Starting phenix.refine on Sat Dec 28 21:06:35 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.17, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 183.6 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 535 0.91 - 1.17: 1114 1.17 - 1.43: 674 1.43 - 1.69: 807 1.69 - 1.95: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 1.522 1.731 -0.209 1.22e-02 6.72e+03 2.95e+02 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.523 1.742 -0.219 1.35e-02 5.49e+03 2.62e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.23e-02 6.61e+03 2.55e+02 bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.112 0.218 1.37e-02 5.33e+03 2.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 2991 4.35 - 8.71: 1859 8.71 - 13.06: 731 13.06 - 17.42: 168 17.42 - 21.77: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA MET A 26 " pdb=" C MET A 26 " pdb=" O MET A 26 " ideal model delta sigma weight residual 120.55 105.53 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 109.59 12.32 9.80e-01 1.04e+00 1.58e+02 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.53 107.45 13.08 1.07e+00 8.73e-01 1.49e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 129.98 -10.78 9.00e-01 1.23e+00 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 942 17.39 - 34.77: 115 34.77 - 52.15: 41 52.15 - 69.54: 10 69.54 - 86.92: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+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 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 30 " pdb=" C GLY A 30 " pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.221: 109 0.221 - 0.441: 73 0.441 - 0.661: 43 0.661 - 0.882: 10 0.882 - 1.102: 8 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 1.42 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.065 2.00e-02 2.50e+03 5.92e-02 1.05e+02 pdb=" CG PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.056 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.023 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.005 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " -0.001 9.50e-02 1.11e+02 6.73e-02 1.02e+02 pdb=" NE ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.145 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.129 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.020 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 632 2.25 - 2.84: 7612 2.84 - 3.43: 10742 3.43 - 4.01: 15415 4.01 - 4.60: 22181 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.667 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.829 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.837 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.841 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.853 2.450 ... (remaining 56577 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_7427252_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= 0.2606 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787967 | | target function (ml) not normalized (work): 232254.397995 | | target function (ml) not normalized (free): 11818.138032 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2100 7.0961 4.9345| | 2: 3.57 - 2.84 1.00 2876 122 0.2420 0.1848 4.3456 4.3397| | 3: 2.84 - 2.48 1.00 2833 165 0.2361 0.1746 4.1222 4.1525| | 4: 2.47 - 2.25 1.00 2825 136 0.2301 0.1475 3.8264 3.835| | 5: 2.25 - 2.09 1.00 2756 127 0.2505 0.1575 3.7932 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2533 0.1655 3.4456 3.5169| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1637 3.149 3.1332| | 8: 1.87 - 1.79 1.00 2789 144 0.2472 0.1972 3.0637 3.1411| | 9: 1.79 - 1.72 1.00 2745 138 0.2442 0.1954 2.9016 2.9303| | 10: 1.72 - 1.66 1.00 2789 158 0.2376 0.1997 2.7862 2.8667| | 11: 1.66 - 1.61 1.00 2740 147 0.2458 0.1645 2.7279 2.6926| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2092 2.6192 2.6936| | 13: 1.56 - 1.52 1.00 2745 130 0.2578 0.1787 2.5586 2.6018| | 14: 1.52 - 1.48 1.00 2803 134 0.2603 0.2114 2.4791 2.5394| | 15: 1.48 - 1.45 1.00 2738 128 0.2569 0.2070 2.4166 2.4525| | 16: 1.45 - 1.42 1.00 2756 161 0.2593 0.2136 2.3732 2.3903| | 17: 1.42 - 1.39 1.00 2785 139 0.2718 0.2229 2.3354 2.4068| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2133 2.2838 2.2854| | 19: 1.36 - 1.34 1.00 2807 134 0.2621 0.2637 2.2297 2.3616| | 20: 1.34 - 1.32 1.00 2696 147 0.2714 0.2407 2.1981 2.2697| | 21: 1.32 - 1.30 1.00 2785 112 0.2725 0.2034 2.1559 2.1463| | 22: 1.29 - 1.27 1.00 2704 152 0.2706 0.2611 2.1352 2.2206| | 23: 1.27 - 1.26 1.00 2802 156 0.2796 0.2391 2.1125 2.1675| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2701 2.0859 2.2093| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2667 2.0551 2.1059| | 26: 1.22 - 1.21 1.00 2727 135 0.2859 0.2656 2.0191 2.2266| | 27: 1.21 - 1.19 1.00 2814 148 0.2930 0.2368 2.0063 1.9466| | 28: 1.19 - 1.18 1.00 2671 147 0.2952 0.2941 1.9787 1.9955| | 29: 1.18 - 1.16 1.00 2800 134 0.2909 0.2823 1.9507 2.0662| | 30: 1.16 - 1.15 1.00 2740 148 0.3047 0.3001 1.9311 1.9703| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.75 0.76 0.23 1460.81| | 2: 3.57 - 2.84 2876 122 0.81 25.84 1.27 0.23 1460.81| | 3: 2.84 - 2.48 2833 165 0.74 31.81 1.24 0.24 1211.45| | 4: 2.47 - 2.25 2825 136 0.81 25.36 1.25 0.25 564.32| | 5: 2.25 - 2.09 2756 127 0.77 29.19 1.29 0.25 564.32| | 6: 2.09 - 1.97 2846 113 0.84 22.55 1.29 0.25 308.52| | 7: 1.97 - 1.87 2787 165 0.90 16.54 1.29 0.26 90.36| | 8: 1.87 - 1.79 2789 144 0.86 20.97 1.24 0.26 90.36| | 9: 1.79 - 1.72 2745 138 0.88 18.17 1.23 0.25 53.72| | 10: 1.72 - 1.66 2789 158 0.87 19.78 1.22 0.25 46.38| | 11: 1.66 - 1.61 2740 147 0.86 21.01 1.23 0.25 44.73| | 12: 1.61 - 1.56 2787 146 0.89 17.77 1.24 0.25 28.03| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.03| | 14: 1.52 - 1.48 2803 134 0.87 20.30 1.24 0.25 25.32| | 15: 1.48 - 1.45 2738 128 0.87 19.80 1.23 0.25 20.35| | 16: 1.45 - 1.42 2756 161 0.86 21.20 1.23 0.25 20.35| | 17: 1.42 - 1.39 2785 139 0.87 20.89 1.24 0.25 17.70| | 18: 1.39 - 1.36 2741 179 0.86 21.36 1.23 0.25 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.43 1.22 0.25 16.17| | 20: 1.34 - 1.32 2696 147 0.86 21.59 1.22 0.24 13.84| | 21: 1.32 - 1.30 2785 112 0.85 22.79 1.21 0.24 13.68| | 22: 1.29 - 1.27 2704 152 0.85 23.09 1.21 0.24 13.39| | 23: 1.27 - 1.26 2802 156 0.85 23.11 1.22 0.24 11.92| | 24: 1.26 - 1.24 2744 132 0.84 23.67 1.20 0.24 11.92| | 25: 1.24 - 1.22 2734 148 0.83 24.79 1.21 0.23 11.33| | 26: 1.22 - 1.21 2727 135 0.83 25.27 1.20 0.23 10.67| | 27: 1.21 - 1.19 2814 148 0.82 26.00 1.20 0.23 10.67| | 28: 1.19 - 1.18 2671 147 0.81 26.80 1.19 0.22 9.97| | 29: 1.18 - 1.16 2800 134 0.81 26.81 1.16 0.22 9.70| | 30: 1.16 - 1.15 2740 148 0.79 28.59 1.16 0.22 9.70| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.70 max = 1460.81 mean = 212.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.87| |phase err.(test): min = 0.00 max = 89.54 mean = 22.88| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.248 1557 Z= 5.560 Angle : 5.208 15.963 2118 Z= 3.657 Chirality : 0.383 1.102 243 Planarity : 0.030 0.088 284 Dihedral : 13.827 86.922 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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: -2.46 (0.44), residues: 224 helix: -2.53 (0.37), residues: 108 sheet: -1.08 (0.81), residues: 28 loop : -0.22 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.024 ARG A 145 TYR 0.084 0.040 TYR A 141 PHE 0.119 0.043 PHE A 162 HIS 0.047 0.024 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= 0.2606 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787967 | | target function (ml) not normalized (work): 232254.397995 | | target function (ml) not normalized (free): 11818.138032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1961 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2000 0.2003 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1629 0.1795 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1628 0.1795 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 0.3839 386.570 358.875 0.678 1.002 0.407 11.894-9.307 99.02 97 4 0.1748 614.048 594.046 0.929 1.003 0.390 9.237-7.194 100.00 213 7 0.2122 502.215 491.443 0.957 1.003 0.350 7.162-5.571 100.00 427 22 0.2161 376.885 365.455 0.931 1.003 0.330 5.546-4.326 100.00 867 58 0.1323 517.370 511.706 0.965 1.003 0.224 4.315-3.360 100.00 1859 96 0.1144 492.022 488.405 1.007 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.233 319.692 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1332 214.274 212.180 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.640 104.032 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2043 46.402 45.161 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2553 29.236 26.996 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0411 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1795 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1630 r_free=0.1798 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.474053 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1998.178276 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 0.1210 0.1469 0.0259 0.008 1.0 1.3 0.5 0.0 0 13.237 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.69 2.59 3.013 19.038 1998.178 0.017 12.44 15.50 3.07 3.192 19.521 1998.178 0.016 Individual atomic B min max mean iso aniso Overall: 8.51 118.54 20.98 2.87 0 1785 Protein: 8.51 118.54 17.87 2.87 0 1519 Water: 11.08 114.48 39.06 N/A 0 258 Other: 23.07 36.37 29.03 N/A 0 8 Chain A: 8.51 118.54 20.98 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.51 1204 19.51 - 30.51 236 30.51 - 41.52 162 41.52 - 52.52 101 52.52 - 63.52 53 63.52 - 74.53 16 74.53 - 85.53 6 85.53 - 96.53 4 96.53 - 107.53 0 107.53 - 118.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1550 r_work=0.1249 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1555 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 = 0.1555 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015432 | | target function (ls_wunit_k1) not normalized (work): 1285.418716 | | target function (ls_wunit_k1) not normalized (free): 115.090964 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1555 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1698 0.1773 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1698 0.1773 n_refl.: 87593 overall B=0.18 to atoms: r(all,work,free)=0.1729 0.1728 0.1793 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1244 0.1548 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1243 0.1548 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 0.3604 299.227 278.365 0.690 0.923 0.380 11.894-9.307 99.02 97 4 0.1591 479.346 467.156 0.982 0.924 0.380 9.237-7.194 100.00 213 7 0.1802 392.046 386.687 1.026 0.924 0.340 7.162-5.571 100.00 427 22 0.1724 294.209 288.427 0.999 0.925 0.290 5.546-4.326 100.00 867 58 0.0918 403.876 401.126 1.026 0.925 0.204 4.315-3.360 100.00 1859 96 0.0771 384.088 383.148 1.073 0.927 0.189 3.356-2.611 100.00 3867 181 0.1018 252.326 251.585 1.073 0.929 0.057 2.608-2.026 99.99 8198 413 0.0976 167.269 166.663 1.082 0.932 0.000 2.025-1.573 100.00 17313 902 0.1214 81.686 81.868 1.082 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1653 36.223 35.684 1.057 0.948 0.000 1.221-1.150 99.97 13689 708 0.2365 22.823 21.345 1.011 0.956 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0409 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1549 | n_water=258 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1254 r_free=0.1548 | n_water=252 | time (s): 26.290 (total time: 28.740) Filter (q & B) r_work=0.1257 r_free=0.1547 | n_water=249 | time (s): 3.820 (total time: 32.560) Compute maps r_work=0.1257 r_free=0.1547 | n_water=249 | time (s): 1.910 (total time: 34.470) Filter (map) r_work=0.1271 r_free=0.1556 | n_water=236 | time (s): 3.900 (total time: 38.370) Find peaks r_work=0.1271 r_free=0.1556 | n_water=236 | time (s): 0.770 (total time: 39.140) Add new water r_work=0.1425 r_free=0.1707 | n_water=453 | time (s): 3.870 (total time: 43.010) Refine new water occ: r_work=0.1337 r_free=0.1579 adp: r_work=0.1258 r_free=0.1529 occ: r_work=0.1273 r_free=0.1515 adp: r_work=0.1235 r_free=0.1505 occ: r_work=0.1239 r_free=0.1490 adp: r_work=0.1229 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1494 r_work=0.1229 r_free=0.1494 | n_water=453 | time (s): 84.050 (total time: 127.060) Filter (q & B) r_work=0.1235 r_free=0.1497 | n_water=432 | time (s): 3.970 (total time: 131.030) Filter (dist only) r_work=0.1236 r_free=0.1497 | n_water=431 | time (s): 44.950 (total time: 175.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.888420 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1489.010355 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 0.1232 0.1515 0.0283 0.007 0.9 1.9 0.5 0.0 0 12.444 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.15 2.83 3.787 23.221 1489.010 0.015 12.05 14.90 2.85 4.140 23.039 1489.010 0.015 Individual atomic B min max mean iso aniso Overall: 8.79 114.86 23.23 2.59 195 1763 Protein: 8.79 114.86 17.71 2.59 0 1519 Water: 10.99 72.90 42.56 N/A 195 236 Other: 25.18 36.35 29.83 N/A 0 8 Chain A: 8.79 114.86 20.37 N/A 0 1763 Chain S: 15.73 69.84 49.02 N/A 195 0 Histogram: Values Number of atoms 8.79 - 19.39 1205 19.39 - 30.00 253 30.00 - 40.61 189 40.61 - 51.22 148 51.22 - 61.82 100 61.82 - 72.43 52 72.43 - 83.04 5 83.04 - 93.65 3 93.65 - 104.25 1 104.25 - 114.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1490 r_work=0.1205 r_free=0.1490 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1490 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1489 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.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1489 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014063 | | target function (ls_wunit_k1) not normalized (work): 1171.371927 | | target function (ls_wunit_k1) not normalized (free): 106.134049 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1205 0.1489 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1605 0.1714 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1605 0.1714 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1614 0.1611 0.1718 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1202 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1214 0.1200 0.1485 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 0.3286 291.918 271.761 0.582 1.002 0.350 11.894-9.307 99.02 97 4 0.1466 479.346 474.759 0.920 1.003 0.350 9.237-7.194 100.00 213 7 0.1680 392.046 392.263 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1513 294.209 290.877 0.940 1.003 0.234 5.546-4.326 100.00 867 58 0.0841 403.876 401.537 0.959 1.003 0.210 4.315-3.360 100.00 1859 96 0.0711 384.088 383.014 1.003 1.002 0.200 3.356-2.611 100.00 3867 181 0.0958 252.326 251.638 1.008 1.002 0.150 2.608-2.026 99.99 8198 413 0.0956 167.269 166.833 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1186 81.686 81.891 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1625 36.223 35.714 1.016 0.998 0.000 1.221-1.150 99.97 13689 708 0.2345 22.823 21.350 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0589 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1485 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1485 | n_water=431 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1199 r_free=0.1486 | n_water=429 | time (s): 38.690 (total time: 40.980) Filter (q & B) r_work=0.1199 r_free=0.1486 | n_water=429 | time (s): 1.290 (total time: 42.270) Compute maps r_work=0.1199 r_free=0.1486 | n_water=429 | time (s): 1.550 (total time: 43.820) Filter (map) r_work=0.1250 r_free=0.1487 | n_water=289 | time (s): 2.580 (total time: 46.400) Find peaks r_work=0.1250 r_free=0.1487 | n_water=289 | time (s): 0.640 (total time: 47.040) Add new water r_work=0.1376 r_free=0.1614 | n_water=488 | time (s): 3.400 (total time: 50.440) Refine new water occ: r_work=0.1266 r_free=0.1525 adp: r_work=0.1268 r_free=0.1526 occ: r_work=0.1243 r_free=0.1500 adp: r_work=0.1241 r_free=0.1501 occ: r_work=0.1227 r_free=0.1483 adp: r_work=0.1221 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1480 r_work=0.1221 r_free=0.1480 | n_water=488 | time (s): 232.250 (total time: 282.690) Filter (q & B) r_work=0.1226 r_free=0.1482 | n_water=450 | time (s): 2.750 (total time: 285.440) Filter (dist only) r_work=0.1226 r_free=0.1480 | n_water=449 | time (s): 38.750 (total time: 324.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.973955 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.768060 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 0.1237 0.1456 0.0219 0.005 0.9 1.6 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.56 2.19 3.626 22.180 48.768 3.731 12.18 14.08 1.90 4.158 21.976 48.768 3.656 Individual atomic B min max mean iso aniso Overall: 9.26 109.98 21.70 2.33 216 1760 Protein: 9.26 109.98 17.24 2.34 0 1519 Water: 11.54 71.98 36.68 N/A 216 233 Other: 21.64 32.47 27.25 N/A 0 8 Chain A: 9.26 109.98 19.91 N/A 0 1760 Chain S: 16.12 64.66 36.30 N/A 216 0 Histogram: Values Number of atoms 9.26 - 19.34 1234 19.34 - 29.41 272 29.41 - 39.48 226 39.48 - 49.55 136 49.55 - 59.62 77 59.62 - 69.69 17 69.69 - 79.77 8 79.77 - 89.84 3 89.84 - 99.91 1 99.91 - 109.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.1218 r_free=0.1408 r_work=0.1219 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1410 target_work(ml) = 3.656 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1410 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.19 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= 0.1214 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.654246 | | target function (ml) not normalized (work): 304369.492992 | | target function (ml) not normalized (free): 16068.828435 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1214 0.1410 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1540 0.1538 0.1605 n_refl.: 87588 remove outliers: r(all,work,free)=0.1540 0.1538 0.1605 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1538 0.1536 0.1604 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1204 0.1383 n_refl.: 87588 remove outliers: r(all,work,free)=0.1208 0.1199 0.1383 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 0.3931 283.839 257.355 0.463 0.999 0.293 11.894-9.307 95.10 93 4 0.2410 469.035 453.691 0.850 1.001 0.273 9.237-7.194 98.18 209 7 0.2290 383.581 385.626 0.945 1.001 0.170 7.162-5.571 100.00 427 22 0.2105 294.209 284.340 0.911 1.001 0.167 5.546-4.326 100.00 867 58 0.1109 403.876 399.591 0.953 1.002 0.156 4.315-3.360 100.00 1859 96 0.0926 384.088 381.384 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1158 252.326 250.201 0.999 1.001 0.130 2.608-2.026 99.99 8198 413 0.1048 167.269 166.248 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1017 81.686 81.816 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.223 35.784 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2131 22.823 21.426 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0296 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1383 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=0.1199 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1383 | n_water=449 | time (s): 2.120 (total time: 2.120) Filter (dist) r_work=0.1199 r_free=0.1383 | n_water=449 | time (s): 35.550 (total time: 37.670) Filter (q & B) r_work=0.1199 r_free=0.1383 | n_water=448 | time (s): 3.440 (total time: 41.110) Compute maps r_work=0.1199 r_free=0.1383 | n_water=448 | time (s): 1.470 (total time: 42.580) Filter (map) r_work=0.1221 r_free=0.1400 | n_water=318 | time (s): 3.620 (total time: 46.200) Find peaks r_work=0.1221 r_free=0.1400 | n_water=318 | time (s): 0.620 (total time: 46.820) Add new water r_work=0.1284 r_free=0.1450 | n_water=487 | time (s): 3.350 (total time: 50.170) Refine new water occ: r_work=0.1211 r_free=0.1385 adp: r_work=0.1211 r_free=0.1387 occ: r_work=0.1197 r_free=0.1373 adp: r_work=0.1195 r_free=0.1376 occ: r_work=0.1186 r_free=0.1368 adp: r_work=0.1182 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1368 r_work=0.1182 r_free=0.1368 | n_water=487 | time (s): 176.620 (total time: 226.790) Filter (q & B) r_work=0.1189 r_free=0.1369 | n_water=450 | time (s): 3.610 (total time: 230.400) Filter (dist only) r_work=0.1189 r_free=0.1368 | n_water=449 | time (s): 40.740 (total time: 271.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.287375 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.910667 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 0.1193 0.1375 0.0182 0.006 1.0 3.8 0.5 0.0 0 1.144 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.75 1.82 3.436 21.544 43.911 3.636 11.85 13.73 1.88 3.745 21.448 43.911 3.625 Individual atomic B min max mean iso aniso Overall: 9.30 105.66 21.33 2.17 218 1758 Protein: 9.30 105.66 17.02 2.17 0 1519 Water: 11.48 71.03 35.83 N/A 218 231 Other: 21.74 30.65 26.46 N/A 0 8 Chain A: 9.30 105.66 19.62 N/A 0 1758 Chain S: 15.75 65.20 35.11 N/A 218 0 Histogram: Values Number of atoms 9.30 - 18.94 1231 18.94 - 28.57 283 28.57 - 38.21 209 38.21 - 47.85 144 47.85 - 57.48 71 57.48 - 67.12 24 67.12 - 76.76 9 76.76 - 86.39 2 86.39 - 96.03 1 96.03 - 105.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1373 r_work=0.1185 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1373 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1370 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.17 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= 0.1181 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623380 | | target function (ml) not normalized (work): 301758.717551 | | target function (ml) not normalized (free): 15950.500584 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1181 0.1370 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1500 0.1498 0.1568 n_refl.: 87577 remove outliers: r(all,work,free)=0.1500 0.1498 0.1568 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1495 0.1567 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1181 0.1370 n_refl.: 87577 remove outliers: r(all,work,free)=0.1189 0.1179 0.1370 n_refl.: 87574 ======================== 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 0.3929 283.839 253.340 0.441 0.999 0.296 11.894-9.307 94.12 92 4 0.2352 472.918 452.247 0.843 1.001 0.224 9.237-7.194 97.27 207 7 0.2442 384.183 377.808 0.910 1.001 0.164 7.162-5.571 100.00 427 22 0.2231 294.209 282.869 0.902 1.002 0.137 5.546-4.326 100.00 867 58 0.1150 403.876 399.436 0.953 1.002 0.124 4.315-3.360 100.00 1859 96 0.0950 384.088 381.607 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1142 252.326 250.581 1.000 1.001 0.100 2.608-2.026 99.99 8198 413 0.1018 167.269 166.416 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0971 81.686 81.975 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.223 35.851 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2127 22.823 21.449 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0417 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1370 After: r_work=0.1180 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1180 r_free=0.1370 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=0.1180 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1370 | n_water=449 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1180 r_free=0.1370 | n_water=449 | time (s): 37.370 (total time: 39.620) Filter (q & B) r_work=0.1180 r_free=0.1371 | n_water=447 | time (s): 3.580 (total time: 43.200) Compute maps r_work=0.1180 r_free=0.1371 | n_water=447 | time (s): 1.440 (total time: 44.640) Filter (map) r_work=0.1201 r_free=0.1382 | n_water=342 | time (s): 2.850 (total time: 47.490) Find peaks r_work=0.1201 r_free=0.1382 | n_water=342 | time (s): 0.620 (total time: 48.110) Add new water r_work=0.1246 r_free=0.1417 | n_water=491 | time (s): 3.190 (total time: 51.300) Refine new water occ: r_work=0.1189 r_free=0.1360 adp: r_work=0.1189 r_free=0.1363 occ: r_work=0.1178 r_free=0.1352 adp: r_work=0.1177 r_free=0.1354 occ: r_work=0.1170 r_free=0.1346 adp: r_work=0.1168 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1348 r_work=0.1168 r_free=0.1348 | n_water=491 | time (s): 247.840 (total time: 299.140) Filter (q & B) r_work=0.1174 r_free=0.1353 | n_water=458 | time (s): 2.670 (total time: 301.810) Filter (dist only) r_work=0.1174 r_free=0.1352 | n_water=457 | time (s): 40.510 (total time: 342.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.959313 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.664500 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 0.1374 0.0177 0.006 1.0 3.5 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.74 1.77 3.316 21.316 35.665 3.632 12.02 13.74 1.72 3.423 21.267 35.665 3.630 Individual atomic B min max mean iso aniso Overall: 9.25 103.14 21.27 2.06 226 1758 Protein: 9.25 103.14 16.89 2.06 0 1519 Water: 11.53 70.73 35.73 N/A 226 231 Other: 21.33 30.07 26.13 N/A 0 8 Chain A: 9.25 103.14 19.50 N/A 0 1758 Chain S: 15.36 58.93 35.06 N/A 226 0 Histogram: Values Number of atoms 9.25 - 18.64 1222 18.64 - 28.03 287 28.03 - 37.42 208 37.42 - 46.81 145 46.81 - 56.20 81 56.20 - 65.58 25 65.58 - 74.97 11 74.97 - 84.36 2 84.36 - 93.75 1 93.75 - 103.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1374 r_work=0.1202 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1374 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1373 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1200 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628775 | | target function (ml) not normalized (work): 302197.084340 | | target function (ml) not normalized (free): 15961.879376 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1416 0.1435 5.6798 5.6529| | 2: 3.57 - 2.84 1.00 2888 124 0.1110 0.1436 5.1994 5.2543| | 3: 2.83 - 2.48 1.00 2820 163 0.1218 0.1257 5.0097 5.0265| | 4: 2.47 - 2.25 1.00 2825 136 0.1028 0.1126 4.71 4.7554| | 5: 2.25 - 2.09 1.00 2756 127 0.0983 0.1138 4.6496 4.7395| | 6: 2.09 - 1.97 1.00 2846 113 0.0988 0.1236 4.363 4.4958| | 7: 1.97 - 1.87 1.00 2787 165 0.0999 0.1202 4.083 4.1691| | 8: 1.87 - 1.79 1.00 2789 144 0.1031 0.1241 3.998 4.0833| | 9: 1.79 - 1.72 1.00 2745 138 0.0969 0.1287 3.728 3.9134| | 10: 1.72 - 1.66 1.00 2831 160 0.1014 0.1297 3.6433 3.7793| | 11: 1.66 - 1.61 1.00 2712 147 0.0974 0.1081 3.5791 3.6043| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1165 3.3536 3.4735| | 13: 1.56 - 1.52 1.00 2745 130 0.0994 0.1074 3.3493 3.4313| | 14: 1.52 - 1.48 1.00 2803 134 0.1005 0.1158 3.2707 3.3536| | 15: 1.48 - 1.45 1.00 2738 128 0.1027 0.1379 3.1808 3.3545| | 16: 1.45 - 1.42 1.00 2756 161 0.1073 0.1239 3.1598 3.2467| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1312 3.1258 3.2414| | 18: 1.39 - 1.36 1.00 2741 179 0.1169 0.1376 3.1002 3.2699| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1636 3.1031 3.2909| | 20: 1.34 - 1.32 1.00 2696 147 0.1327 0.1483 3.0953 3.1454| | 21: 1.32 - 1.30 1.00 2785 112 0.1427 0.1627 3.0948 3.1731| | 22: 1.29 - 1.27 1.00 2704 152 0.1492 0.1930 3.0942 3.2852| | 23: 1.27 - 1.26 1.00 2802 156 0.1591 0.1876 3.1119 3.2155| | 24: 1.26 - 1.24 1.00 2744 132 0.1643 0.1777 3.1024 3.1995| | 25: 1.24 - 1.22 1.00 2733 148 0.1807 0.2329 3.1148 3.2902| | 26: 1.22 - 1.21 1.00 2727 135 0.1870 0.1792 3.1302 3.2105| | 27: 1.21 - 1.19 1.00 2814 148 0.2022 0.2078 3.1462 3.1464| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2330 3.1432 3.1647| | 29: 1.18 - 1.16 1.00 2800 134 0.2229 0.2359 3.1322 3.2204| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2490 3.1208 3.1678| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 9.16 1.00 0.97 6330.25| | 2: 3.57 - 2.84 2888 124 0.92 13.38 1.01 0.97 6330.25| | 3: 2.83 - 2.48 2820 163 0.89 17.58 0.99 0.97 5307.63| | 4: 2.47 - 2.25 2825 136 0.91 14.70 1.00 0.98 2670.63| | 5: 2.25 - 2.09 2756 127 0.89 16.92 1.01 0.98 2670.63| | 6: 2.09 - 1.97 2846 113 0.92 13.67 1.02 0.98 1570.97| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.97 633.11| | 8: 1.87 - 1.79 2789 144 0.91 14.45 0.99 0.97 633.11| | 9: 1.79 - 1.72 2745 138 0.93 11.45 0.98 0.97 343.81| | 10: 1.72 - 1.66 2831 160 0.93 12.35 0.98 0.97 285.88| | 11: 1.66 - 1.61 2712 147 0.93 12.97 0.98 0.97 272.73| | 12: 1.61 - 1.56 2773 144 0.95 9.52 0.99 0.97 148.78| | 13: 1.56 - 1.52 2745 130 0.94 11.14 1.02 0.97 148.78| | 14: 1.52 - 1.48 2803 134 0.94 11.30 1.02 0.98 133.27| | 15: 1.48 - 1.45 2738 128 0.95 10.50 1.01 0.98 104.87| | 16: 1.45 - 1.42 2756 161 0.94 11.70 1.02 0.98 104.87| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 94.88| | 18: 1.39 - 1.36 2741 179 0.94 11.88 1.01 0.98 89.09| | 19: 1.36 - 1.34 2807 134 0.94 12.43 1.00 0.98 89.09| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.97 83.88| | 21: 1.32 - 1.30 2785 112 0.93 13.51 0.98 0.96 83.52| | 22: 1.29 - 1.27 2704 152 0.93 14.00 0.98 0.96 83.56| | 23: 1.27 - 1.26 2802 156 0.92 14.91 0.97 0.95 83.79| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.95 83.79| | 25: 1.24 - 1.22 2733 148 0.91 16.46 0.96 0.94 85.09| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.53| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.53| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 89.44| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 90.53| | 30: 1.16 - 1.15 2739 148 0.86 21.87 0.98 0.93 90.53| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 83.52 max = 6330.25 mean = 987.51| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.10| |phase err.(test): min = 0.00 max = 89.31 mean = 14.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1200 0.1373 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1509 0.1507 0.1577 n_refl.: 87574 remove outliers: r(all,work,free)=0.1509 0.1507 0.1577 n_refl.: 87574 overall B=-0.01 to atoms: r(all,work,free)=0.1507 0.1505 0.1576 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1200 0.1377 n_refl.: 87574 remove outliers: r(all,work,free)=0.1208 0.1199 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 88.54 80 5 0.4156 283.839 250.018 0.427 0.999 0.281 11.894-9.307 92.16 90 4 0.2368 462.711 452.583 0.836 1.001 0.182 9.237-7.194 97.27 207 7 0.2512 384.183 377.507 0.903 1.001 0.105 7.162-5.571 100.00 427 22 0.2289 294.209 282.450 0.896 1.002 0.100 5.546-4.326 100.00 867 58 0.1187 403.876 399.342 0.953 1.002 0.100 4.315-3.360 100.00 1859 96 0.0987 384.088 381.224 0.995 1.002 0.100 3.356-2.611 100.00 3867 181 0.1171 252.326 250.361 1.000 1.001 0.048 2.608-2.026 99.99 8198 413 0.1039 167.269 166.247 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0987 81.686 81.937 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.223 35.839 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2128 22.823 21.435 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0300 ================= 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 : 0.2606 0.1960 0.084 5.208 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1795 0.084 5.208 9.0 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1795 0.084 5.208 9.0 119.5 20.1 258 0.000 1_nqh: 0.1630 0.1798 0.084 5.208 9.0 119.5 20.1 258 0.003 1_weight: 0.1630 0.1798 0.084 5.208 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1210 0.1469 0.008 0.966 9.0 119.5 20.1 258 0.123 1_adp: 0.1244 0.1550 0.008 0.966 8.5 118.5 21.0 258 0.123 1_regHadp: 0.1249 0.1555 0.008 0.966 8.5 118.5 21.0 258 0.123 1_occ: 0.1247 0.1555 0.008 0.966 8.5 118.5 21.0 258 0.123 2_bss: 0.1243 0.1548 0.008 0.966 8.7 118.7 21.2 258 0.123 2_settarget: 0.1243 0.1548 0.008 0.966 8.7 118.7 21.2 258 0.123 2_updatecdl: 0.1243 0.1548 0.008 0.979 8.7 118.7 21.2 258 0.123 2_nqh: 0.1245 0.1549 0.008 0.979 8.7 118.7 21.2 258 0.126 2_sol: 0.1236 0.1497 0.008 0.979 8.7 118.7 23.6 431 n/a 2_weight: 0.1236 0.1497 0.008 0.979 8.7 118.7 23.6 431 n/a 2_xyzrec: 0.1232 0.1515 0.007 0.876 8.7 118.7 23.6 431 n/a 2_adp: 0.1205 0.1490 0.007 0.876 8.8 114.9 23.2 431 n/a 2_regHadp: 0.1205 0.1490 0.007 0.876 8.8 114.9 23.2 431 n/a 2_occ: 0.1205 0.1489 0.007 0.876 8.8 114.9 23.2 431 n/a 3_bss: 0.1200 0.1485 0.007 0.876 8.8 114.9 23.3 431 n/a 3_settarget: 0.1200 0.1485 0.007 0.876 8.8 114.9 23.3 431 n/a 3_updatecdl: 0.1200 0.1485 0.007 0.877 8.8 114.9 23.3 431 n/a 3_nqh: 0.1200 0.1485 0.007 0.877 8.8 114.9 23.3 431 n/a 3_sol: 0.1226 0.1480 0.007 0.877 8.8 114.9 22.1 449 n/a 3_weight: 0.1226 0.1480 0.007 0.877 8.8 114.9 22.1 449 n/a 3_xyzrec: 0.1237 0.1456 0.005 0.909 8.8 114.9 22.1 449 n/a 3_adp: 0.1218 0.1408 0.005 0.909 9.3 110.0 21.7 449 n/a 3_regHadp: 0.1219 0.1410 0.005 0.909 9.3 110.0 21.7 449 n/a 3_occ: 0.1214 0.1410 0.005 0.909 9.3 110.0 21.7 449 n/a 4_bss: 0.1199 0.1383 0.005 0.909 9.3 110.0 21.7 449 n/a 4_settarget: 0.1199 0.1383 0.005 0.909 9.3 110.0 21.7 449 n/a 4_updatecdl: 0.1199 0.1383 0.005 0.908 9.3 110.0 21.7 449 n/a 4_nqh: 0.1199 0.1383 0.005 0.908 9.3 110.0 21.7 449 n/a 4_sol: 0.1189 0.1368 0.005 0.908 9.3 110.0 21.5 449 n/a 4_weight: 0.1189 0.1368 0.005 0.908 9.3 110.0 21.5 449 n/a 4_xyzrec: 0.1193 0.1375 0.006 0.985 9.3 110.0 21.5 449 n/a 4_adp: 0.1185 0.1373 0.006 0.985 9.3 105.7 21.3 449 n/a 4_regHadp: 0.1185 0.1373 0.006 0.985 9.3 105.7 21.3 449 n/a 4_occ: 0.1181 0.1370 0.006 0.985 9.3 105.7 21.3 449 n/a 5_bss: 0.1179 0.1370 0.006 0.985 9.3 105.6 21.3 449 n/a 5_settarget: 0.1179 0.1370 0.006 0.985 9.3 105.6 21.3 449 n/a 5_updatecdl: 0.1179 0.1370 0.006 0.985 9.3 105.6 21.3 449 n/a 5_setrh: 0.1180 0.1370 0.006 0.985 9.3 105.6 21.3 449 n/a 5_nqh: 0.1180 0.1370 0.006 0.985 9.3 105.6 21.3 449 n/a 5_sol: 0.1174 0.1352 0.006 0.985 9.3 105.6 21.4 457 n/a 5_weight: 0.1174 0.1352 0.006 0.985 9.3 105.6 21.4 457 n/a 5_xyzrec: 0.1198 0.1374 0.006 1.024 9.3 105.6 21.4 457 n/a 5_adp: 0.1202 0.1374 0.006 1.024 9.3 103.1 21.3 457 n/a 5_regHadp: 0.1202 0.1374 0.006 1.024 9.3 103.1 21.3 457 n/a 5_occ: 0.1200 0.1373 0.006 1.024 9.3 103.1 21.3 457 n/a end: 0.1199 0.1377 0.006 1.024 9.2 103.1 21.3 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7427252_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7427252_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3554.9900 Write final files (write_after_run_outputs) : 61.7300 Total : 3621.5400 Total CPU time: 60.97 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:58 PST -0800 (1735452718.91 s) Start R-work = 0.1628, R-free = 0.1795 Final R-work = 0.1199, R-free = 0.1377 =============================================================================== Job complete usr+sys time: 3753.17 seconds wall clock time: 67 minutes 4.25 seconds (4024.25 seconds total)