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_3031784.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3031784.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.12, per 1000 atoms: 0.63 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: 0.72 Conformation dependent library (CDL) restraints added in 189.5 milliseconds Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 395 0.89 - 1.15: 1224 1.15 - 1.41: 630 1.41 - 1.67: 858 1.67 - 1.93: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 183 " pdb=" CA ALA A 183 " ideal model delta sigma weight residual 1.462 1.608 -0.146 7.70e-03 1.69e+04 3.58e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.172 0.206 1.10e-02 8.26e+03 3.52e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.034 0.204 1.10e-02 8.26e+03 3.42e+02 bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.040 0.193 1.08e-02 8.57e+03 3.18e+02 bond pdb=" CA ASP A 60 " pdb=" C ASP A 60 " ideal model delta sigma weight residual 1.524 1.745 -0.221 1.26e-02 6.30e+03 3.08e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 3113 4.46 - 8.92: 1829 8.92 - 13.38: 687 13.38 - 17.84: 133 17.84 - 22.30: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ARG A 98 " pdb=" C ARG A 98 " pdb=" O ARG A 98 " ideal model delta sigma weight residual 119.43 137.78 -18.35 1.21e+00 6.83e-01 2.30e+02 angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 136.28 -13.68 1.00e+00 1.00e+00 1.87e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 135.83 -13.76 1.03e+00 9.43e-01 1.78e+02 angle pdb=" N VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta sigma weight residual 110.62 124.46 -13.84 1.05e+00 9.07e-01 1.74e+02 angle pdb=" CA LEU A 92 " pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 120.19 134.73 -14.54 1.15e+00 7.56e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 924 16.65 - 33.30: 130 33.30 - 49.95: 36 49.95 - 66.59: 19 66.59 - 83.24: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " pdb=" HE1 HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" N BGLU A 96 " pdb=" CA BGLU A 96 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 98 0.213 - 0.427: 68 0.427 - 0.640: 44 0.640 - 0.853: 27 0.853 - 1.066: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 1.49 1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.089 2.00e-02 2.50e+03 5.87e-02 1.04e+02 pdb=" CG PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.098 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.072 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.015 2.00e-02 2.50e+03 6.29e-02 8.91e+01 pdb=" CG HIS A 126 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.094 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.060 9.50e-02 1.11e+02 6.44e-02 8.46e+01 pdb=" NE ARG A 5 " -0.090 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.050 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.102 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1120 2.33 - 2.90: 8110 2.90 - 3.47: 10544 3.47 - 4.03: 15209 4.03 - 4.60: 21683 Nonbonded interactions: 56666 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.763 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.823 2.100 nonbonded pdb=" O ILE A 102 " pdb=" H ALEU A 153 " model vdw 1.838 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.838 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.842 2.450 ... (remaining 56661 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_3031784_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795445 | | target function (ml) not normalized (work): 232877.368734 | | target function (ml) not normalized (free): 11855.589639 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3036 0.2009 7.0953 4.9331| | 2: 3.57 - 2.84 1.00 2876 122 0.2429 0.1865 4.3467 4.3474| | 3: 2.84 - 2.48 1.00 2833 165 0.2379 0.1678 4.124 4.1414| | 4: 2.47 - 2.25 1.00 2825 136 0.2351 0.1486 3.8281 3.821| | 5: 2.25 - 2.09 1.00 2756 127 0.2419 0.1579 3.7909 3.8137| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1752 3.4605 3.5289| | 7: 1.97 - 1.87 1.00 2787 165 0.2566 0.1865 3.1449 3.189| | 8: 1.87 - 1.79 1.00 2789 144 0.2476 0.1905 3.0876 3.1358| | 9: 1.79 - 1.72 1.00 2745 138 0.2387 0.2118 2.9019 3.0009| | 10: 1.72 - 1.66 1.00 2789 158 0.2417 0.1900 2.8059 2.8726| | 11: 1.66 - 1.61 1.00 2740 147 0.2543 0.2011 2.7681 2.8502| | 12: 1.61 - 1.56 1.00 2787 146 0.2505 0.2203 2.645 2.7258| | 13: 1.56 - 1.52 1.00 2745 130 0.2592 0.1965 2.5986 2.6429| | 14: 1.52 - 1.48 1.00 2803 134 0.2558 0.1822 2.5003 2.5199| | 15: 1.48 - 1.45 1.00 2738 128 0.2602 0.2220 2.4246 2.5406| | 16: 1.45 - 1.42 1.00 2756 161 0.2606 0.2346 2.3909 2.4845| | 17: 1.42 - 1.39 1.00 2785 139 0.2662 0.2220 2.3425 2.4083| | 18: 1.39 - 1.36 1.00 2741 179 0.2693 0.2197 2.2822 2.3536| | 19: 1.36 - 1.34 1.00 2807 134 0.2694 0.2259 2.246 2.2614| | 20: 1.34 - 1.32 1.00 2696 147 0.2686 0.2164 2.204 2.1344| | 21: 1.32 - 1.30 1.00 2785 112 0.2696 0.2282 2.1568 2.1924| | 22: 1.29 - 1.27 1.00 2704 152 0.2799 0.2756 2.1367 2.2217| | 23: 1.27 - 1.26 1.00 2802 156 0.2778 0.2470 2.1006 2.2166| | 24: 1.26 - 1.24 1.00 2744 132 0.2757 0.2231 2.0833 2.0711| | 25: 1.24 - 1.22 1.00 2734 148 0.2791 0.2647 2.0446 2.0998| | 26: 1.22 - 1.21 1.00 2727 135 0.2810 0.2275 2.0048 2.0668| | 27: 1.21 - 1.19 1.00 2814 148 0.2957 0.2849 2.0006 2.0257| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2843 2.0012 1.9928| | 29: 1.18 - 1.16 1.00 2800 134 0.2964 0.2789 1.9569 2.0639| | 30: 1.16 - 1.15 1.00 2740 148 0.3063 0.3025 1.9336 1.9737| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.74 0.76 0.23 1455.13| | 2: 3.57 - 2.84 2876 122 0.81 25.86 1.27 0.23 1455.13| | 3: 2.84 - 2.48 2833 165 0.74 31.80 1.25 0.23 1207.37| | 4: 2.47 - 2.25 2825 136 0.81 25.40 1.26 0.25 564.40| | 5: 2.25 - 2.09 2756 127 0.78 29.00 1.27 0.25 564.40| | 6: 2.09 - 1.97 2846 113 0.83 22.76 1.29 0.25 310.87| | 7: 1.97 - 1.87 2787 165 0.90 16.85 1.29 0.26 94.64| | 8: 1.87 - 1.79 2789 144 0.85 21.41 1.24 0.26 94.64| | 9: 1.79 - 1.72 2745 138 0.87 19.18 1.22 0.25 58.37| | 10: 1.72 - 1.66 2789 158 0.86 20.84 1.23 0.25 51.10| | 11: 1.66 - 1.61 2740 147 0.85 22.15 1.25 0.25 49.40| | 12: 1.61 - 1.56 2787 146 0.88 19.31 1.23 0.25 32.17| | 13: 1.56 - 1.52 2745 130 0.86 21.17 1.24 0.25 32.17| | 14: 1.52 - 1.48 2803 134 0.86 21.49 1.24 0.25 28.53| | 15: 1.48 - 1.45 2738 128 0.86 20.84 1.23 0.25 21.86| | 16: 1.45 - 1.42 2756 161 0.85 22.17 1.23 0.25 21.86| | 17: 1.42 - 1.39 2785 139 0.86 21.17 1.23 0.25 18.26| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.23 0.25 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.51 1.22 0.25 16.17| | 20: 1.34 - 1.32 2696 147 0.87 20.97 1.21 0.24 12.99| | 21: 1.32 - 1.30 2785 112 0.86 21.90 1.21 0.24 12.77| | 22: 1.29 - 1.27 2704 152 0.85 22.67 1.21 0.24 12.51| | 23: 1.27 - 1.26 2802 156 0.85 22.39 1.21 0.24 11.18| | 24: 1.26 - 1.24 2744 132 0.85 22.80 1.19 0.24 11.18| | 25: 1.24 - 1.22 2734 148 0.84 23.60 1.19 0.24 10.69| | 26: 1.22 - 1.21 2727 135 0.84 24.25 1.19 0.23 10.14| | 27: 1.21 - 1.19 2814 148 0.83 25.36 1.20 0.23 10.14| | 28: 1.19 - 1.18 2671 147 0.82 25.81 1.17 0.23 9.66| | 29: 1.18 - 1.16 2800 134 0.82 26.27 1.17 0.22 9.48| | 30: 1.16 - 1.15 2740 148 0.80 27.94 1.15 0.22 9.48| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.48 max = 1455.13 mean = 212.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.93| |phase err.(test): min = 0.00 max = 89.82 mean = 22.83| |-----------------------------------------------------------------------------| ----------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 0.232 1557 Z= 5.599 Angle : 5.167 19.341 2118 Z= 3.645 Chirality : 0.398 1.066 243 Planarity : 0.030 0.086 284 Dihedral : 14.193 83.240 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 3.73 % Allowed : 1.86 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -1.79 (0.53), residues: 224 helix: -2.16 (0.45), residues: 102 sheet: -1.71 (0.83), residues: 30 loop : 0.61 (0.65), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.016 ARG A 27 TYR 0.089 0.035 TYR A 141 PHE 0.108 0.037 PHE A 162 HIS 0.084 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795445 | | target function (ml) not normalized (work): 232877.368734 | | target function (ml) not normalized (free): 11855.589639 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2608 0.1963 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2608 0.1963 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1983 0.1963 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2006 0.2009 0.1977 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1638 0.1796 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1637 0.1796 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 98.94 88 5 0.3812 386.282 356.300 0.663 1.003 0.401 11.894-9.307 98.04 96 4 0.1730 616.081 590.305 0.925 1.003 0.380 9.237-7.194 100.00 213 7 0.2146 501.842 492.572 0.963 1.004 0.364 7.162-5.571 100.00 427 22 0.2262 376.604 363.041 0.929 1.004 0.297 5.546-4.326 100.00 867 58 0.1259 516.985 510.847 0.962 1.003 0.224 4.315-3.360 100.00 1859 96 0.1143 491.656 488.366 1.005 1.003 0.199 3.356-2.611 100.00 3867 181 0.1450 322.993 319.633 0.996 1.002 0.043 2.608-2.026 99.99 8198 413 0.1337 214.115 212.218 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1662 104.562 103.830 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2062 46.367 45.080 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2582 29.215 26.933 0.975 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1796 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1642 r_free=0.1798 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.317813 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1997.973589 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 0.1209 0.1460 0.0251 0.008 1.0 1.0 0.5 0.0 0 13.159 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.60 2.51 3.013 19.068 1997.974 0.017 12.48 15.49 3.01 3.105 19.487 1997.974 0.015 Individual atomic B min max mean iso aniso Overall: 8.47 118.61 20.89 2.87 0 1785 Protein: 8.47 118.61 17.80 2.87 0 1519 Water: 11.02 114.68 38.86 N/A 0 258 Other: 23.11 35.30 28.50 N/A 0 8 Chain A: 8.47 118.61 20.89 N/A 0 1785 Histogram: Values Number of atoms 8.47 - 19.48 1205 19.48 - 30.50 238 30.50 - 41.51 162 41.51 - 52.53 103 52.53 - 63.54 48 63.54 - 74.55 18 74.55 - 85.57 4 85.57 - 96.58 3 96.58 - 107.60 1 107.60 - 118.61 3 =========================== Idealize ADP of riding H ========================== r_work=0.1248 r_free=0.1549 r_work=0.1252 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1252 r_free = 0.1554 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 = 0.1556 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1251 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015233 | | target function (ls_wunit_k1) not normalized (work): 1268.809492 | | target function (ls_wunit_k1) not normalized (free): 113.987952 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1266 0.1251 0.1556 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1704 0.1703 0.1776 n_refl.: 87592 remove outliers: r(all,work,free)=0.1704 0.1703 0.1776 n_refl.: 87592 overall B=0.15 to atoms: r(all,work,free)=0.1728 0.1727 0.1793 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1263 0.1249 0.1550 n_refl.: 87592 remove outliers: r(all,work,free)=0.1263 0.1249 0.1550 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3580 298.951 278.966 0.688 0.925 0.380 11.894-9.307 98.04 96 4 0.1506 480.846 470.225 0.993 0.925 0.369 9.237-7.194 100.00 213 7 0.1813 391.684 386.813 1.028 0.925 0.340 7.162-5.571 100.00 427 22 0.1746 293.937 288.474 0.998 0.926 0.253 5.546-4.326 100.00 867 58 0.0927 403.503 400.703 1.027 0.927 0.209 4.315-3.360 100.00 1859 96 0.0772 383.734 382.875 1.075 0.928 0.199 3.356-2.611 100.00 3867 181 0.1012 252.093 251.363 1.076 0.930 0.052 2.608-2.026 99.99 8198 413 0.0972 167.115 166.534 1.084 0.933 0.000 2.025-1.573 100.00 17313 902 0.1217 81.610 81.797 1.084 0.938 0.000 1.573-1.221 100.00 36679 1900 0.1678 36.189 35.647 1.059 0.947 0.000 1.221-1.150 99.97 13689 708 0.2384 22.802 21.329 1.013 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0583 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1249 r_free=0.1550 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=0.1250 r_free=0.1551 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1250 r_free=0.1551 | n_water=258 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1258 r_free=0.1547 | n_water=252 | time (s): 25.930 (total time: 28.290) Filter (q & B) r_work=0.1262 r_free=0.1546 | n_water=249 | time (s): 3.660 (total time: 31.950) Compute maps r_work=0.1262 r_free=0.1546 | n_water=249 | time (s): 1.870 (total time: 33.820) Filter (map) r_work=0.1276 r_free=0.1557 | n_water=235 | time (s): 3.870 (total time: 37.690) Find peaks r_work=0.1276 r_free=0.1557 | n_water=235 | time (s): 0.700 (total time: 38.390) Add new water r_work=0.1429 r_free=0.1722 | n_water=452 | time (s): 3.740 (total time: 42.130) Refine new water occ: r_work=0.1335 r_free=0.1573 adp: r_work=0.1260 r_free=0.1538 occ: r_work=0.1273 r_free=0.1521 adp: r_work=0.1239 r_free=0.1512 occ: r_work=0.1241 r_free=0.1499 adp: r_work=0.1231 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1502 r_work=0.1231 r_free=0.1502 | n_water=452 | time (s): 133.080 (total time: 175.210) Filter (q & B) r_work=0.1238 r_free=0.1504 | n_water=431 | time (s): 4.010 (total time: 179.220) Filter (dist only) r_work=0.1239 r_free=0.1505 | n_water=429 | time (s): 44.710 (total time: 223.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.792013 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1426.131779 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 0.1237 0.1527 0.0290 0.007 0.9 2.6 0.5 0.0 0 13.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 15.27 2.90 3.771 23.071 1426.132 0.015 12.05 14.87 2.83 4.112 22.908 1426.132 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 114.75 23.10 2.57 194 1762 Protein: 8.69 114.75 17.64 2.57 0 1519 Water: 11.03 73.29 42.35 N/A 194 235 Other: 24.16 35.18 28.67 N/A 0 8 Chain A: 8.69 114.75 20.28 N/A 0 1762 Chain S: 13.78 70.12 48.70 N/A 194 0 Histogram: Values Number of atoms 8.69 - 19.29 1205 19.29 - 29.90 262 29.90 - 40.51 179 40.51 - 51.11 143 51.11 - 61.72 107 61.72 - 72.33 48 72.33 - 82.93 6 82.93 - 93.54 3 93.54 - 104.14 1 104.14 - 114.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1488 r_work=0.1205 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1487 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 = 0.1205 r_free = 0.1478 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1205 r_free= 0.1478 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014071 | | target function (ls_wunit_k1) not normalized (work): 1172.052184 | | target function (ls_wunit_k1) not normalized (free): 102.326628 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1205 0.1478 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1604 0.1601 0.1697 n_refl.: 87591 remove outliers: r(all,work,free)=0.1604 0.1601 0.1697 n_refl.: 87591 overall B=0.05 to atoms: r(all,work,free)=0.1612 0.1609 0.1702 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1202 0.1477 n_refl.: 87591 remove outliers: r(all,work,free)=0.1214 0.1201 0.1477 n_refl.: 87588 ======================== 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 0.3395 294.889 270.031 0.627 0.938 0.362 11.894-9.307 98.04 96 4 0.1462 480.846 478.266 0.992 0.938 0.356 9.237-7.194 100.00 213 7 0.1715 391.684 392.249 1.040 0.938 0.300 7.162-5.571 100.00 427 22 0.1499 293.937 290.187 0.999 0.939 0.227 5.546-4.326 100.00 867 58 0.0847 403.503 400.591 1.023 0.939 0.217 4.315-3.360 100.00 1859 96 0.0719 383.734 382.734 1.069 0.940 0.210 3.356-2.611 100.00 3867 181 0.0967 252.093 251.247 1.074 0.941 0.062 2.608-2.026 99.99 8198 413 0.0961 167.115 166.661 1.081 0.942 0.000 2.025-1.573 100.00 17313 902 0.1180 81.610 81.821 1.085 0.945 0.000 1.573-1.221 100.00 36679 1900 0.1616 36.189 35.684 1.066 0.950 0.000 1.221-1.150 99.97 13689 708 0.2345 22.802 21.341 1.020 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0744 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1477 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=0.1201 r_free=0.1477 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1477 | n_water=429 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1200 r_free=0.1476 | n_water=427 | time (s): 39.480 (total time: 41.820) Filter (q & B) r_work=0.1200 r_free=0.1476 | n_water=427 | time (s): 1.230 (total time: 43.050) Compute maps r_work=0.1200 r_free=0.1476 | n_water=427 | time (s): 1.280 (total time: 44.330) Filter (map) r_work=0.1235 r_free=0.1483 | n_water=304 | time (s): 3.220 (total time: 47.550) Find peaks r_work=0.1235 r_free=0.1483 | n_water=304 | time (s): 0.600 (total time: 48.150) Add new water r_work=0.1362 r_free=0.1601 | n_water=493 | time (s): 3.080 (total time: 51.230) Refine new water occ: r_work=0.1265 r_free=0.1519 adp: r_work=0.1266 r_free=0.1522 occ: r_work=0.1244 r_free=0.1498 adp: r_work=0.1242 r_free=0.1499 occ: r_work=0.1230 r_free=0.1481 adp: r_work=0.1223 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1223 r_free=0.1480 r_work=0.1223 r_free=0.1480 | n_water=493 | time (s): 222.890 (total time: 274.120) Filter (q & B) r_work=0.1226 r_free=0.1481 | n_water=453 | time (s): 2.880 (total time: 277.000) Filter (dist only) r_work=0.1226 r_free=0.1481 | n_water=453 | time (s): 35.820 (total time: 312.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.063857 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.915076 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1229 0.1445 0.0216 0.006 0.9 1.6 0.5 0.0 0 1.032 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.45 2.16 3.604 22.142 41.915 3.727 12.16 14.03 1.87 4.153 21.934 41.915 3.657 Individual atomic B min max mean iso aniso Overall: 9.15 109.95 21.71 2.29 220 1760 Protein: 9.15 109.95 17.17 2.29 0 1519 Water: 11.49 72.20 36.89 N/A 220 233 Other: 20.51 31.34 25.99 N/A 0 8 Chain A: 9.15 109.95 19.79 N/A 0 1760 Chain S: 15.45 64.33 37.12 N/A 220 0 Histogram: Values Number of atoms 9.15 - 19.23 1234 19.23 - 29.31 282 29.31 - 39.39 215 39.39 - 49.47 137 49.47 - 59.55 78 59.55 - 69.63 22 69.63 - 79.71 6 79.71 - 89.79 3 89.79 - 99.87 1 99.87 - 109.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1403 r_work=0.1217 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1404 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1210 r_free = 0.1403 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1210 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.653991 | | target function (ml) not normalized (work): 304348.252247 | | target function (ml) not normalized (free): 16066.777891 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1210 0.1403 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1538 0.1538 0.1566 n_refl.: 87588 remove outliers: r(all,work,free)=0.1538 0.1538 0.1566 n_refl.: 87588 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1536 0.1566 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1202 0.1372 n_refl.: 87588 remove outliers: r(all,work,free)=0.1207 0.1198 0.1372 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 0.3977 287.025 258.957 0.464 1.001 0.305 11.894-9.307 96.08 94 4 0.2339 474.207 462.819 0.860 1.002 0.293 9.237-7.194 97.73 208 7 0.2344 384.302 385.362 0.945 1.002 0.200 7.162-5.571 100.00 427 22 0.2032 293.937 284.015 0.906 1.002 0.175 5.546-4.326 100.00 867 58 0.1127 403.503 398.826 0.954 1.002 0.164 4.315-3.360 100.00 1859 96 0.0938 383.734 381.147 0.993 1.002 0.156 3.356-2.611 100.00 3867 181 0.1154 252.093 250.005 0.999 1.002 0.062 2.608-2.026 99.99 8198 413 0.1041 167.115 166.146 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1010 81.610 81.768 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1296 36.189 35.761 1.018 0.999 0.000 1.221-1.150 99.97 13689 708 0.2134 22.802 21.409 0.976 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1372 | n_water=453 | time (s): 1.920 (total time: 1.920) Filter (dist) r_work=0.1198 r_free=0.1371 | n_water=452 | time (s): 39.970 (total time: 41.890) Filter (q & B) r_work=0.1198 r_free=0.1370 | n_water=450 | time (s): 3.540 (total time: 45.430) Compute maps r_work=0.1198 r_free=0.1370 | n_water=450 | time (s): 1.510 (total time: 46.940) Filter (map) r_work=0.1221 r_free=0.1384 | n_water=318 | time (s): 2.670 (total time: 49.610) Find peaks r_work=0.1221 r_free=0.1384 | n_water=318 | time (s): 0.650 (total time: 50.260) Add new water r_work=0.1292 r_free=0.1450 | n_water=489 | time (s): 3.480 (total time: 53.740) Refine new water occ: r_work=0.1217 r_free=0.1374 adp: r_work=0.1218 r_free=0.1377 occ: r_work=0.1202 r_free=0.1359 adp: r_work=0.1200 r_free=0.1361 occ: r_work=0.1190 r_free=0.1349 adp: r_work=0.1186 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1349 r_work=0.1186 r_free=0.1349 | n_water=489 | time (s): 194.200 (total time: 247.940) Filter (q & B) r_work=0.1193 r_free=0.1357 | n_water=452 | time (s): 3.020 (total time: 250.960) Filter (dist only) r_work=0.1193 r_free=0.1355 | n_water=451 | time (s): 37.020 (total time: 287.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.005579 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.126727 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 0.1199 0.1367 0.0168 0.006 1.0 1.9 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.67 1.68 3.402 21.459 46.127 3.637 11.81 13.60 1.79 3.840 21.332 46.127 3.618 Individual atomic B min max mean iso aniso Overall: 9.19 105.20 21.22 2.15 221 1757 Protein: 9.19 105.20 16.86 2.15 0 1519 Water: 11.45 70.59 35.85 N/A 221 230 Other: 20.69 28.96 24.56 N/A 0 8 Chain A: 9.19 105.20 19.39 N/A 0 1757 Chain S: 15.83 64.63 35.80 N/A 221 0 Histogram: Values Number of atoms 9.19 - 18.79 1225 18.79 - 28.39 290 28.39 - 37.99 219 37.99 - 47.59 131 47.59 - 57.19 76 57.19 - 66.80 25 66.80 - 76.40 7 76.40 - 86.00 2 86.00 - 95.60 1 95.60 - 105.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1360 r_work=0.1181 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1360 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1177 r_free = 0.1357 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1177 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616023 | | target function (ml) not normalized (work): 301149.599318 | | target function (ml) not normalized (free): 15907.976838 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1177 0.1357 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1493 0.1492 0.1546 n_refl.: 87578 remove outliers: r(all,work,free)=0.1493 0.1492 0.1546 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1492 0.1491 0.1545 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1175 0.1360 n_refl.: 87578 remove outliers: r(all,work,free)=0.1183 0.1174 0.1360 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4206 287.025 247.698 0.442 1.000 0.320 11.894-9.307 94.12 92 4 0.2292 471.926 453.549 0.853 1.002 0.227 9.237-7.194 97.73 208 7 0.2427 384.302 379.144 0.929 1.002 0.140 7.162-5.571 100.00 427 22 0.2158 293.937 283.736 0.912 1.002 0.140 5.546-4.326 100.00 867 58 0.1137 403.503 398.383 0.962 1.002 0.120 4.315-3.360 100.00 1859 96 0.0952 383.734 381.370 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1149 252.093 250.189 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1014 167.115 166.288 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.0952 81.610 81.915 1.035 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.189 35.814 1.027 1.000 0.000 1.221-1.150 99.97 13689 708 0.2129 22.802 21.370 0.980 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1360 After: r_work=0.1175 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1175 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1175 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1360 | n_water=451 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1175 r_free=0.1360 | n_water=451 | time (s): 38.330 (total time: 40.000) Filter (q & B) r_work=0.1175 r_free=0.1359 | n_water=450 | time (s): 2.650 (total time: 42.650) Compute maps r_work=0.1175 r_free=0.1359 | n_water=450 | time (s): 1.350 (total time: 44.000) Filter (map) r_work=0.1202 r_free=0.1374 | n_water=327 | time (s): 3.600 (total time: 47.600) Find peaks r_work=0.1202 r_free=0.1374 | n_water=327 | time (s): 0.650 (total time: 48.250) Add new water r_work=0.1252 r_free=0.1413 | n_water=493 | time (s): 3.660 (total time: 51.910) Refine new water occ: r_work=0.1185 r_free=0.1350 adp: r_work=0.1186 r_free=0.1352 occ: r_work=0.1173 r_free=0.1337 adp: r_work=0.1171 r_free=0.1339 occ: r_work=0.1163 r_free=0.1326 adp: r_work=0.1160 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1160 r_free=0.1328 r_work=0.1160 r_free=0.1328 | n_water=493 | time (s): 215.410 (total time: 267.320) Filter (q & B) r_work=0.1167 r_free=0.1337 | n_water=451 | time (s): 3.200 (total time: 270.520) Filter (dist only) r_work=0.1167 r_free=0.1337 | n_water=450 | time (s): 37.470 (total time: 307.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.036178 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 31.759479 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 0.1187 0.1352 0.0166 0.007 1.1 4.2 0.5 0.0 0 1.018 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.52 1.66 3.271 21.068 31.759 3.621 11.90 13.51 1.62 3.292 21.052 31.759 3.619 Individual atomic B min max mean iso aniso Overall: 9.26 104.45 21.07 2.09 221 1756 Protein: 9.26 104.45 16.82 2.09 0 1519 Water: 11.46 70.50 35.36 N/A 221 229 Other: 20.49 28.75 24.51 N/A 0 8 Chain A: 9.26 104.45 19.33 N/A 0 1756 Chain S: 15.99 59.14 34.93 N/A 221 0 Histogram: Values Number of atoms 9.26 - 18.78 1226 18.78 - 28.30 297 28.30 - 37.82 208 37.82 - 47.34 141 47.34 - 56.86 70 56.86 - 66.38 22 66.38 - 75.89 8 75.89 - 85.41 2 85.41 - 94.93 1 94.93 - 104.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1351 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1185 r_free = 0.1349 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1185 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.616974 | | target function (ml) not normalized (work): 301221.560610 | | target function (ml) not normalized (free): 15909.561915 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1391 0.1391 5.6673 5.6197| | 2: 3.57 - 2.84 1.00 2888 124 0.1104 0.1418 5.1849 5.2504| | 3: 2.83 - 2.48 1.00 2820 163 0.1197 0.1196 4.9857 4.9974| | 4: 2.47 - 2.25 1.00 2825 136 0.1008 0.1167 4.6893 4.7491| | 5: 2.25 - 2.09 1.00 2756 127 0.0978 0.1103 4.6296 4.704| | 6: 2.09 - 1.97 1.00 2846 113 0.0958 0.1164 4.3352 4.4542| | 7: 1.97 - 1.87 1.00 2787 165 0.0987 0.1184 4.0643 4.1396| | 8: 1.87 - 1.79 1.00 2789 144 0.1009 0.1233 3.9711 4.0664| | 9: 1.79 - 1.72 1.00 2745 138 0.0950 0.1261 3.7067 3.8991| | 10: 1.72 - 1.66 1.00 2831 160 0.1005 0.1298 3.6251 3.7699| | 11: 1.66 - 1.61 1.00 2712 147 0.0969 0.1111 3.5605 3.6141| | 12: 1.61 - 1.56 1.00 2773 144 0.0926 0.1193 3.3495 3.4756| | 13: 1.56 - 1.52 1.00 2745 130 0.0982 0.1030 3.3392 3.4158| | 14: 1.52 - 1.48 1.00 2803 134 0.0987 0.1088 3.2583 3.3394| | 15: 1.48 - 1.45 1.00 2738 128 0.1012 0.1314 3.1641 3.3055| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1242 3.1427 3.2294| | 17: 1.42 - 1.39 1.00 2785 139 0.1117 0.1274 3.1139 3.2223| | 18: 1.39 - 1.36 1.00 2741 179 0.1155 0.1388 3.0861 3.2694| | 19: 1.36 - 1.34 1.00 2807 134 0.1218 0.1569 3.0905 3.2814| | 20: 1.34 - 1.32 1.00 2696 147 0.1328 0.1449 3.0881 3.1306| | 21: 1.32 - 1.30 1.00 2785 112 0.1417 0.1638 3.0869 3.174| | 22: 1.29 - 1.27 1.00 2704 152 0.1483 0.1934 3.0883 3.2852| | 23: 1.27 - 1.26 1.00 2802 156 0.1596 0.1838 3.1096 3.2079| | 24: 1.26 - 1.24 1.00 2744 132 0.1638 0.1764 3.0994 3.1957| | 25: 1.24 - 1.22 1.00 2733 148 0.1811 0.2310 3.1141 3.2891| | 26: 1.22 - 1.21 1.00 2727 135 0.1877 0.1785 3.1303 3.1995| | 27: 1.21 - 1.19 1.00 2814 148 0.2018 0.2116 3.1441 3.1516| | 28: 1.19 - 1.18 1.00 2671 147 0.2154 0.2316 3.1431 3.1625| | 29: 1.18 - 1.16 1.00 2800 134 0.2226 0.2339 3.1308 3.2108| | 30: 1.16 - 1.15 1.00 2739 148 0.2385 0.2517 3.1199 3.1737| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 8.89 1.00 0.96 6036.83| | 2: 3.57 - 2.84 2888 124 0.92 13.04 1.01 0.96 6036.83| | 3: 2.83 - 2.48 2820 163 0.89 17.14 0.99 0.96 5058.58| | 4: 2.47 - 2.25 2825 136 0.91 14.29 1.00 0.97 2535.98| | 5: 2.25 - 2.09 2756 127 0.90 16.49 1.01 0.97 2535.98| | 6: 2.09 - 1.97 2846 113 0.92 13.26 1.02 0.96 1489.04| | 7: 1.97 - 1.87 2787 165 0.94 10.46 1.02 0.96 596.14| | 8: 1.87 - 1.79 2789 144 0.92 14.01 1.00 0.96 596.14| | 9: 1.79 - 1.72 2745 138 0.94 11.18 0.98 0.96 327.98| | 10: 1.72 - 1.66 2831 160 0.93 12.09 0.98 0.96 274.28| | 11: 1.66 - 1.61 2712 147 0.93 12.70 0.98 0.96 261.97| | 12: 1.61 - 1.56 2773 144 0.95 9.43 0.99 0.96 145.95| | 13: 1.56 - 1.52 2745 130 0.94 11.03 1.02 0.96 145.95| | 14: 1.52 - 1.48 2803 134 0.94 11.12 1.02 0.96 130.02| | 15: 1.48 - 1.45 2738 128 0.95 10.20 1.01 0.97 100.85| | 16: 1.45 - 1.42 2756 161 0.94 11.37 1.01 0.97 100.85| | 17: 1.42 - 1.39 2785 139 0.95 11.19 1.01 0.97 91.44| | 18: 1.39 - 1.36 2741 179 0.94 11.63 1.01 0.97 86.00| | 19: 1.36 - 1.34 2807 134 0.94 12.14 1.00 0.97 86.00| | 20: 1.34 - 1.32 2696 147 0.94 12.36 0.99 0.96 81.56| | 21: 1.32 - 1.30 2785 112 0.94 13.24 0.98 0.95 81.25| | 22: 1.29 - 1.27 2704 152 0.93 13.75 0.98 0.95 81.49| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 82.69| | 24: 1.26 - 1.24 2744 132 0.93 14.89 0.96 0.94 82.69| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.93 84.32| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.03 0.92 86.13| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.92 86.13| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.92 89.44| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 90.69| | 30: 1.16 - 1.15 2739 148 0.86 21.95 0.98 0.92 90.69| |alpha: min = 0.92 max = 0.97 mean = 0.95| |beta: min = 81.25 max = 6036.83 mean = 941.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.87| |phase err.(test): min = 0.00 max = 88.65 mean = 13.95| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1185 0.1349 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1497 0.1497 0.1527 n_refl.: 87576 remove outliers: r(all,work,free)=0.1497 0.1497 0.1527 n_refl.: 87576 overall B=-0.00 to atoms: r(all,work,free)=0.1496 0.1496 0.1526 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1186 0.1352 n_refl.: 87576 remove outliers: r(all,work,free)=0.1192 0.1184 0.1352 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4132 283.577 250.379 0.425 1.001 0.277 11.894-9.307 91.18 89 4 0.2375 464.195 447.096 0.839 1.002 0.188 9.237-7.194 97.73 208 7 0.2490 384.302 377.284 0.917 1.002 0.130 7.162-5.571 100.00 427 22 0.2175 293.937 283.458 0.905 1.002 0.117 5.546-4.326 100.00 867 58 0.1158 403.503 398.842 0.965 1.002 0.110 4.315-3.360 100.00 1859 96 0.0983 383.734 380.959 1.005 1.002 0.110 3.356-2.611 100.00 3867 181 0.1161 252.093 250.065 1.011 1.001 0.110 2.608-2.026 99.99 8198 413 0.1022 167.115 166.153 1.023 1.000 0.000 2.025-1.573 100.00 17313 902 0.0971 81.610 81.894 1.037 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1231 36.189 35.829 1.030 0.996 0.000 1.221-1.150 99.97 13689 708 0.2129 22.802 21.421 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0132 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1963 0.083 5.167 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1796 0.083 5.167 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1796 0.083 5.167 9.1 119.5 20.1 258 0.000 1_nqh: 0.1642 0.1798 0.083 5.167 9.1 119.5 20.1 258 0.003 1_weight: 0.1642 0.1798 0.083 5.167 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1209 0.1460 0.008 0.964 9.1 119.5 20.1 258 0.123 1_adp: 0.1248 0.1549 0.008 0.964 8.5 118.6 20.9 258 0.123 1_regHadp: 0.1252 0.1554 0.008 0.964 8.5 118.6 20.9 258 0.123 1_occ: 0.1251 0.1556 0.008 0.964 8.5 118.6 20.9 258 0.123 2_bss: 0.1249 0.1550 0.008 0.964 8.6 118.8 21.0 258 0.123 2_settarget: 0.1249 0.1550 0.008 0.964 8.6 118.8 21.0 258 0.123 2_updatecdl: 0.1249 0.1550 0.008 0.968 8.6 118.8 21.0 258 0.123 2_nqh: 0.1250 0.1551 0.008 0.968 8.6 118.8 21.0 258 0.126 2_sol: 0.1239 0.1505 0.008 0.968 8.6 118.8 23.4 429 n/a 2_weight: 0.1239 0.1505 0.008 0.968 8.6 118.8 23.4 429 n/a 2_xyzrec: 0.1237 0.1527 0.007 0.890 8.6 118.8 23.4 429 n/a 2_adp: 0.1205 0.1488 0.007 0.890 8.7 114.8 23.1 429 n/a 2_regHadp: 0.1205 0.1487 0.007 0.890 8.7 114.8 23.1 429 n/a 2_occ: 0.1205 0.1478 0.007 0.890 8.7 114.8 23.1 429 n/a 3_bss: 0.1201 0.1477 0.007 0.890 8.7 114.8 23.1 429 n/a 3_settarget: 0.1201 0.1477 0.007 0.890 8.7 114.8 23.1 429 n/a 3_updatecdl: 0.1201 0.1477 0.007 0.891 8.7 114.8 23.1 429 n/a 3_nqh: 0.1201 0.1477 0.007 0.891 8.7 114.8 23.1 429 n/a 3_sol: 0.1226 0.1481 0.007 0.891 8.7 114.8 22.1 453 n/a 3_weight: 0.1226 0.1481 0.007 0.891 8.7 114.8 22.1 453 n/a 3_xyzrec: 0.1229 0.1445 0.006 0.920 8.7 114.8 22.1 453 n/a 3_adp: 0.1216 0.1403 0.006 0.920 9.1 109.9 21.7 453 n/a 3_regHadp: 0.1217 0.1404 0.006 0.920 9.1 109.9 21.7 453 n/a 3_occ: 0.1210 0.1403 0.006 0.920 9.1 109.9 21.7 453 n/a 4_bss: 0.1198 0.1372 0.006 0.920 9.1 109.9 21.7 453 n/a 4_settarget: 0.1198 0.1372 0.006 0.920 9.1 109.9 21.7 453 n/a 4_updatecdl: 0.1198 0.1372 0.006 0.919 9.1 109.9 21.7 453 n/a 4_nqh: 0.1198 0.1372 0.006 0.919 9.1 109.9 21.7 453 n/a 4_sol: 0.1193 0.1355 0.006 0.919 9.1 109.9 21.5 451 n/a 4_weight: 0.1193 0.1355 0.006 0.919 9.1 109.9 21.5 451 n/a 4_xyzrec: 0.1199 0.1367 0.006 0.955 9.1 109.9 21.5 451 n/a 4_adp: 0.1181 0.1360 0.006 0.955 9.2 105.2 21.2 451 n/a 4_regHadp: 0.1181 0.1360 0.006 0.955 9.2 105.2 21.2 451 n/a 4_occ: 0.1177 0.1357 0.006 0.955 9.2 105.2 21.2 451 n/a 5_bss: 0.1174 0.1360 0.006 0.955 9.2 105.2 21.2 451 n/a 5_settarget: 0.1174 0.1360 0.006 0.955 9.2 105.2 21.2 451 n/a 5_updatecdl: 0.1174 0.1360 0.006 0.957 9.2 105.2 21.2 451 n/a 5_setrh: 0.1175 0.1360 0.006 0.957 9.2 105.2 21.2 451 n/a 5_nqh: 0.1175 0.1360 0.006 0.957 9.2 105.2 21.2 451 n/a 5_sol: 0.1167 0.1337 0.006 0.957 9.2 105.2 21.1 450 n/a 5_weight: 0.1167 0.1337 0.006 0.957 9.2 105.2 21.1 450 n/a 5_xyzrec: 0.1187 0.1352 0.007 1.074 9.2 105.2 21.1 450 n/a 5_adp: 0.1190 0.1351 0.007 1.074 9.3 104.4 21.1 450 n/a 5_regHadp: 0.1190 0.1351 0.007 1.074 9.3 104.4 21.1 450 n/a 5_occ: 0.1185 0.1349 0.007 1.074 9.3 104.4 21.1 450 n/a end: 0.1184 0.1352 0.007 1.074 9.3 104.4 21.1 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3031784_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3031784_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8400 Refinement macro-cycles (run) : 3607.8800 Write final files (write_after_run_outputs) : 60.8000 Total : 3673.5200 Total CPU time: 61.83 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:12:44 PST -0800 (1735452764.11 s) Start R-work = 0.1637, R-free = 0.1796 Final R-work = 0.1184, R-free = 0.1352 =============================================================================== Job complete usr+sys time: 3809.51 seconds wall clock time: 67 minutes 56.42 seconds (4076.42 seconds total)