Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3867824.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } 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 } ordered_solvent { low_resolution = 4 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 } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 4 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: 1.49, per 1000 atoms: 0.44 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 140.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 354 0.88 - 1.13: 1246 1.13 - 1.39: 558 1.39 - 1.64: 924 1.64 - 1.90: 71 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.418 -0.174 9.50e-03 1.11e+04 3.37e+02 bond pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 1.513 1.700 -0.187 1.06e-02 8.90e+03 3.11e+02 bond pdb=" N ALA A 167 " pdb=" CA ALA A 167 " ideal model delta sigma weight residual 1.459 1.246 0.214 1.23e-02 6.61e+03 3.02e+02 bond pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 1.471 1.694 -0.223 1.32e-02 5.74e+03 2.86e+02 bond pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 1.323 1.560 -0.237 1.40e-02 5.10e+03 2.86e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.20: 3866 6.20 - 12.39: 1644 12.39 - 18.58: 249 18.58 - 24.77: 15 24.77 - 30.96: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH2 ARG A 156 " ideal model delta sigma weight residual 119.20 134.60 -15.40 9.00e-01 1.23e+00 2.93e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.87 136.74 -14.87 9.70e-01 1.06e+00 2.35e+02 angle pdb=" O PRO A 43 " pdb=" C PRO A 43 " pdb=" N VAL A 44 " ideal model delta sigma weight residual 122.91 138.98 -16.07 1.21e+00 6.83e-01 1.76e+02 angle pdb=" O GLN A 95 " pdb=" C GLN A 95 " pdb=" N AGLU A 96 " ideal model delta sigma weight residual 122.07 135.69 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 108.30 13.20 1.00e+00 1.00e+00 1.74e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.31: 1291 16.31 - 32.61: 133 32.61 - 48.91: 35 48.91 - 65.21: 18 65.21 - 81.51: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C SER A 161 " pdb=" N SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta harmonic sigma weight residual -122.60 -145.51 22.91 0 2.50e+00 1.60e-01 8.40e+01 dihedral pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CA BASN A 97 " pdb=" CB BASN A 97 " ideal model delta harmonic sigma weight residual 122.80 143.75 -20.95 0 2.50e+00 1.60e-01 7.02e+01 dihedral pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CA SER A 161 " pdb=" CB SER A 161 " ideal model delta harmonic sigma weight residual 122.80 143.02 -20.22 0 2.50e+00 1.60e-01 6.54e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.261: 113 0.261 - 0.520: 82 0.520 - 0.779: 35 0.779 - 1.038: 10 1.038 - 1.297: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.29 -1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA BASN A 97 " pdb=" N BASN A 97 " pdb=" C BASN A 97 " pdb=" CB BASN A 97 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.81e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.023 2.00e-02 2.50e+03 6.75e-02 1.37e+02 pdb=" CG PHE A 119 " -0.126 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.099 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.077 2.00e-02 2.50e+03 7.04e-02 1.11e+02 pdb=" CG HIS A 138 " 0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.091 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.127 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.040 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG TYR A 141 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.043 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.118 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.075 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1044 2.32 - 2.89: 8077 2.89 - 3.46: 10562 3.46 - 4.03: 15165 4.03 - 4.60: 21813 Nonbonded interactions: 56661 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.749 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.779 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.792 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.796 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.808 1.816 ... (remaining 56656 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 2 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 } ordered_solvent { low_resolution = 4 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 } } output { prefix = "shake_3867824_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411094 | | target function (ml) not normalized (work): 71649.401289 | | target function (ml) not normalized (free): 3242.401967 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3190 0.2193 7.598 5.0503| | 2: 3.63 - 2.88 1.00 2711 122 0.2633 0.1660 4.3262 4.3064| | 3: 2.88 - 2.52 1.00 2682 148 0.2577 0.1626 4.1725 4.1664| | 4: 2.52 - 2.29 1.00 2661 139 0.2557 0.1488 3.5021 3.5082| | 5: 2.29 - 2.13 1.00 2678 122 0.2685 0.1302 3.3911 3.3941| | 6: 2.13 - 2.00 1.00 2692 117 0.2723 0.1932 3.3104 3.3817| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.22 0.77 0.23 1272.58| | 2: 3.63 - 2.88 2711 122 0.83 23.53 1.31 0.23 1272.58| | 3: 2.88 - 2.52 2682 148 0.73 32.70 1.29 0.23 1272.58| | 4: 2.52 - 2.29 2661 139 0.94 10.82 1.30 0.26 124.44| | 5: 2.29 - 2.13 2678 122 0.92 12.88 1.32 0.26 124.44| | 6: 2.13 - 2.00 2692 117 0.91 15.35 1.33 0.26 124.44| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 124.44 max = 1272.58 mean = 704.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.86 mean = 18.76| |phase err.(test): min = 0.00 max = 88.59 mean = 18.80| |-----------------------------------------------------------------------------| ----------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 0.239 1557 Z= 5.525 Angle : 5.460 18.696 2118 Z= 3.789 Chirality : 0.400 1.297 243 Planarity : 0.032 0.108 284 Dihedral : 13.864 81.513 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 40.00 % 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: -2.96 (0.48), residues: 224 helix: -2.91 (0.33), residues: 109 sheet: -0.97 (0.80), residues: 38 loop : -0.52 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.014 ARG A 156 TYR 0.080 0.038 TYR A 139 PHE 0.124 0.039 PHE A 119 HIS 0.068 0.035 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411094 | | target function (ml) not normalized (work): 71649.401289 | | target function (ml) not normalized (free): 3242.401967 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2949 percent. r_work = 0.2919 r_free = 0.1956 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2864 0.2919 0.1956 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2864 0.2919 0.1956 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2170 0.1956 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2130 0.2142 0.1936 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1621 0.1620 0.1649 n_refl.: 17045 remove outliers: r(all,work,free)=0.1620 0.1619 0.1649 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4022 394.942 366.141 0.673 1.006 0.404 11.894-9.307 99.02 97 4 0.1870 633.894 616.929 0.937 1.007 0.400 9.237-7.194 100.00 213 7 0.2196 518.461 510.809 0.960 1.007 0.345 7.162-5.571 100.00 427 22 0.2336 389.106 376.174 0.928 1.006 0.331 5.546-4.326 100.00 867 58 0.1375 534.180 530.913 0.967 1.005 0.230 4.315-3.360 100.00 1859 96 0.1306 508.010 504.188 1.019 1.004 0.201 3.356-2.611 100.00 3867 181 0.1651 333.734 329.784 1.012 1.002 0.034 2.608-2.000 99.99 8818 434 0.1663 217.537 213.368 1.022 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4680 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1649 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 144 ASN Total number of N/Q/H flips: 2 r_work=0.1619 r_free=0.1656 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.881246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.908546 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1358 0.1643 0.0285 0.008 1.0 1.0 0.5 0.0 0 10.941 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.58 16.43 2.85 3.013 18.448 0.909 0.023 12.83 16.70 3.86 3.643 18.714 0.909 0.021 Individual atomic B min max mean iso aniso Overall: 6.28 113.89 19.98 4.09 1785 0 Protein: 6.28 112.85 17.22 4.09 1519 0 Water: 8.80 113.89 36.00 N/A 258 0 Other: 21.89 36.58 26.39 N/A 8 0 Chain A: 6.28 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.28 - 17.04 1095 17.04 - 27.80 329 27.80 - 38.56 186 38.56 - 49.32 102 49.32 - 60.09 45 60.09 - 70.85 14 70.85 - 81.61 6 81.61 - 92.37 5 92.37 - 103.13 0 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1283 r_free=0.1670 r_work=0.1286 r_free=0.1676 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1286 r_free = 0.1676 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1282 r_free= 0.1669 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020304 | | target function (ls_wunit_k1) not normalized (work): 329.675389 | | target function (ls_wunit_k1) not normalized (free): 27.605434 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1301 0.1282 0.1669 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1917 0.1916 0.1990 n_refl.: 17044 remove outliers: r(all,work,free)=0.1917 0.1916 0.1990 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1887 0.1886 0.1974 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1298 0.1280 0.1656 n_refl.: 17044 remove outliers: r(all,work,free)=0.1296 0.1278 0.1656 n_refl.: 17042 ======================== 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 0.3549 303.376 278.771 0.626 1.010 0.370 11.894-9.307 99.02 97 4 0.1709 487.933 477.593 0.916 1.010 0.361 9.237-7.194 100.00 213 7 0.1827 399.080 396.139 0.959 1.010 0.341 7.162-5.571 100.00 427 22 0.1872 299.510 294.506 0.931 1.009 0.311 5.546-4.326 100.00 867 58 0.1066 411.179 408.417 0.960 1.007 0.210 4.315-3.360 100.00 1859 96 0.0933 391.035 390.533 1.018 1.004 0.191 3.356-2.611 100.00 3867 181 0.1299 256.888 255.622 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1347 167.447 165.967 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4119 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1280 r_free=0.1659 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1659 | n_water=258 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1285 r_free=0.1643 | n_water=254 | time (s): 19.690 (total time: 20.510) Filter (q & B) r_work=0.1284 r_free=0.1644 | n_water=252 | time (s): 1.690 (total time: 22.200) Compute maps r_work=0.1284 r_free=0.1644 | n_water=252 | time (s): 0.520 (total time: 22.720) Filter (map) r_work=0.1314 r_free=0.1633 | n_water=217 | time (s): 1.470 (total time: 24.190) Find peaks r_work=0.1314 r_free=0.1633 | n_water=217 | time (s): 0.550 (total time: 24.740) Add new water r_work=0.1527 r_free=0.1856 | n_water=375 | time (s): 1.670 (total time: 26.410) Refine new water occ: r_work=0.1330 r_free=0.1573 adp: r_work=0.1273 r_free=0.1574 occ: r_work=0.1278 r_free=0.1536 adp: r_work=0.1246 r_free=0.1546 occ: r_work=0.1248 r_free=0.1531 adp: r_work=0.1235 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1533 r_work=0.1235 r_free=0.1533 | n_water=375 | time (s): 32.160 (total time: 58.570) Filter (q & B) r_work=0.1238 r_free=0.1541 | n_water=363 | time (s): 1.420 (total time: 59.990) Filter (dist only) r_work=0.1239 r_free=0.1541 | n_water=362 | time (s): 28.620 (total time: 88.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.662656 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.970394 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1210 0.1612 0.0402 0.008 0.9 2.6 0.5 0.0 0 11.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 16.12 4.02 4.177 21.075 0.970 0.018 11.98 16.22 4.24 4.201 21.319 0.970 0.018 Individual atomic B min max mean iso aniso Overall: 6.32 107.45 21.33 4.22 1889 0 Protein: 6.32 107.45 17.68 4.21 1519 0 Water: 8.67 65.77 36.36 N/A 362 0 Other: 24.52 43.13 33.41 N/A 8 0 Chain A: 6.32 107.45 19.49 N/A 1744 0 Chain S: 16.40 65.50 43.42 N/A 145 0 Histogram: Values Number of atoms 6.32 - 16.43 1014 16.43 - 26.55 377 26.55 - 36.66 223 36.66 - 46.77 166 46.77 - 56.89 69 56.89 - 67.00 30 67.00 - 77.11 3 77.11 - 87.23 4 87.23 - 97.34 1 97.34 - 107.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1622 r_work=0.1199 r_free=0.1623 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1623 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1618 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1194 r_free= 0.1618 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017036 | | target function (ls_wunit_k1) not normalized (work): 276.581695 | | target function (ls_wunit_k1) not normalized (free): 24.609155 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1194 0.1618 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1754 0.1748 0.1923 n_refl.: 17042 remove outliers: r(all,work,free)=0.1754 0.1748 0.1923 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1729 0.1723 0.1908 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1188 0.1608 n_refl.: 17042 remove outliers: r(all,work,free)=0.1207 0.1187 0.1608 n_refl.: 17041 ======================== 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 0.3207 300.214 286.794 0.603 1.005 0.350 11.894-9.307 99.02 97 4 0.1504 487.933 486.507 0.913 1.006 0.344 9.237-7.194 100.00 213 7 0.1635 399.080 400.234 0.970 1.006 0.295 7.162-5.571 100.00 427 22 0.1601 299.510 295.273 0.934 1.005 0.271 5.546-4.326 100.00 867 58 0.0892 411.179 408.280 0.960 1.005 0.211 4.315-3.360 100.00 1859 96 0.0813 391.035 390.348 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1197 256.888 255.998 1.012 1.001 0.053 2.608-2.000 99.99 8818 434 0.1329 167.447 166.445 1.016 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3501 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1608 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1611 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1611 | n_water=362 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1189 r_free=0.1611 | n_water=362 | time (s): 26.630 (total time: 27.380) Filter (q & B) r_work=0.1189 r_free=0.1611 | n_water=362 | time (s): 1.100 (total time: 28.480) Compute maps r_work=0.1189 r_free=0.1611 | n_water=362 | time (s): 0.660 (total time: 29.140) Filter (map) r_work=0.1254 r_free=0.1601 | n_water=267 | time (s): 2.280 (total time: 31.420) Find peaks r_work=0.1254 r_free=0.1601 | n_water=267 | time (s): 0.600 (total time: 32.020) Add new water r_work=0.1433 r_free=0.1732 | n_water=405 | time (s): 1.580 (total time: 33.600) Refine new water occ: r_work=0.1243 r_free=0.1530 adp: r_work=0.1235 r_free=0.1535 occ: r_work=0.1218 r_free=0.1521 adp: r_work=0.1209 r_free=0.1523 occ: r_work=0.1201 r_free=0.1519 adp: r_work=0.1193 r_free=0.1518 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1518 r_work=0.1193 r_free=0.1518 | n_water=405 | time (s): 33.940 (total time: 67.540) Filter (q & B) r_work=0.1196 r_free=0.1520 | n_water=396 | time (s): 2.000 (total time: 69.540) Filter (dist only) r_work=0.1196 r_free=0.1520 | n_water=395 | time (s): 29.700 (total time: 99.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.902404 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.139898 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1545 0.0379 0.009 1.0 4.5 0.5 0.0 0 0.951 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 15.45 3.79 4.305 21.509 0.140 4.991 11.47 15.64 4.16 4.808 21.397 0.140 4.968 Individual atomic B min max mean iso aniso Overall: 6.28 104.49 20.86 4.54 1922 0 Protein: 6.28 104.49 16.99 4.54 1519 0 Water: 9.16 63.81 35.49 N/A 395 0 Other: 25.63 43.19 32.48 N/A 8 0 Chain A: 6.28 104.49 18.82 N/A 1741 0 Chain S: 16.59 63.81 40.44 N/A 181 0 Histogram: Values Number of atoms 6.28 - 16.10 1057 16.10 - 25.92 355 25.92 - 35.74 218 35.74 - 45.56 169 45.56 - 55.38 84 55.38 - 65.20 27 65.20 - 75.02 4 75.02 - 84.85 3 84.85 - 94.67 3 94.67 - 104.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1564 r_work=0.1148 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1565 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1566 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1566 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.964025 | | target function (ml) not normalized (work): 80585.985685 | | target function (ml) not normalized (free): 4190.324319 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1161 0.1140 0.1566 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1678 0.1669 0.1880 n_refl.: 17041 remove outliers: r(all,work,free)=0.1678 0.1669 0.1880 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1651 0.1642 0.1868 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1159 0.1138 0.1564 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1138 0.1564 n_refl.: 17041 ======================== 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 0.3521 300.214 280.308 0.571 1.005 0.334 11.894-9.307 99.02 97 4 0.1751 487.933 481.344 0.914 1.006 0.329 9.237-7.194 100.00 213 7 0.1785 399.080 400.150 0.981 1.007 0.270 7.162-5.571 100.00 427 22 0.1605 299.510 295.235 0.939 1.006 0.251 5.546-4.326 100.00 867 58 0.0934 411.179 407.527 0.964 1.005 0.215 4.315-3.360 100.00 1859 96 0.0887 391.035 388.954 1.010 1.004 0.201 3.356-2.611 100.00 3867 181 0.1272 256.888 254.704 1.012 1.001 0.121 2.608-2.000 99.99 8818 434 0.1081 167.447 166.090 1.018 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3510 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1564 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1138 r_free=0.1564 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1564 | n_water=395 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1138 r_free=0.1564 | n_water=395 | time (s): 29.130 (total time: 29.910) Filter (q & B) r_work=0.1138 r_free=0.1566 | n_water=394 | time (s): 2.020 (total time: 31.930) Compute maps r_work=0.1138 r_free=0.1566 | n_water=394 | time (s): 0.770 (total time: 32.700) Filter (map) r_work=0.1188 r_free=0.1547 | n_water=317 | time (s): 2.290 (total time: 34.990) Find peaks r_work=0.1188 r_free=0.1547 | n_water=317 | time (s): 0.640 (total time: 35.630) Add new water r_work=0.1337 r_free=0.1697 | n_water=459 | time (s): 1.630 (total time: 37.260) Refine new water occ: r_work=0.1176 r_free=0.1527 adp: r_work=0.1170 r_free=0.1533 occ: r_work=0.1150 r_free=0.1504 adp: r_work=0.1142 r_free=0.1508 occ: r_work=0.1133 r_free=0.1492 adp: r_work=0.1125 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1492 r_work=0.1125 r_free=0.1492 | n_water=459 | time (s): 29.900 (total time: 67.160) Filter (q & B) r_work=0.1128 r_free=0.1502 | n_water=449 | time (s): 2.010 (total time: 69.170) Filter (dist only) r_work=0.1128 r_free=0.1502 | n_water=447 | time (s): 35.070 (total time: 104.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.965983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.172112 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1122 0.1535 0.0413 0.010 1.0 5.1 0.5 0.0 0 0.983 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.35 4.13 4.412 21.092 0.172 4.956 11.08 15.47 4.39 4.654 21.140 0.172 4.951 Individual atomic B min max mean iso aniso Overall: 5.72 102.12 21.07 4.89 1974 0 Protein: 5.72 102.12 16.55 4.87 1519 0 Water: 8.47 62.01 36.22 N/A 447 0 Other: 25.99 46.44 33.80 N/A 8 0 Chain A: 5.72 102.12 18.36 N/A 1741 0 Chain S: 14.25 62.01 41.34 N/A 233 0 Histogram: Values Number of atoms 5.72 - 15.36 1026 15.36 - 25.00 382 25.00 - 34.64 214 34.64 - 44.28 186 44.28 - 53.92 115 53.92 - 63.56 35 63.56 - 73.20 7 73.20 - 82.84 4 82.84 - 92.48 3 92.48 - 102.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1547 r_work=0.1108 r_free=0.1547 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1547 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1546 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.946607 | | target function (ml) not normalized (work): 80303.215540 | | target function (ml) not normalized (free): 4183.727896 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1099 0.1546 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1592 0.1581 0.1835 n_refl.: 17041 remove outliers: r(all,work,free)=0.1592 0.1581 0.1835 n_refl.: 17041 overall B=-0.30 to atoms: r(all,work,free)=0.1573 0.1562 0.1827 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1098 0.1542 n_refl.: 17041 remove outliers: r(all,work,free)=0.1118 0.1097 0.1542 n_refl.: 17040 ======================== 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 0.3648 296.650 282.553 0.555 0.999 0.316 11.894-9.307 99.02 97 4 0.1762 487.933 480.794 0.921 1.001 0.307 9.237-7.194 100.00 213 7 0.1721 399.080 400.784 0.991 1.002 0.250 7.162-5.571 100.00 427 22 0.1496 299.510 293.767 0.945 1.002 0.230 5.546-4.326 100.00 867 58 0.0914 411.179 407.942 0.967 1.003 0.201 4.315-3.360 100.00 1859 96 0.0849 391.035 388.710 1.006 1.002 0.191 3.356-2.611 100.00 3867 181 0.1227 256.888 254.571 1.005 1.002 0.151 2.608-2.000 99.99 8818 434 0.1039 167.447 166.266 1.001 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0244 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1542 After: r_work=0.1099 r_free=0.1541 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1099 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1541 | n_water=447 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1101 r_free=0.1546 | n_water=445 | time (s): 36.440 (total time: 37.340) Filter (q & B) r_work=0.1101 r_free=0.1546 | n_water=444 | time (s): 1.700 (total time: 39.040) Compute maps r_work=0.1101 r_free=0.1546 | n_water=444 | time (s): 0.620 (total time: 39.660) Filter (map) r_work=0.1180 r_free=0.1549 | n_water=340 | time (s): 1.630 (total time: 41.290) Find peaks r_work=0.1180 r_free=0.1549 | n_water=340 | time (s): 0.430 (total time: 41.720) Add new water r_work=0.1300 r_free=0.1656 | n_water=473 | time (s): 1.550 (total time: 43.270) Refine new water occ: r_work=0.1141 r_free=0.1476 adp: r_work=0.1134 r_free=0.1482 occ: r_work=0.1120 r_free=0.1466 adp: r_work=0.1112 r_free=0.1470 occ: r_work=0.1104 r_free=0.1461 adp: r_work=0.1098 r_free=0.1465 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1465 r_work=0.1098 r_free=0.1465 | n_water=473 | time (s): 28.030 (total time: 71.300) Filter (q & B) r_work=0.1100 r_free=0.1485 | n_water=462 | time (s): 2.300 (total time: 73.600) Filter (dist only) r_work=0.1100 r_free=0.1485 | n_water=461 | time (s): 36.320 (total time: 109.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.933154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170389 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1109 0.1509 0.0400 0.010 1.1 6.1 0.5 0.0 0 0.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.09 15.09 4.00 4.569 20.838 0.170 4.940 10.99 14.92 3.94 4.601 20.913 0.170 4.930 Individual atomic B min max mean iso aniso Overall: 5.47 101.26 21.00 5.01 1988 0 Protein: 5.47 101.26 16.29 5.00 1519 0 Water: 8.10 66.06 36.28 N/A 461 0 Other: 25.79 42.69 32.75 N/A 8 0 Chain A: 5.47 101.26 18.02 N/A 1738 0 Chain S: 14.65 66.06 41.66 N/A 250 0 Histogram: Values Number of atoms 5.47 - 15.05 1040 15.05 - 24.63 356 24.63 - 34.21 221 34.21 - 43.79 193 43.79 - 53.36 125 53.36 - 62.94 28 62.94 - 72.52 15 72.52 - 82.10 4 82.10 - 91.68 2 91.68 - 101.26 4 =========================== Idealize ADP of riding H ========================== r_work=0.1099 r_free=0.1492 r_work=0.1099 r_free=0.1493 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1099 r_free = 0.1493 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1092 r_free = 0.1488 target_work(ml) = 4.924 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1092 r_free= 0.1488 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.924299 | | target function (ml) not normalized (work): 79936.141814 | | target function (ml) not normalized (free): 4157.358517 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1085 0.1370 5.43 5.633| | 2: 3.63 - 2.88 1.00 2711 122 0.1074 0.1439 5.1903 5.3272| | 3: 2.88 - 2.52 1.00 2681 148 0.1338 0.1573 5.102 5.1541| | 4: 2.52 - 2.29 1.00 2661 139 0.0936 0.1570 4.6324 4.97| | 5: 2.29 - 2.13 1.00 2678 122 0.0975 0.1565 4.5864 4.937| | 6: 2.13 - 2.00 1.00 2692 117 0.1120 0.1674 4.5763 4.7508| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2810 159 0.95 8.49 1.00 0.96 5898.03| | 2: 3.63 - 2.88 2711 122 0.93 12.16 1.01 0.96 5898.03| | 3: 2.88 - 2.52 2681 148 0.88 18.23 0.99 0.96 5898.03| | 4: 2.52 - 2.29 2661 139 0.93 12.18 1.01 0.97 2151.78| | 5: 2.29 - 2.13 2678 122 0.91 14.37 1.00 0.97 2151.78| | 6: 2.13 - 2.00 2692 117 0.89 16.98 0.99 0.97 2151.78| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2151.78 max = 5898.03 mean = 4044.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.70| |phase err.(test): min = 0.00 max = 87.11 mean = 13.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1112 0.1092 0.1488 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1562 0.1551 0.1796 n_refl.: 17040 remove outliers: r(all,work,free)=0.1562 0.1551 0.1796 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1549 0.1538 0.1789 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1111 0.1092 0.1489 n_refl.: 17040 remove outliers: r(all,work,free)=0.1111 0.1092 0.1489 n_refl.: 17040 ======================== 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 0.3531 296.650 278.569 0.550 1.005 0.330 11.894-9.307 99.02 97 4 0.1704 487.933 482.497 0.916 1.006 0.330 9.237-7.194 100.00 213 7 0.1661 399.080 401.946 0.989 1.006 0.240 7.162-5.571 100.00 427 22 0.1519 299.510 294.753 0.938 1.006 0.220 5.546-4.326 100.00 867 58 0.0901 411.179 407.894 0.962 1.005 0.200 4.315-3.360 100.00 1859 96 0.0857 391.035 388.933 1.000 1.003 0.191 3.356-2.611 100.00 3867 181 0.1216 256.888 254.574 0.999 1.001 0.131 2.608-2.000 99.99 8818 434 0.1039 167.447 166.158 0.992 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7582 ================= 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 : 0.2790 0.1790 0.083 5.460 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1649 0.083 5.460 8.4 118.9 19.5 258 0.000 1_settarget: 0.1619 0.1649 0.083 5.460 8.4 118.9 19.5 258 0.000 1_nqh: 0.1619 0.1656 0.083 5.460 8.4 118.9 19.5 258 0.006 1_weight: 0.1619 0.1656 0.083 5.460 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1358 0.1643 0.008 0.965 8.4 118.9 19.5 258 0.150 1_adp: 0.1283 0.1670 0.008 0.965 6.3 113.9 20.0 258 0.150 1_regHadp: 0.1286 0.1676 0.008 0.965 6.3 113.9 20.0 258 0.150 1_occ: 0.1282 0.1669 0.008 0.965 6.3 113.9 20.0 258 0.150 2_bss: 0.1278 0.1656 0.008 0.965 5.9 113.5 19.6 258 0.150 2_settarget: 0.1278 0.1656 0.008 0.965 5.9 113.5 19.6 258 0.150 2_updatecdl: 0.1278 0.1656 0.008 0.974 5.9 113.5 19.6 258 0.150 2_nqh: 0.1280 0.1659 0.008 0.974 5.9 113.5 19.6 258 0.144 2_sol: 0.1239 0.1541 0.008 0.974 5.9 112.5 20.9 362 n/a 2_weight: 0.1239 0.1541 0.008 0.974 5.9 112.5 20.9 362 n/a 2_xyzrec: 0.1210 0.1612 0.008 0.917 5.9 112.5 20.9 362 n/a 2_adp: 0.1198 0.1622 0.008 0.917 6.3 107.5 21.3 362 n/a 2_regHadp: 0.1199 0.1623 0.008 0.917 6.3 107.5 21.3 362 n/a 2_occ: 0.1194 0.1618 0.008 0.917 6.3 107.5 21.3 362 n/a 3_bss: 0.1187 0.1608 0.008 0.917 5.9 107.1 21.0 362 n/a 3_settarget: 0.1187 0.1608 0.008 0.917 5.9 107.1 21.0 362 n/a 3_updatecdl: 0.1187 0.1608 0.008 0.917 5.9 107.1 21.0 362 n/a 3_nqh: 0.1189 0.1611 0.008 0.917 5.9 107.1 21.0 362 n/a 3_sol: 0.1196 0.1520 0.008 0.917 5.9 107.1 21.1 395 n/a 3_weight: 0.1196 0.1520 0.008 0.917 5.9 107.1 21.1 395 n/a 3_xyzrec: 0.1166 0.1545 0.009 0.969 5.9 107.1 21.1 395 n/a 3_adp: 0.1147 0.1564 0.009 0.969 6.3 104.5 20.9 395 n/a 3_regHadp: 0.1148 0.1565 0.009 0.969 6.3 104.5 20.9 395 n/a 3_occ: 0.1140 0.1566 0.009 0.969 6.3 104.5 20.9 395 n/a 4_bss: 0.1138 0.1564 0.009 0.969 5.9 104.1 20.5 395 n/a 4_settarget: 0.1138 0.1564 0.009 0.969 5.9 104.1 20.5 395 n/a 4_updatecdl: 0.1138 0.1564 0.009 0.969 5.9 104.1 20.5 395 n/a 4_nqh: 0.1138 0.1564 0.009 0.969 5.9 104.1 20.5 395 n/a 4_sol: 0.1128 0.1502 0.009 0.969 5.9 104.1 21.0 447 n/a 4_weight: 0.1128 0.1502 0.009 0.969 5.9 104.1 21.0 447 n/a 4_xyzrec: 0.1122 0.1535 0.010 0.978 5.9 104.1 21.0 447 n/a 4_adp: 0.1108 0.1547 0.010 0.978 5.7 102.1 21.1 447 n/a 4_regHadp: 0.1108 0.1547 0.010 0.978 5.7 102.1 21.1 447 n/a 4_occ: 0.1099 0.1546 0.010 0.978 5.7 102.1 21.1 447 n/a 5_bss: 0.1097 0.1542 0.010 0.978 5.4 101.8 20.8 447 n/a 5_settarget: 0.1097 0.1542 0.010 0.978 5.4 101.8 20.8 447 n/a 5_updatecdl: 0.1097 0.1542 0.010 0.978 5.4 101.8 20.8 447 n/a 5_setrh: 0.1099 0.1541 0.010 0.978 5.4 101.8 20.8 447 n/a 5_nqh: 0.1099 0.1541 0.010 0.978 5.4 101.8 20.8 447 n/a 5_sol: 0.1100 0.1485 0.010 0.978 5.4 101.8 20.9 461 n/a 5_weight: 0.1100 0.1485 0.010 0.978 5.4 101.8 20.9 461 n/a 5_xyzrec: 0.1109 0.1509 0.010 1.084 5.4 101.8 20.9 461 n/a 5_adp: 0.1099 0.1492 0.010 1.084 5.5 101.3 21.0 461 n/a 5_regHadp: 0.1099 0.1493 0.010 1.084 5.5 101.3 21.0 461 n/a 5_occ: 0.1092 0.1488 0.010 1.084 5.5 101.3 21.0 461 n/a end: 0.1092 0.1489 0.010 1.084 5.2 101.0 20.8 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3867824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3867824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1800 Refinement macro-cycles (run) : 935.8700 Write final files (write_after_run_outputs) : 19.0900 Total : 959.1400 Total CPU time: 16.36 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:22 PST -0800 (1735494082.91 s) Start R-work = 0.1619, R-free = 0.1649 Final R-work = 0.1092, R-free = 0.1489 =============================================================================== Job complete usr+sys time: 1002.65 seconds wall clock time: 17 minutes 5.68 seconds (1025.68 seconds total)