Starting phenix.refine on Fri Dec 27 17:58:26 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" 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" 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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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: 1.64, per 1000 atoms: 0.49 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: 0.30 Conformation dependent library (CDL) restraints added in 111.6 milliseconds Time building geometry restraints manager: 0.41 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 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.805 1.850 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 1.850 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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } 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 = 27.037526 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 0.1690 0.1811 0.0121 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1566 0.1713 0.0147 0.001 0.4 3.8 0.0 0.0 0 0.250 0.1438 0.1610 0.0172 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1386 0.1576 0.0190 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1347 0.1549 0.0202 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1359 0.1561 0.0202 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1288 0.1502 0.0213 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1266 0.1491 0.0225 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1255 0.1488 0.0233 0.003 0.7 2.9 0.5 0.0 0 4.000 0.1246 0.1482 0.0236 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1238 0.1476 0.0238 0.004 0.8 3.2 0.5 0.0 0 6.000 0.1236 0.1475 0.0239 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1232 0.1470 0.0238 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1228 0.1469 0.0241 0.006 0.9 3.2 0.5 0.0 0 9.000 0.1229 0.1473 0.0244 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1226 0.1469 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1225 0.1471 0.0246 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1222 0.1471 0.0249 0.008 1.0 3.5 0.5 0.6 0 13.519 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1469 0.0244 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.69 2.44 3.013 19.035 2011.603 0.017 12.26 14.69 2.43 2.995 19.035 60.348 0.017 12.32 14.65 2.33 2.669 19.033 251.450 0.017 12.71 15.35 2.64 2.918 19.305 1005.802 0.016 12.58 15.49 2.92 3.373 19.615 2011.603 0.016 12.42 15.51 3.09 3.363 19.624 3017.405 0.015 12.30 15.39 3.09 3.344 19.608 4023.206 0.015 12.28 15.46 3.18 3.318 19.570 5029.008 0.015 12.19 15.35 3.16 3.356 19.596 6034.809 0.015 12.17 15.38 3.21 3.337 19.580 7040.611 0.015 12.16 15.44 3.28 3.470 19.645 8046.412 0.015 12.11 15.36 3.25 3.311 19.537 9052.214 0.015 12.12 15.44 3.32 3.500 19.629 10058.015 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 251.450 Accepted refinement result: 12.32 14.65 2.33 2.669 19.033 251.450 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.42 20.06 3.31 0 1785 Protein: 9.05 114.98 16.97 3.32 0 1519 Water: 11.43 119.42 38.20 N/A 0 258 Other: 19.67 26.58 22.03 N/A 0 8 Chain A: 9.05 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.12 227 31.12 - 42.16 125 42.16 - 53.20 94 53.20 - 64.24 42 64.24 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1465 r_work=0.1234 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1469 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 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= 0.1228 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016909 | | target function (ls_wunit_k1) not normalized (work): 1408.441936 | | target function (ls_wunit_k1) not normalized (free): 110.902841 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1693 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1669 0.1693 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1676 0.1677 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1455 n_refl.: 87593 remove outliers: r(all,work,free)=0.1238 0.1227 0.1455 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 0.3534 302.538 282.224 0.649 1.003 0.380 11.894-9.307 99.02 97 4 0.1655 484.649 472.682 0.921 1.003 0.372 9.237-7.194 100.00 213 7 0.1900 396.383 390.021 0.961 1.004 0.350 7.162-5.571 100.00 427 22 0.1848 297.464 291.424 0.936 1.004 0.259 5.546-4.326 100.00 867 58 0.1005 408.344 405.449 0.965 1.003 0.230 4.315-3.360 100.00 1859 96 0.0875 388.338 387.173 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1173 255.118 253.973 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1024 169.120 168.365 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.589 82.778 1.025 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.624 36.121 1.018 0.996 0.000 1.221-1.150 99.97 13689 708 0.2252 23.075 21.543 0.980 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0684 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1455 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=0.1227 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1456 | n_water=258 | time (s): 1.830 (total time: 1.830) Filter (dist) r_work=0.1235 r_free=0.1454 | n_water=252 | time (s): 21.280 (total time: 23.110) Filter (q & B) r_work=0.1238 r_free=0.1455 | n_water=249 | time (s): 2.810 (total time: 25.920) Compute maps r_work=0.1238 r_free=0.1455 | n_water=249 | time (s): 1.720 (total time: 27.640) Filter (map) r_work=0.1248 r_free=0.1459 | n_water=230 | time (s): 3.020 (total time: 30.660) Find peaks r_work=0.1248 r_free=0.1459 | n_water=230 | time (s): 0.700 (total time: 31.360) Add new water r_work=0.1393 r_free=0.1639 | n_water=441 | time (s): 2.820 (total time: 34.180) Refine new water occ: r_work=0.1301 r_free=0.1497 adp: r_work=0.1219 r_free=0.1441 occ: r_work=0.1232 r_free=0.1422 adp: r_work=0.1198 r_free=0.1407 occ: r_work=0.1202 r_free=0.1397 adp: r_work=0.1192 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1394 r_work=0.1192 r_free=0.1394 | n_water=441 | time (s): 57.580 (total time: 91.760) Filter (q & B) r_work=0.1197 r_free=0.1395 | n_water=422 | time (s): 3.270 (total time: 95.030) Filter (dist only) r_work=0.1197 r_free=0.1394 | n_water=421 | time (s): 32.970 (total time: 128.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.994730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1496.907828 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 0.1638 0.1758 0.0120 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1553 0.1683 0.0129 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1401 0.1558 0.0157 0.002 0.4 6.4 0.0 0.0 0 0.500 0.1351 0.1523 0.0173 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1305 0.1487 0.0183 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1308 0.1492 0.0184 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1256 0.1459 0.0203 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1224 0.1436 0.0212 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1210 0.1424 0.0214 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1204 0.1424 0.0220 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1200 0.1424 0.0224 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1198 0.1425 0.0227 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1194 0.1421 0.0227 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1192 0.1423 0.0231 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1191 0.1419 0.0228 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1188 0.1421 0.0233 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1187 0.1415 0.0228 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1183 0.1415 0.0232 0.008 0.9 4.8 0.5 0.0 0 13.997 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1183 0.1415 0.0232 0.008 0.9 4.8 0.5 0.0 0 13.997 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 14.15 2.32 3.773 21.800 1496.908 0.016 11.83 14.15 2.32 3.773 21.800 44.907 0.016 11.83 14.15 2.32 3.773 21.800 187.113 0.016 12.03 14.56 2.53 3.620 21.806 748.454 0.015 12.01 14.84 2.83 3.459 22.093 1496.908 0.015 11.92 14.90 2.98 3.517 21.929 2245.362 0.014 11.73 14.65 2.92 3.473 22.104 2993.816 0.014 11.65 14.65 3.00 3.500 21.972 3742.270 0.014 11.74 14.88 3.14 3.544 22.206 4490.723 0.014 11.70 14.90 3.19 3.558 22.202 5239.177 0.014 11.63 14.81 3.17 3.546 22.105 5987.631 0.014 11.60 14.80 3.20 3.564 22.142 6736.085 0.014 11.60 14.87 3.27 3.585 22.125 7484.539 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 187.113 Accepted refinement result: 11.83 14.15 2.32 3.773 21.800 187.113 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.02 22.24 3.31 191 1757 Protein: 9.10 115.02 17.01 3.32 0 1519 Water: 11.47 76.68 41.12 N/A 191 230 Other: 19.72 26.62 22.08 N/A 0 8 Chain A: 9.10 115.02 19.52 N/A 0 1757 Chain S: 17.12 60.00 47.26 N/A 191 0 Histogram: Values Number of atoms 9.10 - 19.69 1260 19.69 - 30.28 242 30.28 - 40.87 161 40.87 - 51.47 139 51.47 - 62.06 123 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.43 0 104.43 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1415 r_work=0.1183 r_free=0.1415 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1415 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1417 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 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= 0.1183 r_free= 0.1417 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014956 | | target function (ls_wunit_k1) not normalized (work): 1245.775371 | | target function (ls_wunit_k1) not normalized (free): 102.429926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1183 0.1417 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1575 0.1574 0.1620 n_refl.: 87592 remove outliers: r(all,work,free)=0.1575 0.1574 0.1620 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1577 0.1577 0.1622 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1179 0.1413 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1413 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 0.3289 298.427 275.743 0.592 1.003 0.350 11.894-9.307 99.02 97 4 0.1644 484.649 476.854 0.919 1.003 0.333 9.237-7.194 100.00 213 7 0.1671 396.383 394.770 0.982 1.003 0.264 7.162-5.571 100.00 427 22 0.1600 297.464 292.888 0.938 1.003 0.230 5.546-4.326 100.00 867 58 0.0865 408.344 405.509 0.961 1.003 0.220 4.315-3.360 100.00 1859 96 0.0784 388.338 387.435 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1074 255.118 254.219 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1004 169.120 168.612 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1093 82.589 82.811 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.624 36.158 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 23.075 21.576 0.986 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0239 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1413 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1413 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1413 | n_water=421 | time (s): 1.890 (total time: 1.890) Filter (dist) r_work=0.1177 r_free=0.1408 | n_water=415 | time (s): 34.160 (total time: 36.050) Filter (q & B) r_work=0.1177 r_free=0.1408 | n_water=415 | time (s): 0.840 (total time: 36.890) Compute maps r_work=0.1177 r_free=0.1408 | n_water=415 | time (s): 1.240 (total time: 38.130) Filter (map) r_work=0.1223 r_free=0.1396 | n_water=283 | time (s): 2.970 (total time: 41.100) Find peaks r_work=0.1223 r_free=0.1396 | n_water=283 | time (s): 0.690 (total time: 41.790) Add new water r_work=0.1342 r_free=0.1529 | n_water=480 | time (s): 2.970 (total time: 44.760) Refine new water occ: r_work=0.1242 r_free=0.1445 adp: r_work=0.1244 r_free=0.1447 occ: r_work=0.1220 r_free=0.1425 adp: r_work=0.1220 r_free=0.1424 occ: r_work=0.1203 r_free=0.1411 adp: r_work=0.1198 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1406 r_work=0.1198 r_free=0.1406 | n_water=480 | time (s): 228.120 (total time: 272.880) Filter (q & B) r_work=0.1204 r_free=0.1412 | n_water=438 | time (s): 3.330 (total time: 276.210) Filter (dist only) r_work=0.1205 r_free=0.1411 | n_water=437 | time (s): 36.320 (total time: 312.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.748145 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 39.284986 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 0.1239 0.1387 0.0148 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1199 0.1356 0.0157 0.003 0.7 3.5 0.5 0.0 0 0.262 0.1180 0.1340 0.0159 0.004 0.8 3.2 0.5 0.0 0 0.524 0.1173 0.1337 0.0164 0.005 0.9 3.2 0.5 0.0 0 0.787 0.1167 0.1333 0.0166 0.006 1.0 3.5 0.5 0.0 0 1.049 0.1166 0.1334 0.0167 0.007 1.0 3.2 0.5 0.0 0 1.311 0.1164 0.1333 0.0169 0.007 1.1 3.5 0.5 0.0 0 1.573 0.1161 0.1332 0.0171 0.008 1.1 3.5 0.5 0.0 0 1.836 0.1171 0.1335 0.0165 0.005 0.9 3.2 0.5 0.0 0 0.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1161 0.1332 0.0171 0.008 1.1 3.5 0.5 0.0 0 1.836 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 13.32 1.71 3.777 21.258 39.285 3.627 11.61 13.32 1.71 3.777 21.258 1.179 3.627 11.61 13.32 1.71 3.777 21.258 4.911 3.627 11.65 13.36 1.72 3.708 21.249 19.642 3.620 11.72 13.49 1.76 3.724 21.218 39.285 3.624 11.62 13.43 1.81 3.752 21.205 58.927 3.616 11.58 13.41 1.84 3.766 21.199 78.570 3.612 11.53 13.37 1.83 3.773 21.198 98.212 3.608 11.52 13.39 1.87 3.786 21.189 117.855 3.606 11.52 13.42 1.90 3.801 21.175 137.497 3.605 11.49 13.40 1.91 3.811 21.171 157.140 3.604 11.49 13.42 1.93 3.823 21.165 176.782 3.603 11.47 13.40 1.93 3.828 21.166 196.425 3.602 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.179 Accepted refinement result: 11.61 13.32 1.71 3.777 21.258 1.179 3.627 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.24 3.31 213 1751 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 35.86 N/A 213 224 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.11 115.03 19.44 N/A 0 1751 Chain S: 17.01 60.02 35.98 N/A 213 0 Histogram: Values Number of atoms 9.11 - 19.70 1263 19.70 - 30.30 289 30.30 - 40.89 207 40.89 - 51.48 124 51.48 - 62.07 58 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1332 r_work=0.1161 r_free=0.1332 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1332 target_work(ml) = 3.627 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1323 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1151 r_free= 0.1323 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.616936 | | target function (ml) not normalized (work): 301265.426079 | | target function (ml) not normalized (free): 15865.689627 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1151 0.1323 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1483 0.1482 0.1528 n_refl.: 87589 remove outliers: r(all,work,free)=0.1483 0.1482 0.1528 n_refl.: 87589 overall B=-0.00 to atoms: r(all,work,free)=0.1482 0.1481 0.1528 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1146 0.1318 n_refl.: 87589 remove outliers: r(all,work,free)=0.1152 0.1143 0.1318 n_refl.: 87581 ======================== 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 0.3901 289.577 270.008 0.483 1.000 0.296 11.894-9.307 97.06 95 4 0.2326 484.874 464.552 0.880 1.001 0.280 9.237-7.194 98.18 209 7 0.2271 387.826 388.335 0.958 1.002 0.208 7.162-5.571 100.00 427 22 0.2020 297.464 287.955 0.928 1.002 0.180 5.546-4.326 100.00 867 58 0.1117 408.344 403.197 0.965 1.002 0.160 4.315-3.360 100.00 1859 96 0.0932 388.338 385.582 1.004 1.002 0.139 3.356-2.611 100.00 3867 181 0.1152 255.118 252.944 1.007 1.002 0.057 2.608-2.026 99.99 8198 413 0.0933 169.120 168.357 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.589 82.889 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.624 36.217 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 23.075 21.617 0.988 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0124 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1318 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=0.1143 r_free=0.1318 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1318 | n_water=437 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1143 r_free=0.1318 | n_water=435 | time (s): 44.040 (total time: 46.210) Filter (q & B) r_work=0.1143 r_free=0.1318 | n_water=435 | time (s): 1.200 (total time: 47.410) Compute maps r_work=0.1143 r_free=0.1318 | n_water=435 | time (s): 1.800 (total time: 49.210) Filter (map) r_work=0.1171 r_free=0.1307 | n_water=320 | time (s): 3.970 (total time: 53.180) Find peaks r_work=0.1171 r_free=0.1307 | n_water=320 | time (s): 0.730 (total time: 53.910) Add new water r_work=0.1242 r_free=0.1372 | n_water=489 | time (s): 3.790 (total time: 57.700) Refine new water occ: r_work=0.1162 r_free=0.1319 adp: r_work=0.1162 r_free=0.1320 occ: r_work=0.1146 r_free=0.1306 adp: r_work=0.1145 r_free=0.1305 occ: r_work=0.1133 r_free=0.1294 adp: r_work=0.1129 r_free=0.1292 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1292 r_work=0.1129 r_free=0.1292 | n_water=489 | time (s): 200.710 (total time: 258.410) Filter (q & B) r_work=0.1136 r_free=0.1297 | n_water=452 | time (s): 3.970 (total time: 262.380) Filter (dist only) r_work=0.1136 r_free=0.1296 | n_water=450 | time (s): 45.890 (total time: 308.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.726829 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.471262 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 0.1334 0.0134 0.002 0.6 4.5 0.5 0.0 0 0.086 0.1162 0.1306 0.0145 0.003 0.7 3.5 0.5 0.0 0 0.259 0.1148 0.1299 0.0151 0.004 0.9 3.8 0.5 0.0 0 0.518 0.1142 0.1298 0.0156 0.005 0.9 3.8 0.5 0.0 0 0.777 0.1138 0.1297 0.0159 0.006 1.0 3.5 0.5 0.0 0 1.036 0.1135 0.1296 0.0161 0.007 1.0 3.5 0.5 0.0 0 1.295 0.1133 0.1292 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.554 0.1131 0.1294 0.0163 0.008 1.1 3.8 0.5 0.0 0 1.813 0.1140 0.1295 0.0155 0.006 1.0 3.8 0.5 0.0 0 0.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1292 0.0159 0.008 1.1 4.2 0.5 0.0 0 1.554 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.92 1.59 3.779 21.241 45.471 3.609 11.33 12.92 1.59 3.779 21.241 1.364 3.609 11.33 12.92 1.59 3.779 21.241 5.684 3.609 11.38 12.98 1.60 3.713 21.226 22.736 3.605 11.38 13.05 1.68 3.742 21.206 45.471 3.604 11.35 13.07 1.73 3.758 21.191 68.207 3.601 11.29 13.03 1.75 3.773 21.190 90.943 3.596 11.26 13.02 1.76 3.783 21.186 113.678 3.593 11.25 13.04 1.79 3.799 21.176 136.414 3.593 11.23 13.04 1.81 3.810 21.174 159.149 3.591 11.21 13.02 1.81 3.816 21.174 181.885 3.590 11.21 13.03 1.82 3.830 21.165 204.621 3.589 11.18 13.00 1.82 3.834 21.164 227.356 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.364 Accepted refinement result: 11.33 12.92 1.59 3.779 21.241 1.364 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.21 3.31 228 1749 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.48 76.69 35.32 N/A 228 222 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.11 115.03 19.43 N/A 0 1749 Chain S: 17.01 60.01 34.82 N/A 228 0 Histogram: Values Number of atoms 9.11 - 19.70 1267 19.70 - 30.29 299 30.29 - 40.88 210 40.88 - 51.48 127 51.48 - 62.07 51 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1292 r_work=0.1133 r_free=0.1292 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1292 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1289 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1289 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606634 | | target function (ml) not normalized (work): 300378.544903 | | target function (ml) not normalized (free): 15823.328056 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1127 0.1289 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1458 0.1458 0.1500 n_refl.: 87581 remove outliers: r(all,work,free)=0.1458 0.1458 0.1500 n_refl.: 87581 overall B=-0.00 to atoms: r(all,work,free)=0.1458 0.1457 0.1500 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1127 0.1289 n_refl.: 87581 remove outliers: r(all,work,free)=0.1132 0.1124 0.1289 n_refl.: 87575 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.4160 286.980 247.284 0.440 1.000 0.305 11.894-9.307 93.14 91 4 0.2155 485.172 466.704 0.882 1.002 0.301 9.237-7.194 98.18 209 7 0.2279 387.826 381.965 0.935 1.002 0.187 7.162-5.571 100.00 427 22 0.2044 297.464 288.128 0.920 1.003 0.163 5.546-4.326 100.00 867 58 0.1108 408.344 403.714 0.965 1.003 0.150 4.315-3.360 100.00 1859 96 0.0900 388.338 386.253 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1106 255.118 252.983 1.009 1.002 0.060 2.608-2.026 99.99 8198 413 0.0911 169.120 168.509 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.589 82.944 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.624 36.240 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.075 21.626 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0075 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1124 r_free=0.1289 After: r_work=0.1125 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1125 r_free=0.1289 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=0.1125 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1125 r_free=0.1289 | n_water=450 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1125 r_free=0.1289 | n_water=449 | time (s): 45.530 (total time: 47.900) Filter (q & B) r_work=0.1125 r_free=0.1289 | n_water=449 | time (s): 1.380 (total time: 49.280) Compute maps r_work=0.1125 r_free=0.1289 | n_water=449 | time (s): 1.810 (total time: 51.090) Filter (map) r_work=0.1148 r_free=0.1281 | n_water=355 | time (s): 3.740 (total time: 54.830) Find peaks r_work=0.1148 r_free=0.1281 | n_water=355 | time (s): 0.620 (total time: 55.450) Add new water r_work=0.1201 r_free=0.1331 | n_water=497 | time (s): 3.540 (total time: 58.990) Refine new water occ: r_work=0.1144 r_free=0.1285 adp: r_work=0.1144 r_free=0.1286 occ: r_work=0.1131 r_free=0.1274 adp: r_work=0.1130 r_free=0.1273 occ: r_work=0.1122 r_free=0.1267 adp: r_work=0.1118 r_free=0.1264 ADP+occupancy (water only), MIN, final r_work=0.1118 r_free=0.1264 r_work=0.1118 r_free=0.1264 | n_water=497 | time (s): 195.260 (total time: 254.250) Filter (q & B) r_work=0.1127 r_free=0.1276 | n_water=458 | time (s): 3.640 (total time: 257.890) Filter (dist only) r_work=0.1130 r_free=0.1272 | n_water=455 | time (s): 47.110 (total time: 305.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.724403 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.269078 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 0.1206 0.1323 0.0117 0.004 0.7 7.7 0.0 0.0 0 0.086 0.1161 0.1292 0.0131 0.004 0.8 6.7 0.0 0.0 0 0.259 0.1142 0.1279 0.0137 0.005 1.0 6.4 0.5 0.0 0 0.517 0.1137 0.1275 0.0139 0.006 1.0 6.1 0.5 0.0 0 0.776 0.1133 0.1273 0.0140 0.007 1.1 6.1 0.5 0.0 0 1.035 0.1131 0.1272 0.0141 0.007 1.1 6.1 0.5 0.0 0 1.293 0.1130 0.1272 0.0142 0.008 1.1 6.1 0.5 0.0 0 1.552 0.1130 0.1272 0.0142 0.008 1.1 6.1 0.5 0.0 0 1.811 0.1135 0.1274 0.0139 0.006 1.0 6.1 0.5 0.0 0 0.862 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1272 0.0142 0.008 1.1 6.1 0.5 0.0 0 1.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.72 1.42 3.778 21.227 43.269 3.604 11.30 12.72 1.42 3.778 21.227 1.298 3.604 11.30 12.72 1.42 3.778 21.227 5.409 3.604 11.31 12.74 1.42 3.713 21.220 21.635 3.599 11.34 12.83 1.49 3.738 21.197 43.269 3.600 11.30 12.83 1.54 3.758 21.182 64.904 3.596 11.25 12.80 1.55 3.771 21.177 86.538 3.591 11.22 12.78 1.56 3.780 21.177 108.173 3.589 11.20 12.79 1.59 3.794 21.171 129.807 3.588 11.19 12.79 1.61 3.806 21.166 151.442 3.586 11.17 12.78 1.61 3.814 21.164 173.076 3.585 11.17 12.79 1.62 3.826 21.160 194.711 3.585 11.15 12.77 1.61 3.830 21.160 216.345 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.298 Accepted refinement result: 11.30 12.72 1.42 3.778 21.227 1.298 3.604 Individual atomic B min max mean iso aniso Overall: 9.10 115.03 21.19 3.31 236 1746 Protein: 9.10 115.03 17.02 3.32 0 1519 Water: 11.48 76.69 35.08 N/A 236 219 Other: 19.72 26.63 22.08 N/A 0 8 Chain A: 9.10 115.03 19.38 N/A 0 1746 Chain S: 15.86 60.01 34.51 N/A 236 0 Histogram: Values Number of atoms 9.10 - 19.70 1267 19.70 - 30.29 299 30.29 - 40.88 216 40.88 - 51.47 127 51.47 - 62.07 50 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.43 0 104.43 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1272 r_work=0.1130 r_free=0.1272 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1272 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1271 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1271 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602052 | | target function (ml) not normalized (work): 299975.322073 | | target function (ml) not normalized (free): 15793.055228 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1291 0.1232 5.6166 5.5215| | 2: 3.57 - 2.84 1.00 2888 124 0.1052 0.1436 5.1397 5.233| | 3: 2.83 - 2.48 1.00 2820 163 0.1105 0.1167 4.923 4.9458| | 4: 2.47 - 2.25 1.00 2825 136 0.0900 0.1022 4.6122 4.6561| | 5: 2.25 - 2.09 1.00 2756 127 0.0872 0.1001 4.5536 4.6209| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.1017 4.2529 4.3459| | 7: 1.97 - 1.87 1.00 2787 165 0.0881 0.1074 3.9741 4.0692| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1094 3.8868 3.9837| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1172 3.648 3.8232| | 10: 1.72 - 1.66 1.00 2831 160 0.0919 0.1191 3.5658 3.7085| | 11: 1.66 - 1.61 1.00 2712 147 0.0876 0.1042 3.4958 3.5677| | 12: 1.61 - 1.56 1.00 2773 144 0.0912 0.1152 3.3352 3.4756| | 13: 1.56 - 1.52 1.00 2745 130 0.0946 0.1013 3.3103 3.3835| | 14: 1.52 - 1.48 1.00 2803 134 0.0983 0.1076 3.2442 3.3356| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1225 3.1596 3.2694| | 16: 1.45 - 1.42 1.00 2756 161 0.1058 0.1270 3.1406 3.2558| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1307 3.1233 3.2375| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1331 3.1082 3.2416| | 19: 1.36 - 1.34 1.00 2807 134 0.1262 0.1552 3.1165 3.2633| | 20: 1.34 - 1.32 1.00 2696 147 0.1372 0.1470 3.1188 3.1523| | 21: 1.32 - 1.30 1.00 2785 112 0.1470 0.1517 3.1187 3.112| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1992 3.1261 3.3018| | 23: 1.27 - 1.26 1.00 2802 156 0.1650 0.1798 3.1364 3.2072| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1834 3.1319 3.2303| | 25: 1.24 - 1.22 1.00 2733 148 0.1887 0.2132 3.1476 3.2602| | 26: 1.22 - 1.21 1.00 2727 135 0.1906 0.1763 3.153 3.2064| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2173 3.1749 3.1684| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2300 3.1701 3.176| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2383 3.1512 3.2355| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2449 3.1479 3.1718| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2917 171 0.95 7.99 1.00 0.97 5297.05| | 2: 3.57 - 2.84 2888 124 0.93 11.83 1.01 0.97 5297.05| | 3: 2.83 - 2.48 2820 163 0.90 15.77 0.99 0.97 4433.88| | 4: 2.47 - 2.25 2825 136 0.92 12.88 1.00 0.98 2208.03| | 5: 2.25 - 2.09 2756 127 0.91 15.02 1.01 0.98 2208.03| | 6: 2.09 - 1.97 2846 113 0.93 12.04 1.02 0.98 1291.11| | 7: 1.97 - 1.87 2787 165 0.95 9.24 1.02 0.98 509.10| | 8: 1.87 - 1.79 2789 144 0.93 12.59 1.00 0.98 509.10| | 9: 1.79 - 1.72 2745 138 0.94 9.98 0.98 0.98 288.63| | 10: 1.72 - 1.66 2831 160 0.94 11.07 0.98 0.98 244.48| | 11: 1.66 - 1.61 2712 147 0.93 11.70 0.98 0.98 234.33| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.98 138.59| | 13: 1.56 - 1.52 2745 130 0.95 10.43 1.03 0.98 138.59| | 14: 1.52 - 1.48 2803 134 0.94 10.75 1.02 0.98 124.51| | 15: 1.48 - 1.45 2738 128 0.95 9.91 1.02 0.99 98.71| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.99 98.71| | 17: 1.42 - 1.39 2785 139 0.95 10.90 1.01 0.99 90.05| | 18: 1.39 - 1.36 2741 179 0.94 11.56 1.01 0.99 85.03| | 19: 1.36 - 1.34 2807 134 0.94 11.90 0.99 0.99 85.03| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 80.91| | 21: 1.32 - 1.30 2785 112 0.94 13.11 0.98 0.97 80.62| | 22: 1.29 - 1.27 2704 152 0.93 13.68 0.98 0.96 81.02| | 23: 1.27 - 1.26 2802 156 0.92 14.86 0.97 0.95 83.07| | 24: 1.26 - 1.24 2744 132 0.92 14.88 0.96 0.95 83.07| | 25: 1.24 - 1.22 2733 148 0.91 16.36 0.96 0.94 85.02| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.02 0.93 87.19| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 87.19| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.90| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.98 0.93 92.30| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.93 92.30| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.62 max = 5297.05 mean = 830.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.33| |phase err.(test): min = 0.00 max = 89.28 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1271 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1444 0.1444 0.1473 n_refl.: 87575 remove outliers: r(all,work,free)=0.1444 0.1444 0.1473 n_refl.: 87575 overall B=-0.00 to atoms: r(all,work,free)=0.1443 0.1443 0.1473 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1124 0.1272 n_refl.: 87575 remove outliers: r(all,work,free)=0.1130 0.1123 0.1272 n_refl.: 87573 ======================== 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 0.3910 289.593 251.578 0.457 1.000 0.314 11.894-9.307 92.16 90 4 0.2151 487.270 470.409 0.889 1.002 0.310 9.237-7.194 98.18 209 7 0.2247 387.826 381.741 0.935 1.002 0.160 7.162-5.571 100.00 427 22 0.2038 297.464 288.942 0.916 1.002 0.150 5.546-4.326 100.00 867 58 0.1097 408.344 403.824 0.964 1.002 0.135 4.315-3.360 100.00 1859 96 0.0902 388.338 386.445 1.003 1.002 0.130 3.356-2.611 100.00 3867 181 0.1104 255.118 253.054 1.010 1.002 0.050 2.608-2.026 99.99 8198 413 0.0912 169.120 168.517 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.589 82.928 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.624 36.245 1.026 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 23.075 21.635 0.988 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0076 ================= 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: 0.1226 0.1469 0.007 0.907 9.0 119.5 20.1 258 0.137 1_adp: 0.1232 0.1465 0.007 0.907 9.1 119.4 20.1 258 0.137 1_regHadp: 0.1234 0.1469 0.007 0.907 9.1 119.4 20.1 258 0.137 1_occ: 0.1228 0.1462 0.007 0.907 9.1 119.4 20.1 258 0.137 2_bss: 0.1227 0.1455 0.007 0.907 9.1 119.5 20.1 258 0.137 2_settarget: 0.1227 0.1455 0.007 0.907 9.1 119.5 20.1 258 0.137 2_updatecdl: 0.1227 0.1455 0.007 0.916 9.1 119.5 20.1 258 0.137 2_nqh: 0.1227 0.1456 0.007 0.916 9.1 119.5 20.1 258 0.134 2_sol: 0.1197 0.1394 0.007 0.916 9.1 115.0 22.2 421 n/a 2_weight: 0.1197 0.1394 0.007 0.916 9.1 115.0 22.2 421 n/a 2_xyzrec: 0.1183 0.1415 0.008 0.938 9.1 115.0 22.2 421 n/a 2_adp: 0.1183 0.1415 0.008 0.938 9.1 115.0 22.2 421 n/a 2_regHadp: 0.1183 0.1415 0.008 0.938 9.1 115.0 22.2 421 n/a 2_occ: 0.1183 0.1417 0.008 0.938 9.1 115.0 22.2 421 n/a 3_bss: 0.1178 0.1413 0.008 0.938 9.1 115.0 22.3 421 n/a 3_settarget: 0.1178 0.1413 0.008 0.938 9.1 115.0 22.3 421 n/a 3_updatecdl: 0.1178 0.1413 0.008 0.937 9.1 115.0 22.3 421 n/a 3_nqh: 0.1178 0.1413 0.008 0.937 9.1 115.0 22.3 421 n/a 3_sol: 0.1205 0.1411 0.008 0.937 9.1 115.0 21.2 437 n/a 3_weight: 0.1205 0.1411 0.008 0.937 9.1 115.0 21.2 437 n/a 3_xyzrec: 0.1161 0.1332 0.008 1.086 9.1 115.0 21.2 437 n/a 3_adp: 0.1161 0.1332 0.008 1.086 9.1 115.0 21.2 437 n/a 3_regHadp: 0.1161 0.1332 0.008 1.086 9.1 115.0 21.2 437 n/a 3_occ: 0.1151 0.1323 0.008 1.086 9.1 115.0 21.2 437 n/a 4_bss: 0.1143 0.1318 0.008 1.086 9.1 115.0 21.2 437 n/a 4_settarget: 0.1143 0.1318 0.008 1.086 9.1 115.0 21.2 437 n/a 4_updatecdl: 0.1143 0.1318 0.008 1.088 9.1 115.0 21.2 437 n/a 4_nqh: 0.1143 0.1318 0.008 1.088 9.1 115.0 21.2 437 n/a 4_sol: 0.1136 0.1296 0.008 1.088 9.1 115.0 21.2 450 n/a 4_weight: 0.1136 0.1296 0.008 1.088 9.1 115.0 21.2 450 n/a 4_xyzrec: 0.1133 0.1292 0.008 1.090 9.1 115.0 21.2 450 n/a 4_adp: 0.1133 0.1292 0.008 1.090 9.1 115.0 21.2 450 n/a 4_regHadp: 0.1133 0.1292 0.008 1.090 9.1 115.0 21.2 450 n/a 4_occ: 0.1127 0.1289 0.008 1.090 9.1 115.0 21.2 450 n/a 5_bss: 0.1124 0.1289 0.008 1.090 9.1 115.0 21.2 450 n/a 5_settarget: 0.1124 0.1289 0.008 1.090 9.1 115.0 21.2 450 n/a 5_updatecdl: 0.1124 0.1289 0.008 1.089 9.1 115.0 21.2 450 n/a 5_setrh: 0.1125 0.1289 0.008 1.089 9.1 115.0 21.2 450 n/a 5_nqh: 0.1125 0.1289 0.008 1.089 9.1 115.0 21.2 450 n/a 5_sol: 0.1130 0.1272 0.008 1.089 9.1 115.0 21.2 455 n/a 5_weight: 0.1130 0.1272 0.008 1.089 9.1 115.0 21.2 455 n/a 5_xyzrec: 0.1130 0.1272 0.008 1.096 9.1 115.0 21.2 455 n/a 5_adp: 0.1130 0.1272 0.008 1.096 9.1 115.0 21.2 455 n/a 5_regHadp: 0.1130 0.1272 0.008 1.096 9.1 115.0 21.2 455 n/a 5_occ: 0.1125 0.1271 0.008 1.096 9.1 115.0 21.2 455 n/a end: 0.1123 0.1272 0.008 1.096 9.1 115.0 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6369642_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6369642_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2300 Refinement macro-cycles (run) : 13149.8300 Write final files (write_after_run_outputs) : 97.0200 Total : 13250.0800 Total CPU time: 3.69 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 21:58:44 PST -0800 (1735365524.62 s) Start R-work = 0.1642, R-free = 0.1772 Final R-work = 0.1123, R-free = 0.1272 =============================================================================== Job complete usr+sys time: 13434.31 seconds wall clock time: 243 minutes 17.35 seconds (14597.35 seconds total)