Starting phenix.refine on Sat Dec 28 21:06:31 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } 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: 2.33, per 1000 atoms: 0.69 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: 0.54 Conformation dependent library (CDL) restraints added in 195.6 milliseconds Time building geometry restraints manager: 0.75 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: 446 0.90 - 1.16: 1198 1.16 - 1.43: 666 1.43 - 1.69: 820 1.69 - 1.96: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.667 -0.130 5.00e-03 4.00e+04 6.81e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.521 1.750 -0.229 1.14e-02 7.69e+03 4.05e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.13e-02 7.83e+03 3.63e+02 bond pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta sigma weight residual 1.459 1.239 0.220 1.21e-02 6.83e+03 3.30e+02 bond pdb=" C SER A 47 " pdb=" O SER A 47 " ideal model delta sigma weight residual 1.236 1.031 0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 3102 4.56 - 9.11: 1867 9.11 - 13.67: 670 13.67 - 18.23: 122 18.23 - 22.79: 16 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.12 135.74 -13.62 1.06e+00 8.90e-01 1.65e+02 angle pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta sigma weight residual 103.52 115.46 -11.94 9.50e-01 1.11e+00 1.58e+02 angle pdb=" O TYR A 141 " pdb=" C TYR A 141 " pdb=" N SER A 142 " ideal model delta sigma weight residual 123.10 137.24 -14.14 1.15e+00 7.56e-01 1.51e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 133.58 -12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.82 133.15 -12.33 1.05e+00 9.07e-01 1.38e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 934 16.33 - 32.65: 116 32.65 - 48.97: 38 48.97 - 65.29: 20 65.29 - 81.62: 3 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 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.209: 81 0.209 - 0.417: 91 0.417 - 0.626: 42 0.626 - 0.834: 20 0.834 - 1.042: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 142 " pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CB SER A 142 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CB VAL A 146 " pdb=" CA VAL A 146 " pdb=" CG1 VAL A 146 " pdb=" CG2 VAL A 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.153 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.041 2.00e-02 2.50e+03 6.27e-02 1.18e+02 pdb=" CG PHE A 119 " -0.177 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.021 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.91: 8328 2.91 - 3.48: 10416 3.48 - 4.04: 15153 4.04 - 4.60: 21502 Nonbonded interactions: 56665 Sorted by model distance: nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.792 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.836 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.847 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.858 2.450 ... (remaining 56660 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_8831905_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= 0.2606 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794496 | | target function (ml) not normalized (work): 232798.252770 | | target function (ml) not normalized (free): 11879.249091 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3023 0.2093 7.0152 4.9403| | 2: 3.57 - 2.84 1.00 2876 122 0.2426 0.1878 4.3546 4.3546| | 3: 2.84 - 2.48 1.00 2833 165 0.2351 0.1695 4.1341 4.1633| | 4: 2.47 - 2.25 1.00 2825 136 0.2366 0.1486 3.8423 3.8551| | 5: 2.25 - 2.09 1.00 2756 127 0.2466 0.1619 3.8027 3.8196| | 6: 2.09 - 1.97 1.00 2846 113 0.2540 0.1857 3.4712 3.612| | 7: 1.97 - 1.87 1.00 2787 165 0.2580 0.1843 3.1454 3.2449| | 8: 1.87 - 1.79 1.00 2789 144 0.2449 0.1910 3.0602 3.1348| | 9: 1.79 - 1.72 1.00 2745 138 0.2383 0.1825 2.8922 2.9833| | 10: 1.72 - 1.66 1.00 2789 158 0.2362 0.1786 2.8149 2.8441| | 11: 1.66 - 1.61 1.00 2740 147 0.2497 0.1940 2.7599 2.8281| | 12: 1.61 - 1.56 1.00 2787 146 0.2568 0.2151 2.6664 2.7039| | 13: 1.56 - 1.52 1.00 2745 130 0.2538 0.1981 2.5845 2.6558| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.1906 2.5171 2.5575| | 15: 1.48 - 1.45 1.00 2738 128 0.2634 0.2244 2.4488 2.5486| | 16: 1.45 - 1.42 1.00 2756 161 0.2583 0.2293 2.3893 2.4889| | 17: 1.42 - 1.39 1.00 2785 139 0.2702 0.2296 2.3416 2.4379| | 18: 1.39 - 1.36 1.00 2741 179 0.2682 0.2216 2.2849 2.3345| | 19: 1.36 - 1.34 1.00 2807 134 0.2683 0.2201 2.2554 2.29| | 20: 1.34 - 1.32 1.00 2696 147 0.2723 0.2381 2.2139 2.2549| | 21: 1.32 - 1.30 1.00 2785 112 0.2721 0.2241 2.1564 2.1812| | 22: 1.29 - 1.27 1.00 2704 152 0.2733 0.2330 2.1311 2.1281| | 23: 1.27 - 1.26 1.00 2802 156 0.2755 0.2596 2.1046 2.2047| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2601 2.067 2.2274| | 25: 1.24 - 1.22 1.00 2734 148 0.2834 0.2282 2.0476 2.0257| | 26: 1.22 - 1.21 1.00 2727 135 0.2867 0.2396 2.0104 2.076| | 27: 1.21 - 1.19 1.00 2814 148 0.2969 0.2719 2.007 2.0407| | 28: 1.19 - 1.18 1.00 2671 147 0.3023 0.2687 1.9832 1.9596| | 29: 1.18 - 1.16 1.00 2800 134 0.2975 0.2696 1.9547 1.9849| | 30: 1.16 - 1.15 1.00 2740 148 0.3027 0.2903 1.9249 1.9496| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1497.92| | 2: 3.57 - 2.84 2876 122 0.80 26.27 1.27 0.23 1497.92| | 3: 2.84 - 2.48 2833 165 0.74 32.13 1.24 0.23 1242.12| | 4: 2.47 - 2.25 2825 136 0.81 25.54 1.26 0.25 578.27| | 5: 2.25 - 2.09 2756 127 0.77 29.40 1.28 0.25 578.27| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 316.51| | 7: 1.97 - 1.87 2787 165 0.90 16.98 1.29 0.26 93.26| | 8: 1.87 - 1.79 2789 144 0.86 21.26 1.25 0.26 93.26| | 9: 1.79 - 1.72 2745 138 0.88 18.96 1.23 0.25 56.25| | 10: 1.72 - 1.66 2789 158 0.87 20.07 1.21 0.25 48.84| | 11: 1.66 - 1.61 2740 147 0.85 21.59 1.24 0.25 47.24| | 12: 1.61 - 1.56 2787 146 0.88 18.78 1.23 0.25 30.95| | 13: 1.56 - 1.52 2745 130 0.86 20.96 1.23 0.25 30.95| | 14: 1.52 - 1.48 2803 134 0.86 21.30 1.24 0.25 27.76| | 15: 1.48 - 1.45 2738 128 0.86 20.81 1.23 0.25 21.93| | 16: 1.45 - 1.42 2756 161 0.85 22.21 1.22 0.25 21.93| | 17: 1.42 - 1.39 2785 139 0.86 21.70 1.24 0.25 18.74| | 18: 1.39 - 1.36 2741 179 0.86 21.85 1.23 0.25 16.89| | 19: 1.36 - 1.34 2807 134 0.85 22.85 1.22 0.25 16.89| | 20: 1.34 - 1.32 2696 147 0.86 21.43 1.21 0.24 13.71| | 21: 1.32 - 1.30 2785 112 0.85 22.97 1.21 0.24 13.48| | 22: 1.29 - 1.27 2704 152 0.85 23.05 1.21 0.24 13.15| | 23: 1.27 - 1.26 2802 156 0.85 22.53 1.21 0.24 11.48| | 24: 1.26 - 1.24 2744 132 0.85 23.24 1.21 0.24 11.48| | 25: 1.24 - 1.22 2734 148 0.84 23.79 1.20 0.24 10.72| | 26: 1.22 - 1.21 2727 135 0.84 23.91 1.20 0.23 9.87| | 27: 1.21 - 1.19 2814 148 0.83 24.59 1.21 0.23 9.87| | 28: 1.19 - 1.18 2671 147 0.83 24.94 1.19 0.23 8.94| | 29: 1.18 - 1.16 2800 134 0.83 24.90 1.16 0.23 8.59| | 30: 1.16 - 1.15 2740 148 0.82 26.24 1.15 0.23 8.59| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.59 max = 1497.92 mean = 217.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.87| |phase err.(test): min = 0.00 max = 89.46 mean = 22.79| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.229 1557 Z= 5.677 Angle : 5.295 16.972 2118 Z= 3.642 Chirality : 0.407 1.042 243 Planarity : 0.030 0.077 284 Dihedral : 14.023 81.616 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.35 % 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: -3.07 (0.46), residues: 224 helix: -2.72 (0.37), residues: 103 sheet: -0.98 (0.81), residues: 38 loop : -1.28 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.026 ARG A 156 TYR 0.084 0.045 TYR A 139 PHE 0.154 0.048 PHE A 119 HIS 0.060 0.034 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794496 | | target function (ml) not normalized (work): 232798.252770 | | target function (ml) not normalized (free): 11879.249091 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1971 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1971 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1984 0.1971 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2005 0.2008 0.1986 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1639 0.1785 n_refl.: 87594 remove outliers: r(all,work,free)=0.1645 0.1638 0.1785 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 0.3825 386.507 358.717 0.681 1.003 0.414 11.894-9.307 99.02 97 4 0.1817 613.947 594.136 0.928 1.004 0.386 9.237-7.194 100.00 213 7 0.2164 502.133 491.155 0.957 1.004 0.370 7.162-5.571 100.00 427 22 0.2188 376.823 363.704 0.930 1.004 0.287 5.546-4.326 100.00 867 58 0.1246 517.285 511.902 0.964 1.004 0.228 4.315-3.360 100.00 1859 96 0.1134 491.941 488.173 1.007 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.180 319.388 0.993 1.003 0.052 2.608-2.026 99.99 8198 413 0.1358 214.239 212.192 1.008 1.001 0.000 2.025-1.573 100.00 17313 902 0.1657 104.623 104.099 1.013 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2070 46.394 45.045 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2578 29.232 26.967 0.978 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1643 r_free=0.1792 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.158658 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1996.527972 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 0.1211 0.1462 0.0251 0.008 1.0 1.0 0.5 0.0 0 13.579 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 14.62 2.51 3.013 19.053 1996.528 0.017 12.45 15.41 2.96 3.322 19.614 1996.528 0.016 Individual atomic B min max mean iso aniso Overall: 8.56 118.80 21.14 2.87 0 1785 Protein: 8.56 118.80 18.00 2.87 0 1519 Water: 11.06 114.49 39.37 N/A 0 258 Other: 23.53 37.33 30.12 N/A 0 8 Chain A: 8.56 118.80 21.14 N/A 0 1785 Histogram: Values Number of atoms 8.56 - 19.59 1204 19.59 - 30.61 230 30.61 - 41.64 163 41.64 - 52.66 104 52.66 - 63.68 50 63.68 - 74.71 18 74.71 - 85.73 9 85.73 - 96.76 2 96.76 - 107.78 2 107.78 - 118.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.1245 r_free=0.1541 r_work=0.1249 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1546 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 = 0.1249 r_free = 0.1553 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 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= 0.1249 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015490 | | target function (ls_wunit_k1) not normalized (work): 1290.272677 | | target function (ls_wunit_k1) not normalized (free): 114.773266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1264 0.1249 0.1553 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1705 0.1703 0.1779 n_refl.: 87593 remove outliers: r(all,work,free)=0.1705 0.1703 0.1779 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 0.1547 n_refl.: 87593 remove outliers: r(all,work,free)=0.1261 0.1247 0.1547 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 0.3610 298.614 278.011 0.637 1.002 0.380 11.894-9.307 99.02 97 4 0.1617 478.363 467.061 0.909 1.003 0.380 9.237-7.194 100.00 213 7 0.1849 391.242 385.072 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1708 293.606 288.353 0.924 1.003 0.248 5.546-4.326 100.00 867 58 0.0907 403.048 400.582 0.950 1.003 0.204 4.315-3.360 100.00 1859 96 0.0769 383.301 382.303 0.996 1.003 0.190 3.356-2.611 100.00 3867 181 0.1022 251.809 251.085 0.997 1.002 0.110 2.608-2.026 99.99 8198 413 0.0980 166.926 166.314 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1221 81.518 81.687 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.148 35.603 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2367 22.776 21.279 0.970 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0500 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1247 r_free=0.1547 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=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1247 r_free=0.1547 | n_water=258 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1258 r_free=0.1544 | n_water=251 | time (s): 27.990 (total time: 30.580) Filter (q & B) r_work=0.1260 r_free=0.1544 | n_water=248 | time (s): 3.850 (total time: 34.430) Compute maps r_work=0.1260 r_free=0.1544 | n_water=248 | time (s): 1.910 (total time: 36.340) Filter (map) r_work=0.1283 r_free=0.1555 | n_water=234 | time (s): 3.920 (total time: 40.260) Find peaks r_work=0.1283 r_free=0.1555 | n_water=234 | time (s): 0.750 (total time: 41.010) Add new water r_work=0.1434 r_free=0.1706 | n_water=448 | time (s): 3.830 (total time: 44.840) Refine new water occ: r_work=0.1330 r_free=0.1566 adp: r_work=0.1254 r_free=0.1518 occ: r_work=0.1268 r_free=0.1519 adp: r_work=0.1233 r_free=0.1498 occ: r_work=0.1236 r_free=0.1493 adp: r_work=0.1228 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1228 r_free=0.1491 r_work=0.1228 r_free=0.1491 | n_water=448 | time (s): 104.010 (total time: 148.850) Filter (q & B) r_work=0.1234 r_free=0.1501 | n_water=429 | time (s): 3.960 (total time: 152.810) Filter (dist only) r_work=0.1234 r_free=0.1501 | n_water=429 | time (s): 40.680 (total time: 193.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.798116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1494.948324 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 0.1232 0.1530 0.0298 0.007 0.9 2.6 0.5 0.0 0 12.899 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 15.30 2.98 3.812 23.248 1494.948 0.015 12.05 15.00 2.94 4.297 23.018 1494.948 0.015 Individual atomic B min max mean iso aniso Overall: 8.69 114.02 23.10 2.62 195 1761 Protein: 8.69 114.02 17.71 2.62 0 1519 Water: 10.77 72.24 42.03 N/A 195 234 Other: 26.51 37.76 31.13 N/A 0 8 Chain A: 8.69 114.02 20.43 N/A 0 1761 Chain S: 16.62 72.22 47.17 N/A 195 0 Histogram: Values Number of atoms 8.69 - 19.23 1204 19.23 - 29.76 250 29.76 - 40.29 201 40.29 - 50.82 131 50.82 - 61.36 105 61.36 - 71.89 51 71.89 - 82.42 8 82.42 - 92.96 3 92.96 - 103.49 1 103.49 - 114.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1500 r_work=0.1205 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1499 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 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= 0.1207 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014054 | | target function (ls_wunit_k1) not normalized (work): 1170.611324 | | target function (ls_wunit_k1) not normalized (free): 101.072331 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1207 0.1486 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1603 0.1599 0.1714 n_refl.: 87592 remove outliers: r(all,work,free)=0.1603 0.1599 0.1714 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1609 0.1605 0.1717 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1205 0.1485 n_refl.: 87592 remove outliers: r(all,work,free)=0.1217 0.1203 0.1485 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3457 294.556 273.123 0.599 1.002 0.370 11.894-9.307 99.02 97 4 0.1597 478.363 475.662 0.916 1.003 0.370 9.237-7.194 100.00 213 7 0.1678 391.242 392.256 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1504 293.606 289.758 0.941 1.003 0.225 5.546-4.326 100.00 867 58 0.0830 403.048 400.707 0.958 1.003 0.210 4.315-3.360 100.00 1859 96 0.0707 383.301 382.035 1.001 1.002 0.200 3.356-2.611 100.00 3867 181 0.0961 251.809 251.161 1.008 1.002 0.130 2.608-2.026 99.99 8198 413 0.0969 166.926 166.563 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1191 81.518 81.725 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1620 36.148 35.642 1.016 0.998 0.000 1.221-1.150 99.97 13689 708 0.2340 22.776 21.315 0.976 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0621 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1485 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1485 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1485 | n_water=429 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1204 r_free=0.1485 | n_water=426 | time (s): 39.610 (total time: 41.670) Filter (q & B) r_work=0.1204 r_free=0.1485 | n_water=426 | time (s): 1.020 (total time: 42.690) Compute maps r_work=0.1204 r_free=0.1485 | n_water=426 | time (s): 1.550 (total time: 44.240) Filter (map) r_work=0.1244 r_free=0.1491 | n_water=294 | time (s): 2.970 (total time: 47.210) Find peaks r_work=0.1244 r_free=0.1491 | n_water=294 | time (s): 0.480 (total time: 47.690) Add new water r_work=0.1375 r_free=0.1612 | n_water=491 | time (s): 2.870 (total time: 50.560) Refine new water occ: r_work=0.1268 r_free=0.1519 adp: r_work=0.1269 r_free=0.1521 occ: r_work=0.1245 r_free=0.1500 adp: r_work=0.1242 r_free=0.1500 occ: r_work=0.1229 r_free=0.1487 adp: r_work=0.1222 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1484 r_work=0.1222 r_free=0.1484 | n_water=491 | time (s): 175.990 (total time: 226.550) Filter (q & B) r_work=0.1226 r_free=0.1486 | n_water=460 | time (s): 3.500 (total time: 230.050) Filter (dist only) r_work=0.1226 r_free=0.1486 | n_water=460 | time (s): 35.190 (total time: 265.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.103724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.693131 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 0.1238 0.1449 0.0211 0.006 0.9 3.2 0.5 0.0 0 1.052 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.49 2.11 3.636 22.191 51.693 3.732 12.19 14.02 1.84 4.192 21.998 51.693 3.657 Individual atomic B min max mean iso aniso Overall: 9.21 109.06 21.76 2.34 230 1757 Protein: 9.21 109.06 17.23 2.35 0 1519 Water: 11.51 70.78 36.64 N/A 230 230 Other: 21.97 33.46 27.64 N/A 0 8 Chain A: 9.21 109.06 19.88 N/A 0 1757 Chain S: 16.84 64.64 36.18 N/A 230 0 Histogram: Values Number of atoms 9.21 - 19.20 1231 19.20 - 29.18 276 29.18 - 39.17 225 39.17 - 49.15 149 49.15 - 59.14 72 59.14 - 69.12 21 69.12 - 79.11 7 79.11 - 89.09 3 89.09 - 99.08 1 99.08 - 109.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1403 r_work=0.1220 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1220 r_free = 0.1404 target_work(ml) = 3.657 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1403 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1214 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.655000 | | target function (ml) not normalized (work): 304435.887837 | | target function (ml) not normalized (free): 16083.674497 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1223 0.1214 0.1403 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1537 0.1537 0.1581 n_refl.: 87589 remove outliers: r(all,work,free)=0.1537 0.1537 0.1581 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1535 0.1534 0.1579 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1204 0.1375 n_refl.: 87589 remove outliers: r(all,work,free)=0.1210 0.1201 0.1375 n_refl.: 87583 ======================== 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 90.62 82 5 0.3850 299.392 261.872 0.472 1.000 0.320 11.894-9.307 97.06 95 4 0.2534 478.585 453.171 0.845 1.002 0.280 9.237-7.194 99.09 211 7 0.2433 385.790 383.477 0.943 1.002 0.190 7.162-5.571 100.00 427 22 0.2031 293.606 284.051 0.911 1.002 0.173 5.546-4.326 100.00 867 58 0.1087 403.048 399.310 0.949 1.003 0.156 4.315-3.360 100.00 1859 96 0.0933 383.301 380.528 0.994 1.002 0.147 3.356-2.611 100.00 3867 181 0.1151 251.809 249.884 0.999 1.002 0.057 2.608-2.026 99.99 8198 413 0.1055 166.926 166.033 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.1015 81.518 81.709 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1294 36.148 35.752 1.020 0.999 0.000 1.221-1.150 99.97 13689 708 0.2129 22.776 21.421 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0357 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1375 | n_water=460 | time (s): 2.150 (total time: 2.150) Filter (dist) r_work=0.1203 r_free=0.1373 | n_water=459 | time (s): 42.050 (total time: 44.200) Filter (q & B) r_work=0.1203 r_free=0.1372 | n_water=457 | time (s): 2.770 (total time: 46.970) Compute maps r_work=0.1203 r_free=0.1372 | n_water=457 | time (s): 1.260 (total time: 48.230) Filter (map) r_work=0.1233 r_free=0.1384 | n_water=318 | time (s): 2.740 (total time: 50.970) Find peaks r_work=0.1233 r_free=0.1384 | n_water=318 | time (s): 0.450 (total time: 51.420) Add new water r_work=0.1293 r_free=0.1446 | n_water=483 | time (s): 2.880 (total time: 54.300) Refine new water occ: r_work=0.1215 r_free=0.1370 adp: r_work=0.1215 r_free=0.1371 occ: r_work=0.1199 r_free=0.1355 adp: r_work=0.1197 r_free=0.1355 occ: r_work=0.1189 r_free=0.1350 adp: r_work=0.1185 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1346 r_work=0.1185 r_free=0.1346 | n_water=483 | time (s): 172.790 (total time: 227.090) Filter (q & B) r_work=0.1190 r_free=0.1350 | n_water=455 | time (s): 2.940 (total time: 230.030) Filter (dist only) r_work=0.1190 r_free=0.1350 | n_water=454 | time (s): 39.140 (total time: 269.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.961793 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.643948 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 0.1197 0.1369 0.0172 0.006 1.0 3.5 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.69 1.72 3.437 21.571 38.644 3.639 11.90 13.70 1.80 3.698 21.496 38.644 3.630 Individual atomic B min max mean iso aniso Overall: 9.29 105.38 21.45 2.15 227 1754 Protein: 9.29 105.38 17.04 2.16 0 1519 Water: 11.58 69.95 36.11 N/A 227 227 Other: 21.10 30.68 26.30 N/A 0 8 Chain A: 9.29 105.38 19.63 N/A 0 1754 Chain S: 15.78 57.74 35.46 N/A 227 0 Histogram: Values Number of atoms 9.29 - 18.90 1229 18.90 - 28.50 285 28.50 - 38.11 198 38.11 - 47.72 153 47.72 - 57.33 77 57.33 - 66.94 24 66.94 - 76.55 10 76.55 - 86.16 2 86.16 - 95.77 1 95.77 - 105.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1370 r_work=0.1191 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1371 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1368 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.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1187 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.629076 | | target function (ml) not normalized (work): 302254.869391 | | target function (ml) not normalized (free): 15962.133723 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1187 0.1368 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1507 0.1505 0.1568 n_refl.: 87583 remove outliers: r(all,work,free)=0.1507 0.1505 0.1568 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1504 0.1503 0.1567 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1186 0.1369 n_refl.: 87583 remove outliers: r(all,work,free)=0.1192 0.1183 0.1369 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 87.50 79 5 0.4021 285.837 263.335 0.463 0.998 0.310 11.894-9.307 95.10 93 4 0.2292 484.532 460.228 0.852 1.001 0.300 9.237-7.194 98.64 210 7 0.2508 384.806 378.687 0.922 1.001 0.170 7.162-5.571 100.00 427 22 0.2136 293.606 283.047 0.908 1.002 0.140 5.546-4.326 100.00 867 58 0.1119 403.048 398.894 0.950 1.002 0.130 4.315-3.360 100.00 1859 96 0.0939 383.301 380.662 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1147 251.809 250.013 1.000 1.002 0.110 2.608-2.026 99.99 8198 413 0.1026 166.926 165.987 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0985 81.518 81.756 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.148 35.770 1.022 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.776 21.407 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0406 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1183 r_free=0.1369 After: r_work=0.1184 r_free=0.1369 ================================== NQH flips ================================== r_work=0.1184 r_free=0.1369 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=0.1184 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1369 | n_water=454 | time (s): 1.580 (total time: 1.580) Filter (dist) r_work=0.1184 r_free=0.1369 | n_water=454 | time (s): 35.500 (total time: 37.080) Filter (q & B) r_work=0.1184 r_free=0.1371 | n_water=450 | time (s): 3.160 (total time: 40.240) Compute maps r_work=0.1184 r_free=0.1371 | n_water=450 | time (s): 1.700 (total time: 41.940) Filter (map) r_work=0.1209 r_free=0.1371 | n_water=337 | time (s): 2.850 (total time: 44.790) Find peaks r_work=0.1209 r_free=0.1371 | n_water=337 | time (s): 0.440 (total time: 45.230) Add new water r_work=0.1259 r_free=0.1418 | n_water=494 | time (s): 2.710 (total time: 47.940) Refine new water occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1194 r_free=0.1359 occ: r_work=0.1182 r_free=0.1349 adp: r_work=0.1181 r_free=0.1349 occ: r_work=0.1174 r_free=0.1343 adp: r_work=0.1171 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1171 r_free=0.1342 r_work=0.1171 r_free=0.1342 | n_water=494 | time (s): 197.870 (total time: 245.810) Filter (q & B) r_work=0.1177 r_free=0.1345 | n_water=460 | time (s): 2.910 (total time: 248.720) Filter (dist only) r_work=0.1177 r_free=0.1345 | n_water=459 | time (s): 38.100 (total time: 286.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.980731 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.497630 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 0.1200 0.1367 0.0167 0.007 1.1 5.4 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.67 1.67 3.316 21.328 48.498 3.634 11.96 13.60 1.64 3.763 21.204 48.498 3.619 Individual atomic B min max mean iso aniso Overall: 9.29 101.31 21.15 2.06 232 1754 Protein: 9.29 101.31 16.71 2.06 0 1519 Water: 11.57 68.21 35.79 N/A 232 227 Other: 20.63 28.58 25.26 N/A 0 8 Chain A: 9.29 101.31 19.28 N/A 0 1754 Chain S: 14.47 57.79 35.27 N/A 232 0 Histogram: Values Number of atoms 9.29 - 18.49 1225 18.49 - 27.69 276 27.69 - 36.89 211 36.89 - 46.09 156 46.09 - 55.30 78 55.30 - 64.50 24 64.50 - 73.70 11 73.70 - 82.90 2 82.90 - 92.10 1 92.10 - 101.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1193 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618075 | | target function (ml) not normalized (work): 301316.942685 | | target function (ml) not normalized (free): 15927.539128 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1424 0.1349 5.7231 5.6012| | 2: 3.57 - 2.84 1.00 2888 124 0.1107 0.1374 5.1787 5.234| | 3: 2.83 - 2.48 1.00 2820 163 0.1215 0.1311 4.9845 5.0148| | 4: 2.47 - 2.25 1.00 2825 136 0.1023 0.1229 4.6902 4.7741| | 5: 2.25 - 2.09 1.00 2756 127 0.1004 0.1123 4.633 4.7099| | 6: 2.09 - 1.97 1.00 2846 113 0.0971 0.1223 4.3439 4.4675| | 7: 1.97 - 1.87 1.00 2787 165 0.1000 0.1219 4.0796 4.1842| | 8: 1.87 - 1.79 1.00 2789 144 0.1004 0.1204 3.9905 4.0689| | 9: 1.79 - 1.72 1.00 2745 138 0.0949 0.1341 3.7148 3.9399| | 10: 1.72 - 1.66 1.00 2831 160 0.0983 0.1236 3.6323 3.7544| | 11: 1.66 - 1.61 1.00 2712 147 0.0948 0.1124 3.5663 3.6132| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1141 3.3401 3.4908| | 13: 1.56 - 1.52 1.00 2745 130 0.0974 0.1018 3.3358 3.4166| | 14: 1.52 - 1.48 1.00 2803 134 0.0989 0.1124 3.26 3.3486| | 15: 1.48 - 1.45 1.00 2738 128 0.1002 0.1317 3.1601 3.3044| | 16: 1.45 - 1.42 1.00 2756 161 0.1068 0.1238 3.1478 3.2317| | 17: 1.42 - 1.39 1.00 2785 139 0.1112 0.1290 3.1081 3.2264| | 18: 1.39 - 1.36 1.00 2741 179 0.1135 0.1381 3.0754 3.2703| | 19: 1.36 - 1.34 1.00 2807 134 0.1214 0.1577 3.0908 3.2675| | 20: 1.34 - 1.32 1.00 2696 147 0.1324 0.1470 3.0852 3.1233| | 21: 1.32 - 1.30 1.00 2785 112 0.1419 0.1600 3.0865 3.1473| | 22: 1.29 - 1.27 1.00 2704 152 0.1474 0.1896 3.0839 3.2942| | 23: 1.27 - 1.26 1.00 2802 156 0.1563 0.1887 3.1008 3.225| | 24: 1.26 - 1.24 1.00 2744 132 0.1621 0.1783 3.094 3.1898| | 25: 1.24 - 1.22 1.00 2733 148 0.1777 0.2312 3.1056 3.294| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1817 3.119 3.2086| | 27: 1.21 - 1.19 1.00 2814 148 0.2005 0.2092 3.1382 3.1524| | 28: 1.19 - 1.18 1.00 2671 147 0.2152 0.2359 3.1403 3.173| | 29: 1.18 - 1.16 1.00 2800 134 0.2212 0.2363 3.1249 3.2163| | 30: 1.16 - 1.15 1.00 2739 148 0.2375 0.2463 3.1136 3.1591| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 8.62 1.00 0.97 5823.12| | 2: 3.57 - 2.84 2888 124 0.92 12.77 1.01 0.97 5823.12| | 3: 2.83 - 2.48 2820 163 0.89 16.88 0.99 0.97 4896.64| | 4: 2.47 - 2.25 2825 136 0.91 14.17 1.00 0.98 2507.54| | 5: 2.25 - 2.09 2756 127 0.90 16.41 1.01 0.98 2507.54| | 6: 2.09 - 1.97 2846 113 0.92 13.49 1.02 0.97 1499.57| | 7: 1.97 - 1.87 2787 165 0.94 10.99 1.02 0.97 639.92| | 8: 1.87 - 1.79 2789 144 0.91 14.63 1.00 0.97 639.92| | 9: 1.79 - 1.72 2745 138 0.93 11.59 0.99 0.97 344.63| | 10: 1.72 - 1.66 2831 160 0.93 12.40 0.98 0.97 285.49| | 11: 1.66 - 1.61 2712 147 0.93 12.99 0.98 0.97 272.34| | 12: 1.61 - 1.56 2773 144 0.95 9.63 0.99 0.97 148.31| | 13: 1.56 - 1.52 2745 130 0.94 11.13 1.02 0.97 148.31| | 14: 1.52 - 1.48 2803 134 0.94 11.32 1.02 0.97 132.06| | 15: 1.48 - 1.45 2738 128 0.95 10.32 1.02 0.98 102.31| | 16: 1.45 - 1.42 2756 161 0.94 11.51 1.02 0.98 102.31| | 17: 1.42 - 1.39 2785 139 0.94 11.40 1.01 0.98 92.37| | 18: 1.39 - 1.36 2741 179 0.94 11.62 1.01 0.98 86.62| | 19: 1.36 - 1.34 2807 134 0.94 12.22 1.00 0.98 86.62| | 20: 1.34 - 1.32 2696 147 0.94 12.40 0.99 0.97 81.65| | 21: 1.32 - 1.30 2785 112 0.94 13.33 0.99 0.97 81.30| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.99 0.96 81.58| | 23: 1.27 - 1.26 2802 156 0.92 14.87 0.98 0.95 83.01| | 24: 1.26 - 1.24 2744 132 0.92 14.98 0.97 0.95 83.01| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.58| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.03 0.93 86.33| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.33| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 89.37| | 29: 1.18 - 1.16 2800 134 0.88 20.48 0.99 0.93 90.52| | 30: 1.16 - 1.15 2739 148 0.86 21.92 0.98 0.93 90.52| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.30 max = 5823.12 mean = 924.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.96| |phase err.(test): min = 0.00 max = 87.24 mean = 14.01| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1193 0.1357 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1510 0.1509 0.1555 n_refl.: 87577 remove outliers: r(all,work,free)=0.1510 0.1509 0.1555 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1507 0.1506 0.1553 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1193 0.1358 n_refl.: 87577 remove outliers: r(all,work,free)=0.1200 0.1192 0.1358 n_refl.: 87574 ======================== 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 87.50 79 5 0.4059 285.837 251.199 0.435 1.000 0.302 11.894-9.307 94.12 92 4 0.2439 477.656 461.531 0.861 1.002 0.233 9.237-7.194 97.73 208 7 0.2599 382.319 376.054 0.909 1.002 0.159 7.162-5.571 100.00 427 22 0.2229 293.606 282.101 0.899 1.002 0.140 5.546-4.326 100.00 867 58 0.1180 403.048 398.714 0.951 1.002 0.113 4.315-3.360 100.00 1859 96 0.0983 383.301 380.199 0.992 1.002 0.099 3.356-2.611 100.00 3867 181 0.1174 251.809 249.764 1.001 1.001 0.034 2.608-2.026 99.99 8198 413 0.1044 166.926 165.923 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0968 81.518 81.733 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1222 36.148 35.771 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2116 22.776 21.401 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0377 ================= 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 : 0.2606 0.1971 0.083 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1785 0.083 5.295 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1785 0.083 5.295 9.0 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1792 0.083 5.295 9.0 119.5 20.1 258 0.007 1_weight: 0.1643 0.1792 0.083 5.295 9.0 119.5 20.1 258 0.007 1_xyzrec: 0.1211 0.1462 0.008 0.983 9.0 119.5 20.1 258 0.127 1_adp: 0.1245 0.1541 0.008 0.983 8.6 118.8 21.1 258 0.127 1_regHadp: 0.1249 0.1546 0.008 0.983 8.6 118.8 21.1 258 0.127 1_occ: 0.1249 0.1553 0.008 0.983 8.6 118.8 21.1 258 0.127 2_bss: 0.1247 0.1547 0.008 0.983 8.7 118.9 21.3 258 0.127 2_settarget: 0.1247 0.1547 0.008 0.983 8.7 118.9 21.3 258 0.127 2_updatecdl: 0.1247 0.1547 0.008 0.984 8.7 118.9 21.3 258 0.127 2_nqh: 0.1247 0.1547 0.008 0.984 8.7 118.9 21.3 258 0.127 2_sol: 0.1234 0.1501 0.008 0.984 8.7 118.9 23.5 429 n/a 2_weight: 0.1234 0.1501 0.008 0.984 8.7 118.9 23.5 429 n/a 2_xyzrec: 0.1232 0.1530 0.007 0.883 8.7 118.9 23.5 429 n/a 2_adp: 0.1205 0.1500 0.007 0.883 8.7 114.0 23.1 429 n/a 2_regHadp: 0.1205 0.1499 0.007 0.883 8.7 114.0 23.1 429 n/a 2_occ: 0.1207 0.1486 0.007 0.883 8.7 114.0 23.1 429 n/a 3_bss: 0.1203 0.1485 0.007 0.883 8.7 114.1 23.1 429 n/a 3_settarget: 0.1203 0.1485 0.007 0.883 8.7 114.1 23.1 429 n/a 3_updatecdl: 0.1203 0.1485 0.007 0.884 8.7 114.1 23.1 429 n/a 3_nqh: 0.1203 0.1485 0.007 0.884 8.7 114.1 23.1 429 n/a 3_sol: 0.1226 0.1486 0.007 0.884 8.7 114.1 22.1 460 n/a 3_weight: 0.1226 0.1486 0.007 0.884 8.7 114.1 22.1 460 n/a 3_xyzrec: 0.1238 0.1449 0.006 0.917 8.7 114.1 22.1 460 n/a 3_adp: 0.1219 0.1403 0.006 0.917 9.2 109.1 21.8 460 n/a 3_regHadp: 0.1220 0.1404 0.006 0.917 9.2 109.1 21.8 460 n/a 3_occ: 0.1214 0.1403 0.006 0.917 9.2 109.1 21.8 460 n/a 4_bss: 0.1201 0.1375 0.006 0.917 9.2 109.0 21.8 460 n/a 4_settarget: 0.1201 0.1375 0.006 0.917 9.2 109.0 21.8 460 n/a 4_updatecdl: 0.1201 0.1375 0.006 0.916 9.2 109.0 21.8 460 n/a 4_nqh: 0.1201 0.1375 0.006 0.916 9.2 109.0 21.8 460 n/a 4_sol: 0.1190 0.1350 0.006 0.916 9.2 109.0 21.6 454 n/a 4_weight: 0.1190 0.1350 0.006 0.916 9.2 109.0 21.6 454 n/a 4_xyzrec: 0.1197 0.1369 0.006 0.954 9.2 109.0 21.6 454 n/a 4_adp: 0.1190 0.1370 0.006 0.954 9.3 105.4 21.4 454 n/a 4_regHadp: 0.1191 0.1371 0.006 0.954 9.3 105.4 21.4 454 n/a 4_occ: 0.1187 0.1368 0.006 0.954 9.3 105.4 21.4 454 n/a 5_bss: 0.1183 0.1369 0.006 0.954 9.3 105.4 21.4 454 n/a 5_settarget: 0.1183 0.1369 0.006 0.954 9.3 105.4 21.4 454 n/a 5_updatecdl: 0.1183 0.1369 0.006 0.956 9.3 105.4 21.4 454 n/a 5_setrh: 0.1184 0.1369 0.006 0.956 9.3 105.4 21.4 454 n/a 5_nqh: 0.1184 0.1369 0.006 0.956 9.3 105.4 21.4 454 n/a 5_sol: 0.1177 0.1345 0.006 0.956 9.3 105.4 21.4 459 n/a 5_weight: 0.1177 0.1345 0.006 0.956 9.3 105.4 21.4 459 n/a 5_xyzrec: 0.1200 0.1367 0.007 1.052 9.3 105.4 21.4 459 n/a 5_adp: 0.1196 0.1360 0.007 1.052 9.3 101.3 21.2 459 n/a 5_regHadp: 0.1196 0.1360 0.007 1.052 9.3 101.3 21.2 459 n/a 5_occ: 0.1193 0.1357 0.007 1.052 9.3 101.3 21.2 459 n/a end: 0.1192 0.1358 0.007 1.052 9.3 101.3 21.1 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8831905_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_8831905_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.7500 Refinement macro-cycles (run) : 3484.8900 Write final files (write_after_run_outputs) : 61.7900 Total : 3551.4300 Total CPU time: 59.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:43 PST -0800 (1735452703.38 s) Start R-work = 0.1638, R-free = 0.1785 Final R-work = 0.1192, R-free = 0.1358 =============================================================================== Job complete usr+sys time: 3682.50 seconds wall clock time: 66 minutes 51.47 seconds (4011.47 seconds total)