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_3657390.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_3657390.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3657390.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 3 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: 2.04, per 1000 atoms: 0.60 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: 0.59 Conformation dependent library (CDL) restraints added in 219.8 milliseconds Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 550 0.92 - 1.17: 1109 1.17 - 1.43: 658 1.43 - 1.68: 799 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 1.334 1.581 -0.247 1.27e-02 6.20e+03 3.77e+02 bond pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.30e-02 5.92e+03 3.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.295 0.229 1.23e-02 6.61e+03 3.47e+02 bond pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 1.237 1.024 0.213 1.17e-02 7.31e+03 3.31e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.049 0.187 1.07e-02 8.73e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 3194 4.61 - 9.21: 1808 9.21 - 13.82: 668 13.82 - 18.43: 100 18.43 - 23.04: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.83 139.60 -17.77 1.03e+00 9.43e-01 2.98e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 120.74 -14.64 1.00e+00 1.00e+00 2.14e+02 angle pdb=" CA ASP A 131 " pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 120.85 134.81 -13.96 1.06e+00 8.90e-01 1.73e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 120.38 -9.93 7.80e-01 1.64e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 920 15.79 - 31.58: 128 31.58 - 47.37: 39 47.37 - 63.16: 22 63.16 - 78.95: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CD2 TYR A 139 " pdb=" CG TYR A 139 " pdb=" CD1 TYR A 139 " pdb=" HD1 TYR A 139 " ideal model delta harmonic sigma weight residual 180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.228: 103 0.228 - 0.451: 84 0.451 - 0.674: 37 0.674 - 0.897: 14 0.897 - 1.120: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.52 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA ASN A 144 " pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CB ASN A 144 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.58 0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.003 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG PHE A 162 " -0.128 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.024 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.007 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.136 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 26 " -0.047 2.00e-02 2.50e+03 9.91e-02 9.82e+01 pdb=" N ARG A 27 " 0.170 2.00e-02 2.50e+03 pdb=" CA ARG A 27 " -0.044 2.00e-02 2.50e+03 pdb=" H ARG A 27 " -0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1028 2.32 - 2.89: 8144 2.89 - 3.46: 10513 3.46 - 4.03: 15152 4.03 - 4.60: 21723 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.754 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.791 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.806 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.830 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.831 2.450 ... (remaining 56555 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_3657390_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= 0.2602 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789427 | | target function (ml) not normalized (work): 232375.964958 | | target function (ml) not normalized (free): 11799.532204 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2045 7.055 4.9454| | 2: 3.57 - 2.84 1.00 2876 122 0.2421 0.1741 4.3459 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2358 0.1679 4.1273 4.1632| | 4: 2.47 - 2.25 1.00 2825 136 0.2310 0.1538 3.8379 3.8355| | 5: 2.25 - 2.09 1.00 2756 127 0.2492 0.1650 3.8009 3.8376| | 6: 2.09 - 1.97 1.00 2846 113 0.2541 0.1643 3.4775 3.4862| | 7: 1.97 - 1.87 1.00 2787 165 0.2516 0.1957 3.1476 3.2513| | 8: 1.87 - 1.79 1.00 2789 144 0.2432 0.1931 3.0596 3.1598| | 9: 1.79 - 1.72 1.00 2745 138 0.2448 0.1770 2.9175 2.9247| | 10: 1.72 - 1.66 1.00 2789 158 0.2455 0.1902 2.8225 2.8217| | 11: 1.66 - 1.61 1.00 2740 147 0.2520 0.1876 2.7436 2.7696| | 12: 1.61 - 1.56 1.00 2787 146 0.2490 0.2100 2.6183 2.679| | 13: 1.56 - 1.52 1.00 2745 130 0.2509 0.1970 2.5529 2.6512| | 14: 1.52 - 1.48 1.00 2803 134 0.2520 0.2069 2.5096 2.6189| | 15: 1.48 - 1.45 1.00 2738 128 0.2585 0.2068 2.4261 2.5128| | 16: 1.45 - 1.42 1.00 2756 161 0.2630 0.2347 2.3597 2.4934| | 17: 1.42 - 1.39 1.00 2785 139 0.2677 0.2042 2.3376 2.3136| | 18: 1.39 - 1.36 1.00 2741 179 0.2631 0.2227 2.2688 2.3443| | 19: 1.36 - 1.34 1.00 2807 134 0.2644 0.2284 2.234 2.2781| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2049 2.1906 2.1216| | 21: 1.32 - 1.30 1.00 2785 112 0.2664 0.2198 2.141 2.1474| | 22: 1.29 - 1.27 1.00 2704 152 0.2727 0.2467 2.145 2.1581| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2469 2.1132 2.1704| | 24: 1.26 - 1.24 1.00 2744 132 0.2802 0.2422 2.07 2.1507| | 25: 1.24 - 1.22 1.00 2734 148 0.2841 0.2230 2.0443 1.9795| | 26: 1.22 - 1.21 1.00 2727 135 0.2832 0.2312 2.0094 2.073| | 27: 1.21 - 1.19 1.00 2814 148 0.2944 0.2686 1.9975 2.0196| | 28: 1.19 - 1.18 1.00 2671 147 0.3029 0.2821 1.9845 1.994| | 29: 1.18 - 1.16 1.00 2800 134 0.2994 0.2643 1.9631 2.0057| | 30: 1.16 - 1.15 1.00 2740 148 0.3092 0.2873 1.9252 1.9772| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.82 0.76 0.23 1487.11| | 2: 3.57 - 2.84 2876 122 0.80 26.11 1.27 0.23 1487.11| | 3: 2.84 - 2.48 2833 165 0.74 32.15 1.24 0.24 1233.96| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.25 0.25 576.98| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.28 0.25 576.98| | 6: 2.09 - 1.97 2846 113 0.83 22.88 1.28 0.25 316.85| | 7: 1.97 - 1.87 2787 165 0.90 16.82 1.27 0.25 94.99| | 8: 1.87 - 1.79 2789 144 0.85 21.57 1.25 0.25 94.99| | 9: 1.79 - 1.72 2745 138 0.88 18.85 1.23 0.25 56.11| | 10: 1.72 - 1.66 2789 158 0.87 20.21 1.23 0.25 48.33| | 11: 1.66 - 1.61 2740 147 0.85 21.46 1.25 0.25 46.68| | 12: 1.61 - 1.56 2787 146 0.88 18.87 1.23 0.25 30.00| | 13: 1.56 - 1.52 2745 130 0.86 20.86 1.24 0.25 30.00| | 14: 1.52 - 1.48 2803 134 0.86 21.04 1.23 0.25 26.93| | 15: 1.48 - 1.45 2738 128 0.87 20.45 1.24 0.25 21.32| | 16: 1.45 - 1.42 2756 161 0.85 22.13 1.24 0.25 21.32| | 17: 1.42 - 1.39 2785 139 0.86 21.16 1.23 0.25 17.87| | 18: 1.39 - 1.36 2741 179 0.86 21.19 1.22 0.25 15.87| | 19: 1.36 - 1.34 2807 134 0.85 22.06 1.22 0.25 15.87| | 20: 1.34 - 1.32 2696 147 0.87 20.66 1.22 0.25 12.78| | 21: 1.32 - 1.30 2785 112 0.86 21.42 1.21 0.25 12.56| | 22: 1.29 - 1.27 2704 152 0.86 21.91 1.20 0.25 12.25| | 23: 1.27 - 1.26 2802 156 0.86 21.73 1.21 0.24 10.68| | 24: 1.26 - 1.24 2744 132 0.86 22.23 1.21 0.24 10.68| | 25: 1.24 - 1.22 2734 148 0.85 23.14 1.21 0.24 10.16| | 26: 1.22 - 1.21 2727 135 0.85 23.49 1.19 0.23 9.57| | 27: 1.21 - 1.19 2814 148 0.84 24.22 1.21 0.23 9.57| | 28: 1.19 - 1.18 2671 147 0.83 25.44 1.20 0.22 9.11| | 29: 1.18 - 1.16 2800 134 0.82 25.78 1.18 0.22 8.94| | 30: 1.16 - 1.15 2740 148 0.80 27.66 1.16 0.22 8.94| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 8.94 max = 1487.11 mean = 216.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.65| |phase err.(test): min = 0.00 max = 89.97 mean = 22.57| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.086 0.247 1557 Z= 5.709 Angle : 5.210 17.773 2118 Z= 3.742 Chirality : 0.378 1.120 243 Planarity : 0.031 0.091 284 Dihedral : 13.578 78.948 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 29.73 % 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: -2.50 (0.48), residues: 224 helix: -2.32 (0.41), residues: 109 sheet: -0.85 (0.73), residues: 38 loop : -0.63 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.019 ARG A 27 TYR 0.091 0.041 TYR A 141 PHE 0.106 0.048 PHE A 162 HIS 0.043 0.022 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= 0.2602 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789427 | | target function (ml) not normalized (work): 232375.964958 | | target function (ml) not normalized (free): 11799.532204 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1938 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1938 n_refl.: 87602 remove outliers: r(all,work,free)=0.1971 0.1974 0.1938 n_refl.: 87594 overall B=0.17 to atoms: r(all,work,free)=0.1991 0.1995 0.1950 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1629 0.1773 n_refl.: 87594 remove outliers: r(all,work,free)=0.1635 0.1628 0.1773 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 0.3774 386.270 359.358 0.726 0.929 0.407 11.894-9.307 99.02 97 4 0.1800 613.572 594.214 1.005 0.930 0.390 9.237-7.194 100.00 213 7 0.2140 501.826 490.685 1.035 0.930 0.339 7.162-5.571 100.00 427 22 0.2179 376.593 364.563 1.002 0.931 0.288 5.546-4.326 100.00 867 58 0.1278 516.969 510.966 1.041 0.931 0.228 4.315-3.360 100.00 1859 96 0.1130 491.641 488.192 1.086 0.931 0.199 3.356-2.611 100.00 3867 181 0.1409 322.983 319.598 1.077 0.931 0.109 2.608-2.026 99.99 8198 413 0.1361 214.108 211.800 1.083 0.930 0.000 2.025-1.573 100.00 17313 902 0.1656 104.559 103.772 1.086 0.929 0.000 1.573-1.221 100.00 36679 1900 0.2040 46.366 45.109 1.078 0.928 0.000 1.221-1.150 99.97 13689 708 0.2576 29.214 27.022 1.052 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0396 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1631 r_free=0.1775 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.942486 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.646566 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 0.1461 0.0252 0.008 1.0 1.0 0.5 0.0 0 12.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 14.61 2.52 3.012 19.031 2021.647 0.017 12.38 15.36 2.98 3.143 19.480 2021.647 0.016 Individual atomic B min max mean iso aniso Overall: 8.49 118.33 20.91 2.88 0 1785 Protein: 8.49 118.33 17.79 2.88 0 1519 Water: 11.09 114.47 39.03 N/A 0 258 Other: 22.52 35.57 28.50 N/A 0 8 Chain A: 8.49 118.33 20.91 N/A 0 1785 Histogram: Values Number of atoms 8.49 - 19.47 1214 19.47 - 30.45 223 30.45 - 41.44 166 41.44 - 52.42 98 52.42 - 63.41 55 63.41 - 74.39 17 74.39 - 85.37 5 85.37 - 96.36 4 96.36 - 107.34 0 107.34 - 118.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1536 r_work=0.1243 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1243 r_free = 0.1541 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 = 0.1242 r_free = 0.1544 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.31 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= 0.1242 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015329 | | target function (ls_wunit_k1) not normalized (work): 1276.900791 | | target function (ls_wunit_k1) not normalized (free): 114.177196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1257 0.1242 0.1544 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1688 0.1686 0.1761 n_refl.: 87593 remove outliers: r(all,work,free)=0.1688 0.1686 0.1761 n_refl.: 87593 overall B=0.19 to atoms: r(all,work,free)=0.1719 0.1718 0.1782 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1257 0.1242 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1257 0.1242 0.1542 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 96.88 88 5 0.3600 302.699 281.678 0.649 1.002 0.393 11.894-9.307 99.02 97 4 0.1585 480.822 468.765 0.906 1.003 0.380 9.237-7.194 100.00 213 7 0.1817 393.253 388.340 0.947 1.003 0.340 7.162-5.571 100.00 427 22 0.1717 295.115 289.926 0.917 1.003 0.253 5.546-4.326 100.00 867 58 0.0927 405.120 402.481 0.948 1.003 0.209 4.315-3.360 100.00 1859 96 0.0779 385.272 384.460 0.993 1.003 0.199 3.356-2.611 100.00 3867 181 0.1022 253.103 252.423 0.997 1.002 0.109 2.608-2.026 99.99 8198 413 0.0970 167.784 167.209 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1211 81.937 82.127 1.015 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1648 36.334 35.788 1.004 0.997 0.000 1.221-1.150 99.97 13689 708 0.2357 22.893 21.386 0.969 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1242 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1245 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1543 | n_water=258 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1254 r_free=0.1541 | n_water=252 | time (s): 26.070 (total time: 28.560) Filter (q & B) r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 3.690 (total time: 32.250) Compute maps r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 1.830 (total time: 34.080) Filter (map) r_work=0.1275 r_free=0.1545 | n_water=235 | time (s): 3.840 (total time: 37.920) Find peaks r_work=0.1275 r_free=0.1545 | n_water=235 | time (s): 0.680 (total time: 38.600) Add new water r_work=0.1430 r_free=0.1691 | n_water=450 | time (s): 3.850 (total time: 42.450) Refine new water occ: r_work=0.1335 r_free=0.1577 adp: r_work=0.1254 r_free=0.1521 occ: r_work=0.1268 r_free=0.1523 adp: r_work=0.1233 r_free=0.1505 occ: r_work=0.1238 r_free=0.1502 adp: r_work=0.1226 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1503 r_work=0.1226 r_free=0.1503 | n_water=450 | time (s): 88.600 (total time: 131.050) Filter (q & B) r_work=0.1232 r_free=0.1507 | n_water=433 | time (s): 4.020 (total time: 135.070) Filter (dist only) r_work=0.1232 r_free=0.1507 | n_water=433 | time (s): 41.410 (total time: 176.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.252370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1436.693170 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1524 0.0293 0.007 0.9 2.9 0.5 0.0 0 12.626 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 15.24 2.93 3.778 23.178 1436.693 0.015 12.05 14.97 2.92 4.179 22.981 1436.693 0.015 Individual atomic B min max mean iso aniso Overall: 8.72 113.94 23.20 2.58 198 1762 Protein: 8.72 113.94 17.62 2.59 0 1519 Water: 11.06 72.34 42.62 N/A 198 235 Other: 25.55 35.80 30.20 N/A 0 8 Chain A: 8.72 113.94 20.32 N/A 0 1762 Chain S: 14.97 70.35 48.85 N/A 198 0 Histogram: Values Number of atoms 8.72 - 19.24 1204 19.24 - 29.76 245 29.76 - 40.29 195 40.29 - 50.81 141 50.81 - 61.33 112 61.33 - 71.85 51 71.85 - 82.38 6 82.38 - 92.90 3 92.90 - 103.42 1 103.42 - 113.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1497 r_work=0.1205 r_free=0.1497 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1497 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 = 0.1209 r_free = 0.1482 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1209 r_free= 0.1482 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.014243 | | target function (ls_wunit_k1) not normalized (work): 1186.423679 | | target function (ls_wunit_k1) not normalized (free): 104.785836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1209 0.1482 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1617 0.1614 0.1718 n_refl.: 87593 remove outliers: r(all,work,free)=0.1617 0.1614 0.1718 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1622 0.1619 0.1721 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1205 0.1478 n_refl.: 87593 remove outliers: r(all,work,free)=0.1217 0.1203 0.1478 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 0.3422 298.703 271.618 0.645 0.936 0.364 11.894-9.307 99.02 97 4 0.1473 480.822 477.875 0.982 0.937 0.360 9.237-7.194 100.00 213 7 0.1667 393.253 393.417 1.046 0.937 0.290 7.162-5.571 100.00 427 22 0.1569 295.115 290.774 1.001 0.938 0.225 5.546-4.326 100.00 867 58 0.0862 405.120 402.128 1.024 0.938 0.215 4.315-3.360 100.00 1859 96 0.0733 385.272 384.047 1.070 0.939 0.210 3.356-2.611 100.00 3867 181 0.0978 253.103 252.268 1.077 0.939 0.160 2.608-2.026 99.99 8198 413 0.0966 167.784 167.270 1.083 0.941 0.000 2.025-1.573 100.00 17313 902 0.1177 81.937 82.138 1.091 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1603 36.334 35.840 1.074 0.946 0.000 1.221-1.150 99.97 13689 708 0.2334 22.893 21.444 1.030 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1478 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1478 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1478 | n_water=433 | time (s): 2.070 (total time: 2.070) Filter (dist) r_work=0.1203 r_free=0.1479 | n_water=432 | time (s): 35.950 (total time: 38.020) Filter (q & B) r_work=0.1204 r_free=0.1481 | n_water=431 | time (s): 3.130 (total time: 41.150) Compute maps r_work=0.1204 r_free=0.1481 | n_water=431 | time (s): 1.800 (total time: 42.950) Filter (map) r_work=0.1242 r_free=0.1484 | n_water=288 | time (s): 2.910 (total time: 45.860) Find peaks r_work=0.1242 r_free=0.1484 | n_water=288 | time (s): 0.490 (total time: 46.350) Add new water r_work=0.1368 r_free=0.1632 | n_water=477 | time (s): 2.850 (total time: 49.200) Refine new water occ: r_work=0.1268 r_free=0.1533 adp: r_work=0.1269 r_free=0.1534 occ: r_work=0.1246 r_free=0.1508 adp: r_work=0.1245 r_free=0.1509 occ: r_work=0.1232 r_free=0.1486 adp: r_work=0.1226 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1226 r_free=0.1485 r_work=0.1226 r_free=0.1485 | n_water=477 | time (s): 205.950 (total time: 255.150) Filter (q & B) r_work=0.1231 r_free=0.1489 | n_water=438 | time (s): 3.730 (total time: 258.880) Filter (dist only) r_work=0.1231 r_free=0.1489 | n_water=438 | time (s): 35.590 (total time: 294.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.033213 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.064750 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1234 0.1457 0.0222 0.006 0.9 1.9 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.57 2.22 3.605 22.010 43.065 3.728 12.29 14.18 1.89 4.074 21.825 43.065 3.660 Individual atomic B min max mean iso aniso Overall: 9.24 109.59 21.54 2.29 205 1760 Protein: 9.24 109.59 17.21 2.29 0 1519 Water: 11.51 71.27 36.43 N/A 205 233 Other: 21.28 31.88 27.20 N/A 0 8 Chain A: 9.24 109.59 19.87 N/A 0 1760 Chain S: 16.86 66.86 35.83 N/A 205 0 Histogram: Values Number of atoms 9.24 - 19.28 1235 19.28 - 29.31 286 29.31 - 39.35 211 39.35 - 49.38 121 49.38 - 59.41 78 59.41 - 69.45 21 69.45 - 79.48 7 79.48 - 89.52 3 89.52 - 99.55 1 99.55 - 109.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1418 r_work=0.1230 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1419 target_work(ml) = 3.661 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1419 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1419 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.658778 | | target function (ml) not normalized (work): 304754.281541 | | target function (ml) not normalized (free): 16092.596482 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1226 0.1419 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1557 0.1559 0.1571 n_refl.: 87590 remove outliers: r(all,work,free)=0.1557 0.1559 0.1571 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1555 0.1556 0.1569 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1217 0.1386 n_refl.: 87590 remove outliers: r(all,work,free)=0.1223 0.1215 0.1386 n_refl.: 87585 ======================== 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 0.4064 293.367 264.644 0.489 0.999 0.330 11.894-9.307 99.02 97 4 0.2289 480.822 470.844 0.860 1.001 0.330 9.237-7.194 98.18 209 7 0.2365 384.763 385.914 0.941 1.001 0.202 7.162-5.571 100.00 427 22 0.2098 295.115 284.988 0.910 1.001 0.173 5.546-4.326 100.00 867 58 0.1115 405.120 399.981 0.950 1.001 0.165 4.315-3.360 100.00 1859 96 0.0969 385.272 382.268 0.992 1.001 0.157 3.356-2.611 100.00 3867 181 0.1180 253.103 251.084 0.999 1.002 0.067 2.608-2.026 99.99 8198 413 0.1075 167.784 166.673 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1024 81.937 82.098 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1289 36.334 35.884 1.017 1.002 0.000 1.221-1.150 99.97 13689 708 0.2129 22.893 21.410 0.971 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1215 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1215 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1215 r_free=0.1386 | n_water=438 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1215 r_free=0.1386 | n_water=437 | time (s): 37.560 (total time: 39.820) Filter (q & B) r_work=0.1215 r_free=0.1385 | n_water=436 | time (s): 3.330 (total time: 43.150) Compute maps r_work=0.1215 r_free=0.1385 | n_water=436 | time (s): 1.410 (total time: 44.560) Filter (map) r_work=0.1236 r_free=0.1383 | n_water=309 | time (s): 3.270 (total time: 47.830) Find peaks r_work=0.1236 r_free=0.1383 | n_water=309 | time (s): 0.670 (total time: 48.500) Add new water r_work=0.1306 r_free=0.1448 | n_water=470 | time (s): 3.220 (total time: 51.720) Refine new water occ: r_work=0.1233 r_free=0.1371 adp: r_work=0.1234 r_free=0.1374 occ: r_work=0.1216 r_free=0.1358 adp: r_work=0.1215 r_free=0.1361 occ: r_work=0.1205 r_free=0.1350 adp: r_work=0.1201 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1350 r_work=0.1201 r_free=0.1350 | n_water=470 | time (s): 194.450 (total time: 246.170) Filter (q & B) r_work=0.1206 r_free=0.1356 | n_water=442 | time (s): 3.590 (total time: 249.760) Filter (dist only) r_work=0.1206 r_free=0.1355 | n_water=441 | time (s): 37.070 (total time: 286.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.959483 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.009800 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 0.1375 0.0163 0.006 1.0 2.2 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 13.75 1.63 3.413 21.483 45.010 3.646 11.94 13.68 1.74 3.844 21.347 45.010 3.630 Individual atomic B min max mean iso aniso Overall: 9.29 105.60 21.19 2.13 211 1757 Protein: 9.29 105.60 16.89 2.14 0 1519 Water: 11.34 69.60 35.90 N/A 211 230 Other: 21.98 30.55 26.34 N/A 0 8 Chain A: 9.29 105.60 19.46 N/A 0 1757 Chain S: 16.17 61.11 35.62 N/A 211 0 Histogram: Values Number of atoms 9.29 - 18.92 1235 18.92 - 28.55 282 28.55 - 38.18 209 38.18 - 47.81 132 47.81 - 57.44 70 57.44 - 67.07 28 67.07 - 76.71 7 76.71 - 86.34 2 86.34 - 95.97 1 95.97 - 105.60 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1368 r_work=0.1194 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1368 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1366 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1190 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628608 | | target function (ml) not normalized (work): 302223.134783 | | target function (ml) not normalized (free): 15949.928765 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1190 0.1366 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1532 0.1533 0.1555 n_refl.: 87585 remove outliers: r(all,work,free)=0.1532 0.1533 0.1555 n_refl.: 87585 overall B=-0.02 to atoms: r(all,work,free)=0.1528 0.1529 0.1552 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1188 0.1360 n_refl.: 87585 remove outliers: r(all,work,free)=0.1192 0.1184 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 0.4136 288.586 251.929 0.455 1.000 0.318 11.894-9.307 94.12 92 4 0.2174 477.467 457.716 0.845 1.002 0.310 9.237-7.194 97.73 208 7 0.2421 385.842 378.705 0.907 1.002 0.160 7.162-5.571 100.00 427 22 0.2207 295.115 284.595 0.905 1.002 0.150 5.546-4.326 100.00 867 58 0.1166 405.120 400.792 0.953 1.002 0.140 4.315-3.360 100.00 1859 96 0.0963 385.272 382.778 0.995 1.002 0.140 3.356-2.611 100.00 3867 181 0.1157 253.103 251.309 1.002 1.002 0.120 2.608-2.026 99.99 8198 413 0.1028 167.784 166.919 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0967 81.937 82.206 1.029 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.334 35.964 1.024 0.998 0.000 1.221-1.150 99.97 13689 708 0.2123 22.893 21.522 0.984 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0572 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1360 After: r_work=0.1185 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1360 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=0.1185 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1360 | n_water=441 | time (s): 1.520 (total time: 1.520) Filter (dist) r_work=0.1185 r_free=0.1360 | n_water=441 | time (s): 36.010 (total time: 37.530) Filter (q & B) r_work=0.1185 r_free=0.1360 | n_water=437 | time (s): 3.020 (total time: 40.550) Compute maps r_work=0.1185 r_free=0.1360 | n_water=437 | time (s): 1.300 (total time: 41.850) Filter (map) r_work=0.1209 r_free=0.1383 | n_water=330 | time (s): 2.770 (total time: 44.620) Find peaks r_work=0.1209 r_free=0.1383 | n_water=330 | time (s): 0.450 (total time: 45.070) Add new water r_work=0.1263 r_free=0.1429 | n_water=471 | time (s): 2.780 (total time: 47.850) Refine new water occ: r_work=0.1204 r_free=0.1362 adp: r_work=0.1205 r_free=0.1366 occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1191 r_free=0.1355 occ: r_work=0.1182 r_free=0.1344 adp: r_work=0.1179 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1347 r_work=0.1179 r_free=0.1347 | n_water=471 | time (s): 181.130 (total time: 228.980) Filter (q & B) r_work=0.1185 r_free=0.1355 | n_water=437 | time (s): 3.050 (total time: 232.030) Filter (dist only) r_work=0.1185 r_free=0.1354 | n_water=436 | time (s): 38.900 (total time: 270.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.892914 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.834759 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 0.1204 0.1373 0.0168 0.007 1.0 2.6 0.5 0.0 0 0.946 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.73 1.68 3.275 21.044 40.835 3.634 12.08 13.73 1.66 3.385 20.997 40.835 3.629 Individual atomic B min max mean iso aniso Overall: 9.28 102.52 20.94 2.03 208 1755 Protein: 9.28 102.52 16.77 2.03 0 1519 Water: 11.34 69.17 35.37 N/A 208 228 Other: 21.98 30.06 26.11 N/A 0 8 Chain A: 9.28 102.52 19.29 N/A 0 1755 Chain S: 15.68 60.03 34.86 N/A 208 0 Histogram: Values Number of atoms 9.28 - 18.61 1228 18.61 - 27.93 282 27.93 - 37.26 203 37.26 - 46.58 141 46.58 - 55.90 68 55.90 - 65.23 25 65.23 - 74.55 12 74.55 - 83.87 1 83.87 - 93.20 1 93.20 - 102.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1373 r_work=0.1208 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1374 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1371 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1204 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.627516 | | target function (ml) not normalized (work): 302099.538122 | | target function (ml) not normalized (free): 15959.663753 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1427 0.1435 5.7045 5.6432| | 2: 3.57 - 2.84 1.00 2888 124 0.1141 0.1444 5.2153 5.269| | 3: 2.83 - 2.48 1.00 2820 163 0.1236 0.1272 5.0109 5.039| | 4: 2.47 - 2.25 1.00 2825 136 0.1043 0.1104 4.7182 4.7514| | 5: 2.25 - 2.09 1.00 2756 127 0.0995 0.1128 4.6541 4.7289| | 6: 2.09 - 1.97 1.00 2846 113 0.0977 0.1253 4.3655 4.4905| | 7: 1.97 - 1.87 1.00 2787 165 0.0998 0.1222 4.0897 4.1897| | 8: 1.87 - 1.79 1.00 2789 144 0.1032 0.1269 4.0037 4.0969| | 9: 1.79 - 1.72 1.00 2745 138 0.0958 0.1308 3.725 3.9246| | 10: 1.72 - 1.66 1.00 2831 160 0.1006 0.1192 3.6423 3.7594| | 11: 1.66 - 1.61 1.00 2712 147 0.0964 0.1109 3.5729 3.6072| | 12: 1.61 - 1.56 1.00 2773 144 0.0919 0.1165 3.3512 3.4847| | 13: 1.56 - 1.52 1.00 2745 130 0.0973 0.1062 3.3414 3.4374| | 14: 1.52 - 1.48 1.00 2803 134 0.0984 0.1112 3.2606 3.3415| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1345 3.1666 3.3248| | 16: 1.45 - 1.42 1.00 2756 161 0.1064 0.1248 3.1524 3.2451| | 17: 1.42 - 1.39 1.00 2785 139 0.1118 0.1287 3.1162 3.2259| | 18: 1.39 - 1.36 1.00 2741 179 0.1150 0.1379 3.0889 3.267| | 19: 1.36 - 1.34 1.00 2807 134 0.1207 0.1639 3.0915 3.2929| | 20: 1.34 - 1.32 1.00 2696 147 0.1318 0.1472 3.0904 3.1362| | 21: 1.32 - 1.30 1.00 2785 112 0.1413 0.1603 3.0883 3.1669| | 22: 1.29 - 1.27 1.00 2704 152 0.1465 0.1917 3.0855 3.2933| | 23: 1.27 - 1.26 1.00 2802 156 0.1573 0.1819 3.1068 3.2047| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1751 3.1009 3.1932| | 25: 1.24 - 1.22 1.00 2733 148 0.1802 0.2329 3.1145 3.2999| | 26: 1.22 - 1.21 1.00 2727 135 0.1859 0.1773 3.1291 3.2042| | 27: 1.21 - 1.19 1.00 2814 148 0.2005 0.2083 3.1442 3.1474| | 28: 1.19 - 1.18 1.00 2671 147 0.2141 0.2311 3.1451 3.1664| | 29: 1.18 - 1.16 1.00 2800 134 0.2222 0.2384 3.132 3.2342| | 30: 1.16 - 1.15 1.00 2739 148 0.2383 0.2500 3.1225 3.1685| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2918 171 0.95 9.07 1.00 0.97 6305.54| | 2: 3.57 - 2.84 2888 124 0.92 13.40 1.01 0.97 6305.54| | 3: 2.83 - 2.48 2820 163 0.89 17.54 0.99 0.97 5290.75| | 4: 2.47 - 2.25 2825 136 0.91 14.60 1.00 0.98 2673.95| | 5: 2.25 - 2.09 2756 127 0.89 16.87 1.01 0.98 2673.95| | 6: 2.09 - 1.97 2846 113 0.92 13.72 1.02 0.98 1579.23| | 7: 1.97 - 1.87 2787 165 0.94 11.01 1.02 0.97 645.58| | 8: 1.87 - 1.79 2789 144 0.91 14.60 0.99 0.97 645.58| | 9: 1.79 - 1.72 2745 138 0.93 11.47 0.98 0.97 346.86| | 10: 1.72 - 1.66 2831 160 0.93 12.37 0.98 0.97 287.04| | 11: 1.66 - 1.61 2712 147 0.93 12.98 0.98 0.97 273.78| | 12: 1.61 - 1.56 2773 144 0.95 9.54 0.99 0.97 148.75| | 13: 1.56 - 1.52 2745 130 0.94 11.06 1.02 0.97 148.75| | 14: 1.52 - 1.48 2803 134 0.94 11.26 1.02 0.98 132.68| | 15: 1.48 - 1.45 2738 128 0.95 10.36 1.01 0.98 103.26| | 16: 1.45 - 1.42 2756 161 0.94 11.49 1.01 0.98 103.26| | 17: 1.42 - 1.39 2785 139 0.95 11.33 1.01 0.98 93.29| | 18: 1.39 - 1.36 2741 179 0.94 11.68 1.01 0.98 87.52| | 19: 1.36 - 1.34 2807 134 0.94 12.22 1.00 0.98 87.52| | 20: 1.34 - 1.32 2696 147 0.94 12.38 0.99 0.97 82.74| | 21: 1.32 - 1.30 2785 112 0.94 13.31 0.98 0.97 82.40| | 22: 1.29 - 1.27 2704 152 0.93 13.80 0.98 0.96 82.57| | 23: 1.27 - 1.26 2802 156 0.92 14.77 0.97 0.95 83.41| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.97 0.95 83.41| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 85.03| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.82| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 86.82| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 90.25| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.93 91.55| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.93 91.55| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.40 max = 6305.54 mean = 986.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 14.04| |phase err.(test): min = 0.00 max = 88.75 mean = 14.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1204 0.1371 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1537 0.1537 0.1574 n_refl.: 87576 remove outliers: r(all,work,free)=0.1537 0.1537 0.1574 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1534 0.1534 0.1572 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1204 0.1373 n_refl.: 87576 remove outliers: r(all,work,free)=0.1213 0.1204 0.1373 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 0.4336 288.586 246.405 0.442 1.001 0.324 11.894-9.307 94.12 92 4 0.2353 477.467 458.808 0.848 1.003 0.320 9.237-7.194 97.73 208 7 0.2507 385.842 377.233 0.901 1.002 0.130 7.162-5.571 100.00 427 22 0.2328 295.115 283.748 0.896 1.003 0.130 5.546-4.326 100.00 867 58 0.1183 405.120 400.527 0.953 1.002 0.130 4.315-3.360 100.00 1859 96 0.1003 385.272 382.518 0.996 1.002 0.130 3.356-2.611 100.00 3867 181 0.1204 253.103 250.908 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1046 167.784 166.812 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0983 81.937 82.181 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.334 35.963 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2118 22.893 21.512 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0395 ================= 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 : 0.2602 0.1939 0.086 5.210 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1773 0.086 5.210 9.0 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1773 0.086 5.210 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1775 0.086 5.210 9.0 119.5 20.1 258 0.003 1_weight: 0.1631 0.1775 0.086 5.210 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1209 0.1461 0.008 0.953 9.0 119.5 20.1 258 0.123 1_adp: 0.1238 0.1536 0.008 0.953 8.5 118.3 20.9 258 0.123 1_regHadp: 0.1243 0.1541 0.008 0.953 8.5 118.3 20.9 258 0.123 1_occ: 0.1242 0.1544 0.008 0.953 8.5 118.3 20.9 258 0.123 2_bss: 0.1242 0.1542 0.008 0.953 8.7 118.5 21.1 258 0.123 2_settarget: 0.1242 0.1542 0.008 0.953 8.7 118.5 21.1 258 0.123 2_updatecdl: 0.1242 0.1542 0.008 0.957 8.7 118.5 21.1 258 0.123 2_nqh: 0.1245 0.1543 0.008 0.957 8.7 118.5 21.1 258 0.123 2_sol: 0.1232 0.1507 0.008 0.957 8.7 118.5 23.6 433 n/a 2_weight: 0.1232 0.1507 0.008 0.957 8.7 118.5 23.6 433 n/a 2_xyzrec: 0.1231 0.1524 0.007 0.885 8.7 118.5 23.6 433 n/a 2_adp: 0.1205 0.1497 0.007 0.885 8.7 113.9 23.2 433 n/a 2_regHadp: 0.1205 0.1497 0.007 0.885 8.7 113.9 23.2 433 n/a 2_occ: 0.1209 0.1482 0.007 0.885 8.7 113.9 23.2 433 n/a 3_bss: 0.1203 0.1478 0.007 0.885 8.7 114.0 23.2 433 n/a 3_settarget: 0.1203 0.1478 0.007 0.885 8.7 114.0 23.2 433 n/a 3_updatecdl: 0.1203 0.1478 0.007 0.886 8.7 114.0 23.2 433 n/a 3_nqh: 0.1203 0.1478 0.007 0.886 8.7 114.0 23.2 433 n/a 3_sol: 0.1231 0.1489 0.007 0.886 8.7 114.0 21.9 438 n/a 3_weight: 0.1231 0.1489 0.007 0.886 8.7 114.0 21.9 438 n/a 3_xyzrec: 0.1234 0.1457 0.006 0.925 8.7 114.0 21.9 438 n/a 3_adp: 0.1229 0.1418 0.006 0.925 9.2 109.6 21.5 438 n/a 3_regHadp: 0.1230 0.1419 0.006 0.925 9.2 109.6 21.5 438 n/a 3_occ: 0.1226 0.1419 0.006 0.925 9.2 109.6 21.5 438 n/a 4_bss: 0.1215 0.1386 0.006 0.925 9.2 109.6 21.5 438 n/a 4_settarget: 0.1215 0.1386 0.006 0.925 9.2 109.6 21.5 438 n/a 4_updatecdl: 0.1215 0.1386 0.006 0.922 9.2 109.6 21.5 438 n/a 4_nqh: 0.1215 0.1386 0.006 0.922 9.2 109.6 21.5 438 n/a 4_sol: 0.1206 0.1355 0.006 0.922 9.2 109.6 21.4 441 n/a 4_weight: 0.1206 0.1355 0.006 0.922 9.2 109.6 21.4 441 n/a 4_xyzrec: 0.1212 0.1375 0.006 0.961 9.2 109.6 21.4 441 n/a 4_adp: 0.1194 0.1368 0.006 0.961 9.3 105.6 21.2 441 n/a 4_regHadp: 0.1194 0.1368 0.006 0.961 9.3 105.6 21.2 441 n/a 4_occ: 0.1190 0.1366 0.006 0.961 9.3 105.6 21.2 441 n/a 5_bss: 0.1184 0.1360 0.006 0.961 9.3 105.6 21.2 441 n/a 5_settarget: 0.1184 0.1360 0.006 0.961 9.3 105.6 21.2 441 n/a 5_updatecdl: 0.1184 0.1360 0.006 0.961 9.3 105.6 21.2 441 n/a 5_setrh: 0.1185 0.1360 0.006 0.961 9.3 105.6 21.2 441 n/a 5_nqh: 0.1185 0.1360 0.006 0.961 9.3 105.6 21.2 441 n/a 5_sol: 0.1185 0.1354 0.006 0.961 9.3 105.6 21.0 436 n/a 5_weight: 0.1185 0.1354 0.006 0.961 9.3 105.6 21.0 436 n/a 5_xyzrec: 0.1204 0.1373 0.007 1.025 9.3 105.6 21.0 436 n/a 5_adp: 0.1208 0.1373 0.007 1.025 9.3 102.5 20.9 436 n/a 5_regHadp: 0.1208 0.1374 0.007 1.025 9.3 102.5 20.9 436 n/a 5_occ: 0.1204 0.1371 0.007 1.025 9.3 102.5 20.9 436 n/a end: 0.1204 0.1373 0.007 1.025 9.3 102.5 20.9 436 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3657390_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_3657390_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9200 Refinement macro-cycles (run) : 3541.0000 Write final files (write_after_run_outputs) : 64.1500 Total : 3610.0700 Total CPU time: 60.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:49 PST -0800 (1735452709.10 s) Start R-work = 0.1628, R-free = 0.1773 Final R-work = 0.1204, R-free = 0.1373 =============================================================================== Job complete usr+sys time: 3742.86 seconds wall clock time: 66 minutes 57.86 seconds (4017.86 seconds total)