Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.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_3975290.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.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 =============================================================================== 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: 2.15, 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: 0.53 Conformation dependent library (CDL) restraints added in 190.5 milliseconds Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 703 0.94 - 1.20: 1000 1.20 - 1.46: 743 1.46 - 1.73: 696 1.73 - 1.99: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.700 -0.241 1.23e-02 6.61e+03 3.83e+02 bond pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " ideal model delta sigma weight residual 1.524 1.753 -0.229 1.26e-02 6.30e+03 3.30e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.669 -0.213 1.18e-02 7.18e+03 3.26e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.458 1.224 0.233 1.30e-02 5.92e+03 3.22e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.437 -0.201 1.13e-02 7.83e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3221 4.84 - 9.68: 1828 9.68 - 14.52: 613 14.52 - 19.36: 100 19.36 - 24.20: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 123.27 144.05 -20.78 1.16e+00 7.43e-01 3.21e+02 angle pdb=" O GLU A 59 " pdb=" C GLU A 59 " pdb=" N ASP A 60 " ideal model delta sigma weight residual 122.12 140.18 -18.06 1.06e+00 8.90e-01 2.90e+02 angle pdb=" C GLY A 40 " pdb=" N ALYS A 41 " pdb=" CA ALYS A 41 " ideal model delta sigma weight residual 120.31 140.41 -20.10 1.52e+00 4.33e-01 1.75e+02 angle pdb=" O GLY A 75 " pdb=" C GLY A 75 " pdb=" N AASN A 76 " ideal model delta sigma weight residual 122.70 105.88 16.82 1.30e+00 5.92e-01 1.67e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 109.05 12.72 1.00e+00 1.00e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 15.69: 916 15.69 - 31.36: 125 31.36 - 47.03: 44 47.03 - 62.70: 22 62.70 - 78.37: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+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 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.240: 116 0.240 - 0.479: 67 0.479 - 0.718: 46 0.718 - 0.956: 13 0.956 - 1.195: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA LYS A 89 " pdb=" N LYS A 89 " pdb=" C LYS A 89 " pdb=" CB LYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.026 9.50e-02 1.11e+02 6.31e-02 8.80e+01 pdb=" NE ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.132 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.043 2.00e-02 2.50e+03 5.24e-02 8.23e+01 pdb=" CG BTYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.148 9.50e-02 1.11e+02 7.69e-02 8.11e+01 pdb=" NE ARG A 156 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1049 2.32 - 2.89: 8078 2.89 - 3.46: 10513 3.46 - 4.03: 15254 4.03 - 4.60: 21801 Nonbonded interactions: 56695 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.750 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.762 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.782 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.784 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.819 2.450 ... (remaining 56690 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_3975290_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= 0.2612 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796841 | | target function (ml) not normalized (work): 232993.643161 | | target function (ml) not normalized (free): 11855.759271 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3018 0.2089 7.0516 4.9487| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1690 4.3494 4.3288| | 3: 2.84 - 2.48 1.00 2833 165 0.2353 0.1771 4.1248 4.1603| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1588 3.8387 3.8502| | 5: 2.25 - 2.09 1.00 2756 127 0.2487 0.1671 3.8016 3.8205| | 6: 2.09 - 1.97 1.00 2846 113 0.2575 0.1853 3.4647 3.5759| | 7: 1.97 - 1.87 1.00 2787 165 0.2534 0.1870 3.1494 3.2297| | 8: 1.87 - 1.79 1.00 2789 144 0.2454 0.1960 3.0807 3.1719| | 9: 1.79 - 1.72 1.00 2745 138 0.2391 0.2044 2.9173 3.0304| | 10: 1.72 - 1.66 1.00 2789 158 0.2422 0.1995 2.8084 2.8686| | 11: 1.66 - 1.61 1.00 2740 147 0.2447 0.1744 2.7588 2.7573| | 12: 1.61 - 1.56 1.00 2787 146 0.2536 0.1985 2.6388 2.6115| | 13: 1.56 - 1.52 1.00 2745 130 0.2601 0.1859 2.5819 2.5964| | 14: 1.52 - 1.48 1.00 2803 134 0.2603 0.2099 2.5093 2.5952| | 15: 1.48 - 1.45 1.00 2738 128 0.2624 0.2330 2.4329 2.5618| | 16: 1.45 - 1.42 1.00 2756 161 0.2709 0.2178 2.3913 2.4203| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2199 2.3271 2.3459| | 18: 1.39 - 1.36 1.00 2741 179 0.2644 0.2217 2.2859 2.3566| | 19: 1.36 - 1.34 1.00 2807 134 0.2682 0.2251 2.2578 2.287| | 20: 1.34 - 1.32 1.00 2696 147 0.2687 0.2148 2.2008 2.1682| | 21: 1.32 - 1.30 1.00 2785 112 0.2737 0.2163 2.1842 2.1136| | 22: 1.29 - 1.27 1.00 2704 152 0.2771 0.2498 2.1415 2.1915| | 23: 1.27 - 1.26 1.00 2802 156 0.2804 0.2548 2.0991 2.1847| | 24: 1.26 - 1.24 1.00 2744 132 0.2832 0.2545 2.0948 2.1452| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2240 2.0489 2.0368| | 26: 1.22 - 1.21 1.00 2727 135 0.2889 0.2615 2.0185 2.1772| | 27: 1.21 - 1.19 1.00 2814 148 0.3011 0.2633 2.0245 2.037| | 28: 1.19 - 1.18 1.00 2671 147 0.2967 0.2888 1.9857 2.0129| | 29: 1.18 - 1.16 1.00 2800 134 0.2947 0.2992 1.9516 2.096| | 30: 1.16 - 1.15 1.00 2740 148 0.3066 0.2820 1.9305 1.9662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.70 0.76 0.23 1470.08| | 2: 3.57 - 2.84 2876 122 0.80 26.06 1.27 0.23 1470.08| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.24 0.23 1221.56| | 4: 2.47 - 2.25 2825 136 0.81 25.75 1.26 0.25 576.63| | 5: 2.25 - 2.09 2756 127 0.77 29.55 1.29 0.25 576.63| | 6: 2.09 - 1.97 2846 113 0.83 23.40 1.30 0.25 319.63| | 7: 1.97 - 1.87 2787 165 0.89 17.64 1.28 0.25 100.44| | 8: 1.87 - 1.79 2789 144 0.85 22.19 1.25 0.25 100.44| | 9: 1.79 - 1.72 2745 138 0.87 19.31 1.23 0.25 59.42| | 10: 1.72 - 1.66 2789 158 0.86 20.89 1.23 0.25 51.21| | 11: 1.66 - 1.61 2740 147 0.85 21.95 1.23 0.25 49.27| | 12: 1.61 - 1.56 2787 146 0.88 18.48 1.24 0.25 29.67| | 13: 1.56 - 1.52 2745 130 0.87 20.44 1.24 0.25 29.67| | 14: 1.52 - 1.48 2803 134 0.86 20.74 1.25 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.16 1.24 0.25 20.88| | 16: 1.45 - 1.42 2756 161 0.85 21.74 1.25 0.25 20.88| | 17: 1.42 - 1.39 2785 139 0.87 20.62 1.23 0.25 17.56| | 18: 1.39 - 1.36 2741 179 0.87 20.95 1.22 0.25 15.64| | 19: 1.36 - 1.34 2807 134 0.86 21.96 1.22 0.25 15.64| | 20: 1.34 - 1.32 2696 147 0.87 20.96 1.21 0.24 13.01| | 21: 1.32 - 1.30 2785 112 0.86 21.67 1.20 0.24 12.83| | 22: 1.29 - 1.27 2704 152 0.85 22.41 1.21 0.24 12.58| | 23: 1.27 - 1.26 2802 156 0.85 22.54 1.22 0.24 11.29| | 24: 1.26 - 1.24 2744 132 0.85 23.01 1.20 0.24 11.29| | 25: 1.24 - 1.22 2734 148 0.84 24.00 1.20 0.24 10.90| | 26: 1.22 - 1.21 2727 135 0.83 24.82 1.21 0.23 10.47| | 27: 1.21 - 1.19 2814 148 0.82 25.67 1.20 0.23 10.47| | 28: 1.19 - 1.18 2671 147 0.81 26.45 1.17 0.23 10.07| | 29: 1.18 - 1.16 2800 134 0.81 27.18 1.16 0.22 9.92| | 30: 1.16 - 1.15 2740 148 0.79 28.83 1.15 0.22 9.92| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.92 max = 1470.08 mean = 215.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 23.01| |phase err.(test): min = 0.00 max = 89.25 mean = 22.99| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.250 1557 Z= 5.583 Angle : 5.396 20.784 2118 Z= 3.828 Chirality : 0.384 1.195 243 Planarity : 0.030 0.116 284 Dihedral : 13.889 78.366 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.44), residues: 224 helix: -2.90 (0.32), residues: 102 sheet: -2.04 (0.75), residues: 30 loop : -0.04 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.016 ARG A 145 TYR 0.082 0.035 TYR A 139 PHE 0.087 0.030 PHE A 164 HIS 0.050 0.028 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= 0.2612 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.796841 | | target function (ml) not normalized (work): 232993.643161 | | target function (ml) not normalized (free): 11855.759271 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2572 0.2612 0.1977 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2572 0.2612 0.1977 n_refl.: 87602 remove outliers: r(all,work,free)=0.1986 0.1989 0.1977 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2009 0.2012 0.1992 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1650 0.1642 0.1801 n_refl.: 87594 remove outliers: r(all,work,free)=0.1649 0.1642 0.1801 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 0.3811 386.680 357.572 0.667 1.001 0.401 11.894-9.307 99.02 97 4 0.1797 614.222 596.480 0.926 1.003 0.380 9.237-7.194 100.00 213 7 0.2155 502.358 492.007 0.957 1.003 0.359 7.162-5.571 100.00 427 22 0.2220 376.992 364.207 0.931 1.003 0.340 5.546-4.326 100.00 867 58 0.1244 517.516 512.512 0.961 1.003 0.209 4.315-3.360 100.00 1859 96 0.1155 492.162 488.770 1.001 1.003 0.153 3.356-2.611 100.00 3867 181 0.1435 323.325 319.600 0.997 1.002 0.119 2.608-2.026 99.99 8198 413 0.1364 214.335 212.023 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1647 104.670 103.967 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2080 46.415 45.114 1.007 0.995 0.000 1.221-1.150 99.97 13689 708 0.2597 29.245 26.928 0.974 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1801 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1642 r_free=0.1801 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.031321 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.879593 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1465 0.0254 0.007 1.0 1.0 0.5 0.0 0 13.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.65 2.54 3.013 19.050 2007.880 0.017 12.33 15.32 2.99 3.006 19.441 2007.880 0.016 Individual atomic B min max mean iso aniso Overall: 8.56 118.05 20.82 2.88 0 1785 Protein: 8.56 118.05 17.72 2.88 0 1519 Water: 11.15 115.08 38.83 N/A 0 258 Other: 22.04 34.61 27.79 N/A 0 8 Chain A: 8.56 118.05 20.82 N/A 0 1785 Histogram: Values Number of atoms 8.56 - 19.51 1214 19.51 - 30.46 235 30.46 - 41.41 158 41.41 - 52.36 96 52.36 - 63.31 53 63.31 - 74.26 18 74.26 - 85.21 4 85.21 - 96.16 4 96.16 - 107.10 0 107.10 - 118.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1532 r_work=0.1237 r_free=0.1536 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1536 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 = 0.1237 r_free = 0.1538 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1237 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015455 | | target function (ls_wunit_k1) not normalized (work): 1287.317407 | | target function (ls_wunit_k1) not normalized (free): 111.714270 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1251 0.1237 0.1538 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1694 0.1692 0.1767 n_refl.: 87593 remove outliers: r(all,work,free)=0.1694 0.1692 0.1767 n_refl.: 87593 overall B=0.12 to atoms: r(all,work,free)=0.1714 0.1713 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1249 0.1235 0.1530 n_refl.: 87593 remove outliers: r(all,work,free)=0.1248 0.1234 0.1530 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 95.83 87 5 0.3611 299.193 277.704 0.639 1.002 0.380 11.894-9.307 98.04 96 4 0.1519 481.236 464.627 0.910 1.002 0.359 9.237-7.194 100.00 213 7 0.1829 392.001 387.152 0.949 1.003 0.319 7.162-5.571 100.00 427 22 0.1748 294.175 288.666 0.925 1.003 0.300 5.546-4.326 100.00 867 58 0.0929 403.830 401.300 0.950 1.003 0.199 4.315-3.360 100.00 1859 96 0.0783 384.045 383.126 0.994 1.002 0.180 3.356-2.611 100.00 3867 181 0.1025 252.298 251.641 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0970 167.250 166.753 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1188 81.676 81.901 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1625 36.219 35.691 1.007 0.999 0.000 1.221-1.150 99.97 13689 708 0.2352 22.820 21.323 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0462 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1530 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=0.1235 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1532 | n_water=258 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1245 r_free=0.1529 | n_water=252 | time (s): 25.600 (total time: 27.970) Filter (q & B) r_work=0.1248 r_free=0.1528 | n_water=249 | time (s): 3.590 (total time: 31.560) Compute maps r_work=0.1248 r_free=0.1528 | n_water=249 | time (s): 1.810 (total time: 33.370) Filter (map) r_work=0.1267 r_free=0.1534 | n_water=234 | time (s): 3.820 (total time: 37.190) Find peaks r_work=0.1267 r_free=0.1534 | n_water=234 | time (s): 0.700 (total time: 37.890) Add new water r_work=0.1426 r_free=0.1684 | n_water=459 | time (s): 3.690 (total time: 41.580) Refine new water occ: r_work=0.1329 r_free=0.1568 adp: r_work=0.1245 r_free=0.1510 occ: r_work=0.1261 r_free=0.1506 adp: r_work=0.1222 r_free=0.1489 occ: r_work=0.1226 r_free=0.1477 adp: r_work=0.1214 r_free=0.1477 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1477 r_work=0.1214 r_free=0.1477 | n_water=459 | time (s): 93.460 (total time: 135.040) Filter (q & B) r_work=0.1220 r_free=0.1486 | n_water=436 | time (s): 3.750 (total time: 138.790) Filter (dist only) r_work=0.1220 r_free=0.1485 | n_water=435 | time (s): 44.340 (total time: 183.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.951871 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1547.312852 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 0.1221 0.1518 0.0297 0.007 0.9 2.9 0.5 0.0 0 12.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 15.18 2.97 3.753 22.987 1547.313 0.015 11.97 14.98 3.01 4.021 22.869 1547.313 0.015 Individual atomic B min max mean iso aniso Overall: 8.85 113.55 23.14 2.60 201 1761 Protein: 8.85 113.55 17.59 2.60 0 1519 Water: 11.12 69.52 42.38 N/A 201 234 Other: 25.02 37.26 30.54 N/A 0 8 Chain A: 8.85 113.55 20.23 N/A 0 1761 Chain S: 15.72 68.19 48.62 N/A 201 0 Histogram: Values Number of atoms 8.85 - 19.32 1208 19.32 - 29.79 251 29.79 - 40.26 188 40.26 - 50.73 139 50.73 - 61.20 113 61.20 - 71.67 53 71.67 - 82.14 4 82.14 - 92.61 3 92.61 - 103.08 1 103.08 - 113.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1498 r_work=0.1197 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1498 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1491 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1199 r_free= 0.1491 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014160 | | target function (ls_wunit_k1) not normalized (work): 1179.489975 | | target function (ls_wunit_k1) not normalized (free): 106.045241 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1199 0.1491 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1600 0.1595 0.1731 n_refl.: 87591 remove outliers: r(all,work,free)=0.1600 0.1595 0.1731 n_refl.: 87591 overall B=0.04 to atoms: r(all,work,free)=0.1607 0.1602 0.1735 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1195 0.1487 n_refl.: 87591 remove outliers: r(all,work,free)=0.1207 0.1193 0.1487 n_refl.: 87587 ======================== 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 0.3282 291.885 272.018 0.628 0.940 0.370 11.894-9.307 98.04 96 4 0.1417 481.236 478.433 0.981 0.940 0.357 9.237-7.194 100.00 213 7 0.1712 392.001 393.388 1.045 0.941 0.262 7.162-5.571 100.00 427 22 0.1529 294.175 289.776 0.999 0.941 0.254 5.546-4.326 100.00 867 58 0.0843 403.830 400.987 1.018 0.941 0.206 4.315-3.360 100.00 1859 96 0.0728 384.045 382.988 1.065 0.941 0.206 3.356-2.611 100.00 3867 181 0.0971 252.298 251.547 1.072 0.942 0.150 2.608-2.026 99.99 8198 413 0.0952 167.250 166.891 1.080 0.943 0.000 2.025-1.573 100.00 17313 902 0.1167 81.676 81.913 1.087 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1596 36.219 35.727 1.071 0.948 0.000 1.221-1.150 99.97 13689 708 0.2329 22.820 21.366 1.025 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0605 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1487 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=0.1193 r_free=0.1487 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1487 | n_water=435 | time (s): 2.110 (total time: 2.110) Filter (dist) r_work=0.1192 r_free=0.1487 | n_water=433 | time (s): 38.810 (total time: 40.920) Filter (q & B) r_work=0.1193 r_free=0.1489 | n_water=432 | time (s): 3.400 (total time: 44.320) Compute maps r_work=0.1193 r_free=0.1489 | n_water=432 | time (s): 1.630 (total time: 45.950) Filter (map) r_work=0.1236 r_free=0.1485 | n_water=293 | time (s): 3.090 (total time: 49.040) Find peaks r_work=0.1236 r_free=0.1485 | n_water=293 | time (s): 0.700 (total time: 49.740) Add new water r_work=0.1358 r_free=0.1613 | n_water=489 | time (s): 3.150 (total time: 52.890) Refine new water occ: r_work=0.1254 r_free=0.1517 adp: r_work=0.1256 r_free=0.1518 occ: r_work=0.1232 r_free=0.1500 adp: r_work=0.1231 r_free=0.1499 occ: r_work=0.1216 r_free=0.1487 adp: r_work=0.1211 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1211 r_free=0.1485 r_work=0.1211 r_free=0.1485 | n_water=489 | time (s): 164.590 (total time: 217.480) Filter (q & B) r_work=0.1216 r_free=0.1488 | n_water=449 | time (s): 3.190 (total time: 220.670) Filter (dist only) r_work=0.1216 r_free=0.1488 | n_water=449 | time (s): 34.800 (total time: 255.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.031005 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.573478 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 0.1221 0.1459 0.0238 0.006 0.9 1.6 0.5 0.0 0 1.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.59 2.38 3.604 22.026 48.573 3.721 12.15 14.21 2.05 4.162 21.817 48.573 3.653 Individual atomic B min max mean iso aniso Overall: 9.23 109.20 21.53 2.31 217 1759 Protein: 9.23 109.20 17.12 2.31 0 1519 Water: 11.52 68.46 36.33 N/A 217 232 Other: 21.30 33.34 27.21 N/A 0 8 Chain A: 9.23 109.20 19.73 N/A 0 1759 Chain S: 16.38 66.09 36.10 N/A 217 0 Histogram: Values Number of atoms 9.23 - 19.23 1234 19.23 - 29.23 277 29.23 - 39.22 226 39.22 - 49.22 135 49.22 - 59.22 71 59.22 - 69.21 23 69.21 - 79.21 4 79.21 - 89.21 3 89.21 - 99.21 1 99.21 - 109.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1215 r_free=0.1421 r_work=0.1217 r_free=0.1421 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1421 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1212 r_free = 0.1420 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.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1212 r_free= 0.1420 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.651338 | | target function (ml) not normalized (work): 304123.570157 | | target function (ml) not normalized (free): 16067.676675 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1212 0.1420 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1541 0.1541 0.1568 n_refl.: 87587 remove outliers: r(all,work,free)=0.1541 0.1541 0.1568 n_refl.: 87587 overall B=-0.02 to atoms: r(all,work,free)=0.1538 0.1538 0.1567 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1201 0.1384 n_refl.: 87587 remove outliers: r(all,work,free)=0.1207 0.1198 0.1384 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 0.3961 288.519 256.211 0.465 1.001 0.320 11.894-9.307 97.06 95 4 0.2413 477.676 467.286 0.850 1.002 0.320 9.237-7.194 98.18 209 7 0.2403 383.538 384.453 0.942 1.002 0.180 7.162-5.571 100.00 427 22 0.2158 294.175 282.549 0.899 1.002 0.170 5.546-4.326 100.00 867 58 0.1122 403.830 398.759 0.952 1.002 0.146 4.315-3.360 100.00 1859 96 0.0937 384.045 381.286 0.992 1.002 0.137 3.356-2.611 100.00 3867 181 0.1157 252.298 250.256 1.000 1.002 0.053 2.608-2.026 99.99 8198 413 0.1046 167.250 166.207 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1002 81.676 81.820 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1283 36.219 35.789 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2129 22.820 21.428 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0445 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1384 | n_water=449 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1198 r_free=0.1382 | n_water=448 | time (s): 37.910 (total time: 39.880) Filter (q & B) r_work=0.1199 r_free=0.1381 | n_water=447 | time (s): 2.700 (total time: 42.580) Compute maps r_work=0.1199 r_free=0.1381 | n_water=447 | time (s): 1.150 (total time: 43.730) Filter (map) r_work=0.1217 r_free=0.1385 | n_water=322 | time (s): 2.580 (total time: 46.310) Find peaks r_work=0.1217 r_free=0.1385 | n_water=322 | time (s): 0.520 (total time: 46.830) Add new water r_work=0.1275 r_free=0.1441 | n_water=480 | time (s): 2.260 (total time: 49.090) Refine new water occ: r_work=0.1210 r_free=0.1366 adp: r_work=0.1210 r_free=0.1370 occ: r_work=0.1196 r_free=0.1350 adp: r_work=0.1194 r_free=0.1352 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1182 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1341 r_work=0.1182 r_free=0.1341 | n_water=480 | time (s): 207.410 (total time: 256.500) Filter (q & B) r_work=0.1188 r_free=0.1344 | n_water=449 | time (s): 2.780 (total time: 259.280) Filter (dist only) r_work=0.1188 r_free=0.1343 | n_water=448 | time (s): 37.730 (total time: 297.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.939371 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.542337 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 0.1192 0.1358 0.0166 0.006 1.0 1.9 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.58 1.66 3.400 21.415 46.542 3.633 11.78 13.51 1.73 3.669 21.334 46.542 3.620 Individual atomic B min max mean iso aniso Overall: 9.25 104.67 21.26 2.15 216 1759 Protein: 9.25 104.67 16.93 2.15 0 1519 Water: 11.56 67.67 35.86 N/A 216 232 Other: 21.67 31.32 26.53 N/A 0 8 Chain A: 9.25 104.67 19.51 N/A 0 1759 Chain S: 15.59 59.47 35.51 N/A 216 0 Histogram: Values Number of atoms 9.25 - 18.80 1222 18.80 - 28.34 283 28.34 - 37.88 216 37.88 - 47.42 136 47.42 - 56.96 80 56.96 - 66.50 25 66.50 - 76.05 8 76.05 - 85.59 2 85.59 - 95.13 1 95.13 - 104.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1178 r_free=0.1351 r_work=0.1179 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1351 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1176 r_free = 0.1350 target_work(ml) = 3.619 | | 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= 0.1176 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.619006 | | target function (ml) not normalized (work): 301405.275236 | | target function (ml) not normalized (free): 15918.840503 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1176 0.1350 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1500 0.1499 0.1542 n_refl.: 87580 remove outliers: r(all,work,free)=0.1500 0.1499 0.1542 n_refl.: 87580 overall B=-0.02 to atoms: r(all,work,free)=0.1497 0.1496 0.1540 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1175 0.1352 n_refl.: 87580 remove outliers: r(all,work,free)=0.1181 0.1172 0.1352 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 0.4150 286.391 246.552 0.437 1.002 0.310 11.894-9.307 93.14 91 4 0.2199 472.181 458.252 0.849 1.003 0.310 9.237-7.194 97.27 207 7 0.2415 384.140 377.617 0.911 1.003 0.125 7.162-5.571 100.00 427 22 0.2195 294.175 282.689 0.899 1.003 0.120 5.546-4.326 100.00 867 58 0.1140 403.830 399.417 0.952 1.002 0.120 4.315-3.360 100.00 1859 96 0.0932 384.045 381.557 0.993 1.002 0.117 3.356-2.611 100.00 3867 181 0.1144 252.298 250.501 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1015 167.250 166.400 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0959 81.676 81.955 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.219 35.852 1.023 0.998 0.000 1.221-1.150 99.97 13689 708 0.2125 22.820 21.450 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0424 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1172 r_free=0.1352 After: r_work=0.1172 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.1173 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1173 r_free=0.1355 | n_water=448 | time (s): 2.080 (total time: 2.080) Filter (dist) r_work=0.1173 r_free=0.1355 | n_water=448 | time (s): 34.190 (total time: 36.270) Filter (q & B) r_work=0.1173 r_free=0.1357 | n_water=446 | time (s): 3.060 (total time: 39.330) Compute maps r_work=0.1173 r_free=0.1357 | n_water=446 | time (s): 1.220 (total time: 40.550) Filter (map) r_work=0.1201 r_free=0.1382 | n_water=336 | time (s): 2.500 (total time: 43.050) Find peaks r_work=0.1201 r_free=0.1382 | n_water=336 | time (s): 0.450 (total time: 43.500) Add new water r_work=0.1244 r_free=0.1416 | n_water=491 | time (s): 3.190 (total time: 46.690) Refine new water occ: r_work=0.1181 r_free=0.1362 adp: r_work=0.1182 r_free=0.1364 occ: r_work=0.1171 r_free=0.1353 adp: r_work=0.1170 r_free=0.1355 occ: r_work=0.1164 r_free=0.1347 adp: r_work=0.1161 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1161 r_free=0.1348 r_work=0.1161 r_free=0.1348 | n_water=491 | time (s): 149.770 (total time: 196.460) Filter (q & B) r_work=0.1170 r_free=0.1357 | n_water=447 | time (s): 3.190 (total time: 199.650) Filter (dist only) r_work=0.1170 r_free=0.1356 | n_water=446 | time (s): 39.140 (total time: 238.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.905595 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.520107 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1388 0.0190 0.007 1.1 3.2 0.5 0.0 0 0.953 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.88 1.90 3.288 21.108 37.520 3.630 12.02 13.91 1.89 3.375 21.068 37.520 3.627 Individual atomic B min max mean iso aniso Overall: 9.27 102.82 21.01 2.05 216 1757 Protein: 9.27 102.82 16.82 2.05 0 1519 Water: 11.54 67.44 35.17 N/A 216 230 Other: 21.72 30.55 26.39 N/A 0 8 Chain A: 9.27 102.82 19.36 N/A 0 1757 Chain S: 15.27 59.42 34.37 N/A 216 0 Histogram: Values Number of atoms 9.27 - 18.62 1220 18.62 - 27.98 294 27.98 - 37.33 205 37.33 - 46.69 141 46.69 - 56.04 71 56.04 - 65.40 28 65.40 - 74.76 10 74.76 - 84.11 1 84.11 - 93.47 1 93.47 - 102.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1391 r_work=0.1202 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1391 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1386 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87572 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625466 | | target function (ml) not normalized (work): 301914.316949 | | target function (ml) not normalized (free): 15955.020665 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2914 171 0.1414 0.1471 5.6753 5.6402| | 2: 3.57 - 2.84 1.00 2888 124 0.1113 0.1497 5.2087 5.2812| | 3: 2.83 - 2.48 1.00 2820 163 0.1227 0.1317 5.0157 5.0398| | 4: 2.47 - 2.25 1.00 2825 136 0.1022 0.1166 4.7093 4.7654| | 5: 2.25 - 2.09 1.00 2756 127 0.0985 0.1099 4.6518 4.7233| | 6: 2.09 - 1.97 1.00 2846 113 0.0982 0.1145 4.3564 4.4807| | 7: 1.97 - 1.87 1.00 2787 165 0.0989 0.1189 4.0726 4.1649| | 8: 1.87 - 1.79 1.00 2789 144 0.1021 0.1245 3.9857 4.0855| | 9: 1.79 - 1.72 1.00 2745 138 0.0962 0.1265 3.7165 3.8812| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1241 3.6341 3.7572| | 11: 1.66 - 1.61 1.00 2712 147 0.0967 0.1093 3.5685 3.61| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1169 3.3542 3.4654| | 13: 1.56 - 1.52 1.00 2745 130 0.0990 0.1053 3.3401 3.4232| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1135 3.2634 3.3575| | 15: 1.48 - 1.45 1.00 2738 128 0.1021 0.1385 3.1766 3.3395| | 16: 1.45 - 1.42 1.00 2756 161 0.1070 0.1263 3.1552 3.2546| | 17: 1.42 - 1.39 1.00 2785 139 0.1125 0.1325 3.1236 3.2492| | 18: 1.39 - 1.36 1.00 2741 179 0.1164 0.1402 3.0969 3.2798| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1653 3.1025 3.3| | 20: 1.34 - 1.32 1.00 2696 147 0.1326 0.1459 3.094 3.1374| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1622 3.0921 3.1694| | 22: 1.29 - 1.27 1.00 2704 152 0.1477 0.1953 3.0889 3.2788| | 23: 1.27 - 1.26 1.00 2802 156 0.1585 0.1869 3.1095 3.2135| | 24: 1.26 - 1.24 1.00 2744 132 0.1640 0.1789 3.1013 3.2023| | 25: 1.24 - 1.22 1.00 2733 148 0.1810 0.2313 3.1159 3.2964| | 26: 1.22 - 1.21 1.00 2727 135 0.1869 0.1773 3.1276 3.2002| | 27: 1.21 - 1.19 1.00 2814 148 0.2022 0.2101 3.1442 3.1498| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2314 3.142 3.1614| | 29: 1.18 - 1.16 1.00 2800 134 0.2227 0.2364 3.1316 3.2218| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2514 3.1197 3.1728| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2914 171 0.94 9.34 1.00 0.97 6445.04| | 2: 3.57 - 2.84 2888 124 0.92 13.52 1.01 0.97 6445.04| | 3: 2.83 - 2.48 2820 163 0.88 17.72 0.99 0.97 5396.23| | 4: 2.47 - 2.25 2825 136 0.91 14.80 1.00 0.98 2691.68| | 5: 2.25 - 2.09 2756 127 0.89 17.08 1.01 0.98 2691.68| | 6: 2.09 - 1.97 2846 113 0.92 13.64 1.02 0.98 1570.92| | 7: 1.97 - 1.87 2787 165 0.94 10.68 1.02 0.97 615.06| | 8: 1.87 - 1.79 2789 144 0.91 14.23 1.00 0.97 615.06| | 9: 1.79 - 1.72 2745 138 0.93 11.31 0.98 0.97 335.27| | 10: 1.72 - 1.66 2831 160 0.93 12.14 0.98 0.97 279.23| | 11: 1.66 - 1.61 2712 147 0.93 12.80 0.98 0.97 266.64| | 12: 1.61 - 1.56 2773 144 0.95 9.48 0.99 0.97 147.91| | 13: 1.56 - 1.52 2745 130 0.94 11.12 1.02 0.97 147.91| | 14: 1.52 - 1.48 2803 134 0.94 11.27 1.02 0.98 132.69| | 15: 1.48 - 1.45 2738 128 0.95 10.50 1.01 0.98 104.82| | 16: 1.45 - 1.42 2756 161 0.94 11.71 1.02 0.98 104.82| | 17: 1.42 - 1.39 2785 139 0.94 11.54 1.01 0.98 95.09| | 18: 1.39 - 1.36 2741 179 0.94 11.91 1.01 0.98 89.46| | 19: 1.36 - 1.34 2807 134 0.94 12.48 1.00 0.98 89.46| | 20: 1.34 - 1.32 2696 147 0.94 12.56 0.99 0.97 84.07| | 21: 1.32 - 1.30 2785 112 0.93 13.53 0.98 0.96 83.69| | 22: 1.29 - 1.27 2704 152 0.93 13.97 0.98 0.96 83.74| | 23: 1.27 - 1.26 2802 156 0.92 14.96 0.98 0.95 83.97| | 24: 1.26 - 1.24 2744 132 0.92 15.07 0.97 0.95 83.97| | 25: 1.24 - 1.22 2733 148 0.91 16.41 0.96 0.94 85.17| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.51| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.51| | 28: 1.19 - 1.18 2671 147 0.88 20.16 1.01 0.93 89.37| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.93 90.45| | 30: 1.16 - 1.15 2739 148 0.86 21.86 0.98 0.93 90.45| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 83.69 max = 6445.04 mean = 997.85| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.09| |phase err.(test): min = 0.00 max = 89.17 mean = 14.24| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1197 0.1386 n_refl.: 87572 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1572 n_refl.: 87572 remove outliers: r(all,work,free)=0.1514 0.1512 0.1572 n_refl.: 87572 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1510 0.1571 n_refl.: 87572 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1198 0.1385 n_refl.: 87572 remove outliers: r(all,work,free)=0.1207 0.1198 0.1385 n_refl.: 87570 ======================== 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 0.4157 286.391 250.065 0.417 1.001 0.277 11.894-9.307 92.16 90 4 0.2391 472.207 451.555 0.837 1.002 0.253 9.237-7.194 96.82 206 7 0.2498 384.683 374.737 0.902 1.002 0.120 7.162-5.571 100.00 427 22 0.2308 294.175 281.536 0.889 1.002 0.110 5.546-4.326 100.00 867 58 0.1195 403.830 399.241 0.952 1.002 0.110 4.315-3.360 100.00 1859 96 0.0975 384.045 381.435 0.994 1.002 0.107 3.356-2.611 100.00 3867 181 0.1183 252.298 250.455 1.000 1.001 0.048 2.608-2.026 99.99 8198 413 0.1038 167.250 166.283 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0979 81.676 81.948 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1237 36.219 35.850 1.022 0.996 0.000 1.221-1.150 99.97 13689 708 0.2128 22.820 21.434 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0280 ================= 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 : 0.2612 0.1977 0.084 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_weight: 0.1642 0.1801 0.084 5.396 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1211 0.1465 0.007 0.956 9.0 119.5 20.1 258 0.124 1_adp: 0.1233 0.1532 0.007 0.956 8.6 118.1 20.8 258 0.124 1_regHadp: 0.1237 0.1536 0.007 0.956 8.6 118.1 20.8 258 0.124 1_occ: 0.1237 0.1538 0.007 0.956 8.6 118.1 20.8 258 0.124 2_bss: 0.1234 0.1530 0.007 0.956 8.7 118.2 20.9 258 0.124 2_settarget: 0.1234 0.1530 0.007 0.956 8.7 118.2 20.9 258 0.124 2_updatecdl: 0.1234 0.1530 0.007 0.965 8.7 118.2 20.9 258 0.124 2_nqh: 0.1235 0.1532 0.007 0.965 8.7 118.2 20.9 258 0.127 2_sol: 0.1220 0.1485 0.007 0.965 8.7 118.2 23.4 435 n/a 2_weight: 0.1220 0.1485 0.007 0.965 8.7 118.2 23.4 435 n/a 2_xyzrec: 0.1221 0.1518 0.007 0.890 8.7 118.2 23.4 435 n/a 2_adp: 0.1197 0.1498 0.007 0.890 8.8 113.6 23.1 435 n/a 2_regHadp: 0.1197 0.1498 0.007 0.890 8.8 113.6 23.1 435 n/a 2_occ: 0.1199 0.1491 0.007 0.890 8.8 113.6 23.1 435 n/a 3_bss: 0.1193 0.1487 0.007 0.890 8.9 113.6 23.2 435 n/a 3_settarget: 0.1193 0.1487 0.007 0.890 8.9 113.6 23.2 435 n/a 3_updatecdl: 0.1193 0.1487 0.007 0.888 8.9 113.6 23.2 435 n/a 3_nqh: 0.1193 0.1487 0.007 0.888 8.9 113.6 23.2 435 n/a 3_sol: 0.1216 0.1488 0.007 0.888 8.9 113.6 21.9 449 n/a 3_weight: 0.1216 0.1488 0.007 0.888 8.9 113.6 21.9 449 n/a 3_xyzrec: 0.1221 0.1459 0.006 0.919 8.9 113.6 21.9 449 n/a 3_adp: 0.1215 0.1421 0.006 0.919 9.2 109.2 21.5 449 n/a 3_regHadp: 0.1217 0.1421 0.006 0.919 9.2 109.2 21.5 449 n/a 3_occ: 0.1212 0.1420 0.006 0.919 9.2 109.2 21.5 449 n/a 4_bss: 0.1198 0.1384 0.006 0.919 9.2 109.2 21.5 449 n/a 4_settarget: 0.1198 0.1384 0.006 0.919 9.2 109.2 21.5 449 n/a 4_updatecdl: 0.1198 0.1384 0.006 0.918 9.2 109.2 21.5 449 n/a 4_nqh: 0.1198 0.1384 0.006 0.918 9.2 109.2 21.5 449 n/a 4_sol: 0.1188 0.1343 0.006 0.918 9.2 109.2 21.4 448 n/a 4_weight: 0.1188 0.1343 0.006 0.918 9.2 109.2 21.4 448 n/a 4_xyzrec: 0.1192 0.1358 0.006 0.954 9.2 109.2 21.4 448 n/a 4_adp: 0.1178 0.1351 0.006 0.954 9.3 104.7 21.3 448 n/a 4_regHadp: 0.1179 0.1351 0.006 0.954 9.3 104.7 21.3 448 n/a 4_occ: 0.1176 0.1350 0.006 0.954 9.3 104.7 21.3 448 n/a 5_bss: 0.1172 0.1352 0.006 0.954 9.2 104.7 21.2 448 n/a 5_settarget: 0.1172 0.1352 0.006 0.954 9.2 104.7 21.2 448 n/a 5_updatecdl: 0.1172 0.1352 0.006 0.956 9.2 104.7 21.2 448 n/a 5_setrh: 0.1172 0.1352 0.006 0.956 9.2 104.7 21.2 448 n/a 5_nqh: 0.1173 0.1355 0.006 0.956 9.2 104.7 21.2 448 n/a 5_sol: 0.1170 0.1356 0.006 0.956 9.2 104.7 21.1 446 n/a 5_weight: 0.1170 0.1356 0.006 0.956 9.2 104.7 21.1 446 n/a 5_xyzrec: 0.1198 0.1388 0.007 1.088 9.2 104.7 21.1 446 n/a 5_adp: 0.1202 0.1391 0.007 1.088 9.3 102.8 21.0 446 n/a 5_regHadp: 0.1202 0.1391 0.007 1.088 9.3 102.8 21.0 446 n/a 5_occ: 0.1197 0.1386 0.007 1.088 9.3 102.8 21.0 446 n/a end: 0.1198 0.1385 0.007 1.088 9.3 102.8 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3975290_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3975290_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7400 Refinement macro-cycles (run) : 3347.1400 Write final files (write_after_run_outputs) : 77.5200 Total : 3429.4000 Total CPU time: 57.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:49 PST -0800 (1735452529.26 s) Start R-work = 0.1642, R-free = 0.1801 Final R-work = 0.1198, R-free = 0.1385 =============================================================================== Job complete usr+sys time: 3588.15 seconds wall clock time: 64 minutes 23.74 seconds (3863.74 seconds total)