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_3850167.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3850167.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } 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: 1.40, per 1000 atoms: 0.41 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: 0.45 Conformation dependent library (CDL) restraints added in 119.3 milliseconds Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 601 0.92 - 1.19: 1081 1.19 - 1.46: 774 1.46 - 1.73: 684 1.73 - 2.00: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.486 -0.147 7.50e-03 1.78e+04 3.83e+02 bond pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta sigma weight residual 1.456 1.688 -0.232 1.22e-02 6.72e+03 3.61e+02 bond pdb=" C ALYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.114 0.220 1.20e-02 6.94e+03 3.38e+02 bond pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta sigma weight residual 1.456 1.235 0.221 1.26e-02 6.30e+03 3.08e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.236 1.419 -0.182 1.10e-02 8.26e+03 2.75e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 2932 4.25 - 8.50: 1862 8.50 - 12.74: 764 12.74 - 16.99: 190 16.99 - 21.24: 29 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ARG A 28 " pdb=" C ARG A 28 " pdb=" N ALA A 29 " ideal model delta sigma weight residual 122.12 138.52 -16.40 1.06e+00 8.90e-01 2.39e+02 angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.99 106.88 13.11 8.70e-01 1.32e+00 2.27e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 139.27 -16.07 1.08e+00 8.57e-01 2.21e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.22 105.67 16.55 1.17e+00 7.31e-01 2.00e+02 angle pdb=" O ASN A 81 " pdb=" C ASN A 81 " pdb=" N LEU A 82 " ideal model delta sigma weight residual 122.12 135.60 -13.48 1.06e+00 8.90e-01 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 943 16.94 - 33.88: 110 33.88 - 50.81: 40 50.81 - 67.75: 16 67.75 - 84.69: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.21 -23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA SER A 57 " pdb=" C SER A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+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 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.194: 76 0.194 - 0.387: 73 0.387 - 0.580: 61 0.580 - 0.773: 21 0.773 - 0.966: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 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 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -3.53 0.94 2.00e-01 2.50e+01 2.21e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.001 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.090 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.059 2.00e-02 2.50e+03 6.54e-02 9.62e+01 pdb=" CG HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.118 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.122 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " -0.049 2.00e-02 2.50e+03 7.85e-02 9.24e+01 pdb=" CG ASN A 173 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " 0.075 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 1486 2.38 - 2.93: 8395 2.93 - 3.49: 10385 3.49 - 4.04: 15036 4.04 - 4.60: 21272 Nonbonded interactions: 56574 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.823 1.850 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.829 1.850 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.832 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.845 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.863 1.850 ... (remaining 56569 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_3850167_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= 0.2613 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794039 | | target function (ml) not normalized (work): 232760.207845 | | target function (ml) not normalized (free): 11789.235816 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3041 0.2086 7.1037 4.9396| | 2: 3.57 - 2.84 1.00 2876 122 0.2456 0.1789 4.3442 4.3365| | 3: 2.84 - 2.48 1.00 2833 165 0.2343 0.1698 4.1209 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2331 0.1412 3.8313 3.8175| | 5: 2.25 - 2.09 1.00 2756 127 0.2447 0.1562 3.7937 3.7903| | 6: 2.09 - 1.97 1.00 2846 113 0.2578 0.1623 3.4684 3.5421| | 7: 1.97 - 1.87 1.00 2787 165 0.2519 0.1613 3.1211 3.092| | 8: 1.87 - 1.79 1.00 2789 144 0.2530 0.2038 3.0597 3.1596| | 9: 1.79 - 1.72 1.00 2745 138 0.2408 0.1979 2.9037 2.9491| | 10: 1.72 - 1.66 1.00 2789 158 0.2416 0.2077 2.8279 2.9512| | 11: 1.66 - 1.61 1.00 2740 147 0.2534 0.1842 2.754 2.8065| | 12: 1.61 - 1.56 1.00 2787 146 0.2557 0.1961 2.6419 2.6624| | 13: 1.56 - 1.52 1.00 2745 130 0.2560 0.1918 2.5832 2.6149| | 14: 1.52 - 1.48 1.00 2803 134 0.2529 0.2192 2.5006 2.6243| | 15: 1.48 - 1.45 1.00 2738 128 0.2517 0.1948 2.4077 2.4397| | 16: 1.45 - 1.42 1.00 2756 161 0.2730 0.2130 2.4141 2.4193| | 17: 1.42 - 1.39 1.00 2785 139 0.2680 0.1967 2.3565 2.329| | 18: 1.39 - 1.36 1.00 2741 179 0.2636 0.2169 2.2612 2.3321| | 19: 1.36 - 1.34 1.00 2807 134 0.2688 0.2030 2.2498 2.2014| | 20: 1.34 - 1.32 1.00 2696 147 0.2659 0.2268 2.1961 2.1672| | 21: 1.32 - 1.30 1.00 2785 112 0.2790 0.2298 2.1816 2.1586| | 22: 1.29 - 1.27 1.00 2704 152 0.2820 0.2414 2.1386 2.1544| | 23: 1.27 - 1.26 1.00 2802 156 0.2771 0.2643 2.0928 2.276| | 24: 1.26 - 1.24 1.00 2744 132 0.2807 0.2223 2.0756 2.0739| | 25: 1.24 - 1.22 1.00 2734 148 0.2885 0.2706 2.056 2.1244| | 26: 1.22 - 1.21 1.00 2727 135 0.2817 0.2481 2.0029 2.1216| | 27: 1.21 - 1.19 1.00 2814 148 0.2943 0.2582 2.0005 2.0035| | 28: 1.19 - 1.18 1.00 2671 147 0.3022 0.2575 1.9895 1.9604| | 29: 1.18 - 1.16 1.00 2800 134 0.2946 0.2712 1.9562 2.004| | 30: 1.16 - 1.15 1.00 2740 148 0.3035 0.2842 1.9296 1.9512| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.78 0.76 0.23 1471.09| | 2: 3.57 - 2.84 2876 122 0.80 26.04 1.28 0.23 1471.09| | 3: 2.84 - 2.48 2833 165 0.74 31.92 1.24 0.24 1218.59| | 4: 2.47 - 2.25 2825 136 0.81 25.31 1.25 0.25 563.31| | 5: 2.25 - 2.09 2756 127 0.78 28.97 1.28 0.25 563.31| | 6: 2.09 - 1.97 2846 113 0.84 22.29 1.30 0.25 306.37| | 7: 1.97 - 1.87 2787 165 0.90 16.12 1.28 0.26 87.23| | 8: 1.87 - 1.79 2789 144 0.86 20.75 1.26 0.26 87.23| | 9: 1.79 - 1.72 2745 138 0.88 18.47 1.23 0.25 54.99| | 10: 1.72 - 1.66 2789 158 0.87 20.08 1.22 0.25 48.53| | 11: 1.66 - 1.61 2740 147 0.85 21.64 1.24 0.25 46.88| | 12: 1.61 - 1.56 2787 146 0.88 18.76 1.24 0.25 30.14| | 13: 1.56 - 1.52 2745 130 0.86 20.99 1.23 0.25 30.14| | 14: 1.52 - 1.48 2803 134 0.86 20.74 1.23 0.25 26.80| | 15: 1.48 - 1.45 2738 128 0.87 20.09 1.23 0.25 20.69| | 16: 1.45 - 1.42 2756 161 0.85 21.76 1.24 0.25 20.69| | 17: 1.42 - 1.39 2785 139 0.87 20.23 1.23 0.25 17.30| | 18: 1.39 - 1.36 2741 179 0.87 20.62 1.23 0.25 15.34| | 19: 1.36 - 1.34 2807 134 0.86 21.33 1.22 0.25 15.34| | 20: 1.34 - 1.32 2696 147 0.87 20.37 1.21 0.25 12.66| | 21: 1.32 - 1.30 2785 112 0.86 21.49 1.21 0.25 12.47| | 22: 1.29 - 1.27 2704 152 0.86 21.98 1.22 0.25 12.22| | 23: 1.27 - 1.26 2802 156 0.86 21.93 1.22 0.24 10.92| | 24: 1.26 - 1.24 2744 132 0.85 22.70 1.20 0.24 10.92| | 25: 1.24 - 1.22 2734 148 0.85 23.26 1.21 0.24 10.39| | 26: 1.22 - 1.21 2727 135 0.85 23.51 1.19 0.24 9.79| | 27: 1.21 - 1.19 2814 148 0.84 24.34 1.21 0.24 9.79| | 28: 1.19 - 1.18 2671 147 0.83 24.77 1.19 0.23 9.00| | 29: 1.18 - 1.16 2800 134 0.83 24.89 1.16 0.23 8.69| | 30: 1.16 - 1.15 2740 148 0.82 26.45 1.15 0.23 8.69| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.69 max = 1471.09 mean = 212.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.36| |phase err.(test): min = 0.00 max = 90.00 mean = 22.34| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.233 1557 Z= 5.612 Angle : 5.255 16.549 2118 Z= 3.695 Chirality : 0.399 0.966 243 Planarity : 0.030 0.087 284 Dihedral : 13.955 84.687 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.46), residues: 224 helix: -2.82 (0.34), residues: 115 sheet: -0.73 (0.81), residues: 28 loop : 0.16 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.018 ARG A 98 TYR 0.084 0.034 TYR A 141 PHE 0.101 0.038 PHE A 162 HIS 0.086 0.052 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2613 r_free= 0.1929 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794039 | | target function (ml) not normalized (work): 232760.207845 | | target function (ml) not normalized (free): 11789.235816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2571 0.2614 0.1929 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2571 0.2614 0.1929 n_refl.: 87602 remove outliers: r(all,work,free)=0.1986 0.1992 0.1929 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2012 0.2017 0.1942 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1652 0.1647 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1651 0.1646 0.1748 n_refl.: 87593 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3833 386.293 369.115 0.688 1.001 0.401 11.894-9.307 99.02 97 4 0.1759 613.608 596.323 0.928 1.002 0.380 9.237-7.194 100.00 213 7 0.2154 501.856 489.639 0.960 1.002 0.360 7.162-5.571 100.00 427 22 0.2214 376.615 364.151 0.928 1.002 0.320 5.546-4.326 100.00 867 58 0.1321 516.999 511.502 0.962 1.002 0.224 4.315-3.360 100.00 1859 96 0.1175 491.670 486.152 1.005 1.002 0.199 3.356-2.611 100.00 3867 181 0.1434 323.002 319.213 0.998 1.002 0.048 2.608-2.026 99.99 8198 413 0.1352 214.121 211.864 1.004 1.002 0.000 2.025-1.573 100.00 17313 902 0.1668 104.565 103.991 1.010 1.002 0.000 1.573-1.221 100.00 36679 1900 0.2074 46.369 45.087 0.999 1.002 0.000 1.221-1.150 99.97 13689 708 0.2566 29.215 26.868 0.964 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1646 r_free=0.1748 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=0.1646 r_free=0.1748 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.358693 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1973.775896 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 0.1683 0.1805 0.0122 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1572 0.1707 0.0135 0.001 0.4 4.2 0.0 0.0 0 0.250 0.1436 0.1598 0.0162 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1393 0.1572 0.0178 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1355 0.1554 0.0198 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1347 0.1541 0.0194 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1291 0.1507 0.0216 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1275 0.1501 0.0225 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1258 0.1490 0.0232 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1250 0.1485 0.0235 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1242 0.1477 0.0235 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1239 0.1475 0.0236 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1234 0.1470 0.0235 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1230 0.1468 0.0237 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1231 0.1467 0.0237 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1228 0.1469 0.0241 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1228 0.1470 0.0243 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1224 0.1470 0.0246 0.008 1.0 4.8 0.5 0.6 0 13.679 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1467 0.0237 0.006 0.9 3.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.67 2.37 3.013 19.066 1973.776 0.017 12.31 14.67 2.36 2.989 19.066 59.213 0.017 12.37 14.63 2.27 2.688 19.065 246.722 0.017 12.71 15.26 2.55 2.728 19.219 986.888 0.017 12.54 15.40 2.86 3.129 19.513 1973.776 0.016 12.50 15.48 2.98 3.334 19.644 2960.664 0.015 12.43 15.50 3.07 3.431 19.686 3947.552 0.015 12.32 15.36 3.04 3.295 19.599 4934.440 0.015 12.22 15.36 3.14 3.365 19.643 5921.328 0.015 12.25 15.43 3.18 3.341 19.617 6908.216 0.015 12.21 15.42 3.21 3.452 19.665 7895.104 0.015 12.18 15.40 3.22 3.351 19.602 8881.992 0.015 12.16 15.38 3.22 3.499 19.676 9868.879 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: 246.722 Accepted refinement result: 12.37 14.63 2.27 2.688 19.065 246.722 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.09 3.35 0 1785 Protein: 9.08 115.20 17.00 3.36 0 1519 Water: 11.49 119.46 38.23 N/A 0 258 Other: 19.66 26.60 22.04 N/A 0 8 Chain A: 9.08 119.46 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 31.15 228 31.15 - 42.19 124 42.19 - 53.23 95 53.23 - 64.27 41 64.27 - 75.31 11 75.31 - 86.34 7 86.34 - 97.38 4 97.38 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1463 r_work=0.1238 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1467 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 = 0.1463 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1234 r_free= 0.1463 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016949 | | target function (ls_wunit_k1) not normalized (work): 1411.824070 | | target function (ls_wunit_k1) not normalized (free): 110.086885 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1463 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1678 0.1679 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1678 0.1679 0.1690 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1684 0.1685 0.1694 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1230 0.1457 n_refl.: 87593 remove outliers: r(all,work,free)=0.1241 0.1230 0.1457 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3630 300.119 286.357 0.660 1.002 0.396 11.894-9.307 99.02 97 4 0.1734 482.077 468.783 0.921 1.003 0.379 9.237-7.194 100.00 213 7 0.1871 394.279 389.049 0.961 1.003 0.350 7.162-5.571 100.00 427 22 0.1830 295.885 289.767 0.932 1.003 0.253 5.546-4.326 100.00 867 58 0.1013 406.177 402.888 0.962 1.003 0.199 4.315-3.360 100.00 1859 96 0.0871 386.277 385.255 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1177 253.764 252.649 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1024 168.222 167.480 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.151 82.345 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1452 36.429 35.932 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.953 21.436 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1457 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=0.1457 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1457 | n_water=258 | time (s): 1.650 (total time: 1.650) Filter (dist) r_work=0.1239 r_free=0.1456 | n_water=252 | time (s): 21.710 (total time: 23.360) Filter (q & B) r_work=0.1241 r_free=0.1455 | n_water=249 | time (s): 2.250 (total time: 25.610) Compute maps r_work=0.1241 r_free=0.1455 | n_water=249 | time (s): 1.290 (total time: 26.900) Filter (map) r_work=0.1262 r_free=0.1462 | n_water=224 | time (s): 3.380 (total time: 30.280) Find peaks r_work=0.1262 r_free=0.1462 | n_water=224 | time (s): 0.610 (total time: 30.890) Add new water r_work=0.1410 r_free=0.1615 | n_water=431 | time (s): 2.520 (total time: 33.410) Refine new water occ: r_work=0.1311 r_free=0.1481 adp: r_work=0.1229 r_free=0.1427 occ: r_work=0.1241 r_free=0.1421 adp: r_work=0.1208 r_free=0.1403 occ: r_work=0.1209 r_free=0.1396 adp: r_work=0.1201 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1394 r_work=0.1201 r_free=0.1394 | n_water=431 | time (s): 55.810 (total time: 89.220) Filter (q & B) r_work=0.1204 r_free=0.1397 | n_water=417 | time (s): 3.470 (total time: 92.690) Filter (dist only) r_work=0.1204 r_free=0.1394 | n_water=416 | time (s): 37.980 (total time: 130.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.511271 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1498.564215 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 0.1629 0.1738 0.0109 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1515 0.1640 0.0125 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1411 0.1555 0.0144 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1349 0.1506 0.0157 0.001 0.5 5.1 0.0 0.0 0 0.750 0.1318 0.1484 0.0167 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1309 0.1476 0.0168 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1251 0.1441 0.0190 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1228 0.1433 0.0204 0.003 0.6 3.8 0.5 0.0 0 3.000 0.1219 0.1426 0.0208 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1210 0.1423 0.0213 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1204 0.1418 0.0213 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1200 0.1420 0.0219 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1196 0.1423 0.0227 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1192 0.1417 0.0225 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1189 0.1416 0.0227 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1188 0.1419 0.0231 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1186 0.1414 0.0228 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1182 0.1412 0.0230 0.008 0.9 5.4 0.5 0.0 0 13.756 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1182 0.1412 0.0230 0.008 0.9 5.4 0.5 0.0 0 13.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 14.12 2.30 3.794 21.810 1498.564 0.015 11.82 14.12 2.30 3.794 21.810 44.957 0.015 11.82 14.12 2.30 3.794 21.810 187.321 0.015 11.96 14.51 2.55 3.653 21.812 749.282 0.015 11.98 14.88 2.91 3.602 21.853 1498.564 0.014 11.89 14.89 3.00 3.485 22.119 2247.846 0.014 11.77 14.83 3.06 3.608 21.869 2997.128 0.014 11.68 14.76 3.09 3.507 22.096 3746.411 0.014 11.69 14.85 3.16 3.522 22.122 4495.693 0.014 11.66 14.87 3.20 3.538 22.159 5244.975 0.013 11.65 14.93 3.27 3.561 22.117 5994.257 0.013 11.63 14.92 3.29 3.575 22.130 6743.539 0.013 11.52 14.74 3.22 3.566 22.101 7492.821 0.013 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.957 Accepted refinement result: 11.82 14.12 2.30 3.794 21.810 44.957 0.015 Individual atomic B min max mean iso aniso Overall: 9.11 115.23 22.24 3.35 192 1751 Protein: 9.11 115.23 17.03 3.36 0 1519 Water: 11.52 76.72 41.25 N/A 192 224 Other: 19.70 26.64 22.07 N/A 0 8 Chain A: 9.11 115.23 19.43 N/A 0 1751 Chain S: 14.86 60.00 47.82 N/A 192 0 Histogram: Values Number of atoms 9.11 - 19.72 1262 19.72 - 30.34 241 30.34 - 40.95 162 40.95 - 51.56 133 51.56 - 62.17 122 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=0.1182 r_free=0.1412 r_work=0.1182 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1182 r_free = 0.1412 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1407 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1407 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014593 | | target function (ls_wunit_k1) not normalized (work): 1215.505975 | | target function (ls_wunit_k1) not normalized (free): 103.407380 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1183 0.1407 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1591 0.1591 0.1619 n_refl.: 87592 remove outliers: r(all,work,free)=0.1591 0.1591 0.1619 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1593 0.1593 0.1620 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1179 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1402 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 0.3522 299.483 273.450 0.597 1.003 0.360 11.894-9.307 99.02 97 4 0.1522 482.077 476.698 0.925 1.003 0.360 9.237-7.194 100.00 213 7 0.1656 394.279 393.163 0.979 1.003 0.269 7.162-5.571 100.00 427 22 0.1558 295.885 291.254 0.938 1.003 0.250 5.546-4.326 100.00 867 58 0.0885 406.177 402.996 0.959 1.003 0.205 4.315-3.360 100.00 1859 96 0.0772 386.277 385.661 1.007 1.003 0.200 3.356-2.611 100.00 3867 181 0.1068 253.764 252.907 1.010 1.002 0.100 2.608-2.026 99.99 8198 413 0.1006 168.222 167.680 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1098 82.151 82.361 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.429 35.964 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 22.953 21.476 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=0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1402 | n_water=416 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1178 r_free=0.1398 | n_water=413 | time (s): 33.270 (total time: 34.890) Filter (q & B) r_work=0.1178 r_free=0.1398 | n_water=413 | time (s): 1.030 (total time: 35.920) Compute maps r_work=0.1178 r_free=0.1398 | n_water=413 | time (s): 1.520 (total time: 37.440) Filter (map) r_work=0.1219 r_free=0.1397 | n_water=285 | time (s): 3.250 (total time: 40.690) Find peaks r_work=0.1219 r_free=0.1397 | n_water=285 | time (s): 0.630 (total time: 41.320) Add new water r_work=0.1344 r_free=0.1530 | n_water=468 | time (s): 2.410 (total time: 43.730) Refine new water occ: r_work=0.1253 r_free=0.1451 adp: r_work=0.1254 r_free=0.1451 occ: r_work=0.1231 r_free=0.1429 adp: r_work=0.1230 r_free=0.1428 occ: r_work=0.1213 r_free=0.1414 adp: r_work=0.1207 r_free=0.1410 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1410 r_work=0.1207 r_free=0.1410 | n_water=468 | time (s): 163.560 (total time: 207.290) Filter (q & B) r_work=0.1212 r_free=0.1419 | n_water=440 | time (s): 3.660 (total time: 210.950) Filter (dist only) r_work=0.1212 r_free=0.1417 | n_water=439 | time (s): 35.940 (total time: 246.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.678454 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.240328 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 0.1382 0.0139 0.002 0.6 4.8 0.5 0.0 0 0.084 0.1203 0.1353 0.0150 0.003 0.7 3.5 0.5 0.0 0 0.252 0.1187 0.1340 0.0152 0.004 0.8 3.2 0.5 0.0 0 0.504 0.1178 0.1336 0.0158 0.005 0.9 2.9 0.5 0.0 0 0.755 0.1174 0.1334 0.0160 0.006 1.0 3.2 0.5 0.0 0 1.007 0.1171 0.1334 0.0164 0.006 1.0 3.2 0.5 0.0 0 1.259 0.1169 0.1334 0.0165 0.007 1.0 3.8 0.5 0.0 0 1.511 0.1167 0.1333 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.762 0.1176 0.1335 0.0158 0.005 0.9 2.9 0.5 0.0 0 0.839 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1167 0.1333 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 13.33 1.66 3.797 21.288 41.240 3.623 11.67 13.33 1.66 3.797 21.288 1.237 3.623 11.68 13.34 1.66 3.787 21.288 5.155 3.623 11.70 13.39 1.69 3.723 21.281 20.620 3.617 11.76 13.47 1.71 3.741 21.250 41.240 3.619 11.68 13.44 1.76 3.765 21.235 61.860 3.612 11.63 13.43 1.80 3.781 21.227 82.481 3.608 11.60 13.41 1.81 3.795 21.223 103.101 3.605 11.58 13.41 1.82 3.803 21.215 123.721 3.603 11.59 13.42 1.84 3.820 21.197 144.341 3.602 11.55 13.39 1.84 3.824 21.207 164.961 3.600 11.58 13.42 1.84 3.843 21.187 185.581 3.600 11.53 13.37 1.84 3.842 21.194 206.202 3.597 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.237 Accepted refinement result: 11.67 13.33 1.66 3.797 21.288 1.237 3.623 Individual atomic B min max mean iso aniso Overall: 9.12 115.24 21.27 3.35 220 1746 Protein: 9.12 115.24 17.04 3.36 0 1519 Water: 11.53 76.73 35.90 N/A 220 219 Other: 19.71 26.65 22.08 N/A 0 8 Chain A: 9.12 115.24 19.33 N/A 0 1746 Chain S: 14.87 60.01 36.67 N/A 220 0 Histogram: Values Number of atoms 9.12 - 19.73 1265 19.73 - 30.35 293 30.35 - 40.96 194 40.96 - 51.57 139 51.57 - 62.18 53 62.18 - 72.79 12 72.79 - 83.40 4 83.40 - 94.02 4 94.02 - 104.63 0 104.63 - 115.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1167 r_free=0.1333 r_work=0.1167 r_free=0.1333 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1167 r_free = 0.1333 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1333 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1154 r_free= 0.1333 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614205 | | target function (ml) not normalized (work): 301041.597346 | | target function (ml) not normalized (free): 15866.618111 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1154 0.1333 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1498 0.1498 0.1546 n_refl.: 87590 remove outliers: r(all,work,free)=0.1498 0.1498 0.1546 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1497 0.1496 0.1545 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1149 0.1329 n_refl.: 87590 remove outliers: r(all,work,free)=0.1156 0.1147 0.1329 n_refl.: 87585 ======================== 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 0.3905 296.843 266.395 0.496 1.000 0.330 11.894-9.307 98.04 96 4 0.2211 482.201 466.370 0.876 1.002 0.330 9.237-7.194 98.64 210 7 0.2202 386.772 387.636 0.954 1.002 0.200 7.162-5.571 100.00 427 22 0.2054 295.885 286.261 0.912 1.002 0.190 5.546-4.326 100.00 867 58 0.1123 406.177 401.497 0.955 1.002 0.180 4.315-3.360 100.00 1859 96 0.0958 386.277 383.803 0.996 1.002 0.170 3.356-2.611 100.00 3867 181 0.1163 253.764 251.350 0.995 1.002 0.038 2.608-2.026 99.99 8198 413 0.0936 168.222 167.404 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.151 82.436 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.429 36.020 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2162 22.953 21.504 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0243 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1329 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=0.1329 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1329 | n_water=439 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1147 r_free=0.1327 | n_water=436 | time (s): 47.520 (total time: 49.750) Filter (q & B) r_work=0.1147 r_free=0.1329 | n_water=434 | time (s): 3.850 (total time: 53.600) Compute maps r_work=0.1147 r_free=0.1329 | n_water=434 | time (s): 1.920 (total time: 55.520) Filter (map) r_work=0.1167 r_free=0.1305 | n_water=323 | time (s): 3.740 (total time: 59.260) Find peaks r_work=0.1167 r_free=0.1305 | n_water=323 | time (s): 0.720 (total time: 59.980) Add new water r_work=0.1238 r_free=0.1372 | n_water=482 | time (s): 3.740 (total time: 63.720) Refine new water occ: r_work=0.1167 r_free=0.1315 adp: r_work=0.1168 r_free=0.1317 occ: r_work=0.1150 r_free=0.1300 adp: r_work=0.1149 r_free=0.1302 occ: r_work=0.1137 r_free=0.1289 adp: r_work=0.1133 r_free=0.1289 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1289 r_work=0.1133 r_free=0.1289 | n_water=482 | time (s): 323.800 (total time: 387.520) Filter (q & B) r_work=0.1141 r_free=0.1294 | n_water=440 | time (s): 3.880 (total time: 391.400) Filter (dist only) r_work=0.1141 r_free=0.1292 | n_water=439 | time (s): 46.010 (total time: 437.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.794799 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 45.179182 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1338 0.0132 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1166 0.1307 0.0141 0.003 0.8 3.2 0.5 0.0 0 0.269 0.1153 0.1299 0.0147 0.005 0.9 3.5 0.5 0.0 0 0.538 0.1146 0.1296 0.0150 0.006 1.0 3.2 0.5 0.0 0 0.808 0.1143 0.1296 0.0153 0.006 1.0 3.2 0.5 0.0 0 1.077 0.1140 0.1294 0.0155 0.007 1.1 3.2 0.5 0.0 0 1.346 0.1138 0.1295 0.0157 0.008 1.1 3.2 0.5 0.0 0 1.615 0.1136 0.1293 0.0157 0.009 1.1 3.5 0.5 0.0 0 1.885 0.1145 0.1291 0.0146 0.006 1.0 4.2 0.5 0.0 0 0.897 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1291 0.0146 0.006 1.0 4.2 0.5 0.0 0 0.897 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.91 1.46 3.798 21.183 45.179 3.609 11.45 12.91 1.46 3.798 21.183 1.355 3.609 11.46 12.91 1.45 3.788 21.183 5.647 3.609 11.48 12.94 1.47 3.727 21.176 22.590 3.605 11.52 13.04 1.52 3.748 21.153 45.179 3.606 11.46 13.04 1.58 3.766 21.142 67.769 3.601 11.42 13.04 1.62 3.779 21.136 90.358 3.597 11.41 13.06 1.66 3.791 21.132 112.948 3.595 11.38 13.05 1.67 3.801 21.131 135.538 3.594 11.37 13.06 1.69 3.815 21.124 158.127 3.593 11.35 13.06 1.70 3.825 21.117 180.717 3.591 11.34 13.04 1.70 3.832 21.118 203.306 3.590 11.33 13.03 1.71 3.838 21.118 225.896 3.589 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.647 Accepted refinement result: 11.46 12.91 1.45 3.788 21.183 5.647 3.609 Individual atomic B min max mean iso aniso Overall: 9.13 115.12 21.09 3.32 221 1745 Protein: 9.13 115.12 17.03 3.32 0 1519 Water: 11.53 76.72 35.11 N/A 221 218 Other: 19.67 26.60 22.07 N/A 0 8 Chain A: 9.13 115.12 19.32 N/A 0 1745 Chain S: 14.85 60.00 35.06 N/A 221 0 Histogram: Values Number of atoms 9.13 - 19.72 1266 19.72 - 30.32 292 30.32 - 40.92 215 40.92 - 51.52 126 51.52 - 62.12 45 62.12 - 72.72 12 72.72 - 83.32 4 83.32 - 93.92 4 93.92 - 104.52 0 104.52 - 115.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1291 r_work=0.1146 r_free=0.1291 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1291 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1290 target_work(ml) = 3.607 | | 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.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1142 r_free= 0.1290 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.606915 | | target function (ml) not normalized (work): 300416.383398 | | target function (ml) not normalized (free): 15810.872900 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1149 0.1142 0.1290 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1484 0.1484 0.1507 n_refl.: 87585 remove outliers: r(all,work,free)=0.1484 0.1484 0.1507 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1483 0.1483 0.1506 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1289 n_refl.: 87585 remove outliers: r(all,work,free)=0.1145 0.1137 0.1289 n_refl.: 87578 ======================== 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 0.3901 296.205 250.288 0.477 1.001 0.330 11.894-9.307 96.08 94 4 0.2323 479.284 467.403 0.867 1.002 0.282 9.237-7.194 97.73 208 7 0.2260 385.287 381.365 0.937 1.003 0.202 7.162-5.571 100.00 427 22 0.2103 295.885 285.583 0.911 1.003 0.170 5.546-4.326 100.00 867 58 0.1155 406.177 401.370 0.963 1.003 0.130 4.315-3.360 100.00 1859 96 0.0940 386.277 384.280 1.005 1.003 0.130 3.356-2.611 100.00 3867 181 0.1108 253.764 251.553 1.009 1.002 0.029 2.608-2.026 99.99 8198 413 0.0917 168.222 167.553 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.151 82.466 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.429 36.024 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.953 21.493 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0160 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1137 r_free=0.1289 After: r_work=0.1138 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1138 r_free=0.1289 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1138 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1289 | n_water=439 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1138 r_free=0.1289 | n_water=439 | time (s): 42.880 (total time: 45.330) Filter (q & B) r_work=0.1138 r_free=0.1290 | n_water=437 | time (s): 3.860 (total time: 49.190) Compute maps r_work=0.1138 r_free=0.1290 | n_water=437 | time (s): 1.840 (total time: 51.030) Filter (map) r_work=0.1168 r_free=0.1292 | n_water=343 | time (s): 3.880 (total time: 54.910) Find peaks r_work=0.1168 r_free=0.1292 | n_water=343 | time (s): 0.690 (total time: 55.600) Add new water r_work=0.1228 r_free=0.1344 | n_water=495 | time (s): 3.750 (total time: 59.350) Refine new water occ: r_work=0.1166 r_free=0.1299 adp: r_work=0.1166 r_free=0.1302 occ: r_work=0.1151 r_free=0.1286 adp: r_work=0.1150 r_free=0.1288 occ: r_work=0.1140 r_free=0.1277 adp: r_work=0.1137 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1276 r_work=0.1137 r_free=0.1276 | n_water=495 | time (s): 303.480 (total time: 362.830) Filter (q & B) r_work=0.1143 r_free=0.1278 | n_water=461 | time (s): 4.080 (total time: 366.910) Filter (dist only) r_work=0.1144 r_free=0.1277 | n_water=460 | time (s): 48.750 (total time: 415.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.747613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.866674 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1234 0.1341 0.0107 0.003 0.7 6.7 0.0 0.0 0 0.087 0.1179 0.1302 0.0123 0.004 0.8 6.1 0.0 0.0 0 0.262 0.1156 0.1287 0.0131 0.005 0.9 5.4 0.5 0.0 0 0.524 0.1145 0.1278 0.0134 0.006 1.0 5.4 0.5 0.0 0 0.786 0.1143 0.1277 0.0134 0.006 1.0 5.4 0.5 0.0 0 1.049 0.1141 0.1277 0.0136 0.007 1.0 5.4 0.5 0.0 0 1.311 0.1139 0.1276 0.0137 0.008 1.1 5.4 0.5 0.0 0 1.573 0.1138 0.1276 0.0138 0.009 1.1 5.8 0.5 0.0 0 1.835 0.1144 0.1278 0.0134 0.006 1.0 5.4 0.5 0.0 0 0.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1276 0.0138 0.009 1.1 5.8 0.5 0.0 0 1.835 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 12.76 1.38 3.782 21.236 48.867 3.600 11.38 12.76 1.38 3.782 21.236 1.466 3.600 11.38 12.76 1.38 3.782 21.236 6.108 3.600 11.40 12.81 1.41 3.717 21.227 24.433 3.596 11.45 12.95 1.50 3.741 21.196 48.867 3.599 11.37 12.91 1.53 3.764 21.190 73.300 3.592 11.35 12.93 1.57 3.774 21.183 97.733 3.589 11.31 12.89 1.58 3.787 21.183 122.167 3.586 11.29 12.88 1.59 3.800 21.178 146.600 3.584 11.30 12.92 1.63 3.820 21.167 171.033 3.585 11.28 12.90 1.63 3.827 21.166 195.467 3.583 11.26 12.89 1.63 3.833 21.167 219.900 3.582 11.25 12.87 1.62 3.834 21.169 244.333 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: 1.466 Accepted refinement result: 11.38 12.76 1.38 3.782 21.236 1.466 3.600 Individual atomic B min max mean iso aniso Overall: 9.12 115.11 21.19 3.32 242 1745 Protein: 9.12 115.11 17.03 3.32 0 1519 Water: 11.52 76.71 34.93 N/A 242 218 Other: 19.67 26.59 22.06 N/A 0 8 Chain A: 9.12 115.11 19.31 N/A 0 1745 Chain S: 14.85 60.00 34.73 N/A 242 0 Histogram: Values Number of atoms 9.12 - 19.72 1266 19.72 - 30.32 306 30.32 - 40.92 222 40.92 - 51.52 126 51.52 - 62.12 45 62.12 - 72.71 12 72.71 - 83.31 4 83.31 - 93.91 4 93.91 - 104.51 0 104.51 - 115.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1138 r_free=0.1276 r_work=0.1138 r_free=0.1276 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1276 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1133 r_free = 0.1274 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1133 r_free= 0.1274 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599404 | | target function (ml) not normalized (work): 299765.583161 | | target function (ml) not normalized (free): 15792.009820 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1356 0.1307 5.6689 5.5934| | 2: 3.57 - 2.84 1.00 2888 124 0.1062 0.1397 5.1535 5.2235| | 3: 2.83 - 2.48 1.00 2820 163 0.1092 0.1183 4.9327 4.9651| | 4: 2.47 - 2.25 1.00 2825 136 0.0901 0.0942 4.6219 4.6455| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0930 4.5682 4.6182| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.1002 4.2544 4.3542| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1127 3.9744 4.0942| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1117 3.8855 3.9919| | 9: 1.79 - 1.72 1.00 2745 138 0.0868 0.1155 3.641 3.8169| | 10: 1.72 - 1.66 1.00 2831 160 0.0910 0.1189 3.557 3.7063| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1018 3.4941 3.5567| | 12: 1.61 - 1.56 1.00 2773 144 0.0896 0.1143 3.3242 3.4702| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1066 3.3041 3.4063| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1062 3.2334 3.3222| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1199 3.1498 3.2512| | 16: 1.45 - 1.42 1.00 2756 161 0.1048 0.1244 3.1285 3.244| | 17: 1.42 - 1.39 1.00 2785 139 0.1135 0.1299 3.1129 3.222| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1326 3.0975 3.228| | 19: 1.36 - 1.34 1.00 2807 134 0.1257 0.1560 3.1062 3.2633| | 20: 1.34 - 1.32 1.00 2696 147 0.1359 0.1439 3.1064 3.1496| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1523 3.1103 3.1075| | 22: 1.29 - 1.27 1.00 2704 152 0.1553 0.1982 3.1184 3.2922| | 23: 1.27 - 1.26 1.00 2802 156 0.1638 0.1784 3.1283 3.193| | 24: 1.26 - 1.24 1.00 2744 132 0.1701 0.1844 3.1239 3.2334| | 25: 1.24 - 1.22 1.00 2733 148 0.1871 0.2148 3.1385 3.2632| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1766 3.1448 3.1996| | 27: 1.21 - 1.19 1.00 2814 148 0.2070 0.2149 3.1675 3.16| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2287 3.1646 3.1714| | 29: 1.18 - 1.16 1.00 2800 134 0.2263 0.2376 3.1453 3.2235| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2454 3.1405 3.1693| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2920 171 0.95 8.38 1.00 0.97 5604.27| | 2: 3.57 - 2.84 2888 124 0.93 12.37 1.01 0.97 5604.27| | 3: 2.83 - 2.48 2820 163 0.90 16.40 0.99 0.97 4683.10| | 4: 2.47 - 2.25 2825 136 0.92 13.31 1.00 0.98 2307.69| | 5: 2.25 - 2.09 2756 127 0.90 15.49 1.01 0.98 2307.69| | 6: 2.09 - 1.97 2846 113 0.93 12.25 1.02 0.98 1335.22| | 7: 1.97 - 1.87 2787 165 0.95 9.31 1.02 0.97 505.83| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.97 505.83| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.99 0.97 287.10| | 10: 1.72 - 1.66 2831 160 0.94 11.11 0.98 0.97 243.30| | 11: 1.66 - 1.61 2712 147 0.94 11.65 0.98 0.97 233.10| | 12: 1.61 - 1.56 2773 144 0.96 8.87 0.99 0.97 136.99| | 13: 1.56 - 1.52 2745 130 0.95 10.40 1.03 0.97 136.99| | 14: 1.52 - 1.48 2803 134 0.94 10.73 1.02 0.98 122.90| | 15: 1.48 - 1.45 2738 128 0.95 9.90 1.02 0.98 97.10| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.98 97.10| | 17: 1.42 - 1.39 2785 139 0.95 10.84 1.01 0.98 88.32| | 18: 1.39 - 1.36 2741 179 0.94 11.48 1.01 0.98 83.24| | 19: 1.36 - 1.34 2807 134 0.94 11.82 1.00 0.98 83.24| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.99 0.96 79.47| | 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 13.61 0.98 0.96 79.63| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.94 81.78| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.94 81.78| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 83.82| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.03 0.93 86.09| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.03 0.93 86.09| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 89.75| | 29: 1.18 - 1.16 2800 134 0.88 20.49 0.99 0.92 91.13| | 30: 1.16 - 1.15 2739 148 0.86 22.03 0.98 0.92 91.13| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.20 max = 5604.27 mean = 867.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.86 mean = 13.40| |phase err.(test): min = 0.00 max = 88.11 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1140 0.1133 0.1274 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1458 0.1459 0.1468 n_refl.: 87578 remove outliers: r(all,work,free)=0.1458 0.1459 0.1468 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1457 0.1458 0.1467 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1140 0.1133 0.1272 n_refl.: 87578 remove outliers: r(all,work,free)=0.1138 0.1131 0.1272 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 87.50 79 5 0.3895 294.970 256.880 0.431 0.999 0.268 11.894-9.307 94.12 92 4 0.2386 472.915 447.761 0.837 1.001 0.253 9.237-7.194 97.73 208 7 0.2329 385.287 378.585 0.919 1.002 0.180 7.162-5.571 100.00 427 22 0.2171 295.885 286.354 0.899 1.002 0.150 5.546-4.326 100.00 867 58 0.1152 406.177 401.467 0.951 1.002 0.098 4.315-3.360 100.00 1859 96 0.0935 386.277 384.518 0.995 1.002 0.080 3.356-2.611 100.00 3867 181 0.1099 253.764 251.795 1.000 1.002 0.019 2.608-2.026 99.99 8198 413 0.0908 168.222 167.665 1.016 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.151 82.526 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1245 36.429 36.058 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2165 22.953 21.518 0.980 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0241 ================= 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 : 0.2613 0.1929 0.084 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_settarget: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_nqh: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_weight: 0.1646 0.1748 0.084 5.255 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1231 0.1467 0.006 0.873 9.1 119.5 20.1 258 0.131 1_adp: 0.1237 0.1463 0.006 0.873 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1238 0.1467 0.006 0.873 9.1 119.5 20.1 258 0.131 1_occ: 0.1234 0.1463 0.006 0.873 9.1 119.5 20.1 258 0.131 2_bss: 0.1230 0.1457 0.006 0.873 9.1 119.5 20.1 258 0.131 2_settarget: 0.1230 0.1457 0.006 0.873 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1230 0.1457 0.006 0.885 9.1 119.5 20.1 258 0.131 2_nqh: 0.1231 0.1457 0.006 0.885 9.1 119.5 20.1 258 0.134 2_sol: 0.1204 0.1394 0.006 0.885 9.1 115.2 22.2 416 n/a 2_weight: 0.1204 0.1394 0.006 0.885 9.1 115.2 22.2 416 n/a 2_xyzrec: 0.1182 0.1412 0.008 0.926 9.1 115.2 22.2 416 n/a 2_adp: 0.1182 0.1412 0.008 0.926 9.1 115.2 22.2 416 n/a 2_regHadp: 0.1182 0.1412 0.008 0.926 9.1 115.2 22.2 416 n/a 2_occ: 0.1183 0.1407 0.008 0.926 9.1 115.2 22.2 416 n/a 3_bss: 0.1178 0.1402 0.008 0.926 9.1 115.2 22.2 416 n/a 3_settarget: 0.1178 0.1402 0.008 0.926 9.1 115.2 22.2 416 n/a 3_updatecdl: 0.1178 0.1402 0.008 0.927 9.1 115.2 22.2 416 n/a 3_nqh: 0.1178 0.1402 0.008 0.927 9.1 115.2 22.2 416 n/a 3_sol: 0.1212 0.1417 0.008 0.927 9.1 115.2 21.3 439 n/a 3_weight: 0.1212 0.1417 0.008 0.927 9.1 115.2 21.3 439 n/a 3_xyzrec: 0.1167 0.1333 0.008 1.072 9.1 115.2 21.3 439 n/a 3_adp: 0.1167 0.1333 0.008 1.072 9.1 115.2 21.3 439 n/a 3_regHadp: 0.1167 0.1333 0.008 1.072 9.1 115.2 21.3 439 n/a 3_occ: 0.1154 0.1333 0.008 1.072 9.1 115.2 21.3 439 n/a 4_bss: 0.1147 0.1329 0.008 1.072 9.1 115.2 21.3 439 n/a 4_settarget: 0.1147 0.1329 0.008 1.072 9.1 115.2 21.3 439 n/a 4_updatecdl: 0.1147 0.1329 0.008 1.073 9.1 115.2 21.3 439 n/a 4_nqh: 0.1147 0.1329 0.008 1.073 9.1 115.2 21.3 439 n/a 4_sol: 0.1141 0.1292 0.008 1.073 9.1 115.2 21.1 439 n/a 4_weight: 0.1141 0.1292 0.008 1.073 9.1 115.2 21.1 439 n/a 4_xyzrec: 0.1145 0.1291 0.006 0.987 9.1 115.2 21.1 439 n/a 4_adp: 0.1146 0.1291 0.006 0.987 9.1 115.1 21.1 439 n/a 4_regHadp: 0.1146 0.1291 0.006 0.987 9.1 115.1 21.1 439 n/a 4_occ: 0.1142 0.1290 0.006 0.987 9.1 115.1 21.1 439 n/a 5_bss: 0.1137 0.1289 0.006 0.987 9.1 115.1 21.1 439 n/a 5_settarget: 0.1137 0.1289 0.006 0.987 9.1 115.1 21.1 439 n/a 5_updatecdl: 0.1137 0.1289 0.006 0.989 9.1 115.1 21.1 439 n/a 5_setrh: 0.1138 0.1289 0.006 0.989 9.1 115.1 21.1 439 n/a 5_nqh: 0.1138 0.1289 0.006 0.989 9.1 115.1 21.1 439 n/a 5_sol: 0.1144 0.1277 0.006 0.989 9.1 115.1 21.2 460 n/a 5_weight: 0.1144 0.1277 0.006 0.989 9.1 115.1 21.2 460 n/a 5_xyzrec: 0.1138 0.1276 0.009 1.126 9.1 115.1 21.2 460 n/a 5_adp: 0.1138 0.1276 0.009 1.126 9.1 115.1 21.2 460 n/a 5_regHadp: 0.1138 0.1276 0.009 1.126 9.1 115.1 21.2 460 n/a 5_occ: 0.1133 0.1274 0.009 1.126 9.1 115.1 21.2 460 n/a end: 0.1131 0.1272 0.009 1.126 9.1 115.1 21.2 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3850167_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3850167_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 13853.4200 Write final files (write_after_run_outputs) : 89.8000 Total : 13946.5400 Total CPU time: 3.88 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:12:13 PST -0800 (1735366333.31 s) Start R-work = 0.1646, R-free = 0.1748 Final R-work = 0.1131, R-free = 0.1272 =============================================================================== Job complete usr+sys time: 14124.93 seconds wall clock time: 256 minutes 22.96 seconds (15382.96 seconds total)