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_3867824.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 4 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: 2.17, per 1000 atoms: 0.64 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 349.8 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 354 0.88 - 1.13: 1246 1.13 - 1.39: 558 1.39 - 1.64: 924 1.64 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.418 -0.174 9.50e-03 1.11e+04 3.37e+02 bond pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 1.513 1.700 -0.187 1.06e-02 8.90e+03 3.11e+02 bond pdb=" N ALA A 167 " pdb=" CA ALA A 167 " ideal model delta sigma weight residual 1.459 1.246 0.214 1.23e-02 6.61e+03 3.02e+02 bond pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 1.471 1.694 -0.223 1.32e-02 5.74e+03 2.86e+02 bond pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.20: 3866 6.20 - 12.39: 1644 12.39 - 18.58: 249 18.58 - 24.77: 15 24.77 - 30.96: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 134.60 -15.40 9.00e-01 1.23e+00 2.93e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.87 136.74 -14.87 9.70e-01 1.06e+00 2.35e+02 angle pdb=" O PRO A 43 " pdb=" C PRO A 43 " pdb=" N VAL A 44 " ideal model delta sigma weight residual 122.91 138.98 -16.07 1.21e+00 6.83e-01 1.76e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N AGLU A 96 " ideal model delta sigma weight residual 122.07 135.69 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 108.30 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.31: 934 16.31 - 32.61: 120 32.61 - 48.91: 35 48.91 - 65.21: 18 65.21 - 81.51: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 155.51 24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CD2 PHE A 119 " pdb=" CG PHE A 119 " pdb=" CD1 PHE A 119 " pdb=" HD1 PHE A 119 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.261: 113 0.261 - 0.520: 82 0.520 - 0.779: 35 0.779 - 1.038: 10 1.038 - 1.297: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.29 -1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.81e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.75e-02 1.37e+02 pdb=" CG PHE A 119 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.077 2.00e-02 2.50e+03 7.04e-02 1.11e+02 pdb=" CG HIS A 138 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.091 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.127 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.040 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1044 2.32 - 2.89: 8077 2.89 - 3.46: 10562 3.46 - 4.03: 15165 4.03 - 4.60: 21813 Nonbonded interactions: 56661 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.779 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.792 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.796 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.808 1.816 ... (remaining 56656 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_3867824_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2605 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790375 | | target function (ml) not normalized (work): 232454.944306 | | target function (ml) not normalized (free): 11857.683327 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3032 0.2142 7.0721 4.9572| | 2: 3.57 - 2.84 1.00 2876 122 0.2419 0.1718 4.3482 4.3272| | 3: 2.84 - 2.48 1.00 2833 165 0.2378 0.1598 4.1236 4.1353| | 4: 2.47 - 2.25 1.00 2825 136 0.2333 0.1376 3.8248 3.8061| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1434 3.7928 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2514 0.1759 3.4599 3.5041| | 7: 1.97 - 1.87 1.00 2787 165 0.2553 0.1848 3.1279 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2529 0.1975 3.054 3.1213| | 9: 1.79 - 1.72 1.00 2745 138 0.2411 0.1913 2.8911 2.9682| | 10: 1.72 - 1.66 1.00 2789 158 0.2370 0.1950 2.7943 2.8839| | 11: 1.66 - 1.61 1.00 2740 147 0.2494 0.1663 2.7486 2.7015| | 12: 1.61 - 1.56 1.00 2787 146 0.2492 0.2044 2.6233 2.6629| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.2030 2.588 2.6711| | 14: 1.52 - 1.48 1.00 2803 134 0.2573 0.2118 2.5093 2.6275| | 15: 1.48 - 1.45 1.00 2738 128 0.2636 0.2259 2.4321 2.5638| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.2236 2.3895 2.451| | 17: 1.42 - 1.39 1.00 2785 139 0.2610 0.2106 2.3449 2.4042| | 18: 1.39 - 1.36 1.00 2741 179 0.2658 0.2122 2.2798 2.3341| | 19: 1.36 - 1.34 1.00 2807 134 0.2654 0.2497 2.2471 2.3881| | 20: 1.34 - 1.32 1.00 2696 147 0.2693 0.2282 2.195 2.2265| | 21: 1.32 - 1.30 1.00 2785 112 0.2733 0.2352 2.1707 2.1783| | 22: 1.29 - 1.27 1.00 2704 152 0.2712 0.2435 2.1196 2.1869| | 23: 1.27 - 1.26 1.00 2802 156 0.2752 0.2589 2.093 2.1823| | 24: 1.26 - 1.24 1.00 2744 132 0.2759 0.2288 2.0737 2.1278| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2682 2.0552 2.1597| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2285 2.0061 2.1084| | 27: 1.21 - 1.19 1.00 2814 148 0.2939 0.2673 2.0095 2.0091| | 28: 1.19 - 1.18 1.00 2671 147 0.2985 0.2724 1.992 1.9988| | 29: 1.18 - 1.16 1.00 2800 134 0.2971 0.2678 1.9607 2.0278| | 30: 1.16 - 1.15 1.00 2740 148 0.3030 0.2811 1.9279 1.9674| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 18.63 0.76 0.23 1465.85| | 2: 3.57 - 2.84 2876 122 0.81 25.95 1.27 0.23 1465.85| | 3: 2.84 - 2.48 2833 165 0.74 32.00 1.25 0.23 1214.53| | 4: 2.47 - 2.25 2825 136 0.81 25.47 1.26 0.25 562.28| | 5: 2.25 - 2.09 2756 127 0.77 29.15 1.28 0.25 562.28| | 6: 2.09 - 1.97 2846 113 0.84 22.23 1.29 0.25 306.09| | 7: 1.97 - 1.87 2787 165 0.90 16.25 1.28 0.26 87.59| | 8: 1.87 - 1.79 2789 144 0.86 20.72 1.26 0.26 87.59| | 9: 1.79 - 1.72 2745 138 0.88 18.74 1.23 0.25 55.37| | 10: 1.72 - 1.66 2789 158 0.86 20.31 1.22 0.25 48.92| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 47.26| | 12: 1.61 - 1.56 2787 146 0.88 18.80 1.24 0.25 30.37| | 13: 1.56 - 1.52 2745 130 0.86 20.65 1.23 0.25 30.37| | 14: 1.52 - 1.48 2803 134 0.86 21.05 1.24 0.25 27.38| | 15: 1.48 - 1.45 2738 128 0.86 20.89 1.24 0.25 21.90| | 16: 1.45 - 1.42 2756 161 0.85 22.47 1.23 0.25 21.90| | 17: 1.42 - 1.39 2785 139 0.86 21.19 1.22 0.25 18.68| | 18: 1.39 - 1.36 2741 179 0.85 21.97 1.23 0.25 16.82| | 19: 1.36 - 1.34 2807 134 0.84 23.06 1.22 0.25 16.82| | 20: 1.34 - 1.32 2696 147 0.86 21.52 1.22 0.24 13.78| | 21: 1.32 - 1.30 2785 112 0.85 22.67 1.21 0.24 13.57| | 22: 1.29 - 1.27 2704 152 0.85 22.99 1.22 0.24 13.23| | 23: 1.27 - 1.26 2802 156 0.85 22.79 1.22 0.24 11.50| | 24: 1.26 - 1.24 2744 132 0.85 23.16 1.21 0.24 11.50| | 25: 1.24 - 1.22 2734 148 0.84 24.18 1.21 0.24 10.92| | 26: 1.22 - 1.21 2727 135 0.84 24.33 1.20 0.23 10.26| | 27: 1.21 - 1.19 2814 148 0.83 25.22 1.20 0.23 10.26| | 28: 1.19 - 1.18 2671 147 0.82 25.91 1.18 0.23 9.67| | 29: 1.18 - 1.16 2800 134 0.82 26.20 1.17 0.22 9.44| | 30: 1.16 - 1.15 2740 148 0.80 27.74 1.16 0.22 9.44| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.44 max = 1465.85 mean = 212.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.92| |phase err.(test): min = 0.00 max = 89.66 mean = 22.81| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.239 1557 Z= 5.525 Angle : 5.460 18.696 2118 Z= 3.789 Chirality : 0.400 1.297 243 Planarity : 0.032 0.108 284 Dihedral : 13.864 81.513 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 40.00 % 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: -2.96 (0.48), residues: 224 helix: -2.91 (0.33), residues: 109 sheet: -0.97 (0.80), residues: 38 loop : -0.52 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.014 ARG A 156 TYR 0.080 0.038 TYR A 139 PHE 0.124 0.039 PHE A 119 HIS 0.068 0.035 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= 0.2605 r_free= 0.1935 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790375 | | target function (ml) not normalized (work): 232454.944306 | | target function (ml) not normalized (free): 11857.683327 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2605 0.1936 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2605 0.1936 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1980 0.1936 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2001 0.2006 0.1949 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1641 0.1634 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1640 0.1634 0.1770 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 0.3766 386.471 360.380 0.680 1.003 0.414 11.894-9.307 99.02 97 4 0.1823 613.891 596.211 0.927 1.004 0.402 9.237-7.194 100.00 213 7 0.2164 502.087 492.086 0.952 1.004 0.349 7.162-5.571 100.00 427 22 0.2219 376.788 365.149 0.930 1.004 0.340 5.546-4.326 100.00 867 58 0.1269 517.237 512.693 0.962 1.003 0.228 4.315-3.360 100.00 1859 96 0.1156 491.896 488.659 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1428 323.150 320.242 0.996 1.002 0.038 2.608-2.026 99.99 8198 413 0.1358 214.219 212.020 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1639 104.613 103.970 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2056 46.390 45.121 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2581 29.229 26.997 0.976 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0467 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1634 r_free=0.1770 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 144 ASN Total number of N/Q/H flips: 2 r_work=0.1637 r_free=0.1773 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.488844 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.209750 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 0.1217 0.1469 0.0252 0.007 0.9 0.6 0.5 0.0 0 11.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 14.69 2.52 3.013 19.063 2007.210 0.017 12.45 15.40 2.95 3.228 19.573 2007.210 0.016 Individual atomic B min max mean iso aniso Overall: 8.56 118.62 21.06 2.88 0 1785 Protein: 8.56 118.62 17.92 2.88 0 1519 Water: 11.03 114.50 39.27 N/A 0 258 Other: 23.11 36.81 29.29 N/A 0 8 Chain A: 8.56 118.62 21.06 N/A 0 1785 Histogram: Values Number of atoms 8.56 - 19.57 1202 19.57 - 30.57 234 30.57 - 41.58 166 41.58 - 52.59 100 52.59 - 63.59 54 63.59 - 74.60 15 74.60 - 85.60 7 85.60 - 96.61 4 96.61 - 107.61 0 107.61 - 118.62 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1540 r_work=0.1250 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1250 r_free = 0.1545 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 = 0.1251 r_free = 0.1550 target_work(ls_wunit_k1) = 0.016 | | 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= 0.1251 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015549 | | target function (ls_wunit_k1) not normalized (work): 1295.179318 | | target function (ls_wunit_k1) not normalized (free): 114.584700 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1251 0.1550 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1706 0.1705 0.1768 n_refl.: 87593 remove outliers: r(all,work,free)=0.1706 0.1705 0.1768 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1729 0.1728 0.1784 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1247 0.1540 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1246 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 0.3571 298.579 279.162 0.684 0.922 0.374 11.894-9.307 99.02 97 4 0.1632 478.307 466.708 0.985 0.923 0.370 9.237-7.194 100.00 213 7 0.1824 391.196 386.602 1.029 0.923 0.319 7.162-5.571 100.00 427 22 0.1712 293.571 288.296 1.004 0.923 0.263 5.546-4.326 100.00 867 58 0.0913 403.001 400.284 1.030 0.924 0.209 4.315-3.360 100.00 1859 96 0.0773 383.256 382.240 1.078 0.926 0.190 3.356-2.611 100.00 3867 181 0.1023 251.780 251.022 1.077 0.928 0.100 2.608-2.026 99.99 8198 413 0.0982 166.907 166.317 1.086 0.931 0.000 2.025-1.573 100.00 17313 902 0.1215 81.509 81.667 1.086 0.937 0.000 1.573-1.221 100.00 36679 1900 0.1656 36.144 35.611 1.061 0.946 0.000 1.221-1.150 99.97 13689 708 0.2367 22.773 21.293 1.014 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0536 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1247 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1540 | n_water=258 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1256 r_free=0.1537 | n_water=252 | time (s): 27.440 (total time: 29.830) Filter (q & B) r_work=0.1259 r_free=0.1536 | n_water=249 | time (s): 3.880 (total time: 33.710) Compute maps r_work=0.1259 r_free=0.1536 | n_water=249 | time (s): 1.940 (total time: 35.650) Filter (map) r_work=0.1283 r_free=0.1548 | n_water=234 | time (s): 3.850 (total time: 39.500) Find peaks r_work=0.1283 r_free=0.1548 | n_water=234 | time (s): 0.700 (total time: 40.200) Add new water r_work=0.1431 r_free=0.1695 | n_water=449 | time (s): 3.650 (total time: 43.850) Refine new water occ: r_work=0.1330 r_free=0.1565 adp: r_work=0.1254 r_free=0.1514 occ: r_work=0.1268 r_free=0.1515 adp: r_work=0.1235 r_free=0.1498 occ: r_work=0.1238 r_free=0.1493 adp: r_work=0.1228 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1494 r_work=0.1228 r_free=0.1494 | n_water=449 | time (s): 86.980 (total time: 130.830) Filter (q & B) r_work=0.1235 r_free=0.1501 | n_water=426 | time (s): 3.920 (total time: 134.750) Filter (dist only) r_work=0.1235 r_free=0.1501 | n_water=426 | time (s): 39.560 (total time: 174.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.762462 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1587.249653 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1521 0.0290 0.007 0.9 2.2 0.5 0.0 0 12.881 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.21 2.90 3.797 23.217 1587.250 0.015 11.97 14.78 2.81 4.221 23.000 1587.250 0.015 Individual atomic B min max mean iso aniso Overall: 8.78 113.99 23.14 2.64 192 1761 Protein: 8.78 113.99 17.70 2.65 0 1519 Water: 11.05 72.69 42.44 N/A 192 234 Other: 23.42 34.98 28.46 N/A 0 8 Chain A: 8.78 113.99 20.42 N/A 0 1761 Chain S: 19.69 71.54 48.12 N/A 192 0 Histogram: Values Number of atoms 8.78 - 19.30 1204 19.30 - 29.82 249 29.82 - 40.34 188 40.34 - 50.86 137 50.86 - 61.38 116 61.38 - 71.90 47 71.90 - 82.42 6 82.42 - 92.94 3 92.94 - 103.47 1 103.47 - 113.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1478 r_work=0.1197 r_free=0.1477 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1477 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 = 0.1197 r_free = 0.1465 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= 0.1197 r_free= 0.1465 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013796 | | target function (ls_wunit_k1) not normalized (work): 1149.142460 | | target function (ls_wunit_k1) not normalized (free): 102.115963 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1197 0.1465 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1615 0.1610 0.1733 n_refl.: 87592 remove outliers: r(all,work,free)=0.1615 0.1610 0.1733 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1620 0.1615 0.1736 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1195 0.1468 n_refl.: 87592 remove outliers: r(all,work,free)=0.1207 0.1194 0.1468 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 0.3458 294.522 271.478 0.633 0.940 0.370 11.894-9.307 99.02 97 4 0.1531 478.307 475.824 0.979 0.940 0.370 9.237-7.194 100.00 213 7 0.1663 391.196 392.923 1.040 0.940 0.290 7.162-5.571 100.00 427 22 0.1485 293.571 290.133 1.004 0.941 0.229 5.546-4.326 100.00 867 58 0.0823 403.001 400.211 1.020 0.941 0.215 4.315-3.360 100.00 1859 96 0.0713 383.256 382.124 1.066 0.941 0.210 3.356-2.611 100.00 3867 181 0.0953 251.780 251.243 1.073 0.941 0.140 2.608-2.026 99.99 8198 413 0.0961 166.907 166.484 1.083 0.942 0.000 2.025-1.573 100.00 17313 902 0.1177 81.509 81.712 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1604 36.144 35.651 1.077 0.944 0.000 1.221-1.150 99.97 13689 708 0.2339 22.773 21.327 1.033 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0452 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1468 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1468 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1468 | n_water=426 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1195 r_free=0.1466 | n_water=423 | time (s): 39.000 (total time: 41.160) Filter (q & B) r_work=0.1195 r_free=0.1466 | n_water=423 | time (s): 1.220 (total time: 42.380) Compute maps r_work=0.1195 r_free=0.1466 | n_water=423 | time (s): 1.790 (total time: 44.170) Filter (map) r_work=0.1236 r_free=0.1481 | n_water=292 | time (s): 3.450 (total time: 47.620) Find peaks r_work=0.1236 r_free=0.1481 | n_water=292 | time (s): 0.700 (total time: 48.320) Add new water r_work=0.1364 r_free=0.1627 | n_water=485 | time (s): 2.730 (total time: 51.050) Refine new water occ: r_work=0.1262 r_free=0.1534 adp: r_work=0.1264 r_free=0.1533 occ: r_work=0.1240 r_free=0.1517 adp: r_work=0.1239 r_free=0.1514 occ: r_work=0.1223 r_free=0.1499 adp: r_work=0.1217 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1217 r_free=0.1496 r_work=0.1217 r_free=0.1496 | n_water=485 | time (s): 247.020 (total time: 298.070) Filter (q & B) r_work=0.1222 r_free=0.1496 | n_water=450 | time (s): 3.470 (total time: 301.540) Filter (dist only) r_work=0.1222 r_free=0.1496 | n_water=450 | time (s): 35.270 (total time: 336.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.052576 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.311602 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 0.1234 0.1473 0.0239 0.006 0.9 3.5 0.0 0.0 0 1.026 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.73 2.39 3.638 22.128 45.312 3.726 12.25 14.35 2.10 4.158 21.936 45.312 3.659 Individual atomic B min max mean iso aniso Overall: 9.23 109.02 21.66 2.32 218 1759 Protein: 9.23 109.02 17.25 2.32 0 1519 Water: 11.58 71.49 36.51 N/A 218 232 Other: 19.30 30.88 25.21 N/A 0 8 Chain A: 9.23 109.02 19.93 N/A 0 1759 Chain S: 16.48 66.28 35.64 N/A 218 0 Histogram: Values Number of atoms 9.23 - 19.21 1229 19.21 - 29.18 278 29.18 - 39.16 228 39.16 - 49.14 131 49.14 - 59.12 75 59.12 - 69.10 23 69.10 - 79.08 7 79.08 - 89.06 3 89.06 - 99.04 1 99.04 - 109.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1225 r_free=0.1436 r_work=0.1226 r_free=0.1436 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1226 r_free = 0.1436 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1220 r_free = 0.1434 target_work(ml) = 3.657 | | 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= 0.1220 r_free= 0.1434 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.657275 | | target function (ml) not normalized (work): 304625.399343 | | target function (ml) not normalized (free): 16088.590962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1220 0.1434 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1552 0.1552 0.1600 n_refl.: 87589 remove outliers: r(all,work,free)=0.1552 0.1552 0.1600 n_refl.: 87589 overall B=-0.02 to atoms: r(all,work,free)=0.1549 0.1548 0.1597 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1209 0.1391 n_refl.: 87589 remove outliers: r(all,work,free)=0.1215 0.1206 0.1391 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3968 286.668 258.135 0.462 1.000 0.297 11.894-9.307 97.06 95 4 0.2482 471.703 456.907 0.847 1.001 0.280 9.237-7.194 98.18 209 7 0.2413 382.750 384.797 0.939 1.002 0.190 7.162-5.571 100.00 427 22 0.2057 293.571 283.230 0.914 1.002 0.160 5.546-4.326 100.00 867 58 0.1110 403.001 398.226 0.951 1.002 0.156 4.315-3.360 100.00 1859 96 0.0947 383.256 380.224 0.994 1.002 0.153 3.356-2.611 100.00 3867 181 0.1156 251.780 249.920 1.000 1.002 0.130 2.608-2.026 99.99 8198 413 0.1058 166.907 165.882 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1018 81.509 81.654 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1295 36.144 35.712 1.023 0.999 0.000 1.221-1.150 99.97 13689 708 0.2136 22.773 21.388 0.982 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0575 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1391 | n_water=450 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1206 r_free=0.1390 | n_water=448 | time (s): 41.330 (total time: 43.390) Filter (q & B) r_work=0.1206 r_free=0.1390 | n_water=447 | time (s): 2.490 (total time: 45.880) Compute maps r_work=0.1206 r_free=0.1390 | n_water=447 | time (s): 1.620 (total time: 47.500) Filter (map) r_work=0.1234 r_free=0.1396 | n_water=300 | time (s): 2.850 (total time: 50.350) Find peaks r_work=0.1234 r_free=0.1396 | n_water=300 | time (s): 0.470 (total time: 50.820) Add new water r_work=0.1297 r_free=0.1456 | n_water=466 | time (s): 2.750 (total time: 53.570) Refine new water occ: r_work=0.1224 r_free=0.1388 adp: r_work=0.1224 r_free=0.1391 occ: r_work=0.1209 r_free=0.1378 adp: r_work=0.1208 r_free=0.1379 occ: r_work=0.1199 r_free=0.1372 adp: r_work=0.1196 r_free=0.1371 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1371 r_work=0.1196 r_free=0.1371 | n_water=466 | time (s): 200.700 (total time: 254.270) Filter (q & B) r_work=0.1203 r_free=0.1371 | n_water=427 | time (s): 3.480 (total time: 257.750) Filter (dist only) r_work=0.1203 r_free=0.1370 | n_water=426 | time (s): 35.910 (total time: 293.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.045777 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.609239 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 0.1205 0.1375 0.0170 0.006 1.0 3.8 0.5 0.0 0 1.023 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.75 1.70 3.423 21.389 47.609 3.639 11.87 13.67 1.80 3.801 21.271 47.609 3.622 Individual atomic B min max mean iso aniso Overall: 9.25 105.26 21.04 2.17 197 1756 Protein: 9.25 105.26 16.96 2.17 0 1519 Water: 11.51 70.10 35.52 N/A 197 229 Other: 20.06 28.32 24.06 N/A 0 8 Chain A: 9.25 105.26 19.55 N/A 0 1756 Chain S: 15.09 57.12 34.31 N/A 197 0 Histogram: Values Number of atoms 9.25 - 18.85 1220 18.85 - 28.45 298 28.45 - 38.05 200 38.05 - 47.65 123 47.65 - 57.25 75 57.25 - 66.86 22 66.86 - 76.46 10 76.46 - 86.06 2 86.06 - 95.66 1 95.66 - 105.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1367 r_work=0.1187 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1367 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1364 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1183 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.620837 | | target function (ml) not normalized (work): 301557.805956 | | target function (ml) not normalized (free): 15928.878440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1183 0.1364 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1519 0.1518 0.1568 n_refl.: 87580 remove outliers: r(all,work,free)=0.1519 0.1518 0.1568 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1516 0.1515 0.1566 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1183 0.1365 n_refl.: 87580 remove outliers: r(all,work,free)=0.1191 0.1182 0.1365 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 88.54 80 5 0.3961 289.256 250.559 0.463 0.999 0.330 11.894-9.307 96.08 94 4 0.2399 465.600 456.562 0.843 1.001 0.269 9.237-7.194 98.18 209 7 0.2552 382.750 374.645 0.907 1.001 0.188 7.162-5.571 100.00 427 22 0.2178 293.571 282.489 0.907 1.001 0.169 5.546-4.326 100.00 867 58 0.1153 403.001 398.327 0.950 1.001 0.140 4.315-3.360 100.00 1859 96 0.0948 383.256 380.908 0.995 1.002 0.137 3.356-2.611 100.00 3867 181 0.1157 251.780 250.114 1.001 1.002 0.120 2.608-2.026 99.99 8198 413 0.1025 166.907 166.024 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0965 81.509 81.785 1.026 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1242 36.144 35.766 1.019 1.001 0.000 1.221-1.150 99.97 13689 708 0.2127 22.773 21.350 0.975 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0410 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1182 r_free=0.1365 After: r_work=0.1183 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1183 r_free=0.1365 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=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1365 | n_water=426 | time (s): 1.720 (total time: 1.720) Filter (dist) r_work=0.1183 r_free=0.1365 | n_water=426 | time (s): 35.710 (total time: 37.430) Filter (q & B) r_work=0.1183 r_free=0.1367 | n_water=422 | time (s): 2.770 (total time: 40.200) Compute maps r_work=0.1183 r_free=0.1367 | n_water=422 | time (s): 1.460 (total time: 41.660) Filter (map) r_work=0.1207 r_free=0.1385 | n_water=317 | time (s): 2.720 (total time: 44.380) Find peaks r_work=0.1207 r_free=0.1385 | n_water=317 | time (s): 0.510 (total time: 44.890) Add new water r_work=0.1267 r_free=0.1443 | n_water=482 | time (s): 2.840 (total time: 47.730) Refine new water occ: r_work=0.1194 r_free=0.1375 adp: r_work=0.1194 r_free=0.1377 occ: r_work=0.1180 r_free=0.1361 adp: r_work=0.1179 r_free=0.1363 occ: r_work=0.1170 r_free=0.1352 adp: r_work=0.1166 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1166 r_free=0.1352 r_work=0.1166 r_free=0.1352 | n_water=482 | time (s): 198.220 (total time: 245.950) Filter (q & B) r_work=0.1175 r_free=0.1357 | n_water=442 | time (s): 2.450 (total time: 248.400) Filter (dist only) r_work=0.1175 r_free=0.1357 | n_water=441 | time (s): 35.670 (total time: 284.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.892648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.233541 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 0.1201 0.1368 0.0168 0.007 1.0 5.1 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.68 1.68 3.298 21.115 42.234 3.629 12.08 13.73 1.65 3.484 21.048 42.234 3.624 Individual atomic B min max mean iso aniso Overall: 9.29 101.33 20.96 2.03 213 1755 Protein: 9.29 101.33 16.78 2.03 0 1519 Water: 11.58 69.37 35.31 N/A 213 228 Other: 19.80 27.65 23.77 N/A 0 8 Chain A: 9.29 101.33 19.34 N/A 0 1755 Chain S: 14.00 60.19 34.32 N/A 213 0 Histogram: Values Number of atoms 9.29 - 18.49 1217 18.49 - 27.70 294 27.70 - 36.90 202 36.90 - 46.10 137 46.10 - 55.31 73 55.31 - 64.51 28 64.51 - 73.72 12 73.72 - 82.92 2 82.92 - 92.12 1 92.12 - 101.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1373 r_work=0.1209 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1373 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1368 target_work(ml) = 3.624 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1206 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.623664 | | target function (ml) not normalized (work): 301785.954260 | | target function (ml) not normalized (free): 15942.238783 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1421 0.1394 5.6877 5.6356| | 2: 3.57 - 2.84 1.00 2888 124 0.1134 0.1455 5.2078 5.2689| | 3: 2.83 - 2.48 1.00 2820 163 0.1235 0.1327 5.0082 5.0317| | 4: 2.47 - 2.25 1.00 2825 136 0.1043 0.1163 4.714 4.7633| | 5: 2.25 - 2.09 1.00 2756 127 0.1022 0.1128 4.6555 4.7153| | 6: 2.09 - 1.97 1.00 2846 113 0.0986 0.1140 4.3605 4.484| | 7: 1.97 - 1.87 1.00 2787 165 0.1013 0.1226 4.0873 4.1764| | 8: 1.87 - 1.79 1.00 2789 144 0.1031 0.1202 3.9954 4.0597| | 9: 1.79 - 1.72 1.00 2745 138 0.0964 0.1356 3.7201 3.9408| | 10: 1.72 - 1.66 1.00 2831 160 0.1014 0.1252 3.6367 3.7567| | 11: 1.66 - 1.61 1.00 2712 147 0.0966 0.1091 3.5668 3.6081| | 12: 1.61 - 1.56 1.00 2773 144 0.0921 0.1153 3.3484 3.494| | 13: 1.56 - 1.52 1.00 2745 130 0.0985 0.1052 3.3418 3.4247| | 14: 1.52 - 1.48 1.00 2803 134 0.0988 0.1126 3.2605 3.3402| | 15: 1.48 - 1.45 1.00 2738 128 0.1014 0.1342 3.1676 3.3243| | 16: 1.45 - 1.42 1.00 2756 161 0.1064 0.1255 3.1479 3.2346| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1274 3.1118 3.2241| | 18: 1.39 - 1.36 1.00 2741 179 0.1160 0.1385 3.0872 3.2754| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1598 3.0928 3.28| | 20: 1.34 - 1.32 1.00 2696 147 0.1318 0.1482 3.0866 3.1361| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1590 3.0891 3.1503| | 22: 1.29 - 1.27 1.00 2704 152 0.1479 0.1940 3.0851 3.2971| | 23: 1.27 - 1.26 1.00 2802 156 0.1578 0.1848 3.1031 3.2077| | 24: 1.26 - 1.24 1.00 2744 132 0.1625 0.1763 3.0937 3.1907| | 25: 1.24 - 1.22 1.00 2733 148 0.1792 0.2275 3.109 3.2878| | 26: 1.22 - 1.21 1.00 2727 135 0.1868 0.1772 3.1257 3.1971| | 27: 1.21 - 1.19 1.00 2814 148 0.2014 0.2090 3.1424 3.1512| | 28: 1.19 - 1.18 1.00 2671 147 0.2152 0.2338 3.1408 3.1652| | 29: 1.18 - 1.16 1.00 2800 134 0.2217 0.2356 3.1266 3.2189| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2489 3.1142 3.1671| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.12 1.00 0.97 6268.79| | 2: 3.57 - 2.84 2888 124 0.92 13.38 1.01 0.97 6268.79| | 3: 2.83 - 2.48 2820 163 0.89 17.56 0.98 0.97 5257.07| | 4: 2.47 - 2.25 2825 136 0.91 14.65 1.00 0.98 2648.15| | 5: 2.25 - 2.09 2756 127 0.89 16.92 1.01 0.98 2648.15| | 6: 2.09 - 1.97 2846 113 0.92 13.70 1.02 0.97 1559.55| | 7: 1.97 - 1.87 2787 165 0.94 10.85 1.02 0.97 631.12| | 8: 1.87 - 1.79 2789 144 0.91 14.48 1.00 0.97 631.12| | 9: 1.79 - 1.72 2745 138 0.93 11.44 0.98 0.97 339.61| | 10: 1.72 - 1.66 2831 160 0.93 12.23 0.98 0.97 281.23| | 11: 1.66 - 1.61 2712 147 0.93 12.90 0.98 0.97 268.39| | 12: 1.61 - 1.56 2773 144 0.95 9.50 0.99 0.97 147.32| | 13: 1.56 - 1.52 2745 130 0.94 11.13 1.02 0.97 147.32| | 14: 1.52 - 1.48 2803 134 0.94 11.27 1.02 0.97 131.50| | 15: 1.48 - 1.45 2738 128 0.95 10.36 1.02 0.98 102.52| | 16: 1.45 - 1.42 2756 161 0.94 11.54 1.02 0.98 102.52| | 17: 1.42 - 1.39 2785 139 0.94 11.45 1.01 0.98 92.69| | 18: 1.39 - 1.36 2741 179 0.94 11.70 1.01 0.98 86.99| | 19: 1.36 - 1.34 2807 134 0.94 12.30 1.00 0.98 86.99| | 20: 1.34 - 1.32 2696 147 0.94 12.42 0.99 0.97 82.14| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 81.80| | 22: 1.29 - 1.27 2704 152 0.93 13.93 0.98 0.96 81.98| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.98 0.95 82.89| | 24: 1.26 - 1.24 2744 132 0.92 14.95 0.97 0.95 82.89| | 25: 1.24 - 1.22 2733 148 0.91 16.37 0.96 0.94 84.45| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.03 0.93 86.19| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.19| | 28: 1.19 - 1.18 2671 147 0.88 20.26 1.01 0.93 89.52| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.93 90.77| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.99 0.93 90.77| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.80 max = 6268.79 mean = 978.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.06| |phase err.(test): min = 0.00 max = 89.73 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1206 0.1368 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1531 0.1529 0.1583 n_refl.: 87578 remove outliers: r(all,work,free)=0.1531 0.1529 0.1583 n_refl.: 87578 overall B=-0.02 to atoms: r(all,work,free)=0.1527 0.1526 0.1580 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1207 0.1368 n_refl.: 87578 remove outliers: r(all,work,free)=0.1214 0.1206 0.1368 n_refl.: 87575 ======================== 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 0.4093 289.256 253.035 0.444 1.000 0.283 11.894-9.307 94.12 92 4 0.2390 465.639 451.273 0.835 1.002 0.263 9.237-7.194 97.73 208 7 0.2515 383.824 375.065 0.904 1.002 0.160 7.162-5.571 100.00 427 22 0.2232 293.571 282.303 0.904 1.002 0.150 5.546-4.326 100.00 867 58 0.1205 403.001 398.846 0.953 1.002 0.136 4.315-3.360 100.00 1859 96 0.0996 383.256 380.435 0.996 1.002 0.130 3.356-2.611 100.00 3867 181 0.1197 251.780 249.969 1.002 1.001 0.110 2.608-2.026 99.99 8198 413 0.1060 166.907 165.846 1.014 1.000 0.000 2.025-1.573 100.00 17313 902 0.0989 81.509 81.774 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1228 36.144 35.782 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2119 22.773 21.411 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0487 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2605 0.1935 0.083 5.460 8.8 119.3 19.9 258 0.000 1_bss: 0.1634 0.1770 0.083 5.460 9.1 119.5 20.1 258 0.000 1_settarget: 0.1634 0.1770 0.083 5.460 9.1 119.5 20.1 258 0.000 1_nqh: 0.1637 0.1773 0.083 5.460 9.1 119.5 20.1 258 0.006 1_weight: 0.1637 0.1773 0.083 5.460 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1217 0.1469 0.007 0.937 9.1 119.5 20.1 258 0.131 1_adp: 0.1245 0.1540 0.007 0.937 8.6 118.6 21.1 258 0.131 1_regHadp: 0.1250 0.1545 0.007 0.937 8.6 118.6 21.1 258 0.131 1_occ: 0.1251 0.1550 0.007 0.937 8.6 118.6 21.1 258 0.131 2_bss: 0.1246 0.1540 0.007 0.937 8.7 118.8 21.2 258 0.131 2_settarget: 0.1246 0.1540 0.007 0.937 8.7 118.8 21.2 258 0.131 2_updatecdl: 0.1246 0.1540 0.007 0.942 8.7 118.8 21.2 258 0.131 2_nqh: 0.1247 0.1540 0.007 0.942 8.7 118.8 21.2 258 0.128 2_sol: 0.1235 0.1501 0.007 0.942 8.7 118.8 23.5 426 n/a 2_weight: 0.1235 0.1501 0.007 0.942 8.7 118.8 23.5 426 n/a 2_xyzrec: 0.1230 0.1521 0.007 0.875 8.7 118.8 23.5 426 n/a 2_adp: 0.1197 0.1478 0.007 0.875 8.8 114.0 23.1 426 n/a 2_regHadp: 0.1197 0.1477 0.007 0.875 8.8 114.0 23.1 426 n/a 2_occ: 0.1197 0.1465 0.007 0.875 8.8 114.0 23.1 426 n/a 3_bss: 0.1194 0.1468 0.007 0.875 8.8 114.0 23.2 426 n/a 3_settarget: 0.1194 0.1468 0.007 0.875 8.8 114.0 23.2 426 n/a 3_updatecdl: 0.1194 0.1468 0.007 0.874 8.8 114.0 23.2 426 n/a 3_nqh: 0.1194 0.1468 0.007 0.874 8.8 114.0 23.2 426 n/a 3_sol: 0.1222 0.1496 0.007 0.874 8.8 114.0 22.0 450 n/a 3_weight: 0.1222 0.1496 0.007 0.874 8.8 114.0 22.0 450 n/a 3_xyzrec: 0.1234 0.1473 0.006 0.918 8.8 114.0 22.0 450 n/a 3_adp: 0.1225 0.1436 0.006 0.918 9.2 109.0 21.7 450 n/a 3_regHadp: 0.1226 0.1436 0.006 0.918 9.2 109.0 21.7 450 n/a 3_occ: 0.1220 0.1434 0.006 0.918 9.2 109.0 21.7 450 n/a 4_bss: 0.1206 0.1391 0.006 0.918 9.2 109.0 21.6 450 n/a 4_settarget: 0.1206 0.1391 0.006 0.918 9.2 109.0 21.6 450 n/a 4_updatecdl: 0.1206 0.1391 0.006 0.917 9.2 109.0 21.6 450 n/a 4_nqh: 0.1206 0.1391 0.006 0.917 9.2 109.0 21.6 450 n/a 4_sol: 0.1203 0.1370 0.006 0.917 9.2 109.0 21.3 426 n/a 4_weight: 0.1203 0.1370 0.006 0.917 9.2 109.0 21.3 426 n/a 4_xyzrec: 0.1205 0.1375 0.006 0.957 9.2 109.0 21.3 426 n/a 4_adp: 0.1187 0.1367 0.006 0.957 9.2 105.3 21.0 426 n/a 4_regHadp: 0.1187 0.1367 0.006 0.957 9.2 105.3 21.0 426 n/a 4_occ: 0.1183 0.1364 0.006 0.957 9.2 105.3 21.0 426 n/a 5_bss: 0.1182 0.1365 0.006 0.957 9.2 105.2 21.0 426 n/a 5_settarget: 0.1182 0.1365 0.006 0.957 9.2 105.2 21.0 426 n/a 5_updatecdl: 0.1182 0.1365 0.006 0.959 9.2 105.2 21.0 426 n/a 5_setrh: 0.1183 0.1365 0.006 0.959 9.2 105.2 21.0 426 n/a 5_nqh: 0.1183 0.1365 0.006 0.959 9.2 105.2 21.0 426 n/a 5_sol: 0.1175 0.1357 0.006 0.959 9.2 105.2 21.1 441 n/a 5_weight: 0.1175 0.1357 0.006 0.959 9.2 105.2 21.1 441 n/a 5_xyzrec: 0.1201 0.1368 0.007 1.037 9.2 105.2 21.1 441 n/a 5_adp: 0.1208 0.1373 0.007 1.037 9.3 101.3 21.0 441 n/a 5_regHadp: 0.1209 0.1373 0.007 1.037 9.3 101.3 21.0 441 n/a 5_occ: 0.1206 0.1368 0.007 1.037 9.3 101.3 21.0 441 n/a end: 0.1206 0.1368 0.007 1.037 9.3 101.3 20.9 441 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3867824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3867824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7900 Refinement macro-cycles (run) : 3513.3900 Write final files (write_after_run_outputs) : 64.2700 Total : 3582.4500 Total CPU time: 60.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:21 PST -0800 (1735452681.90 s) Start R-work = 0.1634, R-free = 0.1770 Final R-work = 0.1206, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 3714.54 seconds wall clock time: 66 minutes 30.51 seconds (3990.51 seconds total)