Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6462862.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.51, per 1000 atoms: 0.45 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: 0.31 Conformation dependent library (CDL) restraints added in 109.4 milliseconds Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 532 0.92 - 1.17: 1105 1.17 - 1.43: 688 1.43 - 1.69: 810 1.69 - 1.95: 18 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALEU A 153 " pdb=" CA ALEU A 153 " ideal model delta sigma weight residual 1.456 1.726 -0.269 1.21e-02 6.83e+03 4.96e+02 bond pdb=" C VAL A 69 " pdb=" O VAL A 69 " ideal model delta sigma weight residual 1.235 1.423 -0.188 1.02e-02 9.61e+03 3.40e+02 bond pdb=" N BLYS A 132 " pdb=" CA BLYS A 132 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.12e+02 bond pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 1.459 1.255 0.204 1.17e-02 7.31e+03 3.03e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.454 1.661 -0.207 1.21e-02 6.83e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 2904 4.22 - 8.44: 1893 8.44 - 12.65: 760 12.65 - 16.87: 193 16.87 - 21.09: 27 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 120.84 136.82 -15.98 1.16e+00 7.43e-01 1.90e+02 angle pdb=" CA LYS A 12 " pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 120.96 105.98 14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.91 135.32 -13.41 9.80e-01 1.04e+00 1.87e+02 angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 107.87 14.25 1.06e+00 8.90e-01 1.81e+02 angle pdb=" C LEU A 72 " pdb=" CA LEU A 72 " pdb=" CB LEU A 72 " ideal model delta sigma weight residual 110.17 123.12 -12.95 9.90e-01 1.02e+00 1.71e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 957 17.98 - 35.96: 103 35.96 - 53.93: 38 53.93 - 71.91: 10 71.91 - 89.89: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CG ATYR A 67 " pdb=" CD1ATYR A 67 " pdb=" CE1ATYR A 67 " pdb=" HE1ATYR A 67 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.272: 117 0.272 - 0.544: 84 0.544 - 0.815: 28 0.815 - 1.086: 12 1.086 - 1.358: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.61e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CA ALA A 86 " pdb=" N ALA A 86 " pdb=" C ALA A 86 " pdb=" CB ALA A 86 " both_signs ideal model delta sigma weight residual False 2.48 1.47 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.072 2.00e-02 2.50e+03 6.94e-02 1.44e+02 pdb=" CG PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.016 2.00e-02 2.50e+03 6.26e-02 1.18e+02 pdb=" CG PHE A 162 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.096 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.079 2.00e-02 2.50e+03 5.99e-02 1.08e+02 pdb=" CG ATYR A 67 " -0.065 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.035 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.115 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.042 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 398 2.19 - 2.80: 7074 2.80 - 3.40: 10882 3.40 - 4.00: 15533 4.00 - 4.60: 22718 Nonbonded interactions: 56605 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.592 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.789 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 1.850 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.810 2.100 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.823 2.100 ... (remaining 56600 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_6462862_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= 0.2612 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789482 | | target function (ml) not normalized (work): 232380.616952 | | target function (ml) not normalized (free): 11799.032408 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2091 7.0263 4.9478| | 2: 3.57 - 2.84 1.00 2876 122 0.2428 0.1855 4.3526 4.3486| | 3: 2.84 - 2.48 1.00 2833 165 0.2387 0.1664 4.1332 4.1735| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1429 3.8325 3.832| | 5: 2.25 - 2.09 1.00 2756 127 0.2471 0.1560 3.8002 3.8215| | 6: 2.09 - 1.97 1.00 2846 113 0.2519 0.1743 3.4686 3.5688| | 7: 1.97 - 1.87 1.00 2787 165 0.2619 0.1753 3.1528 3.1764| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1799 3.0605 3.1021| | 9: 1.79 - 1.72 1.00 2745 138 0.2435 0.1912 2.9112 2.963| | 10: 1.72 - 1.66 1.00 2789 158 0.2405 0.1967 2.7873 2.8858| | 11: 1.66 - 1.61 1.00 2740 147 0.2490 0.1756 2.7383 2.7351| | 12: 1.61 - 1.56 1.00 2787 146 0.2495 0.2035 2.6311 2.7271| | 13: 1.56 - 1.52 1.00 2745 130 0.2594 0.1702 2.5884 2.5296| | 14: 1.52 - 1.48 1.00 2803 134 0.2562 0.2152 2.5022 2.5682| | 15: 1.48 - 1.45 1.00 2738 128 0.2639 0.1974 2.4146 2.4521| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.1940 2.3792 2.3948| | 17: 1.42 - 1.39 1.00 2785 139 0.2707 0.1958 2.3311 2.3007| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2298 2.2628 2.3541| | 19: 1.36 - 1.34 1.00 2807 134 0.2655 0.2276 2.2422 2.2993| | 20: 1.34 - 1.32 1.00 2696 147 0.2683 0.2187 2.2067 2.2198| | 21: 1.32 - 1.30 1.00 2785 112 0.2736 0.2338 2.1697 2.1633| | 22: 1.29 - 1.27 1.00 2704 152 0.2770 0.2580 2.1497 2.2329| | 23: 1.27 - 1.26 1.00 2802 156 0.2710 0.2602 2.0866 2.2206| | 24: 1.26 - 1.24 1.00 2744 132 0.2701 0.2433 2.064 2.1097| | 25: 1.24 - 1.22 1.00 2734 148 0.2842 0.2523 2.0363 2.0674| | 26: 1.22 - 1.21 1.00 2727 135 0.2840 0.2267 2.0085 2.047| | 27: 1.21 - 1.19 1.00 2814 148 0.2968 0.2570 2.0062 1.9761| | 28: 1.19 - 1.18 1.00 2671 147 0.2988 0.2820 1.9851 1.9826| | 29: 1.18 - 1.16 1.00 2800 134 0.2996 0.2915 1.9617 2.0574| | 30: 1.16 - 1.15 1.00 2740 148 0.3067 0.2876 1.941 1.9708| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.96 0.76 0.23 1499.57| | 2: 3.57 - 2.84 2876 122 0.80 26.22 1.27 0.23 1499.57| | 3: 2.84 - 2.48 2833 165 0.74 32.22 1.25 0.23 1242.65| | 4: 2.47 - 2.25 2825 136 0.81 25.65 1.26 0.25 575.90| | 5: 2.25 - 2.09 2756 127 0.77 29.47 1.28 0.25 575.90| | 6: 2.09 - 1.97 2846 113 0.84 22.53 1.29 0.25 313.32| | 7: 1.97 - 1.87 2787 165 0.90 16.62 1.29 0.25 89.37| | 8: 1.87 - 1.79 2789 144 0.86 21.08 1.25 0.25 89.37| | 9: 1.79 - 1.72 2745 138 0.88 18.42 1.23 0.25 54.08| | 10: 1.72 - 1.66 2789 158 0.87 19.85 1.22 0.25 47.01| | 11: 1.66 - 1.61 2740 147 0.86 21.32 1.24 0.25 45.35| | 12: 1.61 - 1.56 2787 146 0.89 18.03 1.23 0.25 28.48| | 13: 1.56 - 1.52 2745 130 0.87 20.07 1.24 0.25 28.48| | 14: 1.52 - 1.48 2803 134 0.87 20.35 1.23 0.25 25.54| | 15: 1.48 - 1.45 2738 128 0.87 20.05 1.25 0.25 20.15| | 16: 1.45 - 1.42 2756 161 0.86 21.41 1.23 0.25 20.15| | 17: 1.42 - 1.39 2785 139 0.87 20.79 1.23 0.25 17.23| | 18: 1.39 - 1.36 2741 179 0.86 21.18 1.24 0.25 15.53| | 19: 1.36 - 1.34 2807 134 0.86 21.94 1.22 0.25 15.53| | 20: 1.34 - 1.32 2696 147 0.87 20.94 1.21 0.24 12.98| | 21: 1.32 - 1.30 2785 112 0.86 21.95 1.21 0.24 12.80| | 22: 1.29 - 1.27 2704 152 0.85 22.34 1.20 0.24 12.52| | 23: 1.27 - 1.26 2802 156 0.86 22.23 1.20 0.24 11.11| | 24: 1.26 - 1.24 2744 132 0.85 22.57 1.20 0.24 11.11| | 25: 1.24 - 1.22 2734 148 0.84 23.97 1.22 0.24 10.59| | 26: 1.22 - 1.21 2727 135 0.84 24.29 1.20 0.23 10.01| | 27: 1.21 - 1.19 2814 148 0.83 24.94 1.20 0.23 10.01| | 28: 1.19 - 1.18 2671 147 0.82 25.76 1.19 0.23 9.40| | 29: 1.18 - 1.16 2800 134 0.82 26.21 1.16 0.22 9.18| | 30: 1.16 - 1.15 2740 148 0.80 27.52 1.15 0.22 9.18| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.18 max = 1499.57 mean = 216.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.63| |phase err.(test): min = 0.00 max = 89.88 mean = 22.40| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.269 1557 Z= 5.407 Angle : 5.189 18.284 2118 Z= 3.660 Chirality : 0.408 1.358 243 Planarity : 0.032 0.088 284 Dihedral : 13.844 89.886 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.42), residues: 224 helix: -2.76 (0.33), residues: 107 sheet: -2.02 (0.79), residues: 24 loop : -1.05 (0.51), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.026 ARG A 98 TYR 0.072 0.044 TYR A 139 PHE 0.095 0.041 PHE A 164 HIS 0.045 0.026 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2612 r_free= 0.1931 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789482 | | target function (ml) not normalized (work): 232380.616952 | | target function (ml) not normalized (free): 11799.032408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2570 0.2613 0.1932 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2570 0.2613 0.1932 n_refl.: 87602 remove outliers: r(all,work,free)=0.1983 0.1988 0.1932 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2008 0.2013 0.1945 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1646 0.1640 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1760 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 0.3874 386.351 358.039 0.667 1.002 0.407 11.894-9.307 99.02 97 4 0.1833 613.700 593.975 0.927 1.003 0.375 9.237-7.194 100.00 213 7 0.2158 501.931 492.314 0.956 1.004 0.344 7.162-5.571 100.00 427 22 0.2215 376.671 364.196 0.925 1.004 0.288 5.546-4.326 100.00 867 58 0.1277 517.076 511.670 0.960 1.004 0.229 4.315-3.360 100.00 1859 96 0.1149 491.743 488.443 1.004 1.003 0.173 3.356-2.611 100.00 3867 181 0.1441 323.050 319.565 0.998 1.002 0.067 2.608-2.026 99.99 8198 413 0.1341 214.153 212.147 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1664 104.581 103.882 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2064 46.375 45.008 1.006 0.994 0.000 1.221-1.150 99.97 13689 708 0.2596 29.220 26.899 0.976 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1641 r_free=0.1762 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.116842 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2004.749329 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 0.1761 0.1874 0.0112 0.001 0.4 5.1 0.0 0.0 0 0.125 0.1573 0.1707 0.0135 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1445 0.1610 0.0164 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1395 0.1581 0.0186 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1355 0.1561 0.0206 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1359 0.1561 0.0202 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1304 0.1524 0.0220 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1275 0.1503 0.0228 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1261 0.1491 0.0230 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1251 0.1486 0.0235 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1244 0.1480 0.0236 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1239 0.1478 0.0239 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1237 0.1479 0.0242 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1232 0.1476 0.0244 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1229 0.1473 0.0244 0.006 0.9 2.9 0.5 0.0 0 10.000 0.1228 0.1472 0.0244 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1476 0.0249 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1226 0.1479 0.0253 0.007 1.0 3.5 0.5 0.6 0 13.058 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1472 0.0244 0.007 0.9 3.5 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.72 2.44 3.013 19.066 2004.749 0.017 12.28 14.72 2.44 3.003 19.066 60.142 0.017 12.34 14.69 2.35 2.669 19.066 250.594 0.017 12.70 15.42 2.72 2.913 19.367 1002.375 0.016 12.50 15.43 2.92 3.273 19.614 2004.749 0.016 12.40 15.46 3.07 3.332 19.647 3007.124 0.015 12.32 15.42 3.10 3.361 19.653 4009.499 0.015 12.29 15.48 3.18 3.438 19.680 5011.873 0.015 12.25 15.43 3.18 3.410 19.662 6014.248 0.015 12.15 15.31 3.17 3.254 19.560 7016.623 0.015 12.18 15.44 3.26 3.385 19.638 8018.997 0.015 12.31 15.80 3.48 3.670 19.751 9021.372 0.015 12.21 15.65 3.44 3.654 19.751 10023.747 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: 250.594 Accepted refinement result: 12.34 14.69 2.35 2.669 19.066 250.594 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.46 20.09 3.31 0 1785 Protein: 9.09 115.00 17.00 3.32 0 1519 Water: 11.48 119.46 38.24 N/A 0 258 Other: 19.72 26.63 22.07 N/A 0 8 Chain A: 9.09 119.46 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1469 r_work=0.1236 r_free=0.1473 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1473 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 = 0.1231 r_free = 0.1471 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= 0.1231 r_free= 0.1471 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016867 | | target function (ls_wunit_k1) not normalized (work): 1404.965939 | | target function (ls_wunit_k1) not normalized (free): 112.011472 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1471 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1675 0.1676 0.1705 n_refl.: 87593 remove outliers: r(all,work,free)=0.1675 0.1676 0.1705 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1680 0.1681 0.1709 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1463 n_refl.: 87593 remove outliers: r(all,work,free)=0.1240 0.1229 0.1463 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 0.3521 301.138 281.046 0.649 1.003 0.380 11.894-9.307 99.02 97 4 0.1632 482.406 469.863 0.922 1.003 0.362 9.237-7.194 100.00 213 7 0.1869 394.549 388.601 0.965 1.003 0.344 7.162-5.571 100.00 427 22 0.1839 296.087 290.070 0.933 1.003 0.258 5.546-4.326 100.00 867 58 0.1020 406.454 403.236 0.962 1.003 0.199 4.315-3.360 100.00 1859 96 0.0875 386.541 385.416 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1172 253.937 252.792 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1025 168.337 167.651 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.207 82.398 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.454 35.960 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2252 22.969 21.458 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1463 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1228 r_free=0.1461 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1461 | n_water=258 | time (s): 1.820 (total time: 1.820) Filter (dist) r_work=0.1236 r_free=0.1461 | n_water=252 | time (s): 20.900 (total time: 22.720) Filter (q & B) r_work=0.1238 r_free=0.1460 | n_water=249 | time (s): 2.650 (total time: 25.370) Compute maps r_work=0.1238 r_free=0.1460 | n_water=249 | time (s): 1.250 (total time: 26.620) Filter (map) r_work=0.1252 r_free=0.1472 | n_water=228 | time (s): 2.680 (total time: 29.300) Find peaks r_work=0.1252 r_free=0.1472 | n_water=228 | time (s): 0.470 (total time: 29.770) Add new water r_work=0.1393 r_free=0.1627 | n_water=438 | time (s): 2.410 (total time: 32.180) Refine new water occ: r_work=0.1298 r_free=0.1495 adp: r_work=0.1218 r_free=0.1441 occ: r_work=0.1229 r_free=0.1428 adp: r_work=0.1198 r_free=0.1417 occ: r_work=0.1201 r_free=0.1410 adp: r_work=0.1191 r_free=0.1408 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1408 r_work=0.1191 r_free=0.1408 | n_water=438 | time (s): 89.650 (total time: 121.830) Filter (q & B) r_work=0.1195 r_free=0.1418 | n_water=421 | time (s): 2.720 (total time: 124.550) Filter (dist only) r_work=0.1195 r_free=0.1417 | n_water=420 | time (s): 35.160 (total time: 159.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.111946 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1494.179460 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 0.1701 0.1824 0.0124 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1559 0.1703 0.0144 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1418 0.1589 0.0170 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1370 0.1553 0.0184 0.002 0.4 5.1 0.0 0.0 0 0.750 0.1317 0.1515 0.0198 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1307 0.1505 0.0198 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1254 0.1467 0.0212 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1224 0.1445 0.0221 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1213 0.1439 0.0226 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1205 0.1432 0.0227 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1200 0.1426 0.0226 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1198 0.1426 0.0228 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1194 0.1422 0.0228 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1190 0.1421 0.0231 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1188 0.1419 0.0231 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1185 0.1414 0.0229 0.007 0.9 6.1 0.5 0.0 0 11.000 0.1183 0.1416 0.0232 0.007 0.9 5.8 0.5 0.0 0 12.000 0.1180 0.1415 0.0235 0.007 0.9 6.4 0.5 0.0 0 13.000 0.1177 0.1412 0.0235 0.008 1.0 6.4 0.5 0.6 0 14.556 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1177 0.1412 0.0235 0.008 1.0 6.4 0.5 0.6 0 14.556 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.77 14.12 2.35 3.776 21.781 1494.179 0.016 11.77 14.12 2.35 3.776 21.781 44.825 0.016 11.77 14.12 2.35 3.776 21.781 186.772 0.016 11.93 14.46 2.53 3.640 21.781 747.090 0.015 11.97 14.81 2.85 3.504 21.899 1494.179 0.015 11.81 14.74 2.93 3.442 22.077 2241.269 0.014 11.71 14.62 2.92 3.476 22.120 2988.359 0.014 11.61 14.66 3.05 3.525 21.922 3735.449 0.014 11.63 14.65 3.02 3.514 22.067 4482.538 0.014 11.60 14.64 3.04 3.532 22.085 5229.628 0.014 11.57 14.69 3.13 3.537 22.046 5976.718 0.014 11.52 14.65 3.13 3.551 22.087 6723.808 0.013 11.52 14.66 3.14 3.592 22.185 7470.897 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: 186.772 Accepted refinement result: 11.77 14.12 2.35 3.776 21.781 186.772 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 22.19 3.31 192 1755 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.50 76.69 40.84 N/A 192 228 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.11 115.03 19.50 N/A 0 1755 Chain S: 12.68 60.00 46.78 N/A 192 0 Histogram: Values Number of atoms 9.11 - 19.71 1260 19.71 - 30.30 244 30.30 - 40.89 160 40.89 - 51.48 139 51.48 - 62.07 121 62.07 - 72.67 12 72.67 - 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=0.1177 r_free=0.1412 r_work=0.1177 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1177 r_free = 0.1412 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 = 0.1177 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 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= 0.1177 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014682 | | target function (ls_wunit_k1) not normalized (work): 1222.943715 | | target function (ls_wunit_k1) not normalized (free): 101.701144 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1188 0.1177 0.1408 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1578 0.1578 0.1617 n_refl.: 87592 remove outliers: r(all,work,free)=0.1578 0.1578 0.1617 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1579 0.1578 0.1617 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1173 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1183 0.1172 0.1402 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 0.3240 297.046 275.554 0.591 1.003 0.350 11.894-9.307 99.02 97 4 0.1695 482.406 474.736 0.917 1.003 0.337 9.237-7.194 100.00 213 7 0.1652 394.549 392.712 0.988 1.003 0.290 7.162-5.571 100.00 427 22 0.1541 296.087 291.611 0.935 1.003 0.209 5.546-4.326 100.00 867 58 0.0864 406.454 403.382 0.960 1.003 0.190 4.315-3.360 100.00 1859 96 0.0763 386.541 385.549 1.006 1.003 0.180 3.356-2.611 100.00 3867 181 0.1066 253.937 252.954 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1002 168.337 167.763 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1089 82.207 82.430 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1439 36.454 35.998 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2247 22.969 21.492 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=0.0062 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1172 r_free=0.1402 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=0.1172 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1402 | n_water=420 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1173 r_free=0.1396 | n_water=415 | time (s): 35.130 (total time: 36.940) Filter (q & B) r_work=0.1173 r_free=0.1396 | n_water=415 | time (s): 1.110 (total time: 38.050) Compute maps r_work=0.1173 r_free=0.1396 | n_water=415 | time (s): 1.780 (total time: 39.830) Filter (map) r_work=0.1215 r_free=0.1383 | n_water=288 | time (s): 3.130 (total time: 42.960) Find peaks r_work=0.1215 r_free=0.1383 | n_water=288 | time (s): 0.640 (total time: 43.600) Add new water r_work=0.1329 r_free=0.1503 | n_water=475 | time (s): 2.740 (total time: 46.340) Refine new water occ: r_work=0.1236 r_free=0.1417 adp: r_work=0.1237 r_free=0.1419 occ: r_work=0.1213 r_free=0.1395 adp: r_work=0.1213 r_free=0.1395 occ: r_work=0.1195 r_free=0.1384 adp: r_work=0.1191 r_free=0.1379 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1379 r_work=0.1191 r_free=0.1379 | n_water=475 | time (s): 210.270 (total time: 256.610) Filter (q & B) r_work=0.1195 r_free=0.1384 | n_water=443 | time (s): 2.880 (total time: 259.490) Filter (dist only) r_work=0.1195 r_free=0.1383 | n_water=442 | time (s): 36.360 (total time: 295.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.774373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.335918 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 0.1374 0.0139 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1187 0.1334 0.0147 0.003 0.7 4.2 0.5 0.0 0 0.266 0.1169 0.1324 0.0155 0.004 0.8 3.8 0.5 0.0 0 0.532 0.1160 0.1318 0.0157 0.005 0.9 3.8 0.5 0.0 0 0.798 0.1159 0.1318 0.0159 0.006 1.0 3.5 0.5 0.0 0 1.065 0.1155 0.1318 0.0162 0.007 1.0 3.8 0.5 0.0 0 1.331 0.1153 0.1318 0.0164 0.007 1.1 3.8 0.5 0.0 0 1.597 0.1151 0.1315 0.0164 0.008 1.1 4.2 0.5 0.0 0 1.863 0.1162 0.1318 0.0156 0.005 0.9 3.5 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1315 0.0164 0.008 1.1 4.2 0.5 0.0 0 1.863 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.15 1.64 3.779 21.249 40.336 3.619 11.51 13.15 1.64 3.779 21.249 1.210 3.619 11.51 13.15 1.64 3.779 21.249 5.042 3.619 11.55 13.23 1.68 3.708 21.243 20.168 3.613 11.65 13.44 1.78 3.714 21.214 40.336 3.617 11.56 13.39 1.82 3.741 21.199 60.504 3.610 11.47 13.31 1.84 3.767 21.197 80.672 3.604 11.44 13.29 1.85 3.776 21.195 100.840 3.601 11.41 13.27 1.86 3.784 21.190 121.008 3.599 11.42 13.31 1.89 3.801 21.177 141.176 3.599 11.40 13.30 1.90 3.811 21.173 161.344 3.598 11.39 13.29 1.90 3.822 21.164 181.512 3.596 11.40 13.30 1.90 3.831 21.160 201.680 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.042 Accepted refinement result: 11.51 13.15 1.64 3.779 21.249 5.042 3.619 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.21 3.31 218 1751 Protein: 9.12 115.04 17.03 3.32 0 1519 Water: 11.51 76.70 35.56 N/A 218 224 Other: 19.75 26.66 22.10 N/A 0 8 Chain A: 9.12 115.04 19.44 N/A 0 1751 Chain S: 12.69 60.00 35.47 N/A 218 0 Histogram: Values Number of atoms 9.12 - 19.71 1264 19.71 - 30.30 288 30.30 - 40.89 217 40.89 - 51.49 129 51.49 - 62.08 48 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1315 r_work=0.1151 r_free=0.1315 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1315 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1317 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.19 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= 0.1142 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.612444 | | target function (ml) not normalized (work): 300891.287920 | | target function (ml) not normalized (free): 15852.902726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1142 0.1317 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1483 0.1481 0.1535 n_refl.: 87589 remove outliers: r(all,work,free)=0.1483 0.1481 0.1535 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1481 0.1480 0.1534 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1137 0.1308 n_refl.: 87589 remove outliers: r(all,work,free)=0.1143 0.1134 0.1308 n_refl.: 87582 ======================== 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 0.3886 297.046 270.256 0.477 1.000 0.293 11.894-9.307 96.08 94 4 0.2444 476.889 454.304 0.870 1.002 0.273 9.237-7.194 98.18 209 7 0.2232 386.030 388.721 0.958 1.002 0.200 7.162-5.571 100.00 427 22 0.2072 296.087 285.482 0.919 1.002 0.173 5.546-4.326 100.00 867 58 0.1098 406.454 401.993 0.964 1.002 0.155 4.315-3.360 100.00 1859 96 0.0922 386.541 383.953 1.006 1.002 0.150 3.356-2.611 100.00 3867 181 0.1125 253.937 251.881 1.008 1.002 0.080 2.608-2.026 99.99 8198 413 0.0915 168.337 167.580 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.207 82.507 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.454 36.047 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 22.969 21.519 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0180 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1134 r_free=0.1308 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 B Total number of N/Q/H flips: 1 r_work=0.1135 r_free=0.1308 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1308 | n_water=442 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1134 r_free=0.1307 | n_water=439 | time (s): 45.180 (total time: 47.640) Filter (q & B) r_work=0.1134 r_free=0.1308 | n_water=438 | time (s): 3.930 (total time: 51.570) Compute maps r_work=0.1134 r_free=0.1308 | n_water=438 | time (s): 1.900 (total time: 53.470) Filter (map) r_work=0.1163 r_free=0.1286 | n_water=339 | time (s): 3.830 (total time: 57.300) Find peaks r_work=0.1163 r_free=0.1286 | n_water=339 | time (s): 0.690 (total time: 57.990) Add new water r_work=0.1225 r_free=0.1356 | n_water=490 | time (s): 3.720 (total time: 61.710) Refine new water occ: r_work=0.1154 r_free=0.1308 adp: r_work=0.1155 r_free=0.1308 occ: r_work=0.1141 r_free=0.1294 adp: r_work=0.1140 r_free=0.1294 occ: r_work=0.1129 r_free=0.1285 adp: r_work=0.1128 r_free=0.1282 ADP+occupancy (water only), MIN, final r_work=0.1128 r_free=0.1282 r_work=0.1128 r_free=0.1282 | n_water=490 | time (s): 217.430 (total time: 279.140) Filter (q & B) r_work=0.1133 r_free=0.1286 | n_water=458 | time (s): 4.250 (total time: 283.390) Filter (dist only) r_work=0.1133 r_free=0.1285 | n_water=457 | time (s): 48.390 (total time: 331.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.867445 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.391591 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 0.1196 0.1326 0.0129 0.002 0.6 4.8 0.5 0.0 0 0.093 0.1160 0.1302 0.0142 0.003 0.8 3.8 0.5 0.0 0 0.280 0.1146 0.1291 0.0145 0.005 0.9 4.2 0.5 0.0 0 0.560 0.1139 0.1290 0.0150 0.006 1.0 4.5 0.5 0.0 0 0.840 0.1135 0.1287 0.0152 0.007 1.0 4.8 0.5 0.0 0 1.120 0.1133 0.1287 0.0154 0.008 1.1 4.8 0.5 0.0 0 1.401 0.1131 0.1287 0.0156 0.008 1.1 4.8 0.5 0.0 0 1.681 0.1129 0.1285 0.0155 0.009 1.1 5.1 0.5 0.0 0 1.961 0.1138 0.1289 0.0151 0.006 1.0 4.2 0.5 0.0 0 0.934 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1129 0.1285 0.0155 0.009 1.1 5.1 0.5 0.0 0 1.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 12.85 1.55 3.779 21.228 45.392 3.603 11.29 12.85 1.55 3.779 21.228 1.362 3.603 11.29 12.85 1.55 3.779 21.228 5.674 3.603 11.33 12.93 1.60 3.713 21.220 22.696 3.597 11.39 13.08 1.69 3.730 21.190 45.392 3.600 11.31 13.04 1.74 3.758 21.181 68.087 3.594 11.25 13.00 1.75 3.772 21.179 90.783 3.589 11.23 12.97 1.74 3.782 21.175 113.479 3.587 11.22 12.99 1.77 3.798 21.166 136.175 3.586 11.21 13.00 1.79 3.809 21.163 158.871 3.585 11.19 12.98 1.79 3.820 21.157 181.566 3.583 11.17 12.97 1.79 3.826 21.157 204.262 3.582 11.17 12.97 1.79 3.836 21.152 226.958 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.674 Accepted refinement result: 11.29 12.85 1.55 3.779 21.228 5.674 3.603 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.18 3.31 234 1750 Protein: 9.11 115.03 17.03 3.32 0 1519 Water: 11.50 76.69 34.97 N/A 234 223 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.11 115.03 19.43 N/A 0 1750 Chain S: 12.68 60.00 34.26 N/A 234 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.30 304 30.30 - 40.89 219 40.89 - 51.48 127 51.48 - 62.07 46 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=0.1129 r_free=0.1285 r_work=0.1129 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1129 r_free = 0.1285 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1283 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1283 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600114 | | target function (ml) not normalized (work): 299839.125447 | | target function (ml) not normalized (free): 15799.244539 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1123 0.1283 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1462 0.1461 0.1501 n_refl.: 87582 remove outliers: r(all,work,free)=0.1462 0.1461 0.1501 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1461 0.1460 0.1500 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1123 0.1287 n_refl.: 87582 remove outliers: r(all,work,free)=0.1129 0.1120 0.1287 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3917 293.020 253.856 0.443 0.999 0.308 11.894-9.307 95.10 93 4 0.2374 480.806 463.145 0.864 1.001 0.236 9.237-7.194 98.18 209 7 0.2281 386.030 380.391 0.933 1.001 0.177 7.162-5.571 100.00 427 22 0.2124 296.087 286.733 0.913 1.002 0.138 5.546-4.326 100.00 867 58 0.1096 406.454 401.961 0.964 1.002 0.116 4.315-3.360 100.00 1859 96 0.0907 386.541 384.672 1.004 1.002 0.097 3.356-2.611 100.00 3867 181 0.1090 253.937 251.973 1.010 1.001 0.010 2.608-2.026 99.99 8198 413 0.0897 168.337 167.719 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.207 82.549 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1248 36.454 36.060 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.969 21.512 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0114 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1120 r_free=0.1287 After: r_work=0.1122 r_free=0.1287 ================================== NQH flips ================================== r_work=0.1122 r_free=0.1287 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=0.1122 r_free=0.1287 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1122 r_free=0.1287 | n_water=457 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1122 r_free=0.1287 | n_water=457 | time (s): 45.310 (total time: 47.600) Filter (q & B) r_work=0.1122 r_free=0.1288 | n_water=456 | time (s): 3.940 (total time: 51.540) Compute maps r_work=0.1122 r_free=0.1288 | n_water=456 | time (s): 1.830 (total time: 53.370) Filter (map) r_work=0.1161 r_free=0.1309 | n_water=359 | time (s): 3.940 (total time: 57.310) Find peaks r_work=0.1161 r_free=0.1309 | n_water=359 | time (s): 0.710 (total time: 58.020) Add new water r_work=0.1206 r_free=0.1349 | n_water=511 | time (s): 3.640 (total time: 61.660) Refine new water occ: r_work=0.1138 r_free=0.1303 adp: r_work=0.1138 r_free=0.1303 occ: r_work=0.1127 r_free=0.1293 adp: r_work=0.1126 r_free=0.1292 occ: r_work=0.1118 r_free=0.1288 adp: r_work=0.1116 r_free=0.1286 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1286 r_work=0.1116 r_free=0.1286 | n_water=511 | time (s): 284.750 (total time: 346.410) Filter (q & B) r_work=0.1124 r_free=0.1285 | n_water=468 | time (s): 3.820 (total time: 350.230) Filter (dist only) r_work=0.1124 r_free=0.1286 | n_water=466 | time (s): 48.290 (total time: 398.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.797233 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.932784 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 0.1217 0.1344 0.0127 0.004 0.7 6.4 0.0 0.0 0 0.090 0.1162 0.1309 0.0147 0.004 0.8 6.1 0.0 0.0 0 0.270 0.1144 0.1297 0.0153 0.005 0.9 5.4 0.5 0.0 0 0.539 0.1137 0.1292 0.0156 0.006 1.0 5.4 0.5 0.0 0 0.809 0.1130 0.1288 0.0158 0.007 1.1 5.1 0.5 0.0 0 1.078 0.1127 0.1286 0.0159 0.008 1.1 5.1 0.5 0.0 0 1.348 0.1125 0.1285 0.0160 0.008 1.1 4.8 0.5 0.0 0 1.618 0.1124 0.1285 0.0161 0.009 1.1 4.8 0.5 0.0 0 1.887 0.1132 0.1289 0.0157 0.006 1.0 5.1 0.5 0.0 0 0.899 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1124 0.1285 0.0161 0.009 1.1 4.8 0.5 0.0 0 1.887 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.24 12.85 1.61 3.779 21.271 42.933 3.601 11.24 12.85 1.61 3.779 21.271 1.288 3.601 11.24 12.85 1.61 3.779 21.271 5.367 3.601 11.27 12.92 1.66 3.712 21.263 21.466 3.596 11.35 13.09 1.74 3.727 21.232 42.933 3.599 11.28 13.07 1.79 3.755 21.221 64.399 3.594 11.21 13.02 1.81 3.772 21.219 85.866 3.588 11.20 13.02 1.82 3.783 21.214 107.332 3.587 11.17 12.99 1.82 3.794 21.211 128.798 3.584 11.14 12.97 1.83 3.803 21.210 150.265 3.583 11.14 13.01 1.86 3.821 21.198 171.731 3.582 11.15 13.01 1.86 3.831 21.194 193.198 3.582 11.13 12.99 1.87 3.837 21.194 214.664 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: 5.367 Accepted refinement result: 11.24 12.85 1.61 3.779 21.271 5.367 3.601 Individual atomic B min max mean iso aniso Overall: 9.11 115.03 21.26 3.31 244 1749 Protein: 9.11 115.03 17.02 3.32 0 1519 Water: 11.50 76.69 35.06 N/A 244 222 Other: 19.74 26.65 22.09 N/A 0 8 Chain A: 9.11 115.03 19.43 N/A 0 1749 Chain S: 12.68 59.99 34.41 N/A 244 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 303 30.29 - 40.88 225 40.88 - 51.47 134 51.47 - 62.07 44 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=0.1124 r_free=0.1285 r_work=0.1124 r_free=0.1285 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1124 r_free = 0.1285 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1123 r_free = 0.1285 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1123 r_free= 0.1285 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600118 | | target function (ml) not normalized (work): 299821.460726 | | target function (ml) not normalized (free): 15789.912690 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1323 0.1353 5.6397 5.615| | 2: 3.57 - 2.84 1.00 2888 124 0.1047 0.1369 5.1539 5.2212| | 3: 2.83 - 2.48 1.00 2820 163 0.1077 0.1219 4.9377 4.9717| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0987 4.6267 4.66| | 5: 2.25 - 2.09 1.00 2756 127 0.0844 0.0942 4.5718 4.6186| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.1026 4.2605 4.3502| | 7: 1.97 - 1.87 1.00 2787 165 0.0876 0.1105 3.9733 4.087| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1105 3.8847 3.9919| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1153 3.6382 3.8026| | 10: 1.72 - 1.66 1.00 2831 160 0.0911 0.1175 3.5572 3.7051| | 11: 1.66 - 1.61 1.00 2712 147 0.0868 0.1020 3.4892 3.5635| | 12: 1.61 - 1.56 1.00 2773 144 0.0904 0.1134 3.3226 3.4586| | 13: 1.56 - 1.52 1.00 2745 130 0.0940 0.1012 3.3003 3.3724| | 14: 1.52 - 1.48 1.00 2803 134 0.0978 0.1048 3.2336 3.3096| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1200 3.1487 3.2502| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1250 3.1325 3.2429| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1301 3.115 3.2254| | 18: 1.39 - 1.36 1.00 2741 179 0.1200 0.1322 3.102 3.2331| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1568 3.1104 3.2679| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1454 3.1096 3.1496| | 21: 1.32 - 1.30 1.00 2785 112 0.1472 0.1530 3.1127 3.1123| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1995 3.1222 3.2975| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1795 3.132 3.1939| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1812 3.1269 3.2219| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2133 3.1417 3.2571| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1785 3.1481 3.2045| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2161 3.1716 3.1616| | 28: 1.19 - 1.18 1.00 2671 147 0.2206 0.2292 3.1664 3.1712| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2395 3.1477 3.2293| | 30: 1.16 - 1.15 1.00 2739 148 0.2452 0.2445 3.1432 3.1662| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.46 1.00 0.97 5754.67| | 2: 3.57 - 2.84 2888 124 0.93 12.62 1.01 0.97 5754.67| | 3: 2.83 - 2.48 2820 163 0.89 16.61 0.99 0.97 4806.76| | 4: 2.47 - 2.25 2825 136 0.92 13.46 1.00 0.98 2362.40| | 5: 2.25 - 2.09 2756 127 0.90 15.62 1.01 0.98 2362.40| | 6: 2.09 - 1.97 2846 113 0.92 12.36 1.02 0.98 1362.42| | 7: 1.97 - 1.87 2787 165 0.95 9.27 1.02 0.98 509.57| | 8: 1.87 - 1.79 2789 144 0.93 12.63 1.00 0.98 509.57| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.97 285.85| | 10: 1.72 - 1.66 2831 160 0.94 10.98 0.98 0.97 241.05| | 11: 1.66 - 1.61 2712 147 0.94 11.67 0.98 0.97 230.90| | 12: 1.61 - 1.56 2773 144 0.96 8.76 0.99 0.97 135.17| | 13: 1.56 - 1.52 2745 130 0.95 10.29 1.03 0.97 135.17| | 14: 1.52 - 1.48 2803 134 0.94 10.62 1.02 0.98 121.36| | 15: 1.48 - 1.45 2738 128 0.95 9.77 1.02 0.98 96.09| | 16: 1.45 - 1.42 2756 161 0.94 10.95 1.02 0.98 96.09| | 17: 1.42 - 1.39 2785 139 0.95 10.82 1.01 0.98 87.84| | 18: 1.39 - 1.36 2741 179 0.94 11.45 1.01 0.98 83.07| | 19: 1.36 - 1.34 2807 134 0.94 11.79 0.99 0.98 83.07| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.60| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.96 79.36| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.96 79.78| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 81.92| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 81.92| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 83.93| | 26: 1.22 - 1.21 2727 135 0.90 18.11 1.02 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 89.88| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.92 91.28| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.97 0.92 91.28| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.36 max = 5754.67 mean = 886.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.41| |phase err.(test): min = 0.00 max = 89.44 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1123 0.1285 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1499 n_refl.: 87577 remove outliers: r(all,work,free)=0.1445 0.1444 0.1499 n_refl.: 87577 overall B=0.00 to atoms: r(all,work,free)=0.1446 0.1444 0.1499 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1286 n_refl.: 87577 remove outliers: r(all,work,free)=0.1131 0.1123 0.1286 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 0.4073 293.020 256.684 0.448 0.999 0.302 11.894-9.307 93.14 91 4 0.2365 477.651 470.567 0.863 1.001 0.290 9.237-7.194 98.18 209 7 0.2356 386.030 379.617 0.926 1.001 0.160 7.162-5.571 100.00 427 22 0.2122 296.087 285.608 0.910 1.001 0.130 5.546-4.326 100.00 867 58 0.1107 406.454 401.805 0.961 1.002 0.100 4.315-3.360 100.00 1859 96 0.0906 386.541 384.318 1.002 1.002 0.100 3.356-2.611 100.00 3867 181 0.1092 253.937 251.961 1.010 1.002 0.000 2.608-2.026 99.99 8198 413 0.0891 168.337 167.726 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.207 82.547 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.454 36.039 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2172 22.969 21.429 0.979 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0042 ================= 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 : 0.2612 0.1931 0.081 5.189 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1760 0.081 5.189 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1760 0.081 5.189 9.1 119.5 20.1 258 0.000 1_nqh: 0.1641 0.1762 0.081 5.189 9.1 119.5 20.1 258 0.003 1_weight: 0.1641 0.1762 0.081 5.189 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1228 0.1472 0.007 0.907 9.1 119.5 20.1 258 0.140 1_adp: 0.1234 0.1469 0.007 0.907 9.1 119.5 20.1 258 0.140 1_regHadp: 0.1236 0.1473 0.007 0.907 9.1 119.5 20.1 258 0.140 1_occ: 0.1231 0.1471 0.007 0.907 9.1 119.5 20.1 258 0.140 2_bss: 0.1229 0.1463 0.007 0.907 9.1 119.5 20.1 258 0.140 2_settarget: 0.1229 0.1463 0.007 0.907 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1229 0.1463 0.007 0.911 9.1 119.5 20.1 258 0.140 2_nqh: 0.1228 0.1461 0.007 0.911 9.1 119.5 20.1 258 0.140 2_sol: 0.1195 0.1417 0.007 0.911 9.1 115.0 22.2 420 n/a 2_weight: 0.1195 0.1417 0.007 0.911 9.1 115.0 22.2 420 n/a 2_xyzrec: 0.1177 0.1412 0.008 0.955 9.1 115.0 22.2 420 n/a 2_adp: 0.1177 0.1412 0.008 0.955 9.1 115.0 22.2 420 n/a 2_regHadp: 0.1177 0.1412 0.008 0.955 9.1 115.0 22.2 420 n/a 2_occ: 0.1177 0.1408 0.008 0.955 9.1 115.0 22.2 420 n/a 3_bss: 0.1172 0.1402 0.008 0.955 9.1 115.0 22.2 420 n/a 3_settarget: 0.1172 0.1402 0.008 0.955 9.1 115.0 22.2 420 n/a 3_updatecdl: 0.1172 0.1402 0.008 0.956 9.1 115.0 22.2 420 n/a 3_nqh: 0.1172 0.1402 0.008 0.956 9.1 115.0 22.2 420 n/a 3_sol: 0.1195 0.1383 0.008 0.956 9.1 115.0 21.2 442 n/a 3_weight: 0.1195 0.1383 0.008 0.956 9.1 115.0 21.2 442 n/a 3_xyzrec: 0.1151 0.1315 0.008 1.087 9.1 115.0 21.2 442 n/a 3_adp: 0.1151 0.1315 0.008 1.087 9.1 115.0 21.2 442 n/a 3_regHadp: 0.1151 0.1315 0.008 1.087 9.1 115.0 21.2 442 n/a 3_occ: 0.1142 0.1317 0.008 1.087 9.1 115.0 21.2 442 n/a 4_bss: 0.1134 0.1308 0.008 1.087 9.1 115.0 21.2 442 n/a 4_settarget: 0.1134 0.1308 0.008 1.087 9.1 115.0 21.2 442 n/a 4_updatecdl: 0.1134 0.1308 0.008 1.088 9.1 115.0 21.2 442 n/a 4_nqh: 0.1135 0.1308 0.008 1.088 9.1 115.0 21.2 442 n/a 4_sol: 0.1133 0.1285 0.008 1.088 9.1 115.0 21.2 457 n/a 4_weight: 0.1133 0.1285 0.008 1.088 9.1 115.0 21.2 457 n/a 4_xyzrec: 0.1129 0.1285 0.009 1.139 9.1 115.0 21.2 457 n/a 4_adp: 0.1129 0.1285 0.009 1.139 9.1 115.0 21.2 457 n/a 4_regHadp: 0.1129 0.1285 0.009 1.139 9.1 115.0 21.2 457 n/a 4_occ: 0.1123 0.1283 0.009 1.139 9.1 115.0 21.2 457 n/a 5_bss: 0.1120 0.1287 0.009 1.139 9.1 115.0 21.2 457 n/a 5_settarget: 0.1120 0.1287 0.009 1.139 9.1 115.0 21.2 457 n/a 5_updatecdl: 0.1120 0.1287 0.009 1.139 9.1 115.0 21.2 457 n/a 5_setrh: 0.1122 0.1287 0.009 1.139 9.1 115.0 21.2 457 n/a 5_nqh: 0.1122 0.1287 0.009 1.139 9.1 115.0 21.2 457 n/a 5_sol: 0.1124 0.1286 0.009 1.139 9.1 115.0 21.3 466 n/a 5_weight: 0.1124 0.1286 0.009 1.139 9.1 115.0 21.3 466 n/a 5_xyzrec: 0.1124 0.1285 0.009 1.148 9.1 115.0 21.3 466 n/a 5_adp: 0.1124 0.1285 0.009 1.148 9.1 115.0 21.3 466 n/a 5_regHadp: 0.1124 0.1285 0.009 1.148 9.1 115.0 21.3 466 n/a 5_occ: 0.1123 0.1285 0.009 1.148 9.1 115.0 21.3 466 n/a end: 0.1123 0.1286 0.009 1.148 9.1 115.0 21.3 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6462862_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6462862_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.7000 Refinement macro-cycles (run) : 13618.0100 Write final files (write_after_run_outputs) : 97.0400 Total : 13717.7500 Total CPU time: 3.82 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:03 PST -0800 (1735366023.21 s) Start R-work = 0.1640, R-free = 0.1760 Final R-work = 0.1123, R-free = 0.1286 =============================================================================== Job complete usr+sys time: 13907.12 seconds wall clock time: 251 minutes 22.85 seconds (15082.85 seconds total)