Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.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_8498250.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8498250.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.29, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 227.0 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: 0.66 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.42: 638 1.42 - 1.68: 824 1.68 - 1.93: 40 Bond restraints: 3153 Sorted by residual: bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.948 0.289 1.16e-02 7.43e+03 6.19e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.65e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.331 1.522 -0.191 1.05e-02 9.07e+03 3.32e+02 bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.455 1.231 0.224 1.25e-02 6.40e+03 3.21e+02 bond pdb=" CA ALA A 165 " pdb=" C ALA A 165 " ideal model delta sigma weight residual 1.524 1.300 0.224 1.29e-02 6.01e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 3296 4.97 - 9.94: 1848 9.94 - 14.91: 558 14.91 - 19.88: 72 19.88 - 24.85: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " pdb=" CE1 HIS A 138 " ideal model delta sigma weight residual 109.00 95.86 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" O ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 122.27 138.23 -15.96 1.23e+00 6.61e-01 1.68e+02 angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 135.57 -12.97 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" N ALYS A 93 " ideal model delta sigma weight residual 117.39 101.55 15.84 1.24e+00 6.50e-01 1.63e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " ideal model delta sigma weight residual 115.61 102.52 13.09 1.03e+00 9.43e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 15.72: 910 15.72 - 31.43: 144 31.43 - 47.13: 31 47.13 - 62.84: 22 62.84 - 78.55: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+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 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 115 0.253 - 0.506: 72 0.506 - 0.759: 40 0.759 - 1.011: 12 1.011 - 1.264: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 72 " pdb=" CB LEU A 72 " pdb=" CD1 LEU A 72 " pdb=" CD2 LEU A 72 " both_signs ideal model delta sigma weight residual False -2.59 -3.85 1.26 2.00e-01 2.50e+01 4.00e+01 chirality pdb=" CA HIS A 138 " pdb=" N HIS A 138 " pdb=" C HIS A 138 " pdb=" CB HIS A 138 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.006 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 141 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.138 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.137 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.094 2.00e-02 2.50e+03 7.07e-02 1.12e+02 pdb=" CG HIS A 126 " -0.124 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.018 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.113 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 620 2.25 - 2.84: 7617 2.84 - 3.42: 10668 3.42 - 4.01: 15427 4.01 - 4.60: 22287 Nonbonded interactions: 56619 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.662 2.100 nonbonded pdb=" O GLY A 37 " pdb=" H LEU A 58 " model vdw 1.810 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.853 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.875 2.270 ... (remaining 56614 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_8498250_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= 0.2599 r_free= 0.1938 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790223 | | target function (ml) not normalized (work): 232442.341864 | | target function (ml) not normalized (free): 11821.779078 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3037 0.2094 7.1009 4.9491| | 2: 3.57 - 2.84 1.00 2876 122 0.2431 0.1797 4.3469 4.3353| | 3: 2.84 - 2.48 1.00 2833 165 0.2329 0.1532 4.1174 4.1375| | 4: 2.47 - 2.25 1.00 2825 136 0.2343 0.1403 3.8257 3.8112| | 5: 2.25 - 2.09 1.00 2756 127 0.2459 0.1777 3.7918 3.8313| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1638 3.4668 3.4897| | 7: 1.97 - 1.87 1.00 2787 165 0.2495 0.1730 3.1246 3.1603| | 8: 1.87 - 1.79 1.00 2789 144 0.2475 0.1835 3.0627 3.112| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.1939 2.8922 3.0102| | 10: 1.72 - 1.66 1.00 2789 158 0.2346 0.2081 2.7974 2.9316| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.2048 2.7485 2.8418| | 12: 1.61 - 1.56 1.00 2787 146 0.2549 0.2012 2.6593 2.6875| | 13: 1.56 - 1.52 1.00 2745 130 0.2527 0.1976 2.5863 2.6666| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2215 2.5195 2.6255| | 15: 1.48 - 1.45 1.00 2738 128 0.2572 0.2096 2.4135 2.4887| | 16: 1.45 - 1.42 1.00 2756 161 0.2665 0.2405 2.3923 2.5309| | 17: 1.42 - 1.39 1.00 2785 139 0.2716 0.2048 2.3369 2.3586| | 18: 1.39 - 1.36 1.00 2741 179 0.2698 0.2323 2.2787 2.3792| | 19: 1.36 - 1.34 1.00 2807 134 0.2598 0.2402 2.2454 2.3188| | 20: 1.34 - 1.32 1.00 2696 147 0.2677 0.2240 2.1899 2.2147| | 21: 1.32 - 1.30 1.00 2785 112 0.2744 0.2262 2.1703 2.1977| | 22: 1.29 - 1.27 1.00 2704 152 0.2737 0.2429 2.1286 2.1841| | 23: 1.27 - 1.26 1.00 2802 156 0.2705 0.2474 2.0963 2.1458| | 24: 1.26 - 1.24 1.00 2744 132 0.2786 0.2369 2.0767 2.1136| | 25: 1.24 - 1.22 1.00 2734 148 0.2811 0.2527 2.0168 2.0718| | 26: 1.22 - 1.21 1.00 2727 135 0.2903 0.2179 2.0127 2.0071| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.2422 1.9924 1.9612| | 28: 1.19 - 1.18 1.00 2671 147 0.2968 0.2308 1.9757 1.9079| | 29: 1.18 - 1.16 1.00 2800 134 0.2960 0.2530 1.9518 1.985| | 30: 1.16 - 1.15 1.00 2740 148 0.3052 0.2776 1.9298 1.9304| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.63 0.76 0.23 1454.69| | 2: 3.57 - 2.84 2876 122 0.81 25.77 1.27 0.23 1454.69| | 3: 2.84 - 2.48 2833 165 0.74 31.71 1.24 0.24 1205.87| | 4: 2.47 - 2.25 2825 136 0.81 25.25 1.25 0.25 560.14| | 5: 2.25 - 2.09 2756 127 0.78 28.98 1.28 0.25 560.14| | 6: 2.09 - 1.97 2846 113 0.84 22.41 1.29 0.25 306.47| | 7: 1.97 - 1.87 2787 165 0.90 16.34 1.27 0.26 90.12| | 8: 1.87 - 1.79 2789 144 0.86 21.00 1.25 0.26 90.12| | 9: 1.79 - 1.72 2745 138 0.88 18.99 1.23 0.25 57.21| | 10: 1.72 - 1.66 2789 158 0.86 20.57 1.22 0.25 50.61| | 11: 1.66 - 1.61 2740 147 0.85 22.08 1.24 0.25 48.96| | 12: 1.61 - 1.56 2787 146 0.87 19.62 1.23 0.25 32.20| | 13: 1.56 - 1.52 2745 130 0.86 21.30 1.23 0.25 32.20| | 14: 1.52 - 1.48 2803 134 0.85 21.93 1.24 0.25 28.88| | 15: 1.48 - 1.45 2738 128 0.86 21.47 1.24 0.25 22.80| | 16: 1.45 - 1.42 2756 161 0.84 23.03 1.24 0.25 22.80| | 17: 1.42 - 1.39 2785 139 0.85 22.06 1.24 0.25 19.18| | 18: 1.39 - 1.36 2741 179 0.85 22.19 1.24 0.25 17.08| | 19: 1.36 - 1.34 2807 134 0.84 23.00 1.21 0.25 17.08| | 20: 1.34 - 1.32 2696 147 0.86 21.44 1.21 0.24 13.43| | 21: 1.32 - 1.30 2785 112 0.85 22.40 1.21 0.24 13.17| | 22: 1.29 - 1.27 2704 152 0.85 22.64 1.21 0.24 12.75| | 23: 1.27 - 1.26 2802 156 0.87 21.25 1.20 0.24 10.62| | 24: 1.26 - 1.24 2744 132 0.86 22.03 1.20 0.24 10.62| | 25: 1.24 - 1.22 2734 148 0.85 22.46 1.21 0.24 9.78| | 26: 1.22 - 1.21 2727 135 0.86 22.26 1.21 0.24 8.86| | 27: 1.21 - 1.19 2814 148 0.85 23.12 1.21 0.24 8.86| | 28: 1.19 - 1.18 2671 147 0.85 22.94 1.19 0.23 7.89| | 29: 1.18 - 1.16 2800 134 0.85 22.86 1.17 0.23 7.52| | 30: 1.16 - 1.15 2740 148 0.84 24.19 1.16 0.23 7.52| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 7.52 max = 1454.69 mean = 211.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.47| |phase err.(test): min = 0.00 max = 89.77 mean = 22.27| |-----------------------------------------------------------------------------| ----------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 0.289 1557 Z= 5.583 Angle : 5.285 17.694 2118 Z= 3.771 Chirality : 0.415 1.264 243 Planarity : 0.033 0.111 284 Dihedral : 13.679 78.546 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % 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: -2.54 (0.34), residues: 108 sheet: -0.48 (0.92), residues: 28 loop : -0.44 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.020 ARG A 5 TYR 0.091 0.043 TYR A 141 PHE 0.105 0.045 PHE A 162 HIS 0.081 0.050 HIS A 115 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= 0.2599 r_free= 0.1938 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790223 | | target function (ml) not normalized (work): 232442.341864 | | target function (ml) not normalized (free): 11821.779078 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2557 0.2599 0.1939 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2557 0.2599 0.1939 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1972 0.1939 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1990 0.1994 0.1950 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1625 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1632 0.1624 0.1785 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 0.3802 386.489 360.633 0.729 0.922 0.407 11.894-9.307 99.02 97 4 0.1803 613.919 593.469 1.014 0.923 0.390 9.237-7.194 100.00 213 7 0.2196 502.110 489.542 1.041 0.923 0.344 7.162-5.571 100.00 427 22 0.2223 376.806 364.554 1.013 0.923 0.330 5.546-4.326 100.00 867 58 0.1300 517.261 510.974 1.050 0.922 0.240 4.315-3.360 100.00 1859 96 0.1120 491.919 487.422 1.093 0.922 0.158 3.356-2.611 100.00 3867 181 0.1417 323.165 320.549 1.086 0.922 0.129 2.608-2.026 99.99 8198 413 0.1351 214.229 211.896 1.097 0.921 0.000 2.025-1.573 100.00 17313 902 0.1635 104.618 103.837 1.096 0.920 0.000 1.573-1.221 100.00 36679 1900 0.2042 46.392 45.119 1.089 0.918 0.000 1.221-1.150 99.97 13689 708 0.2559 29.230 27.080 1.066 0.916 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1624 r_free=0.1785 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.147283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2041.846519 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 0.1209 0.1465 0.0256 0.007 1.0 1.9 0.5 0.0 0 12.574 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.65 2.56 3.013 19.034 2041.847 0.017 12.44 15.48 3.04 3.105 19.459 2041.847 0.016 Individual atomic B min max mean iso aniso Overall: 8.54 118.44 20.87 2.87 0 1785 Protein: 8.54 118.44 17.77 2.87 0 1519 Water: 11.08 114.86 38.89 N/A 0 258 Other: 23.06 36.14 28.58 N/A 0 8 Chain A: 8.54 118.44 20.87 N/A 0 1785 Histogram: Values Number of atoms 8.54 - 19.53 1211 19.53 - 30.52 228 30.52 - 41.51 169 41.51 - 52.50 96 52.50 - 63.49 52 63.49 - 74.48 17 74.48 - 85.47 5 85.47 - 96.46 3 96.46 - 107.45 1 107.45 - 118.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1548 r_work=0.1248 r_free=0.1552 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1552 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 = 0.1558 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 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= 0.1558 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015326 | | target function (ls_wunit_k1) not normalized (work): 1276.642150 | | target function (ls_wunit_k1) not normalized (free): 114.407590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1558 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1699 0.1777 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1699 0.1777 n_refl.: 87593 overall B=0.18 to atoms: r(all,work,free)=0.1729 0.1728 0.1796 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1552 n_refl.: 87593 remove outliers: r(all,work,free)=0.1262 0.1247 0.1552 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 0.3579 299.759 280.757 0.634 1.002 0.380 11.894-9.307 99.02 97 4 0.1615 480.197 468.411 0.904 1.003 0.369 9.237-7.194 100.00 213 7 0.1790 392.742 388.934 0.945 1.003 0.314 7.162-5.571 100.00 427 22 0.1708 294.731 289.441 0.922 1.003 0.290 5.546-4.326 100.00 867 58 0.0908 404.593 402.024 0.947 1.003 0.209 4.315-3.360 100.00 1859 96 0.0767 384.770 383.970 0.992 1.003 0.179 3.356-2.611 100.00 3867 181 0.1012 252.774 252.074 0.997 1.002 0.119 2.608-2.026 99.99 8198 413 0.0974 167.566 167.034 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1221 81.831 82.013 1.015 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1676 36.287 35.729 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2376 22.863 21.353 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1552 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=0.1249 r_free=0.1554 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1554 | n_water=258 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1258 r_free=0.1550 | n_water=252 | time (s): 26.050 (total time: 28.490) Filter (q & B) r_work=0.1261 r_free=0.1549 | n_water=249 | time (s): 3.680 (total time: 32.170) Compute maps r_work=0.1261 r_free=0.1549 | n_water=249 | time (s): 1.780 (total time: 33.950) Filter (map) r_work=0.1287 r_free=0.1559 | n_water=233 | time (s): 3.720 (total time: 37.670) Find peaks r_work=0.1287 r_free=0.1559 | n_water=233 | time (s): 0.740 (total time: 38.410) Add new water r_work=0.1441 r_free=0.1715 | n_water=450 | time (s): 3.890 (total time: 42.300) Refine new water occ: r_work=0.1339 r_free=0.1569 adp: r_work=0.1261 r_free=0.1525 occ: r_work=0.1276 r_free=0.1506 adp: r_work=0.1240 r_free=0.1497 occ: r_work=0.1243 r_free=0.1482 adp: r_work=0.1233 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1480 r_work=0.1233 r_free=0.1480 | n_water=450 | time (s): 89.830 (total time: 132.130) Filter (q & B) r_work=0.1237 r_free=0.1480 | n_water=432 | time (s): 4.050 (total time: 136.180) Filter (dist only) r_work=0.1237 r_free=0.1480 | n_water=431 | time (s): 44.980 (total time: 181.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.985811 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1527.980583 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 0.1236 0.1503 0.0268 0.007 0.9 2.6 0.5 0.0 0 12.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 15.03 2.68 3.765 23.088 1527.981 0.015 12.03 14.74 2.71 4.116 22.953 1527.981 0.015 Individual atomic B min max mean iso aniso Overall: 8.77 114.23 23.19 2.59 198 1760 Protein: 8.77 114.23 17.64 2.59 0 1519 Water: 10.93 73.03 42.67 N/A 198 233 Other: 23.28 33.73 27.73 N/A 0 8 Chain A: 8.77 114.23 20.33 N/A 0 1760 Chain S: 17.73 73.03 48.66 N/A 198 0 Histogram: Values Number of atoms 8.77 - 19.32 1207 19.32 - 29.86 251 29.86 - 40.41 186 40.41 - 50.95 139 50.95 - 61.50 109 61.50 - 72.04 52 72.04 - 82.59 8 82.59 - 93.14 3 93.14 - 103.68 1 103.68 - 114.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1474 r_work=0.1203 r_free=0.1474 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1474 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1472 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 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= 0.1203 r_free= 0.1472 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013980 | | target function (ls_wunit_k1) not normalized (work): 1164.467259 | | target function (ls_wunit_k1) not normalized (free): 100.240310 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1203 0.1472 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1610 0.1606 0.1715 n_refl.: 87592 remove outliers: r(all,work,free)=0.1610 0.1606 0.1715 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1614 0.1610 0.1717 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1200 0.1465 n_refl.: 87592 remove outliers: r(all,work,free)=0.1211 0.1198 0.1465 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 0.3287 292.436 271.745 0.623 0.936 0.350 11.894-9.307 99.02 97 4 0.1531 480.197 476.754 0.984 0.937 0.330 9.237-7.194 100.00 213 7 0.1655 392.742 393.863 1.050 0.938 0.271 7.162-5.571 100.00 427 22 0.1464 294.731 290.852 1.003 0.938 0.263 5.546-4.326 100.00 867 58 0.0831 404.593 401.801 1.023 0.939 0.215 4.315-3.360 100.00 1859 96 0.0729 384.770 383.501 1.069 0.940 0.210 3.356-2.611 100.00 3867 181 0.0962 252.774 252.241 1.075 0.941 0.150 2.608-2.026 99.99 8198 413 0.0955 167.566 167.225 1.081 0.943 0.000 2.025-1.573 100.00 17313 902 0.1182 81.831 82.152 1.085 0.947 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.287 35.920 1.068 0.954 0.000 1.221-1.150 99.97 13689 708 0.2347 22.863 21.512 1.019 0.959 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0354 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1465 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1465 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1465 | n_water=431 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1198 r_free=0.1465 | n_water=429 | time (s): 39.570 (total time: 41.600) Filter (q & B) r_work=0.1198 r_free=0.1465 | n_water=429 | time (s): 1.050 (total time: 42.650) Compute maps r_work=0.1198 r_free=0.1465 | n_water=429 | time (s): 1.590 (total time: 44.240) Filter (map) r_work=0.1240 r_free=0.1476 | n_water=291 | time (s): 3.440 (total time: 47.680) Find peaks r_work=0.1240 r_free=0.1476 | n_water=291 | time (s): 0.690 (total time: 48.370) Add new water r_work=0.1376 r_free=0.1619 | n_water=483 | time (s): 2.840 (total time: 51.210) Refine new water occ: r_work=0.1269 r_free=0.1521 adp: r_work=0.1270 r_free=0.1523 occ: r_work=0.1244 r_free=0.1494 adp: r_work=0.1241 r_free=0.1496 occ: r_work=0.1227 r_free=0.1473 adp: r_work=0.1220 r_free=0.1472 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1472 r_work=0.1220 r_free=0.1472 | n_water=483 | time (s): 257.550 (total time: 308.760) Filter (q & B) r_work=0.1223 r_free=0.1473 | n_water=452 | time (s): 3.710 (total time: 312.470) Filter (dist only) r_work=0.1223 r_free=0.1473 | n_water=452 | time (s): 37.290 (total time: 349.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.049070 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.843852 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 0.1226 0.1443 0.0217 0.006 0.9 1.9 0.5 0.0 0 1.025 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.43 2.17 3.606 22.112 47.844 3.727 12.09 13.97 1.88 4.085 21.932 47.844 3.654 Individual atomic B min max mean iso aniso Overall: 9.22 109.83 21.74 2.32 222 1757 Protein: 9.22 109.83 17.20 2.32 0 1519 Water: 11.47 71.85 36.92 N/A 222 230 Other: 20.24 30.17 25.55 N/A 0 8 Chain A: 9.22 109.83 19.84 N/A 0 1757 Chain S: 15.54 62.46 36.78 N/A 222 0 Histogram: Values Number of atoms 9.22 - 19.28 1233 19.28 - 29.34 277 29.34 - 39.40 210 39.40 - 49.46 149 49.46 - 59.53 77 59.53 - 69.59 21 69.59 - 79.65 6 79.65 - 89.71 3 89.71 - 99.77 1 99.77 - 109.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1397 r_work=0.1210 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1398 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1394 target_work(ml) = 3.651 | | 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= 0.1204 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651348 | | target function (ml) not normalized (work): 304128.071226 | | target function (ml) not normalized (free): 16054.537051 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1394 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1529 0.1528 0.1588 n_refl.: 87588 remove outliers: r(all,work,free)=0.1529 0.1528 0.1588 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1527 0.1526 0.1587 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1196 0.1368 n_refl.: 87588 remove outliers: r(all,work,free)=0.1201 0.1192 0.1368 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3808 284.343 261.529 0.467 0.999 0.295 11.894-9.307 97.06 95 4 0.2443 473.567 461.482 0.855 1.001 0.277 9.237-7.194 98.64 210 7 0.2333 386.281 388.689 0.947 1.002 0.176 7.162-5.571 100.00 427 22 0.1965 294.731 285.708 0.911 1.002 0.169 5.546-4.326 100.00 867 58 0.1101 404.593 400.003 0.952 1.002 0.165 4.315-3.360 100.00 1859 96 0.0928 384.770 382.033 0.994 1.002 0.163 3.356-2.611 100.00 3867 181 0.1145 252.774 250.991 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1036 167.566 166.572 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1014 81.831 81.952 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1293 36.287 35.849 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.863 21.461 0.978 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0295 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1368 | n_water=452 | time (s): 1.600 (total time: 1.600) Filter (dist) r_work=0.1192 r_free=0.1369 | n_water=451 | time (s): 39.660 (total time: 41.260) Filter (q & B) r_work=0.1192 r_free=0.1369 | n_water=450 | time (s): 2.710 (total time: 43.970) Compute maps r_work=0.1192 r_free=0.1369 | n_water=450 | time (s): 1.340 (total time: 45.310) Filter (map) r_work=0.1219 r_free=0.1391 | n_water=312 | time (s): 3.380 (total time: 48.690) Find peaks r_work=0.1219 r_free=0.1391 | n_water=312 | time (s): 0.680 (total time: 49.370) Add new water r_work=0.1288 r_free=0.1453 | n_water=482 | time (s): 3.210 (total time: 52.580) Refine new water occ: r_work=0.1211 r_free=0.1364 adp: r_work=0.1211 r_free=0.1367 occ: r_work=0.1194 r_free=0.1348 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1183 r_free=0.1339 adp: r_work=0.1179 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1340 r_work=0.1179 r_free=0.1340 | n_water=482 | time (s): 240.740 (total time: 293.320) Filter (q & B) r_work=0.1186 r_free=0.1350 | n_water=445 | time (s): 3.330 (total time: 296.650) Filter (dist only) r_work=0.1186 r_free=0.1349 | n_water=444 | time (s): 37.220 (total time: 333.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.938926 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.284490 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 0.1191 0.1365 0.0174 0.006 1.0 1.9 0.5 0.0 0 0.969 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.65 1.74 3.420 21.493 50.284 3.639 11.77 13.56 1.79 3.778 21.384 50.284 3.625 Individual atomic B min max mean iso aniso Overall: 9.26 105.00 21.27 2.18 217 1754 Protein: 9.26 105.00 16.95 2.18 0 1519 Water: 11.53 70.55 36.00 N/A 217 227 Other: 20.48 28.72 24.41 N/A 0 8 Chain A: 9.26 105.00 19.49 N/A 0 1754 Chain S: 14.92 56.05 35.67 N/A 217 0 Histogram: Values Number of atoms 9.26 - 18.83 1226 18.83 - 28.41 286 28.41 - 37.98 201 37.98 - 47.55 138 47.55 - 57.13 84 57.13 - 66.70 22 66.70 - 76.28 9 76.28 - 85.85 2 85.85 - 95.43 1 95.43 - 105.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1177 r_free=0.1356 r_work=0.1178 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1178 r_free = 0.1357 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1170 r_free = 0.1349 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1170 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621944 | | target function (ml) not normalized (work): 301649.948987 | | target function (ml) not normalized (free): 15940.725584 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1179 0.1170 0.1349 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1499 0.1498 0.1554 n_refl.: 87580 remove outliers: r(all,work,free)=0.1499 0.1498 0.1554 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1497 0.1553 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1180 0.1171 0.1353 n_refl.: 87580 remove outliers: r(all,work,free)=0.1178 0.1169 0.1353 n_refl.: 87576 ======================== 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 0.3919 284.343 253.619 0.459 0.998 0.314 11.894-9.307 94.12 92 4 0.2227 476.846 455.952 0.838 1.001 0.310 9.237-7.194 98.18 209 7 0.2377 387.363 381.089 0.927 1.001 0.140 7.162-5.571 100.00 427 22 0.2091 294.731 283.883 0.916 1.001 0.140 5.546-4.326 100.00 867 58 0.1116 404.593 400.293 0.962 1.001 0.150 4.315-3.360 100.00 1859 96 0.0937 384.770 382.446 1.004 1.002 0.150 3.356-2.611 100.00 3867 181 0.1138 252.774 251.111 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1010 167.566 166.743 1.022 1.001 0.000 2.025-1.573 100.00 17313 902 0.0965 81.831 82.126 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.287 35.904 1.028 1.000 0.000 1.221-1.150 99.97 13689 708 0.2127 22.863 21.421 0.981 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1169 r_free=0.1353 After: r_work=0.1170 r_free=0.1353 ================================== NQH flips ================================== r_work=0.1170 r_free=0.1353 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=0.1170 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1170 r_free=0.1353 | n_water=444 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1170 r_free=0.1353 | n_water=444 | time (s): 37.710 (total time: 39.620) Filter (q & B) r_work=0.1170 r_free=0.1351 | n_water=441 | time (s): 3.050 (total time: 42.670) Compute maps r_work=0.1170 r_free=0.1351 | n_water=441 | time (s): 1.860 (total time: 44.530) Filter (map) r_work=0.1192 r_free=0.1358 | n_water=338 | time (s): 3.700 (total time: 48.230) Find peaks r_work=0.1192 r_free=0.1358 | n_water=338 | time (s): 0.690 (total time: 48.920) Add new water r_work=0.1239 r_free=0.1399 | n_water=485 | time (s): 2.670 (total time: 51.590) Refine new water occ: r_work=0.1178 r_free=0.1340 adp: r_work=0.1178 r_free=0.1344 occ: r_work=0.1168 r_free=0.1332 adp: r_work=0.1166 r_free=0.1334 occ: r_work=0.1161 r_free=0.1329 adp: r_work=0.1157 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1157 r_free=0.1330 r_work=0.1157 r_free=0.1330 | n_water=485 | time (s): 218.400 (total time: 269.990) Filter (q & B) r_work=0.1164 r_free=0.1334 | n_water=447 | time (s): 2.620 (total time: 272.610) Filter (dist only) r_work=0.1164 r_free=0.1333 | n_water=446 | time (s): 38.280 (total time: 310.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.904231 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.891754 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 0.1356 0.0163 0.007 1.1 3.2 0.5 0.0 0 0.952 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.56 1.63 3.299 21.182 51.892 3.633 11.97 13.58 1.61 3.648 21.096 51.892 3.625 Individual atomic B min max mean iso aniso Overall: 9.28 100.58 21.05 2.01 219 1754 Protein: 9.28 100.58 16.68 2.02 0 1519 Water: 11.50 68.94 35.87 N/A 219 227 Other: 19.76 27.39 23.42 N/A 0 8 Chain A: 9.28 100.58 19.21 N/A 0 1754 Chain S: 13.56 59.33 35.75 N/A 219 0 Histogram: Values Number of atoms 9.28 - 18.41 1212 18.41 - 27.54 288 27.54 - 36.67 209 36.67 - 45.80 135 45.80 - 54.93 83 54.93 - 64.06 31 64.06 - 73.19 10 73.19 - 82.32 2 82.32 - 91.45 1 91.45 - 100.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1358 r_work=0.1197 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1355 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623999 | | target function (ml) not normalized (work): 301806.612946 | | target function (ml) not normalized (free): 15957.412983 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1398 0.1376 5.6912 5.6029| | 2: 3.57 - 2.84 1.00 2888 124 0.1112 0.1337 5.182 5.2263| | 3: 2.83 - 2.48 1.00 2820 163 0.1232 0.1274 4.9883 5.0153| | 4: 2.47 - 2.25 1.00 2825 136 0.1023 0.1170 4.6902 4.7404| | 5: 2.25 - 2.09 1.00 2756 127 0.0982 0.1098 4.6285 4.7064| | 6: 2.09 - 1.97 1.00 2846 113 0.0976 0.1228 4.3482 4.4803| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1248 4.0823 4.2009| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1249 4.0025 4.0882| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1326 3.7275 3.9119| | 10: 1.72 - 1.66 1.00 2831 160 0.1004 0.1258 3.6431 3.7743| | 11: 1.66 - 1.61 1.00 2712 147 0.0965 0.1108 3.5789 3.6312| | 12: 1.61 - 1.56 1.00 2773 144 0.0920 0.1144 3.353 3.4817| | 13: 1.56 - 1.52 1.00 2745 130 0.0995 0.1070 3.3488 3.4476| | 14: 1.52 - 1.48 1.00 2803 134 0.0992 0.1123 3.2675 3.349| | 15: 1.48 - 1.45 1.00 2738 128 0.1015 0.1341 3.1761 3.326| | 16: 1.45 - 1.42 1.00 2756 161 0.1072 0.1271 3.1571 3.2642| | 17: 1.42 - 1.39 1.00 2785 139 0.1121 0.1314 3.123 3.2468| | 18: 1.39 - 1.36 1.00 2741 179 0.1143 0.1390 3.088 3.2863| | 19: 1.36 - 1.34 1.00 2807 134 0.1220 0.1625 3.1017 3.279| | 20: 1.34 - 1.32 1.00 2696 147 0.1319 0.1462 3.0935 3.1389| | 21: 1.32 - 1.30 1.00 2785 112 0.1409 0.1628 3.0888 3.1691| | 22: 1.29 - 1.27 1.00 2704 152 0.1462 0.1901 3.0872 3.2875| | 23: 1.27 - 1.26 1.00 2802 156 0.1571 0.1878 3.1051 3.2261| | 24: 1.26 - 1.24 1.00 2744 132 0.1626 0.1773 3.099 3.2071| | 25: 1.24 - 1.22 1.00 2733 148 0.1791 0.2294 3.1122 3.2881| | 26: 1.22 - 1.21 1.00 2727 135 0.1863 0.1802 3.127 3.2059| | 27: 1.21 - 1.19 1.00 2814 148 0.2012 0.2110 3.1435 3.16| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2312 3.1437 3.1727| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2361 3.1301 3.2239| | 30: 1.16 - 1.15 1.00 2739 148 0.2380 0.2500 3.1199 3.169| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.61 1.00 0.97 5793.54| | 2: 3.57 - 2.84 2888 124 0.93 12.69 1.01 0.97 5793.54| | 3: 2.83 - 2.48 2820 163 0.89 16.77 0.99 0.97 4873.74| | 4: 2.47 - 2.25 2825 136 0.91 14.14 1.00 0.97 2501.85| | 5: 2.25 - 2.09 2756 127 0.90 16.28 1.01 0.97 2501.85| | 6: 2.09 - 1.97 2846 113 0.92 13.44 1.02 0.97 1499.74| | 7: 1.97 - 1.87 2787 165 0.94 11.01 1.02 0.97 645.08| | 8: 1.87 - 1.79 2789 144 0.91 14.57 1.00 0.97 645.08| | 9: 1.79 - 1.72 2745 138 0.93 11.60 0.98 0.97 349.38| | 10: 1.72 - 1.66 2831 160 0.93 12.49 0.98 0.97 290.17| | 11: 1.66 - 1.61 2712 147 0.93 13.09 0.98 0.97 276.85| | 12: 1.61 - 1.56 2773 144 0.95 9.72 0.99 0.97 151.26| | 13: 1.56 - 1.52 2745 130 0.94 11.30 1.02 0.97 151.26| | 14: 1.52 - 1.48 2803 134 0.94 11.42 1.02 0.97 135.06| | 15: 1.48 - 1.45 2738 128 0.95 10.50 1.01 0.98 105.40| | 16: 1.45 - 1.42 2756 161 0.94 11.70 1.02 0.98 105.40| | 17: 1.42 - 1.39 2785 139 0.94 11.61 1.01 0.98 95.41| | 18: 1.39 - 1.36 2741 179 0.94 11.96 1.01 0.98 89.62| | 19: 1.36 - 1.34 2807 134 0.94 12.46 1.00 0.98 89.62| | 20: 1.34 - 1.32 2696 147 0.94 12.50 0.99 0.96 84.13| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.99 0.96 83.74| | 22: 1.29 - 1.27 2704 152 0.93 13.98 0.98 0.96 83.86| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.98 0.94 84.44| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.94 84.44| | 25: 1.24 - 1.22 2733 148 0.91 16.43 0.96 0.94 85.88| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.03 0.93 87.48| | 27: 1.21 - 1.19 2814 148 0.89 18.86 1.02 0.93 87.48| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.93 90.89| | 29: 1.18 - 1.16 2800 134 0.88 20.69 0.99 0.92 92.17| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.92 92.17| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 83.74 max = 5793.54 mean = 923.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 14.04| |phase err.(test): min = 0.00 max = 88.27 mean = 14.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1193 0.1355 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1516 0.1515 0.1560 n_refl.: 87576 remove outliers: r(all,work,free)=0.1516 0.1515 0.1560 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1514 0.1513 0.1558 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1193 0.1355 n_refl.: 87576 remove outliers: r(all,work,free)=0.1200 0.1192 0.1355 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.4023 286.932 250.665 0.436 1.000 0.306 11.894-9.307 93.14 91 4 0.2336 470.358 448.303 0.848 1.002 0.296 9.237-7.194 97.27 207 7 0.2434 384.866 381.275 0.909 1.002 0.130 7.162-5.571 100.00 427 22 0.2188 294.731 283.311 0.900 1.002 0.129 5.546-4.326 100.00 867 58 0.1182 404.593 399.970 0.952 1.002 0.128 4.315-3.360 100.00 1859 96 0.0985 384.770 382.264 0.994 1.002 0.127 3.356-2.611 100.00 3867 181 0.1188 252.774 250.871 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1034 167.566 166.626 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.831 82.059 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1226 36.287 35.921 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2116 22.863 21.483 0.980 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0279 ================= 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 : 0.2599 0.1938 0.083 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_nqh: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_weight: 0.1624 0.1785 0.083 5.285 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1209 0.1465 0.007 0.962 9.0 119.5 20.1 258 0.124 1_adp: 0.1244 0.1548 0.007 0.962 8.5 118.4 20.9 258 0.124 1_regHadp: 0.1248 0.1552 0.007 0.962 8.5 118.4 20.9 258 0.124 1_occ: 0.1247 0.1558 0.007 0.962 8.5 118.4 20.9 258 0.124 2_bss: 0.1247 0.1552 0.007 0.962 8.7 118.6 21.0 258 0.124 2_settarget: 0.1247 0.1552 0.007 0.962 8.7 118.6 21.0 258 0.124 2_updatecdl: 0.1247 0.1552 0.007 0.959 8.7 118.6 21.0 258 0.124 2_nqh: 0.1249 0.1554 0.007 0.959 8.7 118.6 21.0 258 0.127 2_sol: 0.1237 0.1480 0.007 0.959 8.7 118.6 23.4 431 n/a 2_weight: 0.1237 0.1480 0.007 0.959 8.7 118.6 23.4 431 n/a 2_xyzrec: 0.1236 0.1503 0.007 0.879 8.7 118.6 23.4 431 n/a 2_adp: 0.1203 0.1474 0.007 0.879 8.8 114.2 23.2 431 n/a 2_regHadp: 0.1203 0.1474 0.007 0.879 8.8 114.2 23.2 431 n/a 2_occ: 0.1203 0.1472 0.007 0.879 8.8 114.2 23.2 431 n/a 3_bss: 0.1198 0.1465 0.007 0.879 8.8 114.3 23.2 431 n/a 3_settarget: 0.1198 0.1465 0.007 0.879 8.8 114.3 23.2 431 n/a 3_updatecdl: 0.1198 0.1465 0.007 0.879 8.8 114.3 23.2 431 n/a 3_nqh: 0.1198 0.1465 0.007 0.879 8.8 114.3 23.2 431 n/a 3_sol: 0.1223 0.1473 0.007 0.879 8.8 114.3 22.1 452 n/a 3_weight: 0.1223 0.1473 0.007 0.879 8.8 114.3 22.1 452 n/a 3_xyzrec: 0.1226 0.1443 0.006 0.928 8.8 114.3 22.1 452 n/a 3_adp: 0.1209 0.1397 0.006 0.928 9.2 109.8 21.7 452 n/a 3_regHadp: 0.1210 0.1398 0.006 0.928 9.2 109.8 21.7 452 n/a 3_occ: 0.1204 0.1394 0.006 0.928 9.2 109.8 21.7 452 n/a 4_bss: 0.1192 0.1368 0.006 0.928 9.2 109.8 21.7 452 n/a 4_settarget: 0.1192 0.1368 0.006 0.928 9.2 109.8 21.7 452 n/a 4_updatecdl: 0.1192 0.1368 0.006 0.929 9.2 109.8 21.7 452 n/a 4_nqh: 0.1192 0.1368 0.006 0.929 9.2 109.8 21.7 452 n/a 4_sol: 0.1186 0.1349 0.006 0.929 9.2 109.8 21.5 444 n/a 4_weight: 0.1186 0.1349 0.006 0.929 9.2 109.8 21.5 444 n/a 4_xyzrec: 0.1191 0.1365 0.006 0.960 9.2 109.8 21.5 444 n/a 4_adp: 0.1177 0.1356 0.006 0.960 9.3 105.0 21.3 444 n/a 4_regHadp: 0.1178 0.1357 0.006 0.960 9.3 105.0 21.3 444 n/a 4_occ: 0.1170 0.1349 0.006 0.960 9.3 105.0 21.3 444 n/a 5_bss: 0.1169 0.1353 0.006 0.960 9.3 105.0 21.3 444 n/a 5_settarget: 0.1169 0.1353 0.006 0.960 9.3 105.0 21.3 444 n/a 5_updatecdl: 0.1169 0.1353 0.006 0.959 9.3 105.0 21.3 444 n/a 5_setrh: 0.1170 0.1353 0.006 0.959 9.3 105.0 21.3 444 n/a 5_nqh: 0.1170 0.1353 0.006 0.959 9.3 105.0 21.3 444 n/a 5_sol: 0.1164 0.1333 0.006 0.959 9.3 105.0 21.2 446 n/a 5_weight: 0.1164 0.1333 0.006 0.959 9.3 105.0 21.2 446 n/a 5_xyzrec: 0.1193 0.1356 0.007 1.064 9.3 105.0 21.2 446 n/a 5_adp: 0.1197 0.1358 0.007 1.064 9.3 100.6 21.0 446 n/a 5_regHadp: 0.1197 0.1358 0.007 1.064 9.3 100.6 21.0 446 n/a 5_occ: 0.1193 0.1355 0.007 1.064 9.3 100.6 21.0 446 n/a end: 0.1192 0.1355 0.007 1.064 9.3 100.6 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8498250_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8498250_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0400 Refinement macro-cycles (run) : 3632.7700 Write final files (write_after_run_outputs) : 58.1400 Total : 3695.9500 Total CPU time: 62.23 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:13:27 PST -0800 (1735452807.68 s) Start R-work = 0.1624, R-free = 0.1785 Final R-work = 0.1192, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 3822.84 seconds wall clock time: 68 minutes 29.80 seconds (4109.80 seconds total)