xyzrec: 0.1198 0.1389 0.006 1.015 9.2 106.6 21.1 446 n/a 5_adp: 0.1201 0.1389 0.006 1.015 9.2 103.5 21.1 446 n/a 5_regHadp: 0.1201 0.1389 0.006 1.015 9.2 103.5 21.1 446 n/a 5_occ: 0.1198 0.1385 0.006 1.015 9.2 103.5 21.1 446 n/a end: 0.1198 0.1388 0.006 1.015 9.2 103.5 21.1 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2348261_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2348261_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7200 Refinement macro-cycles (run) : 3654.1400 Write final files (write_after_run_outputs) : 56.7000 Total : 3715.5600 Total CPU time: 62.55 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:26 PST -0800 (1735452806.63 s) Start R-work = 0.1646, R-free = 0.1766 Final R-work = 0.1198, R-free = 0.1388 =============================================================================== Job complete usr+sys time: 3842.03 seconds wall clock time: 68 minutes 28.61 seconds (4108.61 seconds total)