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_5382129.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.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: 1.80, per 1000 atoms: 0.53 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: 0.56 Conformation dependent library (CDL) restraints added in 108.0 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 485 0.90 - 1.16: 1157 1.16 - 1.41: 569 1.41 - 1.66: 886 1.66 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 20 " pdb=" O VAL A 20 " ideal model delta sigma weight residual 1.237 0.986 0.251 1.19e-02 7.06e+03 4.45e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.329 1.538 -0.209 1.15e-02 7.56e+03 3.30e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.501 -0.180 1.00e-02 1.00e+04 3.23e+02 bond pdb=" C THR A 34 " pdb=" O THR A 34 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.17e-02 7.31e+03 3.12e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.732 -0.212 1.23e-02 6.61e+03 2.96e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3268 4.88 - 9.75: 1836 9.75 - 14.62: 581 14.62 - 19.49: 83 19.49 - 24.37: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.62 13.58 9.00e-01 1.23e+00 2.28e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 137.98 -15.86 1.06e+00 8.90e-01 2.24e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.76 134.45 -12.69 8.70e-01 1.32e+00 2.13e+02 angle pdb=" CA BGLU A 96 " pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 120.82 107.13 13.69 1.05e+00 9.07e-01 1.70e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.22 137.81 -14.59 1.14e+00 7.69e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 989 20.64 - 41.28: 86 41.28 - 61.92: 31 61.92 - 82.55: 3 82.55 - 103.19: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CD2 PHE A 164 " pdb=" CG PHE A 164 " pdb=" CD1 PHE A 164 " pdb=" HD1 PHE A 164 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA THR A 110 " pdb=" C THR A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " pdb=" CA ASP A 42 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.228: 111 0.228 - 0.449: 71 0.449 - 0.670: 44 0.670 - 0.892: 13 0.892 - 1.113: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 3.52 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.075 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.052 2.00e-02 2.50e+03 9.22e-02 8.51e+01 pdb=" C ASP A 49 " 0.160 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.053 2.00e-02 2.50e+03 pdb=" N VAL A 50 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1282 2.35 - 2.91: 8208 2.91 - 3.48: 10502 3.48 - 4.04: 15144 4.04 - 4.60: 21424 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.788 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.795 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.820 2.100 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.837 1.850 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.839 2.100 ... (remaining 56555 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_5382129_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= 0.2598 r_free= 0.1945 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789863 | | target function (ml) not normalized (work): 232412.339265 | | target function (ml) not normalized (free): 11799.002663 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3022 0.2063 7.1061 4.9407| | 2: 3.57 - 2.84 1.00 2876 122 0.2420 0.1737 4.3443 4.3257| | 3: 2.84 - 2.48 1.00 2833 165 0.2330 0.1662 4.1217 4.1471| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1545 3.8284 3.8323| | 5: 2.25 - 2.09 1.00 2756 127 0.2442 0.1595 3.7903 3.8191| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1959 3.4633 3.6031| | 7: 1.97 - 1.87 1.00 2787 165 0.2550 0.1820 3.1305 3.181| | 8: 1.87 - 1.79 1.00 2789 144 0.2483 0.1899 3.05 3.1359| | 9: 1.79 - 1.72 1.00 2745 138 0.2409 0.1861 2.9159 2.9822| | 10: 1.72 - 1.66 1.00 2789 158 0.2434 0.2057 2.8101 2.8696| | 11: 1.66 - 1.61 1.00 2740 147 0.2503 0.1793 2.7469 2.7572| | 12: 1.61 - 1.56 1.00 2787 146 0.2472 0.1940 2.6208 2.6172| | 13: 1.56 - 1.52 1.00 2745 130 0.2547 0.1768 2.5614 2.572| | 14: 1.52 - 1.48 1.00 2803 134 0.2635 0.1893 2.509 2.5424| | 15: 1.48 - 1.45 1.00 2738 128 0.2608 0.2168 2.4345 2.493| | 16: 1.45 - 1.42 1.00 2756 161 0.2627 0.2069 2.3706 2.3903| | 17: 1.42 - 1.39 1.00 2785 139 0.2617 0.2028 2.3309 2.3292| | 18: 1.39 - 1.36 1.00 2741 179 0.2731 0.2349 2.2794 2.3587| | 19: 1.36 - 1.34 1.00 2807 134 0.2681 0.2257 2.2512 2.2714| | 20: 1.34 - 1.32 1.00 2696 147 0.2654 0.2327 2.1949 2.23| | 21: 1.32 - 1.30 1.00 2785 112 0.2671 0.2631 2.1559 2.2673| | 22: 1.29 - 1.27 1.00 2704 152 0.2744 0.2531 2.1383 2.2001| | 23: 1.27 - 1.26 1.00 2802 156 0.2729 0.2414 2.0988 2.1773| | 24: 1.26 - 1.24 1.00 2744 132 0.2781 0.2437 2.0692 2.1541| | 25: 1.24 - 1.22 1.00 2734 148 0.2863 0.2558 2.0572 2.0823| | 26: 1.22 - 1.21 1.00 2727 135 0.2889 0.2351 2.0137 2.094| | 27: 1.21 - 1.19 1.00 2814 148 0.2982 0.2503 2.0085 1.9638| | 28: 1.19 - 1.18 1.00 2671 147 0.2935 0.2780 1.9706 1.9949| | 29: 1.18 - 1.16 1.00 2800 134 0.2905 0.2631 1.9419 1.9842| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2908 1.923 1.9584| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.68 0.76 0.23 1451.38| | 2: 3.57 - 2.84 2876 122 0.81 25.78 1.27 0.23 1451.38| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1204.73| | 4: 2.47 - 2.25 2825 136 0.81 25.45 1.26 0.25 564.63| | 5: 2.25 - 2.09 2756 127 0.77 29.10 1.28 0.25 564.63| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 310.81| | 7: 1.97 - 1.87 2787 165 0.90 16.93 1.29 0.25 94.35| | 8: 1.87 - 1.79 2789 144 0.85 21.67 1.26 0.25 94.35| | 9: 1.79 - 1.72 2745 138 0.88 18.64 1.23 0.25 56.41| | 10: 1.72 - 1.66 2789 158 0.87 20.03 1.22 0.25 48.81| | 11: 1.66 - 1.61 2740 147 0.85 21.49 1.24 0.25 47.02| | 12: 1.61 - 1.56 2787 146 0.89 18.13 1.22 0.25 28.80| | 13: 1.56 - 1.52 2745 130 0.87 20.04 1.24 0.25 28.80| | 14: 1.52 - 1.48 2803 134 0.86 20.66 1.24 0.25 25.90| | 15: 1.48 - 1.45 2738 128 0.87 20.15 1.23 0.25 20.60| | 16: 1.45 - 1.42 2756 161 0.86 21.41 1.24 0.25 20.60| | 17: 1.42 - 1.39 2785 139 0.87 20.55 1.22 0.25 17.73| | 18: 1.39 - 1.36 2741 179 0.86 21.75 1.24 0.25 16.07| | 19: 1.36 - 1.34 2807 134 0.85 22.35 1.22 0.25 16.07| | 20: 1.34 - 1.32 2696 147 0.86 21.38 1.21 0.25 13.59| | 21: 1.32 - 1.30 2785 112 0.85 22.38 1.20 0.25 13.42| | 22: 1.29 - 1.27 2704 152 0.85 22.78 1.21 0.24 13.07| | 23: 1.27 - 1.26 2802 156 0.86 22.24 1.21 0.24 11.31| | 24: 1.26 - 1.24 2744 132 0.85 23.10 1.21 0.24 11.31| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.20 0.24 10.65| | 26: 1.22 - 1.21 2727 135 0.84 23.80 1.20 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.69 1.21 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.83 25.08 1.18 0.23 9.12| | 29: 1.18 - 1.16 2800 134 0.83 25.13 1.16 0.22 8.83| | 30: 1.16 - 1.15 2740 148 0.81 26.94 1.15 0.22 8.83| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 8.83 max = 1451.38 mean = 211.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.62| |phase err.(test): min = 0.00 max = 89.90 mean = 22.67| |-----------------------------------------------------------------------------| ----------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 0.258 1557 Z= 5.355 Angle : 5.248 15.864 2118 Z= 3.666 Chirality : 0.382 1.113 243 Planarity : 0.031 0.092 284 Dihedral : 14.092 103.191 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 32.43 % 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: -1.73 (0.51), residues: 224 helix: -1.88 (0.44), residues: 102 sheet: -2.14 (0.85), residues: 28 loop : 0.45 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.024 ARG A 48 TYR 0.089 0.028 TYR A 141 PHE 0.078 0.032 PHE A 119 HIS 0.069 0.031 HIS A 126 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= 0.2598 r_free= 0.1945 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789863 | | target function (ml) not normalized (work): 232412.339265 | | target function (ml) not normalized (free): 11799.002663 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2556 0.2598 0.1946 n_refl.: 87602 remove outliers: r(all,work,free)=0.1968 0.1971 0.1946 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1993 0.1996 0.1961 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1632 0.1626 0.1760 n_refl.: 87594 remove outliers: r(all,work,free)=0.1631 0.1624 0.1760 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3826 381.975 358.101 0.668 1.003 0.401 11.894-9.307 98.04 96 4 0.1737 616.052 589.255 0.928 1.003 0.380 9.237-7.194 100.00 213 7 0.2146 501.818 491.150 0.956 1.003 0.339 7.162-5.571 100.00 427 22 0.2177 376.587 363.853 0.929 1.003 0.320 5.546-4.326 100.00 867 58 0.1283 516.960 511.048 0.963 1.003 0.219 4.315-3.360 100.00 1859 96 0.1140 491.633 487.921 1.003 1.003 0.199 3.356-2.611 100.00 3867 181 0.1421 322.977 319.959 0.997 1.002 0.043 2.608-2.026 99.99 8198 413 0.1335 214.104 212.250 1.005 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.557 103.983 1.015 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2061 46.365 45.072 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2560 29.213 26.984 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0467 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1624 r_free=0.1760 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1624 r_free=0.1760 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.237642 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2031.225959 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 0.1718 0.1842 0.0124 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1572 0.1711 0.0140 0.002 0.4 4.2 0.0 0.0 0 0.250 0.1451 0.1615 0.0164 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1398 0.1581 0.0183 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1364 0.1565 0.0201 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1344 0.1540 0.0196 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1287 0.1499 0.0212 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1275 0.1502 0.0226 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1257 0.1488 0.0231 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1245 0.1478 0.0233 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1240 0.1474 0.0233 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1234 0.1468 0.0235 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1229 0.1464 0.0235 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1227 0.1462 0.0235 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1227 0.1466 0.0239 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1224 0.1461 0.0238 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1223 0.1464 0.0241 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1219 0.1465 0.0246 0.008 1.0 4.2 0.5 0.0 0 13.619 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1224 0.1461 0.0238 0.007 0.9 3.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 14.61 2.38 3.013 19.062 2031.226 0.017 12.24 14.60 2.37 2.986 19.062 60.937 0.017 12.30 14.57 2.28 2.689 19.061 253.903 0.017 12.69 15.29 2.60 2.885 19.351 1015.613 0.016 12.41 15.29 2.88 3.049 19.480 2031.226 0.015 12.47 15.52 3.05 3.432 19.707 3046.839 0.015 12.33 15.43 3.10 3.368 19.661 4062.452 0.015 12.27 15.39 3.12 3.403 19.668 5078.065 0.015 12.19 15.33 3.14 3.335 19.631 6093.678 0.015 12.12 15.27 3.14 3.240 19.570 7109.291 0.015 12.16 15.40 3.23 3.291 19.583 8124.904 0.015 12.15 15.41 3.26 3.520 19.707 9140.517 0.014 12.12 15.39 3.28 3.460 19.663 10156.130 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: 253.903 Accepted refinement result: 12.30 14.57 2.28 2.689 19.061 253.903 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.09 3.35 0 1785 Protein: 9.07 115.20 17.00 3.36 0 1519 Water: 11.48 119.45 38.23 N/A 0 258 Other: 19.69 26.61 22.04 N/A 0 8 Chain A: 9.07 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 228 31.15 - 42.19 124 42.19 - 53.23 95 53.23 - 64.26 41 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1457 r_work=0.1231 r_free=0.1461 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1461 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 = 0.1226 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016639 | | target function (ls_wunit_k1) not normalized (work): 1385.958247 | | target function (ls_wunit_k1) not normalized (free): 108.021006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1226 0.1457 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1669 0.1670 0.1691 n_refl.: 87591 remove outliers: r(all,work,free)=0.1669 0.1670 0.1691 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1675 0.1676 0.1696 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1234 0.1223 0.1451 n_refl.: 87591 remove outliers: r(all,work,free)=0.1234 0.1223 0.1451 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 94.79 86 5 0.3474 297.732 278.007 0.641 1.003 0.380 11.894-9.307 98.04 96 4 0.1532 484.415 473.650 0.934 1.003 0.369 9.237-7.194 100.00 213 7 0.1885 394.590 388.365 0.964 1.003 0.346 7.162-5.571 100.00 427 22 0.1822 296.118 290.290 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1000 406.497 403.606 0.963 1.003 0.204 4.315-3.360 100.00 1859 96 0.0872 386.582 385.450 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1172 253.964 252.774 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.355 167.638 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1107 82.216 82.411 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.458 35.968 1.020 0.996 0.000 1.221-1.150 99.97 13689 708 0.2252 22.971 21.452 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=0.0499 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1451 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=0.1224 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1452 | n_water=258 | time (s): 2.090 (total time: 2.090) Filter (dist) r_work=0.1233 r_free=0.1450 | n_water=252 | time (s): 20.250 (total time: 22.340) Filter (q & B) r_work=0.1235 r_free=0.1450 | n_water=249 | time (s): 3.100 (total time: 25.440) Compute maps r_work=0.1235 r_free=0.1450 | n_water=249 | time (s): 1.670 (total time: 27.110) Filter (map) r_work=0.1251 r_free=0.1456 | n_water=226 | time (s): 3.470 (total time: 30.580) Find peaks r_work=0.1251 r_free=0.1456 | n_water=226 | time (s): 0.630 (total time: 31.210) Add new water r_work=0.1393 r_free=0.1634 | n_water=436 | time (s): 2.680 (total time: 33.890) Refine new water occ: r_work=0.1299 r_free=0.1483 adp: r_work=0.1220 r_free=0.1433 occ: r_work=0.1231 r_free=0.1415 adp: r_work=0.1200 r_free=0.1404 occ: r_work=0.1203 r_free=0.1392 adp: r_work=0.1193 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1393 r_work=0.1193 r_free=0.1393 | n_water=436 | time (s): 56.870 (total time: 90.760) Filter (q & B) r_work=0.1198 r_free=0.1393 | n_water=422 | time (s): 2.920 (total time: 93.680) Filter (dist only) r_work=0.1198 r_free=0.1392 | n_water=421 | time (s): 34.010 (total time: 127.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.983204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1495.076946 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 0.1682 0.1795 0.0113 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1534 0.1666 0.0131 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1405 0.1560 0.0155 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1364 0.1526 0.0163 0.001 0.4 5.1 0.0 0.0 0 0.750 0.1332 0.1508 0.0176 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1320 0.1498 0.0178 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1261 0.1450 0.0188 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1227 0.1438 0.0211 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1213 0.1429 0.0216 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1208 0.1429 0.0220 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1205 0.1433 0.0228 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1201 0.1431 0.0230 0.005 0.8 5.1 0.5 0.0 0 7.000 0.1199 0.1429 0.0230 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1192 0.1423 0.0230 0.006 0.8 5.4 0.5 0.0 0 9.000 0.1190 0.1418 0.0228 0.006 0.9 5.4 0.5 0.0 0 10.000 0.1191 0.1420 0.0229 0.007 0.9 5.4 0.5 0.0 0 11.000 0.1191 0.1414 0.0223 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1188 0.1414 0.0226 0.008 1.0 5.1 0.5 0.0 0 13.992 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1414 0.0223 0.007 0.9 5.4 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 14.14 2.23 3.794 21.813 1495.077 0.016 11.91 14.14 2.23 3.794 21.813 44.852 0.016 11.91 14.14 2.23 3.794 21.813 186.885 0.016 12.18 14.71 2.53 3.581 21.861 747.538 0.015 12.18 15.01 2.83 3.527 22.244 1495.077 0.015 11.94 14.84 2.90 3.482 22.024 2242.615 0.014 11.81 14.79 2.98 3.526 21.971 2990.154 0.014 11.72 14.75 3.03 3.548 21.961 3737.692 0.014 11.77 14.83 3.06 3.561 22.221 4485.231 0.014 11.75 14.85 3.09 3.577 22.180 5232.769 0.014 11.70 14.78 3.08 3.578 22.154 5980.308 0.014 11.70 14.85 3.16 3.605 22.196 6727.846 0.014 11.64 14.80 3.16 3.606 22.164 7475.385 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: 44.852 Accepted refinement result: 11.91 14.14 2.23 3.794 21.813 44.852 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.23 22.25 3.35 195 1753 Protein: 9.11 115.23 17.03 3.36 0 1519 Water: 10.75 76.71 41.08 N/A 195 226 Other: 19.72 26.64 22.07 N/A 0 8 Chain A: 9.11 115.23 19.47 N/A 0 1753 Chain S: 10.75 60.00 47.22 N/A 195 0 Histogram: Values Number of atoms 9.11 - 19.72 1261 19.72 - 30.33 247 30.33 - 40.94 158 40.94 - 51.56 135 51.56 - 62.17 124 62.17 - 72.78 12 72.78 - 83.39 5 83.39 - 94.01 4 94.01 - 104.62 0 104.62 - 115.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1414 r_work=0.1191 r_free=0.1414 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1414 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 = 0.1194 r_free = 0.1421 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1194 r_free= 0.1421 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015112 | | target function (ls_wunit_k1) not normalized (work): 1258.779672 | | target function (ls_wunit_k1) not normalized (free): 104.654949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1194 0.1421 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1587 0.1586 0.1636 n_refl.: 87590 remove outliers: r(all,work,free)=0.1587 0.1586 0.1636 n_refl.: 87590 overall B=0.01 to atoms: r(all,work,free)=0.1588 0.1587 0.1637 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1190 0.1417 n_refl.: 87590 remove outliers: r(all,work,free)=0.1200 0.1189 0.1417 n_refl.: 87588 ======================== 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 0.3309 297.077 272.481 0.586 1.003 0.350 11.894-9.307 98.04 96 4 0.1604 484.415 476.218 0.930 1.003 0.330 9.237-7.194 100.00 213 7 0.1698 394.590 393.940 0.985 1.003 0.280 7.162-5.571 100.00 427 22 0.1557 296.118 292.039 0.937 1.003 0.240 5.546-4.326 100.00 867 58 0.0875 406.497 403.901 0.960 1.003 0.200 4.315-3.360 100.00 1859 96 0.0800 386.582 385.435 1.005 1.003 0.190 3.356-2.611 100.00 3867 181 0.1099 253.964 252.913 1.008 1.002 0.057 2.608-2.026 99.99 8198 413 0.1027 168.355 167.835 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1100 82.216 82.425 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1440 36.458 36.001 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.971 21.487 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0112 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1417 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1190 r_free=0.1418 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1418 | n_water=421 | time (s): 1.720 (total time: 1.720) Filter (dist) r_work=0.1190 r_free=0.1417 | n_water=417 | time (s): 37.360 (total time: 39.080) Filter (q & B) r_work=0.1190 r_free=0.1417 | n_water=417 | time (s): 0.830 (total time: 39.910) Compute maps r_work=0.1190 r_free=0.1417 | n_water=417 | time (s): 1.550 (total time: 41.460) Filter (map) r_work=0.1230 r_free=0.1400 | n_water=278 | time (s): 2.910 (total time: 44.370) Find peaks r_work=0.1230 r_free=0.1400 | n_water=278 | time (s): 0.540 (total time: 44.910) Add new water r_work=0.1343 r_free=0.1519 | n_water=456 | time (s): 2.330 (total time: 47.240) Refine new water occ: r_work=0.1247 r_free=0.1437 adp: r_work=0.1248 r_free=0.1439 occ: r_work=0.1225 r_free=0.1418 adp: r_work=0.1224 r_free=0.1419 occ: r_work=0.1207 r_free=0.1403 adp: r_work=0.1203 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1402 r_work=0.1203 r_free=0.1402 | n_water=456 | time (s): 192.330 (total time: 239.570) Filter (q & B) r_work=0.1208 r_free=0.1400 | n_water=423 | time (s): 2.620 (total time: 242.190) Filter (dist only) r_work=0.1208 r_free=0.1399 | n_water=421 | time (s): 33.810 (total time: 276.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.773613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.623149 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 0.1233 0.1365 0.0132 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1191 0.1334 0.0143 0.003 0.7 3.5 0.5 0.0 0 0.266 0.1176 0.1323 0.0147 0.004 0.8 3.2 0.5 0.0 0 0.532 0.1168 0.1323 0.0155 0.005 0.9 3.2 0.5 0.0 0 0.798 0.1163 0.1322 0.0159 0.006 1.0 2.9 0.5 0.0 0 1.064 0.1160 0.1323 0.0163 0.007 1.0 3.2 0.5 0.0 0 1.330 0.1158 0.1323 0.0165 0.007 1.1 3.2 0.5 0.0 0 1.596 0.1157 0.1324 0.0167 0.008 1.1 3.5 0.5 0.0 0 1.862 0.1166 0.1325 0.0159 0.005 0.9 3.2 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1322 0.0159 0.006 1.0 2.9 0.5 0.0 0 1.064 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 13.22 1.59 3.797 21.179 43.623 3.620 11.63 13.22 1.59 3.797 21.179 1.309 3.620 11.63 13.23 1.59 3.791 21.179 5.453 3.620 11.67 13.30 1.63 3.723 21.171 21.812 3.615 11.73 13.42 1.69 3.731 21.144 43.623 3.618 11.66 13.40 1.74 3.754 21.131 65.435 3.612 11.59 13.37 1.77 3.770 21.124 87.246 3.606 11.57 13.35 1.78 3.779 21.119 109.058 3.604 11.53 13.33 1.80 3.790 21.115 130.869 3.601 11.53 13.36 1.83 3.804 21.098 152.681 3.601 11.50 13.33 1.83 3.813 21.100 174.493 3.599 11.50 13.33 1.83 3.822 21.091 196.304 3.598 11.50 13.34 1.84 3.830 21.089 218.116 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.309 Accepted refinement result: 11.63 13.22 1.59 3.797 21.179 1.309 3.620 Individual atomic B min max mean iso aniso Overall: 9.11 115.24 21.08 3.35 199 1749 Protein: 9.11 115.24 17.03 3.36 0 1519 Water: 10.75 76.72 35.66 N/A 199 222 Other: 19.73 26.65 22.08 N/A 0 8 Chain A: 9.11 115.24 19.41 N/A 0 1749 Chain S: 10.75 60.01 35.77 N/A 199 0 Histogram: Values Number of atoms 9.11 - 19.73 1263 19.73 - 30.34 283 30.34 - 40.95 201 40.95 - 51.56 127 51.56 - 62.18 51 62.18 - 72.79 12 72.79 - 83.40 5 83.40 - 94.01 4 94.01 - 104.63 0 104.63 - 115.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1322 r_work=0.1163 r_free=0.1322 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1322 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1310 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1152 r_free= 0.1310 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.612026 | | target function (ml) not normalized (work): 300852.894289 | | target function (ml) not normalized (free): 15835.125259 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1310 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1492 0.1492 0.1519 n_refl.: 87588 remove outliers: r(all,work,free)=0.1492 0.1492 0.1519 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1491 0.1491 0.1519 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1150 0.1307 n_refl.: 87588 remove outliers: r(all,work,free)=0.1155 0.1147 0.1307 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3944 291.631 265.458 0.497 1.000 0.310 11.894-9.307 96.08 94 4 0.2182 477.726 469.126 0.894 1.002 0.296 9.237-7.194 98.18 209 7 0.2274 386.071 384.878 0.955 1.002 0.219 7.162-5.571 100.00 427 22 0.2130 296.118 285.025 0.922 1.002 0.186 5.546-4.326 100.00 867 58 0.1128 406.497 401.834 0.963 1.002 0.154 4.315-3.360 100.00 1859 96 0.0936 386.582 383.936 1.005 1.002 0.137 3.356-2.611 100.00 3867 181 0.1135 253.964 251.904 1.009 1.001 0.100 2.608-2.026 99.99 8198 413 0.0940 168.355 167.537 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0904 82.216 82.493 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.458 36.039 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 22.971 21.507 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0141 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1307 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=0.1147 r_free=0.1307 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1307 | n_water=421 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1147 r_free=0.1309 | n_water=420 | time (s): 42.060 (total time: 44.510) Filter (q & B) r_work=0.1147 r_free=0.1308 | n_water=419 | time (s): 3.890 (total time: 48.400) Compute maps r_work=0.1147 r_free=0.1308 | n_water=419 | time (s): 1.910 (total time: 50.310) Filter (map) r_work=0.1171 r_free=0.1317 | n_water=317 | time (s): 3.890 (total time: 54.200) Find peaks r_work=0.1171 r_free=0.1317 | n_water=317 | time (s): 0.720 (total time: 54.920) Add new water r_work=0.1243 r_free=0.1392 | n_water=483 | time (s): 3.700 (total time: 58.620) Refine new water occ: r_work=0.1173 r_free=0.1331 adp: r_work=0.1174 r_free=0.1332 occ: r_work=0.1157 r_free=0.1314 adp: r_work=0.1156 r_free=0.1315 occ: r_work=0.1144 r_free=0.1299 adp: r_work=0.1141 r_free=0.1299 ADP+occupancy (water only), MIN, final r_work=0.1141 r_free=0.1299 r_work=0.1141 r_free=0.1299 | n_water=483 | time (s): 210.260 (total time: 268.880) Filter (q & B) r_work=0.1146 r_free=0.1296 | n_water=448 | time (s): 3.970 (total time: 272.850) Filter (dist only) r_work=0.1146 r_free=0.1295 | n_water=447 | time (s): 46.520 (total time: 319.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.805854 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.991332 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 0.1202 0.1333 0.0131 0.002 0.6 4.2 0.5 0.0 0 0.090 0.1167 0.1312 0.0145 0.003 0.7 3.2 0.5 0.0 0 0.271 0.1153 0.1303 0.0151 0.005 0.9 3.5 0.5 0.0 0 0.542 0.1146 0.1300 0.0154 0.006 1.0 3.2 0.5 0.0 0 0.813 0.1142 0.1296 0.0154 0.006 1.0 3.2 0.5 0.0 0 1.084 0.1139 0.1296 0.0158 0.007 1.1 3.2 0.5 0.0 0 1.354 0.1137 0.1294 0.0157 0.008 1.1 3.2 0.5 0.0 0 1.625 0.1136 0.1293 0.0157 0.009 1.1 3.8 0.5 0.0 0 1.896 0.1144 0.1297 0.0153 0.006 1.0 3.2 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1293 0.0157 0.009 1.1 3.8 0.5 0.0 0 1.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.93 1.57 3.798 21.178 48.991 3.602 11.36 12.93 1.57 3.798 21.178 1.470 3.602 11.37 12.93 1.56 3.788 21.178 6.124 3.602 11.43 13.02 1.58 3.725 21.165 24.496 3.600 11.40 13.05 1.66 3.749 21.151 48.991 3.597 11.38 13.08 1.71 3.768 21.133 73.487 3.594 11.34 13.06 1.72 3.777 21.131 97.983 3.591 11.30 13.03 1.73 3.790 21.130 122.478 3.587 11.28 13.02 1.74 3.800 21.127 146.974 3.586 11.29 13.07 1.78 3.820 21.111 171.470 3.586 11.28 13.06 1.78 3.829 21.108 195.965 3.585 11.27 13.04 1.78 3.837 21.107 220.461 3.584 11.25 13.02 1.77 3.841 21.108 244.957 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: 1.470 Accepted refinement result: 11.36 12.93 1.57 3.798 21.178 1.470 3.602 Individual atomic B min max mean iso aniso Overall: 9.11 115.23 21.08 3.35 226 1748 Protein: 9.11 115.23 17.03 3.36 0 1519 Water: 10.75 76.71 34.85 N/A 226 221 Other: 19.72 26.64 22.08 N/A 0 8 Chain A: 9.11 115.23 19.39 N/A 0 1748 Chain S: 10.75 60.00 34.21 N/A 226 0 Histogram: Values Number of atoms 9.11 - 19.72 1265 19.72 - 30.33 303 30.33 - 40.95 211 40.95 - 51.56 126 51.56 - 62.17 46 62.17 - 72.78 12 72.78 - 83.40 5 83.40 - 94.01 4 94.01 - 104.62 0 104.62 - 115.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1293 r_work=0.1136 r_free=0.1293 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1293 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1286 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87581 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1286 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597542 | | target function (ml) not normalized (work): 299621.274247 | | target function (ml) not normalized (free): 15793.820794 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1126 0.1286 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1466 0.1465 0.1519 n_refl.: 87581 remove outliers: r(all,work,free)=0.1466 0.1465 0.1519 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1465 0.1464 0.1518 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1126 0.1288 n_refl.: 87581 remove outliers: r(all,work,free)=0.1132 0.1124 0.1288 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 0.4002 285.682 252.865 0.442 1.000 0.289 11.894-9.307 95.10 93 4 0.2323 477.777 461.857 0.868 1.002 0.273 9.237-7.194 98.18 209 7 0.2253 386.071 379.648 0.934 1.002 0.190 7.162-5.571 100.00 427 22 0.2093 296.118 285.563 0.916 1.002 0.158 5.546-4.326 100.00 867 58 0.1093 406.497 402.386 0.966 1.002 0.150 4.315-3.360 100.00 1859 96 0.0909 386.582 384.512 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1110 253.964 252.227 1.010 1.002 0.048 2.608-2.026 99.99 8198 413 0.0912 168.355 167.755 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0879 82.216 82.579 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1243 36.458 36.079 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.971 21.529 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0155 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1124 r_free=0.1288 After: r_work=0.1125 r_free=0.1288 ================================== NQH flips ================================== r_work=0.1125 r_free=0.1288 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1125 r_free=0.1288 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1125 r_free=0.1288 | n_water=447 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1126 r_free=0.1289 | n_water=445 | time (s): 46.510 (total time: 48.990) Filter (q & B) r_work=0.1126 r_free=0.1289 | n_water=445 | time (s): 1.280 (total time: 50.270) Compute maps r_work=0.1126 r_free=0.1289 | n_water=445 | time (s): 1.740 (total time: 52.010) Filter (map) r_work=0.1150 r_free=0.1299 | n_water=345 | time (s): 3.740 (total time: 55.750) Find peaks r_work=0.1150 r_free=0.1299 | n_water=345 | time (s): 0.650 (total time: 56.400) Add new water r_work=0.1208 r_free=0.1363 | n_water=488 | time (s): 3.440 (total time: 59.840) Refine new water occ: r_work=0.1152 r_free=0.1304 adp: r_work=0.1153 r_free=0.1307 occ: r_work=0.1137 r_free=0.1291 adp: r_work=0.1136 r_free=0.1292 occ: r_work=0.1126 r_free=0.1278 adp: r_work=0.1123 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1279 r_work=0.1123 r_free=0.1279 | n_water=488 | time (s): 227.560 (total time: 287.400) Filter (q & B) r_work=0.1129 r_free=0.1285 | n_water=456 | time (s): 3.640 (total time: 291.040) Filter (dist only) r_work=0.1130 r_free=0.1283 | n_water=455 | time (s): 47.270 (total time: 338.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.809766 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.103696 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 0.1209 0.1332 0.0122 0.004 0.7 5.1 0.0 0.0 0 0.090 0.1161 0.1301 0.0140 0.004 0.8 4.5 0.0 0.0 0 0.271 0.1148 0.1292 0.0144 0.005 0.9 4.2 0.5 0.0 0 0.543 0.1138 0.1286 0.0148 0.006 1.0 3.8 0.5 0.0 0 0.814 0.1134 0.1284 0.0150 0.007 1.1 3.8 0.5 0.0 0 1.086 0.1132 0.1283 0.0152 0.008 1.1 3.8 0.5 0.0 0 1.357 0.1130 0.1283 0.0153 0.009 1.1 3.8 0.5 0.0 0 1.629 0.1130 0.1283 0.0154 0.009 1.1 4.2 0.5 0.0 0 1.900 0.1137 0.1286 0.0149 0.006 1.0 3.8 0.5 0.0 0 0.905 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1283 0.0153 0.009 1.1 3.8 0.5 0.0 0 1.629 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.83 1.53 3.797 21.224 47.104 3.600 11.30 12.83 1.53 3.797 21.224 1.413 3.600 11.30 12.84 1.53 3.786 21.224 5.888 3.599 11.37 12.92 1.56 3.723 21.212 23.552 3.597 11.33 12.93 1.61 3.746 21.202 47.104 3.594 11.35 13.01 1.66 3.754 21.179 70.656 3.592 11.29 12.99 1.69 3.773 21.173 94.207 3.588 11.24 12.92 1.68 3.788 21.176 117.759 3.585 11.22 12.93 1.70 3.801 21.172 141.311 3.583 11.22 12.95 1.73 3.815 21.163 164.863 3.583 11.22 12.96 1.74 3.827 21.157 188.415 3.583 11.20 12.94 1.74 3.836 21.157 211.967 3.581 11.19 12.94 1.75 3.843 21.157 235.518 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.413 Accepted refinement result: 11.30 12.83 1.53 3.797 21.224 1.413 3.600 Individual atomic B min max mean iso aniso Overall: 9.10 115.23 21.17 3.35 236 1746 Protein: 9.10 115.23 17.02 3.36 0 1519 Water: 10.74 76.71 35.01 N/A 236 219 Other: 19.72 26.64 22.07 N/A 0 8 Chain A: 9.10 115.23 19.34 N/A 0 1746 Chain S: 10.74 60.00 34.76 N/A 236 0 Histogram: Values Number of atoms 9.10 - 19.72 1265 19.72 - 30.33 302 30.33 - 40.94 216 40.94 - 51.55 128 51.55 - 62.17 49 62.17 - 72.78 11 72.78 - 83.39 5 83.39 - 94.00 4 94.00 - 104.61 0 104.61 - 115.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1283 r_work=0.1130 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1283 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1279 target_work(ml) = 3.597 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597223 | | target function (ml) not normalized (work): 299580.361208 | | target function (ml) not normalized (free): 15780.965408 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1311 0.1296 5.6327 5.5711| | 2: 3.57 - 2.84 1.00 2888 124 0.1062 0.1351 5.1525 5.2067| | 3: 2.83 - 2.48 1.00 2820 163 0.1105 0.1225 4.9306 4.9694| | 4: 2.47 - 2.25 1.00 2825 136 0.0889 0.1005 4.6152 4.6469| | 5: 2.25 - 2.09 1.00 2756 127 0.0863 0.1009 4.5635 4.6277| | 6: 2.09 - 1.97 1.00 2846 113 0.0854 0.1047 4.2585 4.3623| | 7: 1.97 - 1.87 1.00 2787 165 0.0878 0.1092 3.9735 4.0746| | 8: 1.87 - 1.79 1.00 2789 144 0.0903 0.1091 3.8809 3.9824| | 9: 1.79 - 1.72 1.00 2745 138 0.0863 0.1150 3.6363 3.8159| | 10: 1.72 - 1.66 1.00 2831 160 0.0910 0.1203 3.5567 3.7071| | 11: 1.66 - 1.61 1.00 2712 147 0.0864 0.1002 3.4883 3.5487| | 12: 1.61 - 1.56 1.00 2773 144 0.0895 0.1161 3.3195 3.4618| | 13: 1.56 - 1.52 1.00 2745 130 0.0939 0.1049 3.2967 3.3936| | 14: 1.52 - 1.48 1.00 2803 134 0.0981 0.1040 3.2336 3.3144| | 15: 1.48 - 1.45 1.00 2738 128 0.0993 0.1221 3.1442 3.2604| | 16: 1.45 - 1.42 1.00 2756 161 0.1050 0.1240 3.1298 3.2388| | 17: 1.42 - 1.39 1.00 2785 139 0.1129 0.1283 3.1113 3.2207| | 18: 1.39 - 1.36 1.00 2741 179 0.1191 0.1316 3.0977 3.23| | 19: 1.36 - 1.34 1.00 2807 134 0.1251 0.1550 3.1059 3.2561| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1465 3.1085 3.1528| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1503 3.1105 3.103| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1997 3.1211 3.2983| | 23: 1.27 - 1.26 1.00 2802 156 0.1642 0.1792 3.1307 3.2037| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1842 3.1259 3.2333| | 25: 1.24 - 1.22 1.00 2733 148 0.1878 0.2161 3.1395 3.2623| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1746 3.1471 3.1944| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2171 3.1699 3.1642| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2305 3.1645 3.1732| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2377 3.146 3.2266| | 30: 1.16 - 1.15 1.00 2739 148 0.2448 0.2429 3.1426 3.1623| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.10 1.00 0.97 5497.84| | 2: 3.57 - 2.84 2888 124 0.93 12.17 1.01 0.97 5497.84| | 3: 2.83 - 2.48 2820 163 0.90 16.13 0.99 0.97 4597.97| | 4: 2.47 - 2.25 2825 136 0.92 13.17 1.00 0.98 2277.49| | 5: 2.25 - 2.09 2756 127 0.91 15.30 1.01 0.98 2277.49| | 6: 2.09 - 1.97 2846 113 0.93 12.26 1.02 0.98 1323.51| | 7: 1.97 - 1.87 2787 165 0.95 9.30 1.02 0.97 509.89| | 8: 1.87 - 1.79 2789 144 0.93 12.67 1.00 0.97 509.89| | 9: 1.79 - 1.72 2745 138 0.94 9.95 0.98 0.97 285.99| | 10: 1.72 - 1.66 2831 160 0.94 11.02 0.98 0.97 241.15| | 11: 1.66 - 1.61 2712 147 0.94 11.60 0.98 0.97 230.96| | 12: 1.61 - 1.56 2773 144 0.96 8.79 0.99 0.97 134.86| | 13: 1.56 - 1.52 2745 130 0.95 10.27 1.03 0.97 134.86| | 14: 1.52 - 1.48 2803 134 0.94 10.65 1.02 0.98 121.16| | 15: 1.48 - 1.45 2738 128 0.95 9.80 1.02 0.98 96.07| | 16: 1.45 - 1.42 2756 161 0.94 10.93 1.02 0.98 96.07| | 17: 1.42 - 1.39 2785 139 0.95 10.81 1.01 0.98 87.74| | 18: 1.39 - 1.36 2741 179 0.94 11.46 1.01 0.98 82.92| | 19: 1.36 - 1.34 2807 134 0.94 11.78 0.99 0.98 82.92| | 20: 1.34 - 1.32 2696 147 0.94 12.09 0.98 0.96 79.45| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.96 79.20| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 79.66| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.94 81.98| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 81.98| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 83.97| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 86.16| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.16| | 28: 1.19 - 1.18 2671 147 0.88 20.34 1.01 0.93 89.64| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.98 0.92 90.94| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.92 90.94| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.20 max = 5497.84 mean = 854.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.33| |phase err.(test): min = 0.00 max = 88.82 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1279 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1443 0.1441 0.1506 n_refl.: 87577 remove outliers: r(all,work,free)=0.1443 0.1441 0.1506 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1442 0.1440 0.1505 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1124 0.1277 n_refl.: 87577 remove outliers: r(all,work,free)=0.1131 0.1124 0.1277 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 87.50 79 5 0.3960 288.283 252.997 0.424 0.999 0.271 11.894-9.307 94.12 92 4 0.2419 474.018 462.171 0.870 1.001 0.257 9.237-7.194 98.18 209 7 0.2298 386.071 379.562 0.927 1.002 0.172 7.162-5.571 100.00 427 22 0.2113 296.118 285.926 0.913 1.002 0.160 5.546-4.326 100.00 867 58 0.1096 406.497 402.252 0.965 1.002 0.120 4.315-3.360 100.00 1859 96 0.0911 386.582 384.819 1.003 1.002 0.110 3.356-2.611 100.00 3867 181 0.1105 253.964 252.221 1.011 1.002 0.070 2.608-2.026 99.99 8198 413 0.0904 168.355 167.692 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.216 82.560 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.458 36.066 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.971 21.525 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=-0.0144 ================= 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 : 0.2598 0.1945 0.081 5.248 8.8 119.3 19.9 258 0.000 1_bss: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_settarget: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_nqh: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_weight: 0.1624 0.1760 0.081 5.248 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1224 0.1461 0.007 0.908 9.0 119.5 20.1 258 0.132 1_adp: 0.1230 0.1457 0.007 0.908 9.1 119.5 20.1 258 0.132 1_regHadp: 0.1231 0.1461 0.007 0.908 9.1 119.5 20.1 258 0.132 1_occ: 0.1226 0.1457 0.007 0.908 9.1 119.5 20.1 258 0.132 2_bss: 0.1223 0.1451 0.007 0.908 9.1 119.5 20.1 258 0.132 2_settarget: 0.1223 0.1451 0.007 0.908 9.1 119.5 20.1 258 0.132 2_updatecdl: 0.1223 0.1451 0.007 0.918 9.1 119.5 20.1 258 0.132 2_nqh: 0.1224 0.1452 0.007 0.918 9.1 119.5 20.1 258 0.135 2_sol: 0.1198 0.1392 0.007 0.918 9.1 115.2 22.2 421 n/a 2_weight: 0.1198 0.1392 0.007 0.918 9.1 115.2 22.2 421 n/a 2_xyzrec: 0.1191 0.1414 0.007 0.909 9.1 115.2 22.2 421 n/a 2_adp: 0.1191 0.1414 0.007 0.909 9.1 115.2 22.2 421 n/a 2_regHadp: 0.1191 0.1414 0.007 0.909 9.1 115.2 22.2 421 n/a 2_occ: 0.1194 0.1421 0.007 0.909 9.1 115.2 22.2 421 n/a 3_bss: 0.1189 0.1417 0.007 0.909 9.1 115.2 22.3 421 n/a 3_settarget: 0.1189 0.1417 0.007 0.909 9.1 115.2 22.3 421 n/a 3_updatecdl: 0.1189 0.1417 0.007 0.910 9.1 115.2 22.3 421 n/a 3_nqh: 0.1190 0.1418 0.007 0.910 9.1 115.2 22.3 421 n/a 3_sol: 0.1208 0.1399 0.007 0.910 9.1 115.2 21.1 421 n/a 3_weight: 0.1208 0.1399 0.007 0.910 9.1 115.2 21.1 421 n/a 3_xyzrec: 0.1163 0.1322 0.006 0.970 9.1 115.2 21.1 421 n/a 3_adp: 0.1163 0.1322 0.006 0.970 9.1 115.2 21.1 421 n/a 3_regHadp: 0.1163 0.1322 0.006 0.970 9.1 115.2 21.1 421 n/a 3_occ: 0.1152 0.1310 0.006 0.970 9.1 115.2 21.1 421 n/a 4_bss: 0.1147 0.1307 0.006 0.970 9.1 115.2 21.1 421 n/a 4_settarget: 0.1147 0.1307 0.006 0.970 9.1 115.2 21.1 421 n/a 4_updatecdl: 0.1147 0.1307 0.006 0.973 9.1 115.2 21.1 421 n/a 4_nqh: 0.1147 0.1307 0.006 0.973 9.1 115.2 21.1 421 n/a 4_sol: 0.1146 0.1295 0.006 0.973 9.1 115.2 21.1 447 n/a 4_weight: 0.1146 0.1295 0.006 0.973 9.1 115.2 21.1 447 n/a 4_xyzrec: 0.1136 0.1293 0.009 1.132 9.1 115.2 21.1 447 n/a 4_adp: 0.1136 0.1293 0.009 1.132 9.1 115.2 21.1 447 n/a 4_regHadp: 0.1136 0.1293 0.009 1.132 9.1 115.2 21.1 447 n/a 4_occ: 0.1126 0.1286 0.009 1.132 9.1 115.2 21.1 447 n/a 5_bss: 0.1124 0.1288 0.009 1.132 9.1 115.2 21.1 447 n/a 5_settarget: 0.1124 0.1288 0.009 1.132 9.1 115.2 21.1 447 n/a 5_updatecdl: 0.1124 0.1288 0.009 1.133 9.1 115.2 21.1 447 n/a 5_setrh: 0.1125 0.1288 0.009 1.133 9.1 115.2 21.1 447 n/a 5_nqh: 0.1125 0.1288 0.009 1.133 9.1 115.2 21.1 447 n/a 5_sol: 0.1130 0.1283 0.009 1.133 9.1 115.2 21.2 455 n/a 5_weight: 0.1130 0.1283 0.009 1.133 9.1 115.2 21.2 455 n/a 5_xyzrec: 0.1130 0.1283 0.009 1.132 9.1 115.2 21.2 455 n/a 5_adp: 0.1130 0.1283 0.009 1.132 9.1 115.2 21.2 455 n/a 5_regHadp: 0.1130 0.1283 0.009 1.132 9.1 115.2 21.2 455 n/a 5_occ: 0.1125 0.1279 0.009 1.132 9.1 115.2 21.2 455 n/a end: 0.1124 0.1277 0.009 1.132 9.1 115.2 21.2 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5382129_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5382129_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3500 Refinement macro-cycles (run) : 13289.8300 Write final files (write_after_run_outputs) : 99.8500 Total : 13393.0300 Total CPU time: 3.73 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:17 PST -0800 (1735365977.61 s) Start R-work = 0.1624, R-free = 0.1760 Final R-work = 0.1124, R-free = 0.1277 =============================================================================== Job complete usr+sys time: 13577.74 seconds wall clock time: 250 minutes 36.36 seconds (15036.36 seconds total)