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_6369642.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_6369642.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6369642.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.14, per 1000 atoms: 0.63 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 295.7 milliseconds Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 537 0.91 - 1.18: 1122 1.18 - 1.44: 687 1.44 - 1.71: 785 1.71 - 1.97: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 1.354 1.113 0.241 1.10e-02 8.26e+03 4.82e+02 bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.992 0.244 1.17e-02 7.31e+03 4.37e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.223 0.236 1.24e-02 6.50e+03 3.62e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.459 1.683 -0.224 1.20e-02 6.94e+03 3.49e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.233 0.223 1.23e-02 6.61e+03 3.29e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 3164 4.63 - 9.26: 1869 9.26 - 13.89: 611 13.89 - 18.52: 118 18.52 - 23.15: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 122.14 -16.04 1.00e+00 1.00e+00 2.57e+02 angle pdb=" CA SER A 3 " pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 121.56 140.37 -18.81 1.21e+00 6.83e-01 2.42e+02 angle pdb=" O GLU A 116 " pdb=" C GLU A 116 " pdb=" N ILE A 117 " ideal model delta sigma weight residual 122.55 140.44 -17.89 1.24e+00 6.50e-01 2.08e+02 angle pdb=" O GLY A 174 " pdb=" C GLY A 174 " pdb=" N ALYS A 175 " ideal model delta sigma weight residual 122.87 137.51 -14.64 1.04e+00 9.25e-01 1.98e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.22 138.07 -15.85 1.17e+00 7.31e-01 1.83e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 934 16.81 - 33.61: 119 33.61 - 50.41: 37 50.41 - 67.21: 18 67.21 - 84.02: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ALA A 61 " pdb=" C ALA A 61 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 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 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.226: 118 0.226 - 0.447: 65 0.447 - 0.668: 37 0.668 - 0.889: 17 0.889 - 1.110: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.66e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.111 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.086 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.076 2.00e-02 2.50e+03 6.67e-02 1.00e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.109 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1365 2.36 - 2.92: 8328 2.92 - 3.48: 10431 3.48 - 4.04: 15189 4.04 - 4.60: 21318 Nonbonded interactions: 56631 Sorted by model distance: nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.802 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.805 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.835 2.100 nonbonded pdb=" H ALA A 6 " pdb=" O LYS A 32 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.849 2.100 ... (remaining 56626 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_6369642_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= 0.2604 r_free= 0.1958 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790727 | | target function (ml) not normalized (work): 232484.308406 | | target function (ml) not normalized (free): 11785.465222 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3031 0.2057 7.0394 4.9375| | 2: 3.57 - 2.84 1.00 2876 122 0.2462 0.1844 4.3559 4.3354| | 3: 2.84 - 2.48 1.00 2833 165 0.2337 0.1779 4.1303 4.1655| | 4: 2.47 - 2.25 1.00 2825 136 0.2299 0.1585 3.8352 3.8668| | 5: 2.25 - 2.09 1.00 2756 127 0.2486 0.1602 3.8016 3.8115| | 6: 2.09 - 1.97 1.00 2846 113 0.2520 0.1825 3.4686 3.581| | 7: 1.97 - 1.87 1.00 2787 165 0.2503 0.1901 3.146 3.2025| | 8: 1.87 - 1.79 1.00 2789 144 0.2509 0.1934 3.061 3.1502| | 9: 1.79 - 1.72 1.00 2745 138 0.2421 0.1984 2.9194 3.0003| | 10: 1.72 - 1.66 1.00 2789 158 0.2372 0.1944 2.804 2.8471| | 11: 1.66 - 1.61 1.00 2740 147 0.2517 0.1770 2.7628 2.7636| | 12: 1.61 - 1.56 1.00 2787 146 0.2481 0.1674 2.6303 2.5209| | 13: 1.56 - 1.52 1.00 2745 130 0.2542 0.1762 2.5611 2.5878| | 14: 1.52 - 1.48 1.00 2803 134 0.2647 0.1898 2.5052 2.5132| | 15: 1.48 - 1.45 1.00 2738 128 0.2601 0.1938 2.4251 2.4351| | 16: 1.45 - 1.42 1.00 2756 161 0.2679 0.2227 2.3852 2.4538| | 17: 1.42 - 1.39 1.00 2785 139 0.2672 0.2212 2.3329 2.4077| | 18: 1.39 - 1.36 1.00 2741 179 0.2638 0.2093 2.255 2.2881| | 19: 1.36 - 1.34 1.00 2807 134 0.2621 0.2216 2.2374 2.2801| | 20: 1.34 - 1.32 1.00 2696 147 0.2692 0.2151 2.2253 2.1389| | 21: 1.32 - 1.30 1.00 2785 112 0.2673 0.2210 2.1583 2.1401| | 22: 1.29 - 1.27 1.00 2704 152 0.2769 0.2476 2.1452 2.1557| | 23: 1.27 - 1.26 1.00 2802 156 0.2784 0.2763 2.1013 2.282| | 24: 1.26 - 1.24 1.00 2744 132 0.2752 0.2621 2.0732 2.1892| | 25: 1.24 - 1.22 1.00 2734 148 0.2846 0.2587 2.0413 2.0863| | 26: 1.22 - 1.21 1.00 2727 135 0.2885 0.2212 2.0071 2.031| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2614 1.9974 2.0212| | 28: 1.19 - 1.18 1.00 2671 147 0.2993 0.2719 1.9885 1.9926| | 29: 1.18 - 1.16 1.00 2800 134 0.2900 0.2754 1.9481 1.987| | 30: 1.16 - 1.15 1.00 2740 148 0.3057 0.2872 1.9258 1.9758| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.93 0.76 0.23 1482.75| | 2: 3.57 - 2.84 2876 122 0.80 26.18 1.28 0.23 1482.75| | 3: 2.84 - 2.48 2833 165 0.74 31.95 1.24 0.23 1229.88| | 4: 2.47 - 2.25 2825 136 0.81 25.59 1.25 0.25 573.64| | 5: 2.25 - 2.09 2756 127 0.77 29.37 1.28 0.25 573.64| | 6: 2.09 - 1.97 2846 113 0.84 22.55 1.29 0.25 314.05| | 7: 1.97 - 1.87 2787 165 0.90 16.72 1.27 0.26 92.65| | 8: 1.87 - 1.79 2789 144 0.85 21.44 1.26 0.26 92.65| | 9: 1.79 - 1.72 2745 138 0.88 18.81 1.23 0.25 55.86| | 10: 1.72 - 1.66 2789 158 0.87 20.18 1.21 0.25 48.50| | 11: 1.66 - 1.61 2740 147 0.85 21.54 1.24 0.25 46.65| | 12: 1.61 - 1.56 2787 146 0.89 17.94 1.23 0.25 27.94| | 13: 1.56 - 1.52 2745 130 0.87 20.06 1.23 0.25 27.94| | 14: 1.52 - 1.48 2803 134 0.87 20.26 1.25 0.25 24.95| | 15: 1.48 - 1.45 2738 128 0.87 19.62 1.23 0.25 19.46| | 16: 1.45 - 1.42 2756 161 0.86 20.95 1.24 0.25 19.46| | 17: 1.42 - 1.39 2785 139 0.88 19.92 1.24 0.25 16.73| | 18: 1.39 - 1.36 2741 179 0.87 20.76 1.22 0.25 15.15| | 19: 1.36 - 1.34 2807 134 0.86 21.50 1.21 0.25 15.15| | 20: 1.34 - 1.32 2696 147 0.87 20.27 1.20 0.25 12.78| | 21: 1.32 - 1.30 2785 112 0.86 21.58 1.20 0.25 12.62| | 22: 1.29 - 1.27 2704 152 0.86 21.97 1.21 0.25 12.38| | 23: 1.27 - 1.26 2802 156 0.86 22.01 1.22 0.24 11.18| | 24: 1.26 - 1.24 2744 132 0.85 22.87 1.20 0.24 11.18| | 25: 1.24 - 1.22 2734 148 0.84 23.72 1.20 0.24 10.58| | 26: 1.22 - 1.21 2727 135 0.84 23.98 1.21 0.24 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.84 1.21 0.24 9.93| | 28: 1.19 - 1.18 2671 147 0.83 24.90 1.18 0.23 9.15| | 29: 1.18 - 1.16 2800 134 0.83 24.81 1.17 0.23 8.86| | 30: 1.16 - 1.15 2740 148 0.81 26.76 1.16 0.23 8.86| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.86 max = 1482.75 mean = 215.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.40| |phase err.(test): min = 0.00 max = 89.99 mean = 22.49| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.244 1557 Z= 5.707 Angle : 5.299 18.810 2118 Z= 3.727 Chirality : 0.381 1.110 243 Planarity : 0.029 0.139 284 Dihedral : 14.119 84.017 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % 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: -2.05 (0.47), residues: 224 helix: -2.31 (0.38), residues: 102 sheet: -0.68 (0.86), residues: 28 loop : -0.12 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.030 ARG A 28 TYR 0.108 0.055 TYR A 141 PHE 0.140 0.044 PHE A 119 HIS 0.068 0.038 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= 0.2604 r_free= 0.1958 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790727 | | target function (ml) not normalized (work): 232484.308406 | | target function (ml) not normalized (free): 11785.465222 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2563 0.2604 0.1958 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2563 0.2604 0.1958 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1958 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2002 0.2006 0.1972 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1648 0.1642 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1648 0.1642 0.1772 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 0.3835 386.439 357.732 0.723 0.930 0.407 11.894-9.307 99.02 97 4 0.1793 613.840 592.862 0.999 0.931 0.390 9.237-7.194 100.00 213 7 0.2182 502.045 491.362 1.030 0.931 0.362 7.162-5.571 100.00 427 22 0.2168 376.757 365.224 1.006 0.932 0.295 5.546-4.326 100.00 867 58 0.1267 517.194 511.504 1.043 0.932 0.250 4.315-3.360 100.00 1859 96 0.1158 491.855 487.188 1.085 0.932 0.189 3.356-2.611 100.00 3867 181 0.1457 323.124 319.649 1.079 0.931 0.099 2.608-2.026 99.99 8198 413 0.1362 214.201 212.169 1.081 0.931 0.000 2.025-1.573 100.00 17313 902 0.1656 104.605 103.824 1.084 0.930 0.000 1.573-1.221 100.00 36679 1900 0.2060 46.386 45.135 1.077 0.929 0.000 1.221-1.150 99.97 13689 708 0.2563 29.226 27.044 1.051 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0404 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1642 r_free=0.1772 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 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1645 r_free=0.1779 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.395667 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.603038 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 0.1210 0.1464 0.0253 0.007 0.9 1.0 0.5 0.0 0 12.698 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 14.64 2.53 3.013 19.035 2011.603 0.017 12.40 15.39 2.99 3.173 19.492 2011.603 0.016 Individual atomic B min max mean iso aniso Overall: 8.57 118.65 20.93 2.88 0 1785 Protein: 8.57 118.65 17.81 2.88 0 1519 Water: 10.98 114.64 39.02 N/A 0 258 Other: 22.77 36.20 29.09 N/A 0 8 Chain A: 8.57 118.65 20.93 N/A 0 1785 Histogram: Values Number of atoms 8.57 - 19.57 1211 19.57 - 30.58 227 30.58 - 41.59 167 41.59 - 52.60 99 52.60 - 63.61 52 63.61 - 74.62 17 74.62 - 85.63 5 85.63 - 96.64 4 96.64 - 107.64 0 107.64 - 118.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1241 r_free=0.1539 r_work=0.1245 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1245 r_free = 0.1544 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 = 0.1245 r_free = 0.1547 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1245 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015349 | | target function (ls_wunit_k1) not normalized (work): 1278.551662 | | target function (ls_wunit_k1) not normalized (free): 114.404645 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1260 0.1245 0.1547 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1697 0.1696 0.1770 n_refl.: 87593 remove outliers: r(all,work,free)=0.1697 0.1696 0.1770 n_refl.: 87593 overall B=0.15 to atoms: r(all,work,free)=0.1722 0.1721 0.1788 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1542 n_refl.: 87593 remove outliers: r(all,work,free)=0.1259 0.1244 0.1542 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 0.3589 300.016 279.311 0.638 1.002 0.380 11.894-9.307 99.02 97 4 0.1589 480.610 469.087 0.907 1.003 0.380 9.237-7.194 100.00 213 7 0.1824 393.079 388.151 0.949 1.003 0.340 7.162-5.571 100.00 427 22 0.1721 294.984 289.891 0.925 1.003 0.290 5.546-4.326 100.00 867 58 0.0921 404.941 402.180 0.950 1.003 0.209 4.315-3.360 100.00 1859 96 0.0778 385.101 384.176 0.995 1.003 0.189 3.356-2.611 100.00 3867 181 0.1016 252.992 252.358 1.000 1.002 0.119 2.608-2.026 99.99 8198 413 0.0975 167.710 167.117 1.009 1.002 0.000 2.025-1.573 100.00 17313 902 0.1212 81.901 82.085 1.016 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1657 36.318 35.771 1.005 0.998 0.000 1.221-1.150 99.97 13689 708 0.2362 22.883 21.385 0.968 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0598 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1244 r_free=0.1542 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** A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1244 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1244 r_free=0.1542 | n_water=258 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1254 r_free=0.1540 | n_water=252 | time (s): 25.860 (total time: 28.410) Filter (q & B) r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 3.760 (total time: 32.170) Compute maps r_work=0.1257 r_free=0.1540 | n_water=249 | time (s): 1.920 (total time: 34.090) Filter (map) r_work=0.1268 r_free=0.1548 | n_water=237 | time (s): 3.880 (total time: 37.970) Find peaks r_work=0.1268 r_free=0.1548 | n_water=237 | time (s): 0.730 (total time: 38.700) Add new water r_work=0.1424 r_free=0.1693 | n_water=447 | time (s): 3.820 (total time: 42.520) Refine new water occ: r_work=0.1337 r_free=0.1553 adp: r_work=0.1255 r_free=0.1508 occ: r_work=0.1268 r_free=0.1503 adp: r_work=0.1232 r_free=0.1487 occ: r_work=0.1235 r_free=0.1478 adp: r_work=0.1225 r_free=0.1479 ADP+occupancy (water only), MIN, final r_work=0.1225 r_free=0.1479 r_work=0.1225 r_free=0.1479 | n_water=447 | time (s): 89.470 (total time: 131.990) Filter (q & B) r_work=0.1231 r_free=0.1485 | n_water=426 | time (s): 3.990 (total time: 135.980) Filter (dist only) r_work=0.1231 r_free=0.1485 | n_water=426 | time (s): 40.390 (total time: 176.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.176488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1589.422410 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 0.1227 0.1513 0.0287 0.007 0.9 1.9 0.5 0.0 0 13.088 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 15.13 2.87 3.781 23.114 1589.422 0.015 11.95 14.80 2.85 4.173 22.933 1589.422 0.015 Individual atomic B min max mean iso aniso Overall: 8.71 114.64 23.11 2.62 189 1764 Protein: 8.71 114.64 17.62 2.62 0 1519 Water: 10.92 72.76 42.56 N/A 189 237 Other: 25.70 37.77 30.78 N/A 0 8 Chain A: 8.71 114.64 20.34 N/A 0 1764 Chain S: 15.59 71.26 49.02 N/A 189 0 Histogram: Values Number of atoms 8.71 - 19.30 1206 19.30 - 29.90 251 29.90 - 40.49 182 40.49 - 51.08 147 51.08 - 61.68 104 61.68 - 72.27 52 72.27 - 82.86 5 82.86 - 93.46 3 93.46 - 104.05 1 104.05 - 114.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1481 r_work=0.1195 r_free=0.1481 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1481 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1481 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 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= 0.1196 r_free= 0.1481 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013865 | | target function (ls_wunit_k1) not normalized (work): 1154.907149 | | target function (ls_wunit_k1) not normalized (free): 103.360344 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1196 0.1481 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1599 0.1594 0.1720 n_refl.: 87592 remove outliers: r(all,work,free)=0.1599 0.1594 0.1720 n_refl.: 87592 overall B=0.05 to atoms: r(all,work,free)=0.1606 0.1602 0.1724 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1193 0.1480 n_refl.: 87592 remove outliers: r(all,work,free)=0.1206 0.1192 0.1480 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 0.3383 298.571 273.713 0.602 1.002 0.370 11.894-9.307 99.02 97 4 0.1503 480.610 478.526 0.915 1.003 0.360 9.237-7.194 100.00 213 7 0.1686 393.079 393.805 0.978 1.003 0.280 7.162-5.571 100.00 427 22 0.1504 294.984 290.247 0.939 1.003 0.229 5.546-4.326 100.00 867 58 0.0845 404.941 401.945 0.957 1.003 0.210 4.315-3.360 100.00 1859 96 0.0699 385.101 384.377 1.001 1.002 0.210 3.356-2.611 100.00 3867 181 0.0955 252.992 252.369 1.010 1.002 0.170 2.608-2.026 99.99 8198 413 0.0951 167.710 167.340 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1176 81.901 82.109 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1606 36.318 35.822 1.014 0.998 0.000 1.221-1.150 99.97 13689 708 0.2332 22.883 21.413 0.974 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0724 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1480 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=0.1192 r_free=0.1480 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1480 | n_water=426 | time (s): 1.550 (total time: 1.550) Filter (dist) r_work=0.1192 r_free=0.1480 | n_water=424 | time (s): 37.500 (total time: 39.050) Filter (q & B) r_work=0.1193 r_free=0.1482 | n_water=423 | time (s): 3.540 (total time: 42.590) Compute maps r_work=0.1193 r_free=0.1482 | n_water=423 | time (s): 1.420 (total time: 44.010) Filter (map) r_work=0.1232 r_free=0.1471 | n_water=292 | time (s): 2.980 (total time: 46.990) Find peaks r_work=0.1232 r_free=0.1471 | n_water=292 | time (s): 0.620 (total time: 47.610) Add new water r_work=0.1367 r_free=0.1587 | n_water=488 | time (s): 3.160 (total time: 50.770) Refine new water occ: r_work=0.1263 r_free=0.1510 adp: r_work=0.1263 r_free=0.1511 occ: r_work=0.1239 r_free=0.1491 adp: r_work=0.1237 r_free=0.1491 occ: r_work=0.1224 r_free=0.1477 adp: r_work=0.1216 r_free=0.1474 ADP+occupancy (water only), MIN, final r_work=0.1216 r_free=0.1474 r_work=0.1216 r_free=0.1474 | n_water=488 | time (s): 220.310 (total time: 271.080) Filter (q & B) r_work=0.1221 r_free=0.1473 | n_water=452 | time (s): 3.710 (total time: 274.790) Filter (dist only) r_work=0.1221 r_free=0.1471 | n_water=451 | time (s): 40.330 (total time: 315.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.013441 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.822917 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 0.1223 0.1440 0.0217 0.006 0.9 1.6 0.5 0.0 0 1.007 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 14.40 2.17 3.620 22.145 52.823 3.725 12.11 13.93 1.83 4.158 21.940 52.823 3.654 Individual atomic B min max mean iso aniso Overall: 9.24 109.92 21.73 2.34 216 1762 Protein: 9.24 109.92 17.16 2.34 0 1519 Water: 11.39 71.52 37.02 N/A 216 235 Other: 21.02 33.34 27.05 N/A 0 8 Chain A: 9.24 109.92 19.85 N/A 0 1762 Chain S: 16.01 64.80 37.06 N/A 216 0 Histogram: Values Number of atoms 9.24 - 19.31 1240 19.31 - 29.38 266 29.38 - 39.45 220 39.45 - 49.51 145 49.51 - 59.58 73 59.58 - 69.65 21 69.65 - 79.72 7 79.72 - 89.78 3 89.78 - 99.85 1 99.85 - 109.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1393 r_work=0.1212 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1394 target_work(ml) = 3.654 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1393 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.22 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= 0.1206 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.651928 | | target function (ml) not normalized (work): 304183.650331 | | target function (ml) not normalized (free): 16065.576258 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1206 0.1393 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1534 0.1531 0.1608 n_refl.: 87590 remove outliers: r(all,work,free)=0.1534 0.1531 0.1608 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1534 0.1531 0.1608 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1195 0.1372 n_refl.: 87590 remove outliers: r(all,work,free)=0.1199 0.1190 0.1372 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3944 292.678 269.103 0.478 0.998 0.293 11.894-9.307 93.14 91 4 0.2308 470.363 454.212 0.859 1.000 0.273 9.237-7.194 98.64 210 7 0.2406 385.595 385.455 0.952 1.000 0.170 7.162-5.571 100.00 427 22 0.2049 294.984 284.072 0.916 1.001 0.165 5.546-4.326 100.00 867 58 0.1076 404.941 400.258 0.960 1.001 0.160 4.315-3.360 100.00 1859 96 0.0914 385.101 382.615 1.002 1.001 0.160 3.356-2.611 100.00 3867 181 0.1144 252.992 251.196 1.009 1.001 0.062 2.608-2.026 99.99 8198 413 0.1041 167.710 166.851 1.020 1.002 0.000 2.025-1.573 100.00 17313 902 0.1007 81.901 82.092 1.033 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1291 36.318 35.876 1.023 1.002 0.000 1.221-1.150 99.97 13689 708 0.2130 22.883 21.395 0.975 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0002 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1190 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1372 | n_water=451 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1190 r_free=0.1372 | n_water=451 | time (s): 35.110 (total time: 37.450) Filter (q & B) r_work=0.1190 r_free=0.1372 | n_water=451 | time (s): 1.090 (total time: 38.540) Compute maps r_work=0.1190 r_free=0.1372 | n_water=451 | time (s): 1.320 (total time: 39.860) Filter (map) r_work=0.1212 r_free=0.1388 | n_water=324 | time (s): 3.460 (total time: 43.320) Find peaks r_work=0.1212 r_free=0.1388 | n_water=324 | time (s): 0.530 (total time: 43.850) Add new water r_work=0.1279 r_free=0.1437 | n_water=498 | time (s): 3.110 (total time: 46.960) Refine new water occ: r_work=0.1207 r_free=0.1384 adp: r_work=0.1208 r_free=0.1384 occ: r_work=0.1191 r_free=0.1374 adp: r_work=0.1190 r_free=0.1373 occ: r_work=0.1180 r_free=0.1367 adp: r_work=0.1176 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1176 r_free=0.1364 r_work=0.1176 r_free=0.1364 | n_water=498 | time (s): 161.110 (total time: 208.070) Filter (q & B) r_work=0.1184 r_free=0.1366 | n_water=457 | time (s): 3.170 (total time: 211.240) Filter (dist only) r_work=0.1190 r_free=0.1364 | n_water=455 | time (s): 40.960 (total time: 252.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.885858 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 49.024201 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 0.1195 0.1378 0.0183 0.006 0.9 1.6 0.5 0.0 0 0.943 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.78 1.83 3.421 21.562 49.024 3.642 11.85 13.75 1.90 3.695 21.476 49.024 3.629 Individual atomic B min max mean iso aniso Overall: 9.25 105.90 21.46 2.18 224 1758 Protein: 9.25 105.90 16.97 2.18 0 1519 Water: 11.54 70.60 36.38 N/A 224 231 Other: 20.54 30.79 25.86 N/A 0 8 Chain A: 9.25 105.90 19.57 N/A 0 1758 Chain S: 15.60 65.02 36.33 N/A 224 0 Histogram: Values Number of atoms 9.25 - 18.92 1234 18.92 - 28.58 271 28.58 - 38.25 216 38.25 - 47.91 148 47.91 - 57.57 73 57.57 - 67.24 27 67.24 - 76.90 8 76.90 - 86.57 2 86.57 - 96.23 1 96.23 - 105.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1375 r_work=0.1186 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1376 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1181 r_free = 0.1371 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1181 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627810 | | target function (ml) not normalized (work): 302131.287530 | | target function (ml) not normalized (free): 15977.491133 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1181 0.1371 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1492 0.1490 0.1562 n_refl.: 87578 remove outliers: r(all,work,free)=0.1492 0.1490 0.1562 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1488 0.1561 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1179 0.1370 n_refl.: 87578 remove outliers: r(all,work,free)=0.1187 0.1178 0.1370 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 88.54 80 5 0.4092 284.588 257.005 0.429 0.999 0.285 11.894-9.307 93.14 91 4 0.2374 470.363 450.518 0.834 1.001 0.260 9.237-7.194 98.64 210 7 0.2457 385.595 380.380 0.912 1.002 0.128 7.162-5.571 100.00 427 22 0.2176 294.984 283.763 0.899 1.002 0.123 5.546-4.326 100.00 867 58 0.1143 404.941 400.274 0.951 1.002 0.121 4.315-3.360 100.00 1859 96 0.0933 385.101 382.635 0.994 1.002 0.116 3.356-2.611 100.00 3867 181 0.1151 252.992 251.021 1.001 1.002 0.100 2.608-2.026 99.99 8198 413 0.1024 167.710 166.826 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.0966 81.901 82.187 1.028 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1240 36.318 35.954 1.021 0.999 0.000 1.221-1.150 99.97 13689 708 0.2121 22.883 21.511 0.977 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0332 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1178 r_free=0.1370 After: r_work=0.1178 r_free=0.1370 ================================== NQH flips ================================== r_work=0.1178 r_free=0.1370 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=0.1178 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1370 | n_water=455 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1179 r_free=0.1371 | n_water=454 | time (s): 38.180 (total time: 40.440) Filter (q & B) r_work=0.1179 r_free=0.1371 | n_water=453 | time (s): 2.550 (total time: 42.990) Compute maps r_work=0.1179 r_free=0.1371 | n_water=453 | time (s): 1.290 (total time: 44.280) Filter (map) r_work=0.1205 r_free=0.1374 | n_water=340 | time (s): 2.610 (total time: 46.890) Find peaks r_work=0.1205 r_free=0.1374 | n_water=340 | time (s): 0.560 (total time: 47.450) Add new water r_work=0.1251 r_free=0.1421 | n_water=496 | time (s): 3.190 (total time: 50.640) Refine new water occ: r_work=0.1190 r_free=0.1370 adp: r_work=0.1191 r_free=0.1371 occ: r_work=0.1180 r_free=0.1361 adp: r_work=0.1178 r_free=0.1362 occ: r_work=0.1171 r_free=0.1354 adp: r_work=0.1168 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1168 r_free=0.1354 r_work=0.1168 r_free=0.1354 | n_water=496 | time (s): 197.900 (total time: 248.540) Filter (q & B) r_work=0.1176 r_free=0.1359 | n_water=455 | time (s): 2.790 (total time: 251.330) Filter (dist only) r_work=0.1179 r_free=0.1358 | n_water=452 | time (s): 37.330 (total time: 288.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.908437 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.994567 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1385 0.0182 0.007 1.0 2.2 0.5 0.0 0 0.954 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.85 1.82 3.311 21.294 36.995 3.636 12.04 13.85 1.81 3.345 21.275 36.995 3.635 Individual atomic B min max mean iso aniso Overall: 9.31 104.86 21.33 2.12 222 1757 Protein: 9.31 104.86 16.92 2.12 0 1519 Water: 11.53 70.48 36.10 N/A 222 230 Other: 20.09 30.18 25.63 N/A 0 8 Chain A: 9.31 104.86 19.51 N/A 0 1757 Chain S: 15.42 59.48 35.78 N/A 222 0 Histogram: Values Number of atoms 9.31 - 18.87 1229 18.87 - 28.42 281 28.42 - 37.98 211 37.98 - 47.53 146 47.53 - 57.08 71 57.08 - 66.64 27 66.64 - 76.19 9 76.19 - 85.75 2 85.75 - 95.30 1 95.30 - 104.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1385 r_work=0.1204 r_free=0.1385 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1385 target_work(ml) = 3.635 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1384 target_work(ml) = 3.634 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1201 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.634001 | | target function (ml) not normalized (work): 302639.577885 | | target function (ml) not normalized (free): 15988.531917 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1414 0.1493 5.6845 5.6671| | 2: 3.57 - 2.84 1.00 2888 124 0.1114 0.1397 5.2053 5.2581| | 3: 2.83 - 2.48 1.00 2820 163 0.1212 0.1307 5.0158 5.0425| | 4: 2.47 - 2.25 1.00 2825 136 0.1028 0.1146 4.7161 4.7756| | 5: 2.25 - 2.09 1.00 2756 127 0.0998 0.1067 4.6604 4.7237| | 6: 2.09 - 1.97 1.00 2846 113 0.0980 0.1175 4.3672 4.4909| | 7: 1.97 - 1.87 1.00 2787 165 0.0995 0.1225 4.0836 4.2004| | 8: 1.87 - 1.79 1.00 2789 144 0.1033 0.1256 4.0017 4.094| | 9: 1.79 - 1.72 1.00 2745 138 0.0972 0.1304 3.7307 3.8866| | 10: 1.72 - 1.66 1.00 2831 160 0.1021 0.1292 3.6497 3.7947| | 11: 1.66 - 1.61 1.00 2712 147 0.0985 0.1129 3.5845 3.6267| | 12: 1.61 - 1.56 1.00 2773 144 0.0948 0.1161 3.3727 3.4738| | 13: 1.56 - 1.52 1.00 2745 130 0.0999 0.1080 3.3549 3.4417| | 14: 1.52 - 1.48 1.00 2803 134 0.1006 0.1123 3.2773 3.3561| | 15: 1.48 - 1.45 1.00 2738 128 0.1028 0.1290 3.1859 3.3046| | 16: 1.45 - 1.42 1.00 2756 161 0.1088 0.1298 3.1686 3.2784| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1350 3.134 3.2621| | 18: 1.39 - 1.36 1.00 2741 179 0.1170 0.1416 3.1022 3.29| | 19: 1.36 - 1.34 1.00 2807 134 0.1230 0.1638 3.1084 3.2984| | 20: 1.34 - 1.32 1.00 2696 147 0.1331 0.1442 3.1002 3.1324| | 21: 1.32 - 1.30 1.00 2785 112 0.1424 0.1662 3.0981 3.1849| | 22: 1.29 - 1.27 1.00 2704 152 0.1486 0.1966 3.0968 3.2902| | 23: 1.27 - 1.26 1.00 2802 156 0.1596 0.1860 3.1169 3.2166| | 24: 1.26 - 1.24 1.00 2744 132 0.1640 0.1778 3.1068 3.1928| | 25: 1.24 - 1.22 1.00 2733 148 0.1804 0.2337 3.1189 3.3| | 26: 1.22 - 1.21 1.00 2727 135 0.1877 0.1786 3.1336 3.2073| | 27: 1.21 - 1.19 1.00 2814 148 0.2020 0.2112 3.1482 3.1543| | 28: 1.19 - 1.18 1.00 2671 147 0.2151 0.2309 3.1458 3.1647| | 29: 1.18 - 1.16 1.00 2800 134 0.2226 0.2381 3.1356 3.2289| | 30: 1.16 - 1.15 1.00 2739 148 0.2384 0.2520 3.123 3.1779| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.10 1.00 0.98 6453.57| | 2: 3.57 - 2.84 2888 124 0.92 13.43 1.01 0.98 6453.57| | 3: 2.83 - 2.48 2820 163 0.89 17.58 0.99 0.98 5407.46| | 4: 2.47 - 2.25 2825 136 0.91 14.73 1.00 0.98 2709.91| | 5: 2.25 - 2.09 2756 127 0.89 16.99 1.01 0.98 2709.91| | 6: 2.09 - 1.97 2846 113 0.91 13.76 1.02 0.98 1588.95| | 7: 1.97 - 1.87 2787 165 0.94 10.84 1.02 0.98 632.92| | 8: 1.87 - 1.79 2789 144 0.91 14.41 1.00 0.98 632.92| | 9: 1.79 - 1.72 2745 138 0.93 11.47 0.98 0.98 345.05| | 10: 1.72 - 1.66 2831 160 0.93 12.36 0.98 0.98 287.40| | 11: 1.66 - 1.61 2712 147 0.93 12.95 0.98 0.98 274.34| | 12: 1.61 - 1.56 2773 144 0.95 9.59 0.99 0.98 151.19| | 13: 1.56 - 1.52 2745 130 0.94 11.20 1.02 0.98 151.19| | 14: 1.52 - 1.48 2803 134 0.94 11.37 1.02 0.98 135.14| | 15: 1.48 - 1.45 2738 128 0.95 10.52 1.01 0.99 105.75| | 16: 1.45 - 1.42 2756 161 0.94 11.67 1.01 0.99 105.75| | 17: 1.42 - 1.39 2785 139 0.94 11.58 1.01 0.99 95.99| | 18: 1.39 - 1.36 2741 179 0.94 11.96 1.01 0.99 90.35| | 19: 1.36 - 1.34 2807 134 0.94 12.51 1.00 0.99 90.35| | 20: 1.34 - 1.32 2696 147 0.94 12.60 0.99 0.97 84.74| | 21: 1.32 - 1.30 2785 112 0.93 13.56 0.98 0.97 84.35| | 22: 1.29 - 1.27 2704 152 0.93 13.99 0.98 0.97 84.43| | 23: 1.27 - 1.26 2802 156 0.92 14.98 0.97 0.95 84.82| | 24: 1.26 - 1.24 2744 132 0.92 15.10 0.97 0.95 84.82| | 25: 1.24 - 1.22 2733 148 0.91 16.49 0.96 0.94 86.06| | 26: 1.22 - 1.21 2727 135 0.90 18.19 1.02 0.94 87.43| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.94 87.43| | 28: 1.19 - 1.18 2671 147 0.88 20.28 1.01 0.93 90.50| | 29: 1.18 - 1.16 2800 134 0.88 20.55 0.99 0.93 91.66| | 30: 1.16 - 1.15 2739 148 0.86 21.93 0.98 0.93 91.66| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 84.35 max = 6453.57 mean = 1003.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 14.13| |phase err.(test): min = 0.00 max = 89.50 mean = 14.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1201 0.1384 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1506 0.1504 0.1574 n_refl.: 87576 remove outliers: r(all,work,free)=0.1506 0.1504 0.1574 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1504 0.1502 0.1573 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1202 0.1388 n_refl.: 87576 remove outliers: r(all,work,free)=0.1210 0.1201 0.1388 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 88.54 80 5 0.4207 284.588 245.546 0.416 1.000 0.287 11.894-9.307 92.16 90 4 0.2432 463.931 447.709 0.825 1.001 0.187 9.237-7.194 98.18 209 7 0.2522 385.124 380.639 0.906 1.002 0.110 7.162-5.571 100.00 427 22 0.2244 294.984 283.993 0.892 1.002 0.110 5.546-4.326 100.00 867 58 0.1180 404.941 399.967 0.951 1.002 0.109 4.315-3.360 100.00 1859 96 0.0986 385.101 382.515 0.995 1.002 0.105 3.356-2.611 100.00 3867 181 0.1177 252.992 251.094 1.002 1.001 0.043 2.608-2.026 99.99 8198 413 0.1041 167.710 166.753 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0991 81.901 82.131 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.318 35.950 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2127 22.883 21.499 0.979 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0281 ================= 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 : 0.2604 0.1958 0.084 5.299 8.8 119.3 19.9 258 0.000 1_bss: 0.1642 0.1772 0.084 5.299 9.0 119.5 20.1 258 0.000 1_settarget: 0.1642 0.1772 0.084 5.299 9.0 119.5 20.1 258 0.000 1_nqh: 0.1645 0.1779 0.084 5.299 9.0 119.5 20.1 258 0.006 1_weight: 0.1645 0.1779 0.084 5.299 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1210 0.1464 0.007 0.950 9.0 119.5 20.1 258 0.129 1_adp: 0.1241 0.1539 0.007 0.950 8.6 118.7 20.9 258 0.129 1_regHadp: 0.1245 0.1544 0.007 0.950 8.6 118.7 20.9 258 0.129 1_occ: 0.1245 0.1547 0.007 0.950 8.6 118.7 20.9 258 0.129 2_bss: 0.1244 0.1542 0.007 0.950 8.7 118.8 21.1 258 0.129 2_settarget: 0.1244 0.1542 0.007 0.950 8.7 118.8 21.1 258 0.129 2_updatecdl: 0.1244 0.1542 0.007 0.956 8.7 118.8 21.1 258 0.129 2_nqh: 0.1244 0.1542 0.007 0.956 8.7 118.8 21.1 258 0.126 2_sol: 0.1231 0.1485 0.007 0.956 8.7 118.8 23.4 426 n/a 2_weight: 0.1231 0.1485 0.007 0.956 8.7 118.8 23.4 426 n/a 2_xyzrec: 0.1227 0.1513 0.007 0.884 8.7 118.8 23.4 426 n/a 2_adp: 0.1195 0.1481 0.007 0.884 8.7 114.6 23.1 426 n/a 2_regHadp: 0.1195 0.1481 0.007 0.884 8.7 114.6 23.1 426 n/a 2_occ: 0.1196 0.1481 0.007 0.884 8.7 114.6 23.1 426 n/a 3_bss: 0.1192 0.1480 0.007 0.884 8.8 114.7 23.2 426 n/a 3_settarget: 0.1192 0.1480 0.007 0.884 8.8 114.7 23.2 426 n/a 3_updatecdl: 0.1192 0.1480 0.007 0.885 8.8 114.7 23.2 426 n/a 3_nqh: 0.1192 0.1480 0.007 0.885 8.8 114.7 23.2 426 n/a 3_sol: 0.1221 0.1471 0.007 0.885 8.8 114.7 22.1 451 n/a 3_weight: 0.1221 0.1471 0.007 0.885 8.8 114.7 22.1 451 n/a 3_xyzrec: 0.1223 0.1440 0.006 0.919 8.8 114.7 22.1 451 n/a 3_adp: 0.1211 0.1393 0.006 0.919 9.2 109.9 21.7 451 n/a 3_regHadp: 0.1212 0.1394 0.006 0.919 9.2 109.9 21.7 451 n/a 3_occ: 0.1206 0.1393 0.006 0.919 9.2 109.9 21.7 451 n/a 4_bss: 0.1190 0.1372 0.006 0.919 9.2 109.9 21.7 451 n/a 4_settarget: 0.1190 0.1372 0.006 0.919 9.2 109.9 21.7 451 n/a 4_updatecdl: 0.1190 0.1372 0.006 0.917 9.2 109.9 21.7 451 n/a 4_nqh: 0.1190 0.1372 0.006 0.917 9.2 109.9 21.7 451 n/a 4_sol: 0.1190 0.1364 0.006 0.917 9.2 109.9 21.6 455 n/a 4_weight: 0.1190 0.1364 0.006 0.917 9.2 109.9 21.6 455 n/a 4_xyzrec: 0.1195 0.1378 0.006 0.940 9.2 109.9 21.6 455 n/a 4_adp: 0.1185 0.1375 0.006 0.940 9.3 105.9 21.5 455 n/a 4_regHadp: 0.1186 0.1376 0.006 0.940 9.3 105.9 21.5 455 n/a 4_occ: 0.1181 0.1371 0.006 0.940 9.3 105.9 21.5 455 n/a 5_bss: 0.1178 0.1370 0.006 0.940 9.2 105.9 21.5 455 n/a 5_settarget: 0.1178 0.1370 0.006 0.940 9.2 105.9 21.5 455 n/a 5_updatecdl: 0.1178 0.1370 0.006 0.941 9.2 105.9 21.5 455 n/a 5_setrh: 0.1178 0.1370 0.006 0.941 9.2 105.9 21.5 455 n/a 5_nqh: 0.1178 0.1370 0.006 0.941 9.2 105.9 21.5 455 n/a 5_sol: 0.1179 0.1358 0.006 0.941 9.2 105.9 21.4 452 n/a 5_weight: 0.1179 0.1358 0.006 0.941 9.2 105.9 21.4 452 n/a 5_xyzrec: 0.1203 0.1385 0.007 1.041 9.2 105.9 21.4 452 n/a 5_adp: 0.1204 0.1385 0.007 1.041 9.3 104.9 21.3 452 n/a 5_regHadp: 0.1204 0.1385 0.007 1.041 9.3 104.9 21.3 452 n/a 5_occ: 0.1201 0.1384 0.007 1.041 9.3 104.9 21.3 452 n/a end: 0.1201 0.1388 0.007 1.041 9.3 104.8 21.3 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6369642_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_6369642_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.2600 Refinement macro-cycles (run) : 3543.0000 Write final files (write_after_run_outputs) : 64.7200 Total : 3612.9800 Total CPU time: 60.82 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:53 PST -0800 (1735452713.38 s) Start R-work = 0.1642, R-free = 0.1772 Final R-work = 0.1201, R-free = 0.1388 =============================================================================== Job complete usr+sys time: 3746.12 seconds wall clock time: 67 minutes 3.36 seconds (4023.36 seconds total)