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_3675081.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3675081.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.53, per 1000 atoms: 0.45 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: 0.36 Conformation dependent library (CDL) restraints added in 122.0 milliseconds Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.91: 511 0.91 - 1.15: 1100 1.15 - 1.38: 528 1.38 - 1.61: 887 1.61 - 1.85: 127 Bond restraints: 3153 Sorted by residual: bond pdb=" N LEU A 7 " pdb=" CA LEU A 7 " ideal model delta sigma weight residual 1.458 1.241 0.217 1.22e-02 6.72e+03 3.16e+02 bond pdb=" CE1 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.321 1.495 -0.174 1.00e-02 1.00e+04 3.04e+02 bond pdb=" C THR A 140 " pdb=" N TYR A 141 " ideal model delta sigma weight residual 1.330 1.091 0.239 1.38e-02 5.25e+03 3.00e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.235 1.430 -0.195 1.22e-02 6.72e+03 2.57e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.440 -0.204 1.29e-02 6.01e+03 2.51e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3249 4.84 - 9.68: 1840 9.68 - 14.51: 603 14.51 - 19.35: 78 19.35 - 24.18: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.95 135.23 -14.28 1.04e+00 9.25e-01 1.89e+02 angle pdb=" O VAL A 20 " pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 121.91 134.83 -12.92 9.80e-01 1.04e+00 1.74e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 136.82 -14.67 1.14e+00 7.69e-01 1.66e+02 angle pdb=" O ILE A 91 " pdb=" C ILE A 91 " pdb=" N LEU A 92 " ideal model delta sigma weight residual 121.87 109.39 12.48 9.70e-01 1.06e+00 1.66e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.61 136.53 -13.92 1.09e+00 8.42e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 949 17.80 - 35.59: 109 35.59 - 53.38: 41 53.38 - 71.18: 8 71.18 - 88.97: 4 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER A 121 " pdb=" C SER A 121 " pdb=" N LYS A 122 " pdb=" CA LYS A 122 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG PHE A 162 " pdb=" CD1 PHE A 162 " pdb=" CE1 PHE A 162 " pdb=" HE1 PHE A 162 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.189: 94 0.189 - 0.375: 57 0.375 - 0.561: 52 0.561 - 0.746: 31 0.746 - 0.932: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CB THR A 160 " pdb=" CA THR A 160 " pdb=" OG1 THR A 160 " pdb=" CG2 THR A 160 " both_signs ideal model delta sigma weight residual False 2.55 1.66 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.86 0.86 2.00e-01 2.50e+01 1.85e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.120 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG ATYR A 67 " -0.016 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.078 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.063 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.041 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.094 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.106 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.162 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.017 2.00e-02 2.50e+03 5.68e-02 9.68e+01 pdb=" CG TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.059 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.052 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 611 2.24 - 2.83: 7538 2.83 - 3.42: 10729 3.42 - 4.01: 15393 4.01 - 4.60: 22343 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.656 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.752 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.768 2.100 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.790 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.816 1.850 ... (remaining 56609 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_3675081_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= 0.2603 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789155 | | target function (ml) not normalized (work): 232353.370935 | | target function (ml) not normalized (free): 11858.993040 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3001 0.2132 7.0136 4.9469| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1822 4.3543 4.3487| | 3: 2.84 - 2.48 1.00 2833 165 0.2375 0.1674 4.1303 4.1674| | 4: 2.47 - 2.25 1.00 2825 136 0.2344 0.1393 3.8369 3.8323| | 5: 2.25 - 2.09 1.00 2756 127 0.2486 0.1503 3.8016 3.8201| | 6: 2.09 - 1.97 1.00 2846 113 0.2548 0.1842 3.4821 3.5635| | 7: 1.97 - 1.87 1.00 2787 165 0.2555 0.1898 3.1325 3.2439| | 8: 1.87 - 1.79 1.00 2789 144 0.2442 0.1845 3.0532 3.1635| | 9: 1.79 - 1.72 1.00 2745 138 0.2405 0.1858 2.9069 2.9737| | 10: 1.72 - 1.66 1.00 2789 158 0.2402 0.2057 2.8192 2.9288| | 11: 1.66 - 1.61 1.00 2740 147 0.2470 0.2012 2.7496 2.7921| | 12: 1.61 - 1.56 1.00 2787 146 0.2524 0.2118 2.6198 2.6834| | 13: 1.56 - 1.52 1.00 2745 130 0.2580 0.1971 2.5905 2.6117| | 14: 1.52 - 1.48 1.00 2803 134 0.2530 0.1948 2.5051 2.5353| | 15: 1.48 - 1.45 1.00 2738 128 0.2551 0.2492 2.4129 2.6088| | 16: 1.45 - 1.42 1.00 2756 161 0.2623 0.2040 2.3876 2.4096| | 17: 1.42 - 1.39 1.00 2785 139 0.2715 0.2225 2.3217 2.4309| | 18: 1.39 - 1.36 1.00 2741 179 0.2702 0.2231 2.271 2.3416| | 19: 1.36 - 1.34 1.00 2807 134 0.2660 0.2048 2.2476 2.1961| | 20: 1.34 - 1.32 1.00 2696 147 0.2654 0.2132 2.1877 2.1832| | 21: 1.32 - 1.30 1.00 2785 112 0.2688 0.2105 2.1392 2.1966| | 22: 1.29 - 1.27 1.00 2704 152 0.2748 0.2524 2.1227 2.1667| | 23: 1.27 - 1.26 1.00 2802 156 0.2733 0.2388 2.1014 2.1327| | 24: 1.26 - 1.24 1.00 2744 132 0.2800 0.2522 2.08 2.1014| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2438 2.0401 2.0665| | 26: 1.22 - 1.21 1.00 2727 135 0.2897 0.2430 2.0291 2.1542| | 27: 1.21 - 1.19 1.00 2814 148 0.2964 0.2783 2.0041 2.0349| | 28: 1.19 - 1.18 1.00 2671 147 0.3020 0.2760 1.988 2.0137| | 29: 1.18 - 1.16 1.00 2800 134 0.2955 0.2652 1.9631 2.0031| | 30: 1.16 - 1.15 1.00 2740 148 0.3043 0.2988 1.9288 2.0182| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.94 0.76 0.23 1487.96| | 2: 3.57 - 2.84 2876 122 0.80 26.25 1.27 0.23 1487.96| | 3: 2.84 - 2.48 2833 165 0.74 32.26 1.24 0.23 1234.68| | 4: 2.47 - 2.25 2825 136 0.81 25.80 1.26 0.25 577.37| | 5: 2.25 - 2.09 2756 127 0.77 29.58 1.28 0.25 577.37| | 6: 2.09 - 1.97 2846 113 0.83 23.03 1.29 0.25 317.68| | 7: 1.97 - 1.87 2787 165 0.89 17.27 1.29 0.25 96.20| | 8: 1.87 - 1.79 2789 144 0.85 21.85 1.25 0.25 96.20| | 9: 1.79 - 1.72 2745 138 0.88 19.13 1.23 0.25 58.82| | 10: 1.72 - 1.66 2789 158 0.86 20.83 1.22 0.25 51.34| | 11: 1.66 - 1.61 2740 147 0.85 22.09 1.24 0.25 49.55| | 12: 1.61 - 1.56 2787 146 0.88 19.01 1.24 0.25 31.40| | 13: 1.56 - 1.52 2745 130 0.86 21.08 1.24 0.25 31.40| | 14: 1.52 - 1.48 2803 134 0.86 21.45 1.23 0.25 27.92| | 15: 1.48 - 1.45 2738 128 0.87 20.45 1.22 0.25 21.55| | 16: 1.45 - 1.42 2756 161 0.85 21.95 1.23 0.25 21.55| | 17: 1.42 - 1.39 2785 139 0.86 21.14 1.24 0.25 17.85| | 18: 1.39 - 1.36 2741 179 0.86 21.22 1.24 0.25 15.71| | 19: 1.36 - 1.34 2807 134 0.85 22.10 1.22 0.25 15.71| | 20: 1.34 - 1.32 2696 147 0.87 20.53 1.21 0.25 12.62| | 21: 1.32 - 1.30 2785 112 0.86 21.68 1.21 0.24 12.40| | 22: 1.29 - 1.27 2704 152 0.86 22.05 1.22 0.24 12.12| | 23: 1.27 - 1.26 2802 156 0.86 21.88 1.20 0.24 10.68| | 24: 1.26 - 1.24 2744 132 0.85 22.40 1.20 0.24 10.68| | 25: 1.24 - 1.22 2734 148 0.85 23.24 1.20 0.23 10.28| | 26: 1.22 - 1.21 2727 135 0.84 24.11 1.20 0.23 9.84| | 27: 1.21 - 1.19 2814 148 0.83 24.98 1.20 0.23 9.84| | 28: 1.19 - 1.18 2671 147 0.82 25.88 1.18 0.23 9.45| | 29: 1.18 - 1.16 2800 134 0.82 26.15 1.16 0.22 9.31| | 30: 1.16 - 1.15 2740 148 0.80 27.82 1.15 0.22 9.31| |alpha: min = 0.22 max = 0.25 mean = 0.24| |beta: min = 9.31 max = 1487.96 mean = 217.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.97 mean = 22.87| |phase err.(test): min = 0.00 max = 89.90 mean = 22.51| |-----------------------------------------------------------------------------| ----------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= 5.357 Angle : 5.301 18.512 2118 Z= 3.705 Chirality : 0.382 0.932 243 Planarity : 0.033 0.090 284 Dihedral : 14.152 88.970 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 34.05 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.51), residues: 224 helix: -2.49 (0.38), residues: 103 sheet: -1.14 (0.76), residues: 28 loop : 0.60 (0.67), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.018 ARG A 28 TYR 0.124 0.036 TYR A 139 PHE 0.096 0.028 PHE A 164 HIS 0.086 0.041 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= 0.2603 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789155 | | target function (ml) not normalized (work): 232353.370935 | | target function (ml) not normalized (free): 11858.993040 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2561 0.2603 0.1962 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2561 0.2603 0.1962 n_refl.: 87602 remove outliers: r(all,work,free)=0.1975 0.1978 0.1962 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2001 0.2005 0.1975 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1640 0.1633 0.1784 n_refl.: 87594 remove outliers: r(all,work,free)=0.1639 0.1632 0.1784 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 0.3775 386.247 359.668 0.666 1.004 0.401 11.894-9.307 99.02 97 4 0.1863 613.535 591.413 0.925 1.004 0.380 9.237-7.194 100.00 213 7 0.2131 501.796 490.799 0.958 1.004 0.354 7.162-5.571 100.00 427 22 0.2189 376.570 364.877 0.933 1.004 0.330 5.546-4.326 100.00 867 58 0.1270 516.938 511.290 0.960 1.004 0.226 4.315-3.360 100.00 1859 96 0.1136 491.611 487.852 1.001 1.003 0.203 3.356-2.611 100.00 3867 181 0.1455 322.963 319.506 0.996 1.002 0.109 2.608-2.026 99.99 8198 413 0.1352 214.095 211.842 1.010 1.000 0.000 2.025-1.573 100.00 17313 902 0.1626 104.553 103.929 1.013 0.998 0.000 1.573-1.221 100.00 36679 1900 0.2057 46.363 45.022 1.006 0.993 0.000 1.221-1.150 99.97 13689 708 0.2606 29.212 26.876 0.978 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1784 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** A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1639 r_free=0.1786 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.099222 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2037.625581 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 0.1767 0.1877 0.0110 0.002 0.4 5.4 0.0 0.0 0 0.125 0.1617 0.1748 0.0130 0.002 0.4 5.1 0.0 0.0 0 0.250 0.1458 0.1621 0.0162 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1388 0.1576 0.0188 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1368 0.1565 0.0197 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1370 0.1572 0.0203 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1295 0.1509 0.0214 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1273 0.1505 0.0232 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1260 0.1490 0.0230 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1249 0.1484 0.0234 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1245 0.1478 0.0233 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1239 0.1473 0.0234 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1237 0.1476 0.0239 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1470 0.0237 0.006 0.9 4.2 0.5 0.0 0 9.000 0.1229 0.1470 0.0241 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1229 0.1472 0.0243 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1229 0.1478 0.0248 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1228 0.1486 0.0258 0.008 1.0 4.2 0.5 0.6 0 13.050 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1232 0.1470 0.0237 0.006 0.9 4.2 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.32 14.70 2.37 3.013 19.072 2037.626 0.017 12.32 14.69 2.36 2.988 19.072 61.129 0.017 12.39 14.67 2.28 2.657 19.072 254.703 0.017 12.70 15.31 2.60 2.738 19.233 1018.813 0.017 12.52 15.45 2.93 3.126 19.519 2037.626 0.016 12.48 15.48 3.01 3.296 19.630 3056.438 0.015 12.37 15.48 3.11 3.394 19.676 4075.251 0.015 12.31 15.49 3.17 3.372 19.663 5094.064 0.015 12.25 15.41 3.16 3.310 19.615 6112.877 0.015 12.18 15.36 3.18 3.396 19.658 7131.690 0.015 12.25 15.54 3.29 3.343 19.608 8150.502 0.015 12.26 15.58 3.32 3.370 19.614 9169.315 0.015 12.17 15.44 3.28 3.416 19.635 10188.128 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: 254.703 Accepted refinement result: 12.39 14.67 2.28 2.657 19.072 254.703 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.10 3.29 0 1785 Protein: 9.07 114.89 17.01 3.29 0 1519 Water: 11.49 119.45 38.24 N/A 0 258 Other: 19.76 26.62 22.08 N/A 0 8 Chain A: 9.07 119.45 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 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 - 75.30 11 75.30 - 86.34 7 86.34 - 97.38 4 97.38 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1467 r_work=0.1240 r_free=0.1469 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1469 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 = 0.1235 r_free = 0.1464 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.16 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= 0.1235 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017013 | | target function (ls_wunit_k1) not normalized (work): 1417.138978 | | target function (ls_wunit_k1) not normalized (free): 111.063100 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1246 0.1235 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1679 0.1680 0.1695 n_refl.: 87593 remove outliers: r(all,work,free)=0.1679 0.1680 0.1695 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1684 0.1685 0.1698 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1233 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1232 0.1454 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3591 300.981 281.492 0.644 1.003 0.380 11.894-9.307 99.02 97 4 0.1696 482.155 469.141 0.920 1.003 0.373 9.237-7.194 100.00 213 7 0.1874 394.343 389.390 0.964 1.003 0.329 7.162-5.571 100.00 427 22 0.1845 295.933 289.785 0.937 1.003 0.268 5.546-4.326 100.00 867 58 0.1024 406.243 402.895 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 386.339 385.213 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1178 253.805 252.633 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1023 168.250 167.549 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1116 82.164 82.362 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1457 36.435 35.935 1.020 0.997 0.000 1.221-1.150 99.97 13689 708 0.2257 22.957 21.440 0.983 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0436 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1454 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** A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1231 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1455 | n_water=258 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1241 r_free=0.1452 | n_water=251 | time (s): 21.660 (total time: 23.900) Filter (q & B) r_work=0.1243 r_free=0.1451 | n_water=248 | time (s): 3.400 (total time: 27.300) Compute maps r_work=0.1243 r_free=0.1451 | n_water=248 | time (s): 1.490 (total time: 28.790) Filter (map) r_work=0.1258 r_free=0.1457 | n_water=224 | time (s): 2.880 (total time: 31.670) Find peaks r_work=0.1258 r_free=0.1457 | n_water=224 | time (s): 0.490 (total time: 32.160) Add new water r_work=0.1407 r_free=0.1617 | n_water=435 | time (s): 3.130 (total time: 35.290) Refine new water occ: r_work=0.1311 r_free=0.1490 adp: r_work=0.1230 r_free=0.1430 occ: r_work=0.1242 r_free=0.1419 adp: r_work=0.1210 r_free=0.1403 occ: r_work=0.1213 r_free=0.1398 adp: r_work=0.1201 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1394 r_work=0.1201 r_free=0.1394 | n_water=435 | time (s): 50.470 (total time: 85.760) Filter (q & B) r_work=0.1204 r_free=0.1397 | n_water=419 | time (s): 2.620 (total time: 88.380) Filter (dist only) r_work=0.1204 r_free=0.1395 | n_water=418 | time (s): 35.190 (total time: 123.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.614488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.994421 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 0.1609 0.1729 0.0120 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1518 0.1654 0.0136 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1419 0.1575 0.0156 0.001 0.4 5.4 0.0 0.0 0 0.500 0.1355 0.1527 0.0172 0.001 0.4 4.5 0.0 0.0 0 0.750 0.1330 0.1513 0.0183 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1330 0.1508 0.0179 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1262 0.1466 0.0204 0.002 0.5 4.2 0.5 0.0 0 2.000 0.1229 0.1449 0.0220 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1214 0.1432 0.0218 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1208 0.1430 0.0222 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1203 0.1428 0.0225 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1200 0.1431 0.0231 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1196 0.1425 0.0230 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1195 0.1430 0.0235 0.006 0.8 4.2 0.5 0.0 0 9.000 0.1192 0.1426 0.0234 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1427 0.0237 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1189 0.1425 0.0236 0.007 0.9 4.2 0.5 0.0 0 12.000 0.1187 0.1424 0.0237 0.008 0.9 4.8 0.5 0.0 0 13.000 0.1185 0.1423 0.0237 0.008 0.9 4.5 0.5 0.0 0 14.307 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1185 0.1423 0.0237 0.008 0.9 4.5 0.5 0.0 0 14.307 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.85 14.23 2.37 3.766 21.802 1485.994 0.016 11.85 14.23 2.37 3.766 21.802 44.580 0.016 11.85 14.23 2.37 3.766 21.802 185.749 0.016 12.05 14.62 2.57 3.633 21.802 742.997 0.015 12.05 15.01 2.97 3.551 21.864 1485.994 0.015 11.93 15.01 3.08 3.482 21.947 2228.992 0.014 11.76 14.87 3.11 3.466 21.986 2971.989 0.014 11.73 14.84 3.10 3.469 22.094 3714.986 0.014 11.71 14.89 3.18 3.478 22.123 4457.983 0.014 11.74 15.03 3.29 3.533 22.300 5200.980 0.014 11.70 15.02 3.33 3.533 22.223 5943.978 0.014 11.64 14.98 3.34 3.525 22.123 6686.975 0.014 11.62 14.92 3.30 3.537 22.167 7429.972 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 44.580 Accepted refinement result: 11.85 14.23 2.37 3.766 21.802 44.580 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 114.92 22.22 3.29 194 1751 Protein: 9.10 114.92 17.04 3.29 0 1519 Water: 11.52 76.68 41.07 N/A 194 224 Other: 19.78 26.65 22.11 N/A 0 8 Chain A: 9.10 114.92 19.43 N/A 0 1751 Chain S: 16.60 60.00 47.40 N/A 194 0 Histogram: Values Number of atoms 9.10 - 19.68 1258 19.68 - 30.26 248 30.26 - 40.84 160 40.84 - 51.43 130 51.43 - 62.01 126 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1423 r_work=0.1185 r_free=0.1423 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1423 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 = 0.1184 r_free = 0.1418 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1184 r_free= 0.1418 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014745 | | target function (ls_wunit_k1) not normalized (work): 1228.222634 | | target function (ls_wunit_k1) not normalized (free): 106.384375 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1184 0.1418 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1581 0.1580 0.1627 n_refl.: 87592 remove outliers: r(all,work,free)=0.1581 0.1580 0.1627 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1581 0.1581 0.1628 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1180 0.1410 n_refl.: 87592 remove outliers: r(all,work,free)=0.1191 0.1180 0.1410 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 0.3408 302.983 274.243 0.593 1.003 0.350 11.894-9.307 99.02 97 4 0.1570 482.155 476.975 0.926 1.003 0.350 9.237-7.194 100.00 213 7 0.1624 394.343 395.806 0.993 1.003 0.264 7.162-5.571 100.00 427 22 0.1548 295.933 291.895 0.936 1.003 0.229 5.546-4.326 100.00 867 58 0.0882 406.243 403.122 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0773 386.339 385.653 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1076 253.805 253.039 1.010 1.002 0.057 2.608-2.026 99.99 8198 413 0.1014 168.250 167.659 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1095 82.164 82.374 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.435 35.970 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 22.957 21.469 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0066 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1180 r_free=0.1410 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1180 r_free=0.1410 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1410 | n_water=418 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1179 r_free=0.1406 | n_water=415 | time (s): 37.080 (total time: 39.330) Filter (q & B) r_work=0.1179 r_free=0.1406 | n_water=415 | time (s): 0.940 (total time: 40.270) Compute maps r_work=0.1179 r_free=0.1406 | n_water=415 | time (s): 1.660 (total time: 41.930) Filter (map) r_work=0.1217 r_free=0.1395 | n_water=286 | time (s): 3.290 (total time: 45.220) Find peaks r_work=0.1217 r_free=0.1395 | n_water=286 | time (s): 0.690 (total time: 45.910) Add new water r_work=0.1338 r_free=0.1544 | n_water=466 | time (s): 2.740 (total time: 48.650) Refine new water occ: r_work=0.1248 r_free=0.1451 adp: r_work=0.1250 r_free=0.1453 occ: r_work=0.1225 r_free=0.1426 adp: r_work=0.1225 r_free=0.1427 occ: r_work=0.1207 r_free=0.1399 adp: r_work=0.1203 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1399 r_work=0.1203 r_free=0.1399 | n_water=466 | time (s): 163.280 (total time: 211.930) Filter (q & B) r_work=0.1207 r_free=0.1408 | n_water=438 | time (s): 3.110 (total time: 215.040) Filter (dist only) r_work=0.1207 r_free=0.1406 | n_water=437 | time (s): 36.390 (total time: 251.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.716802 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 35.464439 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 0.1239 0.1374 0.0135 0.002 0.6 4.8 0.5 0.0 0 0.086 0.1196 0.1342 0.0146 0.003 0.7 3.8 0.5 0.0 0 0.258 0.1178 0.1330 0.0152 0.004 0.8 3.2 0.5 0.0 0 0.515 0.1170 0.1328 0.0158 0.005 0.9 2.9 0.5 0.0 0 0.773 0.1166 0.1328 0.0163 0.006 1.0 2.9 0.5 0.0 0 1.030 0.1163 0.1328 0.0165 0.006 1.0 2.9 0.5 0.0 0 1.288 0.1160 0.1326 0.0166 0.007 1.0 3.5 0.5 0.0 0 1.545 0.1159 0.1327 0.0168 0.008 1.1 3.5 0.5 0.0 0 1.803 0.1169 0.1329 0.0160 0.005 0.9 2.9 0.5 0.0 0 0.858 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1160 0.1326 0.0166 0.007 1.0 3.5 0.5 0.0 0 1.545 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.60 13.26 1.66 3.769 21.230 35.464 3.623 11.60 13.26 1.66 3.769 21.230 1.064 3.623 11.60 13.26 1.66 3.769 21.230 4.433 3.623 11.66 13.31 1.65 3.699 21.222 17.732 3.618 11.68 13.38 1.70 3.721 21.201 35.464 3.617 11.67 13.40 1.73 3.736 21.178 53.197 3.615 11.61 13.38 1.77 3.751 21.170 70.929 3.610 11.55 13.33 1.78 3.764 21.171 88.661 3.606 11.55 13.35 1.80 3.774 21.161 106.393 3.604 11.51 13.32 1.81 3.781 21.162 124.126 3.602 11.51 13.36 1.84 3.798 21.149 141.858 3.602 11.51 13.36 1.85 3.808 21.142 159.590 3.601 11.48 13.32 1.85 3.812 21.143 177.322 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.064 Accepted refinement result: 11.60 13.26 1.66 3.769 21.230 1.064 3.623 Individual atomic B min max mean iso aniso Overall: 9.10 114.92 21.17 3.29 218 1746 Protein: 9.10 114.92 17.04 3.29 0 1519 Water: 11.52 76.69 35.52 N/A 218 219 Other: 19.79 26.65 22.12 N/A 0 8 Chain A: 9.10 114.92 19.34 N/A 0 1746 Chain S: 15.90 60.00 35.85 N/A 218 0 Histogram: Values Number of atoms 9.10 - 19.68 1260 19.68 - 30.27 297 30.27 - 40.85 202 40.85 - 51.43 124 51.43 - 62.01 58 62.01 - 72.59 11 72.59 - 83.18 6 83.18 - 93.76 4 93.76 - 104.34 0 104.34 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1326 r_work=0.1160 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1326 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1311 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1150 r_free= 0.1311 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615269 | | target function (ml) not normalized (work): 301133.790353 | | target function (ml) not normalized (free): 15847.733854 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1150 0.1311 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1489 0.1488 0.1527 n_refl.: 87591 remove outliers: r(all,work,free)=0.1489 0.1488 0.1527 n_refl.: 87591 overall B=-0.01 to atoms: r(all,work,free)=0.1487 0.1487 0.1526 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1304 n_refl.: 87591 remove outliers: r(all,work,free)=0.1151 0.1143 0.1304 n_refl.: 87582 ======================== 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 0.3985 299.502 267.171 0.496 1.000 0.320 11.894-9.307 97.06 95 4 0.2225 482.379 463.072 0.878 1.002 0.281 9.237-7.194 98.18 209 7 0.2213 385.829 386.171 0.959 1.002 0.207 7.162-5.571 100.00 427 22 0.2010 295.933 287.124 0.922 1.002 0.174 5.546-4.326 100.00 867 58 0.1114 406.243 401.508 0.967 1.002 0.170 4.315-3.360 100.00 1859 96 0.0938 386.339 384.198 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1136 253.805 251.697 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0934 168.250 167.482 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0902 82.164 82.451 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1262 36.435 36.020 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.957 21.499 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1304 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=0.1143 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1304 | n_water=437 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1143 r_free=0.1305 | n_water=435 | time (s): 43.750 (total time: 46.130) Filter (q & B) r_work=0.1144 r_free=0.1305 | n_water=434 | time (s): 3.750 (total time: 49.880) Compute maps r_work=0.1144 r_free=0.1305 | n_water=434 | time (s): 1.790 (total time: 51.670) Filter (map) r_work=0.1168 r_free=0.1302 | n_water=325 | time (s): 3.780 (total time: 55.450) Find peaks r_work=0.1168 r_free=0.1302 | n_water=325 | time (s): 0.650 (total time: 56.100) Add new water r_work=0.1233 r_free=0.1377 | n_water=469 | time (s): 3.310 (total time: 59.410) Refine new water occ: r_work=0.1170 r_free=0.1325 adp: r_work=0.1170 r_free=0.1327 occ: r_work=0.1155 r_free=0.1308 adp: r_work=0.1154 r_free=0.1310 occ: r_work=0.1143 r_free=0.1292 adp: r_work=0.1140 r_free=0.1293 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1293 r_work=0.1140 r_free=0.1293 | n_water=469 | time (s): 203.590 (total time: 263.000) Filter (q & B) r_work=0.1145 r_free=0.1295 | n_water=443 | time (s): 3.990 (total time: 266.990) Filter (dist only) r_work=0.1151 r_free=0.1295 | n_water=441 | time (s): 45.330 (total time: 312.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.759958 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.277041 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 0.1214 0.1338 0.0124 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1177 0.1312 0.0135 0.003 0.7 3.2 0.5 0.0 0 0.264 0.1162 0.1304 0.0142 0.005 0.9 3.5 0.5 0.0 0 0.528 0.1156 0.1300 0.0144 0.006 0.9 3.8 0.5 0.0 0 0.792 0.1152 0.1301 0.0148 0.006 1.0 3.5 0.5 0.0 0 1.056 0.1149 0.1300 0.0150 0.007 1.0 3.5 0.5 0.0 0 1.320 0.1147 0.1299 0.0152 0.008 1.1 3.5 0.5 0.0 0 1.584 0.1146 0.1296 0.0150 0.008 1.1 3.5 0.5 0.0 0 1.848 0.1155 0.1301 0.0146 0.006 1.0 3.5 0.5 0.0 0 0.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1296 0.0150 0.008 1.1 3.5 0.5 0.0 0 1.848 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 12.96 1.50 3.769 21.149 42.277 3.609 11.46 12.96 1.50 3.769 21.149 1.268 3.609 11.46 12.96 1.50 3.769 21.149 5.285 3.609 11.48 12.99 1.51 3.704 21.140 21.139 3.602 11.56 13.14 1.59 3.727 21.110 42.277 3.606 11.47 13.11 1.64 3.750 21.102 63.416 3.599 11.41 13.06 1.65 3.764 21.100 84.554 3.594 11.38 13.04 1.66 3.773 21.098 105.693 3.591 11.37 13.04 1.67 3.787 21.088 126.831 3.590 11.37 13.06 1.69 3.804 21.078 147.970 3.590 11.35 13.04 1.70 3.811 21.078 169.108 3.588 11.34 13.02 1.68 3.819 21.074 190.247 3.587 11.34 13.03 1.69 3.829 21.072 211.385 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: 1.268 Accepted refinement result: 11.46 12.96 1.50 3.769 21.149 1.268 3.609 Individual atomic B min max mean iso aniso Overall: 9.10 114.92 21.03 3.29 223 1745 Protein: 9.10 114.92 17.03 3.29 0 1519 Water: 11.51 76.68 34.79 N/A 223 218 Other: 19.78 26.65 22.11 N/A 0 8 Chain A: 9.10 114.92 19.33 N/A 0 1745 Chain S: 16.56 60.00 34.35 N/A 223 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 311 30.26 - 40.84 206 40.84 - 51.42 116 51.42 - 62.01 50 62.01 - 72.59 11 72.59 - 83.17 6 83.17 - 93.75 4 93.75 - 104.33 0 104.33 - 114.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1296 r_work=0.1146 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1296 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1141 r_free = 0.1291 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1141 r_free= 0.1291 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605233 | | target function (ml) not normalized (work): 300265.405660 | | target function (ml) not normalized (free): 15811.936863 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1141 0.1291 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1477 0.1478 0.1497 n_refl.: 87582 remove outliers: r(all,work,free)=0.1477 0.1478 0.1497 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1476 0.1477 0.1497 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1139 0.1290 n_refl.: 87582 remove outliers: r(all,work,free)=0.1145 0.1138 0.1290 n_refl.: 87579 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3818 301.765 259.102 0.482 0.999 0.322 11.894-9.307 96.08 94 4 0.2352 475.529 467.192 0.875 1.002 0.238 9.237-7.194 97.73 208 7 0.2312 385.350 380.740 0.931 1.002 0.170 7.162-5.571 100.00 427 22 0.2078 295.933 286.498 0.916 1.002 0.160 5.546-4.326 100.00 867 58 0.1170 406.243 400.955 0.964 1.002 0.140 4.315-3.360 100.00 1859 96 0.0935 386.339 384.238 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1125 253.805 252.000 1.009 1.002 0.019 2.608-2.026 99.99 8198 413 0.0922 168.250 167.577 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.164 82.502 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.435 36.045 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.957 21.510 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1138 r_free=0.1290 After: r_work=0.1139 r_free=0.1290 ================================== NQH flips ================================== r_work=0.1139 r_free=0.1290 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=0.1139 r_free=0.1290 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1139 r_free=0.1290 | n_water=441 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1139 r_free=0.1290 | n_water=441 | time (s): 44.070 (total time: 46.390) Filter (q & B) r_work=0.1141 r_free=0.1289 | n_water=438 | time (s): 3.500 (total time: 49.890) Compute maps r_work=0.1141 r_free=0.1289 | n_water=438 | time (s): 1.660 (total time: 51.550) Filter (map) r_work=0.1175 r_free=0.1316 | n_water=345 | time (s): 3.690 (total time: 55.240) Find peaks r_work=0.1175 r_free=0.1316 | n_water=345 | time (s): 0.700 (total time: 55.940) Add new water r_work=0.1228 r_free=0.1365 | n_water=493 | time (s): 3.620 (total time: 59.560) Refine new water occ: r_work=0.1159 r_free=0.1295 adp: r_work=0.1159 r_free=0.1297 occ: r_work=0.1146 r_free=0.1283 adp: r_work=0.1145 r_free=0.1284 occ: r_work=0.1137 r_free=0.1278 adp: r_work=0.1134 r_free=0.1277 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1277 r_work=0.1134 r_free=0.1277 | n_water=493 | time (s): 233.200 (total time: 292.760) Filter (q & B) r_work=0.1141 r_free=0.1284 | n_water=457 | time (s): 3.980 (total time: 296.740) Filter (dist only) r_work=0.1141 r_free=0.1285 | n_water=455 | time (s): 47.490 (total time: 344.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.800800 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.671408 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 0.1223 0.1340 0.0116 0.004 0.7 6.1 0.0 0.0 0 0.090 0.1182 0.1312 0.0129 0.004 0.8 5.8 0.0 0.0 0 0.270 0.1159 0.1296 0.0136 0.005 0.9 4.8 0.5 0.0 0 0.540 0.1151 0.1289 0.0138 0.006 1.0 4.5 0.5 0.0 0 0.810 0.1147 0.1287 0.0140 0.006 1.1 4.5 0.5 0.0 0 1.080 0.1143 0.1285 0.0141 0.008 1.1 4.5 0.5 0.0 0 1.351 0.1142 0.1284 0.0143 0.008 1.1 4.2 0.5 0.0 0 1.621 0.1141 0.1284 0.0143 0.009 1.1 4.5 0.5 0.0 0 1.891 0.1149 0.1288 0.0139 0.006 1.0 4.5 0.5 0.0 0 0.900 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1141 0.1284 0.0143 0.009 1.1 4.5 0.5 0.0 0 1.891 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.41 12.84 1.43 3.768 21.197 37.671 3.604 11.41 12.84 1.43 3.768 21.197 1.130 3.604 11.41 12.84 1.43 3.768 21.197 4.709 3.604 11.44 12.84 1.40 3.703 21.189 18.836 3.599 11.54 13.01 1.47 3.718 21.162 37.671 3.605 11.46 12.98 1.52 3.745 21.150 56.507 3.599 11.39 12.94 1.55 3.761 21.146 75.343 3.593 11.35 12.90 1.56 3.770 21.147 94.179 3.589 11.35 12.91 1.57 3.783 21.139 113.014 3.588 11.31 12.89 1.58 3.789 21.140 131.850 3.586 11.32 12.92 1.61 3.804 21.132 150.686 3.586 11.33 12.97 1.64 3.823 21.121 169.521 3.586 11.30 12.93 1.63 3.825 21.123 188.357 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: 1.130 Accepted refinement result: 11.41 12.84 1.43 3.768 21.197 1.130 3.604 Individual atomic B min max mean iso aniso Overall: 9.09 114.91 21.12 3.29 238 1744 Protein: 9.09 114.91 17.03 3.29 0 1519 Water: 11.51 76.67 34.79 N/A 238 217 Other: 19.78 26.64 22.10 N/A 0 8 Chain A: 9.09 114.91 19.32 N/A 0 1744 Chain S: 14.98 59.99 34.31 N/A 238 0 Histogram: Values Number of atoms 9.09 - 19.67 1261 19.67 - 30.25 312 30.25 - 40.84 208 40.84 - 51.42 133 51.42 - 62.00 45 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.75 4 93.75 - 104.33 0 104.33 - 114.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1141 r_free=0.1284 r_work=0.1141 r_free=0.1284 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1141 r_free = 0.1284 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1281 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1135 r_free= 0.1281 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602512 | | target function (ml) not normalized (work): 300028.002526 | | target function (ml) not normalized (free): 15795.358803 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1336 0.1375 5.6369 5.6441| | 2: 3.57 - 2.84 1.00 2888 124 0.1081 0.1320 5.1736 5.1964| | 3: 2.83 - 2.48 1.00 2820 163 0.1107 0.1207 4.9516 4.9865| | 4: 2.47 - 2.25 1.00 2825 136 0.0906 0.0973 4.6375 4.6669| | 5: 2.25 - 2.09 1.00 2756 127 0.0864 0.0944 4.5814 4.6292| | 6: 2.09 - 1.97 1.00 2846 113 0.0848 0.1012 4.2656 4.3651| | 7: 1.97 - 1.87 1.00 2787 165 0.0874 0.1088 3.9677 4.078| | 8: 1.87 - 1.79 1.00 2789 144 0.0917 0.1075 3.8841 3.9759| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1122 3.6379 3.7816| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1207 3.5577 3.7264| | 11: 1.66 - 1.61 1.00 2712 147 0.0875 0.1016 3.4924 3.5553| | 12: 1.61 - 1.56 1.00 2773 144 0.0907 0.1179 3.3282 3.4714| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1022 3.3044 3.3825| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1037 3.2387 3.3186| | 15: 1.48 - 1.45 1.00 2738 128 0.0997 0.1196 3.1501 3.2465| | 16: 1.45 - 1.42 1.00 2756 161 0.1051 0.1263 3.133 3.2447| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1293 3.1175 3.2309| | 18: 1.39 - 1.36 1.00 2741 179 0.1205 0.1313 3.1055 3.2355| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1578 3.1094 3.2683| | 20: 1.34 - 1.32 1.00 2696 147 0.1365 0.1439 3.1086 3.1431| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1506 3.112 3.1026| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1990 3.122 3.296| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1800 3.132 3.201| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1830 3.1272 3.2211| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2134 3.142 3.2542| | 26: 1.22 - 1.21 1.00 2727 135 0.1907 0.1764 3.1475 3.1959| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2176 3.1701 3.1629| | 28: 1.19 - 1.18 1.00 2671 147 0.2206 0.2274 3.1659 3.1668| | 29: 1.18 - 1.16 1.00 2800 134 0.2268 0.2386 3.147 3.2291| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2437 3.142 3.1634| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2921 171 0.95 8.67 1.00 0.96 5885.72| | 2: 3.57 - 2.84 2888 124 0.93 12.75 1.01 0.96 5885.72| | 3: 2.83 - 2.48 2820 163 0.89 16.75 0.99 0.97 4910.24| | 4: 2.47 - 2.25 2825 136 0.92 13.59 1.00 0.98 2394.80| | 5: 2.25 - 2.09 2756 127 0.90 15.77 1.01 0.98 2394.80| | 6: 2.09 - 1.97 2846 113 0.92 12.34 1.02 0.98 1371.46| | 7: 1.97 - 1.87 2787 165 0.95 9.12 1.02 0.97 498.69| | 8: 1.87 - 1.79 2789 144 0.93 12.40 1.00 0.97 498.69| | 9: 1.79 - 1.72 2745 138 0.94 9.93 0.98 0.97 283.01| | 10: 1.72 - 1.66 2831 160 0.94 11.00 0.98 0.97 239.82| | 11: 1.66 - 1.61 2712 147 0.94 11.61 0.98 0.97 229.89| | 12: 1.61 - 1.56 2773 144 0.95 8.86 0.99 0.97 136.26| | 13: 1.56 - 1.52 2745 130 0.95 10.31 1.03 0.97 136.26| | 14: 1.52 - 1.48 2803 134 0.94 10.69 1.02 0.98 122.31| | 15: 1.48 - 1.45 2738 128 0.95 9.83 1.02 0.98 96.77| | 16: 1.45 - 1.42 2756 161 0.94 11.01 1.02 0.98 96.77| | 17: 1.42 - 1.39 2785 139 0.95 10.88 1.01 0.98 88.32| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.44| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.98 83.44| | 20: 1.34 - 1.32 2696 147 0.94 12.07 0.98 0.96 79.53| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.25| | 22: 1.29 - 1.27 2704 152 0.93 13.63 0.98 0.96 79.66| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.94 81.75| | 24: 1.26 - 1.24 2744 132 0.93 14.82 0.96 0.94 81.75| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 83.65| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.02 0.93 85.74| | 27: 1.21 - 1.19 2814 148 0.89 18.71 1.02 0.93 85.74| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.92 89.37| | 29: 1.18 - 1.16 2800 134 0.88 20.45 0.99 0.92 90.73| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.73| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.25 max = 5885.72 mean = 901.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.83 mean = 13.42| |phase err.(test): min = 0.00 max = 89.56 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1135 0.1281 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1455 0.1454 0.1485 n_refl.: 87579 remove outliers: r(all,work,free)=0.1455 0.1454 0.1485 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1454 0.1454 0.1484 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1142 0.1135 0.1281 n_refl.: 87579 remove outliers: r(all,work,free)=0.1142 0.1135 0.1281 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.4029 296.253 258.859 0.470 0.999 0.312 11.894-9.307 95.10 93 4 0.2395 469.313 456.883 0.856 1.002 0.228 9.237-7.194 97.73 208 7 0.2266 385.350 379.719 0.929 1.002 0.160 7.162-5.571 100.00 427 22 0.2080 295.933 286.936 0.912 1.002 0.140 5.546-4.326 100.00 867 58 0.1154 406.243 401.106 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0935 386.339 384.197 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1117 253.805 251.822 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0912 168.250 167.544 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.164 82.489 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.435 36.036 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.957 21.501 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0132 ================= 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 : 0.2603 0.1962 0.083 5.301 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1784 0.083 5.301 9.1 119.5 20.1 258 0.000 1_settarget: 0.1632 0.1784 0.083 5.301 9.1 119.5 20.1 258 0.000 1_nqh: 0.1639 0.1786 0.083 5.301 9.1 119.5 20.1 258 0.003 1_weight: 0.1639 0.1786 0.083 5.301 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1232 0.1470 0.006 0.852 9.1 119.5 20.1 258 0.135 1_adp: 0.1239 0.1467 0.006 0.852 9.1 119.5 20.1 258 0.135 1_regHadp: 0.1240 0.1469 0.006 0.852 9.1 119.5 20.1 258 0.135 1_occ: 0.1235 0.1464 0.006 0.852 9.1 119.5 20.1 258 0.135 2_bss: 0.1232 0.1454 0.006 0.852 9.1 119.5 20.1 258 0.135 2_settarget: 0.1232 0.1454 0.006 0.852 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1232 0.1454 0.006 0.863 9.1 119.5 20.1 258 0.135 2_nqh: 0.1231 0.1455 0.006 0.863 9.1 119.5 20.1 258 0.135 2_sol: 0.1204 0.1395 0.006 0.863 9.1 114.9 22.2 418 n/a 2_weight: 0.1204 0.1395 0.006 0.863 9.1 114.9 22.2 418 n/a 2_xyzrec: 0.1185 0.1423 0.008 0.944 9.1 114.9 22.2 418 n/a 2_adp: 0.1185 0.1423 0.008 0.944 9.1 114.9 22.2 418 n/a 2_regHadp: 0.1185 0.1423 0.008 0.944 9.1 114.9 22.2 418 n/a 2_occ: 0.1184 0.1418 0.008 0.944 9.1 114.9 22.2 418 n/a 3_bss: 0.1180 0.1410 0.008 0.944 9.1 114.9 22.2 418 n/a 3_settarget: 0.1180 0.1410 0.008 0.944 9.1 114.9 22.2 418 n/a 3_updatecdl: 0.1180 0.1410 0.008 0.947 9.1 114.9 22.2 418 n/a 3_nqh: 0.1180 0.1410 0.008 0.947 9.1 114.9 22.2 418 n/a 3_sol: 0.1207 0.1406 0.008 0.947 9.1 114.9 21.2 437 n/a 3_weight: 0.1207 0.1406 0.008 0.947 9.1 114.9 21.2 437 n/a 3_xyzrec: 0.1160 0.1326 0.007 1.049 9.1 114.9 21.2 437 n/a 3_adp: 0.1160 0.1326 0.007 1.049 9.1 114.9 21.2 437 n/a 3_regHadp: 0.1160 0.1326 0.007 1.049 9.1 114.9 21.2 437 n/a 3_occ: 0.1150 0.1311 0.007 1.049 9.1 114.9 21.2 437 n/a 4_bss: 0.1143 0.1304 0.007 1.049 9.1 114.9 21.2 437 n/a 4_settarget: 0.1143 0.1304 0.007 1.049 9.1 114.9 21.2 437 n/a 4_updatecdl: 0.1143 0.1304 0.007 1.050 9.1 114.9 21.2 437 n/a 4_nqh: 0.1143 0.1304 0.007 1.050 9.1 114.9 21.2 437 n/a 4_sol: 0.1151 0.1295 0.007 1.050 9.1 114.9 21.0 441 n/a 4_weight: 0.1151 0.1295 0.007 1.050 9.1 114.9 21.0 441 n/a 4_xyzrec: 0.1146 0.1296 0.008 1.118 9.1 114.9 21.0 441 n/a 4_adp: 0.1146 0.1296 0.008 1.118 9.1 114.9 21.0 441 n/a 4_regHadp: 0.1146 0.1296 0.008 1.118 9.1 114.9 21.0 441 n/a 4_occ: 0.1141 0.1291 0.008 1.118 9.1 114.9 21.0 441 n/a 5_bss: 0.1138 0.1290 0.008 1.118 9.1 114.9 21.0 441 n/a 5_settarget: 0.1138 0.1290 0.008 1.118 9.1 114.9 21.0 441 n/a 5_updatecdl: 0.1138 0.1290 0.008 1.119 9.1 114.9 21.0 441 n/a 5_setrh: 0.1139 0.1290 0.008 1.119 9.1 114.9 21.0 441 n/a 5_nqh: 0.1139 0.1290 0.008 1.119 9.1 114.9 21.0 441 n/a 5_sol: 0.1141 0.1285 0.008 1.119 9.1 114.9 21.1 455 n/a 5_weight: 0.1141 0.1285 0.008 1.119 9.1 114.9 21.1 455 n/a 5_xyzrec: 0.1141 0.1284 0.009 1.139 9.1 114.9 21.1 455 n/a 5_adp: 0.1141 0.1284 0.009 1.139 9.1 114.9 21.1 455 n/a 5_regHadp: 0.1141 0.1284 0.009 1.139 9.1 114.9 21.1 455 n/a 5_occ: 0.1135 0.1281 0.009 1.139 9.1 114.9 21.1 455 n/a end: 0.1135 0.1281 0.009 1.139 9.1 114.9 21.1 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3675081_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_3675081_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7000 Refinement macro-cycles (run) : 13250.2200 Write final files (write_after_run_outputs) : 90.2600 Total : 13344.1800 Total CPU time: 3.71 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:00:39 PST -0800 (1735365639.25 s) Start R-work = 0.1632, R-free = 0.1784 Final R-work = 0.1135, R-free = 0.1281 =============================================================================== Job complete usr+sys time: 13519.16 seconds wall clock time: 244 minutes 58.57 seconds (14698.57 seconds total)