Starting phenix.refine on Fri Dec 27 17:58:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8954467.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== 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: 1.63, per 1000 atoms: 0.48 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: 0.34 Conformation dependent library (CDL) restraints added in 108.7 milliseconds Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.93: 641 0.93 - 1.18: 1015 1.18 - 1.43: 645 1.43 - 1.68: 820 1.68 - 1.93: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.444 1.645 -0.201 1.06e-02 8.90e+03 3.60e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.542 1.779 -0.237 1.26e-02 6.30e+03 3.54e+02 bond pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 1.232 1.384 -0.152 8.20e-03 1.49e+04 3.42e+02 bond pdb=" CA LYS A 130 " pdb=" C LYS A 130 " ideal model delta sigma weight residual 1.524 1.749 -0.225 1.24e-02 6.50e+03 3.29e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3324 4.88 - 9.75: 1797 9.75 - 14.63: 571 14.63 - 19.51: 78 19.51 - 24.39: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.17 15.43 1.00e+00 1.00e+00 2.38e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.43 111.66 11.77 8.50e-01 1.38e+00 1.92e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" N GLY A 100 " ideal model delta sigma weight residual 115.67 99.67 16.00 1.23e+00 6.61e-01 1.69e+02 angle pdb=" O ILE A 9 " pdb=" C ILE A 9 " pdb=" N LEU A 10 " ideal model delta sigma weight residual 122.94 138.67 -15.73 1.22e+00 6.72e-01 1.66e+02 angle pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 121.65 136.61 -14.96 1.17e+00 7.31e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 939 17.15 - 34.31: 126 34.31 - 51.46: 33 51.46 - 68.61: 9 68.61 - 85.76: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CD2BTYR A 67 " pdb=" CG BTYR A 67 " pdb=" CD1BTYR A 67 " pdb=" HD1BTYR A 67 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.009 - 0.244: 117 0.244 - 0.480: 77 0.480 - 0.715: 34 0.715 - 0.950: 12 0.950 - 1.185: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA HIS A 115 " pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CB HIS A 115 " both_signs ideal model delta sigma weight residual False 2.51 1.33 1.18 2.00e-01 2.50e+01 3.51e+01 chirality pdb=" CA LEU A 187 " pdb=" N LEU A 187 " pdb=" C LEU A 187 " pdb=" CB LEU A 187 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CG LEU A 101 " pdb=" CB LEU A 101 " pdb=" CD1 LEU A 101 " pdb=" CD2 LEU A 101 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.051 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.135 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.050 2.00e-02 2.50e+03 5.51e-02 9.09e+01 pdb=" CG BTYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.095 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.121 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1413 2.37 - 2.93: 8349 2.93 - 3.48: 10433 3.48 - 4.04: 15097 4.04 - 4.60: 21277 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.811 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.826 1.850 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.840 2.270 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.860 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.873 2.270 ... (remaining 56564 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_8954467_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= 0.2607 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792701 | | target function (ml) not normalized (work): 232648.778296 | | target function (ml) not normalized (free): 11775.498717 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3042 0.1985 7.1501 4.9168| | 2: 3.57 - 2.84 1.00 2876 122 0.2425 0.1835 4.339 4.3445| | 3: 2.84 - 2.48 1.00 2833 165 0.2364 0.1679 4.1156 4.1416| | 4: 2.47 - 2.25 1.00 2825 136 0.2329 0.1423 3.8296 3.8205| | 5: 2.25 - 2.09 1.00 2756 127 0.2449 0.1591 3.7867 3.8037| | 6: 2.09 - 1.97 1.00 2846 113 0.2537 0.1679 3.4585 3.5275| | 7: 1.97 - 1.87 1.00 2787 165 0.2515 0.1841 3.1176 3.2402| | 8: 1.87 - 1.79 1.00 2789 144 0.2489 0.1885 3.0676 3.095| | 9: 1.79 - 1.72 1.00 2745 138 0.2416 0.1950 2.8893 2.9538| | 10: 1.72 - 1.66 1.00 2789 158 0.2414 0.2091 2.7931 2.9327| | 11: 1.66 - 1.61 1.00 2740 147 0.2528 0.1988 2.7435 2.8094| | 12: 1.61 - 1.56 1.00 2787 146 0.2536 0.1863 2.6391 2.6084| | 13: 1.56 - 1.52 1.00 2745 130 0.2585 0.1955 2.5776 2.6317| | 14: 1.52 - 1.48 1.00 2803 134 0.2612 0.1950 2.5179 2.5465| | 15: 1.48 - 1.45 1.00 2738 128 0.2588 0.2074 2.4174 2.475| | 16: 1.45 - 1.42 1.00 2756 161 0.2651 0.2033 2.3803 2.417| | 17: 1.42 - 1.39 1.00 2785 139 0.2676 0.2102 2.3399 2.3844| | 18: 1.39 - 1.36 1.00 2741 179 0.2657 0.2202 2.2778 2.3351| | 19: 1.36 - 1.34 1.00 2807 134 0.2696 0.2293 2.2685 2.3349| | 20: 1.34 - 1.32 1.00 2696 147 0.2720 0.2274 2.2196 2.2143| | 21: 1.32 - 1.30 1.00 2785 112 0.2721 0.2050 2.1609 2.0784| | 22: 1.29 - 1.27 1.00 2704 152 0.2686 0.2484 2.1186 2.1527| | 23: 1.27 - 1.26 1.00 2802 156 0.2803 0.2288 2.1097 2.1382| | 24: 1.26 - 1.24 1.00 2744 132 0.2767 0.2417 2.0707 2.1099| | 25: 1.24 - 1.22 1.00 2734 148 0.2804 0.2409 2.0397 2.0091| | 26: 1.22 - 1.21 1.00 2727 135 0.2886 0.2472 2.0124 2.1193| | 27: 1.21 - 1.19 1.00 2814 148 0.2940 0.2556 2.0072 1.977| | 28: 1.19 - 1.18 1.00 2671 147 0.2999 0.2753 1.9926 2.003| | 29: 1.18 - 1.16 1.00 2800 134 0.2962 0.2603 1.9632 1.9876| | 30: 1.16 - 1.15 1.00 2740 148 0.3004 0.2740 1.9162 1.9528| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.55 0.76 0.23 1443.11| | 2: 3.57 - 2.84 2876 122 0.81 25.67 1.27 0.23 1443.11| | 3: 2.84 - 2.48 2833 165 0.74 31.69 1.24 0.24 1196.66| | 4: 2.47 - 2.25 2825 136 0.82 25.11 1.25 0.25 557.06| | 5: 2.25 - 2.09 2756 127 0.78 28.93 1.28 0.25 557.06| | 6: 2.09 - 1.97 2846 113 0.84 22.38 1.29 0.25 305.09| | 7: 1.97 - 1.87 2787 165 0.90 16.36 1.28 0.26 90.20| | 8: 1.87 - 1.79 2789 144 0.86 20.83 1.25 0.26 90.20| | 9: 1.79 - 1.72 2745 138 0.88 18.46 1.23 0.26 55.22| | 10: 1.72 - 1.66 2789 158 0.87 20.19 1.22 0.25 48.22| | 11: 1.66 - 1.61 2740 147 0.85 21.54 1.24 0.25 46.57| | 12: 1.61 - 1.56 2787 146 0.88 18.56 1.24 0.25 29.84| | 13: 1.56 - 1.52 2745 130 0.87 20.47 1.25 0.25 29.84| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.23 0.25 26.57| | 15: 1.48 - 1.45 2738 128 0.87 20.11 1.24 0.25 20.57| | 16: 1.45 - 1.42 2756 161 0.86 21.68 1.24 0.25 20.57| | 17: 1.42 - 1.39 2785 139 0.87 20.47 1.23 0.25 17.38| | 18: 1.39 - 1.36 2741 179 0.87 20.85 1.22 0.25 15.53| | 19: 1.36 - 1.34 2807 134 0.86 21.67 1.21 0.25 15.53| | 20: 1.34 - 1.32 2696 147 0.87 20.42 1.21 0.25 12.48| | 21: 1.32 - 1.30 2785 112 0.87 21.21 1.22 0.25 12.27| | 22: 1.29 - 1.27 2704 152 0.86 21.67 1.21 0.25 11.97| | 23: 1.27 - 1.26 2802 156 0.87 21.32 1.22 0.24 10.45| | 24: 1.26 - 1.24 2744 132 0.86 21.88 1.20 0.24 10.45| | 25: 1.24 - 1.22 2734 148 0.85 22.85 1.20 0.24 9.94| | 26: 1.22 - 1.21 2727 135 0.85 23.43 1.20 0.23 9.37| | 27: 1.21 - 1.19 2814 148 0.84 23.82 1.20 0.23 9.37| | 28: 1.19 - 1.18 2671 147 0.83 24.70 1.18 0.23 8.84| | 29: 1.18 - 1.16 2800 134 0.84 24.63 1.16 0.23 8.64| | 30: 1.16 - 1.15 2740 148 0.82 26.16 1.15 0.23 8.64| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.64 max = 1443.11 mean = 209.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.21| |phase err.(test): min = 0.00 max = 89.62 mean = 22.11| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.237 1557 Z= 5.365 Angle : 5.131 15.998 2118 Z= 3.654 Chirality : 0.383 1.185 243 Planarity : 0.034 0.111 284 Dihedral : 13.667 85.762 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 33.51 % 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: -2.82 (0.46), residues: 224 helix: -2.43 (0.37), residues: 109 sheet: -0.72 (0.87), residues: 28 loop : -1.20 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.021 ARG A 28 TYR 0.068 0.032 TYR A 139 PHE 0.113 0.037 PHE A 164 HIS 0.045 0.020 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= 0.2607 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.792701 | | target function (ml) not normalized (work): 232648.778296 | | target function (ml) not normalized (free): 11775.498717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2608 0.1919 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2608 0.1919 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1985 0.1919 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2003 0.2009 0.1932 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1645 0.1639 0.1757 n_refl.: 87594 remove outliers: r(all,work,free)=0.1644 0.1638 0.1757 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.87 87 5 0.3825 381.971 355.067 0.672 1.002 0.403 11.894-9.307 99.02 97 4 0.1800 613.554 596.120 0.927 1.003 0.390 9.237-7.194 100.00 213 7 0.2171 501.812 489.822 0.946 1.004 0.359 7.162-5.571 100.00 427 22 0.2224 376.582 363.894 0.926 1.004 0.293 5.546-4.326 100.00 867 58 0.1295 516.954 510.768 0.966 1.004 0.224 4.315-3.360 100.00 1859 96 0.1137 491.627 487.760 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1447 322.973 319.538 0.996 1.003 0.129 2.608-2.026 99.99 8198 413 0.1354 214.102 211.941 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1633 104.556 103.880 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2077 46.364 45.075 1.006 0.995 0.000 1.221-1.150 99.97 13689 708 0.2590 29.213 26.987 0.975 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0449 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1638 r_free=0.1757 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1759 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.989548 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2011.532648 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 0.1641 0.1759 0.0118 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1489 0.1629 0.0139 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1413 0.1572 0.0159 0.001 0.5 4.2 0.0 0.0 0 0.500 0.1361 0.1534 0.0174 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1347 0.1536 0.0188 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1342 0.1534 0.0192 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1297 0.1514 0.0218 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1276 0.1503 0.0227 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1256 0.1489 0.0233 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1244 0.1481 0.0237 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1244 0.1487 0.0243 0.004 0.8 4.2 0.5 0.0 0 6.000 0.1238 0.1476 0.0238 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1237 0.1481 0.0244 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1230 0.1473 0.0243 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1226 0.1471 0.0244 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1227 0.1473 0.0246 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1226 0.1471 0.0245 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1221 0.1468 0.0247 0.008 1.0 3.2 0.5 0.6 0 13.995 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1468 0.0247 0.008 1.0 3.2 0.5 0.6 0 13.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.68 2.47 3.013 19.054 2011.533 0.017 12.21 14.68 2.47 3.007 19.054 60.346 0.017 12.28 14.65 2.36 2.669 19.053 251.442 0.017 12.61 15.23 2.62 2.730 19.207 1005.766 0.016 12.47 15.41 2.94 3.221 19.561 2011.533 0.016 12.35 15.42 3.07 3.279 19.595 3017.299 0.015 12.27 15.40 3.13 3.386 19.652 4023.065 0.015 12.26 15.41 3.15 3.354 19.617 5028.832 0.015 12.20 15.40 3.20 3.324 19.602 6034.598 0.015 12.18 15.41 3.23 3.248 19.545 7040.364 0.015 12.09 15.34 3.25 3.319 19.576 8046.131 0.015 12.08 15.36 3.27 3.303 19.561 9051.897 0.015 12.11 15.42 3.31 3.387 19.597 10057.663 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: 251.442 Accepted refinement result: 12.28 14.65 2.36 2.669 19.053 251.442 0.017 Individual atomic B min max mean iso aniso Overall: 9.05 119.44 20.08 3.31 0 1785 Protein: 9.05 115.00 16.99 3.32 0 1519 Water: 11.45 119.44 38.22 N/A 0 258 Other: 19.72 26.59 22.05 N/A 0 8 Chain A: 9.05 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.05 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.28 11 75.28 - 86.32 7 86.32 - 97.36 4 97.36 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1465 r_work=0.1230 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1460 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1223 r_free= 0.1460 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016612 | | target function (ls_wunit_k1) not normalized (work): 1383.715148 | | target function (ls_wunit_k1) not normalized (free): 109.664389 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1223 0.1460 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1668 0.1669 0.1694 n_refl.: 87592 remove outliers: r(all,work,free)=0.1668 0.1669 0.1694 n_refl.: 87592 overall B=0.04 to atoms: r(all,work,free)=0.1676 0.1677 0.1699 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1222 0.1453 n_refl.: 87592 remove outliers: r(all,work,free)=0.1232 0.1221 0.1453 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3484 298.216 278.090 0.643 1.001 0.380 11.894-9.307 99.02 97 4 0.1636 483.241 469.677 0.923 1.001 0.380 9.237-7.194 100.00 213 7 0.1865 395.232 390.700 0.962 1.002 0.324 7.162-5.571 100.00 427 22 0.1809 296.600 291.241 0.936 1.002 0.269 5.546-4.326 100.00 867 58 0.0987 407.158 404.990 0.966 1.002 0.214 4.315-3.360 100.00 1859 96 0.0866 387.210 385.883 1.008 1.002 0.190 3.356-2.611 100.00 3867 181 0.1167 254.377 253.228 1.008 1.002 0.110 2.608-2.026 99.99 8198 413 0.1018 168.629 167.952 1.017 1.002 0.000 2.025-1.573 100.00 17313 902 0.1108 82.349 82.591 1.024 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.517 36.022 1.013 1.001 0.000 1.221-1.150 99.97 13689 708 0.2247 23.008 21.404 0.970 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0633 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1453 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=0.1221 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1453 | n_water=258 | time (s): 2.130 (total time: 2.130) Filter (dist) r_work=0.1230 r_free=0.1452 | n_water=250 | time (s): 20.910 (total time: 23.040) Filter (q & B) r_work=0.1232 r_free=0.1452 | n_water=247 | time (s): 2.490 (total time: 25.530) Compute maps r_work=0.1232 r_free=0.1452 | n_water=247 | time (s): 1.410 (total time: 26.940) Filter (map) r_work=0.1249 r_free=0.1457 | n_water=226 | time (s): 2.320 (total time: 29.260) Find peaks r_work=0.1249 r_free=0.1457 | n_water=226 | time (s): 0.430 (total time: 29.690) Add new water r_work=0.1396 r_free=0.1622 | n_water=426 | time (s): 2.640 (total time: 32.330) Refine new water occ: r_work=0.1299 r_free=0.1487 adp: r_work=0.1222 r_free=0.1437 occ: r_work=0.1233 r_free=0.1420 adp: r_work=0.1202 r_free=0.1407 occ: r_work=0.1205 r_free=0.1401 adp: r_work=0.1194 r_free=0.1396 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1396 r_work=0.1194 r_free=0.1396 | n_water=426 | time (s): 55.440 (total time: 87.770) Filter (q & B) r_work=0.1197 r_free=0.1399 | n_water=414 | time (s): 3.400 (total time: 91.170) Filter (dist only) r_work=0.1197 r_free=0.1396 | n_water=413 | time (s): 35.150 (total time: 126.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.744276 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1476.353475 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 0.1715 0.1841 0.0126 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1523 0.1667 0.0144 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1425 0.1579 0.0154 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1352 0.1525 0.0173 0.002 0.5 5.1 0.0 0.0 0 0.750 0.1324 0.1506 0.0182 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1310 0.1493 0.0183 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1262 0.1460 0.0198 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1228 0.1440 0.0212 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1215 0.1429 0.0213 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1212 0.1428 0.0216 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1209 0.1427 0.0218 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1204 0.1420 0.0216 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1205 0.1419 0.0214 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1202 0.1421 0.0219 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1196 0.1419 0.0222 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1195 0.1423 0.0229 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1192 0.1421 0.0229 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1191 0.1431 0.0240 0.008 0.9 4.5 0.5 0.6 0 13.372 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1419 0.0222 0.006 0.9 4.5 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.19 2.22 3.775 21.745 1476.353 0.016 11.96 14.19 2.22 3.775 21.745 44.291 0.016 11.96 14.19 2.22 3.775 21.745 184.544 0.016 12.16 14.63 2.47 3.619 21.756 738.177 0.016 12.13 14.87 2.74 3.455 21.997 1476.353 0.015 11.99 14.81 2.82 3.458 22.119 2214.530 0.015 11.91 14.78 2.87 3.489 22.136 2952.707 0.015 11.81 14.81 3.00 3.491 21.965 3690.884 0.014 11.80 14.81 3.01 3.494 22.021 4429.060 0.014 11.72 14.75 3.03 3.515 21.959 5167.237 0.014 11.80 14.96 3.16 3.561 22.137 5905.414 0.014 11.77 14.97 3.20 3.569 22.078 6643.591 0.014 11.74 14.90 3.17 3.587 22.159 7381.767 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: 44.291 Accepted refinement result: 11.96 14.19 2.22 3.775 21.745 44.291 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 22.13 3.31 187 1753 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.49 76.70 40.88 N/A 187 226 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.10 115.04 19.47 N/A 0 1753 Chain S: 16.56 60.00 47.07 N/A 187 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.28 243 30.28 - 40.88 169 40.88 - 51.47 123 51.47 - 62.07 123 62.07 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1419 r_work=0.1196 r_free=0.1419 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1419 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1411 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1198 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015442 | | target function (ls_wunit_k1) not normalized (work): 1286.263123 | | target function (ls_wunit_k1) not normalized (free): 100.875355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1198 0.1411 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1588 0.1586 0.1653 n_refl.: 87591 remove outliers: r(all,work,free)=0.1588 0.1586 0.1653 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1587 0.1654 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1194 0.1404 n_refl.: 87591 remove outliers: r(all,work,free)=0.1203 0.1193 0.1404 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3341 297.560 272.476 0.578 1.002 0.350 11.894-9.307 99.02 97 4 0.1659 483.241 476.683 0.915 1.003 0.350 9.237-7.194 100.00 213 7 0.1738 395.232 394.055 0.980 1.003 0.290 7.162-5.571 100.00 427 22 0.1593 296.600 292.005 0.937 1.003 0.230 5.546-4.326 100.00 867 58 0.0898 407.158 404.169 0.959 1.003 0.205 4.315-3.360 100.00 1859 96 0.0809 387.210 386.410 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1099 254.377 253.468 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.1021 168.629 168.106 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.349 82.564 1.031 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.517 36.050 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 23.008 21.515 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0151 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1404 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1404 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1404 | n_water=413 | time (s): 2.110 (total time: 2.110) Filter (dist) r_work=0.1193 r_free=0.1404 | n_water=410 | time (s): 34.440 (total time: 36.550) Filter (q & B) r_work=0.1193 r_free=0.1404 | n_water=410 | time (s): 1.230 (total time: 37.780) Compute maps r_work=0.1193 r_free=0.1404 | n_water=410 | time (s): 1.520 (total time: 39.300) Filter (map) r_work=0.1225 r_free=0.1394 | n_water=280 | time (s): 3.410 (total time: 42.710) Find peaks r_work=0.1225 r_free=0.1394 | n_water=280 | time (s): 0.550 (total time: 43.260) Add new water r_work=0.1344 r_free=0.1515 | n_water=463 | time (s): 2.810 (total time: 46.070) Refine new water occ: r_work=0.1250 r_free=0.1423 adp: r_work=0.1251 r_free=0.1426 occ: r_work=0.1226 r_free=0.1397 adp: r_work=0.1225 r_free=0.1400 occ: r_work=0.1209 r_free=0.1378 adp: r_work=0.1204 r_free=0.1380 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1380 r_work=0.1204 r_free=0.1380 | n_water=463 | time (s): 246.440 (total time: 292.510) Filter (q & B) r_work=0.1209 r_free=0.1384 | n_water=432 | time (s): 3.670 (total time: 296.180) Filter (dist only) r_work=0.1209 r_free=0.1383 | n_water=431 | time (s): 37.130 (total time: 333.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.751587 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.794484 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 0.1231 0.1348 0.0116 0.002 0.6 4.5 0.5 0.0 0 0.088 0.1193 0.1320 0.0127 0.003 0.7 3.8 0.5 0.0 0 0.263 0.1176 0.1309 0.0133 0.004 0.8 3.2 0.5 0.0 0 0.525 0.1167 0.1303 0.0137 0.005 0.9 3.2 0.5 0.0 0 0.788 0.1162 0.1303 0.0141 0.006 1.0 3.2 0.5 0.0 0 1.051 0.1159 0.1305 0.0145 0.007 1.0 3.2 0.5 0.0 0 1.314 0.1158 0.1304 0.0146 0.007 1.0 3.5 0.5 0.0 0 1.576 0.1156 0.1302 0.0146 0.008 1.1 3.8 0.5 0.0 0 1.839 0.1165 0.1304 0.0139 0.005 0.9 2.9 0.5 0.0 0 0.876 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1156 0.1302 0.0146 0.008 1.1 3.8 0.5 0.0 0 1.839 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.56 13.02 1.46 3.779 21.258 47.794 3.619 11.56 13.02 1.46 3.779 21.258 1.434 3.619 11.56 13.02 1.46 3.769 21.258 5.974 3.619 11.61 13.10 1.49 3.712 21.242 23.897 3.613 11.61 13.17 1.56 3.738 21.211 47.794 3.612 11.56 13.17 1.61 3.756 21.197 71.692 3.607 11.51 13.14 1.64 3.774 21.189 95.589 3.603 11.46 13.10 1.65 3.785 21.187 119.486 3.599 11.43 13.10 1.67 3.797 21.182 143.383 3.597 11.44 13.14 1.70 3.819 21.162 167.281 3.598 11.42 13.11 1.70 3.825 21.164 191.178 3.596 11.40 13.08 1.68 3.831 21.161 215.075 3.594 11.39 13.09 1.69 3.840 21.156 238.972 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.434 Accepted refinement result: 11.56 13.02 1.46 3.779 21.258 1.434 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.22 3.31 210 1748 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.50 76.70 35.96 N/A 210 221 Other: 19.77 26.64 22.10 N/A 0 8 Chain A: 9.11 115.05 19.38 N/A 0 1748 Chain S: 16.05 60.01 36.54 N/A 210 0 Histogram: Values Number of atoms 9.11 - 19.70 1260 19.70 - 30.29 292 30.29 - 40.89 198 40.89 - 51.48 127 51.48 - 62.08 58 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1302 r_work=0.1156 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1301 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1304 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1145 r_free= 0.1304 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.611809 | | target function (ml) not normalized (work): 300838.407638 | | target function (ml) not normalized (free): 15842.998653 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1145 0.1304 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1491 0.1491 0.1525 n_refl.: 87589 remove outliers: r(all,work,free)=0.1491 0.1491 0.1525 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1490 0.1524 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1300 n_refl.: 87589 remove outliers: r(all,work,free)=0.1146 0.1138 0.1300 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 90.62 82 5 0.3821 294.281 263.003 0.497 1.000 0.310 11.894-9.307 97.06 95 4 0.2241 476.569 463.514 0.880 1.001 0.297 9.237-7.194 98.18 209 7 0.2242 386.699 385.889 0.961 1.002 0.220 7.162-5.571 100.00 427 22 0.2000 296.600 287.273 0.923 1.002 0.191 5.546-4.326 100.00 867 58 0.1090 407.158 401.714 0.964 1.002 0.164 4.315-3.360 100.00 1859 96 0.0932 387.210 384.536 1.005 1.002 0.147 3.356-2.611 100.00 3867 181 0.1144 254.377 252.170 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0933 168.629 167.830 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.349 82.621 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.517 36.091 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2165 23.008 21.542 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0188 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1300 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=0.1300 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1300 | n_water=431 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1138 r_free=0.1299 | n_water=428 | time (s): 47.430 (total time: 49.900) Filter (q & B) r_work=0.1138 r_free=0.1299 | n_water=428 | time (s): 1.360 (total time: 51.260) Compute maps r_work=0.1138 r_free=0.1299 | n_water=428 | time (s): 1.860 (total time: 53.120) Filter (map) r_work=0.1159 r_free=0.1303 | n_water=325 | time (s): 3.830 (total time: 56.950) Find peaks r_work=0.1159 r_free=0.1303 | n_water=325 | time (s): 0.720 (total time: 57.670) Add new water r_work=0.1231 r_free=0.1390 | n_water=502 | time (s): 3.710 (total time: 61.380) Refine new water occ: r_work=0.1154 r_free=0.1315 adp: r_work=0.1155 r_free=0.1318 occ: r_work=0.1138 r_free=0.1298 adp: r_work=0.1137 r_free=0.1299 occ: r_work=0.1126 r_free=0.1284 adp: r_work=0.1122 r_free=0.1281 ADP+occupancy (water only), MIN, final r_work=0.1122 r_free=0.1281 r_work=0.1122 r_free=0.1281 | n_water=502 | time (s): 250.220 (total time: 311.600) Filter (q & B) r_work=0.1130 r_free=0.1292 | n_water=458 | time (s): 3.950 (total time: 315.550) Filter (dist only) r_work=0.1130 r_free=0.1290 | n_water=457 | time (s): 48.130 (total time: 363.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.805545 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.568797 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 0.1194 0.1328 0.0135 0.002 0.6 3.8 0.5 0.0 0 0.090 0.1158 0.1305 0.0147 0.003 0.7 2.9 0.5 0.0 0 0.271 0.1143 0.1296 0.0153 0.005 0.9 3.2 0.5 0.0 0 0.542 0.1136 0.1293 0.0158 0.006 1.0 3.2 0.5 0.0 0 0.812 0.1132 0.1293 0.0161 0.007 1.0 2.9 0.5 0.0 0 1.083 0.1130 0.1292 0.0163 0.007 1.1 3.2 0.5 0.0 0 1.354 0.1128 0.1293 0.0165 0.008 1.1 3.2 0.5 0.0 0 1.625 0.1126 0.1292 0.0167 0.009 1.1 3.2 0.5 0.0 0 1.896 0.1135 0.1294 0.0159 0.006 1.0 2.9 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1292 0.0167 0.009 1.1 3.2 0.5 0.0 0 1.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 12.92 1.67 3.780 21.252 41.569 3.603 11.26 12.92 1.67 3.780 21.252 1.247 3.603 11.26 12.92 1.67 3.780 21.252 5.196 3.603 11.29 12.98 1.69 3.713 21.243 20.784 3.599 11.39 13.14 1.75 3.731 21.213 41.569 3.604 11.31 13.11 1.80 3.750 21.202 62.353 3.597 11.25 13.07 1.82 3.770 21.199 83.138 3.593 11.20 13.02 1.82 3.778 21.200 103.922 3.588 11.18 13.04 1.86 3.791 21.194 124.706 3.587 11.16 13.03 1.87 3.800 21.191 145.491 3.586 11.16 13.06 1.90 3.816 21.181 166.275 3.586 11.16 13.06 1.90 3.826 21.175 187.060 3.585 11.16 13.07 1.91 3.836 21.172 207.844 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.196 Accepted refinement result: 11.26 12.92 1.67 3.780 21.252 5.196 3.603 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.22 3.31 237 1747 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 35.12 N/A 237 220 Other: 19.76 26.63 22.09 N/A 0 8 Chain A: 9.10 115.04 19.37 N/A 0 1747 Chain S: 16.56 60.00 34.83 N/A 237 0 Histogram: Values Number of atoms 9.10 - 19.69 1262 19.69 - 30.29 312 30.29 - 40.88 206 40.88 - 51.47 133 51.47 - 62.07 48 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1126 r_free=0.1292 r_work=0.1126 r_free=0.1292 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1126 r_free = 0.1292 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1121 r_free = 0.1286 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.19 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= 0.1121 r_free= 0.1286 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.600706 | | target function (ml) not normalized (work): 299884.820938 | | target function (ml) not normalized (free): 15815.267372 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1121 0.1286 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1455 0.1455 0.1484 n_refl.: 87581 remove outliers: r(all,work,free)=0.1455 0.1455 0.1484 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1453 0.1453 0.1483 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1120 0.1286 n_refl.: 87581 remove outliers: r(all,work,free)=0.1127 0.1119 0.1286 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3990 290.897 261.960 0.462 1.001 0.311 11.894-9.307 96.08 94 4 0.2234 476.600 460.965 0.850 1.002 0.305 9.237-7.194 98.18 209 7 0.2316 386.699 380.942 0.923 1.002 0.200 7.162-5.571 100.00 427 22 0.2063 296.600 286.679 0.906 1.003 0.150 5.546-4.326 100.00 867 58 0.1111 407.158 402.618 0.955 1.003 0.140 4.315-3.360 100.00 1859 96 0.0893 387.210 385.048 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1099 254.377 252.460 0.999 1.002 0.024 2.608-2.026 99.99 8198 413 0.0901 168.629 168.053 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0877 82.349 82.699 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1244 36.517 36.129 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 23.008 21.568 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=-0.0212 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1119 r_free=0.1286 After: r_work=0.1120 r_free=0.1285 ================================== NQH flips ================================== r_work=0.1120 r_free=0.1285 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=0.1120 r_free=0.1285 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1120 r_free=0.1285 | n_water=457 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1120 r_free=0.1285 | n_water=457 | time (s): 44.260 (total time: 46.710) Filter (q & B) r_work=0.1121 r_free=0.1286 | n_water=455 | time (s): 4.180 (total time: 50.890) Compute maps r_work=0.1121 r_free=0.1286 | n_water=455 | time (s): 1.870 (total time: 52.760) Filter (map) r_work=0.1149 r_free=0.1293 | n_water=356 | time (s): 4.010 (total time: 56.770) Find peaks r_work=0.1149 r_free=0.1293 | n_water=356 | time (s): 0.700 (total time: 57.470) Add new water r_work=0.1201 r_free=0.1349 | n_water=500 | time (s): 3.830 (total time: 61.300) Refine new water occ: r_work=0.1145 r_free=0.1291 adp: r_work=0.1145 r_free=0.1294 occ: r_work=0.1133 r_free=0.1278 adp: r_work=0.1132 r_free=0.1279 occ: r_work=0.1124 r_free=0.1267 adp: r_work=0.1121 r_free=0.1268 ADP+occupancy (water only), MIN, final r_work=0.1121 r_free=0.1268 r_work=0.1121 r_free=0.1268 | n_water=500 | time (s): 220.700 (total time: 282.000) Filter (q & B) r_work=0.1126 r_free=0.1275 | n_water=464 | time (s): 3.970 (total time: 285.970) Filter (dist only) r_work=0.1126 r_free=0.1274 | n_water=463 | time (s): 48.990 (total time: 334.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.764848 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.430384 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 0.1331 0.0122 0.004 0.7 5.8 0.0 0.0 0 0.088 0.1165 0.1300 0.0135 0.004 0.8 6.4 0.0 0.0 0 0.265 0.1146 0.1287 0.0141 0.005 0.9 5.4 0.5 0.0 0 0.529 0.1139 0.1281 0.0142 0.006 1.0 5.4 0.5 0.0 0 0.794 0.1133 0.1276 0.0143 0.006 1.1 5.1 0.5 0.0 0 1.059 0.1130 0.1274 0.0144 0.007 1.1 5.1 0.5 0.0 0 1.324 0.1127 0.1273 0.0146 0.008 1.1 5.4 0.5 0.0 0 1.588 0.1126 0.1274 0.0147 0.009 1.1 5.1 0.5 0.0 0 1.853 0.1137 0.1280 0.0143 0.006 1.0 5.1 0.5 0.0 0 0.882 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1127 0.1273 0.0146 0.008 1.1 5.4 0.5 0.0 0 1.588 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.27 12.73 1.46 3.779 21.256 36.430 3.601 11.27 12.73 1.46 3.779 21.256 1.093 3.601 11.27 12.73 1.46 3.779 21.256 4.554 3.601 11.31 12.78 1.48 3.709 21.249 18.215 3.597 11.41 12.95 1.53 3.719 21.226 36.430 3.604 11.34 12.93 1.59 3.741 21.215 54.646 3.598 11.27 12.89 1.63 3.761 21.210 72.861 3.592 11.24 12.86 1.62 3.766 21.211 91.076 3.589 11.21 12.84 1.64 3.776 21.208 109.291 3.587 11.18 12.83 1.65 3.785 21.207 127.506 3.585 11.20 12.88 1.69 3.800 21.194 145.722 3.586 11.18 12.87 1.69 3.810 21.193 163.937 3.584 11.15 12.85 1.69 3.816 21.193 182.152 3.583 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.093 Accepted refinement result: 11.27 12.73 1.46 3.779 21.256 1.093 3.601 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.23 3.31 243 1747 Protein: 9.09 115.03 17.02 3.32 0 1519 Water: 11.49 76.69 35.03 N/A 243 220 Other: 19.76 26.62 22.08 N/A 0 8 Chain A: 9.09 115.03 19.36 N/A 0 1747 Chain S: 15.69 60.00 34.67 N/A 243 0 Histogram: Values Number of atoms 9.09 - 19.68 1264 19.68 - 30.28 310 30.28 - 40.87 211 40.87 - 51.47 132 51.47 - 62.06 50 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1127 r_free=0.1273 r_work=0.1127 r_free=0.1273 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1127 r_free = 0.1273 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1125 r_free = 0.1270 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.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1125 r_free= 0.1270 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599475 | | target function (ml) not normalized (work): 299775.067745 | | target function (ml) not normalized (free): 15790.614409 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1321 0.1263 5.657 5.5549| | 2: 3.57 - 2.84 1.00 2888 124 0.1049 0.1293 5.1321 5.1747| | 3: 2.83 - 2.48 1.00 2820 163 0.1091 0.1283 4.9132 4.9704| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.0995 4.6014 4.6354| | 5: 2.25 - 2.09 1.00 2756 127 0.0859 0.0943 4.5456 4.6016| | 6: 2.09 - 1.97 1.00 2846 113 0.0842 0.0998 4.2465 4.3584| | 7: 1.97 - 1.87 1.00 2787 165 0.0885 0.1106 3.9791 4.0808| | 8: 1.87 - 1.79 1.00 2789 144 0.0919 0.1100 3.888 3.9902| | 9: 1.79 - 1.72 1.00 2745 138 0.0869 0.1200 3.6452 3.8362| | 10: 1.72 - 1.66 1.00 2831 160 0.0910 0.1200 3.561 3.7102| | 11: 1.66 - 1.61 1.00 2712 147 0.0863 0.1030 3.4959 3.5743| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1180 3.3336 3.4851| | 13: 1.56 - 1.52 1.00 2745 130 0.0949 0.1035 3.3121 3.4005| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1053 3.2427 3.327| | 15: 1.48 - 1.45 1.00 2738 128 0.0995 0.1227 3.1539 3.2679| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1231 3.1363 3.2418| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1300 3.1194 3.2319| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1332 3.1032 3.2404| | 19: 1.36 - 1.34 1.00 2807 134 0.1253 0.1554 3.1097 3.2611| | 20: 1.34 - 1.32 1.00 2696 147 0.1368 0.1451 3.1117 3.1525| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1513 3.1126 3.1046| | 22: 1.29 - 1.27 1.00 2704 152 0.1553 0.1976 3.1206 3.2914| | 23: 1.27 - 1.26 1.00 2802 156 0.1642 0.1803 3.1317 3.2042| | 24: 1.26 - 1.24 1.00 2744 132 0.1707 0.1847 3.1278 3.2324| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2147 3.1426 3.2585| | 26: 1.22 - 1.21 1.00 2727 135 0.1904 0.1752 3.1482 3.2007| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2161 3.1716 3.1681| | 28: 1.19 - 1.18 1.00 2671 147 0.2197 0.2288 3.1662 3.1724| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2391 3.1485 3.2311| | 30: 1.16 - 1.15 1.00 2739 148 0.2439 0.2438 3.143 3.1654| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.04 1.00 0.98 5198.93| | 2: 3.57 - 2.84 2888 124 0.93 11.83 1.01 0.98 5198.93| | 3: 2.83 - 2.48 2820 163 0.90 15.67 0.99 0.98 4354.17| | 4: 2.47 - 2.25 2825 136 0.92 12.78 1.00 0.99 2175.81| | 5: 2.25 - 2.09 2756 127 0.91 14.90 1.01 0.99 2175.81| | 6: 2.09 - 1.97 2846 113 0.93 11.98 1.02 0.99 1277.05| | 7: 1.97 - 1.87 2787 165 0.95 9.29 1.02 0.98 510.53| | 8: 1.87 - 1.79 2789 144 0.93 12.62 1.00 0.98 510.53| | 9: 1.79 - 1.72 2745 138 0.94 10.07 0.98 0.98 291.16| | 10: 1.72 - 1.66 2831 160 0.94 11.19 0.98 0.98 247.22| | 11: 1.66 - 1.61 2712 147 0.93 11.81 0.98 0.98 236.92| | 12: 1.61 - 1.56 2773 144 0.95 9.01 0.99 0.98 139.79| | 13: 1.56 - 1.52 2745 130 0.94 10.53 1.03 0.98 139.79| | 14: 1.52 - 1.48 2803 134 0.94 10.86 1.02 0.99 125.23| | 15: 1.48 - 1.45 2738 128 0.95 9.98 1.02 0.99 98.56| | 16: 1.45 - 1.42 2756 161 0.94 11.13 1.02 0.99 98.56| | 17: 1.42 - 1.39 2785 139 0.95 10.92 1.01 0.99 89.43| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.99 84.15| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.99 84.15| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.97 79.86| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.97 79.56| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.97 79.98| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 82.14| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.14| | 25: 1.24 - 1.22 2733 148 0.91 16.30 0.96 0.95 84.10| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.02 0.94 86.27| | 27: 1.21 - 1.19 2814 148 0.89 18.72 1.02 0.94 86.27| | 28: 1.19 - 1.18 2671 147 0.88 20.33 1.01 0.94 89.88| | 29: 1.18 - 1.16 2800 134 0.88 20.43 0.99 0.93 91.23| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.93 91.23| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.56 max = 5198.93 mean = 818.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.32| |phase err.(test): min = 0.00 max = 89.84 mean = 13.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1125 0.1270 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1448 0.1449 0.1458 n_refl.: 87579 remove outliers: r(all,work,free)=0.1448 0.1449 0.1458 n_refl.: 87579 overall B=-0.01 to atoms: r(all,work,free)=0.1447 0.1448 0.1457 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1125 0.1270 n_refl.: 87579 remove outliers: r(all,work,free)=0.1130 0.1123 0.1270 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 0.4107 288.751 253.388 0.440 0.999 0.290 11.894-9.307 93.14 91 4 0.2239 475.952 455.763 0.866 1.002 0.290 9.237-7.194 98.18 209 7 0.2396 386.699 379.057 0.924 1.002 0.160 7.162-5.571 100.00 427 22 0.2044 296.600 287.152 0.914 1.002 0.140 5.546-4.326 100.00 867 58 0.1104 407.158 402.333 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0915 387.210 385.092 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1095 254.377 252.399 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0900 168.629 168.083 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.349 82.717 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.517 36.134 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2167 23.008 21.563 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0145 ================= 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 : 0.2607 0.1919 0.080 5.131 8.8 119.3 19.9 258 0.000 1_bss: 0.1638 0.1757 0.080 5.131 9.0 119.5 20.1 258 0.000 1_settarget: 0.1638 0.1757 0.080 5.131 9.0 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1759 0.080 5.131 9.0 119.5 20.1 258 0.003 1_weight: 0.1639 0.1759 0.080 5.131 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1221 0.1468 0.008 0.978 9.0 119.5 20.1 258 0.133 1_adp: 0.1228 0.1465 0.008 0.978 9.1 119.4 20.1 258 0.133 1_regHadp: 0.1230 0.1468 0.008 0.978 9.1 119.4 20.1 258 0.133 1_occ: 0.1223 0.1460 0.008 0.978 9.1 119.4 20.1 258 0.133 2_bss: 0.1221 0.1453 0.008 0.978 9.1 119.5 20.1 258 0.133 2_settarget: 0.1221 0.1453 0.008 0.978 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1221 0.1453 0.008 0.985 9.1 119.5 20.1 258 0.133 2_nqh: 0.1221 0.1453 0.008 0.985 9.1 119.5 20.1 258 0.133 2_sol: 0.1197 0.1396 0.008 0.985 9.1 115.0 22.1 413 n/a 2_weight: 0.1197 0.1396 0.008 0.985 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1196 0.1419 0.006 0.865 9.1 115.0 22.1 413 n/a 2_adp: 0.1196 0.1419 0.006 0.865 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1196 0.1419 0.006 0.865 9.1 115.0 22.1 413 n/a 2_occ: 0.1198 0.1411 0.006 0.865 9.1 115.0 22.1 413 n/a 3_bss: 0.1193 0.1404 0.006 0.865 9.1 115.0 22.1 413 n/a 3_settarget: 0.1193 0.1404 0.006 0.865 9.1 115.0 22.1 413 n/a 3_updatecdl: 0.1193 0.1404 0.006 0.865 9.1 115.0 22.1 413 n/a 3_nqh: 0.1193 0.1404 0.006 0.865 9.1 115.0 22.1 413 n/a 3_sol: 0.1209 0.1383 0.006 0.865 9.1 115.0 21.2 431 n/a 3_weight: 0.1209 0.1383 0.006 0.865 9.1 115.0 21.2 431 n/a 3_xyzrec: 0.1156 0.1302 0.008 1.084 9.1 115.0 21.2 431 n/a 3_adp: 0.1156 0.1302 0.008 1.084 9.1 115.0 21.2 431 n/a 3_regHadp: 0.1156 0.1301 0.008 1.084 9.1 115.0 21.2 431 n/a 3_occ: 0.1145 0.1304 0.008 1.084 9.1 115.0 21.2 431 n/a 4_bss: 0.1138 0.1300 0.008 1.084 9.1 115.0 21.2 431 n/a 4_settarget: 0.1138 0.1300 0.008 1.084 9.1 115.0 21.2 431 n/a 4_updatecdl: 0.1138 0.1300 0.008 1.087 9.1 115.0 21.2 431 n/a 4_nqh: 0.1138 0.1300 0.008 1.087 9.1 115.0 21.2 431 n/a 4_sol: 0.1130 0.1290 0.008 1.087 9.1 115.0 21.2 457 n/a 4_weight: 0.1130 0.1290 0.008 1.087 9.1 115.0 21.2 457 n/a 4_xyzrec: 0.1126 0.1292 0.009 1.132 9.1 115.0 21.2 457 n/a 4_adp: 0.1126 0.1292 0.009 1.132 9.1 115.0 21.2 457 n/a 4_regHadp: 0.1126 0.1292 0.009 1.132 9.1 115.0 21.2 457 n/a 4_occ: 0.1121 0.1286 0.009 1.132 9.1 115.0 21.2 457 n/a 5_bss: 0.1119 0.1286 0.009 1.132 9.1 115.0 21.2 457 n/a 5_settarget: 0.1119 0.1286 0.009 1.132 9.1 115.0 21.2 457 n/a 5_updatecdl: 0.1119 0.1286 0.009 1.131 9.1 115.0 21.2 457 n/a 5_setrh: 0.1120 0.1285 0.009 1.131 9.1 115.0 21.2 457 n/a 5_nqh: 0.1120 0.1285 0.009 1.131 9.1 115.0 21.2 457 n/a 5_sol: 0.1126 0.1274 0.009 1.131 9.1 115.0 21.2 463 n/a 5_weight: 0.1126 0.1274 0.009 1.131 9.1 115.0 21.2 463 n/a 5_xyzrec: 0.1127 0.1273 0.008 1.131 9.1 115.0 21.2 463 n/a 5_adp: 0.1127 0.1273 0.008 1.131 9.1 115.0 21.2 463 n/a 5_regHadp: 0.1127 0.1273 0.008 1.131 9.1 115.0 21.2 463 n/a 5_occ: 0.1125 0.1270 0.008 1.131 9.1 115.0 21.2 463 n/a end: 0.1123 0.1270 0.008 1.131 9.1 115.0 21.2 463 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8954467_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8954467_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9300 Refinement macro-cycles (run) : 13841.3200 Write final files (write_after_run_outputs) : 90.0300 Total : 13934.2800 Total CPU time: 3.88 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:12:11 PST -0800 (1735366331.46 s) Start R-work = 0.1638, R-free = 0.1757 Final R-work = 0.1123, R-free = 0.1270 =============================================================================== Job complete usr+sys time: 14111.46 seconds wall clock time: 256 minutes 20.63 seconds (15380.63 seconds total)