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_6197065.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_6197065.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6197065.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 =============================================================================== 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: 1.50, per 1000 atoms: 0.44 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 213.5 milliseconds Time building geometry restraints manager: 0.54 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: 546 0.92 - 1.18: 1113 1.18 - 1.45: 756 1.45 - 1.72: 725 1.72 - 1.99: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 1.522 1.303 0.219 1.19e-02 7.06e+03 3.38e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.439 -0.202 1.11e-02 8.12e+03 3.30e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.567 -0.236 1.38e-02 5.25e+03 2.93e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.150 0.171 1.00e-02 1.00e+04 2.92e+02 bond pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 1.238 0.996 0.242 1.42e-02 4.96e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 2838 4.18 - 8.35: 1931 8.35 - 12.52: 780 12.52 - 16.70: 196 16.70 - 20.87: 32 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 122.60 107.47 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" CA GLY A 120 " pdb=" C GLY A 120 " pdb=" O GLY A 120 " ideal model delta sigma weight residual 119.27 133.52 -14.25 1.01e+00 9.80e-01 1.99e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.10 106.77 16.33 1.17e+00 7.31e-01 1.95e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 108.45 13.46 9.80e-01 1.04e+00 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.81: 948 17.81 - 35.60: 111 35.60 - 53.39: 40 53.39 - 71.18: 10 71.18 - 88.97: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 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 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+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 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.209: 97 0.209 - 0.415: 87 0.415 - 0.620: 36 0.620 - 0.826: 18 0.826 - 1.031: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 20 " pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CB VAL A 20 " both_signs ideal model delta sigma weight residual False 2.44 1.41 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA AASN A 76 " pdb=" N AASN A 76 " pdb=" C AASN A 76 " pdb=" CB AASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.35e+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 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 7.04e-02 1.49e+02 pdb=" CG PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.119 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.09e-02 1.11e+02 pdb=" CG PHE A 119 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.096 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 5.59e-02 9.37e+01 pdb=" CG PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.023 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 588 2.24 - 2.83: 7474 2.83 - 3.42: 10735 3.42 - 4.01: 15411 4.01 - 4.60: 22349 Nonbonded interactions: 56557 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.647 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.732 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.800 2.100 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 1.850 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.864 1.850 ... (remaining 56552 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_6197065_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= 0.2606 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788271 | | target function (ml) not normalized (work): 232279.691607 | | target function (ml) not normalized (free): 11804.334416 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3022 0.2079 7.0391 4.9438| | 2: 3.57 - 2.84 1.00 2876 122 0.2410 0.1816 4.3499 4.3437| | 3: 2.84 - 2.48 1.00 2833 165 0.2367 0.1738 4.1311 4.1589| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1367 3.8368 3.8168| | 5: 2.25 - 2.09 1.00 2756 127 0.2487 0.1581 3.8063 3.8196| | 6: 2.09 - 1.97 1.00 2846 113 0.2546 0.1927 3.4703 3.6489| | 7: 1.97 - 1.87 1.00 2787 165 0.2529 0.1887 3.1377 3.221| | 8: 1.87 - 1.79 1.00 2789 144 0.2473 0.2074 3.0675 3.1489| | 9: 1.79 - 1.72 1.00 2745 138 0.2406 0.1853 2.9106 2.9395| | 10: 1.72 - 1.66 1.00 2789 158 0.2399 0.1907 2.8084 2.8528| | 11: 1.66 - 1.61 1.00 2740 147 0.2524 0.1896 2.7492 2.7896| | 12: 1.61 - 1.56 1.00 2787 146 0.2559 0.1947 2.6331 2.6347| | 13: 1.56 - 1.52 1.00 2745 130 0.2547 0.1944 2.5773 2.6514| | 14: 1.52 - 1.48 1.00 2803 134 0.2601 0.2005 2.5088 2.5351| | 15: 1.48 - 1.45 1.00 2738 128 0.2583 0.1962 2.4143 2.4654| | 16: 1.45 - 1.42 1.00 2756 161 0.2618 0.2045 2.3615 2.3674| | 17: 1.42 - 1.39 1.00 2785 139 0.2599 0.1976 2.3047 2.3659| | 18: 1.39 - 1.36 1.00 2741 179 0.2640 0.2047 2.2668 2.2962| | 19: 1.36 - 1.34 1.00 2807 134 0.2730 0.2488 2.2288 2.3664| | 20: 1.34 - 1.32 1.00 2696 147 0.2671 0.2139 2.1821 2.1723| | 21: 1.32 - 1.30 1.00 2785 112 0.2715 0.2181 2.1569 2.1202| | 22: 1.29 - 1.27 1.00 2704 152 0.2752 0.2512 2.1322 2.1961| | 23: 1.27 - 1.26 1.00 2802 156 0.2833 0.2323 2.1204 2.1231| | 24: 1.26 - 1.24 1.00 2744 132 0.2816 0.2323 2.0702 2.0983| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2642 2.0334 2.1041| | 26: 1.22 - 1.21 1.00 2727 135 0.2862 0.2297 2.0081 2.0556| | 27: 1.21 - 1.19 1.00 2814 148 0.3005 0.2834 2.0141 2.0679| | 28: 1.19 - 1.18 1.00 2671 147 0.3017 0.2812 1.9924 2.0267| | 29: 1.18 - 1.16 1.00 2800 134 0.2965 0.2733 1.952 2.0497| | 30: 1.16 - 1.15 1.00 2740 148 0.3059 0.2803 1.9285 1.9314| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.88 0.76 0.23 1490.71| | 2: 3.57 - 2.84 2876 122 0.80 26.12 1.27 0.23 1490.71| | 3: 2.84 - 2.48 2833 165 0.74 32.06 1.25 0.23 1236.86| | 4: 2.47 - 2.25 2825 136 0.81 25.82 1.26 0.25 578.09| | 5: 2.25 - 2.09 2756 127 0.77 29.37 1.28 0.25 578.09| | 6: 2.09 - 1.97 2846 113 0.83 23.06 1.30 0.25 317.73| | 7: 1.97 - 1.87 2787 165 0.90 16.98 1.28 0.26 95.68| | 8: 1.87 - 1.79 2789 144 0.85 21.73 1.25 0.26 95.68| | 9: 1.79 - 1.72 2745 138 0.88 18.95 1.23 0.26 57.36| | 10: 1.72 - 1.66 2789 158 0.86 20.55 1.22 0.26 49.69| | 11: 1.66 - 1.61 2740 147 0.85 21.63 1.24 0.25 47.90| | 12: 1.61 - 1.56 2787 146 0.89 18.35 1.24 0.25 29.81| | 13: 1.56 - 1.52 2745 130 0.87 20.39 1.24 0.25 29.81| | 14: 1.52 - 1.48 2803 134 0.86 20.86 1.24 0.25 26.41| | 15: 1.48 - 1.45 2738 128 0.87 19.80 1.23 0.25 20.16| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 20.16| | 17: 1.42 - 1.39 2785 139 0.87 20.19 1.22 0.25 17.13| | 18: 1.39 - 1.36 2741 179 0.87 20.59 1.23 0.25 15.38| | 19: 1.36 - 1.34 2807 134 0.86 21.90 1.24 0.25 15.38| | 20: 1.34 - 1.32 2696 147 0.87 20.69 1.21 0.25 12.72| | 21: 1.32 - 1.30 2785 112 0.86 21.69 1.20 0.25 12.54| | 22: 1.29 - 1.27 2704 152 0.85 22.32 1.21 0.24 12.28| | 23: 1.27 - 1.26 2802 156 0.86 22.08 1.21 0.24 10.96| | 24: 1.26 - 1.24 2744 132 0.85 22.81 1.21 0.24 10.96| | 25: 1.24 - 1.22 2734 148 0.85 23.44 1.20 0.24 10.46| | 26: 1.22 - 1.21 2727 135 0.84 24.12 1.20 0.23 9.91| | 27: 1.21 - 1.19 2814 148 0.83 24.92 1.21 0.23 9.91| | 28: 1.19 - 1.18 2671 147 0.82 25.72 1.17 0.23 9.34| | 29: 1.18 - 1.16 2800 134 0.82 25.87 1.16 0.22 9.13| | 30: 1.16 - 1.15 2740 148 0.81 27.34 1.15 0.22 9.13| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.13 max = 1490.71 mean = 216.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.92 mean = 22.66| |phase err.(test): min = 0.00 max = 89.55 mean = 22.52| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.248 1557 Z= 5.480 Angle : 5.477 18.164 2118 Z= 3.848 Chirality : 0.364 1.031 243 Planarity : 0.029 0.081 284 Dihedral : 13.920 88.967 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.62 % Allowed : 1.62 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Cbeta Deviations : 26.49 % 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: -2.94 (0.46), residues: 224 helix: -2.72 (0.35), residues: 109 sheet: -1.48 (0.69), residues: 38 loop : -0.50 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.076 0.019 ARG A 5 TYR 0.067 0.032 TYR A 139 PHE 0.122 0.051 PHE A 162 HIS 0.014 0.008 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= 0.2606 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788271 | | target function (ml) not normalized (work): 232279.691607 | | target function (ml) not normalized (free): 11804.334416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1949 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1949 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1983 0.1949 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2004 0.2008 0.1965 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1636 0.1629 0.1772 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1772 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 0.3781 386.383 359.849 0.675 1.003 0.414 11.894-9.307 99.02 97 4 0.1795 613.750 594.255 0.922 1.004 0.400 9.237-7.194 100.00 213 7 0.2159 501.972 489.766 0.955 1.004 0.360 7.162-5.571 100.00 427 22 0.2224 376.702 365.536 0.930 1.004 0.310 5.546-4.326 100.00 867 58 0.1277 517.119 511.669 0.962 1.003 0.234 4.315-3.360 100.00 1859 96 0.1116 491.784 487.993 1.005 1.003 0.219 3.356-2.611 100.00 3867 181 0.1427 323.077 319.764 0.995 1.002 0.080 2.608-2.026 99.99 8198 413 0.1354 214.170 212.017 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1642 104.590 103.866 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.379 45.051 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2603 29.222 26.925 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0464 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1631 r_free=0.1776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.085280 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2014.087296 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 0.1692 0.1822 0.0130 0.002 0.4 4.5 0.0 0.0 0 0.125 0.1549 0.1697 0.0148 0.002 0.5 3.8 0.0 0.0 0 0.250 0.1443 0.1615 0.0172 0.002 0.5 3.2 0.0 0.0 0 0.500 0.1381 0.1574 0.0193 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1355 0.1562 0.0206 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1356 0.1559 0.0203 0.002 0.5 2.6 0.0 0.0 0 1.000 0.1298 0.1519 0.0221 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1264 0.1489 0.0225 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1256 0.1486 0.0229 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1250 0.1479 0.0228 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1239 0.1469 0.0230 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1242 0.1473 0.0232 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1233 0.1464 0.0231 0.005 0.8 3.2 0.5 0.0 0 8.000 0.1234 0.1468 0.0234 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1231 0.1463 0.0232 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1465 0.0238 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1227 0.1468 0.0241 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1226 0.1466 0.0240 0.007 1.0 3.8 0.5 0.0 0 13.043 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1463 0.0232 0.006 0.9 4.2 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 14.63 2.32 3.013 19.061 2014.087 0.017 12.31 14.62 2.31 2.986 19.061 60.423 0.017 12.38 14.61 2.23 2.665 19.061 251.761 0.017 12.71 15.28 2.56 2.747 19.234 1007.044 0.017 12.56 15.39 2.83 3.264 19.597 2014.087 0.016 12.46 15.38 2.92 3.344 19.649 3021.131 0.016 12.36 15.36 2.99 3.349 19.638 4028.175 0.015 12.30 15.36 3.07 3.384 19.650 5035.218 0.015 12.20 15.30 3.09 3.301 19.600 6042.262 0.015 12.21 15.33 3.12 3.433 19.660 7049.306 0.015 12.17 15.34 3.17 3.456 19.660 8056.349 0.015 12.16 15.32 3.17 3.400 19.622 9063.393 0.015 12.15 15.35 3.20 3.435 19.630 10070.436 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: 251.761 Accepted refinement result: 12.38 14.61 2.23 2.665 19.061 251.761 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.44 20.09 3.30 0 1785 Protein: 9.08 114.96 17.00 3.31 0 1519 Water: 11.46 119.44 38.23 N/A 0 258 Other: 19.72 26.60 22.06 N/A 0 8 Chain A: 9.08 119.44 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1461 r_work=0.1239 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1456 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1231 r_free= 0.1456 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016926 | | target function (ls_wunit_k1) not normalized (work): 1409.867059 | | target function (ls_wunit_k1) not normalized (free): 108.996976 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1456 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1678 0.1691 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1678 0.1691 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1684 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1450 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1450 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 96.88 88 5 0.3502 303.693 284.325 0.671 1.002 0.395 11.894-9.307 99.02 97 4 0.1644 482.402 469.722 0.925 1.003 0.384 9.237-7.194 100.00 213 7 0.1926 394.545 387.792 0.964 1.003 0.350 7.162-5.571 100.00 427 22 0.1829 296.084 290.173 0.939 1.003 0.290 5.546-4.326 100.00 867 58 0.0995 406.451 403.569 0.964 1.003 0.209 4.315-3.360 100.00 1859 96 0.0872 386.538 385.331 1.009 1.002 0.190 3.356-2.611 100.00 3867 181 0.1176 253.935 252.799 1.009 1.002 0.090 2.608-2.026 99.99 8198 413 0.1022 168.336 167.622 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.206 82.397 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1451 36.454 35.957 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.968 21.449 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0482 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1450 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=0.1228 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1450 | n_water=258 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1235 r_free=0.1449 | n_water=252 | time (s): 21.490 (total time: 23.650) Filter (q & B) r_work=0.1237 r_free=0.1449 | n_water=249 | time (s): 3.340 (total time: 26.990) Compute maps r_work=0.1237 r_free=0.1449 | n_water=249 | time (s): 1.280 (total time: 28.270) Filter (map) r_work=0.1254 r_free=0.1453 | n_water=226 | time (s): 2.560 (total time: 30.830) Find peaks r_work=0.1254 r_free=0.1453 | n_water=226 | time (s): 0.590 (total time: 31.420) Add new water r_work=0.1407 r_free=0.1627 | n_water=430 | time (s): 2.500 (total time: 33.920) Refine new water occ: r_work=0.1313 r_free=0.1494 adp: r_work=0.1230 r_free=0.1429 occ: r_work=0.1241 r_free=0.1422 adp: r_work=0.1208 r_free=0.1404 occ: r_work=0.1210 r_free=0.1393 adp: r_work=0.1200 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1390 r_work=0.1200 r_free=0.1390 | n_water=430 | time (s): 53.620 (total time: 87.540) Filter (q & B) r_work=0.1203 r_free=0.1391 | n_water=416 | time (s): 3.380 (total time: 90.920) Filter (dist only) r_work=0.1204 r_free=0.1390 | n_water=415 | time (s): 34.140 (total time: 125.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.012072 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.656506 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 0.1645 0.1758 0.0113 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1569 0.1693 0.0124 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1413 0.1563 0.0150 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1343 0.1506 0.0163 0.001 0.4 6.4 0.0 0.0 0 0.750 0.1331 0.1498 0.0167 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1327 0.1497 0.0169 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1260 0.1452 0.0192 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1232 0.1432 0.0201 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1214 0.1419 0.0206 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1210 0.1427 0.0216 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1204 0.1419 0.0214 0.004 0.7 5.1 0.5 0.0 0 6.000 0.1199 0.1410 0.0212 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1200 0.1418 0.0218 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1196 0.1411 0.0215 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1193 0.1419 0.0226 0.006 0.9 5.1 0.5 0.0 0 10.000 0.1189 0.1416 0.0227 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1189 0.1426 0.0237 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1189 0.1429 0.0240 0.008 0.9 4.5 0.5 0.0 0 13.000 0.1189 0.1431 0.0243 0.008 0.9 4.2 0.5 0.0 0 14.006 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1410 0.0212 0.005 0.8 4.5 0.5 0.0 0 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 14.10 2.12 3.773 21.816 1483.657 0.016 11.99 14.10 2.12 3.773 21.816 44.510 0.016 11.99 14.10 2.12 3.773 21.816 185.457 0.016 12.20 14.51 2.31 3.630 21.819 741.828 0.016 12.19 14.90 2.71 3.454 22.135 1483.657 0.015 11.97 14.73 2.76 3.462 22.204 2225.485 0.015 11.91 14.82 2.91 3.488 22.010 2967.313 0.014 11.84 14.84 3.00 3.509 22.013 3709.141 0.014 11.78 14.80 3.02 3.523 22.011 4450.970 0.014 11.83 14.88 3.05 3.539 22.222 5192.798 0.014 11.80 14.88 3.09 3.555 22.220 5934.626 0.014 11.81 14.92 3.12 3.581 22.243 6676.454 0.014 11.78 14.90 3.12 3.584 22.218 7418.283 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.457 Accepted refinement result: 11.99 14.10 2.12 3.773 21.816 185.457 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 114.99 22.25 3.30 189 1753 Protein: 9.11 114.99 17.03 3.31 0 1519 Water: 11.49 76.69 41.38 N/A 189 226 Other: 19.75 26.63 22.10 N/A 0 8 Chain A: 9.11 114.99 19.45 N/A 0 1753 Chain S: 16.33 60.00 48.24 N/A 189 0 Histogram: Values Number of atoms 9.11 - 19.70 1258 19.70 - 30.28 244 30.28 - 40.87 158 40.87 - 51.46 135 51.46 - 62.05 124 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1410 r_work=0.1199 r_free=0.1410 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1410 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1414 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1197 r_free= 0.1414 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015361 | | target function (ls_wunit_k1) not normalized (work): 1279.514095 | | target function (ls_wunit_k1) not normalized (free): 100.324063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1197 0.1414 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1601 0.1599 0.1659 n_refl.: 87593 remove outliers: r(all,work,free)=0.1601 0.1599 0.1659 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1603 0.1602 0.1661 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1194 0.1409 n_refl.: 87593 remove outliers: r(all,work,free)=0.1203 0.1193 0.1409 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 0.3359 299.685 275.525 0.613 1.002 0.360 11.894-9.307 99.02 97 4 0.1609 482.402 476.448 0.929 1.002 0.360 9.237-7.194 100.00 213 7 0.1749 394.545 392.706 0.982 1.002 0.290 7.162-5.571 100.00 427 22 0.1619 296.084 291.382 0.936 1.002 0.270 5.546-4.326 100.00 867 58 0.0906 406.451 403.386 0.959 1.002 0.200 4.315-3.360 100.00 1859 96 0.0791 386.538 385.578 1.004 1.002 0.190 3.356-2.611 100.00 3867 181 0.1096 253.935 252.907 1.008 1.002 0.120 2.608-2.026 99.99 8198 413 0.1015 168.336 167.840 1.018 1.002 0.000 2.025-1.573 100.00 17313 902 0.1107 82.206 82.467 1.028 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.454 35.963 1.019 1.002 0.000 1.221-1.150 99.97 13689 708 0.2254 22.968 21.361 0.976 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0250 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1409 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1409 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1409 | n_water=415 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1193 r_free=0.1411 | n_water=410 | time (s): 34.840 (total time: 36.900) Filter (q & B) r_work=0.1193 r_free=0.1411 | n_water=410 | time (s): 0.850 (total time: 37.750) Compute maps r_work=0.1193 r_free=0.1411 | n_water=410 | time (s): 1.310 (total time: 39.060) Filter (map) r_work=0.1234 r_free=0.1398 | n_water=281 | time (s): 2.720 (total time: 41.780) Find peaks r_work=0.1234 r_free=0.1398 | n_water=281 | time (s): 0.460 (total time: 42.240) Add new water r_work=0.1361 r_free=0.1527 | n_water=472 | time (s): 3.060 (total time: 45.300) Refine new water occ: r_work=0.1263 r_free=0.1438 adp: r_work=0.1264 r_free=0.1440 occ: r_work=0.1239 r_free=0.1416 adp: r_work=0.1237 r_free=0.1415 occ: r_work=0.1220 r_free=0.1394 adp: r_work=0.1214 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1214 r_free=0.1391 r_work=0.1214 r_free=0.1391 | n_water=472 | time (s): 210.070 (total time: 255.370) Filter (q & B) r_work=0.1218 r_free=0.1397 | n_water=440 | time (s): 3.400 (total time: 258.770) Filter (dist only) r_work=0.1218 r_free=0.1395 | n_water=439 | time (s): 36.800 (total time: 295.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.757022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.330818 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 0.1240 0.1367 0.0127 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1194 0.1333 0.0138 0.003 0.7 3.5 0.5 0.0 0 0.264 0.1175 0.1316 0.0141 0.004 0.8 3.2 0.5 0.0 0 0.527 0.1167 0.1311 0.0144 0.005 0.9 3.2 0.5 0.0 0 0.791 0.1163 0.1308 0.0145 0.006 1.0 3.5 0.5 0.0 0 1.054 0.1160 0.1309 0.0150 0.007 1.0 3.8 0.5 0.0 0 1.318 0.1159 0.1312 0.0153 0.007 1.1 3.8 0.5 0.0 0 1.581 0.1157 0.1310 0.0154 0.008 1.1 3.8 0.5 0.0 0 1.845 0.1166 0.1310 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1163 0.1308 0.0145 0.006 1.0 3.5 0.5 0.0 0 1.054 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 13.08 1.45 3.775 21.284 53.331 3.622 11.63 13.08 1.45 3.775 21.284 1.600 3.622 11.64 13.08 1.44 3.765 21.284 6.666 3.621 11.70 13.19 1.49 3.710 21.268 26.665 3.616 11.69 13.28 1.58 3.734 21.235 53.331 3.615 11.63 13.25 1.62 3.756 21.225 79.996 3.609 11.59 13.23 1.65 3.771 21.212 106.662 3.605 11.54 13.20 1.66 3.784 21.211 133.327 3.602 11.55 13.23 1.68 3.802 21.192 159.992 3.602 11.52 13.20 1.68 3.812 21.192 186.658 3.600 11.50 13.18 1.68 3.820 21.190 213.323 3.598 11.49 13.17 1.69 3.828 21.189 239.989 3.597 11.47 13.15 1.69 3.831 21.190 266.654 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.600 Accepted refinement result: 11.63 13.08 1.45 3.775 21.284 1.600 3.622 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.27 3.30 219 1747 Protein: 9.12 115.01 17.04 3.31 0 1519 Water: 11.51 76.70 35.86 N/A 219 220 Other: 19.77 26.65 22.11 N/A 0 8 Chain A: 9.12 115.01 19.35 N/A 0 1747 Chain S: 16.34 60.02 36.58 N/A 219 0 Histogram: Values Number of atoms 9.12 - 19.71 1261 19.71 - 30.30 288 30.30 - 40.89 209 40.89 - 51.48 133 51.48 - 62.06 53 62.06 - 72.65 12 72.65 - 83.24 4 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1308 r_work=0.1163 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1163 r_free = 0.1308 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1308 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1154 r_free= 0.1308 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615584 | | target function (ml) not normalized (work): 301156.427016 | | target function (ml) not normalized (free): 15845.586258 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1154 0.1308 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1496 0.1497 0.1506 n_refl.: 87590 remove outliers: r(all,work,free)=0.1496 0.1497 0.1506 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1494 0.1495 0.1505 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1148 0.1297 n_refl.: 87590 remove outliers: r(all,work,free)=0.1152 0.1144 0.1297 n_refl.: 87581 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3989 291.598 266.854 0.498 1.001 0.330 11.894-9.307 97.06 95 4 0.2244 482.626 461.102 0.872 1.002 0.295 9.237-7.194 97.73 208 7 0.2124 387.110 388.059 0.947 1.002 0.220 7.162-5.571 100.00 427 22 0.2123 296.084 284.824 0.916 1.002 0.200 5.546-4.326 100.00 867 58 0.1108 406.451 402.098 0.952 1.002 0.148 4.315-3.360 100.00 1859 96 0.0943 386.538 383.767 0.994 1.002 0.133 3.356-2.611 100.00 3867 181 0.1128 253.935 251.932 0.998 1.002 0.053 2.608-2.026 99.99 8198 413 0.0939 168.336 167.629 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0903 82.206 82.498 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.454 36.041 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2168 22.968 21.512 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=-0.0234 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1297 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1148 r_free=0.1299 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1299 | n_water=439 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1151 r_free=0.1302 | n_water=436 | time (s): 44.840 (total time: 47.330) Filter (q & B) r_work=0.1151 r_free=0.1303 | n_water=435 | time (s): 3.910 (total time: 51.240) Compute maps r_work=0.1151 r_free=0.1303 | n_water=435 | time (s): 1.880 (total time: 53.120) Filter (map) r_work=0.1174 r_free=0.1297 | n_water=324 | time (s): 3.750 (total time: 56.870) Find peaks r_work=0.1174 r_free=0.1297 | n_water=324 | time (s): 0.700 (total time: 57.570) Add new water r_work=0.1241 r_free=0.1385 | n_water=488 | time (s): 3.840 (total time: 61.410) Refine new water occ: r_work=0.1175 r_free=0.1317 adp: r_work=0.1176 r_free=0.1319 occ: r_work=0.1160 r_free=0.1300 adp: r_work=0.1159 r_free=0.1302 occ: r_work=0.1148 r_free=0.1284 adp: r_work=0.1145 r_free=0.1284 ADP+occupancy (water only), MIN, final r_work=0.1145 r_free=0.1284 r_work=0.1145 r_free=0.1284 | n_water=488 | time (s): 209.770 (total time: 271.180) Filter (q & B) r_work=0.1152 r_free=0.1296 | n_water=450 | time (s): 3.940 (total time: 275.120) Filter (dist only) r_work=0.1159 r_free=0.1298 | n_water=448 | time (s): 46.110 (total time: 321.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.829674 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.935620 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1218 0.1339 0.0121 0.002 0.6 4.5 0.5 0.0 0 0.091 0.1177 0.1313 0.0136 0.003 0.8 3.2 0.5 0.0 0 0.274 0.1162 0.1305 0.0143 0.005 0.9 3.5 0.5 0.0 0 0.549 0.1156 0.1304 0.0148 0.006 1.0 3.5 0.5 0.0 0 0.823 0.1152 0.1303 0.0152 0.007 1.0 3.2 0.5 0.0 0 1.098 0.1149 0.1304 0.0155 0.007 1.1 3.8 0.5 0.0 0 1.372 0.1147 0.1303 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.647 0.1145 0.1302 0.0157 0.009 1.1 3.8 0.5 0.0 0 1.921 0.1154 0.1303 0.0149 0.006 1.0 3.2 0.5 0.0 0 0.915 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1302 0.0157 0.009 1.1 3.8 0.5 0.0 0 1.921 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 13.02 1.57 3.777 21.227 48.936 3.607 11.45 13.02 1.57 3.777 21.227 1.468 3.607 11.46 13.02 1.57 3.767 21.227 6.117 3.606 11.47 13.06 1.59 3.716 21.218 24.468 3.600 11.52 13.20 1.67 3.741 21.182 48.936 3.602 11.44 13.15 1.71 3.762 21.176 73.403 3.596 11.40 13.13 1.73 3.775 21.171 97.871 3.593 11.40 13.16 1.75 3.790 21.159 122.339 3.592 11.37 13.13 1.76 3.803 21.156 146.807 3.589 11.36 13.14 1.78 3.820 21.145 171.275 3.588 11.34 13.11 1.76 3.827 21.145 195.742 3.586 11.33 13.09 1.76 3.834 21.143 220.210 3.585 11.32 13.08 1.76 3.839 21.144 244.678 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.468 Accepted refinement result: 11.45 13.02 1.57 3.777 21.227 1.468 3.607 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.17 3.30 232 1743 Protein: 9.11 115.00 17.04 3.31 0 1519 Water: 11.50 76.69 35.17 N/A 232 216 Other: 19.76 26.64 22.10 N/A 0 8 Chain A: 9.11 115.00 19.30 N/A 0 1743 Chain S: 16.33 60.01 35.24 N/A 232 0 Histogram: Values Number of atoms 9.11 - 19.70 1261 19.70 - 30.29 301 30.29 - 40.88 212 40.88 - 51.47 132 51.47 - 62.06 47 62.06 - 72.64 12 72.64 - 83.23 4 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1302 r_work=0.1145 r_free=0.1302 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1302 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1297 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.22 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= 0.1140 r_free= 0.1297 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603917 | | target function (ml) not normalized (work): 300152.236914 | | target function (ml) not normalized (free): 15813.030003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1140 0.1297 n_refl.: 87581 re-set all scales: r(all,work,free)=0.1478 0.1479 0.1501 n_refl.: 87581 remove outliers: r(all,work,free)=0.1478 0.1479 0.1501 n_refl.: 87581 overall B=-0.01 to atoms: r(all,work,free)=0.1477 0.1477 0.1500 n_refl.: 87581 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1295 n_refl.: 87581 remove outliers: r(all,work,free)=0.1144 0.1136 0.1295 n_refl.: 87576 ======================== 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 0.4001 290.392 254.729 0.453 0.999 0.308 11.894-9.307 94.12 92 4 0.2294 472.035 463.865 0.874 1.001 0.233 9.237-7.194 97.73 208 7 0.2272 387.110 381.061 0.920 1.002 0.170 7.162-5.571 100.00 427 22 0.2121 296.084 285.286 0.904 1.002 0.154 5.546-4.326 100.00 867 58 0.1125 406.451 401.530 0.955 1.003 0.135 4.315-3.360 100.00 1859 96 0.0928 386.538 384.297 0.994 1.002 0.130 3.356-2.611 100.00 3867 181 0.1135 253.935 251.920 0.999 1.002 0.034 2.608-2.026 99.99 8198 413 0.0923 168.336 167.672 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.206 82.507 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.454 36.054 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.968 21.518 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0233 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1295 After: r_work=0.1138 r_free=0.1295 ================================== NQH flips ================================== r_work=0.1138 r_free=0.1295 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=0.1295 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1295 | n_water=448 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1138 r_free=0.1293 | n_water=446 | time (s): 46.940 (total time: 49.340) Filter (q & B) r_work=0.1138 r_free=0.1293 | n_water=446 | time (s): 1.360 (total time: 50.700) Compute maps r_work=0.1138 r_free=0.1293 | n_water=446 | time (s): 1.880 (total time: 52.580) Filter (map) r_work=0.1160 r_free=0.1300 | n_water=351 | time (s): 3.830 (total time: 56.410) Find peaks r_work=0.1160 r_free=0.1300 | n_water=351 | time (s): 0.690 (total time: 57.100) Add new water r_work=0.1207 r_free=0.1347 | n_water=490 | time (s): 3.610 (total time: 60.710) Refine new water occ: r_work=0.1152 r_free=0.1291 adp: r_work=0.1152 r_free=0.1292 occ: r_work=0.1141 r_free=0.1280 adp: r_work=0.1140 r_free=0.1281 occ: r_work=0.1132 r_free=0.1268 adp: r_work=0.1130 r_free=0.1269 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1269 r_work=0.1130 r_free=0.1269 | n_water=490 | time (s): 252.040 (total time: 312.750) Filter (q & B) r_work=0.1138 r_free=0.1279 | n_water=448 | time (s): 3.830 (total time: 316.580) Filter (dist only) r_work=0.1138 r_free=0.1278 | n_water=446 | time (s): 45.690 (total time: 362.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.744290 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 40.421670 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 0.1212 0.1323 0.0111 0.004 0.7 6.4 0.5 0.0 0 0.087 0.1179 0.1302 0.0123 0.004 0.8 5.8 0.0 0.0 0 0.262 0.1159 0.1290 0.0131 0.005 0.9 5.1 0.5 0.0 0 0.523 0.1151 0.1283 0.0133 0.006 1.0 5.4 0.5 0.0 0 0.785 0.1145 0.1280 0.0135 0.006 1.1 5.1 0.5 0.0 0 1.047 0.1141 0.1278 0.0137 0.007 1.1 5.1 0.5 0.0 0 1.308 0.1139 0.1278 0.0139 0.008 1.1 4.8 0.5 0.0 0 1.570 0.1138 0.1278 0.0140 0.009 1.1 4.8 0.5 0.0 0 1.832 0.1147 0.1281 0.0134 0.006 1.0 5.1 0.5 0.0 0 0.872 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1278 0.0139 0.008 1.1 4.8 0.5 0.0 0 1.570 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 12.78 1.39 3.776 21.152 40.422 3.602 11.39 12.78 1.39 3.776 21.152 1.213 3.602 11.39 12.78 1.39 3.776 21.152 5.053 3.602 11.41 12.82 1.41 3.709 21.146 20.211 3.597 11.49 12.98 1.49 3.725 21.116 40.422 3.601 11.43 12.97 1.54 3.740 21.104 60.633 3.595 11.33 12.88 1.55 3.762 21.106 80.843 3.589 11.33 12.91 1.57 3.775 21.094 101.054 3.588 11.29 12.86 1.57 3.783 21.099 121.265 3.585 11.29 12.87 1.59 3.796 21.090 141.476 3.584 11.30 12.91 1.61 3.813 21.078 161.687 3.585 11.28 12.89 1.61 3.822 21.077 181.898 3.583 11.26 12.87 1.61 3.826 21.078 202.108 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.053 Accepted refinement result: 11.39 12.78 1.39 3.776 21.152 5.053 3.602 Individual atomic B min max mean iso aniso Overall: 9.10 114.99 21.04 3.30 230 1743 Protein: 9.10 114.99 17.03 3.31 0 1519 Water: 11.49 76.69 34.70 N/A 230 216 Other: 19.75 26.63 22.09 N/A 0 8 Chain A: 9.10 114.99 19.29 N/A 0 1743 Chain S: 15.87 60.00 34.33 N/A 230 0 Histogram: Values Number of atoms 9.10 - 19.69 1264 19.69 - 30.28 301 30.28 - 40.87 216 40.87 - 51.46 125 51.46 - 62.05 45 62.05 - 72.64 12 72.64 - 83.22 4 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1278 r_work=0.1139 r_free=0.1278 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1278 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1276 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1137 r_free= 0.1276 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601426 | | target function (ml) not normalized (work): 299926.726611 | | target function (ml) not normalized (free): 15792.112310 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1346 0.1278 5.6613 5.5718| | 2: 3.57 - 2.84 1.00 2888 124 0.1075 0.1373 5.1571 5.2069| | 3: 2.83 - 2.48 1.00 2820 163 0.1114 0.1209 4.9308 4.9611| | 4: 2.47 - 2.25 1.00 2825 136 0.0900 0.1009 4.616 4.6473| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0952 4.5612 4.6095| | 6: 2.09 - 1.97 1.00 2846 113 0.0852 0.1031 4.2555 4.3829| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1122 3.9798 4.0877| | 8: 1.87 - 1.79 1.00 2789 144 0.0924 0.1108 3.8886 3.9869| | 9: 1.79 - 1.72 1.00 2745 138 0.0865 0.1190 3.64 3.8256| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1174 3.5627 3.708| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1027 3.4947 3.5703| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1134 3.3294 3.4554| | 13: 1.56 - 1.52 1.00 2745 130 0.0941 0.1038 3.304 3.3952| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1064 3.2383 3.3273| | 15: 1.48 - 1.45 1.00 2738 128 0.0998 0.1259 3.1497 3.2779| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1249 3.1345 3.2316| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1316 3.1176 3.2366| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1310 3.1035 3.2281| | 19: 1.36 - 1.34 1.00 2807 134 0.1260 0.1559 3.1121 3.2662| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1472 3.1113 3.1592| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1516 3.1139 3.1068| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1971 3.1235 3.2935| | 23: 1.27 - 1.26 1.00 2802 156 0.1645 0.1781 3.1321 3.2013| | 24: 1.26 - 1.24 1.00 2744 132 0.1708 0.1831 3.126 3.2295| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2150 3.1424 3.2619| | 26: 1.22 - 1.21 1.00 2727 135 0.1909 0.1742 3.1481 3.1946| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2170 3.1711 3.1614| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2301 3.1653 3.1736| | 29: 1.18 - 1.16 1.00 2800 134 0.2261 0.2377 3.1462 3.2269| | 30: 1.16 - 1.15 1.00 2739 148 0.2444 0.2432 3.1424 3.1628| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.95 8.29 1.00 0.98 5452.20| | 2: 3.57 - 2.84 2888 124 0.93 12.13 1.01 0.98 5452.20| | 3: 2.83 - 2.48 2820 163 0.90 16.09 0.99 0.98 4559.51| | 4: 2.47 - 2.25 2825 136 0.92 13.16 1.00 0.99 2257.57| | 5: 2.25 - 2.09 2756 127 0.91 15.24 1.01 0.99 2257.57| | 6: 2.09 - 1.97 2846 113 0.93 12.10 1.02 0.98 1312.57| | 7: 1.97 - 1.87 2787 165 0.95 9.25 1.02 0.98 506.62| | 8: 1.87 - 1.79 2789 144 0.93 12.55 1.00 0.98 506.62| | 9: 1.79 - 1.72 2745 138 0.94 10.02 0.98 0.98 288.49| | 10: 1.72 - 1.66 2831 160 0.94 11.15 0.98 0.98 244.80| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.98 234.52| | 12: 1.61 - 1.56 2773 144 0.95 8.89 0.99 0.98 137.51| | 13: 1.56 - 1.52 2745 130 0.95 10.38 1.03 0.98 137.51| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.99 123.42| | 15: 1.48 - 1.45 2738 128 0.95 9.93 1.02 0.99 97.62| | 16: 1.45 - 1.42 2756 161 0.94 11.10 1.02 0.99 97.62| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.99 88.94| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.99 83.92| | 19: 1.36 - 1.34 2807 134 0.94 11.88 0.99 0.99 83.92| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 80.05| | 21: 1.32 - 1.30 2785 112 0.94 13.12 0.98 0.97 79.78| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.97 80.17| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.95 82.15| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.15| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.95 84.04| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.94 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.94 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 89.65| | 29: 1.18 - 1.16 2800 134 0.88 20.43 0.99 0.93 90.96| | 30: 1.16 - 1.15 2739 148 0.86 21.96 0.98 0.93 90.96| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.78 max = 5452.20 mean = 849.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.37| |phase err.(test): min = 0.00 max = 88.15 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1137 0.1276 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1461 0.1461 0.1479 n_refl.: 87576 remove outliers: r(all,work,free)=0.1461 0.1461 0.1479 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1459 0.1460 0.1479 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1137 0.1281 n_refl.: 87576 remove outliers: r(all,work,free)=0.1143 0.1135 0.1281 n_refl.: 87573 ======================== 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 0.3917 288.250 254.218 0.450 0.999 0.306 11.894-9.307 93.14 91 4 0.2226 473.987 456.788 0.870 1.001 0.297 9.237-7.194 97.73 208 7 0.2343 387.110 378.250 0.921 1.002 0.170 7.162-5.571 100.00 427 22 0.2174 296.084 284.689 0.907 1.002 0.120 5.546-4.326 100.00 867 58 0.1152 406.451 401.360 0.963 1.002 0.110 4.315-3.360 100.00 1859 96 0.0935 386.538 384.314 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1116 253.935 252.010 1.010 1.002 0.029 2.608-2.026 99.99 8198 413 0.0914 168.336 167.722 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0888 82.206 82.538 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.454 36.060 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.968 21.519 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0158 ================= 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 : 0.2606 0.1949 0.083 5.477 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1772 0.083 5.477 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1772 0.083 5.477 9.0 119.5 20.1 258 0.000 1_nqh: 0.1631 0.1776 0.083 5.477 9.0 119.5 20.1 258 0.006 1_weight: 0.1631 0.1776 0.083 5.477 9.0 119.5 20.1 258 0.006 1_xyzrec: 0.1231 0.1463 0.006 0.881 9.0 119.5 20.1 258 0.138 1_adp: 0.1238 0.1461 0.006 0.881 9.1 119.4 20.1 258 0.138 1_regHadp: 0.1239 0.1464 0.006 0.881 9.1 119.4 20.1 258 0.138 1_occ: 0.1231 0.1456 0.006 0.881 9.1 119.4 20.1 258 0.138 2_bss: 0.1228 0.1450 0.006 0.881 9.1 119.5 20.1 258 0.138 2_settarget: 0.1228 0.1450 0.006 0.881 9.1 119.5 20.1 258 0.138 2_updatecdl: 0.1228 0.1450 0.006 0.887 9.1 119.5 20.1 258 0.138 2_nqh: 0.1228 0.1450 0.006 0.887 9.1 119.5 20.1 258 0.138 2_sol: 0.1204 0.1390 0.006 0.887 9.1 115.0 22.3 415 n/a 2_weight: 0.1204 0.1390 0.006 0.887 9.1 115.0 22.3 415 n/a 2_xyzrec: 0.1199 0.1410 0.005 0.772 9.1 115.0 22.3 415 n/a 2_adp: 0.1199 0.1410 0.005 0.772 9.1 115.0 22.3 415 n/a 2_regHadp: 0.1199 0.1410 0.005 0.772 9.1 115.0 22.3 415 n/a 2_occ: 0.1197 0.1414 0.005 0.772 9.1 115.0 22.3 415 n/a 3_bss: 0.1193 0.1409 0.005 0.772 9.1 115.0 22.3 415 n/a 3_settarget: 0.1193 0.1409 0.005 0.772 9.1 115.0 22.3 415 n/a 3_updatecdl: 0.1193 0.1409 0.005 0.773 9.1 115.0 22.3 415 n/a 3_nqh: 0.1193 0.1409 0.005 0.773 9.1 115.0 22.3 415 n/a 3_sol: 0.1218 0.1395 0.005 0.773 9.1 115.0 21.3 439 n/a 3_weight: 0.1218 0.1395 0.005 0.773 9.1 115.0 21.3 439 n/a 3_xyzrec: 0.1163 0.1308 0.006 0.970 9.1 115.0 21.3 439 n/a 3_adp: 0.1163 0.1308 0.006 0.970 9.1 115.0 21.3 439 n/a 3_regHadp: 0.1163 0.1308 0.006 0.970 9.1 115.0 21.3 439 n/a 3_occ: 0.1154 0.1308 0.006 0.970 9.1 115.0 21.3 439 n/a 4_bss: 0.1144 0.1297 0.006 0.970 9.1 115.0 21.3 439 n/a 4_settarget: 0.1144 0.1297 0.006 0.970 9.1 115.0 21.3 439 n/a 4_updatecdl: 0.1144 0.1297 0.006 0.972 9.1 115.0 21.3 439 n/a 4_nqh: 0.1148 0.1299 0.006 0.972 9.1 115.0 21.3 439 n/a 4_sol: 0.1159 0.1298 0.006 0.972 9.1 115.0 21.2 448 n/a 4_weight: 0.1159 0.1298 0.006 0.972 9.1 115.0 21.2 448 n/a 4_xyzrec: 0.1145 0.1302 0.009 1.139 9.1 115.0 21.2 448 n/a 4_adp: 0.1145 0.1302 0.009 1.139 9.1 115.0 21.2 448 n/a 4_regHadp: 0.1145 0.1302 0.009 1.139 9.1 115.0 21.2 448 n/a 4_occ: 0.1140 0.1297 0.009 1.139 9.1 115.0 21.2 448 n/a 5_bss: 0.1136 0.1295 0.009 1.139 9.1 115.0 21.2 448 n/a 5_settarget: 0.1136 0.1295 0.009 1.139 9.1 115.0 21.2 448 n/a 5_updatecdl: 0.1136 0.1295 0.009 1.140 9.1 115.0 21.2 448 n/a 5_setrh: 0.1138 0.1295 0.009 1.140 9.1 115.0 21.2 448 n/a 5_nqh: 0.1138 0.1295 0.009 1.140 9.1 115.0 21.2 448 n/a 5_sol: 0.1138 0.1278 0.009 1.140 9.1 115.0 21.0 446 n/a 5_weight: 0.1138 0.1278 0.009 1.140 9.1 115.0 21.0 446 n/a 5_xyzrec: 0.1139 0.1278 0.008 1.136 9.1 115.0 21.0 446 n/a 5_adp: 0.1139 0.1278 0.008 1.136 9.1 115.0 21.0 446 n/a 5_regHadp: 0.1139 0.1278 0.008 1.136 9.1 115.0 21.0 446 n/a 5_occ: 0.1137 0.1276 0.008 1.136 9.1 115.0 21.0 446 n/a end: 0.1135 0.1281 0.008 1.136 9.1 115.0 21.0 446 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6197065_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6197065_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1200 Refinement macro-cycles (run) : 13613.6200 Write final files (write_after_run_outputs) : 97.2900 Total : 13715.0300 Total CPU time: 3.82 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:07:45 PST -0800 (1735366065.01 s) Start R-work = 0.1629, R-free = 0.1772 Final R-work = 0.1135, R-free = 0.1281 =============================================================================== Job complete usr+sys time: 13898.01 seconds wall clock time: 251 minutes 58.42 seconds (15118.42 seconds total)