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_7410891.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_7410891.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.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 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: 1.34, per 1000 atoms: 0.40 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: 0.29 Conformation dependent library (CDL) restraints added in 108.6 milliseconds Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 410 0.89 - 1.14: 1196 1.14 - 1.40: 576 1.40 - 1.65: 902 1.65 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.21e-02 6.83e+03 3.35e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.156 0.165 1.00e-02 1.00e+04 2.72e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.730 -0.191 1.18e-02 7.18e+03 2.63e+02 bond pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.540 -0.206 1.27e-02 6.20e+03 2.62e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.428 -0.195 1.21e-02 6.83e+03 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3251 4.93 - 9.86: 1858 9.86 - 14.79: 582 14.79 - 19.71: 81 19.71 - 24.64: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" O ALEU A 153 " ideal model delta sigma weight residual 120.30 134.74 -14.44 1.07e+00 8.73e-01 1.82e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.07 135.58 -13.51 1.03e+00 9.43e-01 1.72e+02 angle pdb=" O ASP A 60 " pdb=" C ASP A 60 " pdb=" N ALA A 61 " ideal model delta sigma weight residual 122.07 135.53 -13.46 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" O LEU A 82 " ideal model delta sigma weight residual 120.90 134.82 -13.92 1.07e+00 8.73e-01 1.69e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 108.24 10.96 9.00e-01 1.23e+00 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 921 16.42 - 32.83: 132 32.83 - 49.24: 41 49.24 - 65.66: 14 65.66 - 82.07: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -154.17 -25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 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 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 111 0.270 - 0.539: 83 0.539 - 0.809: 39 0.809 - 1.079: 8 1.079 - 1.348: 2 Chirality restraints: 243 Sorted by residual: 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 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 1.70 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 " -0.102 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.082 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.065 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG ATYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.121 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.022 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.070 2.00e-02 2.50e+03 6.39e-02 9.18e+01 pdb=" CG HIS A 138 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1162 2.34 - 2.90: 8204 2.90 - 3.47: 10467 3.47 - 4.03: 15210 4.03 - 4.60: 21605 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.771 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.817 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.853 1.850 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.873 1.850 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.878 1.850 ... (remaining 56643 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_7410891_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= 0.2603 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795928 | | target function (ml) not normalized (work): 232917.562073 | | target function (ml) not normalized (free): 11855.320496 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3025 0.2057 7.0711 4.9433| | 2: 3.57 - 2.84 1.00 2876 122 0.2453 0.1776 4.3504 4.3388| | 3: 2.84 - 2.48 1.00 2833 165 0.2319 0.1658 4.1247 4.148| | 4: 2.47 - 2.25 1.00 2825 136 0.2332 0.1366 3.8335 3.821| | 5: 2.25 - 2.09 1.00 2756 127 0.2495 0.1673 3.7978 3.8319| | 6: 2.09 - 1.97 1.00 2846 113 0.2513 0.1648 3.4684 3.5539| | 7: 1.97 - 1.87 1.00 2787 165 0.2562 0.1853 3.1367 3.244| | 8: 1.87 - 1.79 1.00 2789 144 0.2456 0.2014 3.0683 3.158| | 9: 1.79 - 1.72 1.00 2745 138 0.2420 0.1865 2.8912 2.9255| | 10: 1.72 - 1.66 1.00 2789 158 0.2438 0.1885 2.8157 2.8644| | 11: 1.66 - 1.61 1.00 2740 147 0.2523 0.1953 2.7568 2.767| | 12: 1.61 - 1.56 1.00 2787 146 0.2487 0.2124 2.6256 2.7061| | 13: 1.56 - 1.52 1.00 2745 130 0.2507 0.1970 2.5833 2.6492| | 14: 1.52 - 1.48 1.00 2803 134 0.2575 0.2034 2.5003 2.5773| | 15: 1.48 - 1.45 1.00 2738 128 0.2615 0.2158 2.4551 2.55| | 16: 1.45 - 1.42 1.00 2756 161 0.2652 0.2283 2.4053 2.4795| | 17: 1.42 - 1.39 1.00 2785 139 0.2667 0.2090 2.3414 2.3799| | 18: 1.39 - 1.36 1.00 2741 179 0.2665 0.2240 2.2938 2.3523| | 19: 1.36 - 1.34 1.00 2807 134 0.2633 0.2336 2.2527 2.2763| | 20: 1.34 - 1.32 1.00 2696 147 0.2699 0.2101 2.2188 2.1414| | 21: 1.32 - 1.30 1.00 2785 112 0.2666 0.2531 2.1675 2.3024| | 22: 1.29 - 1.27 1.00 2704 152 0.2702 0.2575 2.1226 2.2332| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2371 2.1143 2.168| | 24: 1.26 - 1.24 1.00 2744 132 0.2782 0.2303 2.0633 2.0632| | 25: 1.24 - 1.22 1.00 2734 148 0.2861 0.2520 2.0608 2.0657| | 26: 1.22 - 1.21 1.00 2727 135 0.2836 0.2346 2.013 2.0873| | 27: 1.21 - 1.19 1.00 2814 148 0.2968 0.2691 2.0014 2.0417| | 28: 1.19 - 1.18 1.00 2671 147 0.3000 0.2655 1.9872 2.0097| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2637 1.9645 1.9855| | 30: 1.16 - 1.15 1.00 2740 148 0.3060 0.2856 1.9368 1.9876| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.73 0.76 0.23 1478.00| | 2: 3.57 - 2.84 2876 122 0.80 26.07 1.27 0.23 1478.00| | 3: 2.84 - 2.48 2833 165 0.74 32.05 1.24 0.24 1226.07| | 4: 2.47 - 2.25 2825 136 0.81 25.66 1.25 0.25 572.28| | 5: 2.25 - 2.09 2756 127 0.77 29.42 1.29 0.25 572.28| | 6: 2.09 - 1.97 2846 113 0.83 22.80 1.29 0.25 314.18| | 7: 1.97 - 1.87 2787 165 0.90 16.89 1.29 0.26 94.06| | 8: 1.87 - 1.79 2789 144 0.85 21.44 1.24 0.26 94.06| | 9: 1.79 - 1.72 2745 138 0.87 19.04 1.23 0.26 57.09| | 10: 1.72 - 1.66 2789 158 0.86 20.58 1.23 0.26 49.69| | 11: 1.66 - 1.61 2740 147 0.85 21.67 1.25 0.26 48.01| | 12: 1.61 - 1.56 2787 146 0.88 19.02 1.23 0.25 30.93| | 13: 1.56 - 1.52 2745 130 0.86 20.80 1.23 0.25 30.93| | 14: 1.52 - 1.48 2803 134 0.86 21.37 1.24 0.25 27.69| | 15: 1.48 - 1.45 2738 128 0.87 20.61 1.23 0.25 21.76| | 16: 1.45 - 1.42 2756 161 0.85 22.28 1.23 0.25 21.76| | 17: 1.42 - 1.39 2785 139 0.86 21.11 1.23 0.25 18.28| | 18: 1.39 - 1.36 2741 179 0.86 21.42 1.22 0.25 16.27| | 19: 1.36 - 1.34 2807 134 0.85 22.41 1.21 0.25 16.27| | 20: 1.34 - 1.32 2696 147 0.86 21.47 1.20 0.25 13.44| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.25 13.24| | 22: 1.29 - 1.27 2704 152 0.85 22.65 1.21 0.24 12.91| | 23: 1.27 - 1.26 2802 156 0.86 22.21 1.21 0.24 11.21| | 24: 1.26 - 1.24 2744 132 0.85 22.98 1.21 0.24 11.21| | 25: 1.24 - 1.22 2734 148 0.84 23.71 1.20 0.24 10.60| | 26: 1.22 - 1.21 2727 135 0.84 23.83 1.20 0.24 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.21 0.24 9.93| | 28: 1.19 - 1.18 2671 147 0.83 24.89 1.19 0.23 9.16| | 29: 1.18 - 1.16 2800 134 0.83 24.98 1.15 0.23 8.87| | 30: 1.16 - 1.15 2740 148 0.81 26.55 1.15 0.23 8.87| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.87 max = 1478.00 mean = 215.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.79| |phase err.(test): min = 0.00 max = 89.99 mean = 22.70| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.247 1557 Z= 5.376 Angle : 5.408 18.959 2118 Z= 3.798 Chirality : 0.413 1.348 243 Planarity : 0.034 0.086 284 Dihedral : 13.735 82.074 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 1.86 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.44 (0.44), residues: 224 helix: -2.57 (0.34), residues: 103 sheet: -0.77 (0.90), residues: 28 loop : -0.42 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.024 ARG A 5 TYR 0.069 0.030 TYR A 139 PHE 0.120 0.045 PHE A 164 HIS 0.042 0.017 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= 0.2603 r_free= 0.1941 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.795928 | | target function (ml) not normalized (work): 232917.562073 | | target function (ml) not normalized (free): 11855.320496 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2562 0.2604 0.1941 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2562 0.2604 0.1941 n_refl.: 87602 remove outliers: r(all,work,free)=0.1981 0.1985 0.1941 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2007 0.2012 0.1955 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1651 0.1645 0.1756 n_refl.: 87594 remove outliers: r(all,work,free)=0.1650 0.1644 0.1756 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 97.87 87 5 0.3780 389.574 365.819 0.695 1.000 0.407 11.894-9.307 99.02 97 4 0.1807 613.625 595.566 0.929 1.001 0.390 9.237-7.194 100.00 213 7 0.2169 501.870 492.178 0.959 1.001 0.344 7.162-5.571 100.00 427 22 0.2236 376.625 365.126 0.928 1.002 0.288 5.546-4.326 100.00 867 58 0.1291 517.013 511.174 0.966 1.002 0.234 4.315-3.360 100.00 1859 96 0.1150 491.683 487.838 1.004 1.002 0.209 3.356-2.611 100.00 3867 181 0.1443 323.011 319.548 0.997 1.002 0.052 2.608-2.026 99.99 8198 413 0.1352 214.126 211.859 1.005 1.002 0.000 2.025-1.573 100.00 17313 902 0.1653 104.568 103.807 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2084 46.370 45.072 0.997 1.002 0.000 1.221-1.150 99.97 13689 708 0.2594 29.216 26.885 0.965 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0510 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1644 r_free=0.1756 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1644 r_free=0.1756 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.700835 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2021.918518 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 0.1681 0.1794 0.0113 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1585 0.1716 0.0130 0.002 0.4 4.5 0.0 0.0 0 0.250 0.1474 0.1637 0.0163 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1393 0.1576 0.0183 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1345 0.1546 0.0201 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1352 0.1548 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1306 0.1528 0.0222 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1276 0.1503 0.0228 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1489 0.0231 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1483 0.0233 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 0.1242 0.1480 0.0238 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1237 0.1473 0.0236 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1470 0.0239 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1230 0.1469 0.0239 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1229 0.1474 0.0245 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1226 0.1473 0.0248 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1225 0.1475 0.0249 0.007 1.0 4.2 0.5 0.6 0 13.350 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1230 0.1469 0.0239 0.006 0.9 4.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.69 2.39 3.013 19.081 2021.919 0.017 12.30 14.68 2.38 3.003 19.081 60.658 0.017 12.37 14.65 2.28 2.660 19.079 252.740 0.017 12.75 15.36 2.61 2.903 19.343 1010.959 0.016 12.58 15.49 2.91 3.372 19.662 2021.919 0.016 12.47 15.47 3.00 3.352 19.658 3032.878 0.015 12.35 15.39 3.04 3.317 19.625 4043.837 0.015 12.28 15.32 3.05 3.310 19.608 5054.796 0.015 12.25 15.38 3.12 3.465 19.696 6065.756 0.015 12.20 15.35 3.14 3.387 19.642 7076.715 0.015 12.17 15.35 3.18 3.410 19.652 8087.674 0.015 12.19 15.41 3.22 3.391 19.625 9098.633 0.015 12.17 15.40 3.23 3.424 19.635 10109.593 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: 252.740 Accepted refinement result: 12.37 14.65 2.28 2.660 19.079 252.740 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.29 0 1785 Protein: 9.08 114.93 17.01 3.30 0 1519 Water: 11.49 119.46 38.25 N/A 0 258 Other: 19.76 26.62 22.09 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.16 227 31.16 - 42.20 125 42.20 - 53.24 94 53.24 - 64.27 42 64.27 - 75.31 11 75.31 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1465 r_work=0.1238 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1468 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 = 0.1234 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1234 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016975 | | target function (ls_wunit_k1) not normalized (work): 1413.921443 | | target function (ls_wunit_k1) not normalized (free): 112.110062 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1464 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1678 0.1679 0.1690 n_refl.: 87592 remove outliers: r(all,work,free)=0.1678 0.1679 0.1690 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1684 0.1693 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1231 0.1455 n_refl.: 87592 remove outliers: r(all,work,free)=0.1241 0.1230 0.1455 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 0.3479 300.040 284.110 0.643 1.002 0.375 11.894-9.307 99.02 97 4 0.1744 482.050 468.434 0.917 1.003 0.371 9.237-7.194 100.00 213 7 0.1905 394.258 387.843 0.962 1.003 0.350 7.162-5.571 100.00 427 22 0.1857 295.868 289.593 0.934 1.003 0.259 5.546-4.326 100.00 867 58 0.1012 406.154 402.874 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0867 386.256 385.247 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1175 253.750 252.606 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1023 168.213 167.473 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1115 82.146 82.331 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1454 36.427 35.928 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2256 22.952 21.435 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0434 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1455 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=0.1231 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1456 | n_water=258 | time (s): 1.810 (total time: 1.810) Filter (dist) r_work=0.1241 r_free=0.1455 | n_water=251 | time (s): 22.730 (total time: 24.540) Filter (q & B) r_work=0.1243 r_free=0.1453 | n_water=248 | time (s): 2.750 (total time: 27.290) Compute maps r_work=0.1243 r_free=0.1453 | n_water=248 | time (s): 1.340 (total time: 28.630) Filter (map) r_work=0.1260 r_free=0.1456 | n_water=226 | time (s): 3.040 (total time: 31.670) Find peaks r_work=0.1260 r_free=0.1456 | n_water=226 | time (s): 0.650 (total time: 32.320) Add new water r_work=0.1400 r_free=0.1613 | n_water=428 | time (s): 2.600 (total time: 34.920) Refine new water occ: r_work=0.1309 r_free=0.1485 adp: r_work=0.1231 r_free=0.1430 occ: r_work=0.1243 r_free=0.1426 adp: r_work=0.1212 r_free=0.1411 occ: r_work=0.1213 r_free=0.1403 adp: r_work=0.1205 r_free=0.1403 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1403 r_work=0.1205 r_free=0.1403 | n_water=428 | time (s): 55.140 (total time: 90.060) Filter (q & B) r_work=0.1210 r_free=0.1412 | n_water=410 | time (s): 3.450 (total time: 93.510) Filter (dist only) r_work=0.1210 r_free=0.1410 | n_water=409 | time (s): 36.520 (total time: 130.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.429479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1484.916855 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 0.1705 0.1816 0.0111 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1546 0.1679 0.0133 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1422 0.1581 0.0159 0.001 0.4 4.5 0.0 0.0 0 0.500 0.1369 0.1540 0.0170 0.001 0.4 3.8 0.0 0.0 0 0.750 0.1331 0.1514 0.0184 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1335 0.1519 0.0184 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1269 0.1473 0.0205 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1238 0.1452 0.0214 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1223 0.1437 0.0214 0.004 0.7 3.2 0.5 0.0 0 4.000 0.1219 0.1430 0.0212 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1210 0.1426 0.0216 0.005 0.7 3.5 0.5 0.0 0 6.000 0.1210 0.1426 0.0216 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1205 0.1424 0.0219 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1200 0.1420 0.0220 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1198 0.1423 0.0225 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1196 0.1417 0.0221 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1194 0.1420 0.0227 0.007 0.9 4.2 0.5 0.6 0 12.000 0.1192 0.1416 0.0224 0.008 0.9 4.5 0.5 0.6 0 13.000 0.1192 0.1424 0.0231 0.008 0.9 4.2 0.5 0.6 0 14.215 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1416 0.0224 0.008 0.9 4.5 0.5 0.6 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 14.16 2.24 3.770 21.726 1484.917 0.016 11.92 14.16 2.24 3.770 21.726 44.548 0.016 11.92 14.16 2.24 3.770 21.726 185.615 0.016 12.08 14.56 2.48 3.640 21.727 742.458 0.015 12.04 14.84 2.80 3.486 21.889 1484.917 0.015 11.92 14.88 2.96 3.529 22.083 2227.375 0.014 11.82 14.84 3.02 3.526 21.872 2969.834 0.014 11.75 14.77 3.02 3.530 21.893 3712.292 0.014 11.78 14.89 3.11 3.541 22.096 4454.751 0.014 11.79 14.97 3.18 3.576 22.135 5197.209 0.014 11.70 14.89 3.19 3.565 22.034 5939.667 0.014 11.65 14.85 3.20 3.582 22.054 6682.126 0.014 11.65 14.85 3.20 3.595 22.087 7424.584 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.615 Accepted refinement result: 11.92 14.16 2.24 3.770 21.726 185.615 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 114.96 22.08 3.29 183 1753 Protein: 9.11 114.96 17.04 3.30 0 1519 Water: 11.51 76.69 40.78 N/A 183 226 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.11 114.96 19.47 N/A 0 1753 Chain S: 15.15 60.00 47.07 N/A 183 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.28 246 30.28 - 40.86 160 40.86 - 51.45 122 51.45 - 62.03 126 62.03 - 72.62 10 72.62 - 83.20 6 83.20 - 93.79 4 93.79 - 104.37 0 104.37 - 114.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1416 r_work=0.1192 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1416 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1420 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.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1420 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014904 | | target function (ls_wunit_k1) not normalized (work): 1241.418137 | | target function (ls_wunit_k1) not normalized (free): 106.175079 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1420 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1588 0.1587 0.1643 n_refl.: 87590 remove outliers: r(all,work,free)=0.1588 0.1587 0.1643 n_refl.: 87590 overall B=0.00 to atoms: r(all,work,free)=0.1589 0.1588 0.1643 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1186 0.1415 n_refl.: 87590 remove outliers: r(all,work,free)=0.1196 0.1185 0.1415 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 0.3357 302.077 276.138 0.603 1.003 0.370 11.894-9.307 99.02 97 4 0.1623 482.050 476.303 0.915 1.003 0.350 9.237-7.194 100.00 213 7 0.1666 394.258 393.346 0.986 1.003 0.290 7.162-5.571 100.00 427 22 0.1574 295.868 291.177 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0875 406.154 403.035 0.961 1.003 0.200 4.315-3.360 100.00 1859 96 0.0780 386.256 385.463 1.006 1.003 0.190 3.356-2.611 100.00 3867 181 0.1079 253.750 252.919 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1025 168.213 167.649 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.146 82.359 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.427 35.974 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.952 21.476 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0060 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1415 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=0.1185 r_free=0.1415 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1415 | n_water=409 | time (s): 2.190 (total time: 2.190) Filter (dist) r_work=0.1185 r_free=0.1417 | n_water=407 | time (s): 38.750 (total time: 40.940) Filter (q & B) r_work=0.1185 r_free=0.1417 | n_water=407 | time (s): 1.190 (total time: 42.130) Compute maps r_work=0.1185 r_free=0.1417 | n_water=407 | time (s): 1.540 (total time: 43.670) Filter (map) r_work=0.1224 r_free=0.1390 | n_water=278 | time (s): 2.490 (total time: 46.160) Find peaks r_work=0.1224 r_free=0.1390 | n_water=278 | time (s): 0.620 (total time: 46.780) Add new water r_work=0.1347 r_free=0.1525 | n_water=461 | time (s): 2.600 (total time: 49.380) Refine new water occ: r_work=0.1251 r_free=0.1435 adp: r_work=0.1252 r_free=0.1435 occ: r_work=0.1230 r_free=0.1414 adp: r_work=0.1228 r_free=0.1412 occ: r_work=0.1211 r_free=0.1396 adp: r_work=0.1206 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1390 r_work=0.1206 r_free=0.1390 | n_water=461 | time (s): 156.560 (total time: 205.940) Filter (q & B) r_work=0.1212 r_free=0.1397 | n_water=426 | time (s): 3.740 (total time: 209.680) Filter (dist only) r_work=0.1212 r_free=0.1396 | n_water=424 | time (s): 37.990 (total time: 247.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.745690 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.493649 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 0.1244 0.1369 0.0124 0.002 0.6 4.8 0.5 0.0 0 0.087 0.1202 0.1343 0.0141 0.003 0.7 3.2 0.5 0.0 0 0.262 0.1181 0.1330 0.0149 0.004 0.8 3.2 0.5 0.0 0 0.524 0.1176 0.1329 0.0154 0.005 0.9 3.2 0.5 0.0 0 0.786 0.1171 0.1331 0.0159 0.006 1.0 3.2 0.5 0.0 0 1.047 0.1168 0.1331 0.0163 0.007 1.0 3.2 0.5 0.0 0 1.309 0.1167 0.1332 0.0165 0.007 1.1 3.5 0.5 0.0 0 1.571 0.1164 0.1331 0.0167 0.008 1.1 3.5 0.5 0.0 0 1.833 0.1175 0.1332 0.0157 0.005 0.9 2.9 0.5 0.0 0 0.873 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1176 0.1329 0.0154 0.005 0.9 3.2 0.5 0.0 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 13.29 1.54 3.773 21.196 48.494 3.628 11.76 13.29 1.54 3.773 21.196 1.455 3.628 11.76 13.30 1.54 3.763 21.196 6.062 3.628 11.81 13.40 1.59 3.710 21.181 24.247 3.622 11.77 13.44 1.66 3.740 21.152 48.494 3.619 11.70 13.41 1.71 3.760 21.143 72.740 3.614 11.69 13.41 1.72 3.772 21.129 96.987 3.611 11.66 13.42 1.77 3.791 21.121 121.234 3.608 11.63 13.42 1.79 3.807 21.116 145.481 3.607 11.62 13.42 1.80 3.821 21.107 169.728 3.605 11.59 13.39 1.80 3.825 21.109 193.975 3.603 11.59 13.39 1.80 3.836 21.106 218.221 3.602 11.57 13.37 1.80 3.839 21.106 242.468 3.601 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.455 Accepted refinement result: 11.76 13.29 1.54 3.773 21.196 1.455 3.628 Individual atomic B min max mean iso aniso Overall: 9.12 114.96 21.10 3.29 204 1747 Protein: 9.12 114.96 17.05 3.30 0 1519 Water: 11.52 76.70 35.62 N/A 204 220 Other: 19.79 26.65 22.12 N/A 0 8 Chain A: 9.12 114.96 19.37 N/A 0 1747 Chain S: 15.15 60.00 35.95 N/A 204 0 Histogram: Values Number of atoms 9.12 - 19.70 1263 19.70 - 30.28 289 30.28 - 40.87 201 40.87 - 51.45 122 51.45 - 62.04 54 62.04 - 72.62 10 72.62 - 83.21 6 83.21 - 93.79 4 93.79 - 104.38 0 104.38 - 114.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1176 r_free=0.1329 r_work=0.1176 r_free=0.1329 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1176 r_free = 0.1329 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1166 r_free = 0.1324 target_work(ml) = 3.621 | | occupancies: max = 1.00 min = 0.18 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= 0.1166 r_free= 0.1324 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.620726 | | target function (ml) not normalized (work): 301581.101237 | | target function (ml) not normalized (free): 15846.805019 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1174 0.1166 0.1324 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1509 0.1509 0.1538 n_refl.: 87589 remove outliers: r(all,work,free)=0.1509 0.1509 0.1538 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1508 0.1508 0.1537 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1170 0.1163 0.1316 n_refl.: 87589 remove outliers: r(all,work,free)=0.1168 0.1160 0.1316 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 91.67 83 5 0.3858 299.437 272.553 0.501 1.000 0.297 11.894-9.307 97.06 95 4 0.2279 482.274 463.187 0.876 1.001 0.280 9.237-7.194 98.18 209 7 0.2283 385.746 384.858 0.957 1.002 0.207 7.162-5.571 100.00 427 22 0.2117 295.868 285.725 0.920 1.002 0.180 5.546-4.326 100.00 867 58 0.1125 406.154 401.167 0.966 1.002 0.158 4.315-3.360 100.00 1859 96 0.0950 386.256 384.090 1.005 1.002 0.143 3.356-2.611 100.00 3867 181 0.1162 253.750 251.571 1.008 1.001 0.048 2.608-2.026 99.99 8198 413 0.0947 168.213 167.472 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0916 82.146 82.440 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1274 36.427 36.007 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2174 22.952 21.486 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=-0.0174 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1160 r_free=0.1316 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=0.1160 r_free=0.1316 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1160 r_free=0.1316 | n_water=424 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1160 r_free=0.1318 | n_water=422 | time (s): 46.220 (total time: 48.600) Filter (q & B) r_work=0.1161 r_free=0.1319 | n_water=420 | time (s): 3.760 (total time: 52.360) Compute maps r_work=0.1161 r_free=0.1319 | n_water=420 | time (s): 1.830 (total time: 54.190) Filter (map) r_work=0.1175 r_free=0.1312 | n_water=320 | time (s): 3.790 (total time: 57.980) Find peaks r_work=0.1175 r_free=0.1312 | n_water=320 | time (s): 0.690 (total time: 58.670) Add new water r_work=0.1245 r_free=0.1382 | n_water=490 | time (s): 3.830 (total time: 62.500) Refine new water occ: r_work=0.1177 r_free=0.1326 adp: r_work=0.1178 r_free=0.1327 occ: r_work=0.1165 r_free=0.1315 adp: r_work=0.1164 r_free=0.1316 occ: r_work=0.1154 r_free=0.1311 adp: r_work=0.1151 r_free=0.1310 ADP+occupancy (water only), MIN, final r_work=0.1151 r_free=0.1310 r_work=0.1151 r_free=0.1310 | n_water=490 | time (s): 189.750 (total time: 252.250) Filter (q & B) r_work=0.1157 r_free=0.1318 | n_water=446 | time (s): 3.900 (total time: 256.150) Filter (dist only) r_work=0.1164 r_free=0.1318 | n_water=443 | time (s): 46.480 (total time: 302.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.163598 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 0.1221 0.1357 0.0136 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1183 0.1332 0.0149 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1170 0.1329 0.0158 0.005 0.9 3.8 0.5 0.0 0 0.537 0.1163 0.1322 0.0159 0.006 0.9 3.8 0.5 0.0 0 0.805 0.1159 0.1321 0.0162 0.006 1.0 3.8 0.5 0.0 0 1.074 0.1157 0.1319 0.0162 0.007 1.0 3.8 0.5 0.0 0 1.342 0.1154 0.1320 0.0166 0.008 1.1 3.8 0.5 0.0 0 1.611 0.1153 0.1321 0.0169 0.008 1.1 3.8 0.5 0.0 0 1.879 0.1162 0.1324 0.0162 0.006 1.0 4.2 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1319 0.0162 0.007 1.0 3.8 0.5 0.0 0 1.342 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.19 1.62 3.773 21.146 35.164 3.615 11.57 13.19 1.62 3.773 21.146 1.055 3.615 11.57 13.19 1.62 3.773 21.146 4.395 3.615 11.61 13.23 1.62 3.704 21.141 17.582 3.610 11.71 13.41 1.70 3.719 21.117 35.164 3.616 11.63 13.39 1.76 3.742 21.104 52.745 3.609 11.56 13.33 1.77 3.759 21.100 70.327 3.603 11.52 13.30 1.78 3.770 21.097 87.909 3.600 11.51 13.29 1.78 3.777 21.091 105.491 3.598 11.48 13.27 1.79 3.785 21.094 123.073 3.596 11.49 13.32 1.83 3.802 21.081 140.654 3.596 11.48 13.33 1.84 3.812 21.075 158.236 3.596 11.45 13.30 1.84 3.814 21.081 175.818 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.395 Accepted refinement result: 11.57 13.19 1.62 3.773 21.146 4.395 3.615 Individual atomic B min max mean iso aniso Overall: 9.11 114.95 21.02 3.29 224 1746 Protein: 9.11 114.95 17.04 3.30 0 1519 Water: 11.51 76.69 34.64 N/A 224 219 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.11 114.95 19.36 N/A 0 1746 Chain S: 15.15 60.00 33.93 N/A 224 0 Histogram: Values Number of atoms 9.11 - 19.69 1263 19.69 - 30.28 308 30.28 - 40.86 208 40.86 - 51.45 125 51.45 - 62.03 44 62.03 - 72.62 10 72.62 - 83.20 6 83.20 - 93.78 4 93.78 - 104.37 0 104.37 - 114.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1319 r_work=0.1157 r_free=0.1319 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1319 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1317 target_work(ml) = 3.612 | | 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.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1152 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.612117 | | target function (ml) not normalized (work): 300838.786182 | | target function (ml) not normalized (free): 15841.237538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1317 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1480 0.1480 0.1519 n_refl.: 87582 remove outliers: r(all,work,free)=0.1480 0.1480 0.1519 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1479 0.1478 0.1518 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1150 0.1318 n_refl.: 87582 remove outliers: r(all,work,free)=0.1155 0.1147 0.1318 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 89.58 81 5 0.3987 296.188 255.914 0.447 0.999 0.273 11.894-9.307 92.16 90 4 0.2474 465.321 463.223 0.852 1.001 0.198 9.237-7.194 98.18 209 7 0.2392 385.746 376.542 0.924 1.002 0.160 7.162-5.571 100.00 427 22 0.2155 295.868 284.502 0.909 1.002 0.133 5.546-4.326 100.00 867 58 0.1146 406.154 400.894 0.963 1.002 0.127 4.315-3.360 100.00 1859 96 0.0957 386.256 383.770 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1127 253.750 251.842 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0927 168.213 167.480 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.146 82.461 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1257 36.427 36.011 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2173 22.952 21.482 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=-0.0165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1147 r_free=0.1318 After: r_work=0.1148 r_free=0.1318 ================================== NQH flips ================================== r_work=0.1148 r_free=0.1318 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1148 r_free=0.1318 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1318 | n_water=443 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1148 r_free=0.1319 | n_water=442 | time (s): 48.200 (total time: 50.570) Filter (q & B) r_work=0.1148 r_free=0.1319 | n_water=442 | time (s): 1.310 (total time: 51.880) Compute maps r_work=0.1148 r_free=0.1319 | n_water=442 | time (s): 1.910 (total time: 53.790) Filter (map) r_work=0.1175 r_free=0.1320 | n_water=342 | time (s): 3.950 (total time: 57.740) Find peaks r_work=0.1175 r_free=0.1320 | n_water=342 | time (s): 0.720 (total time: 58.460) Add new water r_work=0.1220 r_free=0.1354 | n_water=504 | time (s): 3.810 (total time: 62.270) Refine new water occ: r_work=0.1163 r_free=0.1302 adp: r_work=0.1163 r_free=0.1305 occ: r_work=0.1151 r_free=0.1294 adp: r_work=0.1150 r_free=0.1295 occ: r_work=0.1141 r_free=0.1288 adp: r_work=0.1139 r_free=0.1287 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1287 r_work=0.1139 r_free=0.1287 | n_water=504 | time (s): 279.410 (total time: 341.680) Filter (q & B) r_work=0.1148 r_free=0.1301 | n_water=449 | time (s): 3.840 (total time: 345.520) Filter (dist only) r_work=0.1148 r_free=0.1300 | n_water=448 | time (s): 46.760 (total time: 392.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.809366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.234566 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 0.1218 0.1343 0.0125 0.003 0.7 5.4 0.0 0.0 0 0.090 0.1176 0.1315 0.0139 0.004 0.8 4.8 0.0 0.0 0 0.271 0.1160 0.1305 0.0145 0.005 0.9 4.5 0.5 0.0 0 0.543 0.1152 0.1301 0.0149 0.006 1.0 4.2 0.5 0.0 0 0.814 0.1148 0.1300 0.0152 0.007 1.1 4.2 0.5 0.0 0 1.086 0.1148 0.1300 0.0152 0.007 1.1 4.2 0.5 0.0 0 1.357 0.1147 0.1300 0.0153 0.007 1.1 4.2 0.5 0.0 0 1.628 0.1147 0.1300 0.0154 0.008 1.1 4.2 0.5 0.0 0 1.900 0.1151 0.1300 0.0150 0.006 1.0 4.2 0.5 0.0 0 0.905 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1300 0.0153 0.007 1.1 4.2 0.5 0.0 0 1.628 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 13.00 1.53 3.772 21.192 36.235 3.609 11.47 13.00 1.53 3.772 21.192 1.087 3.609 11.47 13.00 1.53 3.772 21.192 4.529 3.609 11.51 13.04 1.54 3.704 21.187 18.117 3.604 11.60 13.22 1.62 3.716 21.160 36.235 3.609 11.53 13.20 1.66 3.740 21.148 54.352 3.604 11.47 13.15 1.68 3.760 21.143 72.469 3.599 11.42 13.11 1.69 3.771 21.142 90.586 3.595 11.41 13.09 1.69 3.780 21.137 108.704 3.592 11.39 13.11 1.72 3.792 21.134 126.821 3.592 11.39 13.14 1.75 3.806 21.126 144.938 3.592 11.37 13.13 1.75 3.815 21.122 163.056 3.590 11.37 13.12 1.75 3.824 21.120 181.173 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.529 Accepted refinement result: 11.47 13.00 1.53 3.772 21.192 4.529 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 114.95 21.11 3.29 231 1744 Protein: 9.10 114.95 17.03 3.30 0 1519 Water: 11.51 76.69 34.90 N/A 231 217 Other: 19.78 26.64 22.10 N/A 0 8 Chain A: 9.10 114.95 19.32 N/A 0 1744 Chain S: 15.14 59.99 34.62 N/A 231 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.27 313 30.27 - 40.86 199 40.86 - 51.44 129 51.44 - 62.03 49 62.03 - 72.61 10 72.61 - 83.19 6 83.19 - 93.78 4 93.78 - 104.36 0 104.36 - 114.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1300 r_work=0.1147 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1300 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1293 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87575 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607060 | | target function (ml) not normalized (work): 300392.328004 | | target function (ml) not normalized (free): 15814.666913 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2917 171 0.1346 0.1416 5.6369 5.66| | 2: 3.57 - 2.84 1.00 2888 124 0.1083 0.1323 5.1752 5.1947| | 3: 2.83 - 2.48 1.00 2820 163 0.1119 0.1210 4.9623 4.9996| | 4: 2.47 - 2.25 1.00 2825 136 0.0904 0.0943 4.6415 4.6527| | 5: 2.25 - 2.09 1.00 2756 127 0.0875 0.0947 4.5886 4.634| | 6: 2.09 - 1.97 1.00 2846 113 0.0864 0.1020 4.2771 4.3849| | 7: 1.97 - 1.87 1.00 2787 165 0.0884 0.1107 3.979 4.0832| | 8: 1.87 - 1.79 1.00 2789 144 0.0933 0.1099 3.893 3.9837| | 9: 1.79 - 1.72 1.00 2745 138 0.0880 0.1167 3.6473 3.8035| | 10: 1.72 - 1.66 1.00 2831 160 0.0927 0.1202 3.5652 3.7179| | 11: 1.66 - 1.61 1.00 2712 147 0.0868 0.1028 3.4957 3.5656| | 12: 1.61 - 1.56 1.00 2773 144 0.0917 0.1169 3.337 3.4765| | 13: 1.56 - 1.52 1.00 2745 130 0.0955 0.1059 3.3119 3.3973| | 14: 1.52 - 1.48 1.00 2803 134 0.0991 0.1022 3.244 3.3185| | 15: 1.48 - 1.45 1.00 2738 128 0.1010 0.1217 3.1569 3.2546| | 16: 1.45 - 1.42 1.00 2756 161 0.1060 0.1255 3.1369 3.2449| | 17: 1.42 - 1.39 1.00 2785 139 0.1144 0.1315 3.1208 3.2387| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1320 3.1062 3.2379| | 19: 1.36 - 1.34 1.00 2807 134 0.1266 0.1555 3.1157 3.2579| | 20: 1.34 - 1.32 1.00 2696 147 0.1375 0.1455 3.1132 3.1533| | 21: 1.32 - 1.30 1.00 2785 112 0.1479 0.1520 3.1168 3.1119| | 22: 1.29 - 1.27 1.00 2704 152 0.1570 0.1974 3.1251 3.2919| | 23: 1.27 - 1.26 1.00 2802 156 0.1656 0.1806 3.1346 3.2033| | 24: 1.26 - 1.24 1.00 2744 132 0.1714 0.1836 3.1278 3.2263| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2170 3.1422 3.2604| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1767 3.1482 3.2001| | 27: 1.21 - 1.19 1.00 2814 148 0.2080 0.2170 3.172 3.1614| | 28: 1.19 - 1.18 1.00 2671 147 0.2208 0.2301 3.166 3.1702| | 29: 1.18 - 1.16 1.00 2800 134 0.2270 0.2394 3.1481 3.2301| | 30: 1.16 - 1.15 1.00 2739 148 0.2453 0.2439 3.1434 3.1626| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2917 171 0.95 8.78 1.00 0.97 5950.01| | 2: 3.57 - 2.84 2888 124 0.92 12.81 1.01 0.97 5950.01| | 3: 2.83 - 2.48 2820 163 0.89 16.80 0.99 0.97 4965.09| | 4: 2.47 - 2.25 2825 136 0.92 13.65 1.00 0.98 2425.30| | 5: 2.25 - 2.09 2756 127 0.90 15.89 1.01 0.98 2425.30| | 6: 2.09 - 1.97 2846 113 0.92 12.45 1.02 0.98 1390.97| | 7: 1.97 - 1.87 2787 165 0.95 9.29 1.02 0.97 508.82| | 8: 1.87 - 1.79 2789 144 0.93 12.60 1.00 0.97 508.82| | 9: 1.79 - 1.72 2745 138 0.94 10.09 0.98 0.97 287.72| | 10: 1.72 - 1.66 2831 160 0.94 11.09 0.98 0.97 243.44| | 11: 1.66 - 1.61 2712 147 0.94 11.69 0.98 0.97 233.32| | 12: 1.61 - 1.56 2773 144 0.95 8.92 0.99 0.97 137.92| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.03 0.97 137.92| | 14: 1.52 - 1.48 2803 134 0.94 10.76 1.02 0.98 123.68| | 15: 1.48 - 1.45 2738 128 0.95 9.92 1.02 0.98 97.58| | 16: 1.45 - 1.42 2756 161 0.94 11.08 1.02 0.98 97.58| | 17: 1.42 - 1.39 2785 139 0.95 10.93 1.01 0.98 89.06| | 18: 1.39 - 1.36 2741 179 0.94 11.59 1.01 0.98 84.13| | 19: 1.36 - 1.34 2807 134 0.94 11.90 0.99 0.98 84.13| | 20: 1.34 - 1.32 2696 147 0.94 12.15 0.98 0.96 80.13| | 21: 1.32 - 1.30 2785 112 0.94 13.15 0.98 0.96 79.85| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.96 80.26| | 23: 1.27 - 1.26 2802 156 0.92 14.89 0.97 0.94 82.31| | 24: 1.26 - 1.24 2744 132 0.92 14.91 0.96 0.94 82.31| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.19| | 26: 1.22 - 1.21 2727 135 0.90 18.14 1.02 0.93 86.27| | 27: 1.21 - 1.19 2814 148 0.89 18.80 1.02 0.93 86.27| | 28: 1.19 - 1.18 2671 147 0.88 20.44 1.01 0.92 89.84| | 29: 1.18 - 1.16 2800 134 0.88 20.52 0.99 0.92 91.19| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.92 91.19| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.85 max = 5950.01 mean = 911.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.51| |phase err.(test): min = 0.00 max = 88.03 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1150 0.1143 0.1293 n_refl.: 87575 re-set all scales: r(all,work,free)=0.1458 0.1457 0.1503 n_refl.: 87575 remove outliers: r(all,work,free)=0.1458 0.1457 0.1503 n_refl.: 87575 overall B=-0.01 to atoms: r(all,work,free)=0.1457 0.1456 0.1502 n_refl.: 87575 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1294 n_refl.: 87575 remove outliers: r(all,work,free)=0.1149 0.1141 0.1294 n_refl.: 87574 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4081 296.188 255.949 0.453 0.999 0.297 11.894-9.307 92.16 90 4 0.2387 465.321 447.167 0.839 1.001 0.217 9.237-7.194 97.73 208 7 0.2331 386.828 378.847 0.926 1.002 0.160 7.162-5.571 100.00 427 22 0.2123 295.868 284.856 0.904 1.002 0.120 5.546-4.326 100.00 867 58 0.1150 406.154 400.964 0.962 1.002 0.098 4.315-3.360 100.00 1859 96 0.0943 386.256 384.085 1.003 1.002 0.087 3.356-2.611 100.00 3867 181 0.1122 253.750 251.940 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0918 168.213 167.586 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.146 82.495 1.036 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.427 36.033 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.952 21.499 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0161 ================= 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 : 0.2603 0.1941 0.080 5.408 8.8 119.3 19.9 258 0.000 1_bss: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_settarget: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_weight: 0.1644 0.1756 0.080 5.408 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1230 0.1469 0.006 0.883 9.1 119.5 20.1 258 0.131 1_adp: 0.1237 0.1465 0.006 0.883 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1238 0.1468 0.006 0.883 9.1 119.5 20.1 258 0.131 1_occ: 0.1234 0.1464 0.006 0.883 9.1 119.5 20.1 258 0.131 2_bss: 0.1230 0.1455 0.006 0.883 9.1 119.5 20.1 258 0.131 2_settarget: 0.1230 0.1455 0.006 0.883 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1230 0.1455 0.006 0.896 9.1 119.5 20.1 258 0.131 2_nqh: 0.1231 0.1456 0.006 0.896 9.1 119.5 20.1 258 0.134 2_sol: 0.1210 0.1410 0.006 0.896 9.1 115.0 22.1 409 n/a 2_weight: 0.1210 0.1410 0.006 0.896 9.1 115.0 22.1 409 n/a 2_xyzrec: 0.1192 0.1416 0.008 0.923 9.1 115.0 22.1 409 n/a 2_adp: 0.1192 0.1416 0.008 0.923 9.1 115.0 22.1 409 n/a 2_regHadp: 0.1192 0.1416 0.008 0.923 9.1 115.0 22.1 409 n/a 2_occ: 0.1189 0.1420 0.008 0.923 9.1 115.0 22.1 409 n/a 3_bss: 0.1185 0.1415 0.008 0.923 9.1 115.0 22.1 409 n/a 3_settarget: 0.1185 0.1415 0.008 0.923 9.1 115.0 22.1 409 n/a 3_updatecdl: 0.1185 0.1415 0.008 0.922 9.1 115.0 22.1 409 n/a 3_nqh: 0.1185 0.1415 0.008 0.922 9.1 115.0 22.1 409 n/a 3_sol: 0.1212 0.1396 0.008 0.922 9.1 115.0 21.1 424 n/a 3_weight: 0.1212 0.1396 0.008 0.922 9.1 115.0 21.1 424 n/a 3_xyzrec: 0.1176 0.1329 0.005 0.913 9.1 115.0 21.1 424 n/a 3_adp: 0.1176 0.1329 0.005 0.913 9.1 115.0 21.1 424 n/a 3_regHadp: 0.1176 0.1329 0.005 0.913 9.1 115.0 21.1 424 n/a 3_occ: 0.1166 0.1324 0.005 0.913 9.1 115.0 21.1 424 n/a 4_bss: 0.1160 0.1316 0.005 0.913 9.1 115.0 21.1 424 n/a 4_settarget: 0.1160 0.1316 0.005 0.913 9.1 115.0 21.1 424 n/a 4_updatecdl: 0.1160 0.1316 0.005 0.913 9.1 115.0 21.1 424 n/a 4_nqh: 0.1160 0.1316 0.005 0.913 9.1 115.0 21.1 424 n/a 4_sol: 0.1164 0.1318 0.005 0.913 9.1 115.0 21.0 443 n/a 4_weight: 0.1164 0.1318 0.005 0.913 9.1 115.0 21.0 443 n/a 4_xyzrec: 0.1157 0.1319 0.007 1.050 9.1 115.0 21.0 443 n/a 4_adp: 0.1157 0.1319 0.007 1.050 9.1 115.0 21.0 443 n/a 4_regHadp: 0.1157 0.1319 0.007 1.050 9.1 115.0 21.0 443 n/a 4_occ: 0.1152 0.1317 0.007 1.050 9.1 115.0 21.0 443 n/a 5_bss: 0.1147 0.1318 0.007 1.050 9.1 114.9 21.0 443 n/a 5_settarget: 0.1147 0.1318 0.007 1.050 9.1 114.9 21.0 443 n/a 5_updatecdl: 0.1147 0.1318 0.007 1.051 9.1 114.9 21.0 443 n/a 5_setrh: 0.1148 0.1318 0.007 1.051 9.1 114.9 21.0 443 n/a 5_nqh: 0.1148 0.1318 0.007 1.051 9.1 114.9 21.0 443 n/a 5_sol: 0.1148 0.1300 0.007 1.051 9.1 114.9 21.1 448 n/a 5_weight: 0.1148 0.1300 0.007 1.051 9.1 114.9 21.1 448 n/a 5_xyzrec: 0.1147 0.1300 0.007 1.074 9.1 114.9 21.1 448 n/a 5_adp: 0.1147 0.1300 0.007 1.074 9.1 114.9 21.1 448 n/a 5_regHadp: 0.1147 0.1300 0.007 1.074 9.1 114.9 21.1 448 n/a 5_occ: 0.1143 0.1293 0.007 1.074 9.1 114.9 21.1 448 n/a end: 0.1141 0.1294 0.007 1.074 9.1 114.9 21.1 448 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7410891_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7410891_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8700 Refinement macro-cycles (run) : 13747.0300 Write final files (write_after_run_outputs) : 90.2200 Total : 13841.1200 Total CPU time: 3.85 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:09:28 PST -0800 (1735366168.48 s) Start R-work = 0.1644, R-free = 0.1756 Final R-work = 0.1141, R-free = 0.1294 =============================================================================== Job complete usr+sys time: 14012.75 seconds wall clock time: 253 minutes 32.39 seconds (15212.39 seconds total)