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_5352376.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.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" } 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: 2.18, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 276.7 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 575 0.92 - 1.18: 1088 1.18 - 1.45: 716 1.45 - 1.71: 753 1.71 - 1.97: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.411 0.128 5.40e-03 3.43e+04 5.60e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.778 -0.255 1.24e-02 6.50e+03 4.23e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.683 -0.220 1.08e-02 8.57e+03 4.16e+02 bond pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 1.236 1.469 -0.233 1.16e-02 7.43e+03 4.04e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.237 1.033 0.204 1.10e-02 8.26e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2950 4.24 - 8.47: 1875 8.47 - 12.71: 757 12.71 - 16.94: 167 16.94 - 21.18: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 137.17 -15.08 1.04e+00 9.25e-01 2.10e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.15 138.02 -15.87 1.14e+00 7.69e-01 1.94e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 129.31 -8.89 6.40e-01 2.44e+00 1.93e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 122.99 108.81 14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" O BLYS A 132 " pdb=" C BLYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.15 136.49 -14.34 1.14e+00 7.69e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 949 18.33 - 36.66: 117 36.66 - 54.98: 36 54.98 - 73.31: 8 73.31 - 91.64: 1 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+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 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.197: 107 0.197 - 0.392: 61 0.392 - 0.587: 46 0.587 - 0.782: 20 0.782 - 0.977: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.78 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.072 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.040 2.00e-02 2.50e+03 5.68e-02 9.67e+01 pdb=" CG TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.046 2.00e-02 2.50e+03 5.34e-02 8.55e+01 pdb=" CG ATYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.057 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.075 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.084 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1151 2.33 - 2.90: 8199 2.90 - 3.47: 10484 3.47 - 4.03: 15169 4.03 - 4.60: 21583 Nonbonded interactions: 56586 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.799 2.100 nonbonded pdb=" HB3 LYS A 188 " pdb=" HE2 LYS A 188 " model vdw 1.808 2.440 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.821 2.100 ... (remaining 56581 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_5352376_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= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794328 | | target function (ml) not normalized (work): 232784.303686 | | target function (ml) not normalized (free): 11790.999980 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3019 0.2115 7.0268 4.9462| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1840 4.3523 4.354| | 3: 2.84 - 2.48 1.00 2833 165 0.2355 0.1677 4.1354 4.16| | 4: 2.47 - 2.25 1.00 2825 136 0.2325 0.1540 3.8436 3.8339| | 5: 2.25 - 2.09 1.00 2756 127 0.2540 0.1690 3.8091 3.8245| | 6: 2.09 - 1.97 1.00 2846 113 0.2567 0.1736 3.4844 3.5406| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1874 3.1432 3.2349| | 8: 1.87 - 1.79 1.00 2789 144 0.2460 0.1806 3.0719 3.0883| | 9: 1.79 - 1.72 1.00 2745 138 0.2402 0.1782 2.9013 2.9017| | 10: 1.72 - 1.66 1.00 2789 158 0.2373 0.1902 2.7962 2.844| | 11: 1.66 - 1.61 1.00 2740 147 0.2555 0.1786 2.7534 2.711| | 12: 1.61 - 1.56 1.00 2787 146 0.2510 0.2045 2.6112 2.6798| | 13: 1.56 - 1.52 1.00 2745 130 0.2564 0.2010 2.5779 2.6338| | 14: 1.52 - 1.48 1.00 2803 134 0.2539 0.1964 2.504 2.5197| | 15: 1.48 - 1.45 1.00 2738 128 0.2577 0.2219 2.4267 2.547| | 16: 1.45 - 1.42 1.00 2756 161 0.2610 0.1923 2.3974 2.3719| | 17: 1.42 - 1.39 1.00 2785 139 0.2758 0.2156 2.3391 2.3893| | 18: 1.39 - 1.36 1.00 2741 179 0.2742 0.2151 2.2712 2.2997| | 19: 1.36 - 1.34 1.00 2807 134 0.2647 0.2317 2.2359 2.2668| | 20: 1.34 - 1.32 1.00 2696 147 0.2710 0.2383 2.2054 2.2921| | 21: 1.32 - 1.30 1.00 2785 112 0.2711 0.2233 2.1803 2.1545| | 22: 1.29 - 1.27 1.00 2704 152 0.2794 0.2419 2.1545 2.1745| | 23: 1.27 - 1.26 1.00 2802 156 0.2807 0.2679 2.1115 2.2203| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2564 2.0764 2.1275| | 25: 1.24 - 1.22 1.00 2734 148 0.2834 0.2479 2.0463 2.0708| | 26: 1.22 - 1.21 1.00 2727 135 0.2831 0.2249 2.0121 2.0639| | 27: 1.21 - 1.19 1.00 2814 148 0.3045 0.2621 2.0215 1.9841| | 28: 1.19 - 1.18 1.00 2671 147 0.3015 0.2896 1.9984 1.9764| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2811 1.9605 2.0634| | 30: 1.16 - 1.15 1.00 2740 148 0.3045 0.2711 1.9287 1.9271| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1506.69| | 2: 3.57 - 2.84 2876 122 0.80 26.25 1.27 0.23 1506.69| | 3: 2.84 - 2.48 2833 165 0.74 32.19 1.24 0.24 1249.31| | 4: 2.47 - 2.25 2825 136 0.81 25.60 1.25 0.25 581.36| | 5: 2.25 - 2.09 2756 127 0.77 29.58 1.29 0.25 581.36| | 6: 2.09 - 1.97 2846 113 0.83 22.93 1.29 0.25 317.44| | 7: 1.97 - 1.87 2787 165 0.90 16.62 1.28 0.26 92.35| | 8: 1.87 - 1.79 2789 144 0.86 21.25 1.25 0.26 92.35| | 9: 1.79 - 1.72 2745 138 0.88 18.10 1.23 0.26 54.08| | 10: 1.72 - 1.66 2789 158 0.87 19.68 1.22 0.26 46.42| | 11: 1.66 - 1.61 2740 147 0.86 21.00 1.24 0.25 44.81| | 12: 1.61 - 1.56 2787 146 0.89 17.90 1.24 0.25 28.50| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.50| | 14: 1.52 - 1.48 2803 134 0.87 20.24 1.23 0.25 25.63| | 15: 1.48 - 1.45 2738 128 0.87 20.02 1.23 0.25 20.36| | 16: 1.45 - 1.42 2756 161 0.86 21.14 1.23 0.25 20.36| | 17: 1.42 - 1.39 2785 139 0.86 20.91 1.25 0.25 17.50| | 18: 1.39 - 1.36 2741 179 0.86 21.38 1.24 0.25 15.85| | 19: 1.36 - 1.34 2807 134 0.85 21.99 1.22 0.25 15.85| | 20: 1.34 - 1.32 2696 147 0.87 21.05 1.21 0.25 13.27| | 21: 1.32 - 1.30 2785 112 0.86 21.92 1.19 0.25 13.09| | 22: 1.29 - 1.27 2704 152 0.85 22.72 1.21 0.24 12.78| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.22 0.24 11.20| | 24: 1.26 - 1.24 2744 132 0.85 22.81 1.20 0.24 11.20| | 25: 1.24 - 1.22 2734 148 0.84 23.72 1.20 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 23.82 1.19 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.83 24.85 1.19 0.23 9.13| | 29: 1.18 - 1.16 2800 134 0.83 25.16 1.16 0.23 8.84| | 30: 1.16 - 1.15 2740 148 0.81 26.54 1.16 0.23 8.84| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.84 max = 1506.69 mean = 218.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.52| |phase err.(test): min = 0.00 max = 89.38 mean = 22.66| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.255 1557 Z= 5.584 Angle : 5.278 20.057 2118 Z= 3.756 Chirality : 0.368 0.977 243 Planarity : 0.030 0.080 284 Dihedral : 13.689 91.641 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.97 % Favored : 93.79 % Cbeta Deviations : 27.03 % 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: -2.80 (0.44), residues: 224 helix: -2.46 (0.36), residues: 108 sheet: -1.01 (0.72), residues: 38 loop : -0.95 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 27 TYR 0.085 0.033 TYR A 139 PHE 0.108 0.042 PHE A 119 HIS 0.053 0.025 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2611 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794328 | | target function (ml) not normalized (work): 232784.303686 | | target function (ml) not normalized (free): 11790.999980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2611 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2611 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1990 0.1994 0.1961 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2013 0.2018 0.1974 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1656 0.1650 0.1780 n_refl.: 87594 remove outliers: r(all,work,free)=0.1656 0.1649 0.1780 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 0.3829 386.618 358.733 0.669 1.003 0.407 11.894-9.307 99.02 97 4 0.1775 614.124 594.023 0.927 1.004 0.390 9.237-7.194 100.00 213 7 0.2114 502.278 494.448 0.961 1.004 0.344 7.162-5.571 100.00 427 22 0.2172 376.932 364.723 0.934 1.004 0.293 5.546-4.326 100.00 867 58 0.1286 517.434 511.358 0.959 1.004 0.223 4.315-3.360 100.00 1859 96 0.1155 492.084 488.068 1.003 1.004 0.189 3.356-2.611 100.00 3867 181 0.1451 323.273 320.175 0.997 1.003 0.043 2.608-2.026 99.99 8198 413 0.1379 214.301 212.017 1.008 1.002 0.000 2.025-1.573 100.00 17313 902 0.1656 104.653 103.911 1.011 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2078 46.408 45.072 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2602 29.240 26.974 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0441 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1649 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1651 r_free=0.1783 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.724661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2003.047069 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 0.1461 0.0251 0.007 1.0 1.0 0.5 0.0 0 12.862 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.61 2.51 3.013 19.051 2003.047 0.017 12.45 15.38 2.94 3.431 19.692 2003.047 0.016 Individual atomic B min max mean iso aniso Overall: 8.60 118.84 21.29 2.90 0 1785 Protein: 8.60 118.84 18.10 2.90 0 1519 Water: 11.17 114.49 39.78 N/A 0 258 Other: 23.35 37.72 30.20 N/A 0 8 Chain A: 8.60 118.84 21.29 N/A 0 1785 Histogram: Values Number of atoms 8.60 - 19.63 1203 19.63 - 30.65 229 30.65 - 41.67 161 41.67 - 52.70 100 52.70 - 63.72 57 63.72 - 74.75 20 74.75 - 85.77 8 85.77 - 96.79 2 96.79 - 107.82 2 107.82 - 118.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1538 r_work=0.1249 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1544 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 = 0.1250 r_free = 0.1546 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= 0.1250 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015430 | | target function (ls_wunit_k1) not normalized (work): 1285.251653 | | target function (ls_wunit_k1) not normalized (free): 114.146089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1250 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1712 0.1712 0.1773 n_refl.: 87593 remove outliers: r(all,work,free)=0.1712 0.1712 0.1773 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1733 0.1733 0.1787 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1248 0.1538 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1538 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3598 294.527 278.193 0.677 0.922 0.373 11.894-9.307 99.02 97 4 0.1626 477.264 465.107 0.981 0.922 0.368 9.237-7.194 100.00 213 7 0.1812 390.343 384.785 1.030 0.923 0.340 7.162-5.571 100.00 427 22 0.1715 292.931 287.362 1.001 0.923 0.253 5.546-4.326 100.00 867 58 0.0914 402.121 399.463 1.027 0.924 0.199 4.315-3.360 100.00 1859 96 0.0771 382.420 381.480 1.078 0.925 0.180 3.356-2.611 100.00 3867 181 0.1020 251.230 250.478 1.079 0.927 0.052 2.608-2.026 99.99 8198 413 0.0986 166.543 165.881 1.088 0.930 0.000 2.025-1.573 100.00 17313 902 0.1221 81.331 81.478 1.087 0.936 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.065 35.524 1.063 0.945 0.000 1.221-1.150 99.97 13689 708 0.2363 22.724 21.257 1.017 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=0.0497 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1249 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1249 r_free=0.1540 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1259 r_free=0.1541 | n_water=251 | time (s): 26.070 (total time: 28.470) Filter (q & B) r_work=0.1263 r_free=0.1541 | n_water=248 | time (s): 3.810 (total time: 32.280) Compute maps r_work=0.1263 r_free=0.1541 | n_water=248 | time (s): 1.800 (total time: 34.080) Filter (map) r_work=0.1279 r_free=0.1544 | n_water=236 | time (s): 3.850 (total time: 37.930) Find peaks r_work=0.1279 r_free=0.1544 | n_water=236 | time (s): 0.710 (total time: 38.640) Add new water r_work=0.1427 r_free=0.1684 | n_water=452 | time (s): 3.740 (total time: 42.380) Refine new water occ: r_work=0.1335 r_free=0.1564 adp: r_work=0.1259 r_free=0.1510 occ: r_work=0.1270 r_free=0.1506 adp: r_work=0.1237 r_free=0.1490 occ: r_work=0.1240 r_free=0.1485 adp: r_work=0.1231 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1483 r_work=0.1231 r_free=0.1483 | n_water=452 | time (s): 79.570 (total time: 121.950) Filter (q & B) r_work=0.1238 r_free=0.1491 | n_water=424 | time (s): 3.990 (total time: 125.940) Filter (dist only) r_work=0.1238 r_free=0.1491 | n_water=424 | time (s): 39.650 (total time: 165.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.300868 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1590.417715 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1507 0.0277 0.007 0.9 1.6 0.5 0.0 0 12.650 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.07 2.77 3.841 23.380 1590.418 0.015 11.96 14.76 2.80 4.348 23.151 1590.418 0.014 Individual atomic B min max mean iso aniso Overall: 8.76 113.97 23.23 2.66 188 1763 Protein: 8.76 113.97 17.81 2.66 0 1519 Water: 11.12 73.60 42.61 N/A 188 236 Other: 20.62 33.66 26.48 N/A 0 8 Chain A: 8.76 113.97 20.55 N/A 0 1763 Chain S: 18.58 73.60 48.40 N/A 188 0 Histogram: Values Number of atoms 8.76 - 19.28 1207 19.28 - 29.80 242 29.80 - 40.32 188 40.32 - 50.84 137 50.84 - 61.36 109 61.36 - 71.88 54 71.88 - 82.41 7 82.41 - 92.93 3 92.93 - 103.45 2 103.45 - 113.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1476 r_work=0.1196 r_free=0.1476 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1476 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1469 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1198 r_free= 0.1469 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013781 | | target function (ls_wunit_k1) not normalized (work): 1147.916605 | | target function (ls_wunit_k1) not normalized (free): 99.770656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1198 0.1469 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1615 0.1613 0.1696 n_refl.: 87591 remove outliers: r(all,work,free)=0.1615 0.1613 0.1696 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1619 0.1617 0.1698 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1196 0.1467 n_refl.: 87591 remove outliers: r(all,work,free)=0.1209 0.1195 0.1467 n_refl.: 87589 ======================== 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 92.71 84 5 0.3378 293.879 270.717 0.620 0.936 0.360 11.894-9.307 99.02 97 4 0.1525 477.264 473.548 0.972 0.937 0.360 9.237-7.194 100.00 213 7 0.1727 390.343 389.257 1.044 0.937 0.310 7.162-5.571 100.00 427 22 0.1518 292.931 288.982 1.003 0.938 0.231 5.546-4.326 100.00 867 58 0.0796 402.121 399.195 1.021 0.938 0.210 4.315-3.360 100.00 1859 96 0.0707 382.420 381.405 1.070 0.939 0.200 3.356-2.611 100.00 3867 181 0.0961 251.230 250.665 1.077 0.939 0.067 2.608-2.026 99.99 8198 413 0.0962 166.543 166.126 1.084 0.941 0.000 2.025-1.573 100.00 17313 902 0.1179 81.331 81.536 1.091 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1609 36.065 35.577 1.075 0.947 0.000 1.221-1.150 99.97 13689 708 0.2336 22.724 21.301 1.029 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0416 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1467 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1467 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1467 | n_water=424 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1196 r_free=0.1466 | n_water=423 | time (s): 41.160 (total time: 43.060) Filter (q & B) r_work=0.1196 r_free=0.1466 | n_water=423 | time (s): 1.220 (total time: 44.280) Compute maps r_work=0.1196 r_free=0.1466 | n_water=423 | time (s): 1.700 (total time: 45.980) Filter (map) r_work=0.1236 r_free=0.1483 | n_water=287 | time (s): 3.440 (total time: 49.420) Find peaks r_work=0.1236 r_free=0.1483 | n_water=287 | time (s): 0.730 (total time: 50.150) Add new water r_work=0.1359 r_free=0.1596 | n_water=479 | time (s): 3.440 (total time: 53.590) Refine new water occ: r_work=0.1256 r_free=0.1499 adp: r_work=0.1258 r_free=0.1500 occ: r_work=0.1235 r_free=0.1481 adp: r_work=0.1233 r_free=0.1481 occ: r_work=0.1220 r_free=0.1471 adp: r_work=0.1214 r_free=0.1466 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1466 r_work=0.1214 r_free=0.1466 | n_water=479 | time (s): 226.010 (total time: 279.600) Filter (q & B) r_work=0.1219 r_free=0.1472 | n_water=442 | time (s): 3.740 (total time: 283.340) Filter (dist only) r_work=0.1218 r_free=0.1470 | n_water=441 | time (s): 41.880 (total time: 325.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.052942 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.000134 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1453 0.0223 0.006 0.9 1.9 0.5 0.0 0 1.026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.53 2.23 3.665 22.206 42.000 3.721 12.23 14.11 1.89 4.165 22.017 42.000 3.655 Individual atomic B min max mean iso aniso Overall: 9.25 108.99 21.72 2.33 209 1759 Protein: 9.25 108.99 17.37 2.33 0 1519 Water: 11.54 71.10 36.67 N/A 209 232 Other: 17.90 30.44 24.16 N/A 0 8 Chain A: 9.25 108.99 20.04 N/A 0 1759 Chain S: 16.34 63.90 35.85 N/A 209 0 Histogram: Values Number of atoms 9.25 - 19.23 1228 19.23 - 29.20 277 29.20 - 39.18 218 39.18 - 49.15 131 49.15 - 59.12 76 59.12 - 69.10 25 69.10 - 79.07 7 79.07 - 89.05 2 89.05 - 99.02 2 99.02 - 108.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1223 r_free=0.1411 r_work=0.1224 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1224 r_free = 0.1413 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1410 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1217 r_free= 0.1410 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.653851 | | target function (ml) not normalized (work): 304340.217495 | | target function (ml) not normalized (free): 16068.015343 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1227 0.1217 0.1410 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1558 0.1558 0.1582 n_refl.: 87589 remove outliers: r(all,work,free)=0.1558 0.1558 0.1582 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1553 0.1554 0.1579 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1208 0.1378 n_refl.: 87589 remove outliers: r(all,work,free)=0.1213 0.1205 0.1378 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 89.58 81 5 0.3813 293.247 260.231 0.465 1.000 0.307 11.894-9.307 97.06 95 4 0.2534 470.674 453.356 0.839 1.002 0.290 9.237-7.194 98.18 209 7 0.2397 381.915 382.577 0.940 1.002 0.173 7.162-5.571 100.00 427 22 0.2061 292.931 283.216 0.912 1.002 0.164 5.546-4.326 100.00 867 58 0.1091 402.121 397.442 0.951 1.002 0.156 4.315-3.360 100.00 1859 96 0.0932 382.420 379.634 0.994 1.002 0.150 3.356-2.611 100.00 3867 181 0.1154 251.230 249.228 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1053 166.543 165.560 1.013 1.002 0.000 2.025-1.573 100.00 17313 902 0.1026 81.331 81.476 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1300 36.065 35.635 1.023 1.000 0.000 1.221-1.150 99.97 13689 708 0.2138 22.724 21.334 0.982 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0620 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1378 | n_water=441 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1205 r_free=0.1378 | n_water=441 | time (s): 35.600 (total time: 37.510) Filter (q & B) r_work=0.1205 r_free=0.1378 | n_water=438 | time (s): 3.240 (total time: 40.750) Compute maps r_work=0.1205 r_free=0.1378 | n_water=438 | time (s): 1.310 (total time: 42.060) Filter (map) r_work=0.1240 r_free=0.1401 | n_water=308 | time (s): 3.020 (total time: 45.080) Find peaks r_work=0.1240 r_free=0.1401 | n_water=308 | time (s): 0.500 (total time: 45.580) Add new water r_work=0.1305 r_free=0.1453 | n_water=476 | time (s): 2.790 (total time: 48.370) Refine new water occ: r_work=0.1220 r_free=0.1376 adp: r_work=0.1220 r_free=0.1378 occ: r_work=0.1206 r_free=0.1363 adp: r_work=0.1204 r_free=0.1364 occ: r_work=0.1196 r_free=0.1357 adp: r_work=0.1192 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1356 r_work=0.1192 r_free=0.1356 | n_water=476 | time (s): 200.780 (total time: 249.150) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=442 | time (s): 3.230 (total time: 252.380) Filter (dist only) r_work=0.1198 r_free=0.1359 | n_water=440 | time (s): 39.510 (total time: 291.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.918139 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.846357 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 0.1204 0.1379 0.0175 0.006 1.0 1.9 0.5 0.0 0 0.959 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.79 1.75 3.453 21.575 45.846 3.640 11.84 13.66 1.82 3.841 21.452 45.846 3.622 Individual atomic B min max mean iso aniso Overall: 9.32 104.54 21.25 2.19 210 1757 Protein: 9.32 104.54 17.07 2.20 0 1519 Water: 11.54 69.82 35.65 N/A 210 230 Other: 17.86 27.22 22.31 N/A 0 8 Chain A: 9.32 104.54 19.69 N/A 0 1757 Chain S: 14.43 59.55 34.28 N/A 210 0 Histogram: Values Number of atoms 9.32 - 18.84 1228 18.84 - 28.36 272 28.36 - 37.88 221 37.88 - 47.41 131 47.41 - 56.93 73 56.93 - 66.45 27 66.45 - 75.97 10 75.97 - 85.50 1 85.50 - 95.02 2 95.02 - 104.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1366 r_work=0.1184 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1367 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1180 r_free = 0.1365 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 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= 0.1180 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620461 | | target function (ml) not normalized (work): 301526.487498 | | target function (ml) not normalized (free): 15925.572500 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1180 0.1365 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1513 0.1513 0.1551 n_refl.: 87580 remove outliers: r(all,work,free)=0.1513 0.1513 0.1551 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1509 0.1509 0.1549 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1368 n_refl.: 87580 remove outliers: r(all,work,free)=0.1188 0.1179 0.1368 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 0.4035 288.625 252.122 0.451 1.000 0.320 11.894-9.307 95.10 93 4 0.2238 476.467 453.554 0.826 1.002 0.320 9.237-7.194 97.73 208 7 0.2433 382.987 375.530 0.913 1.002 0.180 7.162-5.571 100.00 427 22 0.2165 292.931 282.598 0.901 1.002 0.145 5.546-4.326 100.00 867 58 0.1120 402.121 397.911 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0943 382.420 380.031 0.995 1.002 0.130 3.356-2.611 100.00 3867 181 0.1158 251.230 249.451 1.002 1.002 0.048 2.608-2.026 99.99 8198 413 0.1016 166.543 165.725 1.013 1.002 0.000 2.025-1.573 100.00 17313 902 0.0968 81.331 81.639 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.065 35.695 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2128 22.724 21.361 0.983 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0576 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1179 r_free=0.1368 After: r_work=0.1179 r_free=0.1368 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1179 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1368 | n_water=440 | time (s): 1.960 (total time: 1.960) Filter (dist) r_work=0.1179 r_free=0.1368 | n_water=439 | time (s): 37.310 (total time: 39.270) Filter (q & B) r_work=0.1180 r_free=0.1368 | n_water=436 | time (s): 2.940 (total time: 42.210) Compute maps r_work=0.1180 r_free=0.1368 | n_water=436 | time (s): 1.780 (total time: 43.990) Filter (map) r_work=0.1201 r_free=0.1376 | n_water=326 | time (s): 2.700 (total time: 46.690) Find peaks r_work=0.1201 r_free=0.1376 | n_water=326 | time (s): 0.450 (total time: 47.140) Add new water r_work=0.1258 r_free=0.1426 | n_water=497 | time (s): 2.850 (total time: 49.990) Refine new water occ: r_work=0.1189 r_free=0.1365 adp: r_work=0.1189 r_free=0.1367 occ: r_work=0.1176 r_free=0.1352 adp: r_work=0.1175 r_free=0.1355 occ: r_work=0.1167 r_free=0.1344 adp: r_work=0.1163 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1163 r_free=0.1345 r_work=0.1163 r_free=0.1345 | n_water=497 | time (s): 206.670 (total time: 256.660) Filter (q & B) r_work=0.1172 r_free=0.1351 | n_water=452 | time (s): 2.570 (total time: 259.230) Filter (dist only) r_work=0.1172 r_free=0.1349 | n_water=450 | time (s): 39.700 (total time: 298.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.979719 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.260167 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 0.1370 0.0177 0.007 1.1 3.5 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.70 1.77 3.327 21.281 44.260 3.626 12.00 13.75 1.75 3.559 21.199 44.260 3.620 Individual atomic B min max mean iso aniso Overall: 9.34 100.72 21.14 2.06 222 1755 Protein: 9.34 100.72 16.86 2.06 0 1519 Water: 11.50 68.97 35.57 N/A 222 228 Other: 17.72 24.89 21.54 N/A 0 8 Chain A: 9.34 100.72 19.43 N/A 0 1755 Chain S: 14.38 60.02 34.62 N/A 222 0 Histogram: Values Number of atoms 9.34 - 18.47 1222 18.47 - 27.61 277 27.61 - 36.75 210 36.75 - 45.89 144 45.89 - 55.03 77 55.03 - 64.16 28 64.16 - 73.30 14 73.30 - 82.44 2 82.44 - 91.58 1 91.58 - 100.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1375 r_work=0.1200 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1375 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1369 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1196 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618403 | | target function (ml) not normalized (work): 301340.618691 | | target function (ml) not normalized (free): 15922.592729 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1380 0.1392 5.6446 5.6187| | 2: 3.57 - 2.84 1.00 2888 124 0.1119 0.1468 5.1902 5.2617| | 3: 2.83 - 2.48 1.00 2820 163 0.1234 0.1324 5.0044 5.0209| | 4: 2.47 - 2.25 1.00 2825 136 0.1039 0.1144 4.7036 4.7534| | 5: 2.25 - 2.09 1.00 2756 127 0.1007 0.1063 4.6442 4.6974| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1205 4.3474 4.4721| | 7: 1.97 - 1.87 1.00 2787 165 0.0997 0.1246 4.0755 4.1883| | 8: 1.87 - 1.79 1.00 2789 144 0.1036 0.1272 3.9923 4.0844| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1309 3.7169 3.9044| | 10: 1.72 - 1.66 1.00 2831 160 0.1011 0.1253 3.6374 3.7686| | 11: 1.66 - 1.61 1.00 2712 147 0.0980 0.1090 3.5729 3.6178| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1138 3.3494 3.4697| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1068 3.3353 3.4293| | 14: 1.52 - 1.48 1.00 2803 134 0.0997 0.1100 3.2599 3.3194| | 15: 1.48 - 1.45 1.00 2738 128 0.1021 0.1375 3.1674 3.3305| | 16: 1.45 - 1.42 1.00 2756 161 0.1071 0.1218 3.1489 3.2331| | 17: 1.42 - 1.39 1.00 2785 139 0.1126 0.1303 3.1136 3.2205| | 18: 1.39 - 1.36 1.00 2741 179 0.1154 0.1374 3.0842 3.2661| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1657 3.0913 3.2873| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1478 3.086 3.132| | 21: 1.32 - 1.30 1.00 2785 112 0.1407 0.1618 3.0826 3.154| | 22: 1.29 - 1.27 1.00 2704 152 0.1473 0.1946 3.081 3.2932| | 23: 1.27 - 1.26 1.00 2802 156 0.1570 0.1841 3.0974 3.1975| | 24: 1.26 - 1.24 1.00 2744 132 0.1628 0.1736 3.0916 3.1815| | 25: 1.24 - 1.22 1.00 2733 148 0.1794 0.2316 3.1064 3.2802| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1783 3.1209 3.198| | 27: 1.21 - 1.19 1.00 2814 148 0.2015 0.2079 3.1384 3.1436| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2292 3.138 3.1554| | 29: 1.18 - 1.16 1.00 2800 134 0.2221 0.2408 3.1256 3.2288| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2490 3.1137 3.1619| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.01 1.00 0.97 6114.05| | 2: 3.57 - 2.84 2888 124 0.92 13.13 1.01 0.97 6114.05| | 3: 2.83 - 2.48 2820 163 0.89 17.28 0.99 0.98 5128.02| | 4: 2.47 - 2.25 2825 136 0.91 14.47 1.00 0.98 2585.36| | 5: 2.25 - 2.09 2756 127 0.90 16.68 1.01 0.98 2585.36| | 6: 2.09 - 1.97 2846 113 0.92 13.53 1.02 0.98 1524.75| | 7: 1.97 - 1.87 2787 165 0.94 10.82 1.02 0.97 620.20| | 8: 1.87 - 1.79 2789 144 0.91 14.35 0.99 0.97 620.20| | 9: 1.79 - 1.72 2745 138 0.93 11.46 0.98 0.97 338.97| | 10: 1.72 - 1.66 2831 160 0.93 12.30 0.98 0.97 282.65| | 11: 1.66 - 1.61 2712 147 0.93 12.92 0.98 0.97 269.67| | 12: 1.61 - 1.56 2773 144 0.95 9.56 0.99 0.97 147.23| | 13: 1.56 - 1.52 2745 130 0.94 11.16 1.02 0.97 147.23| | 14: 1.52 - 1.48 2803 134 0.94 11.27 1.02 0.97 131.31| | 15: 1.48 - 1.45 2738 128 0.95 10.39 1.01 0.98 102.15| | 16: 1.45 - 1.42 2756 161 0.94 11.56 1.02 0.98 102.15| | 17: 1.42 - 1.39 2785 139 0.94 11.41 1.01 0.98 92.46| | 18: 1.39 - 1.36 2741 179 0.94 11.72 1.01 0.98 86.85| | 19: 1.36 - 1.34 2807 134 0.94 12.31 1.00 0.98 86.85| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.97 82.02| | 21: 1.32 - 1.30 2785 112 0.94 13.37 0.99 0.96 81.68| | 22: 1.29 - 1.27 2704 152 0.93 13.92 0.98 0.96 81.81| | 23: 1.27 - 1.26 2802 156 0.92 14.84 0.98 0.95 82.47| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.97 0.95 82.47| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 83.97| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 85.62| | 27: 1.21 - 1.19 2814 148 0.89 18.70 1.02 0.93 85.62| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 88.94| | 29: 1.18 - 1.16 2800 134 0.88 20.58 0.99 0.93 90.19| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.93 90.19| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.68 max = 6114.05 mean = 956.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 14.02| |phase err.(test): min = 0.00 max = 87.57 mean = 14.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1196 0.1369 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1522 0.1522 0.1566 n_refl.: 87576 remove outliers: r(all,work,free)=0.1522 0.1522 0.1566 n_refl.: 87576 overall B=-0.02 to atoms: r(all,work,free)=0.1519 0.1518 0.1563 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1196 0.1369 n_refl.: 87576 remove outliers: r(all,work,free)=0.1204 0.1196 0.1369 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 0.4067 288.625 255.009 0.441 1.000 0.283 11.894-9.307 95.10 93 4 0.2416 476.467 460.989 0.849 1.002 0.264 9.237-7.194 97.73 208 7 0.2481 382.987 377.346 0.907 1.002 0.161 7.162-5.571 100.00 427 22 0.2172 292.931 282.560 0.898 1.002 0.150 5.546-4.326 100.00 867 58 0.1157 402.121 397.795 0.954 1.002 0.130 4.315-3.360 100.00 1859 96 0.0965 382.420 379.867 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1189 251.230 249.306 1.002 1.002 0.048 2.608-2.026 99.99 8198 413 0.1052 166.543 165.586 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0985 81.331 81.616 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.065 35.700 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2119 22.724 21.361 0.983 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0575 ================= 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 0.1961 0.082 5.278 8.8 119.3 19.9 258 0.000 1_bss: 0.1649 0.1780 0.082 5.278 9.0 119.5 20.1 258 0.000 1_settarget: 0.1649 0.1780 0.082 5.278 9.0 119.5 20.1 258 0.000 1_nqh: 0.1651 0.1783 0.082 5.278 9.0 119.5 20.1 258 0.007 1_weight: 0.1651 0.1783 0.082 5.278 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1210 0.1461 0.007 0.957 9.0 119.5 20.1 258 0.128 1_adp: 0.1245 0.1538 0.007 0.957 8.6 118.8 21.3 258 0.128 1_regHadp: 0.1249 0.1544 0.007 0.957 8.6 118.8 21.3 258 0.128 1_occ: 0.1250 0.1546 0.007 0.957 8.6 118.8 21.3 258 0.128 2_bss: 0.1247 0.1538 0.007 0.957 8.7 119.0 21.4 258 0.128 2_settarget: 0.1247 0.1538 0.007 0.957 8.7 119.0 21.4 258 0.128 2_updatecdl: 0.1247 0.1538 0.007 0.967 8.7 119.0 21.4 258 0.128 2_nqh: 0.1249 0.1540 0.007 0.967 8.7 119.0 21.4 258 0.128 2_sol: 0.1238 0.1491 0.007 0.967 8.7 119.0 23.6 424 n/a 2_weight: 0.1238 0.1491 0.007 0.967 8.7 119.0 23.6 424 n/a 2_xyzrec: 0.1230 0.1507 0.007 0.880 8.7 119.0 23.6 424 n/a 2_adp: 0.1196 0.1476 0.007 0.880 8.8 114.0 23.2 424 n/a 2_regHadp: 0.1196 0.1476 0.007 0.880 8.8 114.0 23.2 424 n/a 2_occ: 0.1198 0.1469 0.007 0.880 8.8 114.0 23.2 424 n/a 3_bss: 0.1195 0.1467 0.007 0.880 8.8 114.0 23.3 424 n/a 3_settarget: 0.1195 0.1467 0.007 0.880 8.8 114.0 23.3 424 n/a 3_updatecdl: 0.1195 0.1467 0.007 0.880 8.8 114.0 23.3 424 n/a 3_nqh: 0.1195 0.1467 0.007 0.880 8.8 114.0 23.3 424 n/a 3_sol: 0.1218 0.1470 0.007 0.880 8.8 114.0 22.1 441 n/a 3_weight: 0.1218 0.1470 0.007 0.880 8.8 114.0 22.1 441 n/a 3_xyzrec: 0.1229 0.1453 0.006 0.924 8.8 114.0 22.1 441 n/a 3_adp: 0.1223 0.1411 0.006 0.924 9.3 109.0 21.7 441 n/a 3_regHadp: 0.1224 0.1413 0.006 0.924 9.3 109.0 21.7 441 n/a 3_occ: 0.1217 0.1410 0.006 0.924 9.3 109.0 21.7 441 n/a 4_bss: 0.1205 0.1378 0.006 0.924 9.2 109.0 21.7 441 n/a 4_settarget: 0.1205 0.1378 0.006 0.924 9.2 109.0 21.7 441 n/a 4_updatecdl: 0.1205 0.1378 0.006 0.922 9.2 109.0 21.7 441 n/a 4_nqh: 0.1205 0.1378 0.006 0.922 9.2 109.0 21.7 441 n/a 4_sol: 0.1198 0.1359 0.006 0.922 9.2 109.0 21.5 440 n/a 4_weight: 0.1198 0.1359 0.006 0.922 9.2 109.0 21.5 440 n/a 4_xyzrec: 0.1204 0.1379 0.006 0.950 9.2 109.0 21.5 440 n/a 4_adp: 0.1184 0.1366 0.006 0.950 9.3 104.5 21.3 440 n/a 4_regHadp: 0.1184 0.1367 0.006 0.950 9.3 104.5 21.3 440 n/a 4_occ: 0.1180 0.1365 0.006 0.950 9.3 104.5 21.3 440 n/a 5_bss: 0.1179 0.1368 0.006 0.950 9.3 104.5 21.2 440 n/a 5_settarget: 0.1179 0.1368 0.006 0.950 9.3 104.5 21.2 440 n/a 5_updatecdl: 0.1179 0.1368 0.006 0.950 9.3 104.5 21.2 440 n/a 5_setrh: 0.1179 0.1368 0.006 0.950 9.3 104.5 21.2 440 n/a 5_nqh: 0.1179 0.1368 0.006 0.950 9.3 104.5 21.2 440 n/a 5_sol: 0.1172 0.1349 0.006 0.950 9.3 104.5 21.3 450 n/a 5_weight: 0.1172 0.1349 0.006 0.950 9.3 104.5 21.3 450 n/a 5_xyzrec: 0.1193 0.1370 0.007 1.060 9.3 104.5 21.3 450 n/a 5_adp: 0.1200 0.1375 0.007 1.060 9.3 100.7 21.1 450 n/a 5_regHadp: 0.1200 0.1375 0.007 1.060 9.3 100.7 21.1 450 n/a 5_occ: 0.1196 0.1369 0.007 1.060 9.3 100.7 21.1 450 n/a end: 0.1196 0.1369 0.007 1.060 9.3 100.7 21.1 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5352376_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_5352376_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8600 Refinement macro-cycles (run) : 3559.2800 Write final files (write_after_run_outputs) : 60.3700 Total : 3624.5100 Total CPU time: 61.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:35 PST -0800 (1735452755.34 s) Start R-work = 0.1649, R-free = 0.1780 Final R-work = 0.1196, R-free = 0.1369 =============================================================================== Job complete usr+sys time: 3763.98 seconds wall clock time: 67 minutes 51.33 seconds (4071.33 seconds total)