Starting phenix.refine on Sat Dec 28 21:06:34 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2780949.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.53, per 1000 atoms: 0.75 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: 1.24 Conformation dependent library (CDL) restraints added in 448.5 milliseconds Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 596 0.92 - 1.17: 1062 1.17 - 1.42: 635 1.42 - 1.67: 824 1.67 - 1.92: 36 Bond restraints: 3153 Sorted by residual: bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.456 1.697 -0.241 1.16e-02 7.43e+03 4.32e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.458 1.680 -0.222 1.18e-02 7.18e+03 3.55e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.237 1.025 0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta sigma weight residual 1.459 1.231 0.227 1.28e-02 6.10e+03 3.15e+02 bond pdb=" CA VAL A 69 " pdb=" C VAL A 69 " ideal model delta sigma weight residual 1.522 1.308 0.214 1.26e-02 6.30e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 3141 4.52 - 9.04: 1848 9.04 - 13.56: 658 13.56 - 18.08: 115 18.08 - 22.61: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BLYS A 93 " pdb=" C BLYS A 93 " pdb=" N BGLU A 94 " ideal model delta sigma weight residual 122.03 106.01 16.02 1.04e+00 9.25e-01 2.37e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 105.70 13.50 9.00e-01 1.23e+00 2.25e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.27 140.62 -18.35 1.23e+00 6.61e-01 2.23e+02 angle pdb=" CA ALA A 183 " pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 118.63 131.52 -12.89 9.20e-01 1.18e+00 1.96e+02 angle pdb=" CA VAL A 169 " pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 121.41 106.99 14.42 1.04e+00 9.25e-01 1.92e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 16.93: 932 16.93 - 33.84: 123 33.84 - 50.74: 39 50.74 - 67.64: 14 67.64 - 84.55: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N THR A 160 " pdb=" CA THR A 160 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 126 0.270 - 0.541: 72 0.541 - 0.811: 33 0.811 - 1.081: 10 1.081 - 1.352: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 123 " pdb=" CA VAL A 123 " pdb=" CG1 VAL A 123 " pdb=" CG2 VAL A 123 " both_signs ideal model delta sigma weight residual False -2.63 -1.28 -1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CA ALA A 39 " pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CB ALA A 39 " both_signs ideal model delta sigma weight residual False 2.48 1.40 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.58 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.118 2.00e-02 2.50e+03 7.01e-02 1.48e+02 pdb=" CG PHE A 164 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.101 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.022 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG BTYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.045 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.048 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.096 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.082 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.201 9.50e-02 1.11e+02 9.12e-02 9.07e+01 pdb=" NE ARG A 48 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " 0.043 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.089 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 736 2.27 - 2.86: 7847 2.86 - 3.44: 10631 3.44 - 4.02: 15351 4.02 - 4.60: 22092 Nonbonded interactions: 56657 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.693 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.775 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.804 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.829 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.836 2.450 ... (remaining 56652 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_2780949_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.798304 | | target function (ml) not normalized (work): 233115.507787 | | target function (ml) not normalized (free): 11853.557220 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3049 0.2067 7.0677 4.9451| | 2: 3.57 - 2.84 1.00 2876 122 0.2434 0.1854 4.3509 4.3393| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1667 4.1281 4.1628| | 4: 2.47 - 2.25 1.00 2825 136 0.2354 0.1388 3.8332 3.8188| | 5: 2.25 - 2.09 1.00 2756 127 0.2467 0.1568 3.7996 3.8258| | 6: 2.09 - 1.97 1.00 2846 113 0.2535 0.1793 3.4696 3.5412| | 7: 1.97 - 1.87 1.00 2787 165 0.2533 0.1950 3.1475 3.2211| | 8: 1.87 - 1.79 1.00 2789 144 0.2495 0.1982 3.0853 3.159| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1952 2.9262 2.9834| | 10: 1.72 - 1.66 1.00 2789 158 0.2411 0.2150 2.8306 2.9304| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.2006 2.7586 2.7875| | 12: 1.61 - 1.56 1.00 2787 146 0.2514 0.2084 2.632 2.7252| | 13: 1.56 - 1.52 1.00 2745 130 0.2637 0.1827 2.6197 2.5656| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1953 2.5296 2.5853| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.2114 2.4256 2.5162| | 16: 1.45 - 1.42 1.00 2756 161 0.2626 0.2177 2.3801 2.426| | 17: 1.42 - 1.39 1.00 2785 139 0.2641 0.2174 2.3305 2.3929| | 18: 1.39 - 1.36 1.00 2741 179 0.2639 0.2116 2.2666 2.2686| | 19: 1.36 - 1.34 1.00 2807 134 0.2664 0.2225 2.2403 2.2281| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2060 2.1936 2.1268| | 21: 1.32 - 1.30 1.00 2785 112 0.2675 0.1973 2.1694 2.0926| | 22: 1.29 - 1.27 1.00 2704 152 0.2749 0.2505 2.1461 2.2172| | 23: 1.27 - 1.26 1.00 2802 156 0.2846 0.2608 2.1242 2.2062| | 24: 1.26 - 1.24 1.00 2744 132 0.2742 0.2834 2.0815 2.2604| | 25: 1.24 - 1.22 1.00 2734 148 0.2848 0.2711 2.0521 2.1222| | 26: 1.22 - 1.21 1.00 2727 135 0.2849 0.2457 2.0029 2.1135| | 27: 1.21 - 1.19 1.00 2814 148 0.2932 0.2544 2.004 2.0227| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2702 1.9927 1.9714| | 29: 1.18 - 1.16 1.00 2800 134 0.2999 0.2774 1.9717 2.0477| | 30: 1.16 - 1.15 1.00 2740 148 0.3032 0.2912 1.9332 2.0145| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.84 0.76 0.23 1471.93| | 2: 3.57 - 2.84 2876 122 0.80 25.97 1.27 0.23 1471.93| | 3: 2.84 - 2.48 2833 165 0.74 31.92 1.24 0.23 1221.77| | 4: 2.47 - 2.25 2825 136 0.81 25.67 1.26 0.25 572.58| | 5: 2.25 - 2.09 2756 127 0.77 29.41 1.28 0.25 572.58| | 6: 2.09 - 1.97 2846 113 0.83 22.89 1.29 0.25 315.76| | 7: 1.97 - 1.87 2787 165 0.89 17.18 1.28 0.26 96.74| | 8: 1.87 - 1.79 2789 144 0.85 21.73 1.25 0.26 96.74| | 9: 1.79 - 1.72 2745 138 0.87 19.12 1.23 0.26 59.06| | 10: 1.72 - 1.66 2789 158 0.86 20.69 1.22 0.26 51.51| | 11: 1.66 - 1.61 2740 147 0.85 21.99 1.24 0.26 49.69| | 12: 1.61 - 1.56 2787 146 0.88 18.90 1.23 0.25 31.21| | 13: 1.56 - 1.52 2745 130 0.86 20.96 1.24 0.25 31.21| | 14: 1.52 - 1.48 2803 134 0.86 20.98 1.23 0.25 27.61| | 15: 1.48 - 1.45 2738 128 0.87 20.46 1.24 0.25 21.02| | 16: 1.45 - 1.42 2756 161 0.85 21.75 1.23 0.25 21.02| | 17: 1.42 - 1.39 2785 139 0.87 20.34 1.23 0.25 17.35| | 18: 1.39 - 1.36 2741 179 0.87 20.56 1.22 0.25 15.22| | 19: 1.36 - 1.34 2807 134 0.86 21.48 1.22 0.25 15.22| | 20: 1.34 - 1.32 2696 147 0.87 20.34 1.21 0.25 12.51| | 21: 1.32 - 1.30 2785 112 0.86 21.42 1.19 0.25 12.32| | 22: 1.29 - 1.27 2704 152 0.86 21.82 1.21 0.24 12.14| | 23: 1.27 - 1.26 2802 156 0.86 22.28 1.22 0.24 11.26| | 24: 1.26 - 1.24 2744 132 0.85 22.92 1.19 0.24 11.26| | 25: 1.24 - 1.22 2734 148 0.84 24.10 1.21 0.24 10.86| | 26: 1.22 - 1.21 2727 135 0.83 24.71 1.20 0.23 10.41| | 27: 1.21 - 1.19 2814 148 0.83 25.38 1.20 0.23 10.41| | 28: 1.19 - 1.18 2671 147 0.82 25.97 1.19 0.23 9.70| | 29: 1.18 - 1.16 2800 134 0.82 26.09 1.16 0.23 9.43| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.15 0.23 9.43| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.43 max = 1471.93 mean = 215.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.79| |phase err.(test): min = 0.00 max = 89.16 mean = 22.81| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.241 1557 Z= 5.541 Angle : 5.357 19.115 2118 Z= 3.758 Chirality : 0.407 1.352 243 Planarity : 0.033 0.084 284 Dihedral : 14.093 84.545 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.11 % Allowed : 1.86 % Favored : 95.03 % Cbeta Deviations : 31.35 % 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: -2.57 (0.48), residues: 224 helix: -2.56 (0.41), residues: 102 sheet: -1.40 (0.82), residues: 28 loop : -0.45 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.106 0.021 ARG A 98 TYR 0.090 0.046 TYR A 141 PHE 0.105 0.036 PHE A 164 HIS 0.038 0.019 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.798304 | | target function (ml) not normalized (work): 233115.507787 | | target function (ml) not normalized (free): 11853.557220 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2612 0.1964 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2612 0.1964 n_refl.: 87602 remove outliers: r(all,work,free)=0.1985 0.1988 0.1964 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2010 0.2014 0.1981 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1774 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1774 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 0.3836 386.343 358.939 0.723 0.929 0.409 11.894-9.307 99.02 97 4 0.1806 613.686 593.589 1.001 0.930 0.390 9.237-7.194 100.00 213 7 0.2152 501.920 491.585 1.034 0.930 0.354 7.162-5.571 100.00 427 22 0.2205 376.663 364.240 1.002 0.930 0.299 5.546-4.326 100.00 867 58 0.1247 517.065 511.249 1.044 0.930 0.225 4.315-3.360 100.00 1859 96 0.1143 491.733 487.874 1.082 0.930 0.143 3.356-2.611 100.00 3867 181 0.1445 323.043 320.093 1.074 0.930 0.099 2.608-2.026 99.99 8198 413 0.1367 214.148 211.605 1.084 0.929 0.000 2.025-1.573 100.00 17313 902 0.1653 104.579 103.863 1.088 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2085 46.374 45.025 1.078 0.927 0.000 1.221-1.150 99.97 13689 708 0.2592 29.219 26.973 1.051 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0484 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1774 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=0.1644 r_free=0.1774 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.364148 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.376711 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 0.1212 0.1468 0.0257 0.007 0.9 1.3 0.5 0.0 0 11.682 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.68 2.57 3.013 19.070 1992.377 0.017 12.46 15.50 3.04 3.237 19.565 1992.377 0.016 Individual atomic B min max mean iso aniso Overall: 8.62 118.81 21.03 2.88 0 1785 Protein: 8.62 118.81 17.89 2.88 0 1519 Water: 11.08 114.51 39.31 N/A 0 258 Other: 23.23 36.76 29.31 N/A 0 8 Chain A: 8.62 118.81 21.03 N/A 0 1785 Histogram: Values Number of atoms 8.62 - 19.64 1210 19.64 - 30.66 226 30.66 - 41.68 165 41.68 - 52.70 99 52.70 - 63.71 56 63.71 - 74.73 16 74.73 - 85.75 6 85.75 - 96.77 4 96.77 - 107.79 0 107.79 - 118.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1246 r_free=0.1550 r_work=0.1250 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1250 r_free = 0.1554 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 = 0.1251 r_free = 0.1559 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.18 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= 0.1251 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015512 | | target function (ls_wunit_k1) not normalized (work): 1292.136784 | | target function (ls_wunit_k1) not normalized (free): 116.413298 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1266 0.1251 0.1559 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1702 0.1700 0.1775 n_refl.: 87593 remove outliers: r(all,work,free)=0.1702 0.1700 0.1775 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1725 0.1724 0.1790 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1265 0.1251 0.1551 n_refl.: 87593 remove outliers: r(all,work,free)=0.1265 0.1250 0.1551 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 0.3601 299.224 279.183 0.630 1.002 0.374 11.894-9.307 99.02 97 4 0.1603 479.341 467.867 0.908 1.003 0.369 9.237-7.194 100.00 213 7 0.1845 392.042 387.179 0.948 1.003 0.314 7.162-5.571 100.00 427 22 0.1712 294.206 288.894 0.924 1.003 0.258 5.546-4.326 100.00 867 58 0.0910 403.871 401.382 0.950 1.003 0.199 4.315-3.360 100.00 1859 96 0.0775 384.085 383.041 0.995 1.002 0.170 3.356-2.611 100.00 3867 181 0.1025 252.324 251.627 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0980 167.268 166.681 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1222 81.685 81.854 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1667 36.222 35.679 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2373 22.823 21.318 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0544 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1250 r_free=0.1551 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=0.1252 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1252 r_free=0.1552 | n_water=258 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1262 r_free=0.1550 | n_water=252 | time (s): 26.200 (total time: 28.580) Filter (q & B) r_work=0.1265 r_free=0.1549 | n_water=249 | time (s): 3.750 (total time: 32.330) Compute maps r_work=0.1265 r_free=0.1549 | n_water=249 | time (s): 1.810 (total time: 34.140) Filter (map) r_work=0.1291 r_free=0.1556 | n_water=232 | time (s): 3.800 (total time: 37.940) Find peaks r_work=0.1291 r_free=0.1556 | n_water=232 | time (s): 0.750 (total time: 38.690) Add new water r_work=0.1435 r_free=0.1698 | n_water=451 | time (s): 3.980 (total time: 42.670) Refine new water occ: r_work=0.1339 r_free=0.1556 adp: r_work=0.1262 r_free=0.1509 occ: r_work=0.1276 r_free=0.1500 adp: r_work=0.1243 r_free=0.1490 occ: r_work=0.1246 r_free=0.1482 adp: r_work=0.1237 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1484 r_work=0.1237 r_free=0.1484 | n_water=451 | time (s): 114.790 (total time: 157.460) Filter (q & B) r_work=0.1243 r_free=0.1489 | n_water=434 | time (s): 3.950 (total time: 161.410) Filter (dist only) r_work=0.1243 r_free=0.1489 | n_water=434 | time (s): 41.590 (total time: 203.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.385474 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1518.831083 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 0.1533 0.0294 0.007 0.9 3.2 0.5 0.0 0 12.193 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 15.33 2.94 3.795 23.232 1518.831 0.016 12.05 14.91 2.86 4.255 23.033 1518.831 0.015 Individual atomic B min max mean iso aniso Overall: 8.80 114.27 23.22 2.61 202 1759 Protein: 8.80 114.27 17.65 2.62 0 1519 Water: 10.99 73.31 42.61 N/A 202 232 Other: 24.51 35.10 28.86 N/A 0 8 Chain A: 8.80 114.27 20.34 N/A 0 1759 Chain S: 15.69 73.31 48.37 N/A 202 0 Histogram: Values Number of atoms 8.80 - 19.34 1213 19.34 - 29.89 246 29.89 - 40.44 184 40.44 - 50.99 138 50.99 - 61.53 120 61.53 - 72.08 48 72.08 - 82.63 6 82.63 - 93.17 3 93.17 - 103.72 1 103.72 - 114.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1491 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 = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1485 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= 0.1208 r_free= 0.1485 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014290 | | target function (ls_wunit_k1) not normalized (work): 1190.298900 | | target function (ls_wunit_k1) not normalized (free): 106.007129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1208 0.1485 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1599 0.1743 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1599 0.1743 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1613 0.1607 0.1748 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1219 0.1206 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1217 0.1204 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 0.3307 291.915 272.662 0.572 1.001 0.350 11.894-9.307 99.02 97 4 0.1542 479.341 475.709 0.916 1.001 0.350 9.237-7.194 100.00 213 7 0.1671 392.042 391.947 0.974 1.001 0.264 7.162-5.571 100.00 427 22 0.1533 294.206 290.943 0.942 1.001 0.229 5.546-4.326 100.00 867 58 0.0845 403.871 401.434 0.957 1.001 0.205 4.315-3.360 100.00 1859 96 0.0728 384.085 382.867 1.001 1.001 0.200 3.356-2.611 100.00 3867 181 0.0974 252.324 251.628 1.008 1.001 0.072 2.608-2.026 99.99 8198 413 0.0966 167.268 166.912 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1185 81.685 81.895 1.025 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.222 35.701 1.011 1.001 0.000 1.221-1.150 99.97 13689 708 0.2335 22.823 21.263 0.967 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0820 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1485 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=0.1204 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1485 | n_water=434 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1205 r_free=0.1485 | n_water=432 | time (s): 40.470 (total time: 42.820) Filter (q & B) r_work=0.1205 r_free=0.1485 | n_water=432 | time (s): 1.220 (total time: 44.040) Compute maps r_work=0.1205 r_free=0.1485 | n_water=432 | time (s): 1.310 (total time: 45.350) Filter (map) r_work=0.1237 r_free=0.1476 | n_water=300 | time (s): 3.170 (total time: 48.520) Find peaks r_work=0.1237 r_free=0.1476 | n_water=300 | time (s): 0.720 (total time: 49.240) Add new water r_work=0.1356 r_free=0.1588 | n_water=483 | time (s): 3.470 (total time: 52.710) Refine new water occ: r_work=0.1261 r_free=0.1513 adp: r_work=0.1262 r_free=0.1511 occ: r_work=0.1239 r_free=0.1491 adp: r_work=0.1237 r_free=0.1488 occ: r_work=0.1225 r_free=0.1471 adp: r_work=0.1219 r_free=0.1468 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1468 r_work=0.1219 r_free=0.1468 | n_water=483 | time (s): 306.440 (total time: 359.150) Filter (q & B) r_work=0.1222 r_free=0.1472 | n_water=454 | time (s): 3.660 (total time: 362.810) Filter (dist only) r_work=0.1222 r_free=0.1472 | n_water=454 | time (s): 38.260 (total time: 401.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.092761 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.844230 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1424 0.0196 0.006 0.9 3.5 0.5 0.0 0 1.046 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.24 1.96 3.622 22.187 48.844 3.722 12.15 13.82 1.67 4.093 22.007 48.844 3.653 Individual atomic B min max mean iso aniso Overall: 9.26 110.07 21.83 2.33 223 1758 Protein: 9.26 110.07 17.23 2.33 0 1519 Water: 11.40 68.03 37.14 N/A 223 231 Other: 19.93 31.23 25.93 N/A 0 8 Chain A: 9.26 110.07 19.91 N/A 0 1758 Chain S: 15.88 67.17 37.00 N/A 223 0 Histogram: Values Number of atoms 9.26 - 19.34 1232 19.34 - 29.42 277 29.42 - 39.50 223 39.50 - 49.58 133 49.58 - 59.66 80 59.66 - 69.74 24 69.74 - 79.82 6 79.82 - 89.91 3 89.91 - 99.99 1 99.99 - 110.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1382 r_work=0.1216 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1383 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1381 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.15 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= 0.1210 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650764 | | target function (ml) not normalized (work): 304079.417195 | | target function (ml) not normalized (free): 16061.016239 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1210 0.1381 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1538 0.1537 0.1586 n_refl.: 87588 remove outliers: r(all,work,free)=0.1538 0.1537 0.1586 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1535 0.1585 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1361 n_refl.: 87588 remove outliers: r(all,work,free)=0.1205 0.1197 0.1361 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 86.46 78 5 0.3863 283.870 257.525 0.463 0.999 0.320 11.894-9.307 95.10 93 4 0.2379 469.031 457.161 0.856 1.001 0.277 9.237-7.194 98.18 209 7 0.2342 383.578 383.706 0.937 1.002 0.205 7.162-5.571 100.00 427 22 0.2081 294.206 283.429 0.910 1.002 0.173 5.546-4.326 100.00 867 58 0.1082 403.871 399.908 0.950 1.002 0.158 4.315-3.360 100.00 1859 96 0.0923 384.085 381.342 0.993 1.002 0.147 3.356-2.611 100.00 3867 181 0.1155 252.324 250.495 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1048 167.268 166.277 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1021 81.685 81.822 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1292 36.222 35.781 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2130 22.823 21.429 0.977 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0050 b_overall=-0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 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=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=454 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1197 r_free=0.1361 | n_water=454 | time (s): 38.250 (total time: 40.640) Filter (q & B) r_work=0.1197 r_free=0.1360 | n_water=453 | time (s): 3.640 (total time: 44.280) Compute maps r_work=0.1197 r_free=0.1360 | n_water=453 | time (s): 1.450 (total time: 45.730) Filter (map) r_work=0.1223 r_free=0.1385 | n_water=311 | time (s): 3.170 (total time: 48.900) Find peaks r_work=0.1223 r_free=0.1385 | n_water=311 | time (s): 0.690 (total time: 49.590) Add new water r_work=0.1290 r_free=0.1464 | n_water=480 | time (s): 3.220 (total time: 52.810) Refine new water occ: r_work=0.1215 r_free=0.1381 adp: r_work=0.1216 r_free=0.1383 occ: r_work=0.1200 r_free=0.1368 adp: r_work=0.1199 r_free=0.1368 occ: r_work=0.1188 r_free=0.1356 adp: r_work=0.1185 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1354 r_work=0.1185 r_free=0.1354 | n_water=480 | time (s): 227.920 (total time: 280.730) Filter (q & B) r_work=0.1192 r_free=0.1360 | n_water=441 | time (s): 3.400 (total time: 284.130) Filter (dist only) r_work=0.1199 r_free=0.1356 | n_water=439 | time (s): 40.280 (total time: 324.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.923046 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.406033 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 0.1385 0.0175 0.006 0.9 2.2 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.85 1.75 3.436 21.466 40.406 3.643 12.05 13.85 1.81 3.752 21.363 40.406 3.634 Individual atomic B min max mean iso aniso Overall: 9.28 106.34 21.19 2.15 212 1754 Protein: 9.28 106.34 17.01 2.15 0 1519 Water: 11.52 67.33 35.62 N/A 212 227 Other: 19.55 28.37 24.35 N/A 0 8 Chain A: 9.28 106.34 19.58 N/A 0 1754 Chain S: 14.94 54.81 34.51 N/A 212 0 Histogram: Values Number of atoms 9.28 - 18.98 1229 18.98 - 28.69 280 28.69 - 38.40 220 38.40 - 48.10 137 48.10 - 57.81 67 57.81 - 67.51 21 67.51 - 77.22 7 77.22 - 86.93 2 86.93 - 96.63 1 96.63 - 106.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1385 r_work=0.1205 r_free=0.1386 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1386 target_work(ml) = 3.634 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1383 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1202 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.633099 | | target function (ml) not normalized (work): 302560.836760 | | target function (ml) not normalized (free): 15987.369408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1202 0.1383 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1522 0.1520 0.1582 n_refl.: 87575 remove outliers: r(all,work,free)=0.1522 0.1520 0.1582 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1519 0.1517 0.1581 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1384 n_refl.: 87575 remove outliers: r(all,work,free)=0.1209 0.1200 0.1384 n_refl.: 87573 ======================== 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 86.46 78 5 0.3933 283.870 252.733 0.445 1.000 0.307 11.894-9.307 94.12 92 4 0.2450 472.913 451.529 0.834 1.001 0.235 9.237-7.194 97.73 208 7 0.2540 383.101 376.303 0.902 1.002 0.155 7.162-5.571 100.00 427 22 0.2240 294.206 282.312 0.902 1.002 0.128 5.546-4.326 100.00 867 58 0.1158 403.871 399.595 0.950 1.002 0.121 4.315-3.360 100.00 1859 96 0.0968 384.085 381.473 0.993 1.002 0.113 3.356-2.611 100.00 3867 181 0.1175 252.324 250.590 1.001 1.001 0.090 2.608-2.026 99.99 8198 413 0.1046 167.268 166.383 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0990 81.685 81.940 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.222 35.833 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2124 22.823 21.441 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0383 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1200 r_free=0.1384 After: r_work=0.1201 r_free=0.1384 ================================== NQH flips ================================== r_work=0.1201 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.1201 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1384 | n_water=439 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1201 r_free=0.1384 | n_water=439 | time (s): 36.880 (total time: 39.040) Filter (q & B) r_work=0.1201 r_free=0.1384 | n_water=439 | time (s): 0.890 (total time: 39.930) Compute maps r_work=0.1201 r_free=0.1384 | n_water=439 | time (s): 1.320 (total time: 41.250) Filter (map) r_work=0.1222 r_free=0.1387 | n_water=327 | time (s): 2.710 (total time: 43.960) Find peaks r_work=0.1222 r_free=0.1387 | n_water=327 | time (s): 0.450 (total time: 44.410) Add new water r_work=0.1269 r_free=0.1435 | n_water=487 | time (s): 2.890 (total time: 47.300) Refine new water occ: r_work=0.1205 r_free=0.1368 adp: r_work=0.1205 r_free=0.1371 occ: r_work=0.1194 r_free=0.1356 adp: r_work=0.1193 r_free=0.1358 occ: r_work=0.1186 r_free=0.1349 adp: r_work=0.1183 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1351 r_work=0.1183 r_free=0.1351 | n_water=487 | time (s): 187.830 (total time: 235.130) Filter (q & B) r_work=0.1190 r_free=0.1361 | n_water=449 | time (s): 3.400 (total time: 238.530) Filter (dist only) r_work=0.1190 r_free=0.1361 | n_water=448 | time (s): 38.980 (total time: 277.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.993907 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.627699 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 0.1224 0.1389 0.0166 0.007 1.1 3.2 0.5 0.0 0 0.997 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 13.89 1.66 3.307 21.213 47.628 3.644 12.17 13.86 1.69 3.522 21.148 47.628 3.633 Individual atomic B min max mean iso aniso Overall: 9.22 102.80 21.09 2.07 221 1754 Protein: 9.22 102.80 16.83 2.07 0 1519 Water: 11.57 67.04 35.48 N/A 221 227 Other: 19.63 27.81 23.86 N/A 0 8 Chain A: 9.22 102.80 19.40 N/A 0 1754 Chain S: 15.56 59.33 34.49 N/A 221 0 Histogram: Values Number of atoms 9.22 - 18.58 1220 18.58 - 27.93 281 27.93 - 37.29 224 37.29 - 46.65 136 46.65 - 56.01 75 56.01 - 65.37 23 65.37 - 74.73 11 74.73 - 84.09 2 84.09 - 93.44 1 93.44 - 102.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1386 r_work=0.1217 r_free=0.1386 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1386 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1383 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87573 (all), 4.91 % free)------------| | | | r_work= 0.1214 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.631543 | | target function (ml) not normalized (work): 302424.025648 | | target function (ml) not normalized (free): 15995.731195 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2915 171 0.1461 0.1465 5.7 5.6829| | 2: 3.57 - 2.84 1.00 2888 124 0.1138 0.1392 5.2237 5.2731| | 3: 2.83 - 2.48 1.00 2820 163 0.1235 0.1253 5.0285 5.0399| | 4: 2.47 - 2.25 1.00 2825 136 0.1045 0.1180 4.728 4.7766| | 5: 2.25 - 2.09 1.00 2756 127 0.1016 0.1131 4.6722 4.732| | 6: 2.09 - 1.97 1.00 2846 113 0.0988 0.1177 4.3684 4.4915| | 7: 1.97 - 1.87 1.00 2787 165 0.1005 0.1251 4.0809 4.1961| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1228 3.9968 4.0757| | 9: 1.79 - 1.72 1.00 2745 138 0.0959 0.1316 3.7271 3.9064| | 10: 1.72 - 1.66 1.00 2831 160 0.1012 0.1311 3.6434 3.7987| | 11: 1.66 - 1.61 1.00 2712 147 0.0977 0.1115 3.5811 3.619| | 12: 1.61 - 1.56 1.00 2773 144 0.0923 0.1228 3.3543 3.5049| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1098 3.3484 3.4458| | 14: 1.52 - 1.48 1.00 2803 134 0.1004 0.1133 3.2745 3.3636| | 15: 1.48 - 1.45 1.00 2738 128 0.1017 0.1343 3.1825 3.329| | 16: 1.45 - 1.42 1.00 2756 161 0.1076 0.1300 3.1637 3.2601| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1329 3.1279 3.2539| | 18: 1.39 - 1.36 1.00 2741 179 0.1159 0.1410 3.0982 3.2895| | 19: 1.36 - 1.34 1.00 2807 134 0.1220 0.1648 3.1044 3.2866| | 20: 1.34 - 1.32 1.00 2696 147 0.1323 0.1471 3.0979 3.1418| | 21: 1.32 - 1.30 1.00 2785 112 0.1418 0.1640 3.0919 3.1728| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1918 3.0929 3.2805| | 23: 1.27 - 1.26 1.00 2802 156 0.1572 0.1902 3.1066 3.2306| | 24: 1.26 - 1.24 1.00 2744 132 0.1627 0.1827 3.0977 3.2095| | 25: 1.24 - 1.22 1.00 2733 148 0.1786 0.2354 3.1109 3.3071| | 26: 1.22 - 1.21 1.00 2727 135 0.1867 0.1793 3.1264 3.2017| | 27: 1.21 - 1.19 1.00 2814 148 0.2013 0.2087 3.1404 3.1493| | 28: 1.19 - 1.18 1.00 2671 147 0.2139 0.2341 3.1397 3.1717| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2349 3.1274 3.2195| | 30: 1.16 - 1.15 1.00 2739 148 0.2371 0.2461 3.1171 3.1591| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2915 171 0.94 9.50 1.00 0.97 6666.89| | 2: 3.57 - 2.84 2888 124 0.92 13.81 1.01 0.97 6666.89| | 3: 2.83 - 2.48 2820 163 0.88 18.01 0.99 0.98 5580.13| | 4: 2.47 - 2.25 2825 136 0.91 15.01 1.00 0.98 2777.72| | 5: 2.25 - 2.09 2756 127 0.89 17.23 1.01 0.98 2777.72| | 6: 2.09 - 1.97 2846 113 0.91 13.86 1.02 0.98 1618.38| | 7: 1.97 - 1.87 2787 165 0.94 10.85 1.02 0.98 629.63| | 8: 1.87 - 1.79 2789 144 0.91 14.45 1.00 0.98 629.63| | 9: 1.79 - 1.72 2745 138 0.93 11.51 0.98 0.97 344.37| | 10: 1.72 - 1.66 2831 160 0.93 12.36 0.98 0.97 287.25| | 11: 1.66 - 1.61 2712 147 0.93 13.00 0.98 0.97 274.30| | 12: 1.61 - 1.56 2773 144 0.95 9.75 0.99 0.97 152.20| | 13: 1.56 - 1.52 2745 130 0.94 11.32 1.02 0.97 152.20| | 14: 1.52 - 1.48 2803 134 0.94 11.49 1.02 0.98 136.21| | 15: 1.48 - 1.45 2738 128 0.95 10.63 1.01 0.98 106.93| | 16: 1.45 - 1.42 2756 161 0.94 11.87 1.02 0.98 106.93| | 17: 1.42 - 1.39 2785 139 0.94 11.69 1.01 0.99 96.60| | 18: 1.39 - 1.36 2741 179 0.94 12.01 1.01 0.99 90.62| | 19: 1.36 - 1.34 2807 134 0.94 12.54 1.00 0.99 90.62| | 20: 1.34 - 1.32 2696 147 0.94 12.67 0.99 0.97 84.90| | 21: 1.32 - 1.30 2785 112 0.93 13.63 0.99 0.97 84.50| | 22: 1.29 - 1.27 2704 152 0.93 14.13 0.99 0.96 84.55| | 23: 1.27 - 1.26 2802 156 0.92 14.97 0.98 0.95 84.78| | 24: 1.26 - 1.24 2744 132 0.92 15.17 0.97 0.95 84.78| | 25: 1.24 - 1.22 2733 148 0.91 16.50 0.96 0.94 85.86| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.94 87.06| | 27: 1.21 - 1.19 2814 148 0.89 18.83 1.02 0.94 87.06| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 89.47| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 90.38| | 30: 1.16 - 1.15 2739 148 0.86 21.85 0.98 0.93 90.38| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 84.50 max = 6666.89 mean = 1029.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 14.23| |phase err.(test): min = 0.00 max = 88.61 mean = 14.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1214 0.1383 n_refl.: 87573 re-set all scales: r(all,work,free)=0.1529 0.1527 0.1587 n_refl.: 87573 remove outliers: r(all,work,free)=0.1529 0.1527 0.1587 n_refl.: 87573 overall B=-0.01 to atoms: r(all,work,free)=0.1527 0.1525 0.1586 n_refl.: 87573 bulk-solvent and scaling: r(all,work,free)=0.1222 0.1214 0.1386 n_refl.: 87573 remove outliers: r(all,work,free)=0.1222 0.1214 0.1386 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 86.46 78 5 0.4045 283.870 250.004 0.428 1.000 0.297 11.894-9.307 94.12 92 4 0.2597 472.913 452.239 0.827 1.002 0.197 9.237-7.194 97.27 207 7 0.2537 384.179 376.417 0.895 1.002 0.120 7.162-5.571 100.00 427 22 0.2325 294.206 281.691 0.896 1.002 0.120 5.546-4.326 100.00 867 58 0.1223 403.871 399.336 0.953 1.002 0.119 4.315-3.360 100.00 1859 96 0.1022 384.085 381.203 0.993 1.002 0.119 3.356-2.611 100.00 3867 181 0.1201 252.324 250.376 1.001 1.001 0.080 2.608-2.026 99.99 8198 413 0.1060 167.268 166.316 1.015 1.000 0.000 2.025-1.573 100.00 17313 902 0.0988 81.685 81.910 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1233 36.222 35.843 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2117 22.823 21.446 0.982 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0354 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2611 0.1963 0.083 5.357 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_weight: 0.1644 0.1774 0.083 5.357 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1468 0.007 0.926 9.1 119.5 20.1 258 0.126 1_adp: 0.1246 0.1550 0.007 0.926 8.6 118.8 21.0 258 0.126 1_regHadp: 0.1250 0.1554 0.007 0.926 8.6 118.8 21.0 258 0.126 1_occ: 0.1251 0.1559 0.007 0.926 8.6 118.8 21.0 258 0.126 2_bss: 0.1250 0.1551 0.007 0.926 8.8 118.9 21.2 258 0.126 2_settarget: 0.1250 0.1551 0.007 0.926 8.8 118.9 21.2 258 0.126 2_updatecdl: 0.1250 0.1551 0.007 0.940 8.8 118.9 21.2 258 0.126 2_nqh: 0.1252 0.1552 0.007 0.940 8.8 118.9 21.2 258 0.129 2_sol: 0.1243 0.1489 0.007 0.940 8.8 118.9 23.6 434 n/a 2_weight: 0.1243 0.1489 0.007 0.940 8.8 118.9 23.6 434 n/a 2_xyzrec: 0.1240 0.1533 0.007 0.872 8.8 118.9 23.6 434 n/a 2_adp: 0.1205 0.1491 0.007 0.872 8.8 114.3 23.2 434 n/a 2_regHadp: 0.1205 0.1490 0.007 0.872 8.8 114.3 23.2 434 n/a 2_occ: 0.1208 0.1485 0.007 0.872 8.8 114.3 23.2 434 n/a 3_bss: 0.1204 0.1485 0.007 0.872 8.8 114.3 23.3 434 n/a 3_settarget: 0.1204 0.1485 0.007 0.872 8.8 114.3 23.3 434 n/a 3_updatecdl: 0.1204 0.1485 0.007 0.875 8.8 114.3 23.3 434 n/a 3_nqh: 0.1204 0.1485 0.007 0.875 8.8 114.3 23.3 434 n/a 3_sol: 0.1222 0.1472 0.007 0.875 8.8 114.3 22.2 454 n/a 3_weight: 0.1222 0.1472 0.007 0.875 8.8 114.3 22.2 454 n/a 3_xyzrec: 0.1228 0.1424 0.006 0.924 8.8 114.3 22.2 454 n/a 3_adp: 0.1215 0.1382 0.006 0.924 9.3 110.1 21.8 454 n/a 3_regHadp: 0.1216 0.1383 0.006 0.924 9.3 110.1 21.8 454 n/a 3_occ: 0.1210 0.1381 0.006 0.924 9.3 110.1 21.8 454 n/a 4_bss: 0.1197 0.1361 0.006 0.924 9.3 110.1 21.8 454 n/a 4_settarget: 0.1197 0.1361 0.006 0.924 9.3 110.1 21.8 454 n/a 4_updatecdl: 0.1197 0.1361 0.006 0.923 9.3 110.1 21.8 454 n/a 4_nqh: 0.1197 0.1361 0.006 0.923 9.3 110.1 21.8 454 n/a 4_sol: 0.1199 0.1356 0.006 0.923 9.3 110.1 21.4 439 n/a 4_weight: 0.1199 0.1356 0.006 0.923 9.3 110.1 21.4 439 n/a 4_xyzrec: 0.1210 0.1385 0.006 0.946 9.3 110.1 21.4 439 n/a 4_adp: 0.1205 0.1385 0.006 0.946 9.3 106.3 21.2 439 n/a 4_regHadp: 0.1205 0.1386 0.006 0.946 9.3 106.3 21.2 439 n/a 4_occ: 0.1202 0.1383 0.006 0.946 9.3 106.3 21.2 439 n/a 5_bss: 0.1200 0.1384 0.006 0.946 9.3 106.3 21.2 439 n/a 5_settarget: 0.1200 0.1384 0.006 0.946 9.3 106.3 21.2 439 n/a 5_updatecdl: 0.1200 0.1384 0.006 0.948 9.3 106.3 21.2 439 n/a 5_setrh: 0.1201 0.1384 0.006 0.948 9.3 106.3 21.2 439 n/a 5_nqh: 0.1201 0.1384 0.006 0.948 9.3 106.3 21.2 439 n/a 5_sol: 0.1190 0.1361 0.006 0.948 9.3 106.3 21.2 448 n/a 5_weight: 0.1190 0.1361 0.006 0.948 9.3 106.3 21.2 448 n/a 5_xyzrec: 0.1224 0.1389 0.007 1.086 9.3 106.3 21.2 448 n/a 5_adp: 0.1217 0.1386 0.007 1.086 9.2 102.8 21.1 448 n/a 5_regHadp: 0.1217 0.1386 0.007 1.086 9.2 102.8 21.1 448 n/a 5_occ: 0.1214 0.1383 0.007 1.086 9.2 102.8 21.1 448 n/a end: 0.1214 0.1386 0.007 1.086 9.2 102.8 21.1 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2780949_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2780949_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9100 Refinement macro-cycles (run) : 3655.2900 Write final files (write_after_run_outputs) : 62.2100 Total : 3722.4100 Total CPU time: 62.68 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:14:02 PST -0800 (1735452842.05 s) Start R-work = 0.1644, R-free = 0.1774 Final R-work = 0.1214, R-free = 0.1386 =============================================================================== Job complete usr+sys time: 3862.94 seconds wall clock time: 69 minutes 15.82 seconds (4155.82 seconds total)