Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.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_7848743.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7848743.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.43, per 1000 atoms: 0.72 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: 0.89 Conformation dependent library (CDL) restraints added in 333.5 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 524 0.92 - 1.17: 1131 1.17 - 1.42: 627 1.42 - 1.68: 838 1.68 - 1.93: 33 Bond restraints: 3153 Sorted by residual: bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.463 1.722 -0.259 1.14e-02 7.69e+03 5.15e+02 bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.179 0.160 7.50e-03 1.78e+04 4.57e+02 bond pdb=" C PRO A 43 " pdb=" O PRO A 43 " ideal model delta sigma weight residual 1.233 1.004 0.229 1.10e-02 8.26e+03 4.33e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.234 1.001 0.233 1.16e-02 7.43e+03 4.02e+02 bond pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 1.234 1.014 0.220 1.20e-02 6.94e+03 3.36e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3172 4.79 - 9.58: 1880 9.58 - 14.36: 609 14.36 - 19.15: 107 19.15 - 23.93: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " ideal model delta sigma weight residual 122.07 138.06 -15.99 1.03e+00 9.43e-01 2.41e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.18 107.34 15.84 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.07 129.76 -9.69 7.10e-01 1.98e+00 1.86e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 121.00 110.11 10.89 8.30e-01 1.45e+00 1.72e+02 angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 109.79 12.81 1.00e+00 1.00e+00 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 927 16.05 - 32.10: 118 32.10 - 48.15: 45 48.15 - 64.20: 19 64.20 - 80.25: 2 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 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+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 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.231: 103 0.231 - 0.460: 79 0.460 - 0.690: 47 0.690 - 0.919: 10 0.919 - 1.148: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.59 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" CA APRO A 66 " pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CB APRO A 66 " both_signs ideal model delta sigma weight residual False 2.72 1.72 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 6.86e-02 1.41e+02 pdb=" CG PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.110 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.061 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.090 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CD GLN A 45 " -0.116 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " -0.072 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1007 2.31 - 2.88: 7997 2.88 - 3.46: 10546 3.46 - 4.03: 15328 4.03 - 4.60: 21693 Nonbonded interactions: 56571 Sorted by model distance: nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.741 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.743 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.788 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.803 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.811 2.450 ... (remaining 56566 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_7848743_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= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792487 | | target function (ml) not normalized (work): 232630.945006 | | target function (ml) not normalized (free): 11809.152330 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3029 0.2097 6.9973 4.9487| | 2: 3.57 - 2.84 1.00 2876 122 0.2438 0.1954 4.3585 4.3594| | 3: 2.84 - 2.48 1.00 2833 165 0.2362 0.1631 4.1334 4.1602| | 4: 2.47 - 2.25 1.00 2825 136 0.2338 0.1524 3.8391 3.8528| | 5: 2.25 - 2.09 1.00 2756 127 0.2488 0.1588 3.8089 3.8221| | 6: 2.09 - 1.97 1.00 2846 113 0.2557 0.1833 3.4751 3.563| | 7: 1.97 - 1.87 1.00 2787 165 0.2525 0.1824 3.1401 3.1689| | 8: 1.87 - 1.79 1.00 2789 144 0.2503 0.1903 3.0613 3.1479| | 9: 1.79 - 1.72 1.00 2745 138 0.2401 0.1914 2.9049 2.9989| | 10: 1.72 - 1.66 1.00 2789 158 0.2348 0.1918 2.8023 2.8936| | 11: 1.66 - 1.61 1.00 2740 147 0.2484 0.2101 2.7578 2.8428| | 12: 1.61 - 1.56 1.00 2787 146 0.2496 0.1827 2.6475 2.5759| | 13: 1.56 - 1.52 1.00 2745 130 0.2509 0.2024 2.581 2.6867| | 14: 1.52 - 1.48 1.00 2803 134 0.2538 0.1953 2.5073 2.5349| | 15: 1.48 - 1.45 1.00 2738 128 0.2526 0.2146 2.4281 2.4946| | 16: 1.45 - 1.42 1.00 2756 161 0.2699 0.2231 2.3916 2.45| | 17: 1.42 - 1.39 1.00 2785 139 0.2710 0.2282 2.3353 2.4231| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2068 2.2738 2.313| | 19: 1.36 - 1.34 1.00 2807 134 0.2658 0.2201 2.2498 2.2335| | 20: 1.34 - 1.32 1.00 2696 147 0.2676 0.2296 2.1912 2.1891| | 21: 1.32 - 1.30 1.00 2785 112 0.2747 0.2321 2.1753 2.204| | 22: 1.29 - 1.27 1.00 2704 152 0.2743 0.2472 2.1326 2.1687| | 23: 1.27 - 1.26 1.00 2802 156 0.2835 0.2234 2.1096 2.1083| | 24: 1.26 - 1.24 1.00 2744 132 0.2788 0.2355 2.0724 2.1065| | 25: 1.24 - 1.22 1.00 2734 148 0.2863 0.2664 2.0336 2.1029| | 26: 1.22 - 1.21 1.00 2727 135 0.2906 0.2152 2.0131 2.0447| | 27: 1.21 - 1.19 1.00 2814 148 0.3054 0.2501 2.0287 2.0125| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.2737 1.9889 1.9878| | 29: 1.18 - 1.16 1.00 2800 134 0.2978 0.2549 1.9527 2.0079| | 30: 1.16 - 1.15 1.00 2740 148 0.3086 0.2870 1.93 1.9393| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.08 0.76 0.23 1513.06| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1513.06| | 3: 2.84 - 2.48 2833 165 0.73 32.47 1.25 0.23 1254.31| | 4: 2.47 - 2.25 2825 136 0.81 25.88 1.26 0.25 582.82| | 5: 2.25 - 2.09 2756 127 0.77 29.60 1.28 0.25 582.82| | 6: 2.09 - 1.97 2846 113 0.83 22.82 1.29 0.25 318.61| | 7: 1.97 - 1.87 2787 165 0.90 16.71 1.28 0.25 93.27| | 8: 1.87 - 1.79 2789 144 0.85 21.48 1.25 0.25 93.27| | 9: 1.79 - 1.72 2745 138 0.87 19.23 1.23 0.25 57.66| | 10: 1.72 - 1.66 2789 158 0.86 20.74 1.21 0.25 50.53| | 11: 1.66 - 1.61 2740 147 0.85 21.87 1.24 0.25 48.76| | 12: 1.61 - 1.56 2787 146 0.88 18.97 1.23 0.25 30.87| | 13: 1.56 - 1.52 2745 130 0.86 20.88 1.23 0.25 30.87| | 14: 1.52 - 1.48 2803 134 0.86 21.09 1.23 0.25 27.42| | 15: 1.48 - 1.45 2738 128 0.87 20.19 1.22 0.25 21.11| | 16: 1.45 - 1.42 2756 161 0.85 21.80 1.24 0.25 21.11| | 17: 1.42 - 1.39 2785 139 0.87 20.86 1.24 0.25 17.75| | 18: 1.39 - 1.36 2741 179 0.87 20.92 1.22 0.25 15.80| | 19: 1.36 - 1.34 2807 134 0.85 22.04 1.22 0.25 15.80| | 20: 1.34 - 1.32 2696 147 0.87 20.54 1.21 0.25 12.71| | 21: 1.32 - 1.30 2785 112 0.86 21.46 1.21 0.25 12.50| | 22: 1.29 - 1.27 2704 152 0.86 21.87 1.21 0.25 12.17| | 23: 1.27 - 1.26 2802 156 0.86 21.65 1.22 0.24 10.52| | 24: 1.26 - 1.24 2744 132 0.86 21.89 1.20 0.24 10.52| | 25: 1.24 - 1.22 2734 148 0.85 23.13 1.22 0.24 10.02| | 26: 1.22 - 1.21 2727 135 0.85 23.38 1.20 0.24 9.47| | 27: 1.21 - 1.19 2814 148 0.84 24.01 1.21 0.24 9.47| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.18 0.23 8.99| | 29: 1.18 - 1.16 2800 134 0.83 25.04 1.17 0.23 8.81| | 30: 1.16 - 1.15 2740 148 0.81 26.70 1.16 0.23 8.81| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 8.81 max = 1513.06 mean = 219.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.59| |phase err.(test): min = 0.00 max = 89.88 mean = 22.60| |-----------------------------------------------------------------------------| ----------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 0.259 1557 Z= 5.513 Angle : 5.384 15.993 2118 Z= 3.813 Chirality : 0.384 1.148 243 Planarity : 0.032 0.100 284 Dihedral : 13.568 80.246 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.49), residues: 224 helix: -2.99 (0.35), residues: 108 sheet: -0.53 (0.99), residues: 30 loop : -0.40 (0.61), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 27 TYR 0.071 0.033 TYR A 141 PHE 0.121 0.046 PHE A 164 HIS 0.054 0.030 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= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792487 | | target function (ml) not normalized (work): 232630.945006 | | target function (ml) not normalized (free): 11809.152330 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2568 0.2608 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2568 0.2608 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1963 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2008 0.1979 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1638 0.1788 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1788 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 0.3855 386.460 354.778 0.716 0.921 0.397 11.894-9.307 99.02 97 4 0.1831 613.872 594.149 1.001 0.922 0.380 9.237-7.194 100.00 213 7 0.2135 502.072 491.628 1.041 0.922 0.370 7.162-5.571 100.00 427 22 0.2204 376.777 364.805 1.011 0.922 0.290 5.546-4.326 100.00 867 58 0.1291 517.222 511.737 1.048 0.922 0.218 4.315-3.360 100.00 1859 96 0.1128 491.881 487.777 1.094 0.922 0.189 3.356-2.611 100.00 3867 181 0.1438 323.141 319.535 1.084 0.921 0.129 2.608-2.026 99.99 8198 413 0.1367 214.213 212.207 1.096 0.920 0.000 2.025-1.573 100.00 17313 902 0.1649 104.610 103.933 1.100 0.918 0.000 1.573-1.221 100.00 36679 1900 0.2052 46.388 44.979 1.091 0.915 0.000 1.221-1.150 99.97 13689 708 0.2613 29.228 26.984 1.068 0.913 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1788 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1642 r_free=0.1793 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.762083 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1992.531414 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 0.1207 0.1459 0.0251 0.007 1.0 1.6 0.5 0.0 0 12.881 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 14.59 2.51 3.013 19.057 1992.531 0.017 12.40 15.39 3.00 3.262 19.591 1992.531 0.016 Individual atomic B min max mean iso aniso Overall: 8.58 118.85 21.09 2.86 0 1785 Protein: 8.58 118.85 17.96 2.86 0 1519 Water: 11.10 114.58 39.28 N/A 0 258 Other: 22.79 36.69 29.64 N/A 0 8 Chain A: 8.58 118.85 21.09 N/A 0 1785 Histogram: Values Number of atoms 8.58 - 19.60 1203 19.60 - 30.63 232 30.63 - 41.66 165 41.66 - 52.69 101 52.69 - 63.71 54 63.71 - 74.74 17 74.74 - 85.77 6 85.77 - 96.80 4 96.80 - 107.83 0 107.83 - 118.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1540 r_work=0.1245 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1544 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1244 r_free = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 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= 0.1244 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015337 | | target function (ls_wunit_k1) not normalized (work): 1277.550920 | | target function (ls_wunit_k1) not normalized (free): 113.790371 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1258 0.1244 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1707 0.1705 0.1779 n_refl.: 87593 remove outliers: r(all,work,free)=0.1707 0.1705 0.1779 n_refl.: 87593 overall B=0.11 to atoms: r(all,work,free)=0.1726 0.1724 0.1793 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1244 0.1543 n_refl.: 87593 remove outliers: r(all,work,free)=0.1258 0.1244 0.1543 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 0.3596 298.488 277.753 0.632 1.002 0.376 11.894-9.307 99.02 97 4 0.1600 478.161 467.068 0.908 1.003 0.372 9.237-7.194 100.00 213 7 0.1803 391.077 385.929 0.947 1.003 0.350 7.162-5.571 100.00 427 22 0.1709 293.482 288.501 0.924 1.003 0.248 5.546-4.326 100.00 867 58 0.0908 402.878 400.465 0.950 1.003 0.207 4.315-3.360 100.00 1859 96 0.0773 383.140 382.159 0.996 1.003 0.195 3.356-2.611 100.00 3867 181 0.1022 251.703 250.992 0.998 1.002 0.120 2.608-2.026 99.99 8198 413 0.0978 166.856 166.272 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1214 81.484 81.658 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1654 36.133 35.580 1.006 0.999 0.000 1.221-1.150 99.97 13689 708 0.2364 22.766 21.268 0.971 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A Total number of N/Q/H flips: 2 r_work=0.1245 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1546 | n_water=258 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1254 r_free=0.1543 | n_water=252 | time (s): 28.400 (total time: 30.950) Filter (q & B) r_work=0.1258 r_free=0.1541 | n_water=249 | time (s): 4.000 (total time: 34.950) Compute maps r_work=0.1258 r_free=0.1541 | n_water=249 | time (s): 1.790 (total time: 36.740) Filter (map) r_work=0.1276 r_free=0.1555 | n_water=234 | time (s): 4.050 (total time: 40.790) Find peaks r_work=0.1276 r_free=0.1555 | n_water=234 | time (s): 0.730 (total time: 41.520) Add new water r_work=0.1434 r_free=0.1711 | n_water=456 | time (s): 3.980 (total time: 45.500) Refine new water occ: r_work=0.1344 r_free=0.1589 adp: r_work=0.1260 r_free=0.1532 occ: r_work=0.1273 r_free=0.1533 adp: r_work=0.1238 r_free=0.1514 occ: r_work=0.1242 r_free=0.1514 adp: r_work=0.1232 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1511 r_work=0.1232 r_free=0.1511 | n_water=456 | time (s): 89.170 (total time: 134.670) Filter (q & B) r_work=0.1237 r_free=0.1514 | n_water=435 | time (s): 3.880 (total time: 138.550) Filter (dist only) r_work=0.1237 r_free=0.1514 | n_water=435 | time (s): 41.270 (total time: 179.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.920769 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1488.837395 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 0.1233 0.1521 0.0288 0.007 0.9 1.9 0.5 0.0 0 12.460 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 15.21 2.88 3.800 23.281 1488.837 0.015 12.02 14.82 2.80 4.199 23.089 1488.837 0.015 Individual atomic B min max mean iso aniso Overall: 8.70 114.92 23.26 2.60 201 1761 Protein: 8.70 114.92 17.72 2.60 0 1519 Water: 10.87 72.54 42.46 N/A 201 234 Other: 25.44 37.19 30.61 N/A 0 8 Chain A: 8.70 114.92 20.39 N/A 0 1761 Chain S: 16.52 68.90 48.41 N/A 201 0 Histogram: Values Number of atoms 8.70 - 19.32 1200 19.32 - 29.94 257 29.94 - 40.57 189 40.57 - 51.19 145 51.19 - 61.81 107 61.81 - 72.43 52 72.43 - 83.06 6 83.06 - 93.68 3 93.68 - 104.30 1 104.30 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1482 r_work=0.1202 r_free=0.1482 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1482 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 = 0.1202 r_free = 0.1471 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 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= 0.1202 r_free= 0.1471 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013973 | | target function (ls_wunit_k1) not normalized (work): 1163.857591 | | target function (ls_wunit_k1) not normalized (free): 101.777503 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1202 0.1471 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1605 0.1601 0.1706 n_refl.: 87592 remove outliers: r(all,work,free)=0.1605 0.1601 0.1706 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1612 0.1608 0.1710 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1198 0.1470 n_refl.: 87592 remove outliers: r(all,work,free)=0.1210 0.1197 0.1470 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 0.3362 294.432 272.232 0.633 0.939 0.370 11.894-9.307 99.02 97 4 0.1488 478.161 475.685 0.977 0.940 0.370 9.237-7.194 100.00 213 7 0.1694 391.077 391.857 1.042 0.940 0.277 7.162-5.571 100.00 427 22 0.1456 293.482 289.938 1.006 0.940 0.229 5.546-4.326 100.00 867 58 0.0826 402.878 399.917 1.020 0.941 0.215 4.315-3.360 100.00 1859 96 0.0708 383.140 382.083 1.065 0.941 0.210 3.356-2.611 100.00 3867 181 0.0962 251.703 251.076 1.072 0.942 0.140 2.608-2.026 99.99 8198 413 0.0963 166.856 166.464 1.079 0.944 0.000 2.025-1.573 100.00 17313 902 0.1183 81.484 81.701 1.085 0.946 0.000 1.573-1.221 100.00 36679 1900 0.1612 36.133 35.640 1.067 0.950 0.000 1.221-1.150 99.97 13689 708 0.2340 22.766 21.316 1.022 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0663 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1470 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1199 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1470 | n_water=435 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1200 r_free=0.1474 | n_water=432 | time (s): 42.150 (total time: 44.590) Filter (q & B) r_work=0.1200 r_free=0.1474 | n_water=432 | time (s): 0.830 (total time: 45.420) Compute maps r_work=0.1200 r_free=0.1474 | n_water=432 | time (s): 1.570 (total time: 46.990) Filter (map) r_work=0.1235 r_free=0.1477 | n_water=293 | time (s): 3.690 (total time: 50.680) Find peaks r_work=0.1235 r_free=0.1477 | n_water=293 | time (s): 0.610 (total time: 51.290) Add new water r_work=0.1373 r_free=0.1597 | n_water=487 | time (s): 3.670 (total time: 54.960) Refine new water occ: r_work=0.1270 r_free=0.1515 adp: r_work=0.1271 r_free=0.1518 occ: r_work=0.1248 r_free=0.1493 adp: r_work=0.1245 r_free=0.1496 occ: r_work=0.1232 r_free=0.1478 adp: r_work=0.1224 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1479 r_work=0.1224 r_free=0.1479 | n_water=487 | time (s): 232.360 (total time: 287.320) Filter (q & B) r_work=0.1228 r_free=0.1476 | n_water=453 | time (s): 2.590 (total time: 289.910) Filter (dist only) r_work=0.1228 r_free=0.1476 | n_water=453 | time (s): 39.770 (total time: 329.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.086349 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.965751 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1236 0.1449 0.0214 0.006 0.9 1.6 0.5 0.0 0 1.043 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.49 2.14 3.634 22.209 47.966 3.724 12.20 14.09 1.90 4.165 22.009 47.966 3.653 Individual atomic B min max mean iso aniso Overall: 9.26 109.97 21.74 2.34 222 1758 Protein: 9.26 109.97 17.26 2.34 0 1519 Water: 11.56 71.39 36.68 N/A 222 231 Other: 20.88 32.87 27.06 N/A 0 8 Chain A: 9.26 109.97 19.89 N/A 0 1758 Chain S: 15.35 65.32 36.44 N/A 222 0 Histogram: Values Number of atoms 9.26 - 19.33 1233 19.33 - 29.40 276 29.40 - 39.47 224 39.47 - 49.54 143 49.54 - 59.61 68 59.61 - 69.68 23 69.68 - 79.75 7 79.75 - 89.82 3 89.82 - 99.90 1 99.90 - 109.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1220 r_free=0.1410 r_work=0.1221 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1221 r_free = 0.1411 target_work(ml) = 3.653 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1407 target_work(ml) = 3.650 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1214 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.650009 | | target function (ml) not normalized (work): 304020.224914 | | target function (ml) not normalized (free): 16056.472414 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1214 0.1407 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1543 0.1541 0.1610 n_refl.: 87589 remove outliers: r(all,work,free)=0.1543 0.1541 0.1610 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1541 0.1539 0.1608 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1205 0.1375 n_refl.: 87589 remove outliers: r(all,work,free)=0.1210 0.1201 0.1375 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 0.3917 291.187 260.456 0.469 1.000 0.299 11.894-9.307 97.06 95 4 0.2408 471.560 456.945 0.856 1.001 0.283 9.237-7.194 98.18 209 7 0.2345 382.634 384.230 0.945 1.002 0.180 7.162-5.571 100.00 427 22 0.2044 293.482 283.553 0.912 1.002 0.162 5.546-4.326 100.00 867 58 0.1107 402.878 398.037 0.952 1.002 0.155 4.315-3.360 100.00 1859 96 0.0939 383.140 380.489 0.994 1.002 0.153 3.356-2.611 100.00 3867 181 0.1162 251.703 249.685 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1057 166.856 165.874 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1012 81.484 81.645 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.133 35.706 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2129 22.766 21.382 0.978 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1375 | n_water=453 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1201 r_free=0.1375 | n_water=453 | time (s): 37.740 (total time: 39.470) Filter (q & B) r_work=0.1202 r_free=0.1376 | n_water=449 | time (s): 3.840 (total time: 43.310) Compute maps r_work=0.1202 r_free=0.1376 | n_water=449 | time (s): 1.800 (total time: 45.110) Filter (map) r_work=0.1227 r_free=0.1394 | n_water=309 | time (s): 3.300 (total time: 48.410) Find peaks r_work=0.1227 r_free=0.1394 | n_water=309 | time (s): 0.450 (total time: 48.860) Add new water r_work=0.1296 r_free=0.1455 | n_water=490 | time (s): 3.270 (total time: 52.130) Refine new water occ: r_work=0.1220 r_free=0.1385 adp: r_work=0.1220 r_free=0.1386 occ: r_work=0.1204 r_free=0.1373 adp: r_work=0.1203 r_free=0.1373 occ: r_work=0.1193 r_free=0.1363 adp: r_work=0.1189 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1361 r_work=0.1189 r_free=0.1361 | n_water=490 | time (s): 214.620 (total time: 266.750) Filter (q & B) r_work=0.1196 r_free=0.1367 | n_water=449 | time (s): 3.960 (total time: 270.710) Filter (dist only) r_work=0.1196 r_free=0.1367 | n_water=449 | time (s): 36.520 (total time: 307.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.892046 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.400988 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 0.1203 0.1377 0.0174 0.006 0.9 1.9 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.77 1.74 3.443 21.552 49.401 3.638 11.90 13.73 1.83 3.952 21.394 49.401 3.623 Individual atomic B min max mean iso aniso Overall: 9.22 105.07 21.22 2.17 221 1755 Protein: 9.22 105.07 16.89 2.17 0 1519 Water: 11.47 69.71 35.80 N/A 221 228 Other: 19.57 29.60 24.40 N/A 0 8 Chain A: 9.22 105.07 19.41 N/A 0 1755 Chain S: 14.60 60.34 35.54 N/A 221 0 Histogram: Values Number of atoms 9.22 - 18.81 1227 18.81 - 28.39 286 28.39 - 37.97 217 37.97 - 47.56 131 47.56 - 57.14 74 57.14 - 66.73 26 66.73 - 76.31 10 76.31 - 85.90 2 85.90 - 95.48 1 95.48 - 105.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1373 r_work=0.1190 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1373 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1367 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 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= 0.1185 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621257 | | target function (ml) not normalized (work): 301596.428806 | | target function (ml) not normalized (free): 15927.315444 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1185 0.1367 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1506 0.1504 0.1572 n_refl.: 87581 remove outliers: r(all,work,free)=0.1506 0.1504 0.1572 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1504 0.1502 0.1570 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1184 0.1372 n_refl.: 87581 remove outliers: r(all,work,free)=0.1192 0.1183 0.1372 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 89.58 81 5 0.4104 286.580 253.800 0.437 1.000 0.304 11.894-9.307 93.14 91 4 0.2346 465.458 447.762 0.833 1.001 0.217 9.237-7.194 98.18 209 7 0.2490 382.634 376.730 0.911 1.002 0.130 7.162-5.571 100.00 427 22 0.2214 293.482 282.344 0.902 1.002 0.120 5.546-4.326 100.00 867 58 0.1151 402.878 398.011 0.952 1.002 0.118 4.315-3.360 100.00 1859 96 0.0960 383.140 380.779 0.994 1.002 0.117 3.356-2.611 100.00 3867 181 0.1156 251.703 249.840 1.002 1.002 0.090 2.608-2.026 99.99 8198 413 0.1021 166.856 166.016 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0962 81.484 81.774 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.133 35.758 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2127 22.766 21.392 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=-0.0375 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1372 After: r_work=0.1183 r_free=0.1372 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1372 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=0.1183 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1372 | n_water=449 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1183 r_free=0.1372 | n_water=449 | time (s): 37.830 (total time: 39.650) Filter (q & B) r_work=0.1183 r_free=0.1372 | n_water=448 | time (s): 3.740 (total time: 43.390) Compute maps r_work=0.1183 r_free=0.1372 | n_water=448 | time (s): 1.360 (total time: 44.750) Filter (map) r_work=0.1209 r_free=0.1403 | n_water=332 | time (s): 2.550 (total time: 47.300) Find peaks r_work=0.1209 r_free=0.1403 | n_water=332 | time (s): 0.560 (total time: 47.860) Add new water r_work=0.1254 r_free=0.1427 | n_water=487 | time (s): 3.340 (total time: 51.200) Refine new water occ: r_work=0.1192 r_free=0.1362 adp: r_work=0.1192 r_free=0.1365 occ: r_work=0.1182 r_free=0.1352 adp: r_work=0.1181 r_free=0.1354 occ: r_work=0.1175 r_free=0.1343 adp: r_work=0.1172 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1172 r_free=0.1345 r_work=0.1172 r_free=0.1345 | n_water=487 | time (s): 208.830 (total time: 260.030) Filter (q & B) r_work=0.1181 r_free=0.1359 | n_water=445 | time (s): 3.240 (total time: 263.270) Filter (dist only) r_work=0.1181 r_free=0.1357 | n_water=442 | time (s): 35.800 (total time: 299.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.916039 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.211101 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 0.1200 0.1378 0.0178 0.007 1.1 2.6 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.78 1.78 3.285 21.029 44.211 3.627 12.04 13.78 1.74 3.421 20.975 44.211 3.622 Individual atomic B min max mean iso aniso Overall: 9.21 101.63 20.90 2.05 215 1754 Protein: 9.21 101.63 16.76 2.05 0 1519 Water: 11.47 69.21 35.10 N/A 215 227 Other: 19.86 28.02 24.10 N/A 0 8 Chain A: 9.21 101.63 19.26 N/A 0 1754 Chain S: 14.12 55.96 34.33 N/A 215 0 Histogram: Values Number of atoms 9.21 - 18.46 1221 18.46 - 27.70 284 27.70 - 36.94 210 36.94 - 46.18 141 46.18 - 55.42 71 55.42 - 64.67 25 64.67 - 73.91 12 73.91 - 83.15 2 83.15 - 92.39 1 92.39 - 101.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1378 r_work=0.1204 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1378 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1373 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1201 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620918 | | target function (ml) not normalized (work): 301550.083545 | | target function (ml) not normalized (free): 15940.629007 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1441 0.1419 5.6992 5.6319| | 2: 3.57 - 2.84 1.00 2888 124 0.1126 0.1485 5.1977 5.2618| | 3: 2.83 - 2.48 1.00 2820 163 0.1209 0.1232 5.0026 5.02| | 4: 2.47 - 2.25 1.00 2825 136 0.1033 0.1156 4.7054 4.759| | 5: 2.25 - 2.09 1.00 2756 127 0.1006 0.1159 4.6476 4.7266| | 6: 2.09 - 1.97 1.00 2846 113 0.0980 0.1180 4.353 4.4711| | 7: 1.97 - 1.87 1.00 2787 165 0.1000 0.1213 4.0795 4.1784| | 8: 1.87 - 1.79 1.00 2789 144 0.1026 0.1263 3.9946 4.0918| | 9: 1.79 - 1.72 1.00 2745 138 0.0945 0.1299 3.7126 3.9008| | 10: 1.72 - 1.66 1.00 2831 160 0.1004 0.1258 3.6312 3.7444| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1086 3.5667 3.6002| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1199 3.3454 3.4907| | 13: 1.56 - 1.52 1.00 2745 130 0.0973 0.1053 3.3341 3.4305| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1103 3.2566 3.3443| | 15: 1.48 - 1.45 1.00 2738 128 0.1009 0.1353 3.1651 3.3249| | 16: 1.45 - 1.42 1.00 2756 161 0.1063 0.1253 3.1481 3.2464| | 17: 1.42 - 1.39 1.00 2785 139 0.1115 0.1290 3.1131 3.228| | 18: 1.39 - 1.36 1.00 2741 179 0.1148 0.1404 3.0855 3.2811| | 19: 1.36 - 1.34 1.00 2807 134 0.1212 0.1635 3.0913 3.2793| | 20: 1.34 - 1.32 1.00 2696 147 0.1315 0.1468 3.0853 3.1344| | 21: 1.32 - 1.30 1.00 2785 112 0.1414 0.1628 3.0854 3.1743| | 22: 1.29 - 1.27 1.00 2704 152 0.1464 0.1920 3.0813 3.2782| | 23: 1.27 - 1.26 1.00 2802 156 0.1575 0.1863 3.1028 3.2115| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1795 3.0937 3.1941| | 25: 1.24 - 1.22 1.00 2733 148 0.1799 0.2334 3.11 3.2965| | 26: 1.22 - 1.21 1.00 2727 135 0.1862 0.1742 3.1235 3.1941| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2132 3.1406 3.1595| | 28: 1.19 - 1.18 1.00 2671 147 0.2149 0.2297 3.1389 3.1597| | 29: 1.18 - 1.16 1.00 2800 134 0.2218 0.2380 3.1266 3.2219| | 30: 1.16 - 1.15 1.00 2739 148 0.2382 0.2511 3.1155 3.1638| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.00 1.00 0.97 6181.99| | 2: 3.57 - 2.84 2888 124 0.92 13.23 1.01 0.97 6181.99| | 3: 2.83 - 2.48 2820 163 0.89 17.34 0.99 0.97 5186.12| | 4: 2.47 - 2.25 2825 136 0.91 14.54 1.00 0.98 2618.07| | 5: 2.25 - 2.09 2756 127 0.89 16.82 1.01 0.98 2618.07| | 6: 2.09 - 1.97 2846 113 0.92 13.62 1.02 0.97 1545.01| | 7: 1.97 - 1.87 2787 165 0.94 10.89 1.02 0.97 629.84| | 8: 1.87 - 1.79 2789 144 0.91 14.44 1.00 0.97 629.84| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.97 339.35| | 10: 1.72 - 1.66 2831 160 0.93 12.26 0.98 0.97 281.18| | 11: 1.66 - 1.61 2712 147 0.93 12.86 0.98 0.97 268.37| | 12: 1.61 - 1.56 2773 144 0.95 9.54 0.99 0.97 147.53| | 13: 1.56 - 1.52 2745 130 0.94 11.12 1.02 0.97 147.53| | 14: 1.52 - 1.48 2803 134 0.94 11.28 1.02 0.97 131.87| | 15: 1.48 - 1.45 2738 128 0.95 10.43 1.01 0.98 103.19| | 16: 1.45 - 1.42 2756 161 0.94 11.60 1.01 0.98 103.19| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 93.60| | 18: 1.39 - 1.36 2741 179 0.94 11.82 1.01 0.98 88.04| | 19: 1.36 - 1.34 2807 134 0.94 12.39 1.00 0.98 88.04| | 20: 1.34 - 1.32 2696 147 0.94 12.54 0.99 0.96 83.06| | 21: 1.32 - 1.30 2785 112 0.93 13.46 0.98 0.96 82.71| | 22: 1.29 - 1.27 2704 152 0.93 13.94 0.98 0.96 82.84| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.94 83.53| | 24: 1.26 - 1.24 2744 132 0.92 15.05 0.97 0.94 83.53| | 25: 1.24 - 1.22 2733 148 0.91 16.42 0.96 0.94 84.90| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.42| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.93 86.42| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.92 89.37| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.92 90.48| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.92 90.48| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 82.71 max = 6181.99 mean = 967.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.85 mean = 14.05| |phase err.(test): min = 0.00 max = 87.59 mean = 14.18| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1201 0.1373 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1569 n_refl.: 87576 remove outliers: r(all,work,free)=0.1514 0.1512 0.1569 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1512 0.1511 0.1568 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1372 n_refl.: 87576 remove outliers: r(all,work,free)=0.1210 0.1202 0.1372 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 89.58 81 5 0.4259 286.580 250.764 0.425 1.000 0.297 11.894-9.307 93.14 91 4 0.2543 465.458 444.940 0.831 1.001 0.223 9.237-7.194 98.18 209 7 0.2616 382.634 373.990 0.897 1.002 0.152 7.162-5.571 100.00 427 22 0.2360 293.482 281.039 0.895 1.002 0.136 5.546-4.326 100.00 867 58 0.1205 402.878 398.453 0.953 1.002 0.120 4.315-3.360 100.00 1859 96 0.0990 383.140 380.570 0.995 1.002 0.116 3.356-2.611 100.00 3867 181 0.1183 251.703 249.777 1.001 1.001 0.053 2.608-2.026 99.99 8198 413 0.1045 166.856 165.924 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0978 81.484 81.743 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1224 36.133 35.764 1.021 0.996 0.000 1.221-1.150 99.97 13689 708 0.2120 22.766 21.391 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=-0.0236 ================= 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 : 0.2608 0.1963 0.082 5.384 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1788 0.082 5.384 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1788 0.082 5.384 9.0 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1793 0.082 5.384 9.0 119.5 20.1 258 0.007 1_weight: 0.1642 0.1793 0.082 5.384 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1207 0.1459 0.007 0.954 9.0 119.5 20.1 258 0.128 1_adp: 0.1240 0.1540 0.007 0.954 8.6 118.9 21.1 258 0.128 1_regHadp: 0.1245 0.1544 0.007 0.954 8.6 118.9 21.1 258 0.128 1_occ: 0.1244 0.1546 0.007 0.954 8.6 118.9 21.1 258 0.128 2_bss: 0.1244 0.1543 0.007 0.954 8.7 119.0 21.2 258 0.128 2_settarget: 0.1244 0.1543 0.007 0.954 8.7 119.0 21.2 258 0.128 2_updatecdl: 0.1244 0.1543 0.008 0.957 8.7 119.0 21.2 258 0.128 2_nqh: 0.1245 0.1546 0.008 0.957 8.7 119.0 21.2 258 0.128 2_sol: 0.1237 0.1514 0.008 0.957 8.7 119.0 23.6 435 n/a 2_weight: 0.1237 0.1514 0.008 0.957 8.7 119.0 23.6 435 n/a 2_xyzrec: 0.1233 0.1521 0.007 0.871 8.7 119.0 23.6 435 n/a 2_adp: 0.1202 0.1482 0.007 0.871 8.7 114.9 23.3 435 n/a 2_regHadp: 0.1202 0.1482 0.007 0.871 8.7 114.9 23.3 435 n/a 2_occ: 0.1202 0.1471 0.007 0.871 8.7 114.9 23.3 435 n/a 3_bss: 0.1197 0.1470 0.007 0.871 8.7 115.0 23.3 435 n/a 3_settarget: 0.1197 0.1470 0.007 0.871 8.7 115.0 23.3 435 n/a 3_updatecdl: 0.1197 0.1470 0.007 0.872 8.7 115.0 23.3 435 n/a 3_nqh: 0.1199 0.1470 0.007 0.872 8.7 115.0 23.3 435 n/a 3_sol: 0.1228 0.1476 0.007 0.872 8.7 115.0 22.1 453 n/a 3_weight: 0.1228 0.1476 0.007 0.872 8.7 115.0 22.1 453 n/a 3_xyzrec: 0.1236 0.1449 0.006 0.920 8.7 115.0 22.1 453 n/a 3_adp: 0.1220 0.1410 0.006 0.920 9.3 110.0 21.7 453 n/a 3_regHadp: 0.1221 0.1411 0.006 0.920 9.3 110.0 21.7 453 n/a 3_occ: 0.1214 0.1407 0.006 0.920 9.3 110.0 21.7 453 n/a 4_bss: 0.1201 0.1375 0.006 0.920 9.2 110.0 21.7 453 n/a 4_settarget: 0.1201 0.1375 0.006 0.920 9.2 110.0 21.7 453 n/a 4_updatecdl: 0.1201 0.1375 0.006 0.917 9.2 110.0 21.7 453 n/a 4_nqh: 0.1201 0.1375 0.006 0.917 9.2 110.0 21.7 453 n/a 4_sol: 0.1196 0.1367 0.006 0.917 9.2 110.0 21.5 449 n/a 4_weight: 0.1196 0.1367 0.006 0.917 9.2 110.0 21.5 449 n/a 4_xyzrec: 0.1203 0.1377 0.006 0.943 9.2 110.0 21.5 449 n/a 4_adp: 0.1190 0.1373 0.006 0.943 9.2 105.1 21.2 449 n/a 4_regHadp: 0.1190 0.1373 0.006 0.943 9.2 105.1 21.2 449 n/a 4_occ: 0.1185 0.1367 0.006 0.943 9.2 105.1 21.2 449 n/a 5_bss: 0.1183 0.1372 0.006 0.943 9.2 105.1 21.2 449 n/a 5_settarget: 0.1183 0.1372 0.006 0.943 9.2 105.1 21.2 449 n/a 5_updatecdl: 0.1183 0.1372 0.006 0.945 9.2 105.1 21.2 449 n/a 5_setrh: 0.1183 0.1372 0.006 0.945 9.2 105.1 21.2 449 n/a 5_nqh: 0.1183 0.1372 0.006 0.945 9.2 105.1 21.2 449 n/a 5_sol: 0.1181 0.1357 0.006 0.945 9.2 105.1 21.0 442 n/a 5_weight: 0.1181 0.1357 0.006 0.945 9.2 105.1 21.0 442 n/a 5_xyzrec: 0.1200 0.1378 0.007 1.055 9.2 105.1 21.0 442 n/a 5_adp: 0.1204 0.1378 0.007 1.055 9.2 101.6 20.9 442 n/a 5_regHadp: 0.1204 0.1378 0.007 1.055 9.2 101.6 20.9 442 n/a 5_occ: 0.1201 0.1373 0.007 1.055 9.2 101.6 20.9 442 n/a end: 0.1202 0.1372 0.007 1.055 9.2 101.6 20.9 442 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7848743_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7848743_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0200 Refinement macro-cycles (run) : 3585.9500 Write final files (write_after_run_outputs) : 57.6300 Total : 3648.6000 Total CPU time: 61.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:48 PST -0800 (1735452768.97 s) Start R-work = 0.1638, R-free = 0.1788 Final R-work = 0.1202, R-free = 0.1372 =============================================================================== Job complete usr+sys time: 3782.22 seconds wall clock time: 67 minutes 57.90 seconds (4077.90 seconds total)