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_6712476.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.27, per 1000 atoms: 0.67 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: 0.84 Conformation dependent library (CDL) restraints added in 302.8 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: 0.67 - 0.92: 595 0.92 - 1.18: 1069 1.18 - 1.43: 675 1.43 - 1.69: 783 1.69 - 1.95: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.235 1.007 0.228 1.28e-02 6.10e+03 3.18e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.457 1.674 -0.217 1.23e-02 6.61e+03 3.11e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.060 0.175 1.01e-02 9.80e+03 3.01e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.654 -0.197 1.20e-02 6.94e+03 2.70e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.520 1.329 0.191 1.21e-02 6.83e+03 2.50e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3221 4.82 - 9.65: 1857 9.65 - 14.47: 594 14.47 - 19.29: 94 19.29 - 24.11: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.69 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 136.72 -14.60 1.06e+00 8.90e-01 1.90e+02 angle pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 113.80 100.71 13.09 1.00e+00 1.00e+00 1.71e+02 angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.02 131.02 -14.00 1.11e+00 8.12e-01 1.59e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 108.87 13.25 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 939 17.49 - 34.97: 118 34.97 - 52.46: 37 52.46 - 69.94: 14 69.94 - 87.43: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual 180.00 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+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 180.00 155.59 24.41 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.213: 100 0.213 - 0.421: 63 0.421 - 0.629: 50 0.629 - 0.838: 24 0.838 - 1.046: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALA A 11 " pdb=" N ALA A 11 " pdb=" C ALA A 11 " pdb=" CB ALA A 11 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA LYS A 12 " pdb=" N LYS A 12 " pdb=" C LYS A 12 " pdb=" CB LYS A 12 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.047 2.00e-02 2.50e+03 5.85e-02 1.03e+02 pdb=" CG PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.122 2.00e-02 2.50e+03 5.38e-02 8.69e+01 pdb=" CG PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.059 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 95 " -0.036 2.00e-02 2.50e+03 7.41e-02 8.23e+01 pdb=" CD GLN A 95 " -0.068 2.00e-02 2.50e+03 pdb=" OE1 GLN A 95 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 GLN A 95 " 0.085 2.00e-02 2.50e+03 pdb="HE21 GLN A 95 " 0.055 2.00e-02 2.50e+03 pdb="HE22 GLN A 95 " -0.107 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1115 2.33 - 2.90: 8135 2.90 - 3.46: 10501 3.46 - 4.03: 15194 4.03 - 4.60: 21730 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.760 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 2.450 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.826 2.270 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.849 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.852 2.100 ... (remaining 56670 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_6712476_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= 0.2605 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787811 | | target function (ml) not normalized (work): 232241.375283 | | target function (ml) not normalized (free): 11789.328695 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2103 7.0998 4.9458| | 2: 3.57 - 2.84 1.00 2876 122 0.2424 0.1799 4.3435 4.3313| | 3: 2.84 - 2.48 1.00 2833 165 0.2389 0.1714 4.1291 4.1584| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1363 3.8271 3.8139| | 5: 2.25 - 2.09 1.00 2756 127 0.2476 0.1679 3.7945 3.8377| | 6: 2.09 - 1.97 1.00 2846 113 0.2526 0.1731 3.4738 3.5343| | 7: 1.97 - 1.87 1.00 2787 165 0.2532 0.1787 3.1499 3.2116| | 8: 1.87 - 1.79 1.00 2789 144 0.2489 0.1987 3.0734 3.1287| | 9: 1.79 - 1.72 1.00 2745 138 0.2397 0.1897 2.8902 2.971| | 10: 1.72 - 1.66 1.00 2789 158 0.2446 0.2076 2.7982 2.9192| | 11: 1.66 - 1.61 1.00 2740 147 0.2515 0.1781 2.7594 2.7292| | 12: 1.61 - 1.56 1.00 2787 146 0.2546 0.1797 2.6275 2.5956| | 13: 1.56 - 1.52 1.00 2745 130 0.2486 0.1774 2.5519 2.5472| | 14: 1.52 - 1.48 1.00 2803 134 0.2517 0.1778 2.4852 2.4964| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2205 2.4137 2.518| | 16: 1.45 - 1.42 1.00 2756 161 0.2655 0.2187 2.3701 2.449| | 17: 1.42 - 1.39 1.00 2785 139 0.2726 0.2095 2.3399 2.3493| | 18: 1.39 - 1.36 1.00 2741 179 0.2696 0.2389 2.2799 2.4135| | 19: 1.36 - 1.34 1.00 2807 134 0.2640 0.2370 2.2392 2.2745| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2262 2.1882 2.2188| | 21: 1.32 - 1.30 1.00 2785 112 0.2750 0.2276 2.1671 2.1487| | 22: 1.29 - 1.27 1.00 2704 152 0.2700 0.2531 2.127 2.1993| | 23: 1.27 - 1.26 1.00 2802 156 0.2715 0.2492 2.0867 2.1712| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2500 2.0638 2.1551| | 25: 1.24 - 1.22 1.00 2734 148 0.2802 0.2337 2.0307 2.0564| | 26: 1.22 - 1.21 1.00 2727 135 0.2868 0.2315 2.0073 2.0886| | 27: 1.21 - 1.19 1.00 2814 148 0.2931 0.2379 1.9994 1.9619| | 28: 1.19 - 1.18 1.00 2671 147 0.3005 0.2544 1.9848 1.9667| | 29: 1.18 - 1.16 1.00 2800 134 0.2917 0.2607 1.9501 1.9702| | 30: 1.16 - 1.15 1.00 2740 148 0.3081 0.2888 1.9236 1.9736| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.68 0.76 0.23 1460.06| | 2: 3.57 - 2.84 2876 122 0.81 25.84 1.27 0.23 1460.06| | 3: 2.84 - 2.48 2833 165 0.74 31.72 1.25 0.24 1211.88| | 4: 2.47 - 2.25 2825 136 0.81 25.59 1.26 0.25 567.81| | 5: 2.25 - 2.09 2756 127 0.77 29.31 1.28 0.25 567.81| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 312.48| | 7: 1.97 - 1.87 2787 165 0.90 16.90 1.28 0.26 94.73| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.25 0.26 94.73| | 9: 1.79 - 1.72 2745 138 0.88 18.80 1.23 0.25 56.61| | 10: 1.72 - 1.66 2789 158 0.87 20.24 1.23 0.25 48.97| | 11: 1.66 - 1.61 2740 147 0.86 21.44 1.24 0.25 47.14| | 12: 1.61 - 1.56 2787 146 0.89 18.21 1.24 0.25 28.63| | 13: 1.56 - 1.52 2745 130 0.87 20.00 1.23 0.25 28.63| | 14: 1.52 - 1.48 2803 134 0.87 20.37 1.23 0.25 25.60| | 15: 1.48 - 1.45 2738 128 0.87 19.81 1.23 0.25 20.06| | 16: 1.45 - 1.42 2756 161 0.86 21.51 1.24 0.25 20.06| | 17: 1.42 - 1.39 2785 139 0.87 20.64 1.24 0.25 17.31| | 18: 1.39 - 1.36 2741 179 0.86 21.11 1.23 0.25 15.72| | 19: 1.36 - 1.34 2807 134 0.86 21.72 1.23 0.25 15.72| | 20: 1.34 - 1.32 2696 147 0.87 20.61 1.22 0.25 13.07| | 21: 1.32 - 1.30 2785 112 0.86 21.82 1.21 0.25 12.88| | 22: 1.29 - 1.27 2704 152 0.86 21.92 1.21 0.25 12.57| | 23: 1.27 - 1.26 2802 156 0.86 21.59 1.21 0.24 10.95| | 24: 1.26 - 1.24 2744 132 0.85 22.51 1.20 0.24 10.95| | 25: 1.24 - 1.22 2734 148 0.85 23.22 1.21 0.24 10.23| | 26: 1.22 - 1.21 2727 135 0.85 23.28 1.20 0.23 9.44| | 27: 1.21 - 1.19 2814 148 0.84 23.91 1.20 0.23 9.44| | 28: 1.19 - 1.18 2671 147 0.84 24.20 1.19 0.23 8.71| | 29: 1.18 - 1.16 2800 134 0.84 24.13 1.16 0.23 8.44| | 30: 1.16 - 1.15 2740 148 0.81 26.46 1.15 0.23 8.44| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.44 max = 1460.06 mean = 212.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.33| |phase err.(test): min = 0.00 max = 89.68 mean = 22.21| |-----------------------------------------------------------------------------| ----------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 0.237 1557 Z= 5.394 Angle : 5.266 18.400 2118 Z= 3.699 Chirality : 0.406 1.046 243 Planarity : 0.031 0.102 284 Dihedral : 14.221 87.429 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 28.11 % 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: -2.48 (0.50), residues: 224 helix: -2.80 (0.36), residues: 103 sheet: -1.52 (0.78), residues: 38 loop : 0.39 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.035 ARG A 28 TYR 0.087 0.033 TYR A 141 PHE 0.091 0.041 PHE A 119 HIS 0.081 0.037 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787811 | | target function (ml) not normalized (work): 232241.375283 | | target function (ml) not normalized (free): 11789.328695 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1974 0.1978 0.1941 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1999 0.2004 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1638 0.1631 0.1764 n_refl.: 87594 remove outliers: r(all,work,free)=0.1637 0.1630 0.1764 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 0.3842 386.339 355.645 0.731 0.916 0.401 11.894-9.307 99.02 97 4 0.1808 613.680 594.500 1.011 0.917 0.380 9.237-7.194 100.00 213 7 0.2092 501.915 491.755 1.045 0.917 0.360 7.162-5.571 100.00 427 22 0.2210 376.659 364.272 1.014 0.918 0.340 5.546-4.326 100.00 867 58 0.1271 517.060 510.511 1.049 0.919 0.219 4.315-3.360 100.00 1859 96 0.1154 491.728 487.828 1.095 0.920 0.199 3.356-2.611 100.00 3867 181 0.1438 323.040 320.049 1.084 0.921 0.048 2.608-2.026 99.99 8198 413 0.1352 214.146 212.123 1.093 0.924 0.000 2.025-1.573 100.00 17313 902 0.1645 104.578 103.898 1.087 0.928 0.000 1.573-1.221 100.00 36679 1900 0.2038 46.374 45.071 1.069 0.936 0.000 1.221-1.150 99.97 13689 708 0.2572 29.219 26.998 1.030 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1630 r_free=0.1764 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 173 ASN Total number of N/Q/H flips: 3 r_work=0.1638 r_free=0.1768 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.317120 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.759041 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 0.1466 0.0255 0.007 0.9 1.3 0.5 0.0 0 12.159 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.66 2.55 3.013 19.065 2004.759 0.017 12.44 15.44 3.00 3.230 19.584 2004.759 0.016 Individual atomic B min max mean iso aniso Overall: 8.51 118.64 21.07 2.88 0 1785 Protein: 8.51 118.64 17.93 2.88 0 1519 Water: 11.12 114.84 39.32 N/A 0 258 Other: 23.25 36.77 29.15 N/A 0 8 Chain A: 8.51 118.64 21.07 N/A 0 1785 Histogram: Values Number of atoms 8.51 - 19.52 1202 19.52 - 30.54 235 30.54 - 41.55 162 41.55 - 52.56 101 52.56 - 63.57 56 63.57 - 74.59 15 74.59 - 85.60 7 85.60 - 96.61 4 96.61 - 107.63 0 107.63 - 118.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1544 r_work=0.1249 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1549 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1247 r_free = 0.1549 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015499 | | target function (ls_wunit_k1) not normalized (work): 1291.022701 | | target function (ls_wunit_k1) not normalized (free): 112.898178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1549 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1704 0.1773 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1704 0.1773 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1727 0.1726 0.1789 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1260 0.1246 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1260 0.1246 0.1542 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3616 298.370 278.485 0.635 1.003 0.380 11.894-9.307 99.02 97 4 0.1635 477.973 466.247 0.905 1.003 0.369 9.237-7.194 100.00 213 7 0.1813 390.923 385.620 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1753 293.366 287.635 0.922 1.003 0.300 5.546-4.326 100.00 867 58 0.0921 402.719 400.176 0.948 1.003 0.204 4.315-3.360 100.00 1859 96 0.0773 382.988 382.018 0.994 1.003 0.190 3.356-2.611 100.00 3867 181 0.1019 251.603 250.902 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.0980 166.790 166.179 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1212 81.452 81.626 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1656 36.119 35.578 1.007 0.997 0.000 1.221-1.150 99.97 13689 708 0.2363 22.757 21.267 0.971 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0520 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN Total number of N/Q/H flips: 1 r_work=0.1246 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1541 | n_water=258 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1255 r_free=0.1540 | n_water=252 | time (s): 27.420 (total time: 29.760) Filter (q & B) r_work=0.1258 r_free=0.1540 | n_water=249 | time (s): 3.830 (total time: 33.590) Compute maps r_work=0.1258 r_free=0.1540 | n_water=249 | time (s): 1.850 (total time: 35.440) Filter (map) r_work=0.1270 r_free=0.1543 | n_water=237 | time (s): 3.740 (total time: 39.180) Find peaks r_work=0.1270 r_free=0.1543 | n_water=237 | time (s): 0.710 (total time: 39.890) Add new water r_work=0.1428 r_free=0.1697 | n_water=458 | time (s): 3.860 (total time: 43.750) Refine new water occ: r_work=0.1338 r_free=0.1567 adp: r_work=0.1258 r_free=0.1519 occ: r_work=0.1272 r_free=0.1514 adp: r_work=0.1235 r_free=0.1500 occ: r_work=0.1238 r_free=0.1489 adp: r_work=0.1228 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1487 r_work=0.1228 r_free=0.1487 | n_water=458 | time (s): 88.130 (total time: 131.880) Filter (q & B) r_work=0.1234 r_free=0.1493 | n_water=434 | time (s): 3.830 (total time: 135.710) Filter (dist only) r_work=0.1234 r_free=0.1492 | n_water=433 | time (s): 43.820 (total time: 179.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.334344 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1476.962351 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 0.1510 0.0281 0.007 0.9 2.2 0.5 0.0 0 12.667 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.10 2.81 3.797 23.251 1476.962 0.015 11.99 14.78 2.79 4.249 23.059 1476.962 0.015 Individual atomic B min max mean iso aniso Overall: 8.73 113.77 23.25 2.60 196 1764 Protein: 8.73 113.77 17.67 2.61 0 1519 Water: 11.07 77.63 42.69 N/A 196 237 Other: 26.02 36.21 30.38 N/A 0 8 Chain A: 8.73 113.77 20.40 N/A 0 1764 Chain S: 16.19 77.63 48.85 N/A 196 0 Histogram: Values Number of atoms 8.73 - 19.23 1207 19.23 - 29.74 247 29.74 - 40.24 190 40.24 - 50.75 130 50.75 - 61.25 116 61.25 - 71.76 57 71.76 - 82.26 7 82.26 - 92.77 3 92.77 - 103.27 1 103.27 - 113.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1479 r_work=0.1199 r_free=0.1478 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1478 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1477 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1200 r_free= 0.1477 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014048 | | target function (ls_wunit_k1) not normalized (work): 1170.138717 | | target function (ls_wunit_k1) not normalized (free): 102.611401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1200 0.1477 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1606 0.1602 0.1704 n_refl.: 87592 remove outliers: r(all,work,free)=0.1606 0.1602 0.1704 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1611 0.1608 0.1707 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1196 0.1476 n_refl.: 87592 remove outliers: r(all,work,free)=0.1209 0.1195 0.1476 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 0.3389 294.316 271.160 0.596 1.002 0.370 11.894-9.307 99.02 97 4 0.1508 477.973 475.039 0.916 1.003 0.370 9.237-7.194 100.00 213 7 0.1713 390.923 390.400 0.977 1.003 0.269 7.162-5.571 100.00 427 22 0.1519 293.366 289.508 0.935 1.003 0.250 5.546-4.326 100.00 867 58 0.0839 402.719 399.766 0.956 1.003 0.213 4.315-3.360 100.00 1859 96 0.0715 382.988 382.061 1.001 1.002 0.206 3.356-2.611 100.00 3867 181 0.0958 251.603 250.812 1.009 1.002 0.072 2.608-2.026 99.99 8198 413 0.0955 166.790 166.396 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1176 81.452 81.649 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1607 36.119 35.614 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2331 22.757 21.291 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0540 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1476 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1476 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1476 | n_water=433 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1194 r_free=0.1473 | n_water=431 | time (s): 39.810 (total time: 41.480) Filter (q & B) r_work=0.1194 r_free=0.1473 | n_water=431 | time (s): 1.230 (total time: 42.710) Compute maps r_work=0.1194 r_free=0.1473 | n_water=431 | time (s): 1.600 (total time: 44.310) Filter (map) r_work=0.1234 r_free=0.1480 | n_water=296 | time (s): 2.880 (total time: 47.190) Find peaks r_work=0.1234 r_free=0.1480 | n_water=296 | time (s): 0.490 (total time: 47.680) Add new water r_work=0.1363 r_free=0.1587 | n_water=490 | time (s): 2.470 (total time: 50.150) Refine new water occ: r_work=0.1260 r_free=0.1510 adp: r_work=0.1261 r_free=0.1512 occ: r_work=0.1237 r_free=0.1491 adp: r_work=0.1234 r_free=0.1493 occ: r_work=0.1221 r_free=0.1475 adp: r_work=0.1214 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1476 r_work=0.1214 r_free=0.1476 | n_water=490 | time (s): 203.910 (total time: 254.060) Filter (q & B) r_work=0.1217 r_free=0.1484 | n_water=455 | time (s): 3.450 (total time: 257.510) Filter (dist only) r_work=0.1217 r_free=0.1484 | n_water=455 | time (s): 35.340 (total time: 292.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.048895 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.225947 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 0.1223 0.1442 0.0219 0.006 0.9 1.9 0.5 0.0 0 1.024 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 14.42 2.19 3.620 22.190 52.226 3.720 12.07 13.98 1.91 4.146 21.991 52.226 3.649 Individual atomic B min max mean iso aniso Overall: 9.30 108.81 21.79 2.33 220 1762 Protein: 9.30 108.81 17.20 2.33 0 1519 Water: 11.63 68.50 37.02 N/A 220 235 Other: 21.06 31.87 26.66 N/A 0 8 Chain A: 9.30 108.81 19.90 N/A 0 1762 Chain S: 15.52 61.52 36.90 N/A 220 0 Histogram: Values Number of atoms 9.30 - 19.25 1236 19.25 - 29.20 268 29.20 - 39.15 215 39.15 - 49.10 147 49.10 - 59.05 82 59.05 - 69.00 22 69.00 - 78.96 6 78.96 - 88.91 3 88.91 - 98.86 1 98.86 - 108.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1398 r_work=0.1208 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1399 target_work(ml) = 3.649 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1394 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.16 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= 0.1203 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.646649 | | target function (ml) not normalized (work): 303740.316680 | | target function (ml) not normalized (free): 16049.267687 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1203 0.1394 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87589 remove outliers: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1533 0.1532 0.1578 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1192 0.1359 n_refl.: 87589 remove outliers: r(all,work,free)=0.1197 0.1189 0.1359 n_refl.: 87581 ======================== 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 90.62 82 5 0.3965 291.072 258.140 0.475 1.000 0.324 11.894-9.307 97.06 95 4 0.2312 475.106 461.160 0.858 1.002 0.274 9.237-7.194 98.18 209 7 0.2380 382.483 384.328 0.938 1.002 0.202 7.162-5.571 100.00 427 22 0.2079 293.366 282.741 0.907 1.002 0.177 5.546-4.326 100.00 867 58 0.1086 402.719 398.362 0.951 1.002 0.155 4.315-3.360 100.00 1859 96 0.0909 382.988 380.240 0.993 1.002 0.150 3.356-2.611 100.00 3867 181 0.1139 251.603 249.548 0.998 1.002 0.072 2.608-2.026 99.99 8198 413 0.1038 166.790 165.860 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1004 81.452 81.610 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.119 35.684 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2132 22.757 21.369 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0354 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1359 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=0.1189 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1359 | n_water=455 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1191 r_free=0.1360 | n_water=453 | time (s): 38.350 (total time: 40.410) Filter (q & B) r_work=0.1192 r_free=0.1359 | n_water=451 | time (s): 3.440 (total time: 43.850) Compute maps r_work=0.1192 r_free=0.1359 | n_water=451 | time (s): 1.610 (total time: 45.460) Filter (map) r_work=0.1214 r_free=0.1379 | n_water=316 | time (s): 2.790 (total time: 48.250) Find peaks r_work=0.1214 r_free=0.1379 | n_water=316 | time (s): 0.460 (total time: 48.710) Add new water r_work=0.1280 r_free=0.1438 | n_water=481 | time (s): 2.450 (total time: 51.160) Refine new water occ: r_work=0.1207 r_free=0.1374 adp: r_work=0.1207 r_free=0.1376 occ: r_work=0.1192 r_free=0.1362 adp: r_work=0.1190 r_free=0.1362 occ: r_work=0.1183 r_free=0.1355 adp: r_work=0.1179 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1352 r_work=0.1179 r_free=0.1352 | n_water=481 | time (s): 202.070 (total time: 253.230) Filter (q & B) r_work=0.1186 r_free=0.1356 | n_water=446 | time (s): 2.800 (total time: 256.030) Filter (dist only) r_work=0.1186 r_free=0.1354 | n_water=445 | time (s): 37.630 (total time: 293.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.913547 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.663765 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 0.1375 0.0183 0.006 0.9 1.6 0.5 0.0 0 0.957 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.75 1.83 3.422 21.514 47.664 3.637 11.84 13.69 1.85 3.699 21.426 47.664 3.622 Individual atomic B min max mean iso aniso Overall: 9.30 105.23 21.35 2.17 214 1758 Protein: 9.30 105.23 17.00 2.17 0 1519 Water: 11.59 67.79 36.11 N/A 214 231 Other: 20.13 29.70 25.33 N/A 0 8 Chain A: 9.30 105.23 19.60 N/A 0 1758 Chain S: 15.68 61.75 35.67 N/A 214 0 Histogram: Values Number of atoms 9.30 - 18.89 1227 18.89 - 28.48 278 28.48 - 38.08 207 38.08 - 47.67 144 47.67 - 57.26 74 57.26 - 66.85 29 66.85 - 76.45 8 76.45 - 86.04 2 86.04 - 95.63 1 95.63 - 105.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1369 r_work=0.1184 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1184 r_free = 0.1369 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1371 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1181 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621934 | | target function (ml) not normalized (work): 301652.777289 | | target function (ml) not normalized (free): 15953.679796 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1181 0.1371 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1511 0.1510 0.1556 n_refl.: 87581 remove outliers: r(all,work,free)=0.1511 0.1510 0.1556 n_refl.: 87581 overall B=-0.02 to atoms: r(all,work,free)=0.1507 0.1507 0.1554 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1180 0.1374 n_refl.: 87581 remove outliers: r(all,work,free)=0.1188 0.1178 0.1374 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 0.4068 289.054 252.578 0.454 1.000 0.308 11.894-9.307 94.12 92 4 0.2306 467.198 450.010 0.836 1.002 0.228 9.237-7.194 98.18 209 7 0.2465 382.483 377.121 0.913 1.002 0.160 7.162-5.571 100.00 427 22 0.2160 293.366 282.379 0.901 1.002 0.150 5.546-4.326 100.00 867 58 0.1123 402.719 398.395 0.954 1.002 0.140 4.315-3.360 100.00 1859 96 0.0940 382.988 380.523 0.993 1.002 0.130 3.356-2.611 100.00 3867 181 0.1148 251.603 249.662 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.1034 166.790 165.896 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0970 81.452 81.701 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.119 35.750 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2118 22.757 21.396 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1178 r_free=0.1374 After: r_work=0.1179 r_free=0.1374 ================================== NQH flips ================================== r_work=0.1179 r_free=0.1374 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=0.1179 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1179 r_free=0.1374 | n_water=445 | time (s): 1.940 (total time: 1.940) Filter (dist) r_work=0.1179 r_free=0.1374 | n_water=445 | time (s): 35.860 (total time: 37.800) Filter (q & B) r_work=0.1179 r_free=0.1374 | n_water=445 | time (s): 0.930 (total time: 38.730) Compute maps r_work=0.1179 r_free=0.1374 | n_water=445 | time (s): 1.330 (total time: 40.060) Filter (map) r_work=0.1206 r_free=0.1384 | n_water=335 | time (s): 3.240 (total time: 43.300) Find peaks r_work=0.1206 r_free=0.1384 | n_water=335 | time (s): 0.610 (total time: 43.910) Add new water r_work=0.1256 r_free=0.1422 | n_water=495 | time (s): 2.690 (total time: 46.600) Refine new water occ: r_work=0.1190 r_free=0.1365 adp: r_work=0.1191 r_free=0.1367 occ: r_work=0.1177 r_free=0.1353 adp: r_work=0.1176 r_free=0.1355 occ: r_work=0.1168 r_free=0.1344 adp: r_work=0.1166 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1166 r_free=0.1345 r_work=0.1166 r_free=0.1345 | n_water=495 | time (s): 133.440 (total time: 180.040) Filter (q & B) r_work=0.1174 r_free=0.1350 | n_water=452 | time (s): 2.860 (total time: 182.900) Filter (dist only) r_work=0.1174 r_free=0.1349 | n_water=451 | time (s): 39.750 (total time: 222.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.113773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.703862 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 0.1208 0.1379 0.0171 0.007 1.1 5.1 0.5 0.0 0 1.057 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.79 1.71 3.311 21.265 36.704 3.630 12.06 13.76 1.70 3.332 21.253 36.704 3.628 Individual atomic B min max mean iso aniso Overall: 9.30 104.60 21.28 2.13 222 1756 Protein: 9.30 104.60 16.95 2.13 0 1519 Water: 11.41 67.72 35.78 N/A 222 229 Other: 20.77 29.80 25.47 N/A 0 8 Chain A: 9.30 104.60 19.52 N/A 0 1756 Chain S: 15.54 61.75 35.23 N/A 222 0 Histogram: Values Number of atoms 9.30 - 18.83 1226 18.83 - 28.36 291 28.36 - 37.89 198 37.89 - 47.42 148 47.42 - 56.95 75 56.95 - 66.48 27 66.48 - 76.01 8 76.01 - 85.54 2 85.54 - 95.07 1 95.07 - 104.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1376 r_work=0.1206 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1376 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1376 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1203 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.626767 | | target function (ml) not normalized (work): 302037.165844 | | target function (ml) not normalized (free): 15950.745125 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1420 0.1391 5.6846 5.6368| | 2: 3.57 - 2.84 1.00 2888 124 0.1125 0.1418 5.2005 5.2494| | 3: 2.83 - 2.48 1.00 2820 163 0.1222 0.1342 5.0016 5.0362| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1216 4.7081 4.7738| | 5: 2.25 - 2.09 1.00 2756 127 0.0992 0.1113 4.6471 4.7246| | 6: 2.09 - 1.97 1.00 2846 113 0.0981 0.1248 4.3566 4.4937| | 7: 1.97 - 1.87 1.00 2787 165 0.1011 0.1205 4.0924 4.1803| | 8: 1.87 - 1.79 1.00 2789 144 0.1025 0.1250 4.002 4.092| | 9: 1.79 - 1.72 1.00 2745 138 0.0973 0.1298 3.7278 3.8936| | 10: 1.72 - 1.66 1.00 2831 160 0.1001 0.1265 3.64 3.7596| | 11: 1.66 - 1.61 1.00 2712 147 0.0977 0.1103 3.5785 3.6115| | 12: 1.61 - 1.56 1.00 2773 144 0.0937 0.1219 3.363 3.5009| | 13: 1.56 - 1.52 1.00 2745 130 0.0987 0.1074 3.348 3.4295| | 14: 1.52 - 1.48 1.00 2803 134 0.1003 0.1148 3.2714 3.3605| | 15: 1.48 - 1.45 1.00 2738 128 0.1024 0.1292 3.1764 3.3138| | 16: 1.45 - 1.42 1.00 2756 161 0.1083 0.1276 3.1591 3.2466| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1312 3.1217 3.2423| | 18: 1.39 - 1.36 1.00 2741 179 0.1166 0.1370 3.0924 3.2559| | 19: 1.36 - 1.34 1.00 2807 134 0.1235 0.1584 3.1004 3.2958| | 20: 1.34 - 1.32 1.00 2696 147 0.1326 0.1507 3.0889 3.1413| | 21: 1.32 - 1.30 1.00 2785 112 0.1425 0.1649 3.0904 3.168| | 22: 1.29 - 1.27 1.00 2704 152 0.1488 0.1940 3.0881 3.2949| | 23: 1.27 - 1.26 1.00 2802 156 0.1594 0.1843 3.1099 3.2131| | 24: 1.26 - 1.24 1.00 2744 132 0.1637 0.1747 3.1003 3.1809| | 25: 1.24 - 1.22 1.00 2733 148 0.1802 0.2335 3.1112 3.2957| | 26: 1.22 - 1.21 1.00 2727 135 0.1864 0.1799 3.1251 3.1987| | 27: 1.21 - 1.19 1.00 2814 148 0.2013 0.2093 3.1411 3.1435| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2294 3.1385 3.1583| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2367 3.1277 3.2129| | 30: 1.16 - 1.15 1.00 2739 148 0.2385 0.2506 3.1168 3.1677| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.05 1.00 0.97 6174.06| | 2: 3.57 - 2.84 2888 124 0.92 13.19 1.01 0.97 6174.06| | 3: 2.83 - 2.48 2820 163 0.89 17.43 0.99 0.97 5184.63| | 4: 2.47 - 2.25 2825 136 0.91 14.57 1.00 0.98 2633.22| | 5: 2.25 - 2.09 2756 127 0.89 16.88 1.01 0.98 2633.22| | 6: 2.09 - 1.97 2846 113 0.92 13.77 1.02 0.97 1562.78| | 7: 1.97 - 1.87 2787 165 0.94 11.09 1.02 0.97 649.84| | 8: 1.87 - 1.79 2789 144 0.91 14.74 1.00 0.97 649.84| | 9: 1.79 - 1.72 2745 138 0.93 11.58 0.98 0.97 347.73| | 10: 1.72 - 1.66 2831 160 0.93 12.40 0.98 0.97 287.23| | 11: 1.66 - 1.61 2712 147 0.93 13.11 0.98 0.97 274.10| | 12: 1.61 - 1.56 2773 144 0.95 9.66 0.99 0.97 150.27| | 13: 1.56 - 1.52 2745 130 0.94 11.26 1.02 0.97 150.27| | 14: 1.52 - 1.48 2803 134 0.94 11.39 1.02 0.97 133.77| | 15: 1.48 - 1.45 2738 128 0.95 10.43 1.01 0.98 103.54| | 16: 1.45 - 1.42 2756 161 0.94 11.61 1.01 0.98 103.54| | 17: 1.42 - 1.39 2785 139 0.94 11.46 1.01 0.98 93.50| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 87.68| | 19: 1.36 - 1.34 2807 134 0.94 12.34 1.00 0.98 87.68| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.96 82.71| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.98 0.96 82.36| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.96 82.50| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.98 0.95 83.20| | 24: 1.26 - 1.24 2744 132 0.92 15.00 0.97 0.95 83.20| | 25: 1.24 - 1.22 2733 148 0.91 16.38 0.96 0.94 84.46| | 26: 1.22 - 1.21 2727 135 0.90 18.03 1.02 0.93 85.85| | 27: 1.21 - 1.19 2814 148 0.89 18.67 1.02 0.93 85.85| | 28: 1.19 - 1.18 2671 147 0.88 20.11 1.01 0.93 88.47| | 29: 1.18 - 1.16 2800 134 0.88 20.39 0.99 0.92 89.46| | 30: 1.16 - 1.15 2739 148 0.87 21.77 0.98 0.92 89.46| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.36 max = 6174.06 mean = 970.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.08| |phase err.(test): min = 0.00 max = 89.86 mean = 14.20| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1203 0.1376 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1528 0.1529 0.1555 n_refl.: 87576 remove outliers: r(all,work,free)=0.1528 0.1529 0.1555 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1526 0.1526 0.1553 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1203 0.1379 n_refl.: 87576 remove outliers: r(all,work,free)=0.1211 0.1203 0.1379 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4212 289.054 245.557 0.440 1.000 0.320 11.894-9.307 94.12 92 4 0.2253 467.198 448.314 0.831 1.001 0.222 9.237-7.194 97.27 207 7 0.2518 382.090 375.773 0.903 1.001 0.130 7.162-5.571 100.00 427 22 0.2274 293.366 282.271 0.892 1.002 0.120 5.546-4.326 100.00 867 58 0.1182 402.719 398.421 0.954 1.002 0.120 4.315-3.360 100.00 1859 96 0.0999 382.988 380.267 0.995 1.002 0.120 3.356-2.611 100.00 3867 181 0.1186 251.603 249.681 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1046 166.790 165.742 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0988 81.452 81.731 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1239 36.119 35.770 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2118 22.757 21.377 0.976 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0375 ================= 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 : 0.2605 0.1941 0.082 5.266 8.8 119.3 19.9 258 0.000 1_bss: 0.1630 0.1764 0.082 5.266 9.1 119.5 20.1 258 0.000 1_settarget: 0.1630 0.1764 0.082 5.266 9.1 119.5 20.1 258 0.000 1_nqh: 0.1638 0.1768 0.082 5.266 9.1 119.5 20.1 258 0.009 1_weight: 0.1638 0.1768 0.082 5.266 9.1 119.5 20.1 258 0.009 1_xyzrec: 0.1211 0.1466 0.007 0.946 9.1 119.5 20.1 258 0.134 1_adp: 0.1244 0.1544 0.007 0.946 8.5 118.6 21.1 258 0.134 1_regHadp: 0.1249 0.1549 0.007 0.946 8.5 118.6 21.1 258 0.134 1_occ: 0.1247 0.1549 0.007 0.946 8.5 118.6 21.1 258 0.134 2_bss: 0.1246 0.1542 0.007 0.946 8.6 118.8 21.2 258 0.134 2_settarget: 0.1246 0.1542 0.007 0.946 8.6 118.8 21.2 258 0.134 2_updatecdl: 0.1246 0.1542 0.007 0.946 8.6 118.8 21.2 258 0.134 2_nqh: 0.1246 0.1541 0.007 0.946 8.6 118.8 21.2 258 0.131 2_sol: 0.1234 0.1492 0.007 0.946 8.6 118.8 23.6 433 n/a 2_weight: 0.1234 0.1492 0.007 0.946 8.6 118.8 23.6 433 n/a 2_xyzrec: 0.1229 0.1510 0.007 0.872 8.6 118.8 23.6 433 n/a 2_adp: 0.1199 0.1479 0.007 0.872 8.7 113.8 23.2 433 n/a 2_regHadp: 0.1199 0.1478 0.007 0.872 8.7 113.8 23.2 433 n/a 2_occ: 0.1200 0.1477 0.007 0.872 8.7 113.8 23.2 433 n/a 3_bss: 0.1195 0.1476 0.007 0.872 8.8 113.8 23.3 433 n/a 3_settarget: 0.1195 0.1476 0.007 0.872 8.8 113.8 23.3 433 n/a 3_updatecdl: 0.1195 0.1476 0.007 0.872 8.8 113.8 23.3 433 n/a 3_nqh: 0.1195 0.1476 0.007 0.872 8.8 113.8 23.3 433 n/a 3_sol: 0.1217 0.1484 0.007 0.872 8.8 113.8 22.1 455 n/a 3_weight: 0.1217 0.1484 0.007 0.872 8.8 113.8 22.1 455 n/a 3_xyzrec: 0.1223 0.1442 0.006 0.915 8.8 113.8 22.1 455 n/a 3_adp: 0.1207 0.1398 0.006 0.915 9.3 108.8 21.8 455 n/a 3_regHadp: 0.1208 0.1399 0.006 0.915 9.3 108.8 21.8 455 n/a 3_occ: 0.1203 0.1394 0.006 0.915 9.3 108.8 21.8 455 n/a 4_bss: 0.1189 0.1359 0.006 0.915 9.3 108.8 21.8 455 n/a 4_settarget: 0.1189 0.1359 0.006 0.915 9.3 108.8 21.8 455 n/a 4_updatecdl: 0.1189 0.1359 0.006 0.916 9.3 108.8 21.8 455 n/a 4_nqh: 0.1189 0.1359 0.006 0.916 9.3 108.8 21.8 455 n/a 4_sol: 0.1186 0.1354 0.006 0.916 9.3 108.8 21.5 445 n/a 4_weight: 0.1186 0.1354 0.006 0.916 9.3 108.8 21.5 445 n/a 4_xyzrec: 0.1192 0.1375 0.006 0.945 9.3 108.8 21.5 445 n/a 4_adp: 0.1184 0.1369 0.006 0.945 9.3 105.2 21.3 445 n/a 4_regHadp: 0.1184 0.1369 0.006 0.945 9.3 105.2 21.3 445 n/a 4_occ: 0.1181 0.1371 0.006 0.945 9.3 105.2 21.3 445 n/a 5_bss: 0.1178 0.1374 0.006 0.945 9.3 105.2 21.3 445 n/a 5_settarget: 0.1178 0.1374 0.006 0.945 9.3 105.2 21.3 445 n/a 5_updatecdl: 0.1178 0.1374 0.006 0.945 9.3 105.2 21.3 445 n/a 5_setrh: 0.1179 0.1374 0.006 0.945 9.3 105.2 21.3 445 n/a 5_nqh: 0.1179 0.1374 0.006 0.945 9.3 105.2 21.3 445 n/a 5_sol: 0.1174 0.1349 0.006 0.945 9.3 105.2 21.3 451 n/a 5_weight: 0.1174 0.1349 0.006 0.945 9.3 105.2 21.3 451 n/a 5_xyzrec: 0.1208 0.1379 0.007 1.061 9.3 105.2 21.3 451 n/a 5_adp: 0.1206 0.1376 0.007 1.061 9.3 104.6 21.3 451 n/a 5_regHadp: 0.1206 0.1376 0.007 1.061 9.3 104.6 21.3 451 n/a 5_occ: 0.1203 0.1376 0.007 1.061 9.3 104.6 21.3 451 n/a end: 0.1203 0.1379 0.007 1.061 9.3 104.6 21.3 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6712476_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6712476_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7600 Refinement macro-cycles (run) : 3382.8700 Write final files (write_after_run_outputs) : 71.9500 Total : 3459.5800 Total CPU time: 58.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:09:57 PST -0800 (1735452597.46 s) Start R-work = 0.1630, R-free = 0.1764 Final R-work = 0.1203, R-free = 0.1379 =============================================================================== Job complete usr+sys time: 3613.76 seconds wall clock time: 65 minutes 27.52 seconds (3927.52 seconds total)