Starting phenix.refine on Sat Dec 28 21:06:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.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_7766834.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7766834.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: 2.29, per 1000 atoms: 0.68 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 393.1 milliseconds Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.90: 429 0.90 - 1.17: 1199 1.17 - 1.43: 682 1.43 - 1.70: 820 1.70 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta sigma weight residual 1.456 1.671 -0.215 1.16e-02 7.43e+03 3.43e+02 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.460 1.675 -0.216 1.21e-02 6.83e+03 3.18e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.252 0.207 1.20e-02 6.94e+03 2.98e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.490 -0.169 1.00e-02 1.00e+04 2.85e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.422 -0.185 1.12e-02 7.97e+03 2.74e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 2988 4.38 - 8.76: 1875 8.76 - 13.14: 725 13.14 - 17.52: 160 17.52 - 21.91: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.45 -14.25 9.00e-01 1.23e+00 2.51e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.77 -12.54 8.10e-01 1.52e+00 2.40e+02 angle pdb=" O VAL A 177 " pdb=" C VAL A 177 " pdb=" N ALA A 178 " ideal model delta sigma weight residual 121.94 136.04 -14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.74 12.46 9.00e-01 1.23e+00 1.92e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.61 8.68 6.50e-01 2.37e+00 1.78e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.66: 953 17.66 - 35.30: 105 35.30 - 52.95: 38 52.95 - 70.60: 11 70.60 - 88.25: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA BLYS A 99 " pdb=" C BLYS A 99 " pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta harmonic sigma weight residual 180.00 160.01 19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 85 0.182 - 0.363: 73 0.363 - 0.544: 45 0.544 - 0.726: 33 0.726 - 0.907: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.50 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.69 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA SER A 47 " pdb=" N SER A 47 " pdb=" C SER A 47 " pdb=" CB SER A 47 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.118 2.00e-02 2.50e+03 7.88e-02 1.86e+02 pdb=" CG PHE A 119 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.094 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.124 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.138 2.00e-02 2.50e+03 7.86e-02 1.85e+02 pdb=" CG PHE A 164 " 0.165 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 123 " -0.040 2.00e-02 2.50e+03 9.05e-02 8.19e+01 pdb=" C VAL A 123 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL A 123 " -0.064 2.00e-02 2.50e+03 pdb=" N THR A 124 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 700 2.26 - 2.85: 7720 2.85 - 3.43: 10601 3.43 - 4.02: 15338 4.02 - 4.60: 22374 Nonbonded interactions: 56733 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.677 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.827 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HA3BGLY A 65 " pdb=" HA BPRO A 66 " model vdw 1.830 2.440 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.832 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.849 2.100 ... (remaining 56728 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_7766834_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= 0.2603 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791744 | | target function (ml) not normalized (work): 232569.009453 | | target function (ml) not normalized (free): 11795.763004 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3048 0.2004 7.1171 4.9295| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1840 4.3439 4.3481| | 3: 2.84 - 2.48 1.00 2833 165 0.2332 0.1519 4.1187 4.1289| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1338 3.8243 3.8039| | 5: 2.25 - 2.09 1.00 2756 127 0.2444 0.1603 3.7866 3.8193| | 6: 2.09 - 1.97 1.00 2846 113 0.2545 0.1893 3.4534 3.5836| | 7: 1.97 - 1.87 1.00 2787 165 0.2532 0.1756 3.1389 3.175| | 8: 1.87 - 1.79 1.00 2789 144 0.2479 0.1757 3.052 3.121| | 9: 1.79 - 1.72 1.00 2745 138 0.2432 0.2074 2.8867 2.9335| | 10: 1.72 - 1.66 1.00 2789 158 0.2409 0.1882 2.8056 2.8668| | 11: 1.66 - 1.61 1.00 2740 147 0.2480 0.1935 2.7526 2.8202| | 12: 1.61 - 1.56 1.00 2787 146 0.2451 0.2170 2.6244 2.7102| | 13: 1.56 - 1.52 1.00 2745 130 0.2583 0.1895 2.5928 2.6479| | 14: 1.52 - 1.48 1.00 2803 134 0.2593 0.1777 2.509 2.5164| | 15: 1.48 - 1.45 1.00 2738 128 0.2563 0.2089 2.4298 2.5657| | 16: 1.45 - 1.42 1.00 2756 161 0.2626 0.2165 2.3831 2.4326| | 17: 1.42 - 1.39 1.00 2785 139 0.2672 0.1966 2.3237 2.3101| | 18: 1.39 - 1.36 1.00 2741 179 0.2672 0.2120 2.2717 2.3121| | 19: 1.36 - 1.34 1.00 2807 134 0.2669 0.2224 2.2514 2.2802| | 20: 1.34 - 1.32 1.00 2696 147 0.2657 0.2158 2.1964 2.1622| | 21: 1.32 - 1.30 1.00 2785 112 0.2754 0.2159 2.1785 2.1042| | 22: 1.29 - 1.27 1.00 2704 152 0.2764 0.2545 2.1477 2.1861| | 23: 1.27 - 1.26 1.00 2802 156 0.2808 0.2303 2.1058 2.1232| | 24: 1.26 - 1.24 1.00 2744 132 0.2717 0.2672 2.0589 2.1663| | 25: 1.24 - 1.22 1.00 2734 148 0.2881 0.2689 2.0495 2.0976| | 26: 1.22 - 1.21 1.00 2727 135 0.2862 0.2142 2.0111 2.057| | 27: 1.21 - 1.19 1.00 2814 148 0.2947 0.2613 1.9973 2.0047| | 28: 1.19 - 1.18 1.00 2671 147 0.2979 0.2781 1.9822 1.9853| | 29: 1.18 - 1.16 1.00 2800 134 0.2949 0.2878 1.966 2.0517| | 30: 1.16 - 1.15 1.00 2740 148 0.3085 0.2915 1.9348 1.9989| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1454.19| | 2: 3.57 - 2.84 2876 122 0.81 25.77 1.27 0.23 1454.19| | 3: 2.84 - 2.48 2833 165 0.74 31.72 1.24 0.24 1205.51| | 4: 2.47 - 2.25 2825 136 0.81 25.29 1.26 0.25 560.14| | 5: 2.25 - 2.09 2756 127 0.78 29.00 1.28 0.25 560.14| | 6: 2.09 - 1.97 2846 113 0.84 22.43 1.29 0.25 306.39| | 7: 1.97 - 1.87 2787 165 0.90 16.26 1.28 0.26 89.98| | 8: 1.87 - 1.79 2789 144 0.86 20.88 1.25 0.26 89.98| | 9: 1.79 - 1.72 2745 138 0.88 18.57 1.24 0.26 55.61| | 10: 1.72 - 1.66 2789 158 0.86 20.32 1.22 0.26 48.73| | 11: 1.66 - 1.61 2740 147 0.86 21.38 1.24 0.26 47.08| | 12: 1.61 - 1.56 2787 146 0.88 18.79 1.23 0.25 30.31| | 13: 1.56 - 1.52 2745 130 0.86 20.68 1.24 0.25 30.31| | 14: 1.52 - 1.48 2803 134 0.86 20.87 1.24 0.25 26.89| | 15: 1.48 - 1.45 2738 128 0.87 20.03 1.23 0.25 20.62| | 16: 1.45 - 1.42 2756 161 0.86 21.48 1.23 0.25 20.62| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.24 0.25 17.32| | 18: 1.39 - 1.36 2741 179 0.87 20.88 1.23 0.25 15.41| | 19: 1.36 - 1.34 2807 134 0.86 21.64 1.22 0.25 15.41| | 20: 1.34 - 1.32 2696 147 0.87 20.25 1.20 0.25 12.61| | 21: 1.32 - 1.30 2785 112 0.86 21.34 1.21 0.25 12.41| | 22: 1.29 - 1.27 2704 152 0.86 22.03 1.20 0.25 12.13| | 23: 1.27 - 1.26 2802 156 0.86 21.70 1.22 0.24 10.69| | 24: 1.26 - 1.24 2744 132 0.86 22.11 1.20 0.24 10.69| | 25: 1.24 - 1.22 2734 148 0.84 23.55 1.21 0.24 10.28| | 26: 1.22 - 1.21 2727 135 0.84 23.81 1.20 0.23 9.83| | 27: 1.21 - 1.19 2814 148 0.83 24.66 1.20 0.23 9.83| | 28: 1.19 - 1.18 2671 147 0.83 25.48 1.18 0.23 9.44| | 29: 1.18 - 1.16 2800 134 0.82 25.96 1.15 0.22 9.30| | 30: 1.16 - 1.15 2740 148 0.80 27.77 1.14 0.22 9.30| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.30 max = 1454.19 mean = 211.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.46| |phase err.(test): min = 0.00 max = 89.88 mean = 22.34| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.449 Angle : 5.364 17.071 2118 Z= 3.752 Chirality : 0.368 0.907 243 Planarity : 0.031 0.104 284 Dihedral : 14.050 88.249 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 34.05 % 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: -2.21 (0.50), residues: 224 helix: -2.64 (0.36), residues: 109 sheet: -0.60 (0.93), residues: 28 loop : 0.28 (0.65), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.016 ARG A 28 TYR 0.074 0.023 TYR A 139 PHE 0.168 0.053 PHE A 164 HIS 0.084 0.036 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2603 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791744 | | target function (ml) not normalized (work): 232569.009453 | | target function (ml) not normalized (free): 11795.763004 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1907 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1907 n_refl.: 87602 remove outliers: r(all,work,free)=0.1973 0.1978 0.1907 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.1999 0.2005 0.1921 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1633 0.1749 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1633 0.1749 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 0.3844 386.112 369.228 0.689 1.001 0.401 11.894-9.307 99.02 97 4 0.1784 613.321 592.677 0.926 1.001 0.380 9.237-7.194 100.00 213 7 0.2168 501.621 490.329 0.952 1.002 0.370 7.162-5.571 100.00 427 22 0.2212 376.439 366.686 0.935 1.002 0.288 5.546-4.326 100.00 867 58 0.1277 516.757 510.195 0.965 1.002 0.229 4.315-3.360 100.00 1859 96 0.1149 491.440 487.795 1.005 1.002 0.209 3.356-2.611 100.00 3867 181 0.1439 322.850 319.562 0.995 1.002 0.048 2.608-2.026 99.99 8198 413 0.1329 214.020 211.874 1.004 1.002 0.000 2.025-1.573 100.00 17313 902 0.1639 104.516 103.974 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2072 46.347 45.108 0.999 1.003 0.000 1.221-1.150 99.97 13689 708 0.2592 29.202 26.825 0.961 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0494 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1749 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=0.1635 r_free=0.1754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.546952 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1977.162417 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1212 0.1463 0.0251 0.007 0.9 1.0 0.5 0.0 0 12.273 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.63 2.51 3.013 19.074 1977.162 0.017 12.46 15.42 2.96 3.276 19.592 1977.162 0.016 Individual atomic B min max mean iso aniso Overall: 8.39 118.92 21.08 2.87 0 1785 Protein: 8.39 118.92 17.96 2.87 0 1519 Water: 11.13 114.64 39.20 N/A 0 258 Other: 22.91 36.80 29.54 N/A 0 8 Chain A: 8.39 118.92 21.08 N/A 0 1785 Histogram: Values Number of atoms 8.39 - 19.44 1199 19.44 - 30.50 236 30.50 - 41.55 164 41.55 - 52.60 102 52.60 - 63.65 55 63.65 - 74.71 16 74.71 - 85.76 6 85.76 - 96.81 4 96.81 - 107.86 0 107.86 - 118.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1246 r_free=0.1542 r_work=0.1251 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1251 r_free = 0.1547 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 = 0.1250 r_free = 0.1551 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1250 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015468 | | target function (ls_wunit_k1) not normalized (work): 1288.476112 | | target function (ls_wunit_k1) not normalized (free): 114.274120 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1265 0.1250 0.1551 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1706 0.1704 0.1778 n_refl.: 87593 remove outliers: r(all,work,free)=0.1706 0.1704 0.1778 n_refl.: 87593 overall B=0.13 to atoms: r(all,work,free)=0.1726 0.1725 0.1793 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1262 0.1247 0.1544 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1544 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 0.3609 298.258 278.917 0.635 1.002 0.380 11.894-9.307 99.02 97 4 0.1623 477.793 466.052 0.908 1.003 0.380 9.237-7.194 100.00 213 7 0.1832 390.776 385.646 0.948 1.003 0.340 7.162-5.571 100.00 427 22 0.1698 293.256 288.418 0.927 1.003 0.258 5.546-4.326 100.00 867 58 0.0905 402.568 400.068 0.950 1.003 0.209 4.315-3.360 100.00 1859 96 0.0772 382.845 381.876 0.995 1.003 0.190 3.356-2.611 100.00 3867 181 0.1023 251.509 250.802 0.998 1.002 0.052 2.608-2.026 99.99 8198 413 0.0985 166.728 166.134 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1219 81.421 81.594 1.017 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1655 36.105 35.561 1.005 0.999 0.000 1.221-1.150 99.97 13689 708 0.2368 22.749 21.255 0.969 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0486 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1544 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=0.1247 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1544 | n_water=258 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1256 r_free=0.1542 | n_water=252 | time (s): 26.600 (total time: 29.060) Filter (q & B) r_work=0.1259 r_free=0.1540 | n_water=249 | time (s): 3.950 (total time: 33.010) Compute maps r_work=0.1259 r_free=0.1540 | n_water=249 | time (s): 1.920 (total time: 34.930) Filter (map) r_work=0.1277 r_free=0.1548 | n_water=236 | time (s): 3.920 (total time: 38.850) Find peaks r_work=0.1277 r_free=0.1548 | n_water=236 | time (s): 0.720 (total time: 39.570) Add new water r_work=0.1428 r_free=0.1695 | n_water=448 | time (s): 3.840 (total time: 43.410) Refine new water occ: r_work=0.1336 r_free=0.1571 adp: r_work=0.1257 r_free=0.1515 occ: r_work=0.1269 r_free=0.1513 adp: r_work=0.1236 r_free=0.1497 occ: r_work=0.1238 r_free=0.1496 adp: r_work=0.1229 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1495 r_work=0.1229 r_free=0.1495 | n_water=448 | time (s): 92.770 (total time: 136.180) Filter (q & B) r_work=0.1235 r_free=0.1500 | n_water=428 | time (s): 4.030 (total time: 140.210) Filter (dist only) r_work=0.1235 r_free=0.1500 | n_water=428 | time (s): 40.970 (total time: 181.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.302076 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1414.061437 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 0.1519 0.0289 0.007 0.9 1.3 0.5 0.0 0 12.651 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 15.19 2.89 3.804 23.260 1414.061 0.015 12.03 14.88 2.84 4.199 23.068 1414.061 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 115.22 23.21 2.60 192 1763 Protein: 8.71 115.22 17.76 2.60 0 1519 Water: 10.93 72.62 42.43 N/A 192 236 Other: 23.71 35.87 28.97 N/A 0 8 Chain A: 8.71 115.22 20.47 N/A 0 1763 Chain S: 17.00 69.57 48.35 N/A 192 0 Histogram: Values Number of atoms 8.71 - 19.36 1203 19.36 - 30.01 256 30.01 - 40.67 187 40.67 - 51.32 144 51.32 - 61.97 105 61.97 - 72.62 48 72.62 - 83.27 6 83.27 - 93.92 3 93.92 - 104.57 1 104.57 - 115.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1488 r_work=0.1203 r_free=0.1488 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1488 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 = 0.1204 r_free = 0.1486 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 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= 0.1204 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.013841 | | target function (ls_wunit_k1) not normalized (work): 1152.859030 | | target function (ls_wunit_k1) not normalized (free): 105.838654 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1204 0.1486 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1618 0.1614 0.1741 n_refl.: 87592 remove outliers: r(all,work,free)=0.1618 0.1614 0.1741 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1622 0.1617 0.1743 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1200 0.1483 n_refl.: 87592 remove outliers: r(all,work,free)=0.1213 0.1199 0.1483 n_refl.: 87590 ======================== 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 93.75 85 5 0.3423 296.822 272.248 0.645 0.940 0.380 11.894-9.307 99.02 97 4 0.1536 477.793 474.700 0.980 0.940 0.360 9.237-7.194 100.00 213 7 0.1656 390.776 391.372 1.043 0.940 0.280 7.162-5.571 100.00 427 22 0.1467 293.256 289.496 1.009 0.941 0.229 5.546-4.326 100.00 867 58 0.0829 402.568 399.471 1.020 0.941 0.210 4.315-3.360 100.00 1859 96 0.0710 382.845 381.692 1.066 0.941 0.200 3.356-2.611 100.00 3867 181 0.0953 251.509 250.920 1.073 0.941 0.130 2.608-2.026 99.99 8198 413 0.0965 166.728 166.335 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1185 81.421 81.602 1.091 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1620 36.105 35.615 1.078 0.945 0.000 1.221-1.150 99.97 13689 708 0.2353 22.749 21.303 1.034 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0362 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1483 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=0.1199 r_free=0.1483 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1483 | n_water=428 | time (s): 2.210 (total time: 2.210) Filter (dist) r_work=0.1201 r_free=0.1481 | n_water=427 | time (s): 38.610 (total time: 40.820) Filter (q & B) r_work=0.1201 r_free=0.1481 | n_water=427 | time (s): 1.010 (total time: 41.830) Compute maps r_work=0.1201 r_free=0.1481 | n_water=427 | time (s): 1.510 (total time: 43.340) Filter (map) r_work=0.1242 r_free=0.1483 | n_water=290 | time (s): 3.170 (total time: 46.510) Find peaks r_work=0.1242 r_free=0.1483 | n_water=290 | time (s): 0.720 (total time: 47.230) Add new water r_work=0.1371 r_free=0.1593 | n_water=481 | time (s): 3.250 (total time: 50.480) Refine new water occ: r_work=0.1270 r_free=0.1507 adp: r_work=0.1271 r_free=0.1507 occ: r_work=0.1247 r_free=0.1485 adp: r_work=0.1244 r_free=0.1483 occ: r_work=0.1232 r_free=0.1471 adp: r_work=0.1224 r_free=0.1467 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1467 r_work=0.1224 r_free=0.1467 | n_water=481 | time (s): 263.290 (total time: 313.770) Filter (q & B) r_work=0.1227 r_free=0.1472 | n_water=453 | time (s): 2.580 (total time: 316.350) Filter (dist only) r_work=0.1227 r_free=0.1472 | n_water=453 | time (s): 36.430 (total time: 352.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.006949 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.580950 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1236 0.1443 0.0207 0.006 0.9 2.2 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.43 2.07 3.635 22.285 39.581 3.727 12.26 14.00 1.74 4.140 22.103 39.581 3.657 Individual atomic B min max mean iso aniso Overall: 9.25 110.25 21.90 2.30 218 1762 Protein: 9.25 110.25 17.32 2.30 0 1519 Water: 11.62 71.70 37.20 N/A 218 235 Other: 19.49 31.51 25.96 N/A 0 8 Chain A: 9.25 110.25 20.03 N/A 0 1762 Chain S: 15.57 64.52 37.06 N/A 218 0 Histogram: Values Number of atoms 9.25 - 19.35 1230 19.35 - 29.45 281 29.45 - 39.55 220 39.55 - 49.65 125 49.65 - 59.75 88 59.75 - 69.85 23 69.85 - 79.95 7 79.95 - 90.05 3 90.05 - 100.15 1 100.15 - 110.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1226 r_free=0.1400 r_work=0.1227 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1227 r_free = 0.1401 target_work(ml) = 3.658 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1222 r_free = 0.1399 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1222 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.654866 | | target function (ml) not normalized (work): 304428.381031 | | target function (ml) not normalized (free): 16062.374808 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1222 0.1399 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1558 0.1556 0.1622 n_refl.: 87590 remove outliers: r(all,work,free)=0.1558 0.1556 0.1622 n_refl.: 87590 overall B=-0.03 to atoms: r(all,work,free)=0.1553 0.1551 0.1618 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1212 0.1377 n_refl.: 87590 remove outliers: r(all,work,free)=0.1216 0.1207 0.1377 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3703 293.573 261.235 0.477 1.000 0.305 11.894-9.307 96.08 94 4 0.2440 479.217 453.079 0.845 1.001 0.287 9.237-7.194 98.18 209 7 0.2307 382.339 384.795 0.949 1.002 0.190 7.162-5.571 100.00 427 22 0.2051 293.256 283.305 0.916 1.002 0.173 5.546-4.326 100.00 867 58 0.1082 402.568 398.411 0.953 1.002 0.170 4.315-3.360 100.00 1859 96 0.0924 382.845 380.270 0.996 1.002 0.170 3.356-2.611 100.00 3867 181 0.1169 251.509 249.673 1.000 1.002 0.057 2.608-2.026 99.99 8198 413 0.1063 166.728 165.835 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.1035 81.421 81.615 1.029 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1302 36.105 35.688 1.025 1.000 0.000 1.221-1.150 99.97 13689 708 0.2137 22.749 21.370 0.985 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0710 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1207 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1207 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1377 | n_water=453 | time (s): 1.670 (total time: 1.670) Filter (dist) r_work=0.1207 r_free=0.1377 | n_water=453 | time (s): 37.450 (total time: 39.120) Filter (q & B) r_work=0.1207 r_free=0.1376 | n_water=452 | time (s): 2.690 (total time: 41.810) Compute maps r_work=0.1207 r_free=0.1376 | n_water=452 | time (s): 1.260 (total time: 43.070) Filter (map) r_work=0.1235 r_free=0.1402 | n_water=310 | time (s): 3.660 (total time: 46.730) Find peaks r_work=0.1235 r_free=0.1402 | n_water=310 | time (s): 0.660 (total time: 47.390) Add new water r_work=0.1297 r_free=0.1473 | n_water=474 | time (s): 2.590 (total time: 49.980) Refine new water occ: r_work=0.1223 r_free=0.1384 adp: r_work=0.1223 r_free=0.1386 occ: r_work=0.1208 r_free=0.1374 adp: r_work=0.1207 r_free=0.1374 occ: r_work=0.1197 r_free=0.1368 adp: r_work=0.1194 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1366 r_work=0.1194 r_free=0.1366 | n_water=474 | time (s): 140.640 (total time: 190.620) Filter (q & B) r_work=0.1199 r_free=0.1379 | n_water=441 | time (s): 3.110 (total time: 193.730) Filter (dist only) r_work=0.1205 r_free=0.1377 | n_water=439 | time (s): 40.660 (total time: 234.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.008163 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.043596 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 0.1214 0.1392 0.0177 0.006 0.9 1.9 0.5 0.0 0 1.004 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 13.92 1.77 3.435 21.526 50.044 3.645 11.93 13.83 1.90 3.968 21.362 50.044 3.623 Individual atomic B min max mean iso aniso Overall: 9.33 105.46 21.13 2.18 207 1759 Protein: 9.33 105.46 16.92 2.19 0 1519 Water: 11.53 69.72 35.67 N/A 207 232 Other: 18.88 28.32 23.23 N/A 0 8 Chain A: 9.33 105.46 19.54 N/A 0 1759 Chain S: 15.05 61.05 34.63 N/A 207 0 Histogram: Values Number of atoms 9.33 - 18.94 1229 18.94 - 28.55 287 28.55 - 38.17 214 38.17 - 47.78 129 47.78 - 57.39 66 57.39 - 67.01 28 67.01 - 76.62 8 76.62 - 86.23 2 86.23 - 95.85 1 95.85 - 105.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1383 r_work=0.1193 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1383 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1377 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1190 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.621713 | | target function (ml) not normalized (work): 301627.085719 | | target function (ml) not normalized (free): 15938.991705 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1190 0.1377 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1514 0.1512 0.1567 n_refl.: 87579 remove outliers: r(all,work,free)=0.1514 0.1512 0.1567 n_refl.: 87579 overall B=-0.02 to atoms: r(all,work,free)=0.1510 0.1508 0.1564 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1189 0.1372 n_refl.: 87579 remove outliers: r(all,work,free)=0.1197 0.1188 0.1372 n_refl.: 87577 ======================== 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 0.3905 288.946 259.248 0.451 0.999 0.289 11.894-9.307 95.10 93 4 0.2444 483.168 465.066 0.856 1.001 0.260 9.237-7.194 98.18 209 7 0.2528 382.339 376.742 0.906 1.001 0.142 7.162-5.571 100.00 427 22 0.2243 293.256 282.422 0.903 1.002 0.133 5.546-4.326 100.00 867 58 0.1184 402.568 397.996 0.952 1.002 0.126 4.315-3.360 100.00 1859 96 0.0966 382.845 380.165 0.996 1.002 0.120 3.356-2.611 100.00 3867 181 0.1166 251.509 249.735 1.003 1.001 0.048 2.608-2.026 99.99 8198 413 0.1031 166.728 165.902 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0963 81.421 81.710 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1236 36.105 35.740 1.024 0.999 0.000 1.221-1.150 99.97 13689 708 0.2120 22.749 21.390 0.983 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0618 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1372 After: r_work=0.1188 r_free=0.1372 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1188 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1372 | n_water=439 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1188 r_free=0.1372 | n_water=439 | time (s): 35.580 (total time: 37.200) Filter (q & B) r_work=0.1189 r_free=0.1372 | n_water=438 | time (s): 3.320 (total time: 40.520) Compute maps r_work=0.1189 r_free=0.1372 | n_water=438 | time (s): 1.530 (total time: 42.050) Filter (map) r_work=0.1221 r_free=0.1410 | n_water=325 | time (s): 3.110 (total time: 45.160) Find peaks r_work=0.1221 r_free=0.1410 | n_water=325 | time (s): 0.610 (total time: 45.770) Add new water r_work=0.1267 r_free=0.1460 | n_water=477 | time (s): 3.030 (total time: 48.800) Refine new water occ: r_work=0.1202 r_free=0.1381 adp: r_work=0.1203 r_free=0.1384 occ: r_work=0.1190 r_free=0.1370 adp: r_work=0.1190 r_free=0.1371 occ: r_work=0.1182 r_free=0.1359 adp: r_work=0.1179 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1360 r_work=0.1179 r_free=0.1360 | n_water=477 | time (s): 211.330 (total time: 260.130) Filter (q & B) r_work=0.1187 r_free=0.1372 | n_water=436 | time (s): 3.490 (total time: 263.620) Filter (dist only) r_work=0.1187 r_free=0.1372 | n_water=435 | time (s): 36.090 (total time: 299.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.951581 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 55.757912 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1380 0.0177 0.006 1.0 2.9 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.80 1.77 3.293 21.014 55.758 3.628 12.01 13.75 1.74 3.401 20.973 55.758 3.619 Individual atomic B min max mean iso aniso Overall: 9.25 102.43 20.89 2.09 207 1755 Protein: 9.25 102.43 16.79 2.10 0 1519 Water: 11.56 69.18 35.15 N/A 207 228 Other: 19.00 26.93 23.00 N/A 0 8 Chain A: 9.25 102.43 19.34 N/A 0 1755 Chain S: 14.56 57.96 34.05 N/A 207 0 Histogram: Values Number of atoms 9.25 - 18.57 1219 18.57 - 27.89 292 27.89 - 37.21 212 37.21 - 46.52 129 46.52 - 55.84 65 55.84 - 65.16 28 65.16 - 74.48 12 74.48 - 83.79 2 83.79 - 93.11 1 93.11 - 102.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1376 r_work=0.1202 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1375 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1372 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1199 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618510 | | target function (ml) not normalized (work): 301353.142540 | | target function (ml) not normalized (free): 15938.402255 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1445 0.1472 5.7057 5.6912| | 2: 3.57 - 2.84 1.00 2888 124 0.1130 0.1425 5.2204 5.2689| | 3: 2.83 - 2.48 1.00 2820 163 0.1226 0.1251 5.0229 5.0401| | 4: 2.47 - 2.25 1.00 2825 136 0.1036 0.1156 4.7236 4.7664| | 5: 2.25 - 2.09 1.00 2756 127 0.0995 0.1099 4.6666 4.7315| | 6: 2.09 - 1.97 1.00 2846 113 0.0975 0.1244 4.3623 4.5078| | 7: 1.97 - 1.87 1.00 2787 165 0.0983 0.1188 4.0712 4.1622| | 8: 1.87 - 1.79 1.00 2789 144 0.1021 0.1216 3.9897 4.0738| | 9: 1.79 - 1.72 1.00 2745 138 0.0945 0.1289 3.7074 3.891| | 10: 1.72 - 1.66 1.00 2831 160 0.0993 0.1240 3.6234 3.7533| | 11: 1.66 - 1.61 1.00 2712 147 0.0956 0.1066 3.5593 3.5905| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1208 3.3327 3.4958| | 13: 1.56 - 1.52 1.00 2745 130 0.0957 0.1062 3.3229 3.4294| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1105 3.2522 3.3406| | 15: 1.48 - 1.45 1.00 2738 128 0.0989 0.1320 3.1542 3.2996| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1278 3.1398 3.252| | 17: 1.42 - 1.39 1.00 2785 139 0.1111 0.1275 3.1049 3.2179| | 18: 1.39 - 1.36 1.00 2741 179 0.1136 0.1366 3.0747 3.2636| | 19: 1.36 - 1.34 1.00 2807 134 0.1193 0.1608 3.0793 3.268| | 20: 1.34 - 1.32 1.00 2696 147 0.1296 0.1457 3.075 3.1278| | 21: 1.32 - 1.30 1.00 2785 112 0.1401 0.1614 3.0799 3.1588| | 22: 1.29 - 1.27 1.00 2704 152 0.1458 0.1903 3.076 3.2792| | 23: 1.27 - 1.26 1.00 2802 156 0.1565 0.1857 3.0954 3.2101| | 24: 1.26 - 1.24 1.00 2744 132 0.1609 0.1765 3.0853 3.1902| | 25: 1.24 - 1.22 1.00 2733 148 0.1781 0.2335 3.1029 3.2941| | 26: 1.22 - 1.21 1.00 2727 135 0.1853 0.1749 3.1193 3.1857| | 27: 1.21 - 1.19 1.00 2814 148 0.1999 0.2097 3.1357 3.144| | 28: 1.19 - 1.18 1.00 2671 147 0.2143 0.2303 3.137 3.1589| | 29: 1.18 - 1.16 1.00 2800 134 0.2216 0.2378 3.1244 3.2217| | 30: 1.16 - 1.15 1.00 2739 148 0.2373 0.2499 3.1131 3.1628| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.94 9.43 1.00 0.97 6675.10| | 2: 3.57 - 2.84 2888 124 0.92 13.88 1.01 0.97 6675.10| | 3: 2.83 - 2.48 2820 163 0.88 18.08 0.99 0.97 5586.49| | 4: 2.47 - 2.25 2825 136 0.91 15.08 1.00 0.97 2779.32| | 5: 2.25 - 2.09 2756 127 0.89 17.31 1.01 0.97 2779.32| | 6: 2.09 - 1.97 2846 113 0.91 13.90 1.02 0.97 1616.97| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.97 625.64| | 8: 1.87 - 1.79 2789 144 0.91 14.42 1.00 0.97 625.64| | 9: 1.79 - 1.72 2745 138 0.93 11.40 0.98 0.97 335.85| | 10: 1.72 - 1.66 2831 160 0.93 12.16 0.98 0.97 277.81| | 11: 1.66 - 1.61 2712 147 0.93 12.76 0.98 0.97 265.10| | 12: 1.61 - 1.56 2773 144 0.95 9.47 0.99 0.97 145.21| | 13: 1.56 - 1.52 2745 130 0.94 11.00 1.02 0.97 145.21| | 14: 1.52 - 1.48 2803 134 0.94 11.20 1.02 0.97 129.74| | 15: 1.48 - 1.45 2738 128 0.95 10.26 1.01 0.98 101.41| | 16: 1.45 - 1.42 2756 161 0.94 11.46 1.01 0.98 101.41| | 17: 1.42 - 1.39 2785 139 0.94 11.35 1.01 0.98 91.74| | 18: 1.39 - 1.36 2741 179 0.94 11.61 1.01 0.98 86.14| | 19: 1.36 - 1.34 2807 134 0.94 12.18 1.00 0.98 86.14| | 20: 1.34 - 1.32 2696 147 0.94 12.34 0.99 0.96 81.36| | 21: 1.32 - 1.30 2785 112 0.94 13.28 0.98 0.96 81.03| | 22: 1.29 - 1.27 2704 152 0.93 13.78 0.98 0.96 81.19| | 23: 1.27 - 1.26 2802 156 0.93 14.75 0.98 0.94 81.99| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.97 0.94 81.99| | 25: 1.24 - 1.22 2733 148 0.91 16.29 0.96 0.94 83.62| | 26: 1.22 - 1.21 2727 135 0.90 18.04 1.02 0.93 85.43| | 27: 1.21 - 1.19 2814 148 0.89 18.67 1.02 0.93 85.43| | 28: 1.19 - 1.18 2671 147 0.88 20.20 1.01 0.92 88.93| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.92 90.25| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.92 90.25| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 81.03 max = 6675.10 mean = 1027.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 14.07| |phase err.(test): min = 0.00 max = 89.57 mean = 14.19| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1199 0.1372 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1520 0.1519 0.1573 n_refl.: 87577 remove outliers: r(all,work,free)=0.1520 0.1519 0.1573 n_refl.: 87577 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1516 0.1571 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1200 0.1374 n_refl.: 87577 remove outliers: r(all,work,free)=0.1207 0.1199 0.1374 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 0.4183 288.946 248.436 0.436 1.000 0.291 11.894-9.307 94.12 92 4 0.2451 476.292 463.686 0.859 1.001 0.223 9.237-7.194 97.73 208 7 0.2604 383.412 373.743 0.894 1.002 0.154 7.162-5.571 100.00 427 22 0.2284 293.256 282.051 0.897 1.002 0.130 5.546-4.326 100.00 867 58 0.1232 402.568 397.745 0.952 1.002 0.122 4.315-3.360 100.00 1859 96 0.0990 382.845 380.130 0.996 1.002 0.116 3.356-2.611 100.00 3867 181 0.1193 251.509 249.600 1.002 1.002 0.100 2.608-2.026 99.99 8198 413 0.1046 166.728 165.764 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0971 81.421 81.677 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1211 36.105 35.743 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2112 22.749 21.386 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0442 ================= 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 : 0.2603 0.1906 0.082 5.364 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1749 0.082 5.364 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1749 0.082 5.364 9.1 119.5 20.1 258 0.000 1_nqh: 0.1635 0.1754 0.082 5.364 9.1 119.5 20.1 258 0.003 1_weight: 0.1635 0.1754 0.082 5.364 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1212 0.1463 0.007 0.936 9.1 119.5 20.1 258 0.128 1_adp: 0.1246 0.1542 0.007 0.936 8.4 118.9 21.1 258 0.128 1_regHadp: 0.1251 0.1547 0.007 0.936 8.4 118.9 21.1 258 0.128 1_occ: 0.1250 0.1551 0.007 0.936 8.4 118.9 21.1 258 0.128 2_bss: 0.1247 0.1544 0.007 0.936 8.5 119.0 21.2 258 0.128 2_settarget: 0.1247 0.1544 0.007 0.936 8.5 119.0 21.2 258 0.128 2_updatecdl: 0.1247 0.1544 0.007 0.957 8.5 119.0 21.2 258 0.128 2_nqh: 0.1247 0.1544 0.007 0.957 8.5 119.0 21.2 258 0.128 2_sol: 0.1235 0.1500 0.007 0.957 8.5 119.0 23.6 428 n/a 2_weight: 0.1235 0.1500 0.007 0.957 8.5 119.0 23.6 428 n/a 2_xyzrec: 0.1230 0.1519 0.007 0.872 8.5 119.0 23.6 428 n/a 2_adp: 0.1203 0.1488 0.007 0.872 8.7 115.2 23.2 428 n/a 2_regHadp: 0.1203 0.1488 0.007 0.872 8.7 115.2 23.2 428 n/a 2_occ: 0.1204 0.1486 0.007 0.872 8.7 115.2 23.2 428 n/a 3_bss: 0.1199 0.1483 0.007 0.872 8.7 115.2 23.2 428 n/a 3_settarget: 0.1199 0.1483 0.007 0.872 8.7 115.2 23.2 428 n/a 3_updatecdl: 0.1199 0.1483 0.007 0.873 8.7 115.2 23.2 428 n/a 3_nqh: 0.1199 0.1483 0.007 0.873 8.7 115.2 23.2 428 n/a 3_sol: 0.1227 0.1472 0.007 0.873 8.7 115.2 22.2 453 n/a 3_weight: 0.1227 0.1472 0.007 0.873 8.7 115.2 22.2 453 n/a 3_xyzrec: 0.1236 0.1443 0.006 0.924 8.7 115.2 22.2 453 n/a 3_adp: 0.1226 0.1400 0.006 0.924 9.3 110.2 21.9 453 n/a 3_regHadp: 0.1227 0.1401 0.006 0.924 9.3 110.2 21.9 453 n/a 3_occ: 0.1222 0.1399 0.006 0.924 9.3 110.2 21.9 453 n/a 4_bss: 0.1207 0.1377 0.006 0.924 9.2 110.2 21.9 453 n/a 4_settarget: 0.1207 0.1377 0.006 0.924 9.2 110.2 21.9 453 n/a 4_updatecdl: 0.1207 0.1377 0.006 0.922 9.2 110.2 21.9 453 n/a 4_nqh: 0.1207 0.1377 0.006 0.922 9.2 110.2 21.9 453 n/a 4_sol: 0.1205 0.1377 0.006 0.922 9.2 110.2 21.4 439 n/a 4_weight: 0.1205 0.1377 0.006 0.922 9.2 110.2 21.4 439 n/a 4_xyzrec: 0.1214 0.1392 0.006 0.948 9.2 110.2 21.4 439 n/a 4_adp: 0.1193 0.1383 0.006 0.948 9.3 105.5 21.1 439 n/a 4_regHadp: 0.1193 0.1383 0.006 0.948 9.3 105.5 21.1 439 n/a 4_occ: 0.1190 0.1377 0.006 0.948 9.3 105.5 21.1 439 n/a 5_bss: 0.1188 0.1372 0.006 0.948 9.3 105.4 21.1 439 n/a 5_settarget: 0.1188 0.1372 0.006 0.948 9.3 105.4 21.1 439 n/a 5_updatecdl: 0.1188 0.1372 0.006 0.952 9.3 105.4 21.1 439 n/a 5_setrh: 0.1188 0.1372 0.006 0.952 9.3 105.4 21.1 439 n/a 5_nqh: 0.1188 0.1372 0.006 0.952 9.3 105.4 21.1 439 n/a 5_sol: 0.1187 0.1372 0.006 0.952 9.3 105.4 21.0 435 n/a 5_weight: 0.1187 0.1372 0.006 0.952 9.3 105.4 21.0 435 n/a 5_xyzrec: 0.1203 0.1380 0.006 1.015 9.3 105.4 21.0 435 n/a 5_adp: 0.1201 0.1376 0.006 1.015 9.3 102.4 20.9 435 n/a 5_regHadp: 0.1202 0.1375 0.006 1.015 9.3 102.4 20.9 435 n/a 5_occ: 0.1199 0.1372 0.006 1.015 9.3 102.4 20.9 435 n/a end: 0.1199 0.1374 0.006 1.015 9.2 102.4 20.9 435 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7766834_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_7766834_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9400 Refinement macro-cycles (run) : 3517.6200 Write final files (write_after_run_outputs) : 66.0500 Total : 3588.6100 Total CPU time: 60.44 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.66 s) Start R-work = 0.1633, R-free = 0.1749 Final R-work = 0.1199, R-free = 0.1374 =============================================================================== Job complete usr+sys time: 3719.48 seconds wall clock time: 66 minutes 48.78 seconds (4008.78 seconds total)