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_3337960.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 2.30, per 1000 atoms: 0.68 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: 0.72 Conformation dependent library (CDL) restraints added in 290.1 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 427 0.90 - 1.16: 1204 1.16 - 1.42: 637 1.42 - 1.67: 845 1.67 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.237 1.480 -0.244 1.19e-02 7.06e+03 4.19e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.520 -0.199 1.00e-02 1.00e+04 3.95e+02 bond pdb=" CA LEU A 101 " pdb=" C LEU A 101 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.23e-02 6.61e+03 3.61e+02 bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.319 0.143 7.70e-03 1.69e+04 3.43e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.11e-02 8.12e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 2930 4.28 - 8.55: 1862 8.55 - 12.83: 781 12.83 - 17.11: 179 17.11 - 21.39: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 138.18 -16.09 1.04e+00 9.25e-01 2.39e+02 angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N AGLU A 90 " ideal model delta sigma weight residual 122.09 138.01 -15.92 1.04e+00 9.25e-01 2.34e+02 angle pdb=" C ALYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 122.36 136.29 -13.93 9.70e-01 1.06e+00 2.06e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.52 119.67 -9.15 6.70e-01 2.23e+00 1.86e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 112.03 8.39 6.40e-01 2.44e+00 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 934 17.17 - 34.33: 124 34.33 - 51.50: 38 51.50 - 68.66: 11 68.66 - 85.82: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+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 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.204: 87 0.204 - 0.407: 61 0.407 - 0.610: 55 0.610 - 0.813: 33 0.813 - 1.016: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.61 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=" CB HIS A 115 " -0.071 2.00e-02 2.50e+03 7.77e-02 1.36e+02 pdb=" CG HIS A 115 " 0.129 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " 0.060 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.102 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " -0.122 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.050 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 139 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.112 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.090 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.046 2.00e-02 2.50e+03 6.45e-02 9.35e+01 pdb=" CG HIS A 126 " -0.156 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1380 2.37 - 2.92: 8342 2.92 - 3.48: 10421 3.48 - 4.04: 15124 4.04 - 4.60: 21393 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.808 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.822 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.832 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.837 2.100 ... (remaining 56655 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_3337960_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= 0.2603 r_free= 0.1907 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781820 | | target function (ml) not normalized (work): 231742.301990 | | target function (ml) not normalized (free): 11750.884665 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3025 0.2083 7.0882 4.9446| | 2: 3.57 - 2.84 1.00 2876 122 0.2407 0.1733 4.3431 4.3333| | 3: 2.84 - 2.48 1.00 2833 165 0.2355 0.1689 4.1239 4.1409| | 4: 2.47 - 2.25 1.00 2825 136 0.2391 0.1399 3.8296 3.8111| | 5: 2.25 - 2.09 1.00 2756 127 0.2471 0.1505 3.7883 3.8132| | 6: 2.09 - 1.97 1.00 2846 113 0.2521 0.1808 3.4548 3.5161| | 7: 1.97 - 1.87 1.00 2787 165 0.2553 0.1595 3.1259 3.0929| | 8: 1.87 - 1.79 1.00 2789 144 0.2515 0.1761 3.0493 3.0873| | 9: 1.79 - 1.72 1.00 2745 138 0.2465 0.1991 2.8986 2.9478| | 10: 1.72 - 1.66 1.00 2789 158 0.2389 0.1873 2.7752 2.8283| | 11: 1.66 - 1.61 1.00 2740 147 0.2438 0.1858 2.7164 2.7469| | 12: 1.61 - 1.56 1.00 2787 146 0.2504 0.1856 2.6106 2.6009| | 13: 1.56 - 1.52 1.00 2745 130 0.2575 0.1995 2.568 2.666| | 14: 1.52 - 1.48 1.00 2803 134 0.2591 0.1899 2.507 2.5444| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2044 2.4144 2.4295| | 16: 1.45 - 1.42 1.00 2756 161 0.2670 0.2015 2.3776 2.3791| | 17: 1.42 - 1.39 1.00 2785 139 0.2683 0.2067 2.3216 2.3362| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2244 2.2721 2.3793| | 19: 1.36 - 1.34 1.00 2807 134 0.2621 0.2379 2.2072 2.3091| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2091 2.1861 2.1875| | 21: 1.32 - 1.30 1.00 2785 112 0.2658 0.2193 2.1326 2.1598| | 22: 1.29 - 1.27 1.00 2704 152 0.2723 0.2266 2.1326 2.1212| | 23: 1.27 - 1.26 1.00 2802 156 0.2732 0.2467 2.0969 2.1489| | 24: 1.26 - 1.24 1.00 2744 132 0.2740 0.2505 2.0679 2.1423| | 25: 1.24 - 1.22 1.00 2734 148 0.2794 0.2551 2.0335 2.1027| | 26: 1.22 - 1.21 1.00 2727 135 0.2799 0.2444 1.9989 2.1503| | 27: 1.21 - 1.19 1.00 2814 148 0.2921 0.2650 1.9991 1.9827| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2701 1.9822 1.9873| | 29: 1.18 - 1.16 1.00 2800 134 0.2934 0.2737 1.9676 2.0252| | 30: 1.16 - 1.15 1.00 2740 148 0.3053 0.3016 1.9273 2.0103| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.73 0.76 0.23 1458.10| | 2: 3.57 - 2.84 2876 122 0.81 25.79 1.27 0.23 1458.10| | 3: 2.84 - 2.48 2833 165 0.74 31.75 1.24 0.23 1207.80| | 4: 2.47 - 2.25 2825 136 0.81 25.38 1.26 0.25 558.23| | 5: 2.25 - 2.09 2756 127 0.77 29.06 1.28 0.25 558.23| | 6: 2.09 - 1.97 2846 113 0.84 22.33 1.29 0.25 303.14| | 7: 1.97 - 1.87 2787 165 0.90 16.15 1.29 0.26 85.59| | 8: 1.87 - 1.79 2789 144 0.86 20.52 1.25 0.26 85.59| | 9: 1.79 - 1.72 2745 138 0.88 18.25 1.24 0.25 52.56| | 10: 1.72 - 1.66 2789 158 0.87 19.62 1.22 0.25 45.94| | 11: 1.66 - 1.61 2740 147 0.86 20.87 1.23 0.25 44.36| | 12: 1.61 - 1.56 2787 146 0.88 18.44 1.23 0.25 28.38| | 13: 1.56 - 1.52 2745 130 0.87 19.87 1.24 0.25 28.38| | 14: 1.52 - 1.48 2803 134 0.87 20.36 1.24 0.25 25.37| | 15: 1.48 - 1.45 2738 128 0.88 19.65 1.23 0.25 19.85| | 16: 1.45 - 1.42 2756 161 0.86 21.22 1.24 0.25 19.85| | 17: 1.42 - 1.39 2785 139 0.87 20.52 1.24 0.25 16.96| | 18: 1.39 - 1.36 2741 179 0.87 20.91 1.23 0.25 15.29| | 19: 1.36 - 1.34 2807 134 0.86 21.82 1.23 0.25 15.29| | 20: 1.34 - 1.32 2696 147 0.87 20.54 1.22 0.24 12.58| | 21: 1.32 - 1.30 2785 112 0.86 21.80 1.20 0.24 12.39| | 22: 1.29 - 1.27 2704 152 0.86 21.73 1.21 0.24 12.14| | 23: 1.27 - 1.26 2802 156 0.86 21.80 1.21 0.24 10.87| | 24: 1.26 - 1.24 2744 132 0.85 22.49 1.20 0.24 10.87| | 25: 1.24 - 1.22 2734 148 0.84 23.50 1.20 0.24 10.48| | 26: 1.22 - 1.21 2727 135 0.84 24.19 1.19 0.23 10.03| | 27: 1.21 - 1.19 2814 148 0.83 25.02 1.20 0.23 10.03| | 28: 1.19 - 1.18 2671 147 0.82 25.90 1.19 0.22 9.50| | 29: 1.18 - 1.16 2800 134 0.82 26.24 1.16 0.22 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.90 1.16 0.22 9.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1458.10 mean = 210.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.41| |phase err.(test): min = 0.00 max = 89.87 mean = 22.37| |-----------------------------------------------------------------------------| ----------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 0.267 1557 Z= 5.518 Angle : 5.435 18.859 2118 Z= 3.876 Chirality : 0.419 1.016 243 Planarity : 0.033 0.105 284 Dihedral : 14.574 85.823 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 34.05 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.48), residues: 224 helix: -2.75 (0.40), residues: 103 sheet: 0.14 (1.08), residues: 28 loop : -0.72 (0.50), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.021 ARG A 27 TYR 0.063 0.022 TYR A 139 PHE 0.072 0.032 PHE A 164 HIS 0.109 0.042 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= 0.2603 r_free= 0.1907 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781820 | | target function (ml) not normalized (work): 231742.301990 | | target function (ml) not normalized (free): 11750.884665 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2603 0.1907 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2603 0.1907 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1978 0.1907 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2000 0.2006 0.1924 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1631 0.1730 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1631 0.1730 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3834 386.302 364.292 0.687 1.001 0.412 11.894-9.307 99.02 97 4 0.1853 613.623 590.929 0.924 1.002 0.385 9.237-7.194 100.00 213 7 0.2157 501.868 487.566 0.959 1.002 0.370 7.162-5.571 100.00 427 22 0.2246 376.624 363.998 0.929 1.002 0.340 5.546-4.326 100.00 867 58 0.1284 517.012 511.302 0.960 1.002 0.229 4.315-3.360 100.00 1859 96 0.1131 491.682 488.221 1.001 1.002 0.209 3.356-2.611 100.00 3867 181 0.1423 323.009 320.140 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1370 214.126 211.974 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1633 104.568 103.883 1.010 1.001 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.370 45.056 1.001 1.000 0.000 1.221-1.150 99.97 13689 708 0.2562 29.216 26.834 0.963 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0509 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1730 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** A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1631 r_free=0.1731 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.471195 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2018.128891 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 0.1213 0.1471 0.0258 0.008 1.0 1.3 0.5 0.0 0 13.236 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 14.71 2.58 3.013 19.081 2018.129 0.017 12.44 15.44 3.00 3.293 19.629 2018.129 0.016 Individual atomic B min max mean iso aniso Overall: 8.62 118.62 21.15 2.89 0 1785 Protein: 8.62 118.62 18.00 2.88 0 1519 Water: 11.13 114.52 39.39 N/A 0 258 Other: 23.36 37.37 29.72 N/A 0 8 Chain A: 8.62 118.62 21.15 N/A 0 1785 Histogram: Values Number of atoms 8.62 - 19.62 1207 19.62 - 30.62 230 30.62 - 41.62 160 41.62 - 52.62 105 52.62 - 63.62 52 63.62 - 74.62 16 74.62 - 85.62 8 85.62 - 96.62 3 96.62 - 107.62 1 107.62 - 118.62 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1544 r_work=0.1249 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1549 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 = 0.1249 r_free = 0.1551 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1249 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015426 | | target function (ls_wunit_k1) not normalized (work): 1284.954101 | | target function (ls_wunit_k1) not normalized (free): 116.156460 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1263 0.1249 0.1551 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1712 0.1711 0.1776 n_refl.: 87593 remove outliers: r(all,work,free)=0.1712 0.1711 0.1776 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1732 0.1731 0.1790 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1541 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1244 0.1541 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3589 297.542 277.037 0.685 0.923 0.374 11.894-9.307 99.02 97 4 0.1577 476.646 464.964 0.983 0.924 0.370 9.237-7.194 100.00 213 7 0.1808 389.838 384.444 1.030 0.924 0.350 7.162-5.571 100.00 427 22 0.1692 292.552 287.222 1.001 0.924 0.300 5.546-4.326 100.00 867 58 0.0908 401.601 398.928 1.028 0.925 0.209 4.315-3.360 100.00 1859 96 0.0770 381.926 380.971 1.075 0.926 0.200 3.356-2.611 100.00 3867 181 0.1021 250.905 250.172 1.078 0.928 0.052 2.608-2.026 99.99 8198 413 0.0981 166.327 165.684 1.087 0.931 0.000 2.025-1.573 100.00 17313 902 0.1217 81.226 81.395 1.087 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1654 36.019 35.485 1.065 0.944 0.000 1.221-1.150 99.97 13689 708 0.2363 22.694 21.234 1.020 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0462 ============================ 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=0.1246 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1543 | n_water=258 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1255 r_free=0.1543 | n_water=252 | time (s): 26.210 (total time: 28.600) Filter (q & B) r_work=0.1258 r_free=0.1542 | n_water=249 | time (s): 3.560 (total time: 32.160) Compute maps r_work=0.1258 r_free=0.1542 | n_water=249 | time (s): 1.730 (total time: 33.890) Filter (map) r_work=0.1277 r_free=0.1548 | n_water=234 | time (s): 3.780 (total time: 37.670) Find peaks r_work=0.1277 r_free=0.1548 | n_water=234 | time (s): 0.720 (total time: 38.390) Add new water r_work=0.1440 r_free=0.1710 | n_water=459 | time (s): 3.830 (total time: 42.220) Refine new water occ: r_work=0.1343 r_free=0.1585 adp: r_work=0.1259 r_free=0.1525 occ: r_work=0.1273 r_free=0.1515 adp: r_work=0.1236 r_free=0.1499 occ: r_work=0.1240 r_free=0.1491 adp: r_work=0.1230 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1230 r_free=0.1488 r_work=0.1230 r_free=0.1488 | n_water=459 | time (s): 84.840 (total time: 127.060) Filter (q & B) r_work=0.1237 r_free=0.1498 | n_water=436 | time (s): 3.720 (total time: 130.780) Filter (dist only) r_work=0.1237 r_free=0.1498 | n_water=436 | time (s): 39.860 (total time: 170.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.652733 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1554.358417 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 0.1240 0.1532 0.0293 0.006 0.9 2.2 0.5 0.0 0 11.826 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 15.32 2.93 3.812 23.367 1554.358 0.016 12.10 15.07 2.98 4.306 23.139 1554.358 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 113.74 23.33 2.64 202 1761 Protein: 8.73 113.74 17.68 2.64 0 1519 Water: 11.09 75.23 42.93 N/A 202 234 Other: 24.63 35.64 28.73 N/A 0 8 Chain A: 8.73 113.74 20.39 N/A 0 1761 Chain S: 15.12 75.23 48.94 N/A 202 0 Histogram: Values Number of atoms 8.73 - 19.23 1205 19.23 - 29.73 251 29.73 - 40.23 183 40.23 - 50.73 137 50.73 - 61.23 115 61.23 - 71.74 57 71.74 - 82.24 9 82.24 - 92.74 3 92.74 - 103.24 1 103.24 - 113.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1507 r_work=0.1209 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1507 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 = 0.1211 r_free = 0.1504 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1211 r_free= 0.1504 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014203 | | target function (ls_wunit_k1) not normalized (work): 1183.049921 | | target function (ls_wunit_k1) not normalized (free): 107.949997 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1225 0.1211 0.1504 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1615 0.1611 0.1719 n_refl.: 87592 remove outliers: r(all,work,free)=0.1615 0.1611 0.1719 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1621 0.1617 0.1722 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1222 0.1208 0.1498 n_refl.: 87592 remove outliers: r(all,work,free)=0.1220 0.1206 0.1498 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3340 290.274 271.698 0.614 0.937 0.341 11.894-9.307 99.02 97 4 0.1554 476.646 472.566 0.980 0.937 0.334 9.237-7.194 100.00 213 7 0.1680 389.838 390.421 1.048 0.938 0.290 7.162-5.571 100.00 427 22 0.1491 292.552 289.110 1.003 0.938 0.260 5.546-4.326 100.00 867 58 0.0820 401.601 398.806 1.024 0.938 0.219 4.315-3.360 100.00 1859 96 0.0726 381.926 380.828 1.069 0.939 0.219 3.356-2.611 100.00 3867 181 0.0970 250.905 250.268 1.075 0.940 0.067 2.608-2.026 99.99 8198 413 0.0978 166.327 165.830 1.082 0.941 0.000 2.025-1.573 100.00 17313 902 0.1190 81.226 81.385 1.088 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.019 35.519 1.072 0.947 0.000 1.221-1.150 99.97 13689 708 0.2341 22.694 21.251 1.025 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0586 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1498 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=0.1206 r_free=0.1498 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1498 | n_water=436 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1207 r_free=0.1497 | n_water=435 | time (s): 36.520 (total time: 38.350) Filter (q & B) r_work=0.1207 r_free=0.1497 | n_water=435 | time (s): 0.830 (total time: 39.180) Compute maps r_work=0.1207 r_free=0.1497 | n_water=435 | time (s): 1.580 (total time: 40.760) Filter (map) r_work=0.1245 r_free=0.1485 | n_water=293 | time (s): 3.610 (total time: 44.370) Find peaks r_work=0.1245 r_free=0.1485 | n_water=293 | time (s): 0.600 (total time: 44.970) Add new water r_work=0.1373 r_free=0.1606 | n_water=486 | time (s): 2.770 (total time: 47.740) Refine new water occ: r_work=0.1272 r_free=0.1524 adp: r_work=0.1273 r_free=0.1523 occ: r_work=0.1250 r_free=0.1507 adp: r_work=0.1247 r_free=0.1505 occ: r_work=0.1233 r_free=0.1494 adp: r_work=0.1227 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1489 r_work=0.1227 r_free=0.1489 | n_water=486 | time (s): 156.030 (total time: 203.770) Filter (q & B) r_work=0.1231 r_free=0.1487 | n_water=452 | time (s): 3.300 (total time: 207.070) Filter (dist only) r_work=0.1231 r_free=0.1487 | n_water=452 | time (s): 37.220 (total time: 244.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.126404 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.878404 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 0.1235 0.1462 0.0227 0.006 0.9 2.2 0.5 0.0 0 1.063 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.62 2.27 3.635 22.138 41.878 3.725 12.27 14.23 1.96 4.111 21.970 41.878 3.659 Individual atomic B min max mean iso aniso Overall: 9.24 108.78 21.75 2.30 221 1758 Protein: 9.24 108.78 17.27 2.30 0 1519 Water: 11.52 70.81 36.74 N/A 221 231 Other: 20.21 31.66 26.18 N/A 0 8 Chain A: 9.24 108.78 19.94 N/A 0 1758 Chain S: 15.86 67.18 36.15 N/A 221 0 Histogram: Values Number of atoms 9.24 - 19.19 1229 19.19 - 29.15 271 29.15 - 39.10 226 39.10 - 49.05 138 49.05 - 59.01 80 59.01 - 68.96 22 68.96 - 78.92 7 78.92 - 88.87 3 88.87 - 98.82 1 98.82 - 108.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1423 r_work=0.1229 r_free=0.1423 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1423 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1222 r_free = 0.1421 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1222 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655827 | | target function (ml) not normalized (work): 304501.143571 | | target function (ml) not normalized (free): 16082.326542 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1222 0.1421 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1558 0.1557 0.1613 n_refl.: 87588 remove outliers: r(all,work,free)=0.1558 0.1557 0.1613 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1556 0.1555 0.1611 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1214 0.1397 n_refl.: 87588 remove outliers: r(all,work,free)=0.1220 0.1211 0.1397 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3765 289.521 254.656 0.469 1.000 0.320 11.894-9.307 98.04 96 4 0.2335 476.770 461.178 0.859 1.001 0.320 9.237-7.194 98.18 209 7 0.2277 381.421 384.165 0.951 1.002 0.210 7.162-5.571 100.00 427 22 0.1993 292.552 283.827 0.915 1.002 0.189 5.546-4.326 100.00 867 58 0.1077 401.601 397.473 0.953 1.002 0.167 4.315-3.360 100.00 1859 96 0.0931 381.926 379.512 0.994 1.002 0.156 3.356-2.611 100.00 3867 181 0.1175 250.905 248.835 0.998 1.002 0.062 2.608-2.026 99.99 8198 413 0.1077 166.327 165.277 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1040 81.226 81.365 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1304 36.019 35.585 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.694 21.307 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0293 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1211 r_free=0.1397 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1211 r_free=0.1397 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1211 r_free=0.1397 | n_water=452 | time (s): 2.100 (total time: 2.100) Filter (dist) r_work=0.1211 r_free=0.1398 | n_water=451 | time (s): 40.820 (total time: 42.920) Filter (q & B) r_work=0.1211 r_free=0.1398 | n_water=448 | time (s): 3.350 (total time: 46.270) Compute maps r_work=0.1211 r_free=0.1398 | n_water=448 | time (s): 1.450 (total time: 47.720) Filter (map) r_work=0.1238 r_free=0.1383 | n_water=311 | time (s): 2.610 (total time: 50.330) Find peaks r_work=0.1238 r_free=0.1383 | n_water=311 | time (s): 0.600 (total time: 50.930) Add new water r_work=0.1305 r_free=0.1446 | n_water=465 | time (s): 2.630 (total time: 53.560) Refine new water occ: r_work=0.1230 r_free=0.1387 adp: r_work=0.1231 r_free=0.1387 occ: r_work=0.1216 r_free=0.1381 adp: r_work=0.1214 r_free=0.1379 occ: r_work=0.1204 r_free=0.1378 adp: r_work=0.1201 r_free=0.1374 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1374 r_work=0.1201 r_free=0.1374 | n_water=465 | time (s): 183.930 (total time: 237.490) Filter (q & B) r_work=0.1206 r_free=0.1378 | n_water=431 | time (s): 3.030 (total time: 240.520) Filter (dist only) r_work=0.1206 r_free=0.1376 | n_water=430 | time (s): 37.770 (total time: 278.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.881008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.083060 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 0.1211 0.1378 0.0167 0.006 0.9 1.9 0.5 0.0 0 0.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.78 1.67 3.426 21.469 47.083 3.642 11.88 13.64 1.76 3.776 21.362 47.083 3.623 Individual atomic B min max mean iso aniso Overall: 9.28 104.67 21.17 2.19 203 1754 Protein: 9.28 104.67 17.01 2.19 0 1519 Water: 11.51 69.71 35.81 N/A 203 227 Other: 19.64 29.35 24.53 N/A 0 8 Chain A: 9.28 104.67 19.56 N/A 0 1754 Chain S: 15.07 57.01 35.06 N/A 203 0 Histogram: Values Number of atoms 9.28 - 18.82 1222 18.82 - 28.35 277 28.35 - 37.89 213 37.89 - 47.43 133 47.43 - 56.97 73 56.97 - 66.51 25 66.51 - 76.05 9 76.05 - 85.59 2 85.59 - 95.13 1 95.13 - 104.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1364 r_work=0.1188 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1364 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1361 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1183 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622072 | | target function (ml) not normalized (work): 301660.682671 | | target function (ml) not normalized (free): 15942.822885 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1183 0.1361 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1515 0.1515 0.1565 n_refl.: 87580 remove outliers: r(all,work,free)=0.1515 0.1515 0.1565 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1513 0.1563 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1183 0.1362 n_refl.: 87580 remove outliers: r(all,work,free)=0.1190 0.1182 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 0.3877 289.521 254.918 0.460 1.001 0.320 11.894-9.307 95.10 93 4 0.2200 475.850 462.140 0.853 1.002 0.320 9.237-7.194 98.18 209 7 0.2423 381.421 375.864 0.919 1.002 0.160 7.162-5.571 100.00 427 22 0.2107 292.552 283.277 0.909 1.002 0.160 5.546-4.326 100.00 867 58 0.1145 401.601 397.412 0.953 1.002 0.150 4.315-3.360 100.00 1859 96 0.0943 381.926 379.364 0.994 1.002 0.133 3.356-2.611 100.00 3867 181 0.1160 250.905 249.044 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1029 166.327 165.435 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.0975 81.226 81.487 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.019 35.638 1.020 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.694 21.326 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=-0.0283 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1362 After: r_work=0.1182 r_free=0.1363 ================================== NQH flips ================================== r_work=0.1182 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1363 | n_water=430 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1182 r_free=0.1363 | n_water=430 | time (s): 32.940 (total time: 35.020) Filter (q & B) r_work=0.1182 r_free=0.1364 | n_water=428 | time (s): 3.100 (total time: 38.120) Compute maps r_work=0.1182 r_free=0.1364 | n_water=428 | time (s): 1.550 (total time: 39.670) Filter (map) r_work=0.1207 r_free=0.1376 | n_water=324 | time (s): 2.640 (total time: 42.310) Find peaks r_work=0.1207 r_free=0.1376 | n_water=324 | time (s): 0.500 (total time: 42.810) Add new water r_work=0.1261 r_free=0.1436 | n_water=479 | time (s): 2.540 (total time: 45.350) Refine new water occ: r_work=0.1194 r_free=0.1365 adp: r_work=0.1194 r_free=0.1366 occ: r_work=0.1183 r_free=0.1358 adp: r_work=0.1181 r_free=0.1357 occ: r_work=0.1175 r_free=0.1355 adp: r_work=0.1171 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1351 r_work=0.1171 r_free=0.1351 | n_water=479 | time (s): 207.460 (total time: 252.810) Filter (q & B) r_work=0.1179 r_free=0.1352 | n_water=439 | time (s): 2.890 (total time: 255.700) Filter (dist only) r_work=0.1178 r_free=0.1350 | n_water=437 | time (s): 38.260 (total time: 293.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.942090 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.707664 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 0.1205 0.1381 0.0175 0.007 1.0 2.9 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.81 1.75 3.317 21.159 46.708 3.631 12.10 13.86 1.76 3.525 21.093 46.708 3.625 Individual atomic B min max mean iso aniso Overall: 9.30 101.22 20.99 2.05 210 1754 Protein: 9.30 101.22 16.82 2.05 0 1519 Water: 11.50 68.98 35.39 N/A 210 227 Other: 19.92 28.02 24.15 N/A 0 8 Chain A: 9.30 101.22 19.37 N/A 0 1754 Chain S: 14.37 55.75 34.47 N/A 210 0 Histogram: Values Number of atoms 9.30 - 18.49 1219 18.49 - 27.68 279 27.68 - 36.87 208 36.87 - 46.07 141 46.07 - 55.26 74 55.26 - 64.45 26 64.45 - 73.64 12 73.64 - 82.84 2 82.84 - 92.03 1 92.03 - 101.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1210 r_free=0.1386 r_work=0.1210 r_free=0.1385 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1385 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1385 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.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1208 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.624762 | | target function (ml) not normalized (work): 301873.803989 | | target function (ml) not normalized (free): 15960.440148 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1415 0.1416 5.6795 5.6551| | 2: 3.57 - 2.84 1.00 2888 124 0.1144 0.1426 5.2078 5.2407| | 3: 2.83 - 2.48 1.00 2820 163 0.1231 0.1324 5.0085 5.0315| | 4: 2.47 - 2.25 1.00 2825 136 0.1045 0.1186 4.7144 4.768| | 5: 2.25 - 2.09 1.00 2756 127 0.1015 0.1169 4.6522 4.729| | 6: 2.09 - 1.97 1.00 2846 113 0.0996 0.1218 4.3638 4.5021| | 7: 1.97 - 1.87 1.00 2787 165 0.1007 0.1245 4.0839 4.1954| | 8: 1.87 - 1.79 1.00 2789 144 0.1040 0.1274 4.0032 4.0999| | 9: 1.79 - 1.72 1.00 2745 138 0.0970 0.1295 3.7266 3.8912| | 10: 1.72 - 1.66 1.00 2831 160 0.1014 0.1278 3.6433 3.7815| | 11: 1.66 - 1.61 1.00 2712 147 0.0972 0.1101 3.5801 3.6261| | 12: 1.61 - 1.56 1.00 2773 144 0.0933 0.1208 3.3586 3.4956| | 13: 1.56 - 1.52 1.00 2745 130 0.0996 0.1119 3.3481 3.4635| | 14: 1.52 - 1.48 1.00 2803 134 0.1005 0.1124 3.2705 3.3456| | 15: 1.48 - 1.45 1.00 2738 128 0.1027 0.1383 3.1762 3.339| | 16: 1.45 - 1.42 1.00 2756 161 0.1087 0.1274 3.1598 3.2462| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1320 3.1182 3.2322| | 18: 1.39 - 1.36 1.00 2741 179 0.1161 0.1418 3.0892 3.2832| | 19: 1.36 - 1.34 1.00 2807 134 0.1223 0.1621 3.0944 3.2739| | 20: 1.34 - 1.32 1.00 2696 147 0.1318 0.1474 3.0862 3.1383| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1590 3.0866 3.1361| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1929 3.0825 3.2882| | 23: 1.27 - 1.26 1.00 2802 156 0.1569 0.1859 3.0974 3.2047| | 24: 1.26 - 1.24 1.00 2744 132 0.1624 0.1767 3.0896 3.1921| | 25: 1.24 - 1.22 1.00 2733 148 0.1787 0.2315 3.1035 3.2871| | 26: 1.22 - 1.21 1.00 2727 135 0.1856 0.1793 3.118 3.1982| | 27: 1.21 - 1.19 1.00 2814 148 0.2011 0.2071 3.1355 3.1402| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2296 3.1358 3.1544| | 29: 1.18 - 1.16 1.00 2800 134 0.2223 0.2374 3.1236 3.2238| | 30: 1.16 - 1.15 1.00 2739 148 0.2370 0.2500 3.1109 3.1622| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 9.09 1.00 0.97 6260.77| | 2: 3.57 - 2.84 2888 124 0.92 13.52 1.01 0.97 6260.77| | 3: 2.83 - 2.48 2820 163 0.88 17.63 0.98 0.97 5253.95| | 4: 2.47 - 2.25 2825 136 0.91 14.67 1.00 0.97 2657.69| | 5: 2.25 - 2.09 2756 127 0.89 16.99 1.01 0.97 2657.69| | 6: 2.09 - 1.97 2846 113 0.91 13.86 1.02 0.97 1571.65| | 7: 1.97 - 1.87 2787 165 0.94 11.09 1.02 0.97 645.41| | 8: 1.87 - 1.79 2789 144 0.91 14.73 1.00 0.97 645.41| | 9: 1.79 - 1.72 2745 138 0.93 11.71 0.98 0.97 349.24| | 10: 1.72 - 1.66 2831 160 0.93 12.54 0.98 0.97 289.93| | 11: 1.66 - 1.61 2712 147 0.93 13.15 0.98 0.97 276.70| | 12: 1.61 - 1.56 2773 144 0.95 9.80 0.99 0.97 151.90| | 13: 1.56 - 1.52 2745 130 0.94 11.41 1.02 0.97 151.90| | 14: 1.52 - 1.48 2803 134 0.94 11.59 1.02 0.97 135.53| | 15: 1.48 - 1.45 2738 128 0.95 10.71 1.02 0.98 105.53| | 16: 1.45 - 1.42 2756 161 0.94 11.88 1.02 0.98 105.53| | 17: 1.42 - 1.39 2785 139 0.94 11.67 1.01 0.98 94.84| | 18: 1.39 - 1.36 2741 179 0.94 11.92 1.01 0.98 88.65| | 19: 1.36 - 1.34 2807 134 0.94 12.53 1.00 0.98 88.65| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.96 82.64| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.99 0.96 82.21| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.99 0.96 82.28| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.98 0.94 82.60| | 24: 1.26 - 1.24 2744 132 0.92 15.02 0.97 0.94 82.60| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.00| | 26: 1.22 - 1.21 2727 135 0.90 18.15 1.02 0.93 85.56| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 85.56| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 88.74| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.92 89.94| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.92 89.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.21 max = 6260.77 mean = 981.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.20| |phase err.(test): min = 0.00 max = 89.93 mean = 14.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1208 0.1385 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1533 0.1532 0.1581 n_refl.: 87577 remove outliers: r(all,work,free)=0.1533 0.1532 0.1581 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1530 0.1529 0.1580 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1208 0.1386 n_refl.: 87577 remove outliers: r(all,work,free)=0.1216 0.1207 0.1386 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 87.50 79 5 0.3911 284.811 253.138 0.452 1.001 0.304 11.894-9.307 95.10 93 4 0.2306 475.850 457.758 0.853 1.003 0.300 9.237-7.194 97.73 208 7 0.2557 380.947 375.632 0.905 1.003 0.150 7.162-5.571 100.00 427 22 0.2202 292.552 282.600 0.901 1.003 0.150 5.546-4.326 100.00 867 58 0.1199 401.601 396.971 0.953 1.003 0.132 4.315-3.360 100.00 1859 96 0.0998 381.926 379.051 0.995 1.002 0.127 3.356-2.611 100.00 3867 181 0.1205 250.905 248.726 1.000 1.002 0.120 2.608-2.026 99.99 8198 413 0.1059 166.327 165.264 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0992 81.226 81.450 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.019 35.640 1.022 0.997 0.000 1.221-1.150 99.97 13689 708 0.2113 22.694 21.325 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0349 ================= 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 : 0.2603 0.1907 0.082 5.435 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1730 0.082 5.435 9.1 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1730 0.082 5.435 9.1 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1731 0.082 5.435 9.1 119.5 20.1 258 0.003 1_weight: 0.1631 0.1731 0.082 5.435 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1213 0.1471 0.008 0.971 9.1 119.5 20.1 258 0.125 1_adp: 0.1245 0.1544 0.008 0.971 8.6 118.6 21.1 258 0.125 1_regHadp: 0.1249 0.1549 0.008 0.971 8.6 118.6 21.1 258 0.125 1_occ: 0.1249 0.1551 0.008 0.971 8.6 118.6 21.1 258 0.125 2_bss: 0.1244 0.1541 0.008 0.971 8.7 118.7 21.3 258 0.125 2_settarget: 0.1244 0.1541 0.008 0.971 8.7 118.7 21.3 258 0.125 2_updatecdl: 0.1244 0.1541 0.008 0.975 8.7 118.7 21.3 258 0.125 2_nqh: 0.1246 0.1543 0.008 0.975 8.7 118.7 21.3 258 0.128 2_sol: 0.1237 0.1498 0.008 0.975 8.7 118.7 23.7 436 n/a 2_weight: 0.1237 0.1498 0.008 0.975 8.7 118.7 23.7 436 n/a 2_xyzrec: 0.1240 0.1532 0.006 0.867 8.7 118.7 23.7 436 n/a 2_adp: 0.1210 0.1507 0.006 0.867 8.7 113.7 23.3 436 n/a 2_regHadp: 0.1209 0.1507 0.006 0.867 8.7 113.7 23.3 436 n/a 2_occ: 0.1211 0.1504 0.006 0.867 8.7 113.7 23.3 436 n/a 3_bss: 0.1206 0.1498 0.006 0.867 8.8 113.8 23.4 436 n/a 3_settarget: 0.1206 0.1498 0.006 0.867 8.8 113.8 23.4 436 n/a 3_updatecdl: 0.1206 0.1498 0.006 0.866 8.8 113.8 23.4 436 n/a 3_nqh: 0.1206 0.1498 0.006 0.866 8.8 113.8 23.4 436 n/a 3_sol: 0.1231 0.1487 0.006 0.866 8.8 113.8 22.1 452 n/a 3_weight: 0.1231 0.1487 0.006 0.866 8.8 113.8 22.1 452 n/a 3_xyzrec: 0.1235 0.1462 0.006 0.936 8.8 113.8 22.1 452 n/a 3_adp: 0.1227 0.1423 0.006 0.936 9.2 108.8 21.7 452 n/a 3_regHadp: 0.1229 0.1423 0.006 0.936 9.2 108.8 21.7 452 n/a 3_occ: 0.1222 0.1421 0.006 0.936 9.2 108.8 21.7 452 n/a 4_bss: 0.1211 0.1397 0.006 0.936 9.2 108.8 21.7 452 n/a 4_settarget: 0.1211 0.1397 0.006 0.936 9.2 108.8 21.7 452 n/a 4_updatecdl: 0.1211 0.1397 0.006 0.933 9.2 108.8 21.7 452 n/a 4_nqh: 0.1211 0.1397 0.006 0.933 9.2 108.8 21.7 452 n/a 4_sol: 0.1206 0.1376 0.006 0.933 9.2 108.8 21.4 430 n/a 4_weight: 0.1206 0.1376 0.006 0.933 9.2 108.8 21.4 430 n/a 4_xyzrec: 0.1211 0.1378 0.006 0.945 9.2 108.8 21.4 430 n/a 4_adp: 0.1188 0.1364 0.006 0.945 9.3 104.7 21.2 430 n/a 4_regHadp: 0.1188 0.1364 0.006 0.945 9.3 104.7 21.2 430 n/a 4_occ: 0.1183 0.1361 0.006 0.945 9.3 104.7 21.2 430 n/a 5_bss: 0.1182 0.1362 0.006 0.945 9.3 104.7 21.2 430 n/a 5_settarget: 0.1182 0.1362 0.006 0.945 9.3 104.7 21.2 430 n/a 5_updatecdl: 0.1182 0.1362 0.006 0.947 9.3 104.7 21.2 430 n/a 5_setrh: 0.1182 0.1363 0.006 0.947 9.3 104.7 21.2 430 n/a 5_nqh: 0.1182 0.1363 0.006 0.947 9.3 104.7 21.2 430 n/a 5_sol: 0.1178 0.1350 0.006 0.947 9.3 104.7 21.1 437 n/a 5_weight: 0.1178 0.1350 0.006 0.947 9.3 104.7 21.1 437 n/a 5_xyzrec: 0.1205 0.1381 0.007 1.028 9.3 104.7 21.1 437 n/a 5_adp: 0.1210 0.1386 0.007 1.028 9.3 101.2 21.0 437 n/a 5_regHadp: 0.1210 0.1385 0.007 1.028 9.3 101.2 21.0 437 n/a 5_occ: 0.1208 0.1385 0.007 1.028 9.3 101.2 21.0 437 n/a end: 0.1207 0.1386 0.007 1.028 9.3 101.2 21.0 437 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3337960_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3337960_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8100 Refinement macro-cycles (run) : 3400.4800 Write final files (write_after_run_outputs) : 73.0800 Total : 3478.3700 Total CPU time: 58.58 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:28 PST -0800 (1735452568.96 s) Start R-work = 0.1631, R-free = 0.1730 Final R-work = 0.1207, R-free = 0.1386 =============================================================================== Job complete usr+sys time: 3623.61 seconds wall clock time: 64 minutes 50.76 seconds (3890.76 seconds total)