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_7427252.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_7427252.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7427252.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 1 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: 1.45, per 1000 atoms: 0.43 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 188.4 milliseconds Time building geometry restraints manager: 0.46 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: 535 0.91 - 1.17: 1114 1.17 - 1.43: 674 1.43 - 1.69: 807 1.69 - 1.95: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.01e+02 bond pdb=" CA VAL A 146 " pdb=" C VAL A 146 " ideal model delta sigma weight residual 1.522 1.731 -0.209 1.22e-02 6.72e+03 2.95e+02 bond pdb=" CA SER A 83 " pdb=" C SER A 83 " ideal model delta sigma weight residual 1.523 1.742 -0.219 1.35e-02 5.49e+03 2.62e+02 bond pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 1.335 1.531 -0.196 1.23e-02 6.61e+03 2.55e+02 bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.112 0.218 1.37e-02 5.33e+03 2.52e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 2991 4.35 - 8.71: 1859 8.71 - 13.06: 731 13.06 - 17.42: 168 17.42 - 21.77: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1AASN A 97 " pdb=" CG AASN A 97 " pdb=" ND2AASN A 97 " ideal model delta sigma weight residual 122.60 106.78 15.82 1.00e+00 1.00e+00 2.50e+02 angle pdb=" CA MET A 26 " pdb=" C MET A 26 " pdb=" O MET A 26 " ideal model delta sigma weight residual 120.55 105.53 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 109.59 12.32 9.80e-01 1.04e+00 1.58e+02 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.53 107.45 13.08 1.07e+00 8.73e-01 1.49e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 129.98 -10.78 9.00e-01 1.23e+00 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 942 17.39 - 34.77: 115 34.77 - 52.15: 41 52.15 - 69.54: 10 69.54 - 86.92: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA GLY A 30 " pdb=" C GLY A 30 " pdb=" N ILE A 31 " pdb=" CA ILE A 31 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.221: 109 0.221 - 0.441: 73 0.441 - 0.661: 43 0.661 - 0.882: 10 0.882 - 1.102: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 1.42 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA ALA A 79 " pdb=" N ALA A 79 " pdb=" C ALA A 79 " pdb=" CB ALA A 79 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.75 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.065 2.00e-02 2.50e+03 5.92e-02 1.05e+02 pdb=" CG PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.056 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.023 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.005 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.055 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " -0.001 9.50e-02 1.11e+02 6.73e-02 1.02e+02 pdb=" NE ARG A 28 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.145 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.129 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.020 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 632 2.25 - 2.84: 7612 2.84 - 3.43: 10742 3.43 - 4.01: 15415 4.01 - 4.60: 22181 Nonbonded interactions: 56582 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.667 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.829 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.837 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.841 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.853 1.850 ... (remaining 56577 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_7427252_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787967 | | target function (ml) not normalized (work): 232254.397995 | | target function (ml) not normalized (free): 11818.138032 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2100 7.0961 4.9345| | 2: 3.57 - 2.84 1.00 2876 122 0.2420 0.1848 4.3456 4.3397| | 3: 2.84 - 2.48 1.00 2833 165 0.2361 0.1746 4.1222 4.1525| | 4: 2.47 - 2.25 1.00 2825 136 0.2301 0.1475 3.8264 3.835| | 5: 2.25 - 2.09 1.00 2756 127 0.2505 0.1575 3.7932 3.8127| | 6: 2.09 - 1.97 1.00 2846 113 0.2533 0.1655 3.4456 3.5169| | 7: 1.97 - 1.87 1.00 2787 165 0.2589 0.1637 3.149 3.1332| | 8: 1.87 - 1.79 1.00 2789 144 0.2472 0.1972 3.0637 3.1411| | 9: 1.79 - 1.72 1.00 2745 138 0.2442 0.1954 2.9016 2.9303| | 10: 1.72 - 1.66 1.00 2789 158 0.2376 0.1997 2.7862 2.8667| | 11: 1.66 - 1.61 1.00 2740 147 0.2458 0.1645 2.7279 2.6926| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2092 2.6192 2.6936| | 13: 1.56 - 1.52 1.00 2745 130 0.2578 0.1787 2.5586 2.6018| | 14: 1.52 - 1.48 1.00 2803 134 0.2603 0.2114 2.4791 2.5394| | 15: 1.48 - 1.45 1.00 2738 128 0.2569 0.2070 2.4166 2.4525| | 16: 1.45 - 1.42 1.00 2756 161 0.2593 0.2136 2.3732 2.3903| | 17: 1.42 - 1.39 1.00 2785 139 0.2718 0.2229 2.3354 2.4068| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2133 2.2838 2.2854| | 19: 1.36 - 1.34 1.00 2807 134 0.2621 0.2637 2.2297 2.3616| | 20: 1.34 - 1.32 1.00 2696 147 0.2714 0.2407 2.1981 2.2697| | 21: 1.32 - 1.30 1.00 2785 112 0.2725 0.2034 2.1559 2.1463| | 22: 1.29 - 1.27 1.00 2704 152 0.2706 0.2611 2.1352 2.2206| | 23: 1.27 - 1.26 1.00 2802 156 0.2796 0.2391 2.1125 2.1675| | 24: 1.26 - 1.24 1.00 2744 132 0.2758 0.2701 2.0859 2.2093| | 25: 1.24 - 1.22 1.00 2734 148 0.2868 0.2667 2.0551 2.1059| | 26: 1.22 - 1.21 1.00 2727 135 0.2859 0.2656 2.0191 2.2266| | 27: 1.21 - 1.19 1.00 2814 148 0.2930 0.2368 2.0063 1.9466| | 28: 1.19 - 1.18 1.00 2671 147 0.2952 0.2941 1.9787 1.9955| | 29: 1.18 - 1.16 1.00 2800 134 0.2909 0.2823 1.9507 2.0662| | 30: 1.16 - 1.15 1.00 2740 148 0.3047 0.3001 1.9311 1.9703| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.75 0.76 0.23 1460.81| | 2: 3.57 - 2.84 2876 122 0.81 25.84 1.27 0.23 1460.81| | 3: 2.84 - 2.48 2833 165 0.74 31.81 1.24 0.24 1211.45| | 4: 2.47 - 2.25 2825 136 0.81 25.36 1.25 0.25 564.32| | 5: 2.25 - 2.09 2756 127 0.77 29.19 1.29 0.25 564.32| | 6: 2.09 - 1.97 2846 113 0.84 22.55 1.29 0.25 308.52| | 7: 1.97 - 1.87 2787 165 0.90 16.54 1.29 0.26 90.36| | 8: 1.87 - 1.79 2789 144 0.86 20.97 1.24 0.26 90.36| | 9: 1.79 - 1.72 2745 138 0.88 18.17 1.23 0.25 53.72| | 10: 1.72 - 1.66 2789 158 0.87 19.78 1.22 0.25 46.38| | 11: 1.66 - 1.61 2740 147 0.86 21.01 1.23 0.25 44.73| | 12: 1.61 - 1.56 2787 146 0.89 17.77 1.24 0.25 28.03| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.03| | 14: 1.52 - 1.48 2803 134 0.87 20.30 1.24 0.25 25.32| | 15: 1.48 - 1.45 2738 128 0.87 19.80 1.23 0.25 20.35| | 16: 1.45 - 1.42 2756 161 0.86 21.20 1.23 0.25 20.35| | 17: 1.42 - 1.39 2785 139 0.87 20.89 1.24 0.25 17.70| | 18: 1.39 - 1.36 2741 179 0.86 21.36 1.23 0.25 16.17| | 19: 1.36 - 1.34 2807 134 0.85 22.43 1.22 0.25 16.17| | 20: 1.34 - 1.32 2696 147 0.86 21.59 1.22 0.24 13.84| | 21: 1.32 - 1.30 2785 112 0.85 22.79 1.21 0.24 13.68| | 22: 1.29 - 1.27 2704 152 0.85 23.09 1.21 0.24 13.39| | 23: 1.27 - 1.26 2802 156 0.85 23.11 1.22 0.24 11.92| | 24: 1.26 - 1.24 2744 132 0.84 23.67 1.20 0.24 11.92| | 25: 1.24 - 1.22 2734 148 0.83 24.79 1.21 0.23 11.33| | 26: 1.22 - 1.21 2727 135 0.83 25.27 1.20 0.23 10.67| | 27: 1.21 - 1.19 2814 148 0.82 26.00 1.20 0.23 10.67| | 28: 1.19 - 1.18 2671 147 0.81 26.80 1.19 0.22 9.97| | 29: 1.18 - 1.16 2800 134 0.81 26.81 1.16 0.22 9.70| | 30: 1.16 - 1.15 2740 148 0.79 28.59 1.16 0.22 9.70| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.70 max = 1460.81 mean = 212.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.98 mean = 22.87| |phase err.(test): min = 0.00 max = 89.54 mean = 22.88| |-----------------------------------------------------------------------------| ----------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 0.248 1557 Z= 5.560 Angle : 5.208 15.963 2118 Z= 3.657 Chirality : 0.383 1.102 243 Planarity : 0.030 0.088 284 Dihedral : 13.827 86.922 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.62 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 30.27 % 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: -2.46 (0.44), residues: 224 helix: -2.53 (0.37), residues: 108 sheet: -1.08 (0.81), residues: 28 loop : -0.22 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.024 ARG A 145 TYR 0.084 0.040 TYR A 141 PHE 0.119 0.043 PHE A 162 HIS 0.047 0.024 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= 0.2606 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787967 | | target function (ml) not normalized (work): 232254.397995 | | target function (ml) not normalized (free): 11818.138032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1961 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1961 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1961 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.2000 0.2003 0.1973 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1637 0.1629 0.1795 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1628 0.1795 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 0.3839 386.570 358.875 0.678 1.002 0.407 11.894-9.307 99.02 97 4 0.1748 614.048 594.046 0.929 1.003 0.390 9.237-7.194 100.00 213 7 0.2122 502.215 491.443 0.957 1.003 0.350 7.162-5.571 100.00 427 22 0.2161 376.885 365.455 0.931 1.003 0.330 5.546-4.326 100.00 867 58 0.1323 517.370 511.706 0.965 1.003 0.224 4.315-3.360 100.00 1859 96 0.1144 492.022 488.405 1.007 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.233 319.692 0.995 1.002 0.057 2.608-2.026 99.99 8198 413 0.1332 214.274 212.180 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1649 104.640 104.032 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2043 46.402 45.161 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2553 29.236 26.996 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0411 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1795 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1630 r_free=0.1798 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.906529 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1998.178276 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 0.1594 0.1718 0.0124 0.002 0.5 4.2 0.0 0.0 0 0.125 0.1423 0.1573 0.0149 0.002 0.5 3.5 0.0 0.0 0 0.250 0.1410 0.1571 0.0161 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1346 0.1524 0.0178 0.002 0.5 2.9 0.0 0.0 0 0.750 0.1326 0.1513 0.0187 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1366 0.1554 0.0188 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1285 0.1497 0.0213 0.002 0.6 2.6 0.5 0.0 0 2.000 0.1265 0.1488 0.0223 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1257 0.1489 0.0231 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1241 0.1473 0.0231 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1243 0.1481 0.0239 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1234 0.1470 0.0236 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1231 0.1473 0.0242 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1228 0.1469 0.0242 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1223 0.1463 0.0240 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1223 0.1467 0.0244 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1219 0.1459 0.0240 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1219 0.1467 0.0248 0.008 1.0 3.5 0.5 0.0 0 13.953 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1219 0.1459 0.0240 0.007 0.9 3.5 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 14.59 2.40 3.013 19.038 1998.178 0.017 12.19 14.59 2.40 3.011 19.038 59.945 0.017 12.27 14.57 2.30 2.669 19.037 249.772 0.017 12.63 15.23 2.60 2.723 19.191 999.089 0.016 12.50 15.40 2.90 3.292 19.593 1998.178 0.016 12.33 15.37 3.04 3.120 19.519 2997.267 0.015 12.36 15.49 3.13 3.420 19.653 3996.357 0.015 12.23 15.37 3.15 3.370 19.627 4995.446 0.015 12.22 15.42 3.20 3.219 19.531 5994.535 0.015 12.13 15.34 3.21 3.395 19.628 6993.624 0.015 12.17 15.46 3.29 3.368 19.597 7992.713 0.015 12.13 15.40 3.28 3.409 19.618 8991.802 0.015 12.15 15.50 3.35 3.475 19.639 9990.891 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: 249.772 Accepted refinement result: 12.27 14.57 2.30 2.669 19.037 249.772 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.42 20.06 3.31 0 1785 Protein: 9.04 114.98 16.97 3.32 0 1519 Water: 11.47 119.42 38.20 N/A 0 258 Other: 19.69 26.57 22.03 N/A 0 8 Chain A: 9.04 119.42 20.06 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.15 125 42.15 - 53.19 94 53.19 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.34 4 97.34 - 108.38 1 108.38 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1457 r_work=0.1228 r_free=0.1460 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1228 r_free = 0.1460 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 = 0.1224 r_free = 0.1456 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1224 r_free= 0.1456 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016831 | | target function (ls_wunit_k1) not normalized (work): 1401.992814 | | target function (ls_wunit_k1) not normalized (free): 109.803659 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1224 0.1456 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1684 n_refl.: 87593 remove outliers: r(all,work,free)=0.1668 0.1669 0.1684 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1675 0.1677 0.1689 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1232 0.1221 0.1448 n_refl.: 87593 remove outliers: r(all,work,free)=0.1231 0.1220 0.1448 n_refl.: 87591 ======================== 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 94.79 86 5 0.3526 298.133 282.694 0.648 1.002 0.380 11.894-9.307 99.02 97 4 0.1675 483.107 469.881 0.921 1.003 0.370 9.237-7.194 100.00 213 7 0.1899 395.122 389.800 0.962 1.003 0.322 7.162-5.571 100.00 427 22 0.1860 296.517 290.210 0.934 1.003 0.263 5.546-4.326 100.00 867 58 0.1009 407.045 403.702 0.962 1.003 0.209 4.315-3.360 100.00 1859 96 0.0870 387.102 386.009 1.009 1.003 0.190 3.356-2.611 100.00 3867 181 0.1168 254.306 253.155 1.008 1.002 0.100 2.608-2.026 99.99 8198 413 0.1012 168.582 167.867 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.327 82.545 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1440 36.507 36.018 1.017 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 23.002 21.486 0.979 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0623 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1448 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1222 r_free=0.1449 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1449 | n_water=258 | time (s): 1.970 (total time: 1.970) Filter (dist) r_work=0.1231 r_free=0.1446 | n_water=250 | time (s): 22.420 (total time: 24.390) Filter (q & B) r_work=0.1233 r_free=0.1445 | n_water=247 | time (s): 3.530 (total time: 27.920) Compute maps r_work=0.1233 r_free=0.1445 | n_water=247 | time (s): 1.680 (total time: 29.600) Filter (map) r_work=0.1252 r_free=0.1448 | n_water=226 | time (s): 3.330 (total time: 32.930) Find peaks r_work=0.1252 r_free=0.1448 | n_water=226 | time (s): 0.670 (total time: 33.600) Add new water r_work=0.1397 r_free=0.1616 | n_water=437 | time (s): 3.310 (total time: 36.910) Refine new water occ: r_work=0.1301 r_free=0.1484 adp: r_work=0.1222 r_free=0.1421 occ: r_work=0.1235 r_free=0.1419 adp: r_work=0.1200 r_free=0.1396 occ: r_work=0.1203 r_free=0.1390 adp: r_work=0.1193 r_free=0.1387 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1387 r_work=0.1193 r_free=0.1387 | n_water=437 | time (s): 58.350 (total time: 95.260) Filter (q & B) r_work=0.1195 r_free=0.1387 | n_water=426 | time (s): 3.150 (total time: 98.410) Filter (dist only) r_work=0.1195 r_free=0.1386 | n_water=425 | time (s): 35.050 (total time: 133.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.379071 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1492.039963 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 0.1699 0.1803 0.0104 0.001 0.4 9.0 0.0 0.0 0 0.125 0.1528 0.1652 0.0125 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1405 0.1551 0.0146 0.001 0.4 7.0 0.0 0.0 0 0.500 0.1359 0.1517 0.0158 0.002 0.5 6.4 0.0 0.0 0 0.750 0.1318 0.1488 0.0170 0.002 0.5 6.1 0.0 0.0 0 1.000 0.1302 0.1474 0.0172 0.002 0.5 5.8 0.0 0.0 0 1.000 0.1254 0.1449 0.0195 0.002 0.5 6.1 0.5 0.0 0 2.000 0.1225 0.1430 0.0205 0.003 0.6 6.4 0.5 0.0 0 3.000 0.1210 0.1422 0.0212 0.003 0.7 6.4 0.5 0.0 0 4.000 0.1202 0.1415 0.0213 0.004 0.7 7.4 0.5 0.0 0 5.000 0.1199 0.1412 0.0213 0.005 0.7 7.0 0.5 0.0 0 6.000 0.1194 0.1408 0.0215 0.005 0.8 7.7 0.5 0.0 0 7.000 0.1194 0.1406 0.0212 0.005 0.8 6.7 0.5 0.0 0 8.000 0.1190 0.1403 0.0213 0.006 0.8 7.4 0.5 0.0 0 9.000 0.1186 0.1402 0.0216 0.006 0.8 7.7 0.5 0.0 0 10.000 0.1186 0.1402 0.0216 0.007 0.9 7.4 0.5 0.0 0 11.000 0.1183 0.1405 0.0222 0.007 0.9 8.0 0.5 0.0 0 12.000 0.1181 0.1400 0.0218 0.008 0.9 8.0 0.5 0.6 0 13.690 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1181 0.1400 0.0218 0.008 0.9 8.0 0.5 0.6 0 13.690 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.81 14.00 2.18 3.774 21.802 1492.040 0.015 11.81 14.00 2.18 3.774 21.802 44.761 0.015 11.81 14.00 2.18 3.774 21.802 186.505 0.015 11.96 14.38 2.42 3.635 21.803 746.020 0.015 12.02 14.76 2.74 3.468 22.110 1492.040 0.014 11.80 14.60 2.80 3.459 22.154 2238.060 0.014 11.76 14.65 2.89 3.486 22.152 2984.080 0.014 11.70 14.63 2.93 3.491 22.126 3730.100 0.014 11.64 14.64 3.00 3.494 22.056 4476.120 0.014 11.65 14.68 3.03 3.528 22.178 5222.140 0.013 11.62 14.72 3.09 3.542 22.167 5968.160 0.013 11.59 14.70 3.11 3.563 22.184 6714.180 0.013 11.58 14.72 3.14 3.578 22.184 7460.200 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.761 Accepted refinement result: 11.81 14.00 2.18 3.774 21.802 44.761 0.015 Individual atomic B min max mean iso aniso Overall: 9.08 115.02 22.24 3.31 199 1753 Protein: 9.08 115.02 17.01 3.32 0 1519 Water: 11.51 76.68 40.94 N/A 199 226 Other: 19.73 26.61 22.07 N/A 0 8 Chain A: 9.08 115.02 19.45 N/A 0 1753 Chain S: 12.20 60.00 46.88 N/A 199 0 Histogram: Values Number of atoms 9.08 - 19.67 1261 19.67 - 30.27 246 30.27 - 40.86 167 40.86 - 51.46 126 51.46 - 62.05 129 62.05 - 72.64 12 72.64 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1400 r_work=0.1181 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1400 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1179 r_free = 0.1395 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1179 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014552 | | target function (ls_wunit_k1) not normalized (work): 1212.091166 | | target function (ls_wunit_k1) not normalized (free): 98.824349 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1179 0.1395 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1575 0.1574 0.1624 n_refl.: 87591 remove outliers: r(all,work,free)=0.1575 0.1574 0.1624 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1577 0.1577 0.1625 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1175 0.1392 n_refl.: 87591 remove outliers: r(all,work,free)=0.1185 0.1175 0.1392 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 0.3306 300.123 275.605 0.602 1.002 0.360 11.894-9.307 99.02 97 4 0.1554 483.107 479.084 0.920 1.003 0.350 9.237-7.194 100.00 213 7 0.1604 395.122 395.614 0.983 1.003 0.260 7.162-5.571 100.00 427 22 0.1566 296.517 291.377 0.940 1.003 0.224 5.546-4.326 100.00 867 58 0.0875 407.045 403.797 0.959 1.003 0.210 4.315-3.360 100.00 1859 96 0.0775 387.102 386.408 1.006 1.003 0.190 3.356-2.611 100.00 3867 181 0.1076 254.306 253.595 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1002 168.582 168.093 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.327 82.561 1.029 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1436 36.507 36.055 1.024 0.996 0.000 1.221-1.150 99.97 13689 708 0.2245 23.002 21.519 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0210 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1175 r_free=0.1392 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=0.1175 r_free=0.1392 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1175 r_free=0.1392 | n_water=425 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1174 r_free=0.1389 | n_water=422 | time (s): 34.820 (total time: 36.990) Filter (q & B) r_work=0.1174 r_free=0.1389 | n_water=422 | time (s): 1.040 (total time: 38.030) Compute maps r_work=0.1174 r_free=0.1389 | n_water=422 | time (s): 1.750 (total time: 39.780) Filter (map) r_work=0.1215 r_free=0.1388 | n_water=286 | time (s): 3.240 (total time: 43.020) Find peaks r_work=0.1215 r_free=0.1388 | n_water=286 | time (s): 0.460 (total time: 43.480) Add new water r_work=0.1328 r_free=0.1502 | n_water=465 | time (s): 2.880 (total time: 46.360) Refine new water occ: r_work=0.1238 r_free=0.1422 adp: r_work=0.1239 r_free=0.1423 occ: r_work=0.1217 r_free=0.1402 adp: r_work=0.1216 r_free=0.1401 occ: r_work=0.1201 r_free=0.1385 adp: r_work=0.1197 r_free=0.1380 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1380 r_work=0.1197 r_free=0.1380 | n_water=465 | time (s): 191.110 (total time: 237.470) Filter (q & B) r_work=0.1201 r_free=0.1382 | n_water=433 | time (s): 3.330 (total time: 240.800) Filter (dist only) r_work=0.1201 r_free=0.1381 | n_water=431 | time (s): 35.750 (total time: 276.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.736479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.006884 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1234 0.1358 0.0124 0.002 0.6 4.2 0.5 0.0 0 0.087 0.1190 0.1326 0.0136 0.003 0.7 3.2 0.5 0.0 0 0.260 0.1172 0.1313 0.0141 0.004 0.8 2.9 0.5 0.0 0 0.521 0.1164 0.1309 0.0145 0.005 0.9 2.9 0.5 0.0 0 0.781 0.1160 0.1308 0.0148 0.006 1.0 3.2 0.5 0.0 0 1.042 0.1157 0.1307 0.0150 0.007 1.0 3.5 0.5 0.0 0 1.302 0.1154 0.1305 0.0151 0.007 1.0 3.8 0.5 0.0 0 1.563 0.1153 0.1305 0.0152 0.008 1.1 3.8 0.5 0.0 0 1.823 0.1163 0.1308 0.0145 0.005 0.9 2.9 0.5 0.0 0 0.868 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1305 0.0152 0.008 1.1 3.8 0.5 0.0 0 1.823 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 13.05 1.52 3.778 21.177 44.007 3.617 11.53 13.05 1.52 3.778 21.177 1.320 3.617 11.53 13.05 1.52 3.775 21.177 5.501 3.617 11.56 13.13 1.57 3.710 21.171 22.003 3.610 11.60 13.27 1.67 3.728 21.140 44.007 3.611 11.53 13.25 1.72 3.752 21.129 66.010 3.606 11.47 13.20 1.74 3.767 21.125 88.014 3.601 11.46 13.20 1.74 3.776 21.117 110.017 3.598 11.42 13.16 1.75 3.784 21.119 132.021 3.596 11.44 13.23 1.79 3.805 21.096 154.024 3.596 11.40 13.19 1.79 3.812 21.100 176.028 3.594 11.41 13.21 1.80 3.824 21.093 198.031 3.594 11.40 13.20 1.81 3.832 21.093 220.034 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.320 Accepted refinement result: 11.53 13.05 1.52 3.778 21.177 1.320 3.617 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.09 3.31 208 1750 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.53 76.69 35.39 N/A 208 223 Other: 19.75 26.62 22.08 N/A 0 8 Chain A: 9.09 115.03 19.40 N/A 0 1750 Chain S: 12.21 60.01 35.29 N/A 208 0 Histogram: Values Number of atoms 9.09 - 19.69 1262 19.69 - 30.28 289 30.28 - 40.88 211 40.88 - 51.47 125 51.47 - 62.06 48 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1305 r_work=0.1153 r_free=0.1305 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1305 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1144 r_free = 0.1310 target_work(ml) = 3.610 | | occupancies: max = 1.00 min = 0.14 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= 0.1144 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610473 | | target function (ml) not normalized (work): 300730.732005 | | target function (ml) not normalized (free): 15834.431548 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1144 0.1310 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1494 0.1492 0.1553 n_refl.: 87590 remove outliers: r(all,work,free)=0.1494 0.1492 0.1553 n_refl.: 87590 overall B=0.00 to atoms: r(all,work,free)=0.1494 0.1492 0.1554 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1306 n_refl.: 87590 remove outliers: r(all,work,free)=0.1146 0.1138 0.1306 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3775 300.093 269.201 0.517 1.000 0.330 11.894-9.307 98.04 96 4 0.2215 483.232 470.648 0.886 1.001 0.330 9.237-7.194 98.18 209 7 0.2224 386.591 388.805 0.963 1.001 0.200 7.162-5.571 100.00 427 22 0.1999 296.517 286.922 0.922 1.001 0.185 5.546-4.326 100.00 867 58 0.1103 407.045 402.310 0.964 1.002 0.175 4.315-3.360 100.00 1859 96 0.0938 387.102 384.215 1.004 1.002 0.170 3.356-2.611 100.00 3867 181 0.1139 254.306 252.176 1.005 1.002 0.100 2.608-2.026 99.99 8198 413 0.0929 168.582 167.826 1.022 1.002 0.000 2.025-1.573 100.00 17313 902 0.0896 82.327 82.651 1.032 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.507 36.085 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2163 23.002 21.454 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0020 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1306 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=0.1138 r_free=0.1306 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1306 | n_water=431 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1139 r_free=0.1307 | n_water=430 | time (s): 46.920 (total time: 49.370) Filter (q & B) r_work=0.1139 r_free=0.1308 | n_water=429 | time (s): 3.980 (total time: 53.350) Compute maps r_work=0.1139 r_free=0.1308 | n_water=429 | time (s): 1.920 (total time: 55.270) Filter (map) r_work=0.1162 r_free=0.1282 | n_water=333 | time (s): 3.910 (total time: 59.180) Find peaks r_work=0.1162 r_free=0.1282 | n_water=333 | time (s): 0.780 (total time: 59.960) Add new water r_work=0.1239 r_free=0.1368 | n_water=491 | time (s): 3.930 (total time: 63.890) Refine new water occ: r_work=0.1164 r_free=0.1305 adp: r_work=0.1164 r_free=0.1307 occ: r_work=0.1148 r_free=0.1293 adp: r_work=0.1147 r_free=0.1293 occ: r_work=0.1135 r_free=0.1284 adp: r_work=0.1131 r_free=0.1282 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1282 r_work=0.1131 r_free=0.1282 | n_water=491 | time (s): 248.700 (total time: 312.590) Filter (q & B) r_work=0.1135 r_free=0.1287 | n_water=460 | time (s): 3.990 (total time: 316.580) Filter (dist only) r_work=0.1135 r_free=0.1284 | n_water=459 | time (s): 48.140 (total time: 364.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.849782 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.065031 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 0.1324 0.0129 0.002 0.6 3.8 0.5 0.0 0 0.092 0.1160 0.1298 0.0138 0.003 0.8 3.2 0.5 0.0 0 0.277 0.1146 0.1289 0.0143 0.005 0.9 3.5 0.5 0.0 0 0.555 0.1140 0.1284 0.0144 0.006 1.0 4.2 0.5 0.0 0 0.832 0.1137 0.1289 0.0152 0.007 1.0 3.2 0.5 0.0 0 1.110 0.1134 0.1286 0.0151 0.007 1.1 3.5 0.5 0.0 0 1.387 0.1132 0.1288 0.0156 0.008 1.1 3.5 0.5 0.0 0 1.665 0.1131 0.1288 0.0157 0.009 1.1 3.5 0.5 0.0 0 1.942 0.1139 0.1288 0.0149 0.006 1.0 3.2 0.5 0.0 0 0.925 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1140 0.1284 0.0144 0.006 1.0 4.2 0.5 0.0 0 0.832 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.40 12.84 1.44 3.779 21.247 44.065 3.609 11.40 12.84 1.44 3.779 21.247 1.322 3.609 11.40 12.84 1.44 3.778 21.247 5.508 3.609 11.43 12.90 1.48 3.711 21.242 22.033 3.604 11.49 13.07 1.58 3.729 21.217 44.065 3.607 11.42 13.04 1.62 3.751 21.209 66.098 3.601 11.35 12.99 1.64 3.767 21.206 88.130 3.596 11.35 13.01 1.66 3.775 21.204 110.163 3.595 11.32 13.00 1.67 3.790 21.197 132.195 3.593 11.33 13.03 1.70 3.803 21.192 154.228 3.593 11.30 13.00 1.70 3.811 21.191 176.260 3.591 11.28 12.98 1.70 3.817 21.191 198.293 3.589 11.27 12.97 1.70 3.822 21.193 220.325 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.322 Accepted refinement result: 11.40 12.84 1.44 3.779 21.247 1.322 3.609 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.21 3.31 238 1748 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.53 76.70 35.06 N/A 238 221 Other: 19.75 26.62 22.09 N/A 0 8 Chain A: 9.09 115.03 19.40 N/A 0 1748 Chain S: 12.21 60.01 34.58 N/A 238 0 Histogram: Values Number of atoms 9.09 - 19.69 1266 19.69 - 30.28 294 30.28 - 40.88 229 40.88 - 51.47 130 51.47 - 62.06 44 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1140 r_free=0.1284 r_work=0.1140 r_free=0.1284 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1140 r_free = 0.1284 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1284 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.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1135 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607291 | | target function (ml) not normalized (work): 300440.443059 | | target function (ml) not normalized (free): 15815.196273 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1143 0.1135 0.1284 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1472 0.1471 0.1514 n_refl.: 87583 remove outliers: r(all,work,free)=0.1472 0.1471 0.1514 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1471 0.1470 0.1513 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1133 0.1286 n_refl.: 87583 remove outliers: r(all,work,free)=0.1139 0.1131 0.1286 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3674 293.446 264.957 0.466 1.001 0.293 11.894-9.307 97.06 95 4 0.2522 483.331 466.203 0.865 1.002 0.275 9.237-7.194 98.18 209 7 0.2341 386.591 380.905 0.937 1.002 0.174 7.162-5.571 100.00 427 22 0.2089 296.517 286.719 0.919 1.002 0.150 5.546-4.326 100.00 867 58 0.1109 407.045 402.701 0.965 1.002 0.140 4.315-3.360 100.00 1859 96 0.0911 387.102 384.981 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1094 254.306 252.374 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0917 168.582 167.951 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.327 82.682 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.507 36.119 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2172 23.002 21.547 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=-0.0105 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1131 r_free=0.1286 After: r_work=0.1132 r_free=0.1286 ================================== NQH flips ================================== r_work=0.1132 r_free=0.1286 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=0.1132 r_free=0.1286 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1132 r_free=0.1286 | n_water=459 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1132 r_free=0.1286 | n_water=459 | time (s): 46.170 (total time: 48.470) Filter (q & B) r_work=0.1132 r_free=0.1286 | n_water=459 | time (s): 1.400 (total time: 49.870) Compute maps r_work=0.1132 r_free=0.1286 | n_water=459 | time (s): 1.860 (total time: 51.730) Filter (map) r_work=0.1167 r_free=0.1302 | n_water=358 | time (s): 3.970 (total time: 55.700) Find peaks r_work=0.1167 r_free=0.1302 | n_water=358 | time (s): 0.710 (total time: 56.410) Add new water r_work=0.1218 r_free=0.1351 | n_water=508 | time (s): 3.790 (total time: 60.200) Refine new water occ: r_work=0.1151 r_free=0.1291 adp: r_work=0.1151 r_free=0.1292 occ: r_work=0.1139 r_free=0.1276 adp: r_work=0.1137 r_free=0.1277 occ: r_work=0.1130 r_free=0.1266 adp: r_work=0.1127 r_free=0.1266 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1266 r_work=0.1127 r_free=0.1266 | n_water=508 | time (s): 282.640 (total time: 342.840) Filter (q & B) r_work=0.1133 r_free=0.1268 | n_water=470 | time (s): 3.840 (total time: 346.680) Filter (dist only) r_work=0.1133 r_free=0.1268 | n_water=468 | time (s): 49.110 (total time: 395.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.816265 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.764573 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 0.1208 0.1322 0.0114 0.003 0.7 6.7 0.0 0.0 0 0.091 0.1160 0.1287 0.0127 0.004 0.8 6.7 0.5 0.0 0 0.272 0.1139 0.1271 0.0132 0.005 0.9 7.0 0.5 0.0 0 0.545 0.1132 0.1267 0.0135 0.006 1.0 7.0 0.5 0.0 0 0.817 0.1131 0.1267 0.0136 0.006 1.0 7.0 0.5 0.0 0 1.090 0.1128 0.1265 0.0137 0.007 1.1 7.0 0.5 0.0 0 1.362 0.1126 0.1264 0.0138 0.008 1.1 7.0 0.5 0.0 0 1.635 0.1126 0.1264 0.0138 0.009 1.1 7.0 0.5 0.0 0 1.907 0.1132 0.1267 0.0135 0.006 1.0 7.0 0.5 0.0 0 0.908 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1264 0.0138 0.009 1.1 7.0 0.5 0.0 0 1.907 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.64 1.38 3.779 21.262 44.765 3.600 11.26 12.64 1.38 3.779 21.262 1.343 3.600 11.26 12.64 1.38 3.777 21.262 5.596 3.600 11.28 12.68 1.41 3.713 21.254 22.382 3.594 11.35 12.86 1.51 3.727 21.226 44.765 3.598 11.26 12.81 1.56 3.757 21.218 67.147 3.592 11.21 12.78 1.57 3.770 21.215 89.529 3.587 11.19 12.77 1.58 3.780 21.213 111.911 3.585 11.17 12.78 1.61 3.795 21.206 134.294 3.584 11.15 12.78 1.63 3.807 21.202 156.676 3.582 11.15 12.78 1.64 3.815 21.199 179.058 3.581 11.13 12.77 1.64 3.823 21.200 201.441 3.580 11.12 12.76 1.64 3.831 21.199 223.823 3.580 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.343 Accepted refinement result: 11.26 12.64 1.38 3.779 21.262 1.343 3.600 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.24 3.31 249 1746 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.52 76.69 34.93 N/A 249 219 Other: 19.74 26.62 22.08 N/A 0 8 Chain A: 9.09 115.03 19.37 N/A 0 1746 Chain S: 12.21 60.01 34.35 N/A 249 0 Histogram: Values Number of atoms 9.09 - 19.68 1266 19.68 - 30.28 308 30.28 - 40.87 220 40.87 - 51.47 133 51.47 - 62.06 45 62.06 - 72.65 12 72.65 - 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=0.1126 r_free=0.1264 r_work=0.1126 r_free=0.1264 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1264 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1122 r_free = 0.1261 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1122 r_free= 0.1261 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598181 | | target function (ml) not normalized (work): 299667.280702 | | target function (ml) not normalized (free): 15778.226720 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1317 0.1263 5.6621 5.5505| | 2: 3.57 - 2.84 1.00 2888 124 0.1035 0.1331 5.1281 5.1921| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1184 4.9105 4.9378| | 4: 2.47 - 2.25 1.00 2825 136 0.0884 0.0982 4.6003 4.6341| | 5: 2.25 - 2.09 1.00 2756 127 0.0859 0.0934 4.5475 4.5992| | 6: 2.09 - 1.97 1.00 2846 113 0.0858 0.0998 4.2515 4.3496| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1129 3.9762 4.0918| | 8: 1.87 - 1.79 1.00 2789 144 0.0908 0.1118 3.8868 3.9966| | 9: 1.79 - 1.72 1.00 2745 138 0.0871 0.1189 3.6462 3.8345| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1191 3.5675 3.7145| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1036 3.4941 3.566| | 12: 1.61 - 1.56 1.00 2773 144 0.0899 0.1117 3.325 3.4484| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1018 3.3038 3.3896| | 14: 1.52 - 1.48 1.00 2803 134 0.0972 0.1038 3.2344 3.3151| | 15: 1.48 - 1.45 1.00 2738 128 0.0996 0.1228 3.1502 3.2687| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1228 3.1319 3.2372| | 17: 1.42 - 1.39 1.00 2785 139 0.1131 0.1289 3.1147 3.2301| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1333 3.1023 3.241| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1560 3.109 3.2672| | 20: 1.34 - 1.32 1.00 2696 147 0.1363 0.1437 3.1097 3.1477| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1516 3.1125 3.1096| | 22: 1.29 - 1.27 1.00 2704 152 0.1552 0.1973 3.1182 3.2945| | 23: 1.27 - 1.26 1.00 2802 156 0.1643 0.1801 3.1322 3.2001| | 24: 1.26 - 1.24 1.00 2744 132 0.1703 0.1820 3.126 3.2233| | 25: 1.24 - 1.22 1.00 2733 148 0.1880 0.2145 3.1433 3.2651| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1778 3.1478 3.2019| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2158 3.1702 3.1632| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2277 3.1669 3.1697| | 29: 1.18 - 1.16 1.00 2800 134 0.2271 0.2389 3.1495 3.232| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2459 3.1431 3.1699| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 7.84 1.00 0.97 5224.50| | 2: 3.57 - 2.84 2888 124 0.93 11.82 1.01 0.97 5224.50| | 3: 2.83 - 2.48 2820 163 0.90 15.77 0.99 0.97 4375.22| | 4: 2.47 - 2.25 2825 136 0.92 12.85 1.00 0.98 2185.17| | 5: 2.25 - 2.09 2756 127 0.91 14.93 1.01 0.98 2185.17| | 6: 2.09 - 1.97 2846 113 0.93 12.05 1.02 0.98 1281.14| | 7: 1.97 - 1.87 2787 165 0.95 9.31 1.02 0.98 510.12| | 8: 1.87 - 1.79 2789 144 0.93 12.62 1.00 0.98 510.12| | 9: 1.79 - 1.72 2745 138 0.94 10.05 0.98 0.98 289.97| | 10: 1.72 - 1.66 2831 160 0.94 11.13 0.98 0.97 245.89| | 11: 1.66 - 1.61 2712 147 0.93 11.78 0.98 0.97 235.47| | 12: 1.61 - 1.56 2773 144 0.96 8.86 0.99 0.97 137.25| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 137.25| | 14: 1.52 - 1.48 2803 134 0.94 10.74 1.02 0.98 123.12| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 97.25| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.25| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.98 88.69| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.98 83.74| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.98 83.74| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.97 79.86| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.58| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.01| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.95 82.15| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.96 0.95 82.15| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.16| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.03 0.93 86.39| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 86.39| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.22| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.93 91.66| | 30: 1.16 - 1.15 2739 148 0.86 22.05 0.98 0.93 91.66| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.58 max = 5224.50 mean = 821.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.31| |phase err.(test): min = 0.00 max = 89.55 mean = 13.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1122 0.1261 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1441 0.1440 0.1479 n_refl.: 87579 remove outliers: r(all,work,free)=0.1441 0.1440 0.1479 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1440 0.1439 0.1478 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1122 0.1262 n_refl.: 87579 remove outliers: r(all,work,free)=0.1127 0.1120 0.1262 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 0.3958 288.671 255.267 0.447 0.999 0.300 11.894-9.307 92.16 90 4 0.2274 471.407 463.170 0.878 1.001 0.227 9.237-7.194 98.18 209 7 0.2344 386.591 381.715 0.931 1.002 0.160 7.162-5.571 100.00 427 22 0.2087 296.517 286.606 0.916 1.002 0.130 5.546-4.326 100.00 867 58 0.1099 407.045 402.267 0.962 1.002 0.123 4.315-3.360 100.00 1859 96 0.0910 387.102 384.757 1.002 1.002 0.093 3.356-2.611 100.00 3867 181 0.1083 254.306 252.264 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0902 168.582 167.892 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.327 82.631 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.507 36.100 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 23.002 21.541 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0113 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1960 0.084 5.208 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1795 0.084 5.208 9.0 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1795 0.084 5.208 9.0 119.5 20.1 258 0.000 1_nqh: 0.1630 0.1798 0.084 5.208 9.0 119.5 20.1 258 0.003 1_weight: 0.1630 0.1798 0.084 5.208 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1219 0.1459 0.007 0.936 9.0 119.5 20.1 258 0.128 1_adp: 0.1227 0.1457 0.007 0.936 9.0 119.4 20.1 258 0.128 1_regHadp: 0.1228 0.1460 0.007 0.936 9.0 119.4 20.1 258 0.128 1_occ: 0.1224 0.1456 0.007 0.936 9.0 119.4 20.1 258 0.128 2_bss: 0.1220 0.1448 0.007 0.936 9.1 119.5 20.1 258 0.128 2_settarget: 0.1220 0.1448 0.007 0.936 9.1 119.5 20.1 258 0.128 2_updatecdl: 0.1220 0.1448 0.007 0.947 9.1 119.5 20.1 258 0.128 2_nqh: 0.1222 0.1449 0.007 0.947 9.1 119.5 20.1 258 0.131 2_sol: 0.1195 0.1386 0.007 0.947 9.1 115.0 22.2 425 n/a 2_weight: 0.1195 0.1386 0.007 0.947 9.1 115.0 22.2 425 n/a 2_xyzrec: 0.1181 0.1400 0.008 0.924 9.1 115.0 22.2 425 n/a 2_adp: 0.1181 0.1400 0.008 0.924 9.1 115.0 22.2 425 n/a 2_regHadp: 0.1181 0.1400 0.008 0.924 9.1 115.0 22.2 425 n/a 2_occ: 0.1179 0.1395 0.008 0.924 9.1 115.0 22.2 425 n/a 3_bss: 0.1175 0.1392 0.008 0.924 9.1 115.0 22.3 425 n/a 3_settarget: 0.1175 0.1392 0.008 0.924 9.1 115.0 22.3 425 n/a 3_updatecdl: 0.1175 0.1392 0.008 0.925 9.1 115.0 22.3 425 n/a 3_nqh: 0.1175 0.1392 0.008 0.925 9.1 115.0 22.3 425 n/a 3_sol: 0.1201 0.1381 0.008 0.925 9.1 115.0 21.1 431 n/a 3_weight: 0.1201 0.1381 0.008 0.925 9.1 115.0 21.1 431 n/a 3_xyzrec: 0.1153 0.1305 0.008 1.080 9.1 115.0 21.1 431 n/a 3_adp: 0.1153 0.1305 0.008 1.080 9.1 115.0 21.1 431 n/a 3_regHadp: 0.1153 0.1305 0.008 1.080 9.1 115.0 21.1 431 n/a 3_occ: 0.1144 0.1310 0.008 1.080 9.1 115.0 21.1 431 n/a 4_bss: 0.1138 0.1306 0.008 1.080 9.1 115.0 21.1 431 n/a 4_settarget: 0.1138 0.1306 0.008 1.080 9.1 115.0 21.1 431 n/a 4_updatecdl: 0.1138 0.1306 0.008 1.082 9.1 115.0 21.1 431 n/a 4_nqh: 0.1138 0.1306 0.008 1.082 9.1 115.0 21.1 431 n/a 4_sol: 0.1135 0.1284 0.008 1.082 9.1 115.0 21.2 459 n/a 4_weight: 0.1135 0.1284 0.008 1.082 9.1 115.0 21.2 459 n/a 4_xyzrec: 0.1140 0.1284 0.006 0.966 9.1 115.0 21.2 459 n/a 4_adp: 0.1140 0.1284 0.006 0.966 9.1 115.0 21.2 459 n/a 4_regHadp: 0.1140 0.1284 0.006 0.966 9.1 115.0 21.2 459 n/a 4_occ: 0.1135 0.1284 0.006 0.966 9.1 115.0 21.2 459 n/a 5_bss: 0.1131 0.1286 0.006 0.966 9.1 115.0 21.2 459 n/a 5_settarget: 0.1131 0.1286 0.006 0.966 9.1 115.0 21.2 459 n/a 5_updatecdl: 0.1131 0.1286 0.006 0.965 9.1 115.0 21.2 459 n/a 5_setrh: 0.1132 0.1286 0.006 0.965 9.1 115.0 21.2 459 n/a 5_nqh: 0.1132 0.1286 0.006 0.965 9.1 115.0 21.2 459 n/a 5_sol: 0.1133 0.1268 0.006 0.965 9.1 115.0 21.2 468 n/a 5_weight: 0.1133 0.1268 0.006 0.965 9.1 115.0 21.2 468 n/a 5_xyzrec: 0.1126 0.1264 0.009 1.124 9.1 115.0 21.2 468 n/a 5_adp: 0.1126 0.1264 0.009 1.124 9.1 115.0 21.2 468 n/a 5_regHadp: 0.1126 0.1264 0.009 1.124 9.1 115.0 21.2 468 n/a 5_occ: 0.1122 0.1261 0.009 1.124 9.1 115.0 21.2 468 n/a end: 0.1120 0.1262 0.009 1.124 9.1 115.0 21.2 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7427252_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7427252_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1000 Refinement macro-cycles (run) : 13814.6800 Write final files (write_after_run_outputs) : 97.1900 Total : 13914.9700 Total CPU time: 3.87 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:13:22 PST -0800 (1735366402.53 s) Start R-work = 0.1628, R-free = 0.1795 Final R-work = 0.1120, R-free = 0.1262 =============================================================================== Job complete usr+sys time: 14102.72 seconds wall clock time: 257 minutes 41.49 seconds (15461.49 seconds total)