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_5638674.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_5638674.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5638674.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 2 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: 1.92, per 1000 atoms: 0.57 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: 0.63 Conformation dependent library (CDL) restraints added in 207.9 milliseconds Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.91: 493 0.91 - 1.15: 1126 1.15 - 1.39: 584 1.39 - 1.64: 870 1.64 - 1.88: 80 Bond restraints: 3153 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta sigma weight residual 1.459 1.699 -0.240 1.20e-02 6.94e+03 4.00e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.133 0.188 1.00e-02 1.00e+04 3.53e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.331 1.497 -0.167 8.90e-03 1.26e+04 3.50e+02 bond pdb=" C HIS A 138 " pdb=" O HIS A 138 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.32e-02 5.74e+03 3.24e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.496 -0.175 1.00e-02 1.00e+04 3.07e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 3176 4.87 - 9.74: 1921 9.74 - 14.61: 576 14.61 - 19.48: 98 19.48 - 24.34: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 132.45 -13.25 9.00e-01 1.23e+00 2.17e+02 angle pdb=" O MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 122.09 137.38 -15.29 1.04e+00 9.25e-01 2.16e+02 angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" O ILE A 21 " ideal model delta sigma weight residual 118.69 128.17 -9.48 6.70e-01 2.23e+00 2.00e+02 angle pdb=" CA MET A 17 " pdb=" C MET A 17 " pdb=" N GLU A 18 " ideal model delta sigma weight residual 116.97 100.54 16.43 1.20e+00 6.94e-01 1.88e+02 angle pdb=" N AASN A 76 " pdb=" CA AASN A 76 " pdb=" C AASN A 76 " ideal model delta sigma weight residual 111.33 127.20 -15.87 1.21e+00 6.83e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.17: 923 17.17 - 34.33: 129 34.33 - 51.49: 44 51.49 - 68.65: 12 68.65 - 85.81: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 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 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA CYS A 46 " pdb=" C CYS A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.220: 92 0.220 - 0.439: 82 0.439 - 0.658: 43 0.658 - 0.877: 22 0.877 - 1.095: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA GLU A 16 " pdb=" N GLU A 16 " pdb=" C GLU A 16 " pdb=" CB GLU A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.02e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 173 " 0.011 2.00e-02 2.50e+03 8.15e-02 9.95e+01 pdb=" CG ASN A 173 " -0.120 2.00e-02 2.50e+03 pdb=" OD1 ASN A 173 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 173 " -0.077 2.00e-02 2.50e+03 pdb="HD21 ASN A 173 " -0.010 2.00e-02 2.50e+03 pdb="HD22 ASN A 173 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.120 9.50e-02 1.11e+02 7.64e-02 9.66e+01 pdb=" NE ARG A 48 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.120 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.111 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.026 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " 0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.050 2.00e-02 2.50e+03 5.39e-02 8.71e+01 pdb=" CG PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.068 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.014 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1076 2.33 - 2.89: 8139 2.89 - 3.46: 10488 3.46 - 4.03: 15238 4.03 - 4.60: 21760 Nonbonded interactions: 56701 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.757 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.803 1.850 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.816 1.850 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.844 1.850 x-y,-y,-z-4/3 ... (remaining 56696 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_5638674_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= 0.2608 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789734 | | target function (ml) not normalized (work): 232401.610695 | | target function (ml) not normalized (free): 11828.354149 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3039 0.2122 6.9924 4.9504| | 2: 3.57 - 2.84 1.00 2876 122 0.2417 0.1811 4.3527 4.3609| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1706 4.1339 4.1744| | 4: 2.47 - 2.25 1.00 2825 136 0.2347 0.1415 3.8372 3.8307| | 5: 2.25 - 2.09 1.00 2756 127 0.2479 0.1612 3.8017 3.8297| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1669 3.4572 3.5421| | 7: 1.97 - 1.87 1.00 2787 165 0.2564 0.1701 3.1371 3.1317| | 8: 1.87 - 1.79 1.00 2789 144 0.2397 0.1991 3.0418 3.2021| | 9: 1.79 - 1.72 1.00 2745 138 0.2436 0.2089 2.897 3.0124| | 10: 1.72 - 1.66 1.00 2789 158 0.2436 0.1883 2.802 2.8442| | 11: 1.66 - 1.61 1.00 2740 147 0.2508 0.1851 2.7581 2.7709| | 12: 1.61 - 1.56 1.00 2787 146 0.2519 0.2046 2.6266 2.6512| | 13: 1.56 - 1.52 1.00 2745 130 0.2505 0.1881 2.5697 2.6097| | 14: 1.52 - 1.48 1.00 2803 134 0.2564 0.1875 2.4931 2.5134| | 15: 1.48 - 1.45 1.00 2738 128 0.2695 0.2197 2.4478 2.4767| | 16: 1.45 - 1.42 1.00 2756 161 0.2620 0.2169 2.3887 2.4483| | 17: 1.42 - 1.39 1.00 2785 139 0.2695 0.1934 2.3353 2.3264| | 18: 1.39 - 1.36 1.00 2741 179 0.2697 0.2313 2.2824 2.4053| | 19: 1.36 - 1.34 1.00 2807 134 0.2635 0.2225 2.2444 2.2789| | 20: 1.34 - 1.32 1.00 2696 147 0.2682 0.2197 2.2092 2.2036| | 21: 1.32 - 1.30 1.00 2785 112 0.2716 0.2454 2.1577 2.2358| | 22: 1.29 - 1.27 1.00 2704 152 0.2721 0.2719 2.1358 2.2204| | 23: 1.27 - 1.26 1.00 2802 156 0.2768 0.2403 2.1045 2.1796| | 24: 1.26 - 1.24 1.00 2744 132 0.2720 0.2516 2.0651 2.1711| | 25: 1.24 - 1.22 1.00 2734 148 0.2862 0.2476 2.0496 2.0478| | 26: 1.22 - 1.21 1.00 2727 135 0.2850 0.2429 2.0078 2.1158| | 27: 1.21 - 1.19 1.00 2814 148 0.3003 0.2562 2.0137 1.9795| | 28: 1.19 - 1.18 1.00 2671 147 0.3026 0.2673 1.9973 1.9648| | 29: 1.18 - 1.16 1.00 2800 134 0.3013 0.2936 1.9663 2.0293| | 30: 1.16 - 1.15 1.00 2740 148 0.3071 0.2561 1.9351 1.9506| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.16 0.76 0.23 1523.23| | 2: 3.57 - 2.84 2876 122 0.80 26.43 1.27 0.23 1523.23| | 3: 2.84 - 2.48 2833 165 0.73 32.46 1.24 0.24 1261.56| | 4: 2.47 - 2.25 2825 136 0.81 25.73 1.26 0.25 582.50| | 5: 2.25 - 2.09 2756 127 0.77 29.54 1.28 0.25 582.50| | 6: 2.09 - 1.97 2846 113 0.84 22.53 1.29 0.25 316.11| | 7: 1.97 - 1.87 2787 165 0.90 16.26 1.29 0.26 88.91| | 8: 1.87 - 1.79 2789 144 0.86 20.84 1.24 0.26 88.91| | 9: 1.79 - 1.72 2745 138 0.88 18.78 1.24 0.25 56.34| | 10: 1.72 - 1.66 2789 158 0.86 20.60 1.23 0.25 49.82| | 11: 1.66 - 1.61 2740 147 0.86 21.49 1.24 0.25 48.04| | 12: 1.61 - 1.56 2787 146 0.88 18.62 1.23 0.25 30.04| | 13: 1.56 - 1.52 2745 130 0.87 20.45 1.23 0.25 30.04| | 14: 1.52 - 1.48 2803 134 0.86 20.79 1.24 0.25 26.86| | 15: 1.48 - 1.45 2738 128 0.87 20.59 1.25 0.25 21.04| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 21.04| | 17: 1.42 - 1.39 2785 139 0.86 21.02 1.23 0.25 17.91| | 18: 1.39 - 1.36 2741 179 0.86 21.55 1.23 0.25 16.10| | 19: 1.36 - 1.34 2807 134 0.85 22.17 1.22 0.25 16.10| | 20: 1.34 - 1.32 2696 147 0.86 21.42 1.21 0.24 13.46| | 21: 1.32 - 1.30 2785 112 0.85 22.48 1.21 0.24 13.27| | 22: 1.29 - 1.27 2704 152 0.85 22.91 1.21 0.24 12.97| | 23: 1.27 - 1.26 2802 156 0.85 22.61 1.21 0.24 11.43| | 24: 1.26 - 1.24 2744 132 0.84 23.31 1.20 0.24 11.43| | 25: 1.24 - 1.22 2734 148 0.84 24.02 1.20 0.24 10.74| | 26: 1.22 - 1.21 2727 135 0.84 23.86 1.20 0.23 9.97| | 27: 1.21 - 1.19 2814 148 0.83 24.88 1.20 0.23 9.97| | 28: 1.19 - 1.18 2671 147 0.83 24.85 1.19 0.23 8.99| | 29: 1.18 - 1.16 2800 134 0.83 24.83 1.16 0.23 8.63| | 30: 1.16 - 1.15 2740 148 0.82 26.28 1.15 0.23 8.63| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.63 max = 1523.23 mean = 220.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 22.73| |phase err.(test): min = 0.00 max = 89.78 mean = 22.68| |-----------------------------------------------------------------------------| ----------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 0.260 1557 Z= 5.315 Angle : 5.304 19.146 2118 Z= 3.778 Chirality : 0.398 1.095 243 Planarity : 0.032 0.113 284 Dihedral : 14.211 85.809 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.45), residues: 224 helix: -2.98 (0.34), residues: 109 sheet: -0.98 (0.93), residues: 28 loop : -0.45 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.139 0.024 ARG A 28 TYR 0.070 0.028 TYR A 139 PHE 0.074 0.039 PHE A 164 HIS 0.068 0.027 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2608 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789734 | | target function (ml) not normalized (work): 232401.610695 | | target function (ml) not normalized (free): 11828.354149 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2609 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2609 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1978 0.1982 0.1952 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 0.1770 n_refl.: 87594 remove outliers: r(all,work,free)=0.1636 0.1629 0.1770 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 0.3797 386.381 356.871 0.727 0.916 0.401 11.894-9.307 99.02 97 4 0.1785 613.748 595.966 1.010 0.916 0.380 9.237-7.194 100.00 213 7 0.2119 501.970 490.913 1.048 0.917 0.358 7.162-5.571 100.00 427 22 0.2217 376.701 364.377 1.015 0.917 0.290 5.546-4.326 100.00 867 58 0.1267 517.117 512.140 1.051 0.918 0.217 4.315-3.360 100.00 1859 96 0.1163 491.782 486.963 1.093 0.919 0.189 3.356-2.611 100.00 3867 181 0.1427 323.075 319.496 1.084 0.920 0.119 2.608-2.026 99.99 8198 413 0.1335 214.169 211.835 1.093 0.923 0.000 2.025-1.573 100.00 17313 902 0.1630 104.589 104.054 1.092 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2058 46.379 45.121 1.071 0.934 0.000 1.221-1.150 99.97 13689 708 0.2614 29.222 26.951 1.033 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0465 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1629 r_free=0.1770 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1629 r_free=0.1770 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.081365 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2026.279919 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 0.1631 0.1758 0.0127 0.001 0.4 4.2 0.0 0.0 0 0.125 0.1525 0.1661 0.0136 0.001 0.4 3.5 0.0 0.0 0 0.250 0.1427 0.1579 0.0152 0.001 0.5 3.5 0.0 0.0 0 0.500 0.1375 0.1546 0.0171 0.002 0.5 3.2 0.0 0.0 0 0.750 0.1349 0.1532 0.0184 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1346 0.1537 0.0191 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1294 0.1506 0.0212 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1269 0.1495 0.0225 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1256 0.1487 0.0231 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1243 0.1474 0.0231 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1237 0.1468 0.0232 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1232 0.1467 0.0235 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1230 0.1468 0.0238 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1227 0.1468 0.0241 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1228 0.1470 0.0242 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1222 0.1463 0.0240 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1223 0.1466 0.0243 0.007 0.9 3.2 0.5 0.0 0 12.000 0.1221 0.1461 0.0240 0.007 0.9 4.2 0.5 0.0 0 13.000 0.1220 0.1469 0.0249 0.008 1.0 3.5 0.5 0.6 0 14.041 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1221 0.1461 0.0240 0.007 0.9 4.2 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.21 14.61 2.40 3.013 19.062 2026.280 0.017 12.21 14.61 2.40 3.012 19.062 60.788 0.017 12.29 14.60 2.30 2.657 19.062 253.285 0.017 12.65 15.29 2.65 2.792 19.281 1013.140 0.016 12.48 15.38 2.91 3.361 19.676 2026.280 0.016 12.41 15.47 3.06 3.336 19.649 3039.420 0.015 12.27 15.39 3.12 3.333 19.645 4052.560 0.015 12.20 15.39 3.18 3.310 19.621 5065.700 0.015 12.08 15.27 3.19 3.295 19.612 6078.840 0.015 12.06 15.25 3.19 3.301 19.610 7091.980 0.015 12.05 15.27 3.21 3.326 19.610 8105.120 0.015 12.04 15.33 3.29 3.340 19.610 9118.260 0.015 12.06 15.38 3.32 3.437 19.654 10131.400 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: 253.285 Accepted refinement result: 12.29 14.60 2.30 2.657 19.062 253.285 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.44 20.09 3.29 0 1785 Protein: 9.08 114.88 17.00 3.29 0 1519 Water: 11.48 119.44 38.23 N/A 0 258 Other: 19.74 26.60 22.07 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 1271 20.11 - 31.15 228 31.15 - 42.19 125 42.19 - 53.22 94 53.22 - 64.26 42 64.26 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1460 r_work=0.1231 r_free=0.1463 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1463 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 = 0.1224 r_free = 0.1457 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1224 r_free= 0.1457 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016779 | | target function (ls_wunit_k1) not normalized (work): 1397.668269 | | target function (ls_wunit_k1) not normalized (free): 108.880826 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1224 0.1457 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1697 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1697 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1675 0.1676 0.1701 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1234 0.1223 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 0.3459 303.022 278.802 0.639 1.003 0.370 11.894-9.307 99.02 97 4 0.1656 482.217 470.593 0.920 1.003 0.366 9.237-7.194 100.00 213 7 0.1914 394.394 387.660 0.963 1.003 0.348 7.162-5.571 100.00 427 22 0.1844 295.971 289.810 0.934 1.003 0.249 5.546-4.326 100.00 867 58 0.0997 406.295 403.314 0.964 1.003 0.199 4.315-3.360 100.00 1859 96 0.0865 386.389 385.227 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1169 253.838 252.745 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1019 168.271 167.590 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.175 82.382 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1448 36.440 35.949 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.960 21.446 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0453 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1225 r_free=0.1454 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1454 | n_water=258 | time (s): 1.590 (total time: 1.590) Filter (dist) r_work=0.1234 r_free=0.1453 | n_water=252 | time (s): 20.740 (total time: 22.330) Filter (q & B) r_work=0.1236 r_free=0.1454 | n_water=249 | time (s): 3.320 (total time: 25.650) Compute maps r_work=0.1236 r_free=0.1454 | n_water=249 | time (s): 1.570 (total time: 27.220) Filter (map) r_work=0.1251 r_free=0.1460 | n_water=227 | time (s): 2.480 (total time: 29.700) Find peaks r_work=0.1251 r_free=0.1460 | n_water=227 | time (s): 0.440 (total time: 30.140) Add new water r_work=0.1391 r_free=0.1625 | n_water=438 | time (s): 2.850 (total time: 32.990) Refine new water occ: r_work=0.1298 r_free=0.1484 adp: r_work=0.1219 r_free=0.1431 occ: r_work=0.1233 r_free=0.1420 adp: r_work=0.1200 r_free=0.1409 occ: r_work=0.1203 r_free=0.1397 adp: r_work=0.1194 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1400 r_work=0.1194 r_free=0.1400 | n_water=438 | time (s): 54.570 (total time: 87.560) Filter (q & B) r_work=0.1196 r_free=0.1404 | n_water=421 | time (s): 3.550 (total time: 91.110) Filter (dist only) r_work=0.1197 r_free=0.1403 | n_water=420 | time (s): 34.170 (total time: 125.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.449776 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1504.853160 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 0.1694 0.1815 0.0121 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1562 0.1695 0.0134 0.001 0.4 7.7 0.0 0.0 0 0.250 0.1419 0.1580 0.0161 0.001 0.4 6.1 0.0 0.0 0 0.500 0.1335 0.1512 0.0177 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1314 0.1494 0.0180 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1305 0.1488 0.0183 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1251 0.1448 0.0198 0.002 0.6 4.5 0.5 0.0 0 2.000 0.1233 0.1437 0.0204 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1220 0.1427 0.0207 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1209 0.1423 0.0214 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1208 0.1425 0.0217 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1204 0.1422 0.0218 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1196 0.1418 0.0221 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1195 0.1425 0.0231 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1192 0.1423 0.0231 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1192 0.1423 0.0231 0.007 0.9 5.8 0.5 0.0 0 11.000 0.1190 0.1420 0.0231 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1188 0.1416 0.0229 0.007 0.9 5.4 0.5 0.6 0 13.000 0.1188 0.1421 0.0233 0.008 0.9 5.8 0.5 0.6 0 14.225 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1188 0.1416 0.0229 0.007 0.9 5.4 0.5 0.6 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 14.16 2.29 3.765 21.781 1504.853 0.016 11.88 14.16 2.29 3.765 21.781 45.146 0.016 11.88 14.16 2.29 3.765 21.781 188.107 0.016 12.11 14.69 2.58 3.617 21.788 752.427 0.015 12.09 14.95 2.85 3.462 22.105 1504.853 0.015 11.92 14.85 2.93 3.453 22.012 2257.280 0.015 11.82 14.78 2.97 3.465 22.094 3009.706 0.014 11.72 14.79 3.07 3.528 21.924 3762.133 0.014 11.77 14.88 3.11 3.512 22.152 4514.559 0.014 11.74 14.90 3.16 3.522 22.075 5266.986 0.014 11.70 14.83 3.13 3.528 22.115 6019.413 0.014 11.66 14.80 3.14 3.560 22.207 6771.839 0.014 11.64 14.79 3.15 3.572 22.193 7524.266 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: 45.146 Accepted refinement result: 11.88 14.16 2.29 3.765 21.781 45.146 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.91 22.19 3.29 193 1754 Protein: 9.10 114.91 17.03 3.29 0 1519 Water: 11.51 76.67 40.86 N/A 193 227 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.10 114.91 19.48 N/A 0 1754 Chain S: 12.79 60.00 46.80 N/A 193 0 Histogram: Values Number of atoms 9.10 - 19.69 1259 19.69 - 30.27 252 30.27 - 40.85 159 40.85 - 51.43 130 51.43 - 62.01 124 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1416 r_work=0.1188 r_free=0.1416 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1416 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1411 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 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= 0.1186 r_free= 0.1411 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014895 | | target function (ls_wunit_k1) not normalized (work): 1240.716320 | | target function (ls_wunit_k1) not normalized (free): 102.215290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1186 0.1411 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1530 0.1527 0.1615 n_refl.: 87591 remove outliers: r(all,work,free)=0.1530 0.1527 0.1615 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1531 0.1529 0.1615 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1182 0.1406 n_refl.: 87591 remove outliers: r(all,work,free)=0.1192 0.1181 0.1406 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 0.3475 299.570 280.132 0.593 1.002 0.340 11.894-9.307 99.02 97 4 0.1629 482.217 476.858 0.918 1.003 0.327 9.237-7.194 100.00 213 7 0.1667 394.394 394.205 0.987 1.003 0.290 7.162-5.571 100.00 427 22 0.1496 295.971 291.552 0.935 1.003 0.225 5.546-4.326 100.00 867 58 0.0882 406.295 402.494 0.962 1.003 0.220 4.315-3.360 100.00 1859 96 0.0792 386.389 385.148 1.004 1.002 0.190 3.356-2.611 100.00 3867 181 0.1077 253.838 253.010 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1007 168.271 167.659 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1098 82.175 82.387 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.440 35.972 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.960 21.469 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=0.0109 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1406 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1182 r_free=0.1406 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1406 | n_water=420 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1182 r_free=0.1404 | n_water=415 | time (s): 35.060 (total time: 36.820) Filter (q & B) r_work=0.1182 r_free=0.1404 | n_water=415 | time (s): 0.990 (total time: 37.810) Compute maps r_work=0.1182 r_free=0.1404 | n_water=415 | time (s): 1.340 (total time: 39.150) Filter (map) r_work=0.1212 r_free=0.1412 | n_water=291 | time (s): 2.400 (total time: 41.550) Find peaks r_work=0.1212 r_free=0.1412 | n_water=291 | time (s): 0.450 (total time: 42.000) Add new water r_work=0.1322 r_free=0.1534 | n_water=462 | time (s): 2.640 (total time: 44.640) Refine new water occ: r_work=0.1240 r_free=0.1444 adp: r_work=0.1242 r_free=0.1445 occ: r_work=0.1219 r_free=0.1420 adp: r_work=0.1218 r_free=0.1420 occ: r_work=0.1202 r_free=0.1398 adp: r_work=0.1197 r_free=0.1396 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1396 r_work=0.1197 r_free=0.1396 | n_water=462 | time (s): 190.200 (total time: 234.840) Filter (q & B) r_work=0.1201 r_free=0.1405 | n_water=433 | time (s): 3.320 (total time: 238.160) Filter (dist only) r_work=0.1202 r_free=0.1404 | n_water=432 | time (s): 37.810 (total time: 275.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.806140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.958873 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 0.1227 0.1368 0.0142 0.002 0.6 4.8 0.5 0.0 0 0.090 0.1187 0.1339 0.0152 0.003 0.7 3.5 0.5 0.0 0 0.271 0.1172 0.1326 0.0154 0.004 0.8 2.9 0.5 0.0 0 0.542 0.1163 0.1320 0.0157 0.005 0.9 3.2 0.5 0.0 0 0.813 0.1159 0.1319 0.0160 0.006 1.0 3.2 0.5 0.0 0 1.084 0.1156 0.1319 0.0163 0.007 1.0 3.5 0.5 0.0 0 1.355 0.1155 0.1317 0.0162 0.007 1.1 3.5 0.5 0.6 0 1.626 0.1151 0.1316 0.0165 0.008 1.1 4.2 0.5 0.6 0 1.896 0.1162 0.1321 0.0159 0.005 0.9 3.2 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1316 0.0165 0.008 1.1 4.2 0.5 0.6 0 1.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.16 1.65 3.768 21.243 43.959 3.616 11.51 13.16 1.65 3.768 21.243 1.319 3.616 11.52 13.17 1.65 3.758 21.243 5.495 3.616 11.54 13.22 1.68 3.706 21.235 21.979 3.609 11.60 13.33 1.73 3.726 21.195 43.959 3.610 11.51 13.29 1.78 3.756 21.185 65.938 3.604 11.45 13.25 1.80 3.770 21.181 87.918 3.599 11.42 13.23 1.81 3.780 21.176 109.897 3.596 11.42 13.27 1.85 3.799 21.161 131.877 3.595 11.42 13.29 1.87 3.817 21.147 153.856 3.595 11.39 13.25 1.86 3.822 21.146 175.835 3.592 11.37 13.23 1.86 3.828 21.147 197.815 3.591 11.37 13.23 1.87 3.839 21.141 219.794 3.590 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.319 Accepted refinement result: 11.51 13.16 1.65 3.768 21.243 1.319 3.616 Individual atomic B min max mean iso aniso Overall: 9.11 114.91 21.20 3.29 206 1753 Protein: 9.11 114.91 17.03 3.29 0 1519 Water: 11.51 76.68 35.84 N/A 206 226 Other: 19.78 26.63 22.11 N/A 0 8 Chain A: 9.11 114.91 19.47 N/A 0 1753 Chain S: 12.80 60.01 35.96 N/A 206 0 Histogram: Values Number of atoms 9.11 - 19.69 1264 19.69 - 30.27 284 30.27 - 40.85 205 40.85 - 51.43 126 51.43 - 62.01 57 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1316 r_work=0.1151 r_free=0.1317 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1317 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1316 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 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= 0.1143 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.609152 | | target function (ml) not normalized (work): 300620.685688 | | target function (ml) not normalized (free): 15829.543218 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1152 0.1143 0.1316 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1492 0.1490 0.1544 n_refl.: 87590 remove outliers: r(all,work,free)=0.1492 0.1490 0.1544 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1490 0.1489 0.1543 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1310 n_refl.: 87590 remove outliers: r(all,work,free)=0.1147 0.1138 0.1310 n_refl.: 87585 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3876 296.929 272.222 0.504 1.001 0.309 11.894-9.307 98.04 96 4 0.2327 482.342 466.459 0.881 1.002 0.294 9.237-7.194 98.64 210 7 0.2216 386.885 386.907 0.964 1.002 0.205 7.162-5.571 100.00 427 22 0.2026 295.971 286.851 0.923 1.003 0.184 5.546-4.326 100.00 867 58 0.1098 406.295 401.654 0.965 1.002 0.170 4.315-3.360 100.00 1859 96 0.0921 386.389 383.679 1.004 1.002 0.160 3.356-2.611 100.00 3867 181 0.1137 253.838 251.793 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0931 168.271 167.491 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0895 82.175 82.442 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.440 36.025 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 22.960 21.502 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0166 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1310 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=0.1310 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1310 | n_water=432 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1138 r_free=0.1310 | n_water=429 | time (s): 47.240 (total time: 49.730) Filter (q & B) r_work=0.1139 r_free=0.1311 | n_water=427 | time (s): 3.910 (total time: 53.640) Compute maps r_work=0.1139 r_free=0.1311 | n_water=427 | time (s): 1.890 (total time: 55.530) Filter (map) r_work=0.1162 r_free=0.1310 | n_water=325 | time (s): 3.950 (total time: 59.480) Find peaks r_work=0.1162 r_free=0.1310 | n_water=325 | time (s): 0.680 (total time: 60.160) Add new water r_work=0.1238 r_free=0.1399 | n_water=483 | time (s): 3.770 (total time: 63.930) Refine new water occ: r_work=0.1171 r_free=0.1325 adp: r_work=0.1171 r_free=0.1327 occ: r_work=0.1156 r_free=0.1306 adp: r_work=0.1155 r_free=0.1307 occ: r_work=0.1143 r_free=0.1287 adp: r_work=0.1139 r_free=0.1288 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1288 r_work=0.1139 r_free=0.1288 | n_water=483 | time (s): 259.510 (total time: 323.440) Filter (q & B) r_work=0.1144 r_free=0.1295 | n_water=449 | time (s): 3.800 (total time: 327.240) Filter (dist only) r_work=0.1144 r_free=0.1293 | n_water=448 | time (s): 46.440 (total time: 373.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.800796 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.676990 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 0.1338 0.0126 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1173 0.1309 0.0137 0.003 0.7 3.5 0.5 0.0 0 0.270 0.1157 0.1302 0.0145 0.005 0.9 3.5 0.5 0.0 0 0.540 0.1151 0.1300 0.0148 0.006 0.9 3.2 0.5 0.0 0 0.810 0.1147 0.1296 0.0149 0.007 1.0 3.2 0.5 0.0 0 1.080 0.1145 0.1295 0.0150 0.007 1.1 3.5 0.5 0.0 0 1.351 0.1142 0.1300 0.0158 0.008 1.1 3.2 0.5 0.0 0 1.621 0.1141 0.1299 0.0158 0.009 1.1 3.2 0.5 0.0 0 1.891 0.1150 0.1299 0.0149 0.006 1.0 3.2 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1295 0.0150 0.007 1.1 3.5 0.5 0.0 0 1.351 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.95 1.50 3.769 21.222 46.677 3.609 11.45 12.95 1.50 3.769 21.222 1.400 3.609 11.45 12.95 1.50 3.759 21.222 5.835 3.609 11.47 12.99 1.53 3.709 21.213 23.338 3.603 11.52 13.11 1.59 3.736 21.178 46.677 3.605 11.46 13.11 1.65 3.756 21.167 70.015 3.599 11.41 13.07 1.66 3.772 21.165 93.354 3.596 11.36 13.02 1.66 3.782 21.164 116.692 3.592 11.35 13.05 1.70 3.799 21.155 140.031 3.591 11.36 13.08 1.72 3.818 21.139 163.369 3.591 11.33 13.07 1.73 3.828 21.140 186.708 3.590 11.32 13.04 1.72 3.835 21.138 210.046 3.588 11.31 13.03 1.72 3.840 21.137 233.385 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.835 Accepted refinement result: 11.45 12.95 1.50 3.759 21.222 5.835 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 114.79 21.17 3.26 223 1752 Protein: 9.11 114.79 17.03 3.26 0 1519 Water: 11.51 76.67 35.18 N/A 223 225 Other: 19.74 26.59 22.10 N/A 0 8 Chain A: 9.11 114.79 19.46 N/A 0 1752 Chain S: 12.78 60.00 34.60 N/A 223 0 Histogram: Values Number of atoms 9.11 - 19.68 1261 19.68 - 30.25 302 30.25 - 40.82 212 40.82 - 51.38 128 51.38 - 61.95 49 61.95 - 72.52 11 72.52 - 83.09 6 83.09 - 93.65 4 93.65 - 104.22 0 104.22 - 114.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1295 r_work=0.1145 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1295 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1292 target_work(ml) = 3.607 | | 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.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1141 r_free= 0.1292 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607334 | | target function (ml) not normalized (work): 300451.260131 | | target function (ml) not normalized (free): 15813.225617 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1141 0.1292 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1470 0.1469 0.1512 n_refl.: 87585 remove outliers: r(all,work,free)=0.1470 0.1469 0.1512 n_refl.: 87585 overall B=-0.01 to atoms: r(all,work,free)=0.1468 0.1467 0.1511 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1146 0.1139 0.1293 n_refl.: 87585 remove outliers: r(all,work,free)=0.1143 0.1136 0.1293 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4173 290.692 258.323 0.448 1.000 0.304 11.894-9.307 95.10 93 4 0.2453 469.373 457.221 0.851 1.002 0.234 9.237-7.194 98.18 209 7 0.2386 385.879 380.384 0.922 1.002 0.170 7.162-5.571 100.00 427 22 0.2208 295.971 284.352 0.902 1.002 0.130 5.546-4.326 100.00 867 58 0.1133 406.295 401.588 0.956 1.002 0.130 4.315-3.360 100.00 1859 96 0.0914 386.389 383.771 0.994 1.002 0.120 3.356-2.611 100.00 3867 181 0.1112 253.838 251.909 1.001 1.002 0.029 2.608-2.026 99.99 8198 413 0.0910 168.271 167.606 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.175 82.494 1.026 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1254 36.440 36.037 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.960 21.504 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0215 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1293 After: r_work=0.1137 r_free=0.1292 ================================== NQH flips ================================== r_work=0.1137 r_free=0.1292 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=0.1137 r_free=0.1292 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1292 | n_water=448 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1137 r_free=0.1292 | n_water=448 | time (s): 44.080 (total time: 46.690) Filter (q & B) r_work=0.1137 r_free=0.1293 | n_water=447 | time (s): 4.000 (total time: 50.690) Compute maps r_work=0.1137 r_free=0.1293 | n_water=447 | time (s): 1.850 (total time: 52.540) Filter (map) r_work=0.1160 r_free=0.1304 | n_water=347 | time (s): 4.070 (total time: 56.610) Find peaks r_work=0.1160 r_free=0.1304 | n_water=347 | time (s): 0.710 (total time: 57.320) Add new water r_work=0.1208 r_free=0.1357 | n_water=491 | time (s): 3.750 (total time: 61.070) Refine new water occ: r_work=0.1154 r_free=0.1295 adp: r_work=0.1155 r_free=0.1298 occ: r_work=0.1143 r_free=0.1281 adp: r_work=0.1142 r_free=0.1284 occ: r_work=0.1134 r_free=0.1269 adp: r_work=0.1131 r_free=0.1270 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1270 r_work=0.1131 r_free=0.1270 | n_water=491 | time (s): 240.020 (total time: 301.090) Filter (q & B) r_work=0.1138 r_free=0.1272 | n_water=450 | time (s): 4.170 (total time: 305.260) Filter (dist only) r_work=0.1138 r_free=0.1272 | n_water=449 | time (s): 47.800 (total time: 353.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.747937 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.121904 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1334 0.0101 0.003 0.7 5.8 0.0 0.0 0 0.087 0.1181 0.1299 0.0118 0.004 0.8 4.8 0.0 0.0 0 0.262 0.1159 0.1286 0.0127 0.005 0.9 4.5 0.5 0.0 0 0.524 0.1152 0.1282 0.0130 0.006 1.0 4.5 0.5 0.0 0 0.787 0.1143 0.1275 0.0132 0.006 1.1 4.2 0.5 0.0 0 1.049 0.1139 0.1272 0.0134 0.007 1.1 3.8 0.5 0.0 0 1.311 0.1137 0.1271 0.0134 0.008 1.1 3.8 0.5 0.0 0 1.573 0.1136 0.1271 0.0135 0.008 1.1 3.8 0.5 0.0 0 1.835 0.1147 0.1278 0.0131 0.006 1.0 4.2 0.5 0.0 0 0.874 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1136 0.1271 0.0135 0.008 1.1 3.8 0.5 0.0 0 1.835 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.36 12.71 1.35 3.754 21.198 36.122 3.601 11.36 12.71 1.35 3.754 21.198 1.084 3.601 11.36 12.71 1.35 3.754 21.198 4.515 3.601 11.39 12.75 1.36 3.691 21.191 18.061 3.597 11.38 12.80 1.42 3.709 21.179 36.122 3.595 11.41 12.87 1.46 3.733 21.151 54.183 3.597 11.34 12.82 1.48 3.751 21.147 72.244 3.590 11.31 12.81 1.50 3.762 21.145 90.305 3.588 11.27 12.77 1.50 3.768 21.146 108.366 3.585 11.25 12.76 1.51 3.778 21.143 126.427 3.583 11.27 12.82 1.56 3.802 21.127 144.488 3.584 11.26 12.83 1.57 3.813 21.122 162.549 3.584 11.23 12.79 1.56 3.815 21.126 180.610 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.084 Accepted refinement result: 11.36 12.71 1.35 3.754 21.198 1.084 3.601 Individual atomic B min max mean iso aniso Overall: 9.11 114.78 21.13 3.26 225 1751 Protein: 9.11 114.78 17.02 3.26 0 1519 Water: 11.51 76.66 35.03 N/A 225 224 Other: 19.74 26.58 22.09 N/A 0 8 Chain A: 9.11 114.78 19.43 N/A 0 1751 Chain S: 12.77 59.99 34.37 N/A 225 0 Histogram: Values Number of atoms 9.11 - 19.67 1262 19.67 - 30.24 304 30.24 - 40.81 213 40.81 - 51.38 126 51.38 - 61.94 48 61.94 - 72.51 11 72.51 - 83.08 6 83.08 - 93.64 4 93.64 - 104.21 0 104.21 - 114.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1136 r_free=0.1271 r_work=0.1136 r_free=0.1271 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1136 r_free = 0.1271 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1268 target_work(ml) = 3.599 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1268 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.599074 | | target function (ml) not normalized (work): 299738.098026 | | target function (ml) not normalized (free): 15772.346065 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2920 171 0.1350 0.1284 5.6696 5.5732| | 2: 3.57 - 2.84 1.00 2888 124 0.1057 0.1332 5.1454 5.1883| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1210 4.9252 4.9508| | 4: 2.47 - 2.25 1.00 2825 136 0.0892 0.1000 4.6102 4.6369| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0939 4.5559 4.6033| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.0994 4.252 4.3387| | 7: 1.97 - 1.87 1.00 2787 165 0.0875 0.1101 3.9681 4.0802| | 8: 1.87 - 1.79 1.00 2789 144 0.0908 0.1114 3.8792 3.9878| | 9: 1.79 - 1.72 1.00 2745 138 0.0879 0.1195 3.6438 3.828| | 10: 1.72 - 1.66 1.00 2831 160 0.0918 0.1209 3.5591 3.7158| | 11: 1.66 - 1.61 1.00 2712 147 0.0869 0.1008 3.4922 3.5614| | 12: 1.61 - 1.56 1.00 2773 144 0.0906 0.1139 3.3267 3.4461| | 13: 1.56 - 1.52 1.00 2745 130 0.0944 0.1037 3.3048 3.3953| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1066 3.2363 3.3255| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1194 3.1507 3.2549| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1241 3.1319 3.2381| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1268 3.1166 3.2118| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1316 3.0994 3.2324| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1566 3.1077 3.2658| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1462 3.1103 3.1507| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1513 3.1111 3.102| | 22: 1.29 - 1.27 1.00 2704 152 0.1561 0.1977 3.1209 3.2945| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1784 3.1318 3.1972| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1841 3.1269 3.2322| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2158 3.1426 3.2644| | 26: 1.22 - 1.21 1.00 2727 135 0.1911 0.1767 3.1477 3.1999| | 27: 1.21 - 1.19 1.00 2814 148 0.2071 0.2169 3.1694 3.162| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2283 3.1646 3.1672| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2373 3.1457 3.2236| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2441 3.142 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 2920 171 0.95 8.18 1.00 0.98 5413.31| | 2: 3.57 - 2.84 2888 124 0.93 12.10 1.01 0.98 5413.31| | 3: 2.83 - 2.48 2820 163 0.90 16.02 0.99 0.98 4526.26| | 4: 2.47 - 2.25 2825 136 0.92 13.06 1.00 0.99 2238.84| | 5: 2.25 - 2.09 2756 127 0.91 15.19 1.01 0.99 2238.84| | 6: 2.09 - 1.97 2846 113 0.93 12.08 1.02 0.98 1300.61| | 7: 1.97 - 1.87 2787 165 0.95 9.13 1.02 0.98 500.42| | 8: 1.87 - 1.79 2789 144 0.93 12.49 1.00 0.98 500.42| | 9: 1.79 - 1.72 2745 138 0.94 9.96 0.98 0.98 285.60| | 10: 1.72 - 1.66 2831 160 0.94 11.12 0.98 0.98 242.57| | 11: 1.66 - 1.61 2712 147 0.93 11.73 0.98 0.98 232.42| | 12: 1.61 - 1.56 2773 144 0.96 8.84 0.99 0.98 136.62| | 13: 1.56 - 1.52 2745 130 0.95 10.36 1.03 0.98 136.62| | 14: 1.52 - 1.48 2803 134 0.94 10.71 1.02 0.98 122.57| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.99 96.86| | 16: 1.45 - 1.42 2756 161 0.94 11.05 1.02 0.99 96.86| | 17: 1.42 - 1.39 2785 139 0.95 10.86 1.01 0.99 88.11| | 18: 1.39 - 1.36 2741 179 0.94 11.47 1.01 0.99 83.04| | 19: 1.36 - 1.34 2807 134 0.94 11.80 0.99 0.99 83.04| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 79.48| | 21: 1.32 - 1.30 2785 112 0.94 13.06 0.98 0.97 79.23| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.97 79.67| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 81.91| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 81.91| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.95 83.87| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.94 86.04| | 27: 1.21 - 1.19 2814 148 0.89 18.70 1.02 0.94 86.04| | 28: 1.19 - 1.18 2671 147 0.88 20.32 1.01 0.93 89.35| | 29: 1.18 - 1.16 2800 134 0.88 20.40 0.99 0.93 90.60| | 30: 1.16 - 1.15 2739 148 0.86 21.94 0.98 0.93 90.60| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.23 max = 5413.31 mean = 842.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.92 mean = 13.32| |phase err.(test): min = 0.00 max = 89.38 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1268 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1460 0.1460 0.1477 n_refl.: 87578 remove outliers: r(all,work,free)=0.1460 0.1460 0.1477 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1459 0.1459 0.1477 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1132 0.1269 n_refl.: 87578 remove outliers: r(all,work,free)=0.1137 0.1130 0.1269 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 86.46 78 5 0.3973 290.259 246.326 0.423 1.000 0.266 11.894-9.307 95.10 93 4 0.2560 469.373 454.688 0.854 1.002 0.250 9.237-7.194 97.73 208 7 0.2263 387.599 378.443 0.923 1.002 0.159 7.162-5.571 100.00 427 22 0.2161 295.971 284.937 0.907 1.002 0.130 5.546-4.326 100.00 867 58 0.1147 406.295 401.954 0.965 1.002 0.120 4.315-3.360 100.00 1859 96 0.0922 386.389 383.949 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1100 253.838 252.093 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0904 168.271 167.740 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.175 82.552 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.440 36.059 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.960 21.518 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=-0.0161 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2608 0.1951 0.080 5.304 8.8 119.3 19.9 258 0.000 1_bss: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_settarget: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_nqh: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_weight: 0.1629 0.1770 0.080 5.304 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1221 0.1461 0.007 0.942 9.0 119.5 20.1 258 0.133 1_adp: 0.1229 0.1460 0.007 0.942 9.1 119.4 20.1 258 0.133 1_regHadp: 0.1231 0.1463 0.007 0.942 9.1 119.4 20.1 258 0.133 1_occ: 0.1224 0.1457 0.007 0.942 9.1 119.4 20.1 258 0.133 2_bss: 0.1223 0.1453 0.007 0.942 9.1 119.5 20.1 258 0.133 2_settarget: 0.1223 0.1453 0.007 0.942 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1223 0.1453 0.007 0.962 9.1 119.5 20.1 258 0.133 2_nqh: 0.1225 0.1454 0.007 0.962 9.1 119.5 20.1 258 0.136 2_sol: 0.1197 0.1403 0.007 0.962 9.1 114.9 22.2 420 n/a 2_weight: 0.1197 0.1403 0.007 0.962 9.1 114.9 22.2 420 n/a 2_xyzrec: 0.1188 0.1416 0.007 0.925 9.1 114.9 22.2 420 n/a 2_adp: 0.1188 0.1416 0.007 0.925 9.1 114.9 22.2 420 n/a 2_regHadp: 0.1188 0.1416 0.007 0.925 9.1 114.9 22.2 420 n/a 2_occ: 0.1186 0.1411 0.007 0.925 9.1 114.9 22.2 420 n/a 3_bss: 0.1181 0.1406 0.007 0.925 9.1 114.9 22.2 420 n/a 3_settarget: 0.1181 0.1406 0.007 0.925 9.1 114.9 22.2 420 n/a 3_updatecdl: 0.1181 0.1406 0.007 0.924 9.1 114.9 22.2 420 n/a 3_nqh: 0.1182 0.1406 0.007 0.924 9.1 114.9 22.2 420 n/a 3_sol: 0.1202 0.1404 0.007 0.924 9.1 114.9 21.2 432 n/a 3_weight: 0.1202 0.1404 0.007 0.924 9.1 114.9 21.2 432 n/a 3_xyzrec: 0.1151 0.1316 0.008 1.088 9.1 114.9 21.2 432 n/a 3_adp: 0.1151 0.1316 0.008 1.088 9.1 114.9 21.2 432 n/a 3_regHadp: 0.1151 0.1317 0.008 1.088 9.1 114.9 21.2 432 n/a 3_occ: 0.1143 0.1316 0.008 1.088 9.1 114.9 21.2 432 n/a 4_bss: 0.1138 0.1310 0.008 1.088 9.1 114.9 21.2 432 n/a 4_settarget: 0.1138 0.1310 0.008 1.088 9.1 114.9 21.2 432 n/a 4_updatecdl: 0.1138 0.1310 0.008 1.089 9.1 114.9 21.2 432 n/a 4_nqh: 0.1138 0.1310 0.008 1.089 9.1 114.9 21.2 432 n/a 4_sol: 0.1144 0.1293 0.008 1.089 9.1 114.9 21.2 448 n/a 4_weight: 0.1144 0.1293 0.008 1.089 9.1 114.9 21.2 448 n/a 4_xyzrec: 0.1145 0.1295 0.007 1.057 9.1 114.9 21.2 448 n/a 4_adp: 0.1145 0.1295 0.007 1.057 9.1 114.8 21.2 448 n/a 4_regHadp: 0.1145 0.1295 0.007 1.057 9.1 114.8 21.2 448 n/a 4_occ: 0.1141 0.1292 0.007 1.057 9.1 114.8 21.2 448 n/a 5_bss: 0.1136 0.1293 0.007 1.057 9.1 114.8 21.2 448 n/a 5_settarget: 0.1136 0.1293 0.007 1.057 9.1 114.8 21.2 448 n/a 5_updatecdl: 0.1136 0.1293 0.007 1.056 9.1 114.8 21.2 448 n/a 5_setrh: 0.1137 0.1292 0.007 1.056 9.1 114.8 21.2 448 n/a 5_nqh: 0.1137 0.1292 0.007 1.056 9.1 114.8 21.2 448 n/a 5_sol: 0.1138 0.1272 0.007 1.056 9.1 114.8 21.1 449 n/a 5_weight: 0.1138 0.1272 0.007 1.056 9.1 114.8 21.1 449 n/a 5_xyzrec: 0.1136 0.1271 0.008 1.107 9.1 114.8 21.1 449 n/a 5_adp: 0.1136 0.1271 0.008 1.107 9.1 114.8 21.1 449 n/a 5_regHadp: 0.1136 0.1271 0.008 1.107 9.1 114.8 21.1 449 n/a 5_occ: 0.1132 0.1268 0.008 1.107 9.1 114.8 21.1 449 n/a end: 0.1130 0.1269 0.008 1.107 9.1 114.8 21.1 449 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5638674_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_5638674_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.3500 Refinement macro-cycles (run) : 13973.8000 Write final files (write_after_run_outputs) : 82.7400 Total : 14060.8900 Total CPU time: 3.91 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:16:44 PST -0800 (1735366604.97 s) Start R-work = 0.1629, R-free = 0.1770 Final R-work = 0.1130, R-free = 0.1269 =============================================================================== Job complete usr+sys time: 14215.67 seconds wall clock time: 260 minutes 26.99 seconds (15626.99 seconds total)