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_2963595.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2963595.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): 0.01s 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: 2.30, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 301.1 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 528 0.91 - 1.16: 1115 1.16 - 1.42: 620 1.42 - 1.67: 851 1.67 - 1.93: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.524 1.772 -0.248 1.26e-02 6.30e+03 3.87e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.163 0.215 1.10e-02 8.26e+03 3.82e+02 bond pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 1.456 1.240 0.215 1.11e-02 8.12e+03 3.76e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.512 -0.191 1.00e-02 1.00e+04 3.63e+02 bond pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 1.466 1.242 0.223 1.19e-02 7.06e+03 3.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3338 4.85 - 9.69: 1833 9.69 - 14.54: 495 14.54 - 19.39: 105 19.39 - 24.23: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 71 " pdb=" C VAL A 71 " pdb=" N LEU A 72 " ideal model delta sigma weight residual 123.18 104.97 18.21 1.05e+00 9.07e-01 3.01e+02 angle pdb=" O SER A 47 " pdb=" C SER A 47 " pdb=" N ARG A 48 " ideal model delta sigma weight residual 122.12 138.53 -16.41 1.06e+00 8.90e-01 2.40e+02 angle pdb=" CA AGLU A 94 " pdb=" C AGLU A 94 " pdb=" O AGLU A 94 " ideal model delta sigma weight residual 119.97 104.45 15.52 1.15e+00 7.56e-01 1.82e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.76 -12.41 9.20e-01 1.18e+00 1.82e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.83 108.18 13.65 1.03e+00 9.43e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 18.44: 958 18.44 - 36.87: 110 36.87 - 55.30: 30 55.30 - 73.73: 10 73.73 - 92.15: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+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 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.218: 109 0.218 - 0.430: 74 0.430 - 0.641: 31 0.641 - 0.853: 24 0.853 - 1.064: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.69 1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA BLYS A 175 " pdb=" N BLYS A 175 " pdb=" C BLYS A 175 " pdb=" CB BLYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 3.39 -0.95 2.00e-01 2.50e+01 2.27e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.043 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.110 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.145 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.126 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.058 2.00e-02 2.50e+03 6.04e-02 1.10e+02 pdb=" CG PHE A 119 " -0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.098 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.002 2.00e-02 2.50e+03 7.06e-02 7.48e+01 pdb=" CG ASN A 173 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.126 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " 0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.101 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 717 2.27 - 2.85: 7812 2.85 - 3.43: 10581 3.43 - 4.02: 15362 4.02 - 4.60: 22067 Nonbonded interactions: 56539 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.685 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.771 2.450 x-y,-y,-z-4/3 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.773 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.801 2.450 x-y,-y,-z-4/3 ... (remaining 56534 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_2963595_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= 0.1942 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788674 | | target function (ml) not normalized (work): 232313.244986 | | target function (ml) not normalized (free): 11816.781129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3025 0.2109 6.9723 4.9545| | 2: 3.57 - 2.84 1.00 2876 122 0.2460 0.1880 4.3633 4.3511| | 3: 2.84 - 2.48 1.00 2833 165 0.2372 0.1637 4.1385 4.1733| | 4: 2.47 - 2.25 1.00 2825 136 0.2319 0.1416 3.8415 3.8422| | 5: 2.25 - 2.09 1.00 2756 127 0.2482 0.1609 3.8086 3.8266| | 6: 2.09 - 1.97 1.00 2846 113 0.2534 0.1688 3.4703 3.5705| | 7: 1.97 - 1.87 1.00 2787 165 0.2567 0.1663 3.1387 3.1434| | 8: 1.87 - 1.79 1.00 2789 144 0.2510 0.1820 3.0614 3.1107| | 9: 1.79 - 1.72 1.00 2745 138 0.2450 0.1938 2.8989 2.9754| | 10: 1.72 - 1.66 1.00 2789 158 0.2375 0.2054 2.795 2.9489| | 11: 1.66 - 1.61 1.00 2740 147 0.2547 0.1919 2.7728 2.7862| | 12: 1.61 - 1.56 1.00 2787 146 0.2497 0.2030 2.6228 2.6419| | 13: 1.56 - 1.52 1.00 2745 130 0.2466 0.1782 2.5546 2.5611| | 14: 1.52 - 1.48 1.00 2803 134 0.2515 0.1863 2.4862 2.4811| | 15: 1.48 - 1.45 1.00 2738 128 0.2556 0.2178 2.4115 2.554| | 16: 1.45 - 1.42 1.00 2756 161 0.2657 0.2030 2.3725 2.3647| | 17: 1.42 - 1.39 1.00 2785 139 0.2688 0.2171 2.3429 2.3967| | 18: 1.39 - 1.36 1.00 2741 179 0.2732 0.2105 2.2793 2.2733| | 19: 1.36 - 1.34 1.00 2807 134 0.2636 0.2317 2.2462 2.3025| | 20: 1.34 - 1.32 1.00 2696 147 0.2672 0.2397 2.1892 2.2274| | 21: 1.32 - 1.30 1.00 2785 112 0.2718 0.2192 2.1692 2.1198| | 22: 1.29 - 1.27 1.00 2704 152 0.2682 0.2561 2.1347 2.2004| | 23: 1.27 - 1.26 1.00 2802 156 0.2815 0.2367 2.1002 2.1509| | 24: 1.26 - 1.24 1.00 2744 132 0.2748 0.2552 2.0746 2.1784| | 25: 1.24 - 1.22 1.00 2734 148 0.2838 0.2514 2.0493 2.0718| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2639 2.0095 2.1379| | 27: 1.21 - 1.19 1.00 2814 148 0.2937 0.2812 2.0135 2.0714| | 28: 1.19 - 1.18 1.00 2671 147 0.3029 0.2611 2.0037 1.9786| | 29: 1.18 - 1.16 1.00 2800 134 0.2933 0.2702 1.9587 2.0116| | 30: 1.16 - 1.15 1.00 2740 148 0.3062 0.2923 1.9288 1.9827| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.23 0.76 0.23 1534.41| | 2: 3.57 - 2.84 2876 122 0.80 26.55 1.28 0.23 1534.41| | 3: 2.84 - 2.48 2833 165 0.73 32.66 1.25 0.23 1271.71| | 4: 2.47 - 2.25 2825 136 0.81 26.07 1.25 0.25 589.97| | 5: 2.25 - 2.09 2756 127 0.77 29.81 1.29 0.25 589.97| | 6: 2.09 - 1.97 2846 113 0.83 23.22 1.29 0.25 321.63| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.29 0.25 92.77| | 8: 1.87 - 1.79 2789 144 0.85 21.41 1.25 0.25 92.77| | 9: 1.79 - 1.72 2745 138 0.88 18.72 1.24 0.25 55.90| | 10: 1.72 - 1.66 2789 158 0.87 20.22 1.22 0.25 48.51| | 11: 1.66 - 1.61 2740 147 0.86 21.26 1.24 0.25 46.80| | 12: 1.61 - 1.56 2787 146 0.88 18.63 1.23 0.25 29.38| | 13: 1.56 - 1.52 2745 130 0.87 20.24 1.23 0.25 29.38| | 14: 1.52 - 1.48 2803 134 0.86 20.67 1.23 0.25 26.03| | 15: 1.48 - 1.45 2738 128 0.88 19.67 1.23 0.25 19.90| | 16: 1.45 - 1.42 2756 161 0.86 21.32 1.24 0.25 19.90| | 17: 1.42 - 1.39 2785 139 0.87 20.34 1.23 0.25 16.93| | 18: 1.39 - 1.36 2741 179 0.87 20.68 1.23 0.25 15.22| | 19: 1.36 - 1.34 2807 134 0.86 21.40 1.21 0.25 15.22| | 20: 1.34 - 1.32 2696 147 0.87 20.42 1.21 0.25 12.76| | 21: 1.32 - 1.30 2785 112 0.86 21.49 1.20 0.25 12.59| | 22: 1.29 - 1.27 2704 152 0.86 21.83 1.20 0.25 12.36| | 23: 1.27 - 1.26 2802 156 0.86 22.26 1.21 0.24 11.17| | 24: 1.26 - 1.24 2744 132 0.85 22.80 1.19 0.24 11.17| | 25: 1.24 - 1.22 2734 148 0.84 23.74 1.20 0.24 10.70| | 26: 1.22 - 1.21 2727 135 0.84 24.13 1.19 0.23 10.18| | 27: 1.21 - 1.19 2814 148 0.83 24.88 1.20 0.23 10.18| | 28: 1.19 - 1.18 2671 147 0.82 25.58 1.18 0.23 9.51| | 29: 1.18 - 1.16 2800 134 0.83 25.52 1.17 0.23 9.25| | 30: 1.16 - 1.15 2740 148 0.80 27.58 1.15 0.23 9.25| |alpha: min = 0.23 max = 0.25 mean = 0.24| |beta: min = 9.25 max = 1534.41 mean = 221.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.65| |phase err.(test): min = 0.00 max = 89.78 mean = 22.57| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.538 Angle : 5.254 18.207 2118 Z= 3.716 Chirality : 0.387 1.064 243 Planarity : 0.031 0.106 284 Dihedral : 14.341 92.155 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.47), residues: 224 helix: -2.83 (0.34), residues: 102 sheet: -0.89 (1.00), residues: 28 loop : -0.57 (0.57), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.012 ARG A 145 TYR 0.073 0.033 TYR A 139 PHE 0.119 0.037 PHE A 119 HIS 0.065 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1942 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788674 | | target function (ml) not normalized (work): 232313.244986 | | target function (ml) not normalized (free): 11816.781129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1943 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1943 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1943 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2007 0.2011 0.1958 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1636 0.1771 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1636 0.1771 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 0.3789 386.315 359.591 0.669 1.002 0.407 11.894-9.307 99.02 97 4 0.1818 613.643 596.067 0.930 1.003 0.390 9.237-7.194 100.00 213 7 0.2144 501.884 491.676 0.953 1.003 0.354 7.162-5.571 100.00 427 22 0.2140 376.636 365.225 0.925 1.003 0.292 5.546-4.326 100.00 867 58 0.1268 517.029 510.577 0.961 1.003 0.229 4.315-3.360 100.00 1859 96 0.1143 491.698 487.620 1.001 1.003 0.209 3.356-2.611 100.00 3867 181 0.1461 323.020 319.579 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1344 214.133 211.740 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1652 104.571 103.930 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.371 45.021 1.002 0.996 0.000 1.221-1.150 99.97 13689 708 0.2591 29.217 26.977 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0515 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1771 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1636 r_free=0.1771 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.225499 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.776446 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 0.1212 0.1463 0.0251 0.008 1.0 1.6 0.5 0.0 0 13.113 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.63 2.51 3.013 19.083 2020.776 0.017 12.41 15.38 2.97 3.187 19.559 2020.776 0.016 Individual atomic B min max mean iso aniso Overall: 8.53 118.64 21.01 2.87 0 1785 Protein: 8.53 118.64 17.89 2.87 0 1519 Water: 11.11 114.52 39.17 N/A 0 258 Other: 22.98 36.30 29.13 N/A 0 8 Chain A: 8.53 118.64 21.01 N/A 0 1785 Histogram: Values Number of atoms 8.53 - 19.54 1206 19.54 - 30.55 230 30.55 - 41.56 165 41.56 - 52.57 101 52.57 - 63.59 54 63.59 - 74.60 17 74.60 - 85.61 5 85.61 - 96.62 4 96.62 - 107.63 0 107.63 - 118.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1538 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 = 0.1246 r_free = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1246 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015390 | | target function (ls_wunit_k1) not normalized (work): 1281.928293 | | target function (ls_wunit_k1) not normalized (free): 114.629802 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1246 0.1546 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1703 0.1702 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1703 0.1702 0.1770 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1725 0.1724 0.1786 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1258 0.1243 0.1540 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1243 0.1540 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 0.3628 298.427 277.375 0.690 0.923 0.380 11.894-9.307 99.02 97 4 0.1607 478.063 466.044 0.985 0.923 0.380 9.237-7.194 100.00 213 7 0.1827 390.997 385.724 1.029 0.924 0.340 7.162-5.571 100.00 427 22 0.1737 293.421 288.063 0.998 0.924 0.280 5.546-4.326 100.00 867 58 0.0926 402.795 399.956 1.028 0.925 0.209 4.315-3.360 100.00 1859 96 0.0780 383.061 382.055 1.075 0.926 0.200 3.356-2.611 100.00 3867 181 0.1018 251.651 250.927 1.079 0.928 0.110 2.608-2.026 99.99 8198 413 0.0975 166.822 166.241 1.085 0.932 0.000 2.025-1.573 100.00 17313 902 0.1207 81.467 81.650 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1651 36.126 35.593 1.061 0.946 0.000 1.221-1.150 99.97 13689 708 0.2361 22.762 21.303 1.015 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0518 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1243 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1245 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1541 | n_water=258 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1254 r_free=0.1539 | n_water=252 | time (s): 25.760 (total time: 28.070) Filter (q & B) r_work=0.1257 r_free=0.1539 | n_water=249 | time (s): 3.480 (total time: 31.550) Compute maps r_work=0.1257 r_free=0.1539 | n_water=249 | time (s): 1.790 (total time: 33.340) Filter (map) r_work=0.1270 r_free=0.1547 | n_water=236 | time (s): 3.880 (total time: 37.220) Find peaks r_work=0.1270 r_free=0.1547 | n_water=236 | time (s): 0.710 (total time: 37.930) Add new water r_work=0.1423 r_free=0.1696 | n_water=448 | time (s): 3.750 (total time: 41.680) Refine new water occ: r_work=0.1332 r_free=0.1577 adp: r_work=0.1255 r_free=0.1528 occ: r_work=0.1268 r_free=0.1519 adp: r_work=0.1234 r_free=0.1508 occ: r_work=0.1237 r_free=0.1495 adp: r_work=0.1228 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1497 r_work=0.1228 r_free=0.1497 | n_water=448 | time (s): 83.220 (total time: 124.900) Filter (q & B) r_work=0.1235 r_free=0.1501 | n_water=423 | time (s): 3.850 (total time: 128.750) Filter (dist only) r_work=0.1235 r_free=0.1501 | n_water=423 | time (s): 39.910 (total time: 168.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.411976 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1578.204310 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 0.1231 0.1518 0.0287 0.007 0.9 1.9 0.5 0.0 0 13.206 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 15.18 2.87 3.789 23.128 1578.204 0.015 12.03 14.95 2.92 4.174 22.934 1578.204 0.015 Individual atomic B min max mean iso aniso Overall: 8.76 114.69 23.06 2.61 187 1763 Protein: 8.76 114.69 17.67 2.62 0 1519 Water: 11.21 71.98 42.26 N/A 187 236 Other: 25.60 37.09 30.24 N/A 0 8 Chain A: 8.76 114.69 20.37 N/A 0 1763 Chain S: 18.32 70.26 48.42 N/A 187 0 Histogram: Values Number of atoms 8.76 - 19.35 1207 19.35 - 29.95 245 29.95 - 40.54 193 40.54 - 51.13 142 51.13 - 61.72 105 61.72 - 72.32 48 72.32 - 82.91 4 82.91 - 93.50 3 93.50 - 104.09 1 104.09 - 114.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1496 r_work=0.1203 r_free=0.1496 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1496 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 = 0.1206 r_free = 0.1491 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1206 r_free= 0.1491 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014087 | | target function (ls_wunit_k1) not normalized (work): 1173.398313 | | target function (ls_wunit_k1) not normalized (free): 103.904915 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1206 0.1491 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1614 0.1611 0.1716 n_refl.: 87592 remove outliers: r(all,work,free)=0.1614 0.1611 0.1716 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1621 0.1618 0.1720 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1205 0.1488 n_refl.: 87592 remove outliers: r(all,work,free)=0.1217 0.1203 0.1488 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 0.3356 294.372 272.845 0.593 1.000 0.364 11.894-9.307 99.02 97 4 0.1537 478.063 473.099 0.912 1.001 0.360 9.237-7.194 100.00 213 7 0.1725 390.997 389.581 0.976 1.002 0.290 7.162-5.571 100.00 427 22 0.1521 293.421 289.463 0.939 1.002 0.250 5.546-4.326 100.00 867 58 0.0824 402.795 400.170 0.957 1.002 0.215 4.315-3.360 100.00 1859 96 0.0716 383.061 382.076 1.001 1.002 0.210 3.356-2.611 100.00 3867 181 0.0959 251.651 251.002 1.009 1.002 0.150 2.608-2.026 99.99 8198 413 0.0966 166.822 166.446 1.016 1.002 0.000 2.025-1.573 100.00 17313 902 0.1190 81.467 81.690 1.025 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1622 36.126 35.613 1.012 1.002 0.000 1.221-1.150 99.97 13689 708 0.2338 22.762 21.200 0.967 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0704 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1488 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1488 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1488 | n_water=423 | time (s): 1.930 (total time: 1.930) Filter (dist) r_work=0.1203 r_free=0.1486 | n_water=421 | time (s): 36.690 (total time: 38.620) Filter (q & B) r_work=0.1203 r_free=0.1486 | n_water=421 | time (s): 1.330 (total time: 39.950) Compute maps r_work=0.1203 r_free=0.1486 | n_water=421 | time (s): 1.600 (total time: 41.550) Filter (map) r_work=0.1252 r_free=0.1482 | n_water=284 | time (s): 3.400 (total time: 44.950) Find peaks r_work=0.1252 r_free=0.1482 | n_water=284 | time (s): 0.530 (total time: 45.480) Add new water r_work=0.1383 r_free=0.1600 | n_water=472 | time (s): 2.940 (total time: 48.420) Refine new water occ: r_work=0.1272 r_free=0.1531 adp: r_work=0.1273 r_free=0.1530 occ: r_work=0.1250 r_free=0.1514 adp: r_work=0.1247 r_free=0.1511 occ: r_work=0.1235 r_free=0.1500 adp: r_work=0.1226 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1494 r_work=0.1226 r_free=0.1494 | n_water=472 | time (s): 195.460 (total time: 243.880) Filter (q & B) r_work=0.1230 r_free=0.1494 | n_water=446 | time (s): 2.910 (total time: 246.790) Filter (dist only) r_work=0.1230 r_free=0.1494 | n_water=446 | time (s): 36.040 (total time: 282.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.322918 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.900012 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 0.1454 0.0221 0.006 0.9 1.9 0.5 0.0 0 1.161 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.54 2.21 3.628 22.107 48.900 3.725 12.13 14.07 1.93 4.196 21.893 48.900 3.650 Individual atomic B min max mean iso aniso Overall: 9.24 109.73 21.58 2.33 213 1760 Protein: 9.24 109.73 17.20 2.33 0 1519 Water: 11.60 70.70 36.44 N/A 213 233 Other: 20.64 32.19 26.18 N/A 0 8 Chain A: 9.24 109.73 19.85 N/A 0 1760 Chain S: 15.95 64.11 35.91 N/A 213 0 Histogram: Values Number of atoms 9.24 - 19.29 1238 19.29 - 29.34 278 29.34 - 39.39 217 39.39 - 49.44 133 49.44 - 59.49 76 59.49 - 69.54 18 69.54 - 79.58 7 79.58 - 89.63 3 89.63 - 99.68 1 99.68 - 109.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1407 r_work=0.1215 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1407 target_work(ml) = 3.651 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1405 target_work(ml) = 3.648 | | occupancies: max = 1.00 min = 0.20 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= 0.1208 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.647810 | | target function (ml) not normalized (work): 303837.022352 | | target function (ml) not normalized (free): 16044.328199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1208 0.1405 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1542 0.1541 0.1583 n_refl.: 87589 remove outliers: r(all,work,free)=0.1542 0.1541 0.1583 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1539 0.1539 0.1582 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1197 0.1373 n_refl.: 87589 remove outliers: r(all,work,free)=0.1202 0.1193 0.1373 n_refl.: 87579 ======================== 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 0.3742 293.739 261.749 0.480 1.000 0.330 11.894-9.307 97.06 95 4 0.2445 471.463 458.069 0.851 1.002 0.283 9.237-7.194 97.73 208 7 0.2300 383.628 385.382 0.949 1.002 0.180 7.162-5.571 100.00 427 22 0.2030 293.421 283.474 0.907 1.002 0.164 5.546-4.326 100.00 867 58 0.1098 402.795 398.351 0.950 1.002 0.158 4.315-3.360 100.00 1859 96 0.0919 383.061 380.485 0.993 1.002 0.157 3.356-2.611 100.00 3867 181 0.1158 251.651 249.760 1.001 1.002 0.067 2.608-2.026 99.99 8198 413 0.1043 166.822 165.922 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.467 81.628 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1288 36.126 35.709 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2131 22.762 21.387 0.979 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0411 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1373 | n_water=446 | time (s): 2.010 (total time: 2.010) Filter (dist) r_work=0.1196 r_free=0.1373 | n_water=444 | time (s): 42.480 (total time: 44.490) Filter (q & B) r_work=0.1196 r_free=0.1373 | n_water=444 | time (s): 0.880 (total time: 45.370) Compute maps r_work=0.1196 r_free=0.1373 | n_water=444 | time (s): 1.830 (total time: 47.200) Filter (map) r_work=0.1221 r_free=0.1372 | n_water=314 | time (s): 3.710 (total time: 50.910) Find peaks r_work=0.1221 r_free=0.1372 | n_water=314 | time (s): 0.670 (total time: 51.580) Add new water r_work=0.1283 r_free=0.1432 | n_water=466 | time (s): 3.350 (total time: 54.930) Refine new water occ: r_work=0.1211 r_free=0.1373 adp: r_work=0.1211 r_free=0.1374 occ: r_work=0.1195 r_free=0.1363 adp: r_work=0.1194 r_free=0.1363 occ: r_work=0.1184 r_free=0.1359 adp: r_work=0.1180 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1356 r_work=0.1180 r_free=0.1356 | n_water=466 | time (s): 184.090 (total time: 239.020) Filter (q & B) r_work=0.1188 r_free=0.1361 | n_water=436 | time (s): 2.590 (total time: 241.610) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=434 | time (s): 38.600 (total time: 280.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.969086 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.952647 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 0.1202 0.1378 0.0175 0.006 1.0 1.9 0.5 0.0 0 0.985 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.78 1.75 3.420 21.426 46.953 3.638 11.93 13.72 1.79 3.698 21.345 46.953 3.624 Individual atomic B min max mean iso aniso Overall: 9.33 105.62 21.20 2.17 206 1755 Protein: 9.33 105.62 17.00 2.18 0 1519 Water: 11.39 69.68 35.86 N/A 206 228 Other: 18.95 29.40 24.43 N/A 0 8 Chain A: 9.33 105.62 19.56 N/A 0 1755 Chain S: 15.55 60.27 35.23 N/A 206 0 Histogram: Values Number of atoms 9.33 - 18.96 1237 18.96 - 28.59 273 28.59 - 38.22 209 38.22 - 47.85 135 47.85 - 57.48 69 57.48 - 67.10 25 67.10 - 76.73 8 76.73 - 86.36 2 86.36 - 95.99 1 95.99 - 105.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1372 r_work=0.1193 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1372 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1375 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1188 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.622644 | | target function (ml) not normalized (work): 301704.621261 | | target function (ml) not normalized (free): 15941.127935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1188 0.1375 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1577 n_refl.: 87579 remove outliers: r(all,work,free)=0.1522 0.1521 0.1577 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1519 0.1518 0.1575 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1188 0.1378 n_refl.: 87579 remove outliers: r(all,work,free)=0.1197 0.1188 0.1378 n_refl.: 87578 ======================== 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 0.4088 293.739 256.864 0.456 0.998 0.308 11.894-9.307 96.08 94 4 0.2524 465.363 450.873 0.839 1.000 0.224 9.237-7.194 97.73 208 7 0.2418 383.628 378.019 0.917 1.001 0.150 7.162-5.571 100.00 427 22 0.2141 293.421 282.905 0.899 1.001 0.150 5.546-4.326 100.00 867 58 0.1147 402.795 397.789 0.952 1.001 0.150 4.315-3.360 100.00 1859 96 0.0953 383.061 380.390 0.994 1.001 0.150 3.356-2.611 100.00 3867 181 0.1167 251.651 249.819 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1036 166.822 165.899 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0979 81.467 81.746 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.126 35.751 1.020 1.001 0.000 1.221-1.150 99.97 13689 708 0.2119 22.762 21.345 0.975 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0440 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1378 After: r_work=0.1188 r_free=0.1378 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1378 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=0.1188 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1378 | n_water=434 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1188 r_free=0.1378 | n_water=434 | time (s): 36.570 (total time: 38.380) Filter (q & B) r_work=0.1188 r_free=0.1377 | n_water=431 | time (s): 2.910 (total time: 41.290) Compute maps r_work=0.1188 r_free=0.1377 | n_water=431 | time (s): 1.200 (total time: 42.490) Filter (map) r_work=0.1210 r_free=0.1373 | n_water=326 | time (s): 3.010 (total time: 45.500) Find peaks r_work=0.1210 r_free=0.1373 | n_water=326 | time (s): 0.660 (total time: 46.160) Add new water r_work=0.1266 r_free=0.1427 | n_water=482 | time (s): 3.190 (total time: 49.350) Refine new water occ: r_work=0.1201 r_free=0.1385 adp: r_work=0.1201 r_free=0.1388 occ: r_work=0.1189 r_free=0.1375 adp: r_work=0.1188 r_free=0.1377 occ: r_work=0.1179 r_free=0.1366 adp: r_work=0.1176 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1368 r_work=0.1176 r_free=0.1368 | n_water=482 | time (s): 212.920 (total time: 262.270) Filter (q & B) r_work=0.1182 r_free=0.1366 | n_water=447 | time (s): 2.790 (total time: 265.060) Filter (dist only) r_work=0.1182 r_free=0.1364 | n_water=446 | time (s): 38.100 (total time: 303.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.968482 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.627033 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 0.1202 0.1378 0.0175 0.007 1.1 3.2 0.5 0.0 0 0.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.78 1.75 3.310 21.205 43.627 3.629 12.06 13.77 1.71 3.549 21.122 43.627 3.625 Individual atomic B min max mean iso aniso Overall: 9.27 101.45 21.04 2.04 218 1755 Protein: 9.27 101.45 16.79 2.04 0 1519 Water: 11.44 68.88 35.46 N/A 218 228 Other: 19.49 27.41 23.66 N/A 0 8 Chain A: 9.27 101.45 19.34 N/A 0 1755 Chain S: 14.95 57.26 34.77 N/A 218 0 Histogram: Values Number of atoms 9.27 - 18.49 1223 18.49 - 27.71 283 27.71 - 36.93 211 36.93 - 46.14 139 46.14 - 55.36 73 55.36 - 64.58 28 64.58 - 73.80 11 73.80 - 83.01 2 83.01 - 92.23 1 92.23 - 101.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1377 r_work=0.1206 r_free=0.1377 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1377 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1380 target_work(ml) = 3.625 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1204 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.625337 | | target function (ml) not normalized (work): 301925.334819 | | target function (ml) not normalized (free): 15950.880282 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1383 0.1429 5.6376 5.6471| | 2: 3.57 - 2.84 1.00 2888 124 0.1135 0.1429 5.2065 5.2581| | 3: 2.83 - 2.48 1.00 2820 163 0.1243 0.1367 5.0174 5.0503| | 4: 2.47 - 2.25 1.00 2825 136 0.1060 0.1122 4.7218 4.748| | 5: 2.25 - 2.09 1.00 2756 127 0.1013 0.1110 4.6595 4.7239| | 6: 2.09 - 1.97 1.00 2846 113 0.0985 0.1223 4.361 4.4884| | 7: 1.97 - 1.87 1.00 2787 165 0.1005 0.1167 4.0851 4.1623| | 8: 1.87 - 1.79 1.00 2789 144 0.1050 0.1310 4.0047 4.1027| | 9: 1.79 - 1.72 1.00 2745 138 0.0970 0.1293 3.7267 3.8866| | 10: 1.72 - 1.66 1.00 2831 160 0.1019 0.1287 3.6468 3.7929| | 11: 1.66 - 1.61 1.00 2712 147 0.0973 0.1121 3.5763 3.6242| | 12: 1.61 - 1.56 1.00 2773 144 0.0930 0.1208 3.3561 3.4941| | 13: 1.56 - 1.52 1.00 2745 130 0.0992 0.1071 3.3505 3.4356| | 14: 1.52 - 1.48 1.00 2803 134 0.1007 0.1096 3.2717 3.3307| | 15: 1.48 - 1.45 1.00 2738 128 0.1021 0.1351 3.1737 3.3255| | 16: 1.45 - 1.42 1.00 2756 161 0.1084 0.1294 3.1591 3.2676| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1303 3.1216 3.2302| | 18: 1.39 - 1.36 1.00 2741 179 0.1165 0.1394 3.0918 3.2666| | 19: 1.36 - 1.34 1.00 2807 134 0.1219 0.1615 3.0946 3.2701| | 20: 1.34 - 1.32 1.00 2696 147 0.1320 0.1490 3.0891 3.1411| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1610 3.0865 3.1582| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1921 3.0856 3.2904| | 23: 1.27 - 1.26 1.00 2802 156 0.1572 0.1842 3.0989 3.205| | 24: 1.26 - 1.24 1.00 2744 132 0.1630 0.1745 3.0939 3.1791| | 25: 1.24 - 1.22 1.00 2733 148 0.1789 0.2332 3.1067 3.2912| | 26: 1.22 - 1.21 1.00 2727 135 0.1866 0.1778 3.1232 3.197| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2083 3.1408 3.1475| | 28: 1.19 - 1.18 1.00 2671 147 0.2148 0.2301 3.1395 3.1571| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2361 3.1246 3.2262| | 30: 1.16 - 1.15 1.00 2739 148 0.2381 0.2472 3.1155 3.1603| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 9.19 1.00 0.97 6331.80| | 2: 3.57 - 2.84 2888 124 0.92 13.41 1.01 0.97 6331.80| | 3: 2.83 - 2.48 2820 163 0.88 17.62 0.99 0.97 5309.01| | 4: 2.47 - 2.25 2825 136 0.91 14.75 1.00 0.98 2671.57| | 5: 2.25 - 2.09 2756 127 0.89 16.91 1.01 0.98 2671.57| | 6: 2.09 - 1.97 2846 113 0.92 13.77 1.02 0.98 1572.72| | 7: 1.97 - 1.87 2787 165 0.94 10.91 1.02 0.97 635.56| | 8: 1.87 - 1.79 2789 144 0.91 14.55 1.00 0.97 635.56| | 9: 1.79 - 1.72 2745 138 0.93 11.63 0.98 0.97 346.45| | 10: 1.72 - 1.66 2831 160 0.93 12.45 0.98 0.97 288.56| | 11: 1.66 - 1.61 2712 147 0.92 13.16 0.98 0.97 275.37| | 12: 1.61 - 1.56 2773 144 0.95 9.71 0.99 0.97 150.96| | 13: 1.56 - 1.52 2745 130 0.94 11.32 1.02 0.97 150.96| | 14: 1.52 - 1.48 2803 134 0.94 11.49 1.02 0.97 134.54| | 15: 1.48 - 1.45 2738 128 0.95 10.62 1.01 0.98 104.47| | 16: 1.45 - 1.42 2756 161 0.94 11.72 1.02 0.98 104.47| | 17: 1.42 - 1.39 2785 139 0.94 11.53 1.01 0.98 93.95| | 18: 1.39 - 1.36 2741 179 0.94 11.83 1.01 0.98 87.86| | 19: 1.36 - 1.34 2807 134 0.94 12.36 1.00 0.98 87.86| | 20: 1.34 - 1.32 2696 147 0.94 12.45 0.99 0.97 82.43| | 21: 1.32 - 1.30 2785 112 0.94 13.37 0.98 0.97 82.04| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.96 82.13| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.98 0.95 82.58| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 82.58| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.11| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.94 85.79| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.94 85.79| | 28: 1.19 - 1.18 2671 147 0.88 20.21 1.01 0.93 89.14| | 29: 1.18 - 1.16 2800 134 0.88 20.57 0.99 0.93 90.40| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.93 90.40| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.04 max = 6331.80 mean = 988.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 14.13| |phase err.(test): min = 0.00 max = 89.86 mean = 14.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1204 0.1380 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1531 0.1529 0.1594 n_refl.: 87578 remove outliers: r(all,work,free)=0.1531 0.1529 0.1594 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1528 0.1526 0.1592 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1205 0.1379 n_refl.: 87578 remove outliers: r(all,work,free)=0.1213 0.1204 0.1379 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 0.3924 289.109 262.260 0.454 0.998 0.281 11.894-9.307 95.10 93 4 0.2381 469.170 447.842 0.834 1.000 0.234 9.237-7.194 97.73 208 7 0.2413 383.628 379.030 0.916 1.000 0.190 7.162-5.571 100.00 427 22 0.2135 293.421 283.762 0.899 1.001 0.158 5.546-4.326 100.00 867 58 0.1182 402.795 397.149 0.953 1.001 0.146 4.315-3.360 100.00 1859 96 0.0990 383.061 380.564 0.997 1.001 0.133 3.356-2.611 100.00 3867 181 0.1203 251.651 249.468 1.002 1.001 0.100 2.608-2.026 99.99 8198 413 0.1065 166.822 165.811 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0994 81.467 81.727 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.126 35.781 1.021 1.001 0.000 1.221-1.150 99.97 13689 708 0.2116 22.762 21.378 0.977 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0513 ================= 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 0.1942 0.082 5.254 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_weight: 0.1636 0.1771 0.082 5.254 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1212 0.1463 0.008 0.966 9.1 119.5 20.1 258 0.121 1_adp: 0.1241 0.1538 0.008 0.966 8.5 118.6 21.0 258 0.121 1_regHadp: 0.1245 0.1544 0.008 0.966 8.5 118.6 21.0 258 0.121 1_occ: 0.1246 0.1546 0.008 0.966 8.5 118.6 21.0 258 0.121 2_bss: 0.1243 0.1540 0.008 0.966 8.7 118.8 21.1 258 0.121 2_settarget: 0.1243 0.1540 0.008 0.966 8.7 118.8 21.1 258 0.121 2_updatecdl: 0.1243 0.1540 0.008 0.968 8.7 118.8 21.1 258 0.121 2_nqh: 0.1245 0.1541 0.008 0.968 8.7 118.8 21.1 258 0.124 2_sol: 0.1235 0.1501 0.008 0.968 8.7 118.8 23.4 423 n/a 2_weight: 0.1235 0.1501 0.008 0.968 8.7 118.8 23.4 423 n/a 2_xyzrec: 0.1231 0.1518 0.007 0.882 8.7 118.8 23.4 423 n/a 2_adp: 0.1204 0.1496 0.007 0.882 8.8 114.7 23.1 423 n/a 2_regHadp: 0.1203 0.1496 0.007 0.882 8.8 114.7 23.1 423 n/a 2_occ: 0.1206 0.1491 0.007 0.882 8.8 114.7 23.1 423 n/a 3_bss: 0.1203 0.1488 0.007 0.882 8.8 114.7 23.1 423 n/a 3_settarget: 0.1203 0.1488 0.007 0.882 8.8 114.7 23.1 423 n/a 3_updatecdl: 0.1203 0.1488 0.007 0.882 8.8 114.7 23.1 423 n/a 3_nqh: 0.1203 0.1488 0.007 0.882 8.8 114.7 23.1 423 n/a 3_sol: 0.1230 0.1494 0.007 0.882 8.8 114.7 22.0 446 n/a 3_weight: 0.1230 0.1494 0.007 0.882 8.8 114.7 22.0 446 n/a 3_xyzrec: 0.1233 0.1454 0.006 0.941 8.8 114.7 22.0 446 n/a 3_adp: 0.1214 0.1407 0.006 0.941 9.2 109.7 21.6 446 n/a 3_regHadp: 0.1215 0.1407 0.006 0.941 9.2 109.7 21.6 446 n/a 3_occ: 0.1208 0.1405 0.006 0.941 9.2 109.7 21.6 446 n/a 4_bss: 0.1193 0.1373 0.006 0.941 9.2 109.7 21.6 446 n/a 4_settarget: 0.1193 0.1373 0.006 0.941 9.2 109.7 21.6 446 n/a 4_updatecdl: 0.1193 0.1373 0.006 0.940 9.2 109.7 21.6 446 n/a 4_nqh: 0.1193 0.1373 0.006 0.940 9.2 109.7 21.6 446 n/a 4_sol: 0.1194 0.1357 0.006 0.940 9.2 109.7 21.4 434 n/a 4_weight: 0.1194 0.1357 0.006 0.940 9.2 109.7 21.4 434 n/a 4_xyzrec: 0.1202 0.1378 0.006 0.953 9.2 109.7 21.4 434 n/a 4_adp: 0.1193 0.1372 0.006 0.953 9.3 105.6 21.2 434 n/a 4_regHadp: 0.1193 0.1372 0.006 0.953 9.3 105.6 21.2 434 n/a 4_occ: 0.1188 0.1375 0.006 0.953 9.3 105.6 21.2 434 n/a 5_bss: 0.1188 0.1378 0.006 0.953 9.3 105.6 21.2 434 n/a 5_settarget: 0.1188 0.1378 0.006 0.953 9.3 105.6 21.2 434 n/a 5_updatecdl: 0.1188 0.1378 0.006 0.952 9.3 105.6 21.2 434 n/a 5_setrh: 0.1188 0.1378 0.006 0.952 9.3 105.6 21.2 434 n/a 5_nqh: 0.1188 0.1378 0.006 0.952 9.3 105.6 21.2 434 n/a 5_sol: 0.1182 0.1364 0.006 0.952 9.3 105.6 21.2 446 n/a 5_weight: 0.1182 0.1364 0.006 0.952 9.3 105.6 21.2 446 n/a 5_xyzrec: 0.1202 0.1378 0.007 1.062 9.3 105.6 21.2 446 n/a 5_adp: 0.1206 0.1377 0.007 1.062 9.3 101.4 21.0 446 n/a 5_regHadp: 0.1206 0.1377 0.007 1.062 9.3 101.4 21.0 446 n/a 5_occ: 0.1204 0.1380 0.007 1.062 9.3 101.4 21.0 446 n/a end: 0.1204 0.1379 0.007 1.062 9.3 101.4 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2963595_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_2963595_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0600 Refinement macro-cycles (run) : 3466.1100 Write final files (write_after_run_outputs) : 64.5100 Total : 3535.6800 Total CPU time: 59.55 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:13 PST -0800 (1735452673.93 s) Start R-work = 0.1636, R-free = 0.1771 Final R-work = 0.1204, R-free = 0.1379 =============================================================================== Job complete usr+sys time: 3663.52 seconds wall clock time: 66 minutes 17.25 seconds (3977.25 seconds total)